Starting phenix.real_space_refine on Sun Apr 14 21:32:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hu1_35022/04_2024/8hu1_35022_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hu1_35022/04_2024/8hu1_35022.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hu1_35022/04_2024/8hu1_35022_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hu1_35022/04_2024/8hu1_35022_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hu1_35022/04_2024/8hu1_35022_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hu1_35022/04_2024/8hu1_35022.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hu1_35022/04_2024/8hu1_35022.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hu1_35022/04_2024/8hu1_35022_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hu1_35022/04_2024/8hu1_35022_updated.pdb" } resolution = 2.69 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians K 1 8.98 5 P 4554 5.49 5 Mg 314 5.21 5 S 151 5.16 5 C 71052 2.51 5 N 26410 2.21 5 O 39393 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ASP 116": "OD1" <-> "OD2" Residue "C GLU 85": "OE1" <-> "OE2" Residue "C GLU 110": "OE1" <-> "OE2" Residue "C GLU 188": "OE1" <-> "OE2" Residue "D GLU 202": "OE1" <-> "OE2" Residue "E GLU 13": "OE1" <-> "OE2" Residue "E PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 43": "OE1" <-> "OE2" Residue "H GLU 52": "OE1" <-> "OE2" Residue "H GLU 58": "OE1" <-> "OE2" Residue "I TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 60": "OD1" <-> "OD2" Residue "K ASP 112": "OD1" <-> "OD2" Residue "M GLU 66": "OE1" <-> "OE2" Residue "N GLU 92": "OE1" <-> "OE2" Residue "Q ASP 15": "OD1" <-> "OD2" Residue "R ASP 72": "OD1" <-> "OD2" Residue "S GLU 73": "OE1" <-> "OE2" Residue "S TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 168": "OD1" <-> "OD2" Residue "c GLU 194": "OE1" <-> "OE2" Residue "c ASP 264": "OD1" <-> "OD2" Residue "d ASP 43": "OD1" <-> "OD2" Residue "d GLU 86": "OE1" <-> "OE2" Residue "d ASP 108": "OD1" <-> "OD2" Residue "f GLU 32": "OE1" <-> "OE2" Residue "f TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ASP 113": "OD1" <-> "OD2" Residue "f GLU 134": "OE1" <-> "OE2" Residue "f GLU 140": "OE1" <-> "OE2" Residue "f ASP 174": "OD1" <-> "OD2" Residue "g PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ASP 14": "OD1" <-> "OD2" Residue "i ASP 19": "OD1" <-> "OD2" Residue "k GLU 10": "OE1" <-> "OE2" Residue "k PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k GLU 115": "OE1" <-> "OE2" Residue "m GLU 43": "OE1" <-> "OE2" Residue "n ASP 93": "OD1" <-> "OD2" Residue "n GLU 112": "OE1" <-> "OE2" Residue "o GLU 71": "OE1" <-> "OE2" Residue "p ASP 49": "OD1" <-> "OD2" Residue "r GLU 2": "OE1" <-> "OE2" Residue "r ASP 65": "OD1" <-> "OD2" Residue "r ASP 77": "OD1" <-> "OD2" Residue "t GLU 10": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 141875 Number of models: 1 Model: "" Number of chains: 64 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': 268, 'rna2p_pyr': 139, 'rna3p': 16, 'rna3p_pur': 1317, 'rna3p_pyr': 1005} Link IDs: {'rna2p': 413, 'rna3p': 2339} 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: 1646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1646 Classifications: {'RNA': 76} Modifications used: {'rna2p': 4, 'rna2p_pur': 3, 'rna2p_pyr': 4, 'rna3p': 7, 'rna3p_pur': 32, 'rna3p_pyr': 26} Link IDs: {'rna2p': 11, 'rna3p': 64} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 5 Chain: "A" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 93 Unusual residues: {' K': 1, ' MG': 92} Classifications: {'undetermined': 93} Link IDs: {None: 92} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} 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: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 210 Unusual residues: {' MG': 210} Classifications: {'undetermined': 210} Link IDs: {None: 209} 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: "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: "X" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 56.05, per 1000 atoms: 0.40 Number of scatterers: 141875 At special positions: 0 Unit cell: (251.864, 235.294, 251.035, 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 151 16.00 P 4554 15.00 Mg 314 11.99 O 39393 8.00 N 26410 7.00 C 71052 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: 60.67 Conformation dependent library (CDL) restraints added in 7.2 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: 162 helices and 64 sheets defined 38.2% alpha, 18.7% beta 1592 base pairs and 2341 stacking pairs defined. Time for finding SS restraints: 78.22 Creating SS restraints... Processing helix chain 'B' and resid 5 through 13 removed outlier: 4.822A pdb=" N MET B 9 " --> pdb=" O SER B 5 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY B 13 " --> pdb=" O MET B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 64 Proline residue: B 48 - end of helix removed outlier: 3.899A pdb=" N ARG B 63 " --> pdb=" O LYS B 59 " (cutoff:3.500A) removed outlier: 3.840A 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: 4.917A pdb=" N GLN B 109 " --> pdb=" O LYS B 105 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N SER B 110 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY B 124 " --> pdb=" O GLN B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 148 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: 3.601A pdb=" N GLN B 227 " --> pdb=" O GLU B 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 12 removed outlier: 4.017A pdb=" N ARG C 11 " --> pdb=" O PRO C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 48 removed outlier: 3.506A pdb=" N ALA C 48 " --> pdb=" O THR C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 78 removed outlier: 3.716A 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: 3.939A pdb=" N ASP C 112 " --> pdb=" O LYS C 108 " (cutoff:3.500A) removed outlier: 5.559A 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 removed outlier: 3.656A pdb=" N GLY C 145 " --> pdb=" O ALA C 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 16 removed outlier: 4.714A pdb=" N LEU D 11 " --> pdb=" O PRO D 7 " (cutoff:3.500A) removed outlier: 3.559A 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: 5.322A pdb=" N LYS D 83 " --> pdb=" O ALA D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 97 removed outlier: 3.600A pdb=" N ASN D 89 " --> pdb=" O ASN D 85 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ARG D 97 " --> pdb=" O LEU D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 106 Processing helix chain 'D' and resid 110 through 121 removed outlier: 4.074A pdb=" N LYS D 121 " --> pdb=" O LEU D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 166 removed outlier: 3.754A pdb=" N GLN D 164 " --> pdb=" O GLU D 160 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ARG D 165 " --> pdb=" O LEU D 161 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N GLU D 166 " --> pdb=" O ALA D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 205 removed outlier: 4.042A pdb=" N ILE D 200 " --> pdb=" O ASN D 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 71 removed outlier: 4.131A 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: 3.618A 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 removed outlier: 3.589A pdb=" N LEU E 165 " --> pdb=" O VAL E 161 " (cutoff:3.500A) Processing helix chain 'F' and resid 11 through 16 removed outlier: 4.018A pdb=" N SER F 15 " --> pdb=" O HIS F 11 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N GLU F 16 " --> pdb=" O PRO F 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 11 through 16' Processing helix chain 'F' and resid 17 through 33 removed outlier: 3.549A pdb=" N GLU F 33 " --> pdb=" O ILE F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 81 Processing helix chain 'G' and resid 20 through 31 removed outlier: 3.835A pdb=" N ALA G 24 " --> pdb=" O SER G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 35 through 55 removed outlier: 3.646A pdb=" N ALA G 39 " --> pdb=" O LYS G 35 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 70 removed outlier: 3.601A pdb=" N ASN G 68 " --> pdb=" O VAL G 64 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL G 69 " --> pdb=" O ALA G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 112 removed outlier: 5.494A pdb=" N GLY G 112 " --> pdb=" O ALA G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 115 through 130 removed outlier: 3.524A pdb=" N GLU G 129 " --> pdb=" O SER G 125 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 149 removed outlier: 3.681A pdb=" N ASN G 148 " --> pdb=" O MET G 144 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LYS G 149 " --> pdb=" O ALA G 145 " (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 92 removed outlier: 3.758A pdb=" N GLU I 92 " --> pdb=" O MET I 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 94 through 102 Processing helix chain 'J' and resid 14 through 33 removed outlier: 4.078A pdb=" N THR J 32 " --> pdb=" O THR J 28 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N GLY J 33 " --> pdb=" O ALA J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 80 through 90 removed outlier: 3.675A pdb=" N ARG J 89 " --> pdb=" O ASP J 85 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N LEU J 90 " --> pdb=" O ALA J 86 " (cutoff:3.500A) Processing helix chain 'K' and resid 46 through 51 removed outlier: 4.861A pdb=" N GLY K 51 " --> pdb=" O ALA K 47 " (cutoff:3.500A) Processing helix chain 'K' and resid 54 through 59 removed outlier: 3.813A pdb=" N SER K 58 " --> pdb=" O GLY K 54 " (cutoff:3.500A) removed outlier: 4.129A 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 92 through 104 removed outlier: 4.699A pdb=" N THR K 96 " --> pdb=" O GLY K 92 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ILE K 97 " --> pdb=" O ARG K 93 " (cutoff:3.500A) removed outlier: 4.103A 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 Processing helix chain 'M' and resid 14 through 22 removed outlier: 3.838A pdb=" N SER M 21 " --> pdb=" O ILE M 17 " (cutoff:3.500A) removed outlier: 4.534A 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: 4.133A pdb=" N LEU M 48 " --> pdb=" O LYS M 44 " (cutoff:3.500A) removed outlier: 5.711A 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 84 removed outlier: 3.816A pdb=" N PHE M 63 " --> pdb=" O GLU M 59 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N VAL M 64 " --> pdb=" O VAL M 60 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N VAL M 65 " --> pdb=" O ALA M 61 " (cutoff:3.500A) removed outlier: 11.014A pdb=" N GLU M 66 " --> pdb=" O LYS M 62 " (cutoff:3.500A) removed outlier: 8.758A pdb=" N GLY M 67 " --> pdb=" O PHE M 63 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ASP M 68 " --> pdb=" O VAL M 64 " (cutoff:3.500A) removed outlier: 3.761A 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 removed outlier: 3.552A pdb=" N LYS M 110 " --> pdb=" O ALA M 106 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 21 removed outlier: 3.543A pdb=" N LYS N 7 " --> pdb=" O LYS N 3 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE N 21 " --> pdb=" O ALA N 17 " (cutoff:3.500A) Processing helix chain 'N' and resid 22 through 33 Processing helix chain 'N' and resid 37 through 52 Proline residue: N 52 - end of helix 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: 4.233A pdb=" N GLY O 41 " --> pdb=" O ASN O 37 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N HIS O 42 " --> pdb=" O HIS O 38 " (cutoff:3.500A) Processing helix chain 'O' and resid 49 through 74 removed outlier: 3.725A 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 removed outlier: 3.544A pdb=" N ILE P 57 " --> pdb=" O ASP P 53 " (cutoff:3.500A) Processing helix chain 'P' and resid 68 through 80 removed outlier: 3.548A pdb=" N ASN P 79 " --> pdb=" O ILE P 75 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LYS P 80 " --> pdb=" O LYS P 76 " (cutoff:3.500A) Processing helix chain 'R' and resid 11 through 17 removed outlier: 3.806A pdb=" N ALA R 15 " --> pdb=" O CYS R 11 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N GLU R 16 " --> pdb=" O ARG R 12 " (cutoff:3.500A) Processing helix chain 'R' and resid 25 through 34 removed outlier: 4.054A pdb=" N ASN R 31 " --> pdb=" O ALA R 27 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N TYR R 32 " --> pdb=" O THR R 28 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ILE R 33 " --> pdb=" O LEU R 29 " (cutoff:3.500A) removed outlier: 5.774A 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: 4.457A pdb=" N PHE S 74 " --> pdb=" O LYS S 70 " (cutoff:3.500A) removed outlier: 4.165A 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 removed outlier: 3.577A pdb=" N LYS T 8 " --> pdb=" O ILE T 4 " (cutoff:3.500A) Processing helix chain 'T' and resid 43 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: 5.291A pdb=" N PHE U 37 " --> pdb=" O ARG U 33 " (cutoff:3.500A) Processing helix chain 'U' and resid 40 through 69 removed outlier: 3.875A pdb=" N ARG U 67 " --> pdb=" O GLU U 63 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N THR U 68 " --> pdb=" O ASN U 64 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ARG U 69 " --> pdb=" O ALA U 65 " (cutoff:3.500A) Processing helix chain 'c' and resid 10 through 17 removed outlier: 4.892A pdb=" N HIS c 15 " --> pdb=" O PRO c 11 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N VAL c 16 " --> pdb=" O GLY c 12 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N VAL c 17 " --> pdb=" O ARG c 13 " (cutoff:3.500A) Processing helix chain 'c' and resid 30 through 35 removed outlier: 4.078A pdb=" N LEU c 34 " --> pdb=" O PHE c 30 " (cutoff:3.500A) removed outlier: 5.741A 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: 3.592A 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: 3.646A pdb=" N ALA c 211 " --> pdb=" O LYS c 207 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG c 214 " --> pdb=" O ALA c 210 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLY c 215 " --> pdb=" O ALA c 211 " (cutoff:3.500A) Processing helix chain 'c' and resid 221 through 226 removed outlier: 4.166A pdb=" N MET c 225 " --> pdb=" O ARG c 221 " (cutoff:3.500A) removed outlier: 5.417A 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 265 removed outlier: 4.888A pdb=" N LYS c 265 " --> pdb=" O LYS c 261 " (cutoff:3.500A) Processing helix chain 'd' and resid 61 through 72 Processing helix chain 'd' and resid 98 through 105 removed outlier: 4.287A pdb=" N ALA d 102 " --> pdb=" O VAL d 98 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N ASP d 103 " --> pdb=" O GLU d 99 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N VAL d 104 " --> pdb=" O LEU d 100 " (cutoff:3.500A) removed outlier: 5.462A 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 24 through 40 removed outlier: 3.551A pdb=" N ALA e 39 " --> pdb=" O TYR e 35 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ARG e 40 " --> pdb=" O ALA e 36 " (cutoff:3.500A) Processing helix chain 'e' and resid 48 through 53 removed outlier: 6.499A pdb=" N THR e 53 " --> pdb=" O ARG e 49 " (cutoff:3.500A) Processing helix chain 'e' and resid 97 through 116 Processing helix chain 'e' and resid 130 through 142 removed outlier: 3.652A pdb=" N LEU e 134 " --> pdb=" O LYS e 130 " (cutoff:3.500A) Processing helix chain 'e' and resid 154 through 163 removed outlier: 4.826A 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 removed outlier: 3.590A pdb=" N ALA e 201 " --> pdb=" O GLU e 197 " (cutoff:3.500A) Processing helix chain 'e' and resid 16 through 21 Processing helix chain 'f' and resid 2 through 21 removed outlier: 5.612A pdb=" N VAL f 13 " --> pdb=" O LYS f 9 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N LYS f 14 " --> pdb=" O ASP f 10 " (cutoff:3.500A) Processing helix chain 'f' and resid 46 through 62 removed outlier: 4.160A pdb=" N LEU f 50 " --> pdb=" O ASP f 46 " (cutoff:3.500A) Processing helix chain 'f' and resid 93 through 111 removed outlier: 4.611A 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 Processing helix chain 'f' and resid 134 through 139 removed outlier: 3.792A 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 8 Proline residue: g 8 - end of helix Processing helix chain 'g' and resid 60 through 81 removed outlier: 6.106A pdb=" N GLN g 64 " --> pdb=" O ASP g 60 " (cutoff:3.500A) Processing helix chain 'g' and resid 137 through 153 removed outlier: 4.214A pdb=" N ARG g 152 " --> pdb=" O LEU g 148 " (cutoff:3.500A) Processing helix chain 'h' and resid 22 through 29 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: 4.103A pdb=" N ILE i 101 " --> pdb=" O PRO i 97 " (cutoff:3.500A) removed outlier: 3.645A 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: 3.998A pdb=" N LYS i 121 " --> pdb=" O ALA i 117 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LEU i 122 " --> pdb=" O MET i 118 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N LYS i 123 " --> pdb=" O PHE i 119 " (cutoff:3.500A) Processing helix chain 'j' and resid 112 through 119 Processing helix chain 'k' and resid 37 through 42 removed outlier: 3.653A pdb=" N ARG k 41 " --> pdb=" O GLY k 37 " (cutoff:3.500A) removed outlier: 5.854A 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 Proline residue: k 62 - end of helix Processing helix chain 'k' and resid 68 through 75 removed outlier: 3.760A pdb=" N ALA k 72 " --> pdb=" O SER k 68 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N ALA k 75 " --> pdb=" O ALA k 71 " (cutoff:3.500A) Processing helix chain 'k' and resid 78 through 86 removed outlier: 4.191A pdb=" N LEU k 82 " --> pdb=" O ARG k 78 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ALA k 83 " --> pdb=" O LEU k 79 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N LYS k 84 " --> pdb=" O SER k 80 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL k 85 " --> pdb=" O ASP k 81 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N GLU k 86 " --> pdb=" O LEU k 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 78 through 86' Processing helix chain 'k' and resid 91 through 99 Processing helix chain 'k' and resid 128 through 139 Processing helix chain 'l' and resid 42 through 58 Processing helix chain 'l' and resid 109 through 125 removed outlier: 3.862A pdb=" N LYS l 123 " --> pdb=" O LEU l 119 " (cutoff:3.500A) removed outlier: 3.772A 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: 4.289A pdb=" N ARG m 46 " --> pdb=" O LYS m 42 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL m 47 " --> pdb=" O GLU m 43 " (cutoff:3.500A) Proline residue: m 50 - end of helix removed outlier: 4.631A pdb=" N THR m 57 " --> pdb=" O THR m 53 " (cutoff:3.500A) Processing helix chain 'm' and resid 59 through 71 removed outlier: 3.531A pdb=" N ARG m 69 " --> pdb=" O LEU m 65 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N THR m 70 " --> pdb=" O ALA m 66 " (cutoff:3.500A) Processing helix chain 'm' and resid 72 through 88 removed outlier: 5.242A 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: 4.495A pdb=" N ALA n 6 " --> pdb=" O ASP n 2 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ARG n 13 " --> pdb=" O ARG n 9 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N ALA n 14 " --> pdb=" O ARG n 10 " (cutoff:3.500A) Processing helix chain 'n' and resid 55 through 63 removed outlier: 4.575A pdb=" N GLN n 61 " --> pdb=" O ALA n 57 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N LEU n 62 " --> pdb=" O ILE n 58 " (cutoff:3.500A) removed outlier: 5.878A 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: 3.564A pdb=" N GLY n 114 " --> pdb=" O ALA n 110 " (cutoff:3.500A) Processing helix chain 'o' and resid 2 through 13 removed outlier: 3.530A pdb=" N GLU o 11 " --> pdb=" O GLN o 7 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLN o 12 " --> pdb=" O LEU o 8 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N MET o 13 " --> pdb=" O GLU o 9 " (cutoff:3.500A) Processing helix chain 'o' and resid 97 through 104 removed outlier: 4.653A pdb=" N ARG o 101 " --> pdb=" O LEU o 97 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N GLU o 102 " --> pdb=" O TYR o 98 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ARG o 103 " --> pdb=" O TYR o 99 " (cutoff:3.500A) removed outlier: 5.395A 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: 3.709A pdb=" N LYS p 22 " --> pdb=" O LEU p 18 " (cutoff:3.500A) Processing helix chain 'p' and resid 26 through 31 removed outlier: 3.693A pdb=" N ARG p 30 " --> pdb=" O GLY p 26 " (cutoff:3.500A) Processing helix chain 'p' and resid 36 through 73 removed outlier: 3.820A pdb=" N ARG p 51 " --> pdb=" O TYR p 47 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N LYS p 54 " --> pdb=" O ARG p 50 " (cutoff:3.500A) removed outlier: 3.947A 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: 4.455A pdb=" N LEU r 23 " --> pdb=" O LEU r 19 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ILE r 24 " --> pdb=" O VAL r 20 " (cutoff:3.500A) removed outlier: 3.704A 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: 4.844A 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 51 Processing helix chain 't' and resid 66 through 71 removed outlier: 4.046A pdb=" N VAL t 70 " --> pdb=" O GLN t 66 " (cutoff:3.500A) removed outlier: 5.116A 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: 3.790A pdb=" N SER u 17 " --> pdb=" O GLY u 13 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA u 23 " --> pdb=" O ARG u 19 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ASN u 24 " --> pdb=" O LEU u 20 " (cutoff:3.500A) Processing helix chain 'u' and resid 43 through 53 removed outlier: 3.723A pdb=" N ALA u 52 " --> pdb=" O MET u 48 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N LYS u 53 " --> pdb=" O ASN u 49 " (cutoff:3.500A) Processing helix chain 'u' and resid 54 through 59 removed outlier: 3.847A 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: 4.569A pdb=" N LYS x 9 " --> pdb=" O GLU x 5 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N SER x 10 " --> pdb=" O LEU x 6 " (cutoff:3.500A) Processing helix chain 'x' and resid 11 through 35 Processing helix chain 'x' and resid 40 through 62 removed outlier: 4.107A 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 removed outlier: 3.531A pdb=" N VAL y 51 " --> pdb=" O MET y 47 " (cutoff:3.500A) 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: 4.405A pdb=" N THR 1 24 " --> pdb=" O ALA 1 20 " (cutoff:3.500A) removed outlier: 5.511A 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: 3.891A 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: 3.526A pdb=" N LEU 2 55 " --> pdb=" O SER 2 51 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N GLY 2 56 " --> pdb=" O LYS 2 52 " (cutoff:3.500A) removed outlier: 5.304A 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: 4.201A pdb=" N ARG 4 59 " --> pdb=" O GLY 4 55 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'B' and resid 15 through 18 removed outlier: 5.797A pdb=" N HIS B 15 " --> pdb=" O ILE B 41 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N HIS B 39 " --> pdb=" O GLY B 17 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'B' and resid 67 through 71 removed outlier: 3.990A pdb=" N LEU B 68 " --> pdb=" O ALA B 160 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'C' and resid 53 through 59 removed outlier: 3.540A 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: 3.646A pdb=" N GLY C 148 " --> pdb=" O PHE C 203 " (cutoff:3.500A) removed outlier: 4.960A 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: 3.568A pdb=" N ASP D 141 " --> pdb=" O PHE D 182 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU D 179 " --> pdb=" O ASP D 174 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU D 172 " --> pdb=" O THR D 181 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'E' and resid 12 through 16 removed outlier: 6.834A 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: 3.619A pdb=" N ALA E 99 " --> pdb=" O ASN E 122 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N ASN E 122 " --> pdb=" O ALA E 99 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'E' and resid 32 through 40 Processing sheet with id= 9, first strand: chain 'F' and resid 38 through 43 removed outlier: 3.717A pdb=" N ARG F 38 " --> pdb=" O ASN F 63 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N TYR F 59 " --> pdb=" O TRP F 42 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N HIS F 3 " --> pdb=" O THR F 92 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG F 86 " --> pdb=" O MET F 9 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'F' and resid 44 through 47 removed outlier: 6.757A 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: 6.210A 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: 6.471A pdb=" N ALA H 23 " --> pdb=" O LEU H 63 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER H 29 " --> pdb=" O PRO H 57 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU H 52 " --> pdb=" O GLU H 58 " (cutoff:3.500A) removed outlier: 3.560A 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: 3.656A pdb=" N CYS H 127 " --> pdb=" O VAL H 103 " (cutoff:3.500A) removed outlier: 6.692A 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: 3.514A pdb=" N GLY I 10 " --> pdb=" O ALA I 17 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS I 22 " --> pdb=" O ASP I 62 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LYS I 60 " --> pdb=" O GLY I 24 " (cutoff:3.500A) removed outlier: 4.180A 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: 3.578A pdb=" N ALA J 12 " --> pdb=" O HIS J 70 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'J' and resid 42 through 52 removed outlier: 4.684A pdb=" N LEU J 71 " --> pdb=" O PRO J 43 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG J 45 " --> pdb=" O THR J 69 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR J 69 " --> pdb=" O ARG J 45 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'K' and resid 30 through 35 Processing sheet with id= 18, first strand: chain 'L' and resid 29 through 33 removed outlier: 3.644A pdb=" N LYS L 30 " --> pdb=" O ILE L 82 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N LEU L 81 " --> pdb=" O VAL L 98 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'L' and resid 35 through 41 removed outlier: 3.598A pdb=" N ARG L 36 " --> pdb=" O ARG L 54 " (cutoff:3.500A) removed outlier: 5.359A 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 Processing sheet with id= 21, first strand: chain 'Q' and resid 7 through 11 removed outlier: 6.889A 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 'S' and resid 30 through 33 removed outlier: 3.723A pdb=" N VAL S 60 " --> pdb=" O ILE S 49 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL S 51 " --> pdb=" O VAL S 58 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'c' and resid 80 through 83 removed outlier: 6.653A pdb=" N LEU c 93 " --> pdb=" O GLU c 79 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ASP c 114 " --> pdb=" O VAL c 78 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N GLY c 127 " --> pdb=" O GLN c 115 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N GLN c 117 " --> pdb=" O GLY c 127 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'c' and resid 138 through 142 removed outlier: 4.194A pdb=" N SER c 139 " --> pdb=" O ILE c 164 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N THR c 173 " --> pdb=" O VAL c 165 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N GLU c 180 " --> pdb=" O LEU c 176 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'c' and resid 91 through 96 removed outlier: 3.791A pdb=" N GLU c 100 " --> pdb=" O TYR c 96 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'd' and resid 3 through 8 removed outlier: 4.346A pdb=" N SER d 199 " --> pdb=" O LYS d 8 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N ASP d 200 " --> pdb=" O THR d 112 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N THR d 112 " --> pdb=" O ASP d 200 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLU d 168 " --> pdb=" O SER d 113 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'd' and resid 11 through 16 removed outlier: 4.684A pdb=" N VAL d 20 " --> pdb=" O THR d 16 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL d 189 " --> pdb=" O THR d 25 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'd' and resid 36 through 39 removed outlier: 4.377A pdb=" N GLN d 94 " --> pdb=" O VAL d 34 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'd' and resid 46 through 51 removed outlier: 6.007A pdb=" N ARG d 46 " --> pdb=" O LEU d 84 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'e' and resid 1 through 6 removed outlier: 4.582A pdb=" N SER e 10 " --> pdb=" O LEU e 5 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'e' and resid 42 through 47 removed outlier: 7.817A pdb=" N GLY e 42 " --> pdb=" O ASP e 91 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N ASP e 91 " --> pdb=" O GLY e 42 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ARG e 44 " --> pdb=" O PRO e 89 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N ALA e 87 " --> pdb=" O GLN e 46 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'e' and resid 117 through 120 removed outlier: 3.905A pdb=" N LYS e 185 " --> pdb=" O ASP e 145 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'f' and resid 65 through 69 removed outlier: 5.153A pdb=" N ILE f 85 " --> pdb=" O VAL f 40 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'g' and resid 16 through 19 removed outlier: 3.884A pdb=" N ILE g 24 " --> pdb=" O ARG g 35 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'g' and resid 94 through 98 removed outlier: 3.854A pdb=" N ARG g 95 " --> pdb=" O SER g 106 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N HIS g 115 " --> pdb=" O ILE g 103 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU g 105 " --> pdb=" O VAL g 113 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL g 113 " --> pdb=" O LEU g 105 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'g' and resid 121 through 125 removed outlier: 6.013A pdb=" N THR g 129 " --> pdb=" O LEU g 89 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL g 90 " --> pdb=" O GLY g 161 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'i' and resid 14 through 19 Processing sheet with id= 39, first strand: chain 'i' and resid 74 through 78 removed outlier: 7.879A pdb=" N GLY i 83 " --> pdb=" O THR i 78 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'j' and resid 56 through 60 removed outlier: 4.642A pdb=" N ASP j 56 " --> pdb=" O ILE j 43 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LYS j 40 " --> pdb=" O ILE j 22 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N THR j 6 " --> pdb=" O CYS j 21 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N ASN j 82 " --> pdb=" O MET j 7 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'l' and resid 62 through 66 removed outlier: 6.373A pdb=" N LEU l 102 " --> pdb=" O ARG l 66 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N SER l 30 " --> pdb=" O LYS l 133 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N LYS l 127 " --> pdb=" O VAL l 36 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'm' and resid 33 through 37 removed outlier: 6.219A pdb=" N MET m 110 " --> pdb=" O CYS m 100 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'n' and resid 49 through 52 removed outlier: 3.675A pdb=" N VAL n 49 " --> pdb=" O VAL n 39 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG n 25 " --> pdb=" O ILE n 40 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'o' and resid 38 through 45 removed outlier: 6.406A pdb=" N THR o 25 " --> pdb=" O LYS o 87 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER o 83 " --> pdb=" O LYS o 29 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'o' and resid 49 through 53 removed outlier: 3.669A pdb=" N ALA o 49 " --> pdb=" O THR o 60 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N ARG o 53 " --> pdb=" O HIS o 56 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N SER o 57 " --> pdb=" O THR o 76 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'q' and resid 11 through 14 removed outlier: 7.330A pdb=" N LEU q 39 " --> pdb=" O GLY q 50 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLU q 46 " --> pdb=" O ASN q 43 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'q' and resid 17 through 23 removed outlier: 4.408A pdb=" N GLN q 18 " --> pdb=" O ILE q 98 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ASP q 95 " --> pdb=" O VAL q 64 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N LYS q 60 " --> pdb=" O THR q 99 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'q' and resid 57 through 60 Processing sheet with id= 49, first strand: chain 'q' and resid 65 through 68 Processing sheet with id= 50, first strand: chain 'q' and resid 71 through 78 removed outlier: 4.092A pdb=" N TYR q 83 " --> pdb=" O ARG q 78 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'r' and resid 2 through 8 Processing sheet with id= 52, first strand: chain 's' and resid 28 through 33 removed outlier: 6.411A pdb=" N ASN s 28 " --> pdb=" O LEU s 87 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N LYS s 66 " --> pdb=" O ARG s 77 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N ASP s 79 " --> pdb=" O LYS s 64 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N LYS s 64 " --> pdb=" O ASP s 79 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LYS s 81 " --> pdb=" O VAL s 62 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL s 62 " --> pdb=" O LYS s 81 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ALA s 83 " --> pdb=" O THR s 60 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N THR s 60 " --> pdb=" O ALA s 83 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N VAL s 85 " --> pdb=" O VAL s 58 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL s 58 " --> pdb=" O VAL s 85 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 't' and resid 9 through 12 removed outlier: 4.791A pdb=" N ASP t 9 " --> pdb=" O VAL t 25 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 't' and resid 26 through 29 removed outlier: 3.676A pdb=" N ASN t 27 " --> pdb=" O ILE t 35 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LYS t 33 " --> pdb=" O LEU t 29 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 't' and resid 83 through 87 Processing sheet with id= 56, first strand: chain 'u' and resid 69 through 72 removed outlier: 3.749A pdb=" N VAL u 72 " --> pdb=" O LEU u 61 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE u 26 " --> pdb=" O LEU u 42 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE u 89 " --> pdb=" O PRO u 27 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'v' and resid 28 through 31 removed outlier: 4.256A pdb=" N GLU v 29 " --> pdb=" O VAL v 67 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N ILE v 82 " --> pdb=" O GLY v 48 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'v' and resid 50 through 54 removed outlier: 6.996A pdb=" N ASN v 50 " --> pdb=" O LYS v 62 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N THR v 58 " --> pdb=" O GLY v 54 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'w' and resid 12 through 19 removed outlier: 4.774A pdb=" N ASN w 23 " --> pdb=" O SER w 19 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'y' and resid 33 through 39 removed outlier: 4.309A pdb=" N HIS y 34 " --> pdb=" O GLN y 9 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS y 6 " --> pdb=" O GLU y 58 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU y 58 " --> pdb=" O LYS y 6 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N MET y 54 " --> pdb=" O THR y 10 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain '0' and resid 19 through 24 removed outlier: 5.675A pdb=" N HIS 0 19 " --> pdb=" O SER 0 13 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ILE 0 48 " --> pdb=" O SER 0 14 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LEU 0 34 " --> pdb=" O GLU 0 51 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain '2' and resid 22 through 25 No H-bonds generated for sheet with id= 62 Processing sheet with id= 63, first strand: chain '3' and resid 1 through 5 removed outlier: 7.091A pdb=" N HIS 3 33 " --> pdb=" O CYS 3 27 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N CYS 3 27 " --> pdb=" O HIS 3 33 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N ILE 3 23 " --> pdb=" O GLN 3 37 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N SER 3 28 " --> pdb=" O ASN 3 13 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N ASN 3 13 " --> pdb=" O SER 3 28 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain '4' and resid 20 through 25 removed outlier: 4.332A pdb=" N ASN 4 20 " --> pdb=" O CYS 4 16 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE 4 24 " --> pdb=" O ILE 4 12 " (cutoff:3.500A) 1840 hydrogen bonds defined for protein. 5448 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 4007 hydrogen bonds 6290 hydrogen bond angles 0 basepair planarities 1592 basepair parallelities 2341 stacking parallelities Total time for adding SS restraints: 253.82 Time building geometry restraints manager: 65.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 11420 1.29 - 1.44: 70234 1.44 - 1.58: 62850 1.58 - 1.72: 9108 1.72 - 1.86: 264 Bond restraints: 153876 Sorted by residual: bond pdb=" C5 5MU a1939 " pdb=" C6 5MU a1939 " ideal model delta sigma weight residual 1.155 1.451 -0.296 2.00e-02 2.50e+03 2.20e+02 bond pdb=" C5 5MU V 54 " pdb=" C6 5MU V 54 " ideal model delta sigma weight residual 1.155 1.451 -0.296 2.00e-02 2.50e+03 2.19e+02 bond pdb=" C5 5MU a 747 " pdb=" C6 5MU a 747 " ideal model delta sigma weight residual 1.155 1.450 -0.295 2.00e-02 2.50e+03 2.18e+02 bond pdb=" C5 5MU X 54 " pdb=" C6 5MU X 54 " ideal model delta sigma weight residual 1.155 1.441 -0.286 2.00e-02 2.50e+03 2.04e+02 bond pdb=" C MS6 l 82 " pdb=" S MS6 l 82 " ideal model delta sigma weight residual 1.829 1.579 0.250 2.00e-02 2.50e+03 1.57e+02 ... (remaining 153871 not shown) Histogram of bond angle deviations from ideal: 98.35 - 107.54: 30606 107.54 - 116.73: 107365 116.73 - 125.92: 76481 125.92 - 135.11: 15821 135.11 - 144.30: 2 Bond angle restraints: 230275 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 106.32 144.30 -37.98 3.00e+00 1.11e-01 1.60e+02 angle pdb=" C1' 2MA a2503 " pdb=" N9 2MA a2503 " pdb=" C8 2MA a2503 " ideal model delta sigma weight residual 106.32 143.00 -36.68 3.00e+00 1.11e-01 1.49e+02 angle pdb=" C1' 2MA V 38 " pdb=" N9 2MA V 38 " pdb=" C4 2MA V 38 " ideal model delta sigma weight residual 138.88 108.29 30.59 3.00e+00 1.11e-01 1.04e+02 angle pdb=" C1' 2MA a2503 " pdb=" N9 2MA a2503 " pdb=" C4 2MA a2503 " ideal model delta sigma weight residual 138.88 109.85 29.03 3.00e+00 1.11e-01 9.36e+01 angle pdb=" C1' 2MG A1516 " pdb=" N9 2MG A1516 " pdb=" C8 2MG A1516 " ideal model delta sigma weight residual 110.07 130.39 -20.32 3.00e+00 1.11e-01 4.59e+01 ... (remaining 230270 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.75: 86958 35.75 - 71.49: 10175 71.49 - 107.24: 1279 107.24 - 142.98: 14 142.98 - 178.73: 8 Dihedral angle restraints: 98434 sinusoidal: 82529 harmonic: 15905 Sorted by residual: dihedral pdb=" CA ASP g 47 " pdb=" C ASP g 47 " pdb=" N ASN g 48 " pdb=" CA ASN g 48 " ideal model delta harmonic sigma weight residual -180.00 -122.19 -57.81 0 5.00e+00 4.00e-02 1.34e+02 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 -134.65 -45.35 0 5.00e+00 4.00e-02 8.23e+01 dihedral pdb=" O4' U a1779 " pdb=" C1' U a1779 " pdb=" N1 U a1779 " pdb=" C2 U a1779 " ideal model delta sinusoidal sigma weight residual 200.00 46.37 153.63 1 1.50e+01 4.44e-03 8.09e+01 ... (remaining 98431 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 27540 0.068 - 0.135: 1626 0.135 - 0.203: 119 0.203 - 0.271: 16 0.271 - 0.338: 5 Chirality restraints: 29306 Sorted by residual: 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 0.34 2.00e-01 2.50e+01 2.86e+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 2.82 -0.32 2.00e-01 2.50e+01 2.58e+00 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 2.70 -0.32 2.00e-01 2.50e+01 2.52e+00 ... (remaining 29303 not shown) Planarity restraints: 12253 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 2MG A1516 " -0.075 2.00e-02 2.50e+03 6.10e-01 8.37e+03 pdb=" C4' 2MG A1516 " -0.435 2.00e-02 2.50e+03 pdb=" O4' 2MG A1516 " -0.616 2.00e-02 2.50e+03 pdb=" C3' 2MG A1516 " 0.600 2.00e-02 2.50e+03 pdb=" O3' 2MG A1516 " 0.667 2.00e-02 2.50e+03 pdb=" C2' 2MG A1516 " 0.157 2.00e-02 2.50e+03 pdb=" O2' 2MG A1516 " -1.010 2.00e-02 2.50e+03 pdb=" C1' 2MG A1516 " -0.223 2.00e-02 2.50e+03 pdb=" N9 2MG A1516 " 0.935 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMG X 18 " -0.920 2.00e-02 2.50e+03 6.02e-01 8.16e+03 pdb=" C4' OMG X 18 " 0.197 2.00e-02 2.50e+03 pdb=" O4' OMG X 18 " 0.790 2.00e-02 2.50e+03 pdb=" C3' OMG X 18 " -0.234 2.00e-02 2.50e+03 pdb=" O3' OMG X 18 " 0.878 2.00e-02 2.50e+03 pdb=" C2' OMG X 18 " -0.601 2.00e-02 2.50e+03 pdb=" O2' OMG X 18 " -0.591 2.00e-02 2.50e+03 pdb=" C1' OMG X 18 " 0.467 2.00e-02 2.50e+03 pdb=" N9 OMG X 18 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 5MC A1407 " -0.054 2.00e-02 2.50e+03 5.91e-01 7.85e+03 pdb=" C4' 5MC A1407 " -0.440 2.00e-02 2.50e+03 pdb=" O4' 5MC A1407 " -0.625 2.00e-02 2.50e+03 pdb=" C3' 5MC A1407 " 0.592 2.00e-02 2.50e+03 pdb=" O3' 5MC A1407 " 0.622 2.00e-02 2.50e+03 pdb=" C2' 5MC A1407 " 0.186 2.00e-02 2.50e+03 pdb=" O2' 5MC A1407 " -0.957 2.00e-02 2.50e+03 pdb=" C1' 5MC A1407 " -0.226 2.00e-02 2.50e+03 pdb=" N1 5MC A1407 " 0.902 2.00e-02 2.50e+03 ... (remaining 12250 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.58: 1236 2.58 - 3.22: 121064 3.22 - 3.86: 349001 3.86 - 4.50: 467956 4.50 - 5.14: 608658 Nonbonded interactions: 1547915 Sorted by model distance: nonbonded pdb=" OP2 G a2057 " pdb="MG MG a6052 " model vdw 1.935 2.170 nonbonded pdb=" OP2 C a2575 " pdb="MG MG a6089 " model vdw 1.944 2.170 nonbonded pdb=" O6 G A1222 " pdb="MG MG A1604 " model vdw 1.950 2.170 nonbonded pdb=" OP2 U a 511 " pdb="MG MG a6100 " model vdw 1.953 2.170 nonbonded pdb=" OP2 A a1156 " pdb="MG MG a6031 " model vdw 1.954 2.170 ... (remaining 1547910 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: 5.480 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: 0.100 Extract box with map and model: 34.980 Check model and map are aligned: 1.540 Set scattering table: 1.030 Process input model: 557.520 Find NCS groups from input model: 3.090 Set up NCS constraints: 0.350 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:10.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 615.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 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 : 0.004 0.296 153876 Z= 0.260 Angle : 0.577 37.985 230275 Z= 0.287 Chirality : 0.034 0.338 29306 Planarity : 0.022 0.610 12253 Dihedral : 22.690 178.727 88174 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.29 % Favored : 95.63 % Rotamer: Outliers : 0.02 % Allowed : 0.26 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.11), residues: 5474 helix: 0.98 (0.12), residues: 1856 sheet: -0.43 (0.16), residues: 1048 loop : -0.90 (0.12), residues: 2570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 201 HIS 0.007 0.001 HIS F 3 PHE 0.040 0.001 PHE F 78 TYR 0.019 0.002 TYR D 204 ARG 0.008 0.000 ARG j 98 *********************** 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 1014 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1013 time to evaluate : 6.215 Fit side-chains REVERT: I 55 VAL cc_start: 0.6975 (p) cc_final: 0.6692 (p) REVERT: T 32 ILE cc_start: 0.7696 (mt) cc_final: 0.7364 (mt) REVERT: i 90 GLU cc_start: 0.7275 (pt0) cc_final: 0.7075 (pt0) REVERT: l 1 MET cc_start: 0.5697 (tpt) cc_final: 0.4411 (ppp) REVERT: n 104 GLN cc_start: 0.7465 (tt0) cc_final: 0.7033 (tt0) REVERT: x 40 SER cc_start: 0.7849 (p) cc_final: 0.7597 (p) REVERT: z 52 ARG cc_start: 0.6919 (ptm-80) cc_final: 0.6645 (ttt180) outliers start: 1 outliers final: 1 residues processed: 1014 average time/residue: 2.2538 time to fit residues: 3198.6260 Evaluate side-chains 799 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 798 time to evaluate : 6.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain t residue 103 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 988 random chunks: chunk 834 optimal weight: 7.9990 chunk 748 optimal weight: 6.9990 chunk 415 optimal weight: 10.0000 chunk 255 optimal weight: 10.0000 chunk 505 optimal weight: 10.0000 chunk 400 optimal weight: 10.0000 chunk 774 optimal weight: 9.9990 chunk 299 optimal weight: 0.9990 chunk 470 optimal weight: 40.0000 chunk 576 optimal weight: 10.0000 chunk 897 optimal weight: 1.9990 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 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 178 ASN E 122 ASN F 58 HIS G 142 HIS H 18 GLN H 118 GLN I 4 ASN I 5 GLN I 32 GLN I 126 GLN K 38 GLN N 49 GLN O 62 GLN T 70 ASN T 84 ASN ** d 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 173 GLN e 163 ASN f 21 ASN g 104 ASN o 52 ASN p 59 GLN q 86 GLN ** t 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 87 GLN ** 4 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.0888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 153876 Z= 0.289 Angle : 0.727 17.807 230275 Z= 0.387 Chirality : 0.040 0.347 29306 Planarity : 0.007 0.140 12253 Dihedral : 23.084 179.969 77148 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.66 % Favored : 95.27 % Rotamer: Outliers : 2.71 % Allowed : 12.84 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.11), residues: 5474 helix: 0.89 (0.12), residues: 1863 sheet: -0.50 (0.16), residues: 1039 loop : -0.96 (0.12), residues: 2572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 201 HIS 0.010 0.001 HIS 2 31 PHE 0.019 0.002 PHE B 184 TYR 0.021 0.002 TYR g 94 ARG 0.008 0.001 ARG u 79 *********************** 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 951 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 827 time to evaluate : 6.298 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 198 PHE cc_start: 0.6301 (m-80) cc_final: 0.5908 (m-80) REVERT: C 129 MET cc_start: 0.5758 (OUTLIER) cc_final: 0.5375 (mmt) REVERT: C 166 GLU cc_start: 0.6766 (OUTLIER) cc_final: 0.5712 (mt-10) REVERT: D 200 ILE cc_start: 0.7080 (OUTLIER) cc_final: 0.6820 (mm) REVERT: E 12 GLN cc_start: 0.7016 (OUTLIER) cc_final: 0.6530 (mp10) REVERT: G 86 GLN cc_start: 0.6857 (OUTLIER) cc_final: 0.6042 (mt0) REVERT: G 139 GLU cc_start: 0.5883 (OUTLIER) cc_final: 0.5115 (mp0) REVERT: L 54 ARG cc_start: 0.7115 (OUTLIER) cc_final: 0.6887 (mmt180) REVERT: M 71 ARG cc_start: 0.6098 (tpp80) cc_final: 0.5867 (mtt90) REVERT: M 75 MET cc_start: 0.6844 (mmt) cc_final: 0.6629 (mmp) REVERT: O 84 ARG cc_start: 0.7095 (OUTLIER) cc_final: 0.6248 (ttp-110) REVERT: c 35 GLU cc_start: 0.6675 (OUTLIER) cc_final: 0.6267 (tt0) REVERT: d 128 ARG cc_start: 0.7381 (OUTLIER) cc_final: 0.6660 (mmp80) REVERT: f 10 ASP cc_start: 0.5738 (OUTLIER) cc_final: 0.5475 (m-30) REVERT: f 78 LYS cc_start: 0.6562 (mptt) cc_final: 0.6356 (mptt) REVERT: k 1 MET cc_start: 0.7148 (OUTLIER) cc_final: 0.6689 (ptm) REVERT: k 10 GLU cc_start: 0.7025 (mm-30) cc_final: 0.6814 (mm-30) REVERT: l 1 MET cc_start: 0.5924 (tpt) cc_final: 0.4422 (ppp) REVERT: l 22 GLN cc_start: 0.7733 (OUTLIER) cc_final: 0.7390 (mp10) REVERT: n 104 GLN cc_start: 0.7558 (tt0) cc_final: 0.7341 (tt0) REVERT: r 78 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7531 (mp0) REVERT: s 1 MET cc_start: 0.5192 (OUTLIER) cc_final: 0.4820 (ptt) REVERT: v 29 GLU cc_start: 0.7655 (mt-10) cc_final: 0.6998 (tp30) REVERT: x 7 ARG cc_start: 0.6462 (ttm-80) cc_final: 0.6203 (tpp-160) REVERT: z 52 ARG cc_start: 0.6923 (ptm-80) cc_final: 0.6706 (ttt180) REVERT: 0 27 LYS cc_start: 0.7272 (OUTLIER) cc_final: 0.6841 (ttmt) REVERT: 3 2 LYS cc_start: 0.7931 (OUTLIER) cc_final: 0.7370 (ptmt) REVERT: 4 11 GLU cc_start: 0.6223 (OUTLIER) cc_final: 0.5591 (tm-30) REVERT: 4 22 MET cc_start: 0.6328 (OUTLIER) cc_final: 0.5978 (mmp) REVERT: 4 28 VAL cc_start: 0.7026 (t) cc_final: 0.6664 (p) outliers start: 124 outliers final: 53 residues processed: 882 average time/residue: 2.2357 time to fit residues: 2786.6778 Evaluate side-chains 850 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 778 time to evaluate : 5.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 129 MET Chi-restraints excluded: chain C residue 166 GLU Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain E residue 12 GLN Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain F residue 93 LYS Chi-restraints excluded: chain G residue 40 GLU Chi-restraints excluded: chain G residue 86 GLN Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain H residue 107 SER Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 46 MET Chi-restraints excluded: chain I residue 73 SER Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain L residue 54 ARG Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain M residue 7 ILE Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain N residue 98 LYS Chi-restraints excluded: chain O residue 84 ARG Chi-restraints excluded: chain Q residue 79 VAL Chi-restraints excluded: chain R residue 24 LYS Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain U residue 4 ILE Chi-restraints excluded: chain c residue 35 GLU Chi-restraints excluded: chain d residue 128 ARG Chi-restraints excluded: chain e residue 15 SER Chi-restraints excluded: chain f residue 10 ASP Chi-restraints excluded: chain f residue 149 VAL Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 110 SER Chi-restraints excluded: chain i residue 92 MET Chi-restraints excluded: chain j residue 19 VAL Chi-restraints excluded: chain k residue 1 MET Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain l residue 22 GLN Chi-restraints excluded: chain l residue 57 VAL Chi-restraints excluded: chain l residue 89 VAL Chi-restraints excluded: chain n residue 60 GLU Chi-restraints excluded: chain n residue 91 SER Chi-restraints excluded: chain o residue 19 SER Chi-restraints excluded: chain p residue 107 THR Chi-restraints excluded: chain q residue 7 SER Chi-restraints excluded: chain q residue 60 LYS Chi-restraints excluded: chain r residue 4 ILE Chi-restraints excluded: chain r residue 13 SER Chi-restraints excluded: chain r residue 71 VAL Chi-restraints excluded: chain r residue 78 GLU Chi-restraints excluded: chain s residue 1 MET Chi-restraints excluded: chain s residue 22 THR Chi-restraints excluded: chain s residue 85 VAL Chi-restraints excluded: chain t residue 58 ILE Chi-restraints excluded: chain u residue 69 GLU Chi-restraints excluded: chain w residue 42 SER Chi-restraints excluded: chain x residue 30 MET Chi-restraints excluded: chain x residue 46 VAL Chi-restraints excluded: chain y residue 10 THR Chi-restraints excluded: chain y residue 52 SER Chi-restraints excluded: chain 0 residue 17 THR Chi-restraints excluded: chain 0 residue 27 LYS Chi-restraints excluded: chain 3 residue 2 LYS Chi-restraints excluded: chain 4 residue 11 GLU Chi-restraints excluded: chain 4 residue 22 MET 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: 9.9990 chunk 746 optimal weight: 20.0000 chunk 610 optimal weight: 10.0000 chunk 247 optimal weight: 9.9990 chunk 898 optimal weight: 4.9990 chunk 970 optimal weight: 4.9990 chunk 800 optimal weight: 0.0050 chunk 891 optimal weight: 5.9990 chunk 306 optimal weight: 8.9990 chunk 721 optimal weight: 0.9980 overall best weight: 3.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 178 ASN ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 142 HIS H 18 GLN I 4 ASN I 5 GLN I 32 GLN I 126 GLN N 49 GLN O 35 GLN O 62 GLN P 40 ASN Q 9 GLN T 84 ASN U 9 ASN ** d 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 42 ASN g 104 ASN k 104 GLN o 52 ASN q 86 GLN ** t 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.0823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 153876 Z= 0.192 Angle : 0.640 15.240 230275 Z= 0.351 Chirality : 0.036 0.336 29306 Planarity : 0.006 0.134 12253 Dihedral : 22.997 179.095 77146 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.06 % Favored : 95.89 % Rotamer: Outliers : 2.89 % Allowed : 16.01 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.11), residues: 5474 helix: 1.16 (0.12), residues: 1859 sheet: -0.40 (0.16), residues: 1026 loop : -0.87 (0.12), residues: 2589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 201 HIS 0.006 0.001 HIS E 89 PHE 0.020 0.002 PHE B 50 TYR 0.019 0.002 TYR g 94 ARG 0.008 0.000 ARG u 79 *********************** 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 973 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 841 time to evaluate : 6.279 Fit side-chains revert: symmetry clash REVERT: B 49 MET cc_start: 0.5005 (mtt) cc_final: 0.4747 (mtt) REVERT: C 129 MET cc_start: 0.5735 (OUTLIER) cc_final: 0.5159 (mmt) REVERT: C 166 GLU cc_start: 0.6817 (OUTLIER) cc_final: 0.5773 (mt-10) REVERT: D 200 ILE cc_start: 0.7037 (OUTLIER) cc_final: 0.6803 (mm) REVERT: E 12 GLN cc_start: 0.7059 (OUTLIER) cc_final: 0.6547 (mp10) REVERT: E 48 PHE cc_start: 0.8053 (OUTLIER) cc_final: 0.7668 (p90) REVERT: G 42 ILE cc_start: 0.7201 (OUTLIER) cc_final: 0.6953 (mp) REVERT: G 86 GLN cc_start: 0.6862 (OUTLIER) cc_final: 0.6025 (mt0) REVERT: G 139 GLU cc_start: 0.5794 (OUTLIER) cc_final: 0.5131 (mp0) REVERT: O 84 ARG cc_start: 0.7110 (OUTLIER) cc_final: 0.6258 (ttp-110) REVERT: Q 30 LYS cc_start: 0.7947 (OUTLIER) cc_final: 0.7198 (ttpp) REVERT: d 128 ARG cc_start: 0.7414 (OUTLIER) cc_final: 0.6781 (mmp80) REVERT: f 50 LEU cc_start: 0.7453 (OUTLIER) cc_final: 0.7218 (tp) REVERT: h 2 GLN cc_start: 0.5576 (OUTLIER) cc_final: 0.5074 (mt0) REVERT: j 111 LYS cc_start: 0.6704 (mtpp) cc_final: 0.6376 (mtmm) REVERT: j 113 MET cc_start: 0.6047 (mmt) cc_final: 0.5834 (mmt) REVERT: k 1 MET cc_start: 0.7090 (OUTLIER) cc_final: 0.6715 (ptm) REVERT: l 1 MET cc_start: 0.5969 (tpt) cc_final: 0.4403 (ttt) REVERT: l 22 GLN cc_start: 0.7754 (OUTLIER) cc_final: 0.7300 (mp10) REVERT: l 104 GLU cc_start: 0.7258 (tt0) cc_final: 0.6975 (mt-10) REVERT: m 86 ARG cc_start: 0.7501 (OUTLIER) cc_final: 0.6055 (ttp80) REVERT: n 104 GLN cc_start: 0.7433 (tt0) cc_final: 0.6978 (tt0) REVERT: o 13 MET cc_start: 0.7734 (OUTLIER) cc_final: 0.7434 (ptm) REVERT: o 115 ASN cc_start: 0.3466 (OUTLIER) cc_final: 0.2855 (m-40) REVERT: p 117 LEU cc_start: 0.6554 (OUTLIER) cc_final: 0.6134 (mt) REVERT: r 78 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7456 (mp0) REVERT: v 29 GLU cc_start: 0.7623 (mt-10) cc_final: 0.6966 (tp30) REVERT: z 52 ARG cc_start: 0.6904 (ptm-80) cc_final: 0.6700 (ttt180) REVERT: 0 27 LYS cc_start: 0.7267 (OUTLIER) cc_final: 0.6841 (ttmt) REVERT: 4 11 GLU cc_start: 0.6239 (OUTLIER) cc_final: 0.5644 (tm-30) REVERT: 4 28 VAL cc_start: 0.6961 (t) cc_final: 0.6618 (p) outliers start: 132 outliers final: 52 residues processed: 904 average time/residue: 2.3535 time to fit residues: 3056.0874 Evaluate side-chains 865 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 791 time to evaluate : 6.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 129 MET Chi-restraints excluded: chain C residue 166 GLU Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain E residue 12 GLN Chi-restraints excluded: chain E residue 48 PHE Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain F residue 93 LYS Chi-restraints excluded: chain G residue 42 ILE Chi-restraints excluded: chain G residue 86 GLN Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 107 SER Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 46 MET Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain O residue 84 ARG Chi-restraints excluded: chain Q residue 30 LYS Chi-restraints excluded: chain Q residue 79 VAL Chi-restraints excluded: chain R residue 24 LYS Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain S residue 62 VAL Chi-restraints excluded: chain d residue 128 ARG Chi-restraints excluded: chain e residue 15 SER Chi-restraints excluded: chain f residue 50 LEU Chi-restraints excluded: chain f residue 149 VAL Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 11 VAL Chi-restraints excluded: chain g residue 110 SER Chi-restraints excluded: chain h residue 2 GLN Chi-restraints excluded: chain i residue 92 MET Chi-restraints excluded: chain j residue 76 VAL Chi-restraints excluded: chain k residue 1 MET Chi-restraints excluded: chain k residue 23 ILE Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 112 LEU Chi-restraints excluded: chain l residue 22 GLN Chi-restraints excluded: chain l residue 57 VAL Chi-restraints excluded: chain l residue 89 VAL Chi-restraints excluded: chain m residue 86 ARG Chi-restraints excluded: chain n residue 91 SER Chi-restraints excluded: chain o residue 13 MET Chi-restraints excluded: chain o residue 19 SER Chi-restraints excluded: chain o residue 70 VAL Chi-restraints excluded: chain o residue 115 ASN Chi-restraints excluded: chain p residue 107 THR Chi-restraints excluded: chain p residue 117 LEU Chi-restraints excluded: chain q residue 7 SER Chi-restraints excluded: chain q residue 60 LYS Chi-restraints excluded: chain r residue 4 ILE Chi-restraints excluded: chain r residue 13 SER Chi-restraints excluded: chain r residue 78 GLU Chi-restraints excluded: chain s residue 22 THR Chi-restraints excluded: chain s residue 85 VAL Chi-restraints excluded: chain t residue 58 ILE Chi-restraints excluded: chain t residue 72 ILE Chi-restraints excluded: chain t residue 103 ILE Chi-restraints excluded: chain v residue 43 THR Chi-restraints excluded: chain w residue 42 SER Chi-restraints excluded: chain y residue 52 SER Chi-restraints excluded: chain 0 residue 17 THR Chi-restraints excluded: chain 0 residue 27 LYS Chi-restraints excluded: chain 4 residue 11 GLU Chi-restraints excluded: chain 4 residue 66 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 988 random chunks: chunk 888 optimal weight: 9.9990 chunk 675 optimal weight: 9.9990 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: 10.0000 chunk 955 optimal weight: 0.9990 chunk 471 optimal weight: 40.0000 chunk 854 optimal weight: 10.0000 chunk 257 optimal weight: 10.0000 overall best weight: 8.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 HIS G 142 HIS H 18 GLN H 118 GLN I 4 ASN I 5 GLN I 32 GLN I 126 GLN K 22 HIS K 38 GLN N 49 GLN P 40 ASN T 84 ASN ** d 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 104 ASN n 100 HIS o 52 ASN q 86 GLN ** t 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 20 ASN ** 4 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.1266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.092 153876 Z= 0.398 Angle : 0.831 17.441 230275 Z= 0.431 Chirality : 0.045 0.408 29306 Planarity : 0.008 0.148 12253 Dihedral : 23.147 179.803 77146 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.19 % Favored : 94.76 % Rotamer: Outliers : 4.77 % Allowed : 17.80 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.11), residues: 5474 helix: 0.59 (0.12), residues: 1863 sheet: -0.55 (0.16), residues: 1050 loop : -1.11 (0.12), residues: 2561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 201 HIS 0.012 0.002 HIS F 3 PHE 0.022 0.003 PHE F 8 TYR 0.029 0.003 TYR g 94 ARG 0.009 0.001 ARG R 61 *********************** 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 1023 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 218 poor density : 805 time to evaluate : 6.359 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 59 LYS cc_start: 0.5220 (OUTLIER) cc_final: 0.4894 (tmtt) REVERT: C 166 GLU cc_start: 0.6868 (OUTLIER) cc_final: 0.5758 (mt-10) REVERT: D 200 ILE cc_start: 0.7094 (OUTLIER) cc_final: 0.6894 (mm) REVERT: E 12 GLN cc_start: 0.7089 (OUTLIER) cc_final: 0.6566 (mp10) REVERT: E 68 ARG cc_start: 0.7277 (OUTLIER) cc_final: 0.7032 (mtm110) REVERT: E 152 MET cc_start: 0.7058 (OUTLIER) cc_final: 0.6780 (mpp) REVERT: G 86 GLN cc_start: 0.6961 (OUTLIER) cc_final: 0.6203 (mt0) REVERT: G 114 LYS cc_start: 0.5963 (OUTLIER) cc_final: 0.5301 (ttmm) REVERT: M 45 ILE cc_start: 0.6388 (OUTLIER) cc_final: 0.5982 (pt) REVERT: O 84 ARG cc_start: 0.7159 (OUTLIER) cc_final: 0.6331 (ttp-110) REVERT: Q 30 LYS cc_start: 0.7955 (OUTLIER) cc_final: 0.7183 (ttpp) REVERT: R 57 ARG cc_start: 0.7546 (OUTLIER) cc_final: 0.6525 (mtp180) REVERT: T 84 ASN cc_start: 0.6611 (m-40) cc_final: 0.6395 (m110) REVERT: c 35 GLU cc_start: 0.6745 (OUTLIER) cc_final: 0.6496 (mt-10) REVERT: e 198 GLU cc_start: 0.6873 (OUTLIER) cc_final: 0.6200 (tp30) REVERT: f 10 ASP cc_start: 0.5813 (OUTLIER) cc_final: 0.5523 (m-30) REVERT: g 130 GLU cc_start: 0.6900 (pp20) cc_final: 0.6699 (pp20) REVERT: j 111 LYS cc_start: 0.6882 (mtpp) cc_final: 0.6525 (mtmm) REVERT: j 113 MET cc_start: 0.6016 (mmt) cc_final: 0.5766 (mmt) REVERT: k 1 MET cc_start: 0.7187 (OUTLIER) cc_final: 0.6842 (ptm) REVERT: l 1 MET cc_start: 0.6118 (tpt) cc_final: 0.4769 (tpp) REVERT: l 22 GLN cc_start: 0.7840 (OUTLIER) cc_final: 0.7242 (mp10) REVERT: l 104 GLU cc_start: 0.7385 (tt0) cc_final: 0.7134 (mt-10) REVERT: m 82 GLU cc_start: 0.6902 (OUTLIER) cc_final: 0.6567 (tt0) REVERT: m 86 ARG cc_start: 0.7477 (OUTLIER) cc_final: 0.6054 (ttp80) REVERT: n 104 GLN cc_start: 0.7582 (tt0) cc_final: 0.7379 (tt0) REVERT: o 13 MET cc_start: 0.7856 (OUTLIER) cc_final: 0.7548 (ptm) REVERT: r 78 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7636 (mp0) REVERT: s 1 MET cc_start: 0.5110 (OUTLIER) cc_final: 0.4735 (ptt) REVERT: u 87 GLN cc_start: 0.7642 (mm-40) cc_final: 0.7378 (mm-40) REVERT: v 29 GLU cc_start: 0.7692 (mt-10) cc_final: 0.6904 (tp30) REVERT: v 66 LYS cc_start: 0.8331 (OUTLIER) cc_final: 0.7961 (mtpp) REVERT: x 5 GLU cc_start: 0.6285 (OUTLIER) cc_final: 0.5477 (pm20) REVERT: 0 27 LYS cc_start: 0.7464 (OUTLIER) cc_final: 0.7094 (ttmt) REVERT: 1 25 LYS cc_start: 0.8172 (OUTLIER) cc_final: 0.7362 (ttpp) REVERT: 3 2 LYS cc_start: 0.8059 (OUTLIER) cc_final: 0.7460 (ptmt) REVERT: 4 22 MET cc_start: 0.5753 (OUTLIER) cc_final: 0.5404 (mmp) REVERT: 4 28 VAL cc_start: 0.7107 (t) cc_final: 0.6713 (p) outliers start: 218 outliers final: 99 residues processed: 920 average time/residue: 2.2005 time to fit residues: 2869.6171 Evaluate side-chains 912 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 785 time to evaluate : 6.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 166 GLU Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain E residue 12 GLN Chi-restraints excluded: chain E residue 68 ARG Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 62 MET Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 93 LYS Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain G residue 86 GLN Chi-restraints excluded: chain G residue 114 LYS Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 107 SER Chi-restraints excluded: chain I residue 46 MET Chi-restraints excluded: chain I residue 65 ILE Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 73 SER Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 45 ILE Chi-restraints excluded: chain M residue 55 THR Chi-restraints excluded: chain M residue 74 SER Chi-restraints excluded: chain N residue 16 LEU Chi-restraints excluded: chain N residue 98 LYS Chi-restraints excluded: chain O residue 84 ARG Chi-restraints excluded: chain Q residue 27 ARG Chi-restraints excluded: chain Q residue 30 LYS Chi-restraints excluded: chain Q residue 36 LYS Chi-restraints excluded: chain R residue 24 LYS Chi-restraints excluded: chain R residue 57 ARG Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain S residue 62 VAL Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain U residue 3 VAL Chi-restraints excluded: chain c residue 35 GLU Chi-restraints excluded: chain c residue 229 ASP Chi-restraints excluded: chain d residue 128 ARG Chi-restraints excluded: chain e residue 15 SER Chi-restraints excluded: chain e residue 126 VAL Chi-restraints excluded: chain e residue 169 VAL Chi-restraints excluded: chain e residue 198 GLU Chi-restraints excluded: chain f residue 10 ASP Chi-restraints excluded: chain f residue 25 VAL Chi-restraints excluded: chain f residue 132 VAL Chi-restraints excluded: chain f residue 149 VAL Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 11 VAL Chi-restraints excluded: chain g residue 60 ASP Chi-restraints excluded: chain g residue 79 VAL Chi-restraints excluded: chain g residue 110 SER Chi-restraints excluded: chain g residue 168 VAL Chi-restraints excluded: chain h residue 30 LEU Chi-restraints excluded: chain i residue 14 ASP Chi-restraints excluded: chain i residue 92 MET 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 j residue 76 VAL Chi-restraints excluded: chain k residue 1 MET Chi-restraints excluded: chain k residue 23 ILE Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain l residue 22 GLN Chi-restraints excluded: chain l residue 57 VAL Chi-restraints excluded: chain l residue 89 VAL Chi-restraints excluded: chain l residue 105 MET Chi-restraints excluded: chain m residue 82 GLU Chi-restraints excluded: chain m residue 86 ARG Chi-restraints excluded: chain n residue 24 THR Chi-restraints excluded: chain n residue 60 GLU Chi-restraints excluded: chain n residue 91 SER Chi-restraints excluded: chain o residue 13 MET Chi-restraints excluded: chain o residue 19 SER Chi-restraints excluded: chain o residue 70 VAL Chi-restraints excluded: chain p residue 107 THR Chi-restraints excluded: chain q residue 7 SER Chi-restraints excluded: chain q residue 60 LYS Chi-restraints excluded: chain r residue 3 THR Chi-restraints excluded: chain r residue 13 SER Chi-restraints excluded: chain r residue 29 VAL Chi-restraints excluded: chain r residue 37 THR Chi-restraints excluded: chain r residue 71 VAL Chi-restraints excluded: chain r residue 78 GLU Chi-restraints excluded: chain r residue 100 THR Chi-restraints excluded: chain s residue 1 MET Chi-restraints excluded: chain s residue 22 THR Chi-restraints excluded: chain s residue 85 VAL Chi-restraints excluded: chain t residue 58 ILE Chi-restraints excluded: chain t residue 72 ILE Chi-restraints excluded: chain t residue 103 ILE Chi-restraints excluded: chain v residue 43 THR Chi-restraints excluded: chain v residue 66 LYS Chi-restraints excluded: chain w residue 13 VAL Chi-restraints excluded: chain w residue 42 SER Chi-restraints excluded: chain x residue 5 GLU Chi-restraints excluded: chain x residue 46 VAL Chi-restraints excluded: chain x residue 54 LYS Chi-restraints excluded: chain y residue 10 THR Chi-restraints excluded: chain y residue 52 SER Chi-restraints excluded: chain z residue 43 ILE Chi-restraints excluded: chain 0 residue 17 THR Chi-restraints excluded: chain 0 residue 27 LYS Chi-restraints excluded: chain 1 residue 25 LYS Chi-restraints excluded: chain 1 residue 45 SER Chi-restraints excluded: chain 2 residue 54 ASP Chi-restraints excluded: chain 3 residue 2 LYS Chi-restraints excluded: chain 4 residue 22 MET Chi-restraints excluded: chain 4 residue 66 ILE 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: 4.9990 chunk 394 optimal weight: 10.0000 chunk 814 optimal weight: 2.9990 chunk 660 optimal weight: 20.0000 chunk 1 optimal weight: 10.0000 chunk 487 optimal weight: 20.0000 chunk 857 optimal weight: 6.9990 chunk 240 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 142 HIS H 18 GLN H 118 GLN I 4 ASN I 5 GLN I 32 GLN K 38 GLN N 49 GLN O 35 GLN P 40 ASN U 9 ASN ** d 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 42 ASN g 104 ASN o 52 ASN q 86 GLN t 69 ASN ** 4 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.1175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 153876 Z= 0.295 Angle : 0.738 14.946 230275 Z= 0.393 Chirality : 0.041 0.367 29306 Planarity : 0.007 0.142 12253 Dihedral : 23.086 179.617 77146 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.53 % Favored : 95.41 % Rotamer: Outliers : 4.53 % Allowed : 19.58 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.11), residues: 5474 helix: 0.70 (0.12), residues: 1865 sheet: -0.53 (0.16), residues: 1044 loop : -1.08 (0.12), residues: 2565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 201 HIS 0.008 0.001 HIS F 3 PHE 0.021 0.002 PHE B 50 TYR 0.023 0.002 TYR g 94 ARG 0.010 0.001 ARG u 79 *********************** 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: 207 poor density : 805 time to evaluate : 6.326 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 59 LYS cc_start: 0.5244 (OUTLIER) cc_final: 0.4903 (tmtt) REVERT: C 166 GLU cc_start: 0.6872 (OUTLIER) cc_final: 0.5722 (mt-10) REVERT: D 200 ILE cc_start: 0.7055 (OUTLIER) cc_final: 0.6847 (mm) REVERT: E 68 ARG cc_start: 0.7214 (OUTLIER) cc_final: 0.6980 (mtm110) REVERT: G 42 ILE cc_start: 0.7283 (OUTLIER) cc_final: 0.6978 (mp) REVERT: G 86 GLN cc_start: 0.6892 (OUTLIER) cc_final: 0.6090 (mt0) REVERT: M 45 ILE cc_start: 0.6302 (OUTLIER) cc_final: 0.5909 (pt) REVERT: O 84 ARG cc_start: 0.7108 (OUTLIER) cc_final: 0.6289 (ttp-110) REVERT: Q 30 LYS cc_start: 0.7929 (OUTLIER) cc_final: 0.7165 (ttpp) REVERT: T 84 ASN cc_start: 0.6670 (m-40) cc_final: 0.6433 (m110) REVERT: e 198 GLU cc_start: 0.6860 (OUTLIER) cc_final: 0.6140 (tp30) REVERT: f 10 ASP cc_start: 0.5767 (OUTLIER) cc_final: 0.5504 (m-30) REVERT: f 44 ILE cc_start: 0.6034 (mm) cc_final: 0.5816 (mt) REVERT: f 133 ARG cc_start: 0.5969 (OUTLIER) cc_final: 0.5507 (mtt90) REVERT: j 1 MET cc_start: 0.8437 (OUTLIER) cc_final: 0.8234 (mtt) REVERT: j 111 LYS cc_start: 0.6841 (mtpp) cc_final: 0.6493 (mtmm) REVERT: j 113 MET cc_start: 0.6094 (mmt) cc_final: 0.5717 (mmm) REVERT: l 1 MET cc_start: 0.6078 (tpt) cc_final: 0.4552 (tpp) REVERT: l 22 GLN cc_start: 0.7841 (OUTLIER) cc_final: 0.7247 (mp10) REVERT: l 104 GLU cc_start: 0.7356 (tt0) cc_final: 0.7097 (mt-10) REVERT: m 82 GLU cc_start: 0.6973 (OUTLIER) cc_final: 0.6631 (tt0) REVERT: n 104 GLN cc_start: 0.7521 (tt0) cc_final: 0.7105 (tt0) REVERT: o 13 MET cc_start: 0.7806 (OUTLIER) cc_final: 0.7528 (ptm) REVERT: r 78 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7545 (mp0) REVERT: s 1 MET cc_start: 0.5118 (OUTLIER) cc_final: 0.4755 (ptt) REVERT: u 63 ILE cc_start: 0.7836 (OUTLIER) cc_final: 0.7611 (mt) REVERT: u 87 GLN cc_start: 0.7638 (mm-40) cc_final: 0.7373 (mm-40) REVERT: v 29 GLU cc_start: 0.7679 (mt-10) cc_final: 0.6915 (tp30) REVERT: v 66 LYS cc_start: 0.8318 (OUTLIER) cc_final: 0.8030 (mtpp) REVERT: 0 27 LYS cc_start: 0.7434 (OUTLIER) cc_final: 0.7093 (ttmt) REVERT: 3 2 LYS cc_start: 0.7994 (OUTLIER) cc_final: 0.7403 (ptmt) REVERT: 3 36 ARG cc_start: 0.8458 (OUTLIER) cc_final: 0.8248 (ptm160) REVERT: 4 22 MET cc_start: 0.5697 (OUTLIER) cc_final: 0.5418 (mmp) REVERT: 4 28 VAL cc_start: 0.7106 (t) cc_final: 0.6746 (p) outliers start: 207 outliers final: 108 residues processed: 922 average time/residue: 2.1677 time to fit residues: 2843.8103 Evaluate side-chains 916 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 784 time to evaluate : 6.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 166 GLU Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain E residue 68 ARG Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 93 LYS Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 40 GLU Chi-restraints excluded: chain G residue 42 ILE Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 86 GLN Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 107 SER Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 46 MET Chi-restraints excluded: chain I residue 65 ILE Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 73 SER Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 129 VAL Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain M residue 7 ILE Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 45 ILE Chi-restraints excluded: chain M residue 55 THR Chi-restraints excluded: chain N residue 16 LEU Chi-restraints excluded: chain N residue 30 ILE Chi-restraints excluded: chain N residue 98 LYS Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain O residue 84 ARG Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 27 ARG Chi-restraints excluded: chain Q residue 30 LYS Chi-restraints excluded: chain Q residue 36 LYS Chi-restraints excluded: chain R residue 24 LYS Chi-restraints excluded: chain R residue 57 ARG Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain S residue 62 VAL Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain U residue 3 VAL Chi-restraints excluded: chain c residue 229 ASP Chi-restraints excluded: chain d residue 128 ARG Chi-restraints excluded: chain d residue 180 VAL Chi-restraints excluded: chain e residue 15 SER Chi-restraints excluded: chain e residue 169 VAL Chi-restraints excluded: chain e residue 198 GLU Chi-restraints excluded: chain f residue 10 ASP Chi-restraints excluded: chain f residue 132 VAL Chi-restraints excluded: chain f residue 133 ARG Chi-restraints excluded: chain f residue 149 VAL Chi-restraints excluded: chain f residue 164 GLU Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 11 VAL Chi-restraints excluded: chain g residue 49 THR Chi-restraints excluded: chain g residue 60 ASP Chi-restraints excluded: chain g residue 110 SER Chi-restraints excluded: chain g residue 168 VAL Chi-restraints excluded: chain h residue 30 LEU Chi-restraints excluded: chain i residue 92 MET Chi-restraints excluded: chain j residue 1 MET Chi-restraints excluded: chain j residue 19 VAL Chi-restraints excluded: chain j residue 62 VAL Chi-restraints excluded: chain j residue 76 VAL Chi-restraints excluded: chain j residue 116 ILE Chi-restraints excluded: chain k residue 23 ILE Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain l residue 22 GLN Chi-restraints excluded: chain l residue 57 VAL Chi-restraints excluded: chain l residue 89 VAL Chi-restraints excluded: chain l residue 105 MET Chi-restraints excluded: chain l residue 108 VAL Chi-restraints excluded: chain m residue 82 GLU Chi-restraints excluded: chain n residue 60 GLU Chi-restraints excluded: chain n residue 91 SER Chi-restraints excluded: chain o residue 13 MET Chi-restraints excluded: chain o residue 19 SER Chi-restraints excluded: chain o residue 70 VAL Chi-restraints excluded: chain p residue 19 LYS Chi-restraints excluded: chain p residue 107 THR Chi-restraints excluded: chain q residue 7 SER Chi-restraints excluded: chain q residue 60 LYS Chi-restraints excluded: chain r residue 3 THR Chi-restraints excluded: chain r residue 13 SER Chi-restraints excluded: chain r residue 78 GLU Chi-restraints excluded: chain r residue 100 THR Chi-restraints excluded: chain s residue 1 MET Chi-restraints excluded: chain s residue 22 THR Chi-restraints excluded: chain s residue 85 VAL Chi-restraints excluded: chain t residue 58 ILE Chi-restraints excluded: chain t residue 72 ILE Chi-restraints excluded: chain t residue 103 ILE Chi-restraints excluded: chain u residue 63 ILE Chi-restraints excluded: chain v residue 43 THR Chi-restraints excluded: chain v residue 66 LYS Chi-restraints excluded: chain w residue 13 VAL Chi-restraints excluded: chain w residue 42 SER Chi-restraints excluded: chain x residue 30 MET Chi-restraints excluded: chain x residue 46 VAL Chi-restraints excluded: chain x residue 57 LEU Chi-restraints excluded: chain y residue 6 LYS Chi-restraints excluded: chain y residue 10 THR Chi-restraints excluded: chain y residue 52 SER Chi-restraints excluded: chain 0 residue 17 THR Chi-restraints excluded: chain 0 residue 27 LYS Chi-restraints excluded: chain 1 residue 45 SER Chi-restraints excluded: chain 3 residue 2 LYS Chi-restraints excluded: chain 3 residue 36 ARG Chi-restraints excluded: chain 4 residue 22 MET Chi-restraints excluded: chain 4 residue 66 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 988 random chunks: chunk 321 optimal weight: 6.9990 chunk 860 optimal weight: 3.9990 chunk 188 optimal weight: 8.9990 chunk 560 optimal weight: 10.0000 chunk 235 optimal weight: 0.8980 chunk 955 optimal weight: 0.7980 chunk 793 optimal weight: 2.9990 chunk 442 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 316 optimal weight: 0.9990 chunk 501 optimal weight: 10.0000 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 58 ASN B 178 ASN D 116 GLN G 142 HIS I 4 ASN I 5 GLN I 32 GLN K 38 GLN N 49 GLN O 62 GLN U 9 ASN ** d 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 104 ASN k 104 GLN o 52 ASN q 86 GLN t 69 ASN u 80 HIS u 87 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.1064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 153876 Z= 0.146 Angle : 0.636 13.624 230275 Z= 0.352 Chirality : 0.036 0.364 29306 Planarity : 0.006 0.130 12253 Dihedral : 23.054 179.313 77146 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.95 % Favored : 96.00 % Rotamer: Outliers : 3.35 % Allowed : 21.13 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.11), residues: 5474 helix: 1.11 (0.12), residues: 1863 sheet: -0.44 (0.16), residues: 1045 loop : -0.91 (0.12), residues: 2566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 201 HIS 0.005 0.001 HIS i 47 PHE 0.026 0.002 PHE B 50 TYR 0.021 0.002 TYR q 2 ARG 0.011 0.000 ARG u 79 *********************** 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 947 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 794 time to evaluate : 6.369 Fit side-chains revert: symmetry clash REVERT: B 59 LYS cc_start: 0.5235 (OUTLIER) cc_final: 0.4844 (tmtt) REVERT: B 91 PHE cc_start: 0.6601 (p90) cc_final: 0.6190 (p90) REVERT: C 166 GLU cc_start: 0.6834 (OUTLIER) cc_final: 0.5711 (mt-10) REVERT: D 200 ILE cc_start: 0.7044 (OUTLIER) cc_final: 0.6842 (mm) REVERT: G 42 ILE cc_start: 0.7200 (OUTLIER) cc_final: 0.6942 (mp) REVERT: G 78 ARG cc_start: 0.6427 (OUTLIER) cc_final: 0.4257 (tpt-90) REVERT: G 86 GLN cc_start: 0.6901 (OUTLIER) cc_final: 0.6060 (mt0) REVERT: G 114 LYS cc_start: 0.5731 (OUTLIER) cc_final: 0.5075 (ttmm) REVERT: M 45 ILE cc_start: 0.6199 (OUTLIER) cc_final: 0.5826 (pt) REVERT: O 84 ARG cc_start: 0.7072 (OUTLIER) cc_final: 0.6255 (ttp-110) REVERT: T 43 ASP cc_start: 0.5183 (OUTLIER) cc_final: 0.4525 (m-30) REVERT: T 84 ASN cc_start: 0.6419 (m-40) cc_final: 0.6187 (m110) REVERT: d 128 ARG cc_start: 0.7342 (OUTLIER) cc_final: 0.6898 (mmp80) REVERT: f 133 ARG cc_start: 0.5965 (OUTLIER) cc_final: 0.5513 (mtt90) REVERT: g 60 ASP cc_start: 0.4383 (OUTLIER) cc_final: 0.3892 (p0) REVERT: j 1 MET cc_start: 0.8418 (OUTLIER) cc_final: 0.8206 (mtt) REVERT: j 49 ARG cc_start: 0.6308 (OUTLIER) cc_final: 0.5933 (mpp-170) REVERT: j 106 GLU cc_start: 0.6847 (mp0) cc_final: 0.6435 (mp0) REVERT: j 111 LYS cc_start: 0.6826 (mtpp) cc_final: 0.6461 (mtmm) REVERT: j 113 MET cc_start: 0.6044 (mmt) cc_final: 0.5718 (mmm) REVERT: l 1 MET cc_start: 0.5992 (tpt) cc_final: 0.4395 (tpp) REVERT: l 22 GLN cc_start: 0.7792 (OUTLIER) cc_final: 0.7175 (mp10) REVERT: l 104 GLU cc_start: 0.7219 (tt0) cc_final: 0.6937 (mt-10) REVERT: n 104 GLN cc_start: 0.7516 (tt0) cc_final: 0.7133 (tt0) REVERT: r 78 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7443 (mp0) REVERT: u 87 GLN cc_start: 0.7594 (OUTLIER) cc_final: 0.7321 (mm-40) REVERT: v 29 GLU cc_start: 0.7621 (mt-10) cc_final: 0.6919 (tp30) REVERT: 3 2 LYS cc_start: 0.7909 (OUTLIER) cc_final: 0.7426 (ptmt) REVERT: 4 11 GLU cc_start: 0.6209 (mm-30) cc_final: 0.5561 (tm-30) REVERT: 4 28 VAL cc_start: 0.7004 (t) cc_final: 0.6660 (p) outliers start: 153 outliers final: 75 residues processed: 880 average time/residue: 2.1970 time to fit residues: 2750.0412 Evaluate side-chains 861 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 767 time to evaluate : 6.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 166 GLU Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain F residue 62 MET Chi-restraints excluded: chain F residue 93 LYS Chi-restraints excluded: chain G residue 42 ILE Chi-restraints excluded: chain G residue 78 ARG Chi-restraints excluded: chain G residue 86 GLN Chi-restraints excluded: chain G residue 114 LYS Chi-restraints excluded: chain G residue 130 ASN Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 107 SER Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 46 MET Chi-restraints excluded: chain I residue 65 ILE Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain J residue 66 GLU Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 45 ILE Chi-restraints excluded: chain M residue 74 SER Chi-restraints excluded: chain N residue 16 LEU Chi-restraints excluded: chain N residue 98 LYS Chi-restraints excluded: chain O residue 84 ARG Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain Q residue 67 LEU Chi-restraints excluded: chain R residue 24 LYS Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain S residue 62 VAL Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain T residue 43 ASP Chi-restraints excluded: chain U residue 3 VAL Chi-restraints excluded: chain d residue 128 ARG Chi-restraints excluded: chain d residue 180 VAL Chi-restraints excluded: chain e residue 15 SER Chi-restraints excluded: chain e residue 169 VAL Chi-restraints excluded: chain f residue 50 LEU Chi-restraints excluded: chain f residue 132 VAL Chi-restraints excluded: chain f residue 133 ARG Chi-restraints excluded: chain f residue 149 VAL Chi-restraints excluded: chain f residue 164 GLU Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 11 VAL Chi-restraints excluded: chain g residue 49 THR Chi-restraints excluded: chain g residue 60 ASP Chi-restraints excluded: chain g residue 75 MET Chi-restraints excluded: chain g residue 79 VAL Chi-restraints excluded: chain g residue 110 SER Chi-restraints excluded: chain g residue 168 VAL Chi-restraints excluded: chain i residue 92 MET Chi-restraints excluded: chain i residue 138 GLN Chi-restraints excluded: chain j residue 1 MET Chi-restraints excluded: chain j residue 19 VAL Chi-restraints excluded: chain j residue 49 ARG Chi-restraints excluded: chain j residue 62 VAL Chi-restraints excluded: chain j residue 76 VAL Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain l residue 22 GLN Chi-restraints excluded: chain l residue 57 VAL Chi-restraints excluded: chain l residue 89 VAL Chi-restraints excluded: chain l residue 108 VAL Chi-restraints excluded: chain n residue 24 THR Chi-restraints excluded: chain n residue 60 GLU Chi-restraints excluded: chain o residue 19 SER Chi-restraints excluded: chain p residue 107 THR Chi-restraints excluded: chain p residue 117 LEU Chi-restraints excluded: chain q residue 60 LYS Chi-restraints excluded: chain r residue 13 SER Chi-restraints excluded: chain r residue 78 GLU Chi-restraints excluded: chain s residue 22 THR Chi-restraints excluded: chain s residue 85 VAL Chi-restraints excluded: chain t residue 58 ILE Chi-restraints excluded: chain t residue 72 ILE Chi-restraints excluded: chain t residue 103 ILE Chi-restraints excluded: chain u residue 87 GLN Chi-restraints excluded: chain v residue 43 THR Chi-restraints excluded: chain w residue 42 SER Chi-restraints excluded: chain x residue 54 LYS Chi-restraints excluded: chain x residue 56 LEU Chi-restraints excluded: chain y residue 6 LYS Chi-restraints excluded: chain y residue 10 THR Chi-restraints excluded: chain y residue 52 SER Chi-restraints excluded: chain 0 residue 17 THR Chi-restraints excluded: chain 2 residue 55 LEU Chi-restraints excluded: chain 3 residue 2 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 988 random chunks: chunk 921 optimal weight: 10.0000 chunk 107 optimal weight: 10.0000 chunk 544 optimal weight: 10.0000 chunk 698 optimal weight: 5.9990 chunk 540 optimal weight: 10.0000 chunk 804 optimal weight: 8.9990 chunk 533 optimal weight: 10.0000 chunk 952 optimal weight: 7.9990 chunk 595 optimal weight: 10.0000 chunk 580 optimal weight: 10.0000 chunk 439 optimal weight: 10.0000 overall best weight: 8.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 116 GLN G 142 HIS H 118 GLN I 4 ASN I 5 GLN I 32 GLN K 38 GLN M 8 ASN N 49 GLN O 35 GLN P 40 ASN U 9 ASN ** d 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 104 ASN o 52 ASN q 86 GLN t 69 ASN x 20 ASN ** 4 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.091 153876 Z= 0.414 Angle : 0.844 16.355 230275 Z= 0.436 Chirality : 0.046 0.415 29306 Planarity : 0.008 0.149 12253 Dihedral : 23.141 179.428 77146 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.28 % Favored : 94.67 % Rotamer: Outliers : 4.75 % Allowed : 20.69 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.11), residues: 5474 helix: 0.55 (0.12), residues: 1863 sheet: -0.52 (0.16), residues: 1041 loop : -1.12 (0.12), residues: 2570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 201 HIS 0.010 0.002 HIS F 3 PHE 0.023 0.003 PHE B 50 TYR 0.026 0.003 TYR g 94 ARG 0.011 0.001 ARG u 79 *********************** 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 1016 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 217 poor density : 799 time to evaluate : 6.271 Fit side-chains revert: symmetry clash REVERT: B 59 LYS cc_start: 0.5280 (OUTLIER) cc_final: 0.4949 (tmtt) REVERT: C 166 GLU cc_start: 0.6898 (OUTLIER) cc_final: 0.5787 (mt-10) REVERT: E 68 ARG cc_start: 0.7234 (OUTLIER) cc_final: 0.7006 (mtm110) REVERT: E 152 MET cc_start: 0.7050 (OUTLIER) cc_final: 0.6750 (mpp) REVERT: G 40 GLU cc_start: 0.6331 (OUTLIER) cc_final: 0.6079 (mt-10) REVERT: G 78 ARG cc_start: 0.6505 (OUTLIER) cc_final: 0.4735 (tpt-90) REVERT: G 86 GLN cc_start: 0.6919 (OUTLIER) cc_final: 0.6268 (mt0) REVERT: G 114 LYS cc_start: 0.5951 (OUTLIER) cc_final: 0.5291 (ttmm) REVERT: M 45 ILE cc_start: 0.6338 (OUTLIER) cc_final: 0.5938 (pt) REVERT: O 84 ARG cc_start: 0.7157 (OUTLIER) cc_final: 0.6328 (ttp-110) REVERT: Q 30 LYS cc_start: 0.7942 (OUTLIER) cc_final: 0.7163 (ttpp) REVERT: T 43 ASP cc_start: 0.5321 (OUTLIER) cc_final: 0.4569 (m-30) REVERT: U 63 GLU cc_start: 0.2472 (OUTLIER) cc_final: 0.2029 (mm-30) REVERT: e 198 GLU cc_start: 0.6873 (OUTLIER) cc_final: 0.6152 (tp30) REVERT: f 10 ASP cc_start: 0.5756 (OUTLIER) cc_final: 0.5429 (m-30) REVERT: f 21 ASN cc_start: 0.5795 (OUTLIER) cc_final: 0.5365 (m110) REVERT: f 133 ARG cc_start: 0.6006 (OUTLIER) cc_final: 0.5335 (mtt180) REVERT: j 105 ARG cc_start: 0.6451 (mmt180) cc_final: 0.6103 (tpp80) REVERT: j 113 MET cc_start: 0.6001 (mmt) cc_final: 0.5615 (mmm) REVERT: l 1 MET cc_start: 0.6140 (tpt) cc_final: 0.4610 (tpp) REVERT: l 22 GLN cc_start: 0.7863 (OUTLIER) cc_final: 0.7236 (mp10) REVERT: l 104 GLU cc_start: 0.7367 (tt0) cc_final: 0.7108 (mt-10) REVERT: m 82 GLU cc_start: 0.6977 (OUTLIER) cc_final: 0.6609 (tt0) REVERT: r 4 ILE cc_start: 0.8047 (mp) cc_final: 0.7714 (mp) REVERT: r 78 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7656 (mp0) REVERT: s 26 LYS cc_start: 0.7073 (mmpt) cc_final: 0.6871 (mttm) REVERT: u 87 GLN cc_start: 0.7834 (mt0) cc_final: 0.7494 (mm-40) REVERT: v 66 LYS cc_start: 0.8343 (OUTLIER) cc_final: 0.8061 (mtpp) REVERT: x 5 GLU cc_start: 0.6324 (OUTLIER) cc_final: 0.5462 (pm20) REVERT: 1 25 LYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7408 (ttpp) REVERT: 1 42 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.7919 (mp) REVERT: 3 2 LYS cc_start: 0.8032 (OUTLIER) cc_final: 0.7438 (ptmt) REVERT: 3 36 ARG cc_start: 0.8479 (OUTLIER) cc_final: 0.8240 (ptm160) REVERT: 4 22 MET cc_start: 0.5712 (OUTLIER) cc_final: 0.5407 (mmp) REVERT: 4 28 VAL cc_start: 0.7179 (t) cc_final: 0.6771 (p) outliers start: 217 outliers final: 120 residues processed: 924 average time/residue: 2.1485 time to fit residues: 2830.0285 Evaluate side-chains 922 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 775 time to evaluate : 6.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 166 GLU Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain E residue 68 ARG Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 142 ASP Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 93 LYS Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 40 GLU Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 78 ARG Chi-restraints excluded: chain G residue 86 GLN Chi-restraints excluded: chain G residue 114 LYS Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 107 SER Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 46 MET Chi-restraints excluded: chain I residue 65 ILE Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain J residue 66 GLU Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 129 VAL Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 45 ILE Chi-restraints excluded: chain M residue 74 SER Chi-restraints excluded: chain N residue 16 LEU Chi-restraints excluded: chain N residue 30 ILE Chi-restraints excluded: chain N residue 98 LYS Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain O residue 84 ARG Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 27 ARG Chi-restraints excluded: chain Q residue 30 LYS Chi-restraints excluded: chain Q residue 79 VAL Chi-restraints excluded: chain R residue 24 LYS Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain S residue 17 LYS Chi-restraints excluded: chain S residue 62 VAL Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain T residue 43 ASP Chi-restraints excluded: chain U residue 3 VAL Chi-restraints excluded: chain U residue 63 GLU Chi-restraints excluded: chain c residue 229 ASP Chi-restraints excluded: chain d residue 128 ARG Chi-restraints excluded: chain d residue 180 VAL Chi-restraints excluded: chain e residue 15 SER Chi-restraints excluded: chain e residue 126 VAL Chi-restraints excluded: chain e residue 169 VAL Chi-restraints excluded: chain e residue 198 GLU Chi-restraints excluded: chain f residue 10 ASP Chi-restraints excluded: chain f residue 21 ASN Chi-restraints excluded: chain f residue 25 VAL Chi-restraints excluded: chain f residue 132 VAL Chi-restraints excluded: chain f residue 133 ARG Chi-restraints excluded: chain f residue 149 VAL Chi-restraints excluded: chain f residue 164 GLU Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 11 VAL Chi-restraints excluded: chain g residue 17 VAL Chi-restraints excluded: chain g residue 49 THR Chi-restraints excluded: chain g residue 60 ASP Chi-restraints excluded: chain g residue 75 MET Chi-restraints excluded: chain g residue 79 VAL Chi-restraints excluded: chain g residue 110 SER Chi-restraints excluded: chain g residue 168 VAL Chi-restraints excluded: chain h residue 2 GLN Chi-restraints excluded: chain h residue 30 LEU Chi-restraints excluded: chain i residue 92 MET Chi-restraints excluded: chain j residue 19 VAL Chi-restraints excluded: chain j residue 62 VAL Chi-restraints excluded: chain j residue 76 VAL Chi-restraints excluded: chain j residue 116 ILE Chi-restraints excluded: chain k residue 23 ILE Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain l residue 22 GLN Chi-restraints excluded: chain l residue 57 VAL Chi-restraints excluded: chain l residue 89 VAL Chi-restraints excluded: chain l residue 105 MET Chi-restraints excluded: chain l residue 108 VAL Chi-restraints excluded: chain m residue 54 LEU Chi-restraints excluded: chain m residue 82 GLU Chi-restraints excluded: chain n residue 24 THR Chi-restraints excluded: chain n residue 60 GLU Chi-restraints excluded: chain n residue 91 SER Chi-restraints excluded: chain o residue 19 SER Chi-restraints excluded: chain o residue 40 LEU Chi-restraints excluded: chain o residue 70 VAL Chi-restraints excluded: chain p residue 107 THR Chi-restraints excluded: chain q residue 60 LYS Chi-restraints excluded: chain r residue 3 THR Chi-restraints excluded: chain r residue 13 SER Chi-restraints excluded: chain r residue 29 VAL Chi-restraints excluded: chain r residue 37 THR Chi-restraints excluded: chain r residue 71 VAL Chi-restraints excluded: chain r residue 78 GLU Chi-restraints excluded: chain r residue 100 THR Chi-restraints excluded: chain r residue 101 SER Chi-restraints excluded: chain s residue 22 THR Chi-restraints excluded: chain s residue 85 VAL Chi-restraints excluded: chain t residue 58 ILE Chi-restraints excluded: chain t residue 72 ILE Chi-restraints excluded: chain t residue 103 ILE Chi-restraints excluded: chain v residue 43 THR Chi-restraints excluded: chain v residue 66 LYS Chi-restraints excluded: chain w residue 13 VAL Chi-restraints excluded: chain w residue 42 SER Chi-restraints excluded: chain x residue 5 GLU Chi-restraints excluded: chain x residue 46 VAL Chi-restraints excluded: chain x residue 54 LYS Chi-restraints excluded: chain x residue 57 LEU Chi-restraints excluded: chain y residue 6 LYS Chi-restraints excluded: chain y residue 10 THR Chi-restraints excluded: chain y residue 52 SER Chi-restraints excluded: chain 0 residue 17 THR Chi-restraints excluded: chain 0 residue 27 LYS Chi-restraints excluded: chain 1 residue 25 LYS Chi-restraints excluded: chain 1 residue 42 LEU Chi-restraints excluded: chain 1 residue 45 SER Chi-restraints excluded: chain 2 residue 54 ASP Chi-restraints excluded: chain 2 residue 59 ILE Chi-restraints excluded: chain 3 residue 2 LYS Chi-restraints excluded: chain 3 residue 36 ARG Chi-restraints excluded: chain 4 residue 22 MET Chi-restraints excluded: chain 4 residue 66 ILE 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: 6.9990 chunk 568 optimal weight: 10.0000 chunk 286 optimal weight: 20.0000 chunk 187 optimal weight: 0.9980 chunk 184 optimal weight: 6.9990 chunk 605 optimal weight: 10.0000 chunk 648 optimal weight: 10.0000 chunk 470 optimal weight: 30.0000 chunk 88 optimal weight: 10.0000 chunk 748 optimal weight: 7.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 GLN G 142 HIS I 4 ASN I 5 GLN I 32 GLN K 38 GLN N 49 GLN N 60 GLN O 62 GLN ** d 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 42 ASN g 104 ASN o 52 ASN q 86 GLN t 69 ASN u 87 GLN ** 4 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.110 153876 Z= 0.331 Angle : 0.774 15.285 230275 Z= 0.409 Chirality : 0.043 0.389 29306 Planarity : 0.008 0.144 12253 Dihedral : 23.133 179.358 77146 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.99 % Favored : 94.96 % Rotamer: Outliers : 4.51 % Allowed : 21.78 % Favored : 73.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.11), residues: 5474 helix: 0.52 (0.12), residues: 1865 sheet: -0.57 (0.16), residues: 1049 loop : -1.12 (0.12), residues: 2560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 201 HIS 0.009 0.001 HIS D 198 PHE 0.024 0.002 PHE B 50 TYR 0.021 0.002 TYR q 2 ARG 0.012 0.001 ARG u 79 *********************** 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 986 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 206 poor density : 780 time to evaluate : 5.868 Fit side-chains revert: symmetry clash REVERT: B 59 LYS cc_start: 0.5301 (OUTLIER) cc_final: 0.4920 (tmtt) REVERT: B 141 LEU cc_start: 0.5117 (mt) cc_final: 0.4897 (mt) REVERT: B 184 PHE cc_start: 0.6603 (OUTLIER) cc_final: 0.5787 (m-80) REVERT: C 129 MET cc_start: 0.5810 (OUTLIER) cc_final: 0.5477 (mmt) REVERT: C 166 GLU cc_start: 0.6891 (OUTLIER) cc_final: 0.5727 (mt-10) REVERT: E 68 ARG cc_start: 0.7207 (OUTLIER) cc_final: 0.6998 (mtm110) REVERT: E 152 MET cc_start: 0.7027 (OUTLIER) cc_final: 0.6699 (mpp) REVERT: G 40 GLU cc_start: 0.6321 (OUTLIER) cc_final: 0.6074 (mt-10) REVERT: G 42 ILE cc_start: 0.7392 (mp) cc_final: 0.7061 (mp) REVERT: G 78 ARG cc_start: 0.6540 (OUTLIER) cc_final: 0.4422 (tpt-90) REVERT: G 86 GLN cc_start: 0.6899 (OUTLIER) cc_final: 0.6174 (mt0) REVERT: G 114 LYS cc_start: 0.5853 (OUTLIER) cc_final: 0.5199 (ttmm) REVERT: I 88 MET cc_start: 0.6737 (OUTLIER) cc_final: 0.6308 (mpp) REVERT: K 116 ILE cc_start: 0.7834 (OUTLIER) cc_final: 0.7286 (tp) REVERT: M 45 ILE cc_start: 0.6320 (OUTLIER) cc_final: 0.5925 (pt) REVERT: O 84 ARG cc_start: 0.7108 (OUTLIER) cc_final: 0.6283 (ttp-110) REVERT: T 43 ASP cc_start: 0.5259 (OUTLIER) cc_final: 0.4517 (m-30) REVERT: e 198 GLU cc_start: 0.6877 (OUTLIER) cc_final: 0.6155 (tp30) REVERT: f 10 ASP cc_start: 0.5767 (OUTLIER) cc_final: 0.5479 (m-30) REVERT: f 21 ASN cc_start: 0.5803 (OUTLIER) cc_final: 0.5373 (m110) REVERT: f 133 ARG cc_start: 0.5993 (OUTLIER) cc_final: 0.5336 (mtt180) REVERT: j 105 ARG cc_start: 0.6497 (mmt180) cc_final: 0.6222 (tpp80) REVERT: j 113 MET cc_start: 0.6057 (mmt) cc_final: 0.5711 (mmm) REVERT: l 1 MET cc_start: 0.6158 (tpt) cc_final: 0.4559 (tpp) REVERT: l 22 GLN cc_start: 0.7850 (OUTLIER) cc_final: 0.7237 (mp10) REVERT: l 104 GLU cc_start: 0.7347 (tt0) cc_final: 0.7116 (mt-10) REVERT: l 127 LYS cc_start: 0.7635 (OUTLIER) cc_final: 0.7189 (mmmm) REVERT: m 82 GLU cc_start: 0.6990 (OUTLIER) cc_final: 0.6608 (tt0) REVERT: r 78 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7614 (mp0) REVERT: u 87 GLN cc_start: 0.7659 (OUTLIER) cc_final: 0.7328 (mm-40) REVERT: v 29 GLU cc_start: 0.7675 (mt-10) cc_final: 0.6891 (tp30) REVERT: v 66 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.8033 (mtpp) REVERT: x 5 GLU cc_start: 0.6307 (OUTLIER) cc_final: 0.5447 (pm20) REVERT: 1 25 LYS cc_start: 0.8166 (OUTLIER) cc_final: 0.7389 (ttpp) REVERT: 1 42 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.7928 (mp) REVERT: 3 2 LYS cc_start: 0.8032 (OUTLIER) cc_final: 0.7446 (ptmt) REVERT: 3 36 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.8228 (ptm160) REVERT: 4 11 GLU cc_start: 0.6193 (mm-30) cc_final: 0.5563 (tm-30) REVERT: 4 22 MET cc_start: 0.5699 (OUTLIER) cc_final: 0.5398 (mmp) REVERT: 4 28 VAL cc_start: 0.7089 (t) cc_final: 0.6708 (p) outliers start: 206 outliers final: 122 residues processed: 905 average time/residue: 2.1891 time to fit residues: 2826.8527 Evaluate side-chains 926 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 773 time to evaluate : 6.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 184 PHE Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 129 MET Chi-restraints excluded: chain C residue 166 GLU Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain E residue 68 ARG Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 142 ASP Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 93 LYS Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 40 GLU Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 78 ARG Chi-restraints excluded: chain G residue 86 GLN Chi-restraints excluded: chain G residue 114 LYS Chi-restraints excluded: chain G residue 130 ASN Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 107 SER Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain I residue 46 MET Chi-restraints excluded: chain I residue 65 ILE Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 88 MET Chi-restraints excluded: chain J residue 66 GLU Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain K residue 129 VAL Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 45 ILE Chi-restraints excluded: chain M residue 74 SER Chi-restraints excluded: chain M residue 83 LEU Chi-restraints excluded: chain N residue 16 LEU Chi-restraints excluded: chain N residue 30 ILE Chi-restraints excluded: chain N residue 98 LYS Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain O residue 84 ARG Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 27 ARG Chi-restraints excluded: chain R residue 24 LYS Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain S residue 62 VAL Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain T residue 43 ASP Chi-restraints excluded: chain U residue 3 VAL Chi-restraints excluded: chain c residue 180 GLU Chi-restraints excluded: chain c residue 229 ASP Chi-restraints excluded: chain d residue 128 ARG Chi-restraints excluded: chain d residue 180 VAL Chi-restraints excluded: chain e residue 15 SER Chi-restraints excluded: chain e residue 126 VAL Chi-restraints excluded: chain e residue 169 VAL Chi-restraints excluded: chain e residue 198 GLU Chi-restraints excluded: chain f residue 10 ASP Chi-restraints excluded: chain f residue 21 ASN Chi-restraints excluded: chain f residue 25 VAL Chi-restraints excluded: chain f residue 50 LEU Chi-restraints excluded: chain f residue 132 VAL Chi-restraints excluded: chain f residue 133 ARG Chi-restraints excluded: chain f residue 149 VAL Chi-restraints excluded: chain f residue 164 GLU Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 11 VAL Chi-restraints excluded: chain g residue 17 VAL Chi-restraints excluded: chain g residue 49 THR Chi-restraints excluded: chain g residue 60 ASP Chi-restraints excluded: chain g residue 75 MET Chi-restraints excluded: chain g residue 79 VAL Chi-restraints excluded: chain g residue 110 SER Chi-restraints excluded: chain g residue 168 VAL Chi-restraints excluded: chain h residue 2 GLN Chi-restraints excluded: chain h residue 30 LEU Chi-restraints excluded: chain i residue 92 MET Chi-restraints excluded: chain j residue 19 VAL Chi-restraints excluded: chain j residue 62 VAL Chi-restraints excluded: chain j residue 76 VAL Chi-restraints excluded: chain k residue 23 ILE Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain l residue 22 GLN Chi-restraints excluded: chain l residue 57 VAL Chi-restraints excluded: chain l residue 89 VAL Chi-restraints excluded: chain l residue 105 MET Chi-restraints excluded: chain l residue 108 VAL Chi-restraints excluded: chain l residue 127 LYS Chi-restraints excluded: chain m residue 82 GLU Chi-restraints excluded: chain n residue 24 THR Chi-restraints excluded: chain n residue 60 GLU Chi-restraints excluded: chain n residue 91 SER Chi-restraints excluded: chain o residue 19 SER Chi-restraints excluded: chain o residue 40 LEU Chi-restraints excluded: chain o residue 70 VAL Chi-restraints excluded: chain p residue 107 THR Chi-restraints excluded: chain q residue 60 LYS Chi-restraints excluded: chain q residue 96 VAL Chi-restraints excluded: chain r residue 3 THR Chi-restraints excluded: chain r residue 13 SER Chi-restraints excluded: chain r residue 29 VAL Chi-restraints excluded: chain r residue 37 THR Chi-restraints excluded: chain r residue 78 GLU Chi-restraints excluded: chain r residue 100 THR Chi-restraints excluded: chain r residue 101 SER Chi-restraints excluded: chain s residue 22 THR Chi-restraints excluded: chain s residue 85 VAL Chi-restraints excluded: chain t residue 58 ILE Chi-restraints excluded: chain t residue 60 GLU Chi-restraints excluded: chain t residue 72 ILE Chi-restraints excluded: chain t residue 103 ILE Chi-restraints excluded: chain u residue 87 GLN Chi-restraints excluded: chain v residue 43 THR Chi-restraints excluded: chain v residue 66 LYS Chi-restraints excluded: chain w residue 13 VAL Chi-restraints excluded: chain w residue 42 SER Chi-restraints excluded: chain x residue 5 GLU Chi-restraints excluded: chain x residue 30 MET Chi-restraints excluded: chain x residue 46 VAL Chi-restraints excluded: chain x residue 54 LYS Chi-restraints excluded: chain x residue 56 LEU Chi-restraints excluded: chain x residue 57 LEU Chi-restraints excluded: chain y residue 6 LYS Chi-restraints excluded: chain y residue 10 THR Chi-restraints excluded: chain y residue 52 SER Chi-restraints excluded: chain z residue 39 LEU Chi-restraints excluded: chain 0 residue 17 THR Chi-restraints excluded: chain 0 residue 27 LYS Chi-restraints excluded: chain 1 residue 25 LYS Chi-restraints excluded: chain 1 residue 42 LEU Chi-restraints excluded: chain 1 residue 45 SER Chi-restraints excluded: chain 2 residue 54 ASP Chi-restraints excluded: chain 2 residue 59 ILE Chi-restraints excluded: chain 3 residue 2 LYS Chi-restraints excluded: chain 3 residue 36 ARG Chi-restraints excluded: chain 4 residue 22 MET Chi-restraints excluded: chain 4 residue 66 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 988 random chunks: chunk 866 optimal weight: 4.9990 chunk 912 optimal weight: 8.9990 chunk 832 optimal weight: 0.9980 chunk 887 optimal weight: 9.9990 chunk 534 optimal weight: 20.0000 chunk 386 optimal weight: 10.0000 chunk 696 optimal weight: 5.9990 chunk 272 optimal weight: 9.9990 chunk 801 optimal weight: 3.9990 chunk 839 optimal weight: 10.0000 chunk 884 optimal weight: 0.8980 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 GLN G 142 HIS I 4 ASN I 5 GLN I 32 GLN K 38 GLN N 49 GLN N 60 GLN O 62 GLN ** d 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 104 ASN o 52 ASN q 86 GLN t 69 ASN 0 26 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.1114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 153876 Z= 0.200 Angle : 0.662 13.954 230275 Z= 0.362 Chirality : 0.037 0.349 29306 Planarity : 0.007 0.134 12253 Dihedral : 23.020 178.965 77146 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.29 % Favored : 95.65 % Rotamer: Outliers : 3.54 % Allowed : 23.03 % Favored : 73.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.11), residues: 5474 helix: 0.91 (0.12), residues: 1869 sheet: -0.45 (0.16), residues: 1051 loop : -0.99 (0.12), residues: 2554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 201 HIS 0.018 0.001 HIS u 88 PHE 0.022 0.002 PHE B 50 TYR 0.022 0.002 TYR q 2 ARG 0.014 0.000 ARG u 79 *********************** 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 958 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 796 time to evaluate : 6.250 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 184 PHE cc_start: 0.6583 (OUTLIER) cc_final: 0.5783 (m-80) REVERT: C 166 GLU cc_start: 0.6834 (OUTLIER) cc_final: 0.5711 (mt-10) REVERT: G 78 ARG cc_start: 0.6474 (OUTLIER) cc_final: 0.4277 (tpt-90) REVERT: G 86 GLN cc_start: 0.6843 (OUTLIER) cc_final: 0.6019 (mt0) REVERT: G 114 LYS cc_start: 0.5710 (OUTLIER) cc_final: 0.5047 (ttmm) REVERT: K 116 ILE cc_start: 0.7738 (OUTLIER) cc_final: 0.7213 (tp) REVERT: M 45 ILE cc_start: 0.6200 (OUTLIER) cc_final: 0.5811 (pt) REVERT: O 84 ARG cc_start: 0.7078 (OUTLIER) cc_final: 0.6262 (ttp-110) REVERT: Q 30 LYS cc_start: 0.7921 (OUTLIER) cc_final: 0.7171 (ttpp) REVERT: S 44 MET cc_start: 0.5627 (mtt) cc_final: 0.5369 (mtt) REVERT: T 43 ASP cc_start: 0.5253 (OUTLIER) cc_final: 0.4545 (m-30) REVERT: d 128 ARG cc_start: 0.7388 (OUTLIER) cc_final: 0.6843 (mmp80) REVERT: f 10 ASP cc_start: 0.5587 (OUTLIER) cc_final: 0.5360 (m-30) REVERT: f 21 ASN cc_start: 0.5757 (OUTLIER) cc_final: 0.5306 (m110) REVERT: f 133 ARG cc_start: 0.5970 (OUTLIER) cc_final: 0.5525 (mtt90) REVERT: j 105 ARG cc_start: 0.6454 (mmt180) cc_final: 0.6201 (tpp80) REVERT: j 111 LYS cc_start: 0.6885 (mtpp) cc_final: 0.6515 (mtmm) REVERT: j 113 MET cc_start: 0.6069 (mmt) cc_final: 0.5752 (mmm) REVERT: l 1 MET cc_start: 0.6093 (tpt) cc_final: 0.4465 (tpp) REVERT: l 22 GLN cc_start: 0.7819 (OUTLIER) cc_final: 0.7179 (mp10) REVERT: l 104 GLU cc_start: 0.7271 (tt0) cc_final: 0.7027 (mt-10) REVERT: o 13 MET cc_start: 0.7685 (OUTLIER) cc_final: 0.7428 (ptm) REVERT: o 38 LYS cc_start: 0.7090 (ptmm) cc_final: 0.6836 (ptmm) REVERT: r 78 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7420 (mp0) REVERT: v 29 GLU cc_start: 0.7639 (mt-10) cc_final: 0.6907 (tp30) REVERT: v 66 LYS cc_start: 0.8297 (OUTLIER) cc_final: 0.8010 (mtpp) REVERT: x 5 GLU cc_start: 0.6333 (OUTLIER) cc_final: 0.5406 (pm20) REVERT: 1 25 LYS cc_start: 0.8126 (OUTLIER) cc_final: 0.7434 (ttpp) REVERT: 1 42 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.7919 (mp) REVERT: 3 2 LYS cc_start: 0.7938 (OUTLIER) cc_final: 0.7458 (ptmt) REVERT: 4 11 GLU cc_start: 0.6226 (OUTLIER) cc_final: 0.5597 (tm-30) REVERT: 4 28 VAL cc_start: 0.6909 (t) cc_final: 0.6571 (p) outliers start: 162 outliers final: 109 residues processed: 899 average time/residue: 2.1597 time to fit residues: 2763.9765 Evaluate side-chains 909 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 777 time to evaluate : 6.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 184 PHE Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 166 GLU Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain E residue 64 MET Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 142 ASP Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 93 LYS Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 78 ARG Chi-restraints excluded: chain G residue 86 GLN Chi-restraints excluded: chain G residue 114 LYS Chi-restraints excluded: chain G residue 130 ASN Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 107 SER Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 46 MET Chi-restraints excluded: chain I residue 65 ILE Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain J residue 66 GLU Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain K residue 129 VAL Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 45 ILE Chi-restraints excluded: chain N residue 16 LEU Chi-restraints excluded: chain N residue 30 ILE Chi-restraints excluded: chain N residue 98 LYS Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain O residue 84 ARG Chi-restraints excluded: chain Q residue 8 LEU Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 27 ARG Chi-restraints excluded: chain Q residue 30 LYS Chi-restraints excluded: chain R residue 24 LYS Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain S residue 62 VAL Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain T residue 43 ASP Chi-restraints excluded: chain U residue 3 VAL Chi-restraints excluded: chain c residue 180 GLU Chi-restraints excluded: chain d residue 128 ARG Chi-restraints excluded: chain d residue 180 VAL Chi-restraints excluded: chain e residue 15 SER Chi-restraints excluded: chain e residue 169 VAL Chi-restraints excluded: chain f residue 10 ASP Chi-restraints excluded: chain f residue 21 ASN Chi-restraints excluded: chain f residue 25 VAL Chi-restraints excluded: chain f residue 50 LEU Chi-restraints excluded: chain f residue 132 VAL Chi-restraints excluded: chain f residue 133 ARG Chi-restraints excluded: chain f residue 149 VAL Chi-restraints excluded: chain f residue 164 GLU Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 11 VAL Chi-restraints excluded: chain g residue 17 VAL Chi-restraints excluded: chain g residue 49 THR Chi-restraints excluded: chain g residue 79 VAL Chi-restraints excluded: chain g residue 110 SER Chi-restraints excluded: chain g residue 168 VAL Chi-restraints excluded: chain h residue 30 LEU Chi-restraints excluded: chain i residue 92 MET Chi-restraints excluded: chain i residue 138 GLN Chi-restraints excluded: chain j residue 19 VAL Chi-restraints excluded: chain j residue 62 VAL Chi-restraints excluded: chain j residue 76 VAL Chi-restraints excluded: chain k residue 23 ILE Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain l residue 22 GLN Chi-restraints excluded: chain l residue 57 VAL Chi-restraints excluded: chain l residue 89 VAL Chi-restraints excluded: chain l residue 105 MET Chi-restraints excluded: chain l residue 108 VAL Chi-restraints excluded: chain m residue 54 LEU Chi-restraints excluded: chain n residue 24 THR Chi-restraints excluded: chain n residue 60 GLU Chi-restraints excluded: chain n residue 91 SER Chi-restraints excluded: chain o residue 13 MET Chi-restraints excluded: chain o residue 19 SER Chi-restraints excluded: chain o residue 36 SER Chi-restraints excluded: chain o residue 40 LEU Chi-restraints excluded: chain o residue 70 VAL Chi-restraints excluded: chain p residue 107 THR Chi-restraints excluded: chain q residue 60 LYS Chi-restraints excluded: chain r residue 3 THR Chi-restraints excluded: chain r residue 13 SER Chi-restraints excluded: chain r residue 78 GLU Chi-restraints excluded: chain r residue 100 THR Chi-restraints excluded: chain r residue 101 SER Chi-restraints excluded: chain s residue 22 THR Chi-restraints excluded: chain s residue 85 VAL Chi-restraints excluded: chain t residue 58 ILE Chi-restraints excluded: chain t residue 72 ILE Chi-restraints excluded: chain t residue 103 ILE Chi-restraints excluded: chain v residue 43 THR Chi-restraints excluded: chain v residue 66 LYS Chi-restraints excluded: chain w residue 13 VAL Chi-restraints excluded: chain w residue 42 SER Chi-restraints excluded: chain x residue 5 GLU Chi-restraints excluded: chain x residue 19 LEU Chi-restraints excluded: chain x residue 54 LYS Chi-restraints excluded: chain x residue 56 LEU Chi-restraints excluded: chain x residue 57 LEU Chi-restraints excluded: chain y residue 6 LYS Chi-restraints excluded: chain y residue 10 THR Chi-restraints excluded: chain y residue 52 SER Chi-restraints excluded: chain 0 residue 17 THR Chi-restraints excluded: chain 1 residue 25 LYS Chi-restraints excluded: chain 1 residue 42 LEU Chi-restraints excluded: chain 2 residue 54 ASP Chi-restraints excluded: chain 2 residue 55 LEU Chi-restraints excluded: chain 2 residue 59 ILE Chi-restraints excluded: chain 3 residue 2 LYS Chi-restraints excluded: chain 4 residue 11 GLU Chi-restraints excluded: chain 4 residue 66 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 988 random chunks: chunk 582 optimal weight: 10.0000 chunk 938 optimal weight: 6.9990 chunk 572 optimal weight: 9.9990 chunk 445 optimal weight: 10.0000 chunk 652 optimal weight: 10.0000 chunk 984 optimal weight: 10.0000 chunk 905 optimal weight: 8.9990 chunk 783 optimal weight: 9.9990 chunk 81 optimal weight: 10.0000 chunk 605 optimal weight: 10.0000 chunk 480 optimal weight: 10.0000 overall best weight: 9.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 GLN G 142 HIS H 118 GLN I 4 ASN I 5 GLN I 32 GLN K 38 GLN N 49 GLN N 60 GLN O 62 GLN P 40 ASN T 84 ASN ** d 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 104 ASN o 52 ASN q 86 GLN t 69 ASN ** 4 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.097 153876 Z= 0.440 Angle : 0.874 16.852 230275 Z= 0.448 Chirality : 0.048 0.467 29306 Planarity : 0.008 0.150 12253 Dihedral : 23.161 179.412 77146 Min Nonbonded Distance : 1.768 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.59 % Favored : 94.36 % Rotamer: Outliers : 3.96 % Allowed : 22.77 % Favored : 73.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.11), residues: 5474 helix: 0.36 (0.11), residues: 1868 sheet: -0.58 (0.16), residues: 1047 loop : -1.18 (0.12), residues: 2559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP w 39 HIS 0.012 0.002 HIS F 3 PHE 0.023 0.003 PHE B 50 TYR 0.027 0.003 TYR R 51 ARG 0.016 0.001 ARG u 79 ********************** 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 960 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 779 time to evaluate : 6.377 Fit side-chains revert: symmetry clash REVERT: B 184 PHE cc_start: 0.6572 (OUTLIER) cc_final: 0.5968 (m-80) REVERT: C 166 GLU cc_start: 0.6856 (OUTLIER) cc_final: 0.5703 (mt-10) REVERT: E 152 MET cc_start: 0.7058 (OUTLIER) cc_final: 0.6756 (mpp) REVERT: G 78 ARG cc_start: 0.6518 (OUTLIER) cc_final: 0.4787 (tpt-90) REVERT: G 86 GLN cc_start: 0.6903 (OUTLIER) cc_final: 0.6289 (mt0) REVERT: G 114 LYS cc_start: 0.5915 (OUTLIER) cc_final: 0.5274 (ttmm) REVERT: M 45 ILE cc_start: 0.6401 (OUTLIER) cc_final: 0.6007 (pt) REVERT: O 84 ARG cc_start: 0.7168 (OUTLIER) cc_final: 0.6340 (ttp-110) REVERT: Q 30 LYS cc_start: 0.7937 (OUTLIER) cc_final: 0.7167 (ttpp) REVERT: T 43 ASP cc_start: 0.5262 (OUTLIER) cc_final: 0.4516 (m-30) REVERT: e 198 GLU cc_start: 0.6891 (OUTLIER) cc_final: 0.6170 (tp30) REVERT: f 10 ASP cc_start: 0.5722 (OUTLIER) cc_final: 0.5450 (m-30) REVERT: f 21 ASN cc_start: 0.5802 (OUTLIER) cc_final: 0.5372 (m110) REVERT: f 133 ARG cc_start: 0.6023 (OUTLIER) cc_final: 0.5531 (mtt90) REVERT: j 105 ARG cc_start: 0.6463 (mmt180) cc_final: 0.6202 (tpp80) REVERT: j 113 MET cc_start: 0.6041 (mmt) cc_final: 0.5718 (mmm) REVERT: l 1 MET cc_start: 0.6354 (tpt) cc_final: 0.4902 (tpp) REVERT: l 22 GLN cc_start: 0.7871 (OUTLIER) cc_final: 0.7195 (mp10) REVERT: l 104 GLU cc_start: 0.7415 (tt0) cc_final: 0.7135 (mt-10) REVERT: r 66 ILE cc_start: 0.6607 (OUTLIER) cc_final: 0.6186 (tp) REVERT: r 78 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7616 (mp0) REVERT: v 66 LYS cc_start: 0.8324 (OUTLIER) cc_final: 0.7927 (mtpp) REVERT: x 5 GLU cc_start: 0.6333 (OUTLIER) cc_final: 0.5453 (pm20) REVERT: 1 25 LYS cc_start: 0.8171 (OUTLIER) cc_final: 0.7391 (ttpp) REVERT: 1 42 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.7921 (mp) REVERT: 3 2 LYS cc_start: 0.8060 (OUTLIER) cc_final: 0.7472 (ptmt) REVERT: 3 36 ARG cc_start: 0.8480 (OUTLIER) cc_final: 0.8231 (ptm160) REVERT: 4 11 GLU cc_start: 0.6200 (OUTLIER) cc_final: 0.5571 (tm-30) REVERT: 4 22 MET cc_start: 0.5699 (OUTLIER) cc_final: 0.5385 (mmp) outliers start: 181 outliers final: 120 residues processed: 890 average time/residue: 2.1299 time to fit residues: 2714.7222 Evaluate side-chains 915 residues out of total 4573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 770 time to evaluate : 6.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 184 PHE Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 166 GLU Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain E residue 64 MET Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 142 ASP Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 93 LYS Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 78 ARG Chi-restraints excluded: chain G residue 86 GLN Chi-restraints excluded: chain G residue 114 LYS Chi-restraints excluded: chain G residue 130 ASN Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 107 SER Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain I residue 46 MET Chi-restraints excluded: chain I residue 65 ILE Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain J residue 66 GLU Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain K residue 129 VAL Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 45 ILE Chi-restraints excluded: chain M residue 55 THR Chi-restraints excluded: chain N residue 16 LEU Chi-restraints excluded: chain N residue 30 ILE Chi-restraints excluded: chain N residue 49 GLN Chi-restraints excluded: chain N residue 98 LYS Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain O residue 84 ARG Chi-restraints excluded: chain Q residue 8 LEU Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 27 ARG Chi-restraints excluded: chain Q residue 30 LYS Chi-restraints excluded: chain R residue 24 LYS Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain S residue 17 LYS Chi-restraints excluded: chain S residue 62 VAL Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain T residue 43 ASP Chi-restraints excluded: chain U residue 3 VAL Chi-restraints excluded: chain c residue 229 ASP Chi-restraints excluded: chain d residue 128 ARG Chi-restraints excluded: chain d residue 180 VAL Chi-restraints excluded: chain e residue 15 SER Chi-restraints excluded: chain e residue 169 VAL Chi-restraints excluded: chain e residue 198 GLU Chi-restraints excluded: chain f residue 10 ASP Chi-restraints excluded: chain f residue 21 ASN Chi-restraints excluded: chain f residue 25 VAL Chi-restraints excluded: chain f residue 50 LEU Chi-restraints excluded: chain f residue 132 VAL Chi-restraints excluded: chain f residue 133 ARG Chi-restraints excluded: chain f residue 149 VAL Chi-restraints excluded: chain f residue 164 GLU Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 11 VAL Chi-restraints excluded: chain g residue 17 VAL Chi-restraints excluded: chain g residue 49 THR Chi-restraints excluded: chain g residue 79 VAL Chi-restraints excluded: chain g residue 110 SER Chi-restraints excluded: chain g residue 168 VAL Chi-restraints excluded: chain h residue 2 GLN Chi-restraints excluded: chain i residue 92 MET Chi-restraints excluded: chain j residue 19 VAL Chi-restraints excluded: chain j residue 62 VAL Chi-restraints excluded: chain j residue 76 VAL Chi-restraints excluded: chain k residue 23 ILE Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain l residue 22 GLN Chi-restraints excluded: chain l residue 57 VAL Chi-restraints excluded: chain l residue 89 VAL Chi-restraints excluded: chain l residue 105 MET Chi-restraints excluded: chain l residue 108 VAL Chi-restraints excluded: chain m residue 54 LEU Chi-restraints excluded: chain n residue 24 THR Chi-restraints excluded: chain n residue 60 GLU Chi-restraints excluded: chain n residue 91 SER Chi-restraints excluded: chain o residue 19 SER Chi-restraints excluded: chain o residue 36 SER Chi-restraints excluded: chain o residue 40 LEU Chi-restraints excluded: chain o residue 70 VAL Chi-restraints excluded: chain p residue 107 THR Chi-restraints excluded: chain q residue 7 SER Chi-restraints excluded: chain q residue 60 LYS Chi-restraints excluded: chain q residue 96 VAL Chi-restraints excluded: chain r residue 3 THR Chi-restraints excluded: chain r residue 13 SER Chi-restraints excluded: chain r residue 29 VAL Chi-restraints excluded: chain r residue 37 THR Chi-restraints excluded: chain r residue 66 ILE Chi-restraints excluded: chain r residue 78 GLU Chi-restraints excluded: chain r residue 100 THR Chi-restraints excluded: chain r residue 101 SER Chi-restraints excluded: chain s residue 22 THR Chi-restraints excluded: chain s residue 85 VAL Chi-restraints excluded: chain t residue 58 ILE Chi-restraints excluded: chain t residue 72 ILE Chi-restraints excluded: chain t residue 103 ILE Chi-restraints excluded: chain v residue 43 THR Chi-restraints excluded: chain v residue 66 LYS Chi-restraints excluded: chain w residue 13 VAL Chi-restraints excluded: chain w residue 42 SER Chi-restraints excluded: chain x residue 5 GLU Chi-restraints excluded: chain x residue 54 LYS Chi-restraints excluded: chain x residue 57 LEU Chi-restraints excluded: chain y residue 6 LYS Chi-restraints excluded: chain y residue 10 THR Chi-restraints excluded: chain y residue 52 SER Chi-restraints excluded: chain 0 residue 17 THR Chi-restraints excluded: chain 1 residue 25 LYS Chi-restraints excluded: chain 1 residue 42 LEU Chi-restraints excluded: chain 1 residue 45 SER Chi-restraints excluded: chain 2 residue 54 ASP Chi-restraints excluded: chain 2 residue 59 ILE Chi-restraints excluded: chain 3 residue 2 LYS Chi-restraints excluded: chain 3 residue 36 ARG Chi-restraints excluded: chain 4 residue 11 GLU Chi-restraints excluded: chain 4 residue 22 MET Chi-restraints excluded: chain 4 residue 66 ILE 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: 4.9990 chunk 240 optimal weight: 5.9990 chunk 722 optimal weight: 3.9990 chunk 115 optimal weight: 20.0000 chunk 217 optimal weight: 9.9990 chunk 785 optimal weight: 2.9990 chunk 328 optimal weight: 0.7980 chunk 806 optimal weight: 10.0000 chunk 99 optimal weight: 30.0000 chunk 144 optimal weight: 10.0000 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 GLN G 142 HIS H 118 GLN I 4 ASN I 5 GLN I 32 GLN K 38 GLN N 49 GLN N 60 GLN O 62 GLN T 84 ASN ** d 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 104 ASN o 66 ASN q 86 GLN t 69 ASN ** 4 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.148910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.124210 restraints weight = 180811.681| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 0.47 r_work: 0.3286 rms_B_bonded: 1.39 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 2.35 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 153876 Z= 0.213 Angle : 0.682 14.130 230275 Z= 0.371 Chirality : 0.038 0.345 29306 Planarity : 0.007 0.136 12253 Dihedral : 23.054 178.687 77146 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.22 % Favored : 95.73 % Rotamer: Outliers : 3.30 % Allowed : 23.64 % Favored : 73.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.11), residues: 5474 helix: 0.78 (0.12), residues: 1869 sheet: -0.53 (0.16), residues: 1058 loop : -1.02 (0.12), residues: 2547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP w 39 HIS 0.006 0.001 HIS E 89 PHE 0.024 0.002 PHE B 50 TYR 0.024 0.002 TYR q 2 ARG 0.014 0.001 ARG u 79 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 40927.67 seconds wall clock time: 710 minutes 53.26 seconds (42653.26 seconds total)