Starting phenix.real_space_refine on Sat Mar 23 04:56:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fto_29449/03_2024/8fto_29449_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fto_29449/03_2024/8fto_29449.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fto_29449/03_2024/8fto_29449_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fto_29449/03_2024/8fto_29449_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fto_29449/03_2024/8fto_29449_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fto_29449/03_2024/8fto_29449.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fto_29449/03_2024/8fto_29449.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fto_29449/03_2024/8fto_29449_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fto_29449/03_2024/8fto_29449_updated.pdb" } resolution = 1.85 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= 0.269 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: 6 Type Number sf(0) Gaussians P 4490 5.49 5 Mg 284 5.21 5 S 150 5.16 5 C 70422 2.51 5 N 26156 2.21 5 O 45060 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "0 GLU 35": "OE1" <-> "OE2" Residue "B GLU 52": "OE1" <-> "OE2" Residue "B GLU 56": "OE1" <-> "OE2" Residue "B GLU 133": "OE1" <-> "OE2" Residue "B GLU 140": "OE1" <-> "OE2" Residue "B GLU 169": "OE1" <-> "OE2" Residue "C GLU 85": "OE1" <-> "OE2" Residue "C GLU 105": "OE1" <-> "OE2" Residue "D GLU 78": "OE1" <-> "OE2" Residue "D GLU 160": "OE1" <-> "OE2" Residue "D GLU 163": "OE1" <-> "OE2" Residue "D GLU 166": "OE1" <-> "OE2" Residue "D GLU 197": "OE1" <-> "OE2" Residue "E GLU 10": "OE1" <-> "OE2" Residue "E GLU 65": "OE1" <-> "OE2" Residue "E GLU 101": "OE1" <-> "OE2" Residue "E GLU 145": "OE1" <-> "OE2" Residue "E GLU 162": "OE1" <-> "OE2" Residue "F GLU 16": "OE1" <-> "OE2" Residue "F GLU 23": "OE1" <-> "OE2" Residue "F GLU 69": "OE1" <-> "OE2" Residue "G GLU 40": "OE1" <-> "OE2" Residue "G GLU 60": "OE1" <-> "OE2" Residue "G GLU 106": "OE1" <-> "OE2" Residue "G GLU 129": "OE1" <-> "OE2" Residue "H GLU 42": "OE1" <-> "OE2" Residue "H GLU 60": "OE1" <-> "OE2" Residue "H GLU 73": "OE1" <-> "OE2" Residue "H GLU 91": "OE1" <-> "OE2" Residue "I GLU 92": "OE1" <-> "OE2" Residue "I GLU 112": "OE1" <-> "OE2" Residue "J GLU 27": "OE1" <-> "OE2" Residue "J GLU 66": "OE1" <-> "OE2" Residue "L GLU 62": "OE1" <-> "OE2" Residue "L GLU 70": "OE1" <-> "OE2" Residue "L GLU 76": "OE1" <-> "OE2" Residue "M GLU 41": "OE1" <-> "OE2" Residue "M GLU 47": "OE1" <-> "OE2" Residue "M GLU 66": "OE1" <-> "OE2" Residue "N PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 39": "OE1" <-> "OE2" Residue "N GLU 86": "OE1" <-> "OE2" Residue "N GLU 92": "OE1" <-> "OE2" Residue "O GLU 83": "OE1" <-> "OE2" Residue "P GLU 48": "OE1" <-> "OE2" Residue "P GLU 77": "OE1" <-> "OE2" Residue "Q GLU 18": "OE1" <-> "OE2" Residue "S GLU 65": "OE1" <-> "OE2" Residue "T GLU 40": "OE1" <-> "OE2" Residue "T GLU 53": "OE1" <-> "OE2" Residue "U GLU 31": "OE1" <-> "OE2" Residue "U GLU 44": "OE1" <-> "OE2" Residue "c GLU 185": "OE1" <-> "OE2" Residue "d GLU 89": "OE1" <-> "OE2" Residue "e GLU 16": "OE1" <-> "OE2" Residue "e GLU 25": "OE1" <-> "OE2" Residue "f GLU 32": "OE1" <-> "OE2" Residue "f GLU 42": "OE1" <-> "OE2" Residue "f GLU 98": "OE1" <-> "OE2" Residue "f GLU 101": "OE1" <-> "OE2" Residue "f GLU 164": "OE1" <-> "OE2" Residue "g GLU 124": "OE1" <-> "OE2" Residue "g GLU 155": "OE1" <-> "OE2" Residue "k GLU 143": "OE1" <-> "OE2" Residue "l PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 74": "OE1" <-> "OE2" Residue "o GLU 34": "OE1" <-> "OE2" Residue "o GLU 44": "OE1" <-> "OE2" Residue "q GLU 31": "OE1" <-> "OE2" Residue "q GLU 37": "OE1" <-> "OE2" Residue "s GLU 18": "OE1" <-> "OE2" Residue "s GLU 25": "OE1" <-> "OE2" Residue "s GLU 54": "OE1" <-> "OE2" Residue "u GLU 55": "OE1" <-> "OE2" Residue "u GLU 59": "OE1" <-> "OE2" Residue "v GLU 70": "OE1" <-> "OE2" Residue "w GLU 43": "OE1" <-> "OE2" Residue "x GLU 17": "OE1" <-> "OE2" Residue "y GLU 37": "OE1" <-> "OE2" Residue "y GLU 58": "OE1" <-> "OE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 146562 Number of models: 1 Model: "" Number of chains: 111 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: "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': 124, 'rna2p_pyr': 84, 'rna3p': 10, 'rna3p_pur': 738, 'rna3p_pyr': 562} Link IDs: {'rna2p': 209, 'rna3p': 1309} 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: "X" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 189 Classifications: {'RNA': 9} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pur': 3, 'rna3p_pyr': 3} Link IDs: {'rna2p': 2, 'rna3p': 6} Chain: "Z" Number of atoms: 1623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1623 Unusual residues: {'8AN': 1} Classifications: {'RNA': 75, 'undetermined': 1} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 4, 'rna3p_pur': 33, 'rna3p_pyr': 33} Link IDs: {'p': 1, 'rna2p': 9, 'rna3p': 65} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "a" Number of atoms: 59422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2767, 59422 Classifications: {'RNA': 2767} Modifications used: {'rna2p': 7, 'rna2p_pur': 267, 'rna2p_pyr': 144, 'rna3p': 17, 'rna3p_pur': 1323, 'rna3p_pyr': 1009} Link IDs: {'rna2p': 417, 'rna3p': 2349} Chain breaks: 4 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: 1076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1076 Unusual residues: {'MV6': 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="MV6 l 82 " Not linked: pdbres="MV6 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: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 576 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 74} 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: "A" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 81 Unusual residues: {' MG': 81} Classifications: {'undetermined': 81} Link IDs: {None: 80} Chain: "a" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 205 Unusual residues: {' MG': 195} Classifications: {'peptide': 1, 'undetermined': 195} Link IDs: {None: 195} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "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: "c" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "d" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "0" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "1" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Chain: "2" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "3" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 1650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1650, 1650 Classifications: {'water': 1650} Link IDs: {None: 1649} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 39 Classifications: {'water': 39} Link IDs: {None: 38} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "G" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "H" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "I" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "J" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "K" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "L" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "M" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "N" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "O" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "P" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "Q" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "R" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "S" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "T" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "X" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "Z" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Chain: "a" Number of atoms: 3559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3559, 3559 Classifications: {'water': 3559} Link IDs: {None: 3558} Chain: "b" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 93 Classifications: {'water': 93} Link IDs: {None: 92} Chain: "c" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 90 Classifications: {'water': 90} Link IDs: {None: 89} Chain: "d" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Classifications: {'water': 40} Link IDs: {None: 39} Chain: "e" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 44 Classifications: {'water': 44} Link IDs: {None: 43} Chain: "f" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "h" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "i" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "j" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "k" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 42 Classifications: {'water': 42} Link IDs: {None: 41} Chain: "l" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "m" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Chain: "n" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "o" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "q" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "r" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Chain: "s" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "t" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "u" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "v" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "w" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "x" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "y" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Time building chain proxies: 59.39, per 1000 atoms: 0.41 Number of scatterers: 146562 At special positions: 0 Unit cell: (240.842, 264.761, 264.761, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 150 16.00 P 4490 15.00 Mg 284 11.99 O 45060 8.00 N 26156 7.00 C 70422 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: 70.86 Conformation dependent library (CDL) restraints added in 7.1 seconds 10944 Ramachandran restraints generated. 5472 Oldfield, 0 Emsley, 5472 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: 171 helices and 69 sheets defined 39.1% alpha, 19.4% beta 1553 base pairs and 2330 stacking pairs defined. Time for finding SS restraints: 78.38 Creating SS restraints... Processing helix chain '1' and resid 8 through 16 Processing helix chain '1' and resid 17 through 24 removed outlier: 4.301A pdb=" N THR 1 24 " --> pdb=" O ALA 1 20 " (cutoff:3.500A) Processing helix chain '1' and resid 25 through 38 Processing helix chain '2' and resid 7 through 14 removed outlier: 3.674A pdb=" N ARG 2 13 " --> pdb=" O GLY 2 9 " (cutoff:3.500A) Processing helix chain '2' and resid 32 through 37 removed outlier: 5.134A pdb=" N LYS 2 36 " --> pdb=" O ILE 2 32 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N ALA 2 37 " --> pdb=" O LEU 2 33 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 32 through 37' Processing helix chain '2' and resid 38 through 46 Proline residue: 2 46 - end of helix Processing helix chain '2' and resid 51 through 63 removed outlier: 4.482A pdb=" N GLY 2 56 " --> pdb=" O LYS 2 52 " (cutoff:3.500A) removed outlier: 4.973A 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: 3.695A pdb=" N ARG 4 59 " --> pdb=" O GLY 4 55 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ARG 4 63 " --> pdb=" O ARG 4 59 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ASN 4 65 " --> pdb=" O ASN 4 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 13 removed outlier: 4.660A pdb=" N MET B 9 " --> pdb=" O SER B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 removed outlier: 4.239A pdb=" N LYS B 28 " --> pdb=" O ASN B 24 " (cutoff:3.500A) Proline residue: B 29 - end of helix No H-bonds generated for 'chain 'B' and resid 24 through 29' Processing helix chain 'B' and resid 42 through 64 Proline residue: B 48 - end of helix removed outlier: 4.603A pdb=" N ARG B 63 " --> pdb=" O LYS B 59 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N LYS B 64 " --> pdb=" O ILE B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 88 removed outlier: 5.426A pdb=" N GLU B 78 " --> pdb=" O ARG B 74 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ALA B 79 " --> pdb=" O ALA B 75 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASP B 82 " --> pdb=" O GLU B 78 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA B 83 " --> pdb=" O ALA B 79 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N CYS B 87 " --> pdb=" O ALA B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 124 removed outlier: 4.191A pdb=" N GLN B 109 " --> pdb=" O LYS B 105 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER B 110 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N GLN B 120 " --> pdb=" O ASP B 116 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN B 122 " --> pdb=" O GLU B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 148 removed outlier: 6.495A pdb=" N ALA B 134 " --> pdb=" O THR B 130 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU B 135 " --> pdb=" O LYS B 131 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N MET B 136 " --> pdb=" O LYS B 132 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ARG B 139 " --> pdb=" O LEU B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 170 Processing helix chain 'B' and resid 171 through 180 Processing helix chain 'B' and resid 206 through 227 Processing helix chain 'C' and resid 6 through 12 removed outlier: 3.815A pdb=" N ARG C 11 " --> pdb=" O PRO C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 48 Processing helix chain 'C' and resid 72 through 78 removed outlier: 3.708A 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: 3.961A pdb=" N ASP C 112 " --> pdb=" O LYS C 108 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N ALA C 113 " --> pdb=" O PRO C 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 108 through 113' Processing helix chain 'C' and resid 114 through 127 Processing helix chain 'C' and resid 129 through 145 Processing helix chain 'D' and resid 7 through 16 removed outlier: 4.491A pdb=" N LEU D 11 " --> pdb=" O PRO D 7 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER D 12 " --> pdb=" O LYS D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 32 removed outlier: 3.796A pdb=" N LYS D 31 " --> pdb=" O ALA D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 66 Processing helix chain 'D' and resid 68 through 83 removed outlier: 5.410A pdb=" N LYS D 83 " --> pdb=" O ALA D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 97 removed outlier: 3.594A pdb=" N ARG D 97 " --> pdb=" O LEU D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 106 removed outlier: 3.553A pdb=" N GLY D 106 " --> pdb=" O VAL D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 121 removed outlier: 3.546A pdb=" N LYS D 121 " --> pdb=" O LEU D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 151 removed outlier: 4.726A pdb=" N LYS D 151 " --> pdb=" O GLU D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 166 removed outlier: 3.573A pdb=" N LYS D 156 " --> pdb=" O GLN D 152 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLN D 164 " --> pdb=" O GLU D 160 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ARG D 165 " --> pdb=" O LEU D 161 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N GLU D 166 " --> pdb=" O ALA D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 192 removed outlier: 3.676A pdb=" N LEU D 191 " --> pdb=" O GLU D 187 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N SER D 192 " --> pdb=" O ARG D 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 187 through 192' Processing helix chain 'D' and resid 196 through 206 removed outlier: 4.103A pdb=" N ILE D 200 " --> pdb=" O ASN D 196 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS D 206 " --> pdb=" O GLU D 202 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 71 removed outlier: 3.564A pdb=" N ARG E 69 " --> pdb=" O GLU E 65 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N MET E 71 " --> pdb=" O ALA E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 119 Processing helix chain 'E' and resid 132 through 147 removed outlier: 3.640A pdb=" N MET E 147 " --> pdb=" O GLY E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 149 through 158 Processing helix chain 'E' and resid 160 through 165 Processing helix chain 'F' and resid 14 through 33 removed outlier: 3.687A pdb=" N VAL F 18 " --> pdb=" O GLN F 14 " (cutoff:3.500A) Proline residue: F 19 - end of helix Processing helix chain 'F' and resid 67 through 82 removed outlier: 3.528A pdb=" N ILE F 71 " --> pdb=" O PRO F 67 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N ASP F 82 " --> pdb=" O PHE F 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 31 Processing helix chain 'G' and resid 35 through 55 Processing helix chain 'G' and resid 57 through 70 removed outlier: 3.669A pdb=" N ASN G 68 " --> pdb=" O VAL G 64 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL G 69 " --> pdb=" O ALA G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 112 removed outlier: 5.849A pdb=" N GLY G 112 " --> pdb=" O ALA G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 115 through 130 removed outlier: 3.602A pdb=" N GLU G 129 " --> pdb=" O SER G 125 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 149 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 40 removed outlier: 4.401A pdb=" N GLY I 40 " --> pdb=" O GLU I 36 " (cutoff:3.500A) Processing helix chain 'I' and resid 41 through 56 Proline residue: I 51 - end of helix removed outlier: 3.503A pdb=" N LEU I 54 " --> pdb=" O GLN I 50 " (cutoff:3.500A) Processing helix chain 'I' and resid 71 through 92 removed outlier: 3.506A pdb=" N GLU I 89 " --> pdb=" O ARG I 85 " (cutoff:3.500A) removed outlier: 3.504A 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: 3.807A pdb=" N ALA J 23 " --> pdb=" O ASP J 19 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU J 27 " --> pdb=" O ALA J 23 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N THR J 32 " --> pdb=" O THR J 28 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N GLY J 33 " --> pdb=" O ALA J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 82 through 91 removed outlier: 5.140A pdb=" N ASP J 91 " --> pdb=" O LEU J 87 " (cutoff:3.500A) Processing helix chain 'K' and resid 46 through 51 removed outlier: 4.543A pdb=" N GLY K 51 " --> pdb=" O ALA K 47 " (cutoff:3.500A) Processing helix chain 'K' and resid 54 through 59 removed outlier: 3.937A pdb=" N SER K 58 " --> pdb=" O GLY K 54 " (cutoff:3.500A) removed outlier: 4.675A 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 76 removed outlier: 3.660A pdb=" N LYS K 75 " --> pdb=" O ALA K 71 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N GLU K 76 " --> pdb=" O ASP K 72 " (cutoff:3.500A) Processing helix chain 'K' and resid 92 through 104 removed outlier: 3.675A pdb=" N THR K 96 " --> pdb=" O GLY K 92 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ILE K 97 " --> pdb=" O ARG K 93 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLY K 104 " --> pdb=" O LEU K 100 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 11 Proline residue: L 11 - end of helix Processing helix chain 'L' and resid 113 through 118 removed outlier: 3.899A pdb=" N TYR L 117 " --> pdb=" O ALA L 113 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N GLY L 118 " --> pdb=" O ARG L 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 113 through 118' Processing helix chain 'M' and resid 14 through 22 removed outlier: 3.767A pdb=" N THR M 20 " --> pdb=" O VAL M 16 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N SER M 21 " --> pdb=" O ILE M 17 " (cutoff:3.500A) removed outlier: 4.890A 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 49 through 64 removed outlier: 3.606A pdb=" N LYS M 62 " --> pdb=" O ASP M 58 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N PHE M 63 " --> pdb=" O GLU M 59 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N VAL M 64 " --> pdb=" O VAL M 60 " (cutoff:3.500A) Processing helix chain 'M' and resid 66 through 84 Processing helix chain 'M' and resid 85 through 94 Processing helix chain 'M' and resid 106 through 111 Processing helix chain 'N' and resid 3 through 21 Processing helix chain 'N' and resid 22 through 33 removed outlier: 3.828A pdb=" N ILE N 30 " --> pdb=" O GLU N 26 " (cutoff:3.500A) Processing helix chain 'N' and resid 37 through 52 removed outlier: 3.685A pdb=" N GLN N 49 " --> pdb=" O VAL N 45 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N THR N 50 " --> pdb=" O LEU N 46 " (cutoff:3.500A) Proline residue: N 52 - end of helix Processing helix chain 'N' and resid 80 through 91 removed outlier: 3.542A pdb=" N ARG N 90 " --> pdb=" O GLU N 86 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY N 91 " --> pdb=" O ALA N 87 " (cutoff:3.500A) Processing helix chain 'O' and resid 4 through 16 Processing helix chain 'O' and resid 24 through 43 removed outlier: 4.274A pdb=" N GLY O 41 " --> pdb=" O ASN O 37 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N HIS O 42 " --> pdb=" O HIS O 38 " (cutoff:3.500A) Processing helix chain 'O' and resid 49 through 74 removed outlier: 3.747A 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: 3.535A pdb=" N GLN P 63 " --> pdb=" O HIS P 59 " (cutoff:3.500A) Processing helix chain 'P' and resid 68 through 80 Processing helix chain 'R' and resid 11 through 17 removed outlier: 4.008A pdb=" N ALA R 15 " --> pdb=" O CYS R 11 " (cutoff:3.500A) Processing helix chain 'R' and resid 25 through 34 removed outlier: 3.660A pdb=" N ASN R 31 " --> pdb=" O ALA R 27 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N TYR R 32 " --> pdb=" O THR R 28 " (cutoff:3.500A) removed outlier: 5.541A 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: 4.331A pdb=" N PHE S 74 " --> pdb=" O LYS S 70 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA S 75 " --> pdb=" O LEU S 71 " (cutoff:3.500A) Proline residue: S 76 - end of helix No H-bonds generated for 'chain 'S' and resid 70 through 76' Processing helix chain 'T' and resid 4 through 41 Processing helix chain 'T' and resid 44 through 65 Proline residue: T 56 - end of helix Processing helix chain 'T' and resid 68 through 87 removed outlier: 4.290A pdb=" N LEU T 86 " --> pdb=" O GLN T 82 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N ALA T 87 " --> pdb=" O ILE T 83 " (cutoff:3.500A) Processing helix chain 'U' and resid 11 through 27 Processing helix chain 'U' and resid 28 through 37 removed outlier: 4.921A pdb=" N PHE U 37 " --> pdb=" O ARG U 33 " (cutoff:3.500A) Processing helix chain 'U' and resid 40 through 69 removed outlier: 3.904A pdb=" N ARG U 67 " --> pdb=" O GLU U 63 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N THR U 68 " --> pdb=" O ASN U 64 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N ARG U 69 " --> pdb=" O ALA U 65 " (cutoff:3.500A) Processing helix chain 'c' and resid 10 through 17 removed outlier: 4.737A pdb=" N HIS c 15 " --> pdb=" O PRO c 11 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N VAL c 16 " --> pdb=" O GLY c 12 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N VAL c 17 " --> pdb=" O ARG c 13 " (cutoff:3.500A) Processing helix chain 'c' and resid 30 through 35 removed outlier: 3.847A pdb=" N LEU c 34 " --> pdb=" O PHE c 30 " (cutoff:3.500A) removed outlier: 5.642A 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: 3.712A 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: 3.795A pdb=" N ALA c 211 " --> pdb=" O LYS c 207 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG c 214 " --> pdb=" O ALA c 210 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY c 215 " --> pdb=" O ALA c 211 " (cutoff:3.500A) Processing helix chain 'c' and resid 221 through 226 removed outlier: 3.950A pdb=" N MET c 225 " --> pdb=" O ARG c 221 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N ASN c 226 " --> pdb=" O GLY c 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 221 through 226' Processing helix chain 'c' and resid 260 through 268 removed outlier: 4.996A pdb=" N LYS c 265 " --> pdb=" O LYS c 261 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N PHE c 266 " --> pdb=" O ARG c 262 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ILE c 267 " --> pdb=" O THR c 263 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N VAL c 268 " --> pdb=" O ASP c 264 " (cutoff:3.500A) Processing helix chain 'd' and resid 56 through 61 removed outlier: 5.389A pdb=" N THR d 61 " --> pdb=" O ALA d 57 " (cutoff:3.500A) Processing helix chain 'd' and resid 62 through 72 removed outlier: 3.570A pdb=" N ALA d 71 " --> pdb=" O HIS d 67 " (cutoff:3.500A) Processing helix chain 'd' and resid 98 through 103 removed outlier: 4.204A pdb=" N ALA d 102 " --> pdb=" O VAL d 98 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N ASP d 103 " --> pdb=" O GLU d 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 98 through 103' Processing helix chain 'd' and resid 120 through 125 Processing helix chain 'd' and resid 39 through 44 Processing helix chain 'e' and resid 15 through 20 Processing helix chain 'e' and resid 24 through 40 removed outlier: 3.807A pdb=" N ARG e 40 " --> pdb=" O ALA e 36 " (cutoff:3.500A) Processing helix chain 'e' and resid 48 through 53 removed outlier: 6.388A 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 Processing helix chain 'e' and resid 154 through 163 removed outlier: 4.576A pdb=" N ASN e 163 " --> pdb=" O LEU e 159 " (cutoff:3.500A) Processing helix chain 'e' and resid 176 through 183 Processing helix chain 'e' and resid 189 through 201 Processing helix chain 'f' and resid 2 through 21 removed outlier: 4.772A pdb=" N ASP f 6 " --> pdb=" O ALA f 2 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N VAL f 13 " --> pdb=" O LYS f 9 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N LYS f 14 " --> pdb=" O ASP f 10 " (cutoff:3.500A) Processing helix chain 'f' and resid 40 through 46 removed outlier: 4.722A pdb=" N ILE f 44 " --> pdb=" O VAL f 40 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N ALA f 45 " --> pdb=" O GLY f 41 " (cutoff:3.500A) Processing helix chain 'f' and resid 47 through 62 Processing helix chain 'f' and resid 93 through 111 removed outlier: 4.793A pdb=" N VAL f 108 " --> pdb=" O ILE f 104 " (cutoff:3.500A) Proline residue: f 109 - end of helix Processing helix chain 'f' and resid 162 through 174 removed outlier: 3.698A pdb=" N PHE f 173 " --> pdb=" O LEU f 169 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASP f 174 " --> pdb=" O LEU f 170 " (cutoff:3.500A) Processing helix chain 'f' and resid 24 through 29 Proline residue: f 29 - end of helix Processing helix chain 'f' and resid 134 through 139 removed outlier: 4.425A 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 removed outlier: 3.726A pdb=" N ALA g 7 " --> pdb=" O ARG g 3 " (cutoff:3.500A) Proline residue: g 8 - end of helix Processing helix chain 'g' and resid 60 through 81 removed outlier: 4.086A pdb=" N VAL g 79 " --> pdb=" O MET g 75 " (cutoff:3.500A) Processing helix chain 'g' and resid 137 through 153 removed outlier: 3.725A pdb=" N TYR g 151 " --> pdb=" O ASP g 147 " (cutoff:3.500A) removed outlier: 4.645A 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 removed outlier: 3.817A pdb=" N GLU i 31 " --> pdb=" O ARG i 27 " (cutoff:3.500A) Processing helix chain 'i' and resid 88 through 96 Processing helix chain 'i' and resid 97 through 110 removed outlier: 4.271A pdb=" N ILE i 101 " --> pdb=" O PRO i 97 " (cutoff:3.500A) Proline residue: i 110 - end of helix Processing helix chain 'i' and resid 112 through 122 removed outlier: 3.846A pdb=" N LYS i 121 " --> pdb=" O ALA i 117 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N LEU i 122 " --> pdb=" O MET i 118 " (cutoff:3.500A) Processing helix chain 'j' and resid 112 through 119 Processing helix chain 'k' and resid 37 through 42 removed outlier: 3.682A pdb=" N ARG k 41 " --> pdb=" O GLY k 37 " (cutoff:3.500A) removed outlier: 5.620A 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: 3.901A pdb=" N ALA k 72 " --> pdb=" O SER k 68 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE k 73 " --> pdb=" O ARG k 69 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N ALA k 75 " --> pdb=" O ALA k 71 " (cutoff:3.500A) Processing helix chain 'k' and resid 78 through 85 removed outlier: 3.761A pdb=" N LEU k 82 " --> pdb=" O ARG k 78 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ALA k 83 " --> pdb=" O LEU k 79 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N LYS k 84 " --> pdb=" O SER k 80 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL k 85 " --> pdb=" O ASP k 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 78 through 85' Processing helix chain 'k' and resid 91 through 99 Processing helix chain 'k' and resid 128 through 139 Processing helix chain 'l' and resid 42 through 58 Processing helix chain 'l' and resid 109 through 125 removed outlier: 4.059A pdb=" N LYS l 123 " --> pdb=" O LEU l 119 " (cutoff:3.500A) removed outlier: 3.931A 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: 4.172A pdb=" N ARG m 46 " --> pdb=" O LYS m 42 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL m 47 " --> pdb=" O GLU m 43 " (cutoff:3.500A) Proline residue: m 50 - end of helix removed outlier: 4.259A pdb=" N THR m 57 " --> pdb=" O THR m 53 " (cutoff:3.500A) Processing helix chain 'm' and resid 59 through 71 removed outlier: 3.850A pdb=" N THR m 70 " --> pdb=" O ALA m 66 " (cutoff:3.500A) Processing helix chain 'm' and resid 72 through 88 removed outlier: 4.696A 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: 4.518A pdb=" N ARG n 13 " --> pdb=" O ARG n 9 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N ALA n 14 " --> pdb=" O ARG n 10 " (cutoff:3.500A) Processing helix chain 'n' and resid 55 through 63 removed outlier: 4.742A pdb=" N GLN n 61 " --> pdb=" O ALA n 57 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU n 62 " --> pdb=" O ILE n 58 " (cutoff:3.500A) removed outlier: 5.034A 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 Processing helix chain 'o' and resid 2 through 13 removed outlier: 4.057A pdb=" N GLN o 12 " --> pdb=" O LEU o 8 " (cutoff:3.500A) Processing helix chain 'o' and resid 97 through 104 removed outlier: 4.471A pdb=" N ARG o 101 " --> pdb=" O LEU o 97 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N GLU o 102 " --> pdb=" O TYR o 98 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ARG o 103 " --> pdb=" O TYR o 99 " (cutoff:3.500A) removed outlier: 5.112A 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: 3.584A pdb=" N LYS p 22 " --> pdb=" O LEU p 18 " (cutoff:3.500A) Processing helix chain 'p' and resid 26 through 31 removed outlier: 3.698A pdb=" N ARG p 30 " --> pdb=" O GLY p 26 " (cutoff:3.500A) Processing helix chain 'p' and resid 32 through 37 removed outlier: 3.620A pdb=" N GLN p 37 " --> pdb=" O ARG p 33 " (cutoff:3.500A) Processing helix chain 'p' and resid 39 through 73 removed outlier: 4.026A pdb=" N ARG p 51 " --> pdb=" O TYR p 47 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS p 54 " --> pdb=" O ARG p 50 " (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: 3.522A pdb=" N LEU r 19 " --> pdb=" O GLN r 15 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL r 20 " --> pdb=" O LYS r 16 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU r 23 " --> pdb=" O LEU r 19 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILE r 24 " --> pdb=" O VAL r 20 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG r 25 " --> pdb=" O ALA r 21 " (cutoff:3.500A) Processing helix chain 'r' and resid 28 through 40 removed outlier: 5.632A pdb=" N ASN r 40 " --> pdb=" O LEU r 36 " (cutoff:3.500A) Processing helix chain 'r' and resid 41 through 61 removed outlier: 3.535A pdb=" N VAL r 45 " --> pdb=" O LYS r 41 " (cutoff:3.500A) Processing helix chain 'r' and resid 65 through 70 removed outlier: 3.996A pdb=" N LEU r 69 " --> pdb=" O ASP r 65 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N LYS r 70 " --> pdb=" O ILE r 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 65 through 70' Processing helix chain 's' and resid 3 through 11 removed outlier: 4.110A pdb=" N LEU s 11 " --> pdb=" O LEU s 7 " (cutoff:3.500A) Processing helix chain 's' and resid 17 through 27 Processing helix chain 's' and resid 39 through 50 Processing helix chain 't' and resid 66 through 71 removed outlier: 3.963A pdb=" N VAL t 70 " --> pdb=" O GLN t 66 " (cutoff:3.500A) removed outlier: 5.199A 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: 3.568A pdb=" N ASN u 24 " --> pdb=" O LEU u 20 " (cutoff:3.500A) Processing helix chain 'u' and resid 43 through 53 removed outlier: 4.219A pdb=" N LYS u 53 " --> pdb=" O ASN u 49 " (cutoff:3.500A) Processing helix chain 'u' and resid 54 through 59 removed outlier: 3.937A pdb=" N SER u 58 " --> pdb=" O ALA u 54 " (cutoff:3.500A) Processing helix chain 'w' and resid 52 through 63 Processing helix chain 'w' and resid 64 through 75 Processing helix chain 'x' and resid 2 through 10 removed outlier: 3.900A pdb=" N GLU x 8 " --> pdb=" O LYS x 4 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LYS x 9 " --> pdb=" O GLU x 5 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N SER x 10 " --> pdb=" O LEU x 6 " (cutoff:3.500A) Processing helix chain 'x' and resid 11 through 35 removed outlier: 3.537A pdb=" N GLY x 35 " --> pdb=" O GLN x 31 " (cutoff:3.500A) Processing helix chain 'x' and resid 39 through 62 removed outlier: 4.794A pdb=" N LEU x 43 " --> pdb=" O GLN x 39 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LYS x 44 " --> pdb=" O SER x 40 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY x 62 " --> pdb=" O ASN x 58 " (cutoff:3.500A) Processing helix chain 'y' and resid 17 through 28 Processing helix chain 'y' and resid 41 through 52 Processing helix chain 'z' and resid 9 through 19 removed outlier: 4.864A pdb=" N HIS z 19 " --> pdb=" O MET z 15 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain '0' and resid 19 through 25 removed outlier: 6.103A pdb=" N HIS 0 19 " --> pdb=" O SER 0 13 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N LEU 0 34 " --> pdb=" O GLU 0 51 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain '2' and resid 22 through 25 No H-bonds generated for sheet with id= 2 Processing sheet with id= 3, first strand: chain '3' and resid 1 through 5 removed outlier: 5.487A pdb=" N ILE 3 23 " --> pdb=" O GLN 3 37 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain '4' and resid 20 through 25 removed outlier: 4.317A pdb=" N ASN 4 20 " --> pdb=" O CYS 4 16 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU 4 34 " --> pdb=" O SER 4 15 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'B' and resid 15 through 18 removed outlier: 5.295A pdb=" N HIS B 15 " --> pdb=" O ILE B 41 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N HIS B 39 " --> pdb=" O GLY B 17 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'B' and resid 67 through 71 Processing sheet with id= 7, first strand: chain 'C' and resid 53 through 59 removed outlier: 3.552A pdb=" N ARG C 54 " --> pdb=" O HIS C 69 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'C' and resid 164 through 169 removed outlier: 6.144A pdb=" N ASP C 181 " --> pdb=" O LYS C 204 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'D' and resid 141 through 145 removed outlier: 3.743A pdb=" N ASP D 141 " --> pdb=" O PHE D 182 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N MET D 178 " --> pdb=" O ILE D 145 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'E' and resid 12 through 16 removed outlier: 6.680A pdb=" N LEU E 36 " --> pdb=" O ILE E 16 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'E' and resid 84 through 88 removed outlier: 3.802A pdb=" N ALA E 99 " --> pdb=" O ASN E 122 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N ASN E 122 " --> pdb=" O ALA E 99 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'E' and resid 33 through 40 Processing sheet with id= 13, first strand: chain 'F' and resid 38 through 42 removed outlier: 5.724A pdb=" N TYR F 59 " --> pdb=" O TRP F 42 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N HIS F 3 " --> pdb=" O THR F 92 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG F 86 " --> pdb=" O MET F 9 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'F' and resid 43 through 46 removed outlier: 3.551A pdb=" N GLY F 43 " --> pdb=" O TYR F 59 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'G' and resid 72 through 79 removed outlier: 6.007A pdb=" N THR G 72 " --> pdb=" O VAL G 91 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'H' and resid 23 through 29 removed outlier: 6.371A pdb=" N ALA H 23 " --> pdb=" O LEU H 63 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASP H 48 " --> pdb=" O THR H 62 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'H' and resid 74 through 77 removed outlier: 3.630A pdb=" N CYS H 127 " --> pdb=" O VAL H 103 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL H 103 " --> pdb=" O ILE H 126 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'I' and resid 5 through 11 removed outlier: 3.597A pdb=" N LYS I 60 " --> pdb=" O GLY I 24 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N LYS I 27 " --> pdb=" O LEU I 61 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'J' and resid 35 through 38 removed outlier: 3.513A pdb=" N GLN J 35 " --> pdb=" O VAL J 77 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'J' and resid 39 through 42 removed outlier: 4.412A pdb=" N LEU J 71 " --> pdb=" O LEU J 42 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'J' and resid 44 through 52 Processing sheet with id= 22, first strand: chain 'K' and resid 42 through 45 Processing sheet with id= 23, first strand: chain 'L' and resid 29 through 32 removed outlier: 5.137A pdb=" N LEU L 81 " --> pdb=" O VAL L 98 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'L' and resid 36 through 41 removed outlier: 3.979A pdb=" N TYR L 38 " --> pdb=" O VAL L 52 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N VAL L 52 " --> pdb=" O TYR L 38 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N LYS L 51 " --> pdb=" O ILE L 67 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N PHE L 61 " --> pdb=" O LEU L 57 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'P' and resid 16 through 20 removed outlier: 3.524A pdb=" N GLY P 37 " --> pdb=" O VAL P 19 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'Q' and resid 7 through 11 removed outlier: 6.711A pdb=" N GLU Q 60 " --> pdb=" O VAL Q 76 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'Q' and resid 19 through 30 No H-bonds generated for sheet with id= 27 Processing sheet with id= 28, first strand: chain 'S' and resid 30 through 34 removed outlier: 4.711A pdb=" N LEU S 47 " --> pdb=" O VAL S 62 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'c' and resid 80 through 83 removed outlier: 6.795A pdb=" N LEU c 93 " --> pdb=" O GLU c 79 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N ILE c 74 " --> pdb=" O SER c 118 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N SER c 118 " --> pdb=" O ILE c 74 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ASP c 114 " --> pdb=" O VAL c 78 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N GLY c 127 " --> pdb=" O GLN c 115 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N GLN c 117 " --> pdb=" O GLY c 127 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'c' and resid 138 through 142 removed outlier: 3.972A pdb=" N SER c 139 " --> pdb=" O ILE c 164 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N THR c 173 " --> pdb=" O VAL c 165 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLU c 180 " --> pdb=" O LEU c 176 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'c' and resid 90 through 96 removed outlier: 5.396A pdb=" N ASN c 90 " --> pdb=" O ALA c 106 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLU c 100 " --> pdb=" O TYR c 96 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'd' and resid 3 through 6 removed outlier: 6.461A pdb=" N LYS d 105 " --> pdb=" O VAL d 177 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'd' and resid 10 through 16 removed outlier: 3.646A pdb=" N GLY d 10 " --> pdb=" O VAL d 26 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N VAL d 20 " --> pdb=" O THR d 16 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'd' and resid 79 through 84 removed outlier: 5.929A pdb=" N ARG d 46 " --> pdb=" O LEU d 84 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N GLN d 49 " --> pdb=" O THR d 35 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLN d 94 " --> pdb=" O VAL d 34 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'e' and resid 1 through 6 removed outlier: 4.740A pdb=" N SER e 10 " --> pdb=" O LEU e 5 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'e' and resid 117 through 120 removed outlier: 5.702A pdb=" N ARG e 117 " --> pdb=" O ASP e 184 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'f' and resid 65 through 69 removed outlier: 3.596A pdb=" N GLY f 86 " --> pdb=" O THR f 68 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS f 33 " --> pdb=" O THR f 157 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N GLY f 39 " --> pdb=" O GLY f 151 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N GLY f 151 " --> pdb=" O GLY f 39 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'g' and resid 15 through 20 removed outlier: 6.432A pdb=" N GLN g 22 " --> pdb=" O LEU g 37 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU g 33 " --> pdb=" O ILE g 26 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY g 28 " --> pdb=" O GLY g 31 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLY g 31 " --> pdb=" O GLY g 28 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'g' and resid 40 through 45 removed outlier: 6.073A pdb=" N ALA g 40 " --> pdb=" O ARG g 55 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY g 53 " --> pdb=" O GLU g 42 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N THR g 51 " --> pdb=" O LYS g 44 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'g' and resid 94 through 99 removed outlier: 7.081A pdb=" N ASN g 101 " --> pdb=" O LEU g 117 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'g' and resid 121 through 125 removed outlier: 5.943A pdb=" N THR g 129 " --> pdb=" O LEU g 89 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'h' and resid 17 through 21 removed outlier: 4.564A pdb=" N ASP h 17 " --> pdb=" O LEU h 5 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N GLN h 2 " --> pdb=" O ALA h 39 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'i' and resid 14 through 19 Processing sheet with id= 44, first strand: chain 'i' and resid 74 through 78 removed outlier: 7.338A pdb=" N GLY i 83 " --> pdb=" O THR i 78 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'j' and resid 18 through 21 removed outlier: 4.149A pdb=" N THR j 6 " --> pdb=" O CYS j 21 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N ASN j 82 " --> pdb=" O MET j 7 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'l' and resid 37 through 40 No H-bonds generated for sheet with id= 46 Processing sheet with id= 47, first strand: chain 'l' and resid 62 through 65 removed outlier: 3.520A pdb=" N TYR l 103 " --> pdb=" O LEU l 33 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU l 33 " --> pdb=" O LEU l 102 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LYS l 100 " --> pdb=" O ALA l 35 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'l' and resid 73 through 76 removed outlier: 6.855A pdb=" N ILE l 73 " --> pdb=" O GLU l 90 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'l' and resid 30 through 36 removed outlier: 7.636A pdb=" N SER l 30 " --> pdb=" O LYS l 133 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LYS l 127 " --> pdb=" O VAL l 36 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'm' and resid 33 through 37 removed outlier: 5.788A pdb=" N ALA m 108 " --> pdb=" O PHE m 102 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N PHE m 102 " --> pdb=" O ALA m 108 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N MET m 110 " --> pdb=" O CYS m 100 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'n' and resid 49 through 52 removed outlier: 3.506A pdb=" N VAL n 49 " --> pdb=" O VAL n 39 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'o' and resid 38 through 45 removed outlier: 6.417A pdb=" N THR o 25 " --> pdb=" O LYS o 87 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'o' and resid 49 through 52 removed outlier: 3.720A pdb=" N ALA o 49 " --> pdb=" O THR o 60 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N SER o 57 " --> pdb=" O THR o 76 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'q' and resid 11 through 15 removed outlier: 3.562A pdb=" N MET q 40 " --> pdb=" O VAL q 4 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'q' and resid 18 through 23 removed outlier: 4.200A pdb=" N GLN q 18 " --> pdb=" O ILE q 98 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ASP q 95 " --> pdb=" O VAL q 64 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LYS q 60 " --> pdb=" O THR q 99 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'q' and resid 57 through 60 Processing sheet with id= 57, first strand: chain 'q' and resid 65 through 68 removed outlier: 3.514A pdb=" N ALA q 65 " --> pdb=" O ASP q 95 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'q' and resid 71 through 78 removed outlier: 4.170A pdb=" N TYR q 83 " --> pdb=" O ARG q 78 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'r' and resid 2 through 8 Processing sheet with id= 60, first strand: chain 's' and resid 12 through 15 removed outlier: 5.258A pdb=" N VAL s 31 " --> pdb=" O HIS s 15 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ASN s 28 " --> pdb=" O LEU s 87 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LYS s 81 " --> pdb=" O VAL s 34 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LYS s 66 " --> pdb=" O ARG s 77 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N ASP s 79 " --> pdb=" O LYS s 64 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N LYS s 64 " --> pdb=" O ASP s 79 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LYS s 81 " --> pdb=" O VAL s 62 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N VAL s 62 " --> pdb=" O LYS s 81 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ALA s 83 " --> pdb=" O THR s 60 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N THR s 60 " --> pdb=" O ALA s 83 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N VAL s 85 " --> pdb=" O VAL s 58 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL s 58 " --> pdb=" O VAL s 85 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 't' and resid 40 through 45 removed outlier: 4.671A pdb=" N ASN t 40 " --> pdb=" O ALA t 63 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 't' and resid 83 through 87 Processing sheet with id= 63, first strand: chain 'u' and resid 69 through 72 removed outlier: 6.900A pdb=" N ALA u 39 " --> pdb=" O ARG u 9 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE u 89 " --> pdb=" O PRO u 27 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'v' and resid 51 through 54 removed outlier: 4.302A pdb=" N THR v 58 " --> pdb=" O GLY v 54 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'v' and resid 65 through 71 Processing sheet with id= 66, first strand: chain 'w' and resid 12 through 19 removed outlier: 4.483A pdb=" N ASN w 23 " --> pdb=" O SER w 19 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'w' and resid 35 through 41 Processing sheet with id= 68, first strand: chain 'y' and resid 33 through 39 removed outlier: 4.439A pdb=" N HIS y 34 " --> pdb=" O GLN y 9 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N MET y 54 " --> pdb=" O THR y 10 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'z' and resid 29 through 32 removed outlier: 4.408A pdb=" N GLU z 36 " --> pdb=" O ASP z 31 " (cutoff:3.500A) 1882 hydrogen bonds defined for protein. 5559 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3899 hydrogen bonds 6082 hydrogen bond angles 0 basepair planarities 1553 basepair parallelities 2330 stacking parallelities Total time for adding SS restraints: 699.12 Time building geometry restraints manager: 75.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.39: 56438 1.39 - 1.63: 95608 1.63 - 1.87: 269 1.87 - 2.11: 0 2.11 - 2.35: 1 Bond restraints: 152316 Sorted by residual: bond pdb=" O3' C a1914 " pdb=" P 3TD a1915 " ideal model delta sigma weight residual 1.607 2.354 -0.747 1.50e-02 4.44e+03 2.48e+03 bond pdb=" C4 5MU a 747 " pdb=" C5 5MU a 747 " ideal model delta sigma weight residual 1.802 1.446 0.356 2.00e-02 2.50e+03 3.17e+02 bond pdb=" C4 5MU a1939 " pdb=" C5 5MU a1939 " ideal model delta sigma weight residual 1.802 1.447 0.355 2.00e-02 2.50e+03 3.15e+02 bond pdb=" N1 5MU a1939 " pdb=" C6 5MU a1939 " ideal model delta sigma weight residual 1.635 1.388 0.247 2.00e-02 2.50e+03 1.52e+02 bond pdb=" N1 5MU a 747 " pdb=" C6 5MU a 747 " ideal model delta sigma weight residual 1.635 1.389 0.246 2.00e-02 2.50e+03 1.51e+02 ... (remaining 152311 not shown) Histogram of bond angle deviations from ideal: 90.95 - 100.39: 268 100.39 - 109.82: 66195 109.82 - 119.26: 90337 119.26 - 128.69: 65781 128.69 - 138.12: 5266 Bond angle restraints: 227847 Sorted by residual: angle pdb=" O3' A A 547 " pdb=" C3' A A 547 " pdb=" C2' A A 547 " ideal model delta sigma weight residual 109.50 123.34 -13.84 1.50e+00 4.44e-01 8.51e+01 angle pdb=" O3' U A 5 " pdb=" C3' U A 5 " pdb=" C2' U A 5 " ideal model delta sigma weight residual 109.50 96.57 12.93 1.50e+00 4.44e-01 7.43e+01 angle pdb=" C4' G A 537 " pdb=" C3' G A 537 " pdb=" O3' G A 537 " ideal model delta sigma weight residual 113.00 100.23 12.77 1.50e+00 4.44e-01 7.25e+01 angle pdb=" N SER B 121 " pdb=" CA SER B 121 " pdb=" C SER B 121 " ideal model delta sigma weight residual 111.82 103.00 8.82 1.16e+00 7.43e-01 5.79e+01 angle pdb=" N ARG m 69 " pdb=" CA ARG m 69 " pdb=" C ARG m 69 " ideal model delta sigma weight residual 110.52 99.28 11.24 1.48e+00 4.57e-01 5.77e+01 ... (remaining 227842 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.65: 85411 35.65 - 71.31: 10764 71.31 - 106.96: 1248 106.96 - 142.62: 28 142.62 - 178.27: 11 Dihedral angle restraints: 97462 sinusoidal: 81559 harmonic: 15903 Sorted by residual: dihedral pdb=" CA HIS 2 31 " pdb=" C HIS 2 31 " pdb=" N ILE 2 32 " pdb=" CA ILE 2 32 " ideal model delta harmonic sigma weight residual -180.00 -129.27 -50.73 0 5.00e+00 4.00e-02 1.03e+02 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 60.25 139.75 1 1.50e+01 4.44e-03 7.52e+01 dihedral pdb=" O4' U A 365 " pdb=" C1' U A 365 " pdb=" N1 U A 365 " pdb=" C2 U A 365 " ideal model delta sinusoidal sigma weight residual 200.00 63.99 136.01 1 1.50e+01 4.44e-03 7.34e+01 ... (remaining 97459 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 27105 0.106 - 0.212: 1764 0.212 - 0.317: 134 0.317 - 0.423: 13 0.423 - 0.529: 1 Chirality restraints: 29017 Sorted by residual: chirality pdb=" C3' A A 547 " pdb=" C4' A A 547 " pdb=" O3' A A 547 " pdb=" C2' A A 547 " both_signs ideal model delta sigma weight residual False -2.74 -2.22 -0.53 2.00e-01 2.50e+01 7.00e+00 chirality pdb=" CA LYS B 37 " pdb=" N LYS B 37 " pdb=" C LYS B 37 " pdb=" CB LYS B 37 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.59e+00 chirality pdb=" CB D2T L 89 " pdb=" CA D2T L 89 " pdb=" SB D2T L 89 " pdb=" CG D2T L 89 " both_signs ideal model delta sigma weight residual False -3.02 -3.39 0.37 2.00e-01 2.50e+01 3.50e+00 ... (remaining 29014 not shown) Planarity restraints: 12181 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 2MG A1516 " -0.074 2.00e-02 2.50e+03 6.00e-01 8.09e+03 pdb=" C4' 2MG A1516 " -0.434 2.00e-02 2.50e+03 pdb=" O4' 2MG A1516 " -0.598 2.00e-02 2.50e+03 pdb=" C3' 2MG A1516 " 0.592 2.00e-02 2.50e+03 pdb=" O3' 2MG A1516 " 0.649 2.00e-02 2.50e+03 pdb=" C2' 2MG A1516 " 0.163 2.00e-02 2.50e+03 pdb=" O2' 2MG A1516 " -0.992 2.00e-02 2.50e+03 pdb=" C1' 2MG A1516 " -0.229 2.00e-02 2.50e+03 pdb=" N9 2MG A1516 " 0.922 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMG a2251 " -0.055 2.00e-02 2.50e+03 5.96e-01 8.00e+03 pdb=" C4' OMG a2251 " -0.436 2.00e-02 2.50e+03 pdb=" O4' OMG a2251 " -0.654 2.00e-02 2.50e+03 pdb=" C3' OMG a2251 " 0.608 2.00e-02 2.50e+03 pdb=" O3' OMG a2251 " 0.618 2.00e-02 2.50e+03 pdb=" C2' OMG a2251 " 0.197 2.00e-02 2.50e+03 pdb=" O2' OMG a2251 " -0.966 2.00e-02 2.50e+03 pdb=" C1' OMG a2251 " -0.212 2.00e-02 2.50e+03 pdb=" N9 OMG a2251 " 0.901 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 5MC A1407 " -0.062 2.00e-02 2.50e+03 5.93e-01 7.91e+03 pdb=" C4' 5MC A1407 " -0.437 2.00e-02 2.50e+03 pdb=" O4' 5MC A1407 " -0.614 2.00e-02 2.50e+03 pdb=" C3' 5MC A1407 " 0.594 2.00e-02 2.50e+03 pdb=" O3' 5MC A1407 " 0.635 2.00e-02 2.50e+03 pdb=" C2' 5MC A1407 " 0.179 2.00e-02 2.50e+03 pdb=" O2' 5MC A1407 " -0.972 2.00e-02 2.50e+03 pdb=" C1' 5MC A1407 " -0.224 2.00e-02 2.50e+03 pdb=" N1 5MC A1407 " 0.900 2.00e-02 2.50e+03 ... (remaining 12178 not shown) Histogram of nonbonded interaction distances: 0.35 - 1.26: 1 1.26 - 2.17: 764 2.17 - 3.08: 102592 3.08 - 3.99: 520839 3.99 - 4.90: 840117 Warning: very small nonbonded interaction distances. Nonbonded interactions: 1464313 Sorted by model distance: nonbonded pdb=" O HOH Z 104 " pdb=" O HOH Z 109 " model vdw 0.347 2.440 nonbonded pdb="MG MG A1626 " pdb=" O HOH A3169 " model vdw 1.355 2.170 nonbonded pdb=" OG SER S 25 " pdb=" OD1 ASP S 27 " model vdw 1.408 2.440 nonbonded pdb=" NH2 ARG 4 56 " pdb=" CD2 HIS S 69 " model vdw 1.548 3.340 nonbonded pdb=" OP2 C a1941 " pdb="MG MG a4176 " model vdw 1.551 2.170 ... (remaining 1464308 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: 3.920 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.110 Extract box with map and model: 24.000 Check model and map are aligned: 1.660 Set scattering table: 1.050 Process input model: 1013.320 Find NCS groups from input model: 3.440 Set up NCS constraints: 0.450 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.040 Load rotamer database and sin/cos tables:12.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 1060.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.747 152316 Z= 0.490 Angle : 0.914 19.336 227847 Z= 0.507 Chirality : 0.055 0.529 29017 Planarity : 0.020 0.600 12181 Dihedral : 23.314 178.269 87202 Min Nonbonded Distance : 0.347 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.66 % Allowed : 3.73 % Favored : 95.61 % Rotamer: Outliers : 3.59 % Allowed : 15.69 % Favored : 80.73 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 1.63 % Cis-general : 0.00 % Twisted Proline : 0.54 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.11), residues: 5472 helix: 0.67 (0.12), residues: 1821 sheet: -0.24 (0.15), residues: 1073 loop : -0.48 (0.12), residues: 2578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP c 248 HIS 0.014 0.002 HIS k 35 PHE 0.026 0.003 PHE B 32 TYR 0.037 0.003 TYR L 117 ARG 0.012 0.001 ARG L 110 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10944 Ramachandran restraints generated. 5472 Oldfield, 0 Emsley, 5472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10944 Ramachandran restraints generated. 5472 Oldfield, 0 Emsley, 5472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1164 residues out of total 4572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 1000 time to evaluate : 6.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 10 LEU cc_start: 0.5976 (mm) cc_final: 0.5769 (mt) REVERT: B 59 LYS cc_start: 0.6245 (OUTLIER) cc_final: 0.5802 (ttpp) REVERT: B 100 MET cc_start: 0.7894 (OUTLIER) cc_final: 0.7476 (mtm) REVERT: B 127 ASP cc_start: 0.3243 (OUTLIER) cc_final: 0.2396 (t70) REVERT: B 132 LYS cc_start: 0.3648 (mmtp) cc_final: 0.3334 (mmmm) REVERT: B 142 GLU cc_start: 0.6627 (OUTLIER) cc_final: 0.6367 (tp30) REVERT: B 146 ASN cc_start: 0.6837 (t0) cc_final: 0.6590 (t0) REVERT: B 154 MET cc_start: 0.6839 (ttt) cc_final: 0.6531 (ttp) REVERT: B 174 LYS cc_start: 0.7373 (OUTLIER) cc_final: 0.6906 (tttm) REVERT: B 207 ILE cc_start: 0.5777 (tp) cc_final: 0.5502 (OUTLIER) REVERT: B 222 ARG cc_start: 0.5958 (mtm-85) cc_final: 0.5645 (mtm-85) REVERT: C 45 LYS cc_start: 0.7799 (tttp) cc_final: 0.7540 (tptt) REVERT: C 62 LYS cc_start: 0.6239 (OUTLIER) cc_final: 0.5922 (mttp) REVERT: C 65 ARG cc_start: 0.7680 (ttp-170) cc_final: 0.7165 (ttp80) REVERT: C 82 GLU cc_start: 0.5870 (tt0) cc_final: 0.5297 (tt0) REVERT: C 86 LYS cc_start: 0.7207 (mttm) cc_final: 0.6872 (pttm) REVERT: C 144 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.8034 (mm) REVERT: D 35 GLU cc_start: 0.6878 (pm20) cc_final: 0.6565 (pm20) REVERT: D 36 GLN cc_start: 0.8324 (tt0) cc_final: 0.7905 (tt0) REVERT: D 183 LYS cc_start: 0.8179 (mtpt) cc_final: 0.7744 (mtpt) REVERT: D 194 ASP cc_start: 0.7184 (m-30) cc_final: 0.6881 (m-30) REVERT: E 45 ARG cc_start: 0.8105 (mtp-110) cc_final: 0.7788 (mtp-110) REVERT: E 147 MET cc_start: 0.8407 (ttp) cc_final: 0.7905 (ttp) REVERT: F 14 GLN cc_start: 0.7994 (mm-40) cc_final: 0.7384 (mm110) REVERT: F 17 GLN cc_start: 0.7315 (mp10) cc_final: 0.6702 (mp10) REVERT: F 93 LYS cc_start: 0.7567 (mttt) cc_final: 0.7348 (mtpp) REVERT: F 102 MET cc_start: 0.8192 (mpt) cc_final: 0.7801 (mpt) REVERT: G 11 LYS cc_start: 0.6993 (tttp) cc_final: 0.6729 (ptpp) REVERT: G 76 LYS cc_start: 0.7201 (mtpm) cc_final: 0.6450 (mmtt) REVERT: G 90 GLU cc_start: 0.7338 (tt0) cc_final: 0.7122 (tp30) REVERT: G 146 GLU cc_start: 0.7347 (tp30) cc_final: 0.6973 (mm-30) REVERT: G 154 TYR cc_start: 0.4188 (OUTLIER) cc_final: 0.3453 (m-10) REVERT: H 69 LYS cc_start: 0.7913 (mtpt) cc_final: 0.7633 (mtmm) REVERT: I 36 GLU cc_start: 0.7091 (mp0) cc_final: 0.6701 (mp0) REVERT: I 41 ARG cc_start: 0.6755 (OUTLIER) cc_final: 0.6139 (ttt180) REVERT: I 46 MET cc_start: 0.6725 (tmm) cc_final: 0.5966 (tmt) REVERT: J 36 VAL cc_start: 0.5581 (OUTLIER) cc_final: 0.5317 (m) REVERT: J 37 ARG cc_start: 0.5186 (OUTLIER) cc_final: 0.4974 (mmm160) REVERT: K 15 GLN cc_start: 0.6829 (mm-40) cc_final: 0.6133 (mm110) REVERT: L 35 THR cc_start: 0.8129 (OUTLIER) cc_final: 0.7862 (p) REVERT: L 76 GLU cc_start: 0.7016 (OUTLIER) cc_final: 0.6749 (tm-30) REVERT: L 79 VAL cc_start: 0.8386 (OUTLIER) cc_final: 0.8080 (t) REVERT: M 16 VAL cc_start: 0.7976 (OUTLIER) cc_final: 0.7636 (p) REVERT: M 69 LEU cc_start: 0.8197 (tp) cc_final: 0.7969 (tp) REVERT: M 75 MET cc_start: 0.7500 (ttp) cc_final: 0.6881 (tpp) REVERT: M 78 LYS cc_start: 0.7100 (tptp) cc_final: 0.6791 (ttpt) REVERT: M 95 LEU cc_start: 0.8847 (mt) cc_final: 0.8604 (mt) REVERT: N 47 LYS cc_start: 0.7394 (tptm) cc_final: 0.7042 (tppt) REVERT: O 2 SER cc_start: 0.7502 (OUTLIER) cc_final: 0.7083 (t) REVERT: O 26 GLU cc_start: 0.8943 (mp0) cc_final: 0.8741 (mp0) REVERT: O 62 GLN cc_start: 0.8540 (mm110) cc_final: 0.8209 (tt0) REVERT: O 73 LYS cc_start: 0.7957 (tptt) cc_final: 0.7552 (tppt) REVERT: P 55 ASP cc_start: 0.7491 (m-30) cc_final: 0.7132 (p0) REVERT: P 76 LYS cc_start: 0.8278 (mtpp) cc_final: 0.7766 (mttp) REVERT: Q 11 ARG cc_start: 0.7731 (ttm-80) cc_final: 0.7354 (ttp80) REVERT: Q 27 ARG cc_start: 0.7643 (ptt90) cc_final: 0.7434 (ptt-90) REVERT: Q 40 ARG cc_start: 0.8199 (mmp-170) cc_final: 0.7989 (mmm160) REVERT: Q 51 ASN cc_start: 0.7754 (m-40) cc_final: 0.7431 (m110) REVERT: Q 62 ARG cc_start: 0.8554 (ptt90) cc_final: 0.8261 (ptt90) REVERT: Q 77 ARG cc_start: 0.7626 (ptt90) cc_final: 0.7354 (ptt90) REVERT: R 30 LYS cc_start: 0.8376 (mttt) cc_final: 0.8134 (mttp) REVERT: R 48 ARG cc_start: 0.7653 (mtp85) cc_final: 0.7211 (mtt90) REVERT: S 48 THR cc_start: 0.7242 (m) cc_final: 0.6818 (p) REVERT: T 49 LYS cc_start: 0.7821 (ttpp) cc_final: 0.7454 (tmmt) REVERT: U 14 VAL cc_start: 0.6156 (OUTLIER) cc_final: 0.5854 (t) REVERT: U 17 ARG cc_start: 0.6309 (tpp80) cc_final: 0.6082 (mtt-85) REVERT: U 31 GLU cc_start: 0.7315 (tp30) cc_final: 0.6776 (tt0) REVERT: U 58 LYS cc_start: 0.4482 (OUTLIER) cc_final: 0.4150 (ttpp) REVERT: f 144 ASP cc_start: 0.5472 (OUTLIER) cc_final: 0.5163 (m-30) REVERT: f 148 ARG cc_start: 0.5809 (mtp180) cc_final: 0.5527 (ttm170) REVERT: k 81 ASP cc_start: 0.8093 (m-30) cc_final: 0.7740 (m-30) REVERT: s 18 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7554 (mp0) REVERT: s 48 GLN cc_start: 0.8619 (mt0) cc_final: 0.8391 (mt0) REVERT: u 59 GLU cc_start: 0.6913 (mt-10) cc_final: 0.6697 (pt0) outliers start: 164 outliers final: 41 residues processed: 1113 average time/residue: 2.5823 time to fit residues: 3971.7675 Evaluate side-chains 935 residues out of total 4572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 875 time to evaluate : 6.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 8 LYS Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 136 MET Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 142 GLU Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain B residue 174 LYS Chi-restraints excluded: chain C residue 62 LYS Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain G residue 6 VAL Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 154 TYR Chi-restraints excluded: chain I residue 41 ARG Chi-restraints excluded: chain I residue 72 ILE Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 37 ARG Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 89 ARG Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 35 THR Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 76 GLU Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 115 SER Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain N residue 30 ILE Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain O residue 2 SER Chi-restraints excluded: chain S residue 31 LEU Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain U residue 14 VAL Chi-restraints excluded: chain U residue 58 LYS Chi-restraints excluded: chain d residue 17 GLU Chi-restraints excluded: chain d residue 73 VAL Chi-restraints excluded: chain e residue 107 SER Chi-restraints excluded: chain f residue 133 ARG Chi-restraints excluded: chain f residue 144 ASP Chi-restraints excluded: chain f residue 152 LEU Chi-restraints excluded: chain g residue 47 ASP Chi-restraints excluded: chain g residue 55 ARG Chi-restraints excluded: chain h residue 3 VAL Chi-restraints excluded: chain m residue 33 ILE Chi-restraints excluded: chain n residue 52 SER Chi-restraints excluded: chain q residue 20 VAL Chi-restraints excluded: chain s residue 18 GLU Chi-restraints excluded: chain s residue 27 SER Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain t residue 49 VAL Chi-restraints excluded: chain t residue 59 VAL Chi-restraints excluded: chain z residue 23 THR Chi-restraints excluded: chain z residue 26 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 981 random chunks: chunk 828 optimal weight: 6.9990 chunk 743 optimal weight: 5.9990 chunk 412 optimal weight: 30.0000 chunk 253 optimal weight: 30.0000 chunk 501 optimal weight: 30.0000 chunk 397 optimal weight: 8.9990 chunk 768 optimal weight: 2.9990 chunk 297 optimal weight: 5.9990 chunk 467 optimal weight: 20.0000 chunk 572 optimal weight: 10.0000 chunk 890 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 3 HIS G 130 ASN I 32 GLN J 15 HIS J 58 ASN K 40 ASN K 81 ASN ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 40 GLN Q 50 ASN S 69 HIS T 3 ASN c 117 GLN e 136 GLN e 165 HIS e 195 GLN f 52 ASN g 48 ASN g 64 GLN g 111 HIS h 20 ASN i 80 HIS n 19 GLN n 104 GLN r 31 GLN u 49 ASN w 20 HIS x 15 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.1003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 152316 Z= 0.281 Angle : 0.797 21.536 227847 Z= 0.418 Chirality : 0.042 0.390 29017 Planarity : 0.008 0.144 12181 Dihedral : 23.331 178.909 76295 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.12 % Favored : 96.75 % Rotamer: Outliers : 3.19 % Allowed : 15.10 % Favored : 81.71 % 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: 0.23 (0.11), residues: 5472 helix: 1.09 (0.12), residues: 1861 sheet: -0.14 (0.15), residues: 1102 loop : -0.32 (0.12), residues: 2509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP c 248 HIS 0.011 0.002 HIS k 35 PHE 0.028 0.002 PHE F 8 TYR 0.030 0.002 TYR L 117 ARG 0.010 0.001 ARG z 40 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10944 Ramachandran restraints generated. 5472 Oldfield, 0 Emsley, 5472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10944 Ramachandran restraints generated. 5472 Oldfield, 0 Emsley, 5472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1028 residues out of total 4572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 882 time to evaluate : 6.830 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 16 PHE cc_start: 0.5474 (m-80) cc_final: 0.5237 (m-10) REVERT: B 44 GLU cc_start: 0.6533 (mt-10) cc_final: 0.6146 (tm-30) REVERT: B 50 PHE cc_start: 0.6866 (t80) cc_final: 0.6563 (t80) REVERT: B 56 GLU cc_start: 0.7153 (tp30) cc_final: 0.6924 (mm-30) REVERT: B 59 LYS cc_start: 0.6188 (OUTLIER) cc_final: 0.5765 (tttm) REVERT: B 88 ASP cc_start: 0.4985 (m-30) cc_final: 0.4764 (m-30) REVERT: B 100 MET cc_start: 0.7726 (mtt) cc_final: 0.7436 (mtp) REVERT: B 108 ARG cc_start: 0.6793 (ttp-170) cc_final: 0.6515 (ptp90) REVERT: B 127 ASP cc_start: 0.3389 (OUTLIER) cc_final: 0.2995 (m-30) REVERT: B 136 MET cc_start: 0.5201 (mtm) cc_final: 0.4673 (mmt) REVERT: B 139 ARG cc_start: 0.5402 (OUTLIER) cc_final: 0.5071 (mtp-110) REVERT: B 145 GLU cc_start: 0.6780 (OUTLIER) cc_final: 0.6463 (tm-30) REVERT: B 146 ASN cc_start: 0.6664 (t0) cc_final: 0.6344 (t0) REVERT: B 154 MET cc_start: 0.6846 (ttt) cc_final: 0.6510 (ttp) REVERT: B 167 ASP cc_start: 0.6648 (t70) cc_final: 0.6410 (t70) REVERT: B 178 ASN cc_start: 0.7331 (t0) cc_final: 0.7098 (t0) REVERT: C 45 LYS cc_start: 0.7777 (tttp) cc_final: 0.7505 (tptt) REVERT: C 62 LYS cc_start: 0.6191 (OUTLIER) cc_final: 0.5888 (mptp) REVERT: C 86 LYS cc_start: 0.7129 (mttm) cc_final: 0.6785 (mtmp) REVERT: C 100 GLN cc_start: 0.7546 (tt0) cc_final: 0.7323 (tt0) REVERT: C 144 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7706 (mm) REVERT: D 26 ARG cc_start: 0.7722 (OUTLIER) cc_final: 0.6414 (mtm-85) REVERT: D 35 GLU cc_start: 0.6941 (pm20) cc_final: 0.6599 (pm20) REVERT: D 36 GLN cc_start: 0.8314 (tt0) cc_final: 0.7972 (tt0) REVERT: D 161 LEU cc_start: 0.8031 (mp) cc_final: 0.7749 (mt) REVERT: D 172 GLU cc_start: 0.6716 (tp30) cc_final: 0.6503 (tp30) REVERT: D 183 LYS cc_start: 0.8129 (mtpt) cc_final: 0.7745 (mtpt) REVERT: D 194 ASP cc_start: 0.7081 (m-30) cc_final: 0.6774 (m-30) REVERT: E 45 ARG cc_start: 0.8061 (mtp-110) cc_final: 0.7814 (mtp-110) REVERT: E 147 MET cc_start: 0.8379 (ttp) cc_final: 0.7883 (ttp) REVERT: F 14 GLN cc_start: 0.8070 (OUTLIER) cc_final: 0.7429 (mm-40) REVERT: F 17 GLN cc_start: 0.7435 (mp10) cc_final: 0.6846 (mp10) REVERT: F 102 MET cc_start: 0.8208 (mpt) cc_final: 0.7794 (mpt) REVERT: G 143 ARG cc_start: 0.7442 (OUTLIER) cc_final: 0.7048 (ptp90) REVERT: G 154 TYR cc_start: 0.4412 (OUTLIER) cc_final: 0.4061 (m-10) REVERT: H 43 GLU cc_start: 0.8676 (mm-30) cc_final: 0.8472 (mm-30) REVERT: H 69 LYS cc_start: 0.7931 (mtpt) cc_final: 0.7650 (mtmm) REVERT: H 90 ASP cc_start: 0.7724 (OUTLIER) cc_final: 0.7505 (m-30) REVERT: I 36 GLU cc_start: 0.7057 (mp0) cc_final: 0.6775 (mp0) REVERT: I 41 ARG cc_start: 0.6631 (mtp180) cc_final: 0.5900 (ttt180) REVERT: I 46 MET cc_start: 0.6956 (tmm) cc_final: 0.6227 (tmt) REVERT: I 57 MET cc_start: 0.6768 (mtp) cc_final: 0.6481 (mtp) REVERT: I 85 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.8165 (mtt-85) REVERT: I 97 GLU cc_start: 0.6861 (OUTLIER) cc_final: 0.6649 (tp30) REVERT: J 14 ASP cc_start: 0.7664 (t0) cc_final: 0.7437 (t0) REVERT: J 37 ARG cc_start: 0.5043 (OUTLIER) cc_final: 0.4600 (mmm160) REVERT: K 15 GLN cc_start: 0.6864 (mm-40) cc_final: 0.6168 (mm110) REVERT: L 41 THR cc_start: 0.8599 (OUTLIER) cc_final: 0.8374 (p) REVERT: L 76 GLU cc_start: 0.7062 (OUTLIER) cc_final: 0.6792 (tm-30) REVERT: M 75 MET cc_start: 0.7456 (ttp) cc_final: 0.6808 (tpp) REVERT: M 78 LYS cc_start: 0.7063 (OUTLIER) cc_final: 0.6770 (tmmt) REVERT: M 95 LEU cc_start: 0.8791 (mt) cc_final: 0.8483 (mt) REVERT: N 49 GLN cc_start: 0.7894 (OUTLIER) cc_final: 0.7653 (pt0) REVERT: O 2 SER cc_start: 0.7484 (m) cc_final: 0.7267 (t) REVERT: O 62 GLN cc_start: 0.8557 (mm110) cc_final: 0.8264 (tt0) REVERT: P 55 ASP cc_start: 0.7438 (m-30) cc_final: 0.7015 (p0) REVERT: P 76 LYS cc_start: 0.8081 (mtpp) cc_final: 0.7529 (mttp) REVERT: Q 11 ARG cc_start: 0.7741 (ttm-80) cc_final: 0.7372 (ttp80) REVERT: Q 27 ARG cc_start: 0.7735 (ptt90) cc_final: 0.7517 (ptt-90) REVERT: R 48 ARG cc_start: 0.7583 (mtp85) cc_final: 0.7127 (mtt90) REVERT: S 20 GLU cc_start: 0.6006 (OUTLIER) cc_final: 0.5672 (tt0) REVERT: S 48 THR cc_start: 0.7244 (m) cc_final: 0.6697 (p) REVERT: T 53 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7306 (tt0) REVERT: U 17 ARG cc_start: 0.6331 (tpp80) cc_final: 0.6006 (mtt-85) REVERT: U 21 ARG cc_start: 0.6072 (OUTLIER) cc_final: 0.5634 (mpt-90) REVERT: U 31 GLU cc_start: 0.7252 (tp30) cc_final: 0.6702 (tt0) REVERT: U 58 LYS cc_start: 0.4454 (OUTLIER) cc_final: 0.4053 (ttpp) REVERT: f 148 ARG cc_start: 0.5898 (mtp85) cc_final: 0.5604 (ttm170) REVERT: k 81 ASP cc_start: 0.8024 (m-30) cc_final: 0.7689 (m-30) REVERT: r 1 MET cc_start: 0.6427 (tmt) cc_final: 0.6082 (tmt) REVERT: y 19 LYS cc_start: 0.8403 (OUTLIER) cc_final: 0.8180 (tttt) outliers start: 146 outliers final: 48 residues processed: 972 average time/residue: 2.6602 time to fit residues: 3608.6438 Evaluate side-chains 920 residues out of total 4572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 849 time to evaluate : 6.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 5 ILE Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain C residue 62 LYS Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain D residue 26 ARG Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 166 GLU Chi-restraints excluded: chain F residue 14 GLN Chi-restraints excluded: chain G residue 143 ARG Chi-restraints excluded: chain G residue 154 TYR Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain I residue 85 ARG Chi-restraints excluded: chain I residue 94 LEU Chi-restraints excluded: chain I residue 97 GLU Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain J residue 37 ARG Chi-restraints excluded: chain J residue 81 GLU Chi-restraints excluded: chain L residue 35 THR Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 76 GLU Chi-restraints excluded: chain L residue 94 ARG Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 78 LYS Chi-restraints excluded: chain N residue 30 ILE Chi-restraints excluded: chain N residue 49 GLN Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain S residue 20 GLU Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain T residue 53 GLU Chi-restraints excluded: chain U residue 21 ARG Chi-restraints excluded: chain U residue 36 GLU Chi-restraints excluded: chain U residue 58 LYS Chi-restraints excluded: chain U residue 60 LEU Chi-restraints excluded: chain c residue 182 ARG Chi-restraints excluded: chain d residue 17 GLU Chi-restraints excluded: chain d residue 73 VAL Chi-restraints excluded: chain d residue 95 SER Chi-restraints excluded: chain e residue 107 SER Chi-restraints excluded: chain f residue 35 THR Chi-restraints excluded: chain f residue 133 ARG Chi-restraints excluded: chain f residue 152 LEU Chi-restraints excluded: chain g residue 47 ASP Chi-restraints excluded: chain g residue 127 THR Chi-restraints excluded: chain h residue 14 SER Chi-restraints excluded: chain i residue 101 ILE Chi-restraints excluded: chain k residue 54 GLN Chi-restraints excluded: chain l residue 8 LYS Chi-restraints excluded: chain n residue 40 ILE Chi-restraints excluded: chain q residue 15 SER Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain t residue 49 VAL Chi-restraints excluded: chain t residue 59 VAL Chi-restraints excluded: chain u residue 41 GLU Chi-restraints excluded: chain y residue 19 LYS Chi-restraints excluded: chain z residue 23 THR Chi-restraints excluded: chain z residue 26 THR Chi-restraints excluded: chain z residue 27 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 981 random chunks: chunk 495 optimal weight: 10.0000 chunk 276 optimal weight: 20.0000 chunk 741 optimal weight: 6.9990 chunk 606 optimal weight: 9.9990 chunk 245 optimal weight: 9.9990 chunk 892 optimal weight: 9.9990 chunk 964 optimal weight: 9.9990 chunk 794 optimal weight: 20.0000 chunk 885 optimal weight: 5.9990 chunk 304 optimal weight: 10.0000 chunk 715 optimal weight: 7.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 58 ASN E 148 ASN G 68 ASN K 81 ASN L 20 ASN ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 40 GLN P 63 GLN Q 51 ASN T 52 ASN c 90 ASN c 251 GLN d 42 ASN e 136 GLN e 165 HIS e 195 GLN g 64 GLN g 111 HIS j 5 GLN l 3 GLN n 104 GLN s 48 GLN s 72 GLN u 49 ASN w 20 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.1221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 152316 Z= 0.380 Angle : 0.907 23.315 227847 Z= 0.463 Chirality : 0.047 0.430 29017 Planarity : 0.009 0.156 12181 Dihedral : 23.345 174.006 76235 Min Nonbonded Distance : 1.762 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.38 % Favored : 96.47 % Rotamer: Outliers : 3.70 % Allowed : 14.88 % Favored : 81.43 % 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: 0.12 (0.11), residues: 5472 helix: 0.91 (0.12), residues: 1874 sheet: -0.14 (0.15), residues: 1078 loop : -0.34 (0.12), residues: 2520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP c 248 HIS 0.015 0.002 HIS k 35 PHE 0.028 0.003 PHE F 8 TYR 0.030 0.003 TYR L 117 ARG 0.015 0.001 ARG z 40 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10944 Ramachandran restraints generated. 5472 Oldfield, 0 Emsley, 5472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10944 Ramachandran restraints generated. 5472 Oldfield, 0 Emsley, 5472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1038 residues out of total 4572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 869 time to evaluate : 6.883 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 16 PHE cc_start: 0.5424 (m-80) cc_final: 0.5170 (m-10) REVERT: B 44 GLU cc_start: 0.6261 (mt-10) cc_final: 0.5841 (tm-30) REVERT: B 59 LYS cc_start: 0.5780 (OUTLIER) cc_final: 0.5334 (tttm) REVERT: B 88 ASP cc_start: 0.5057 (m-30) cc_final: 0.4564 (t0) REVERT: B 100 MET cc_start: 0.7875 (mtt) cc_final: 0.7504 (mtp) REVERT: B 145 GLU cc_start: 0.6819 (OUTLIER) cc_final: 0.6520 (tm-30) REVERT: B 207 ILE cc_start: 0.6000 (tp) cc_final: 0.5558 (OUTLIER) REVERT: C 45 LYS cc_start: 0.7740 (tttp) cc_final: 0.7450 (tptt) REVERT: C 58 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.8023 (mt-10) REVERT: C 62 LYS cc_start: 0.6303 (OUTLIER) cc_final: 0.5964 (mptp) REVERT: C 100 GLN cc_start: 0.7550 (tt0) cc_final: 0.7310 (tt0) REVERT: C 144 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7712 (mm) REVERT: D 26 ARG cc_start: 0.7744 (OUTLIER) cc_final: 0.6666 (mtm-85) REVERT: D 161 LEU cc_start: 0.7971 (mp) cc_final: 0.7681 (mt) REVERT: D 183 LYS cc_start: 0.8113 (mtpt) cc_final: 0.7786 (mtpt) REVERT: D 187 GLU cc_start: 0.7309 (mm-30) cc_final: 0.6823 (tp30) REVERT: D 188 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.7433 (mmm160) REVERT: E 147 MET cc_start: 0.8465 (ttp) cc_final: 0.8199 (ttp) REVERT: F 14 GLN cc_start: 0.7966 (OUTLIER) cc_final: 0.7401 (mm-40) REVERT: F 17 GLN cc_start: 0.7555 (mp10) cc_final: 0.6991 (mp10) REVERT: F 36 ILE cc_start: 0.8521 (mm) cc_final: 0.8209 (mm) REVERT: G 143 ARG cc_start: 0.7548 (OUTLIER) cc_final: 0.7177 (ptp90) REVERT: G 154 TYR cc_start: 0.4329 (OUTLIER) cc_final: 0.3947 (m-80) REVERT: H 69 LYS cc_start: 0.7934 (mtpt) cc_final: 0.7634 (mtmm) REVERT: H 90 ASP cc_start: 0.7760 (OUTLIER) cc_final: 0.7507 (m-30) REVERT: I 46 MET cc_start: 0.6813 (tmm) cc_final: 0.6087 (tmt) REVERT: I 85 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.8187 (mtt-85) REVERT: I 97 GLU cc_start: 0.6972 (OUTLIER) cc_final: 0.6706 (tp30) REVERT: K 15 GLN cc_start: 0.6837 (mm-40) cc_final: 0.6114 (mm110) REVERT: L 54 ARG cc_start: 0.8330 (OUTLIER) cc_final: 0.7662 (ttm-80) REVERT: L 76 GLU cc_start: 0.7183 (OUTLIER) cc_final: 0.6935 (tm-30) REVERT: L 123 LYS cc_start: 0.5850 (OUTLIER) cc_final: 0.4878 (tptt) REVERT: M 53 ILE cc_start: 0.8262 (OUTLIER) cc_final: 0.7956 (mm) REVERT: M 75 MET cc_start: 0.7447 (OUTLIER) cc_final: 0.6813 (tpp) REVERT: M 78 LYS cc_start: 0.7088 (OUTLIER) cc_final: 0.6876 (tmmt) REVERT: M 95 LEU cc_start: 0.8762 (mt) cc_final: 0.8486 (mt) REVERT: N 49 GLN cc_start: 0.7923 (OUTLIER) cc_final: 0.7680 (pt0) REVERT: O 62 GLN cc_start: 0.8566 (mm110) cc_final: 0.8258 (tt0) REVERT: P 55 ASP cc_start: 0.7424 (m-30) cc_final: 0.7093 (p0) REVERT: P 76 LYS cc_start: 0.8098 (mtpp) cc_final: 0.7703 (mtmm) REVERT: R 48 ARG cc_start: 0.7624 (mtp85) cc_final: 0.7149 (mtt90) REVERT: S 20 GLU cc_start: 0.6047 (OUTLIER) cc_final: 0.5725 (tt0) REVERT: S 48 THR cc_start: 0.7515 (m) cc_final: 0.6776 (p) REVERT: S 56 GLN cc_start: 0.7935 (OUTLIER) cc_final: 0.7384 (pt0) REVERT: T 53 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7431 (tt0) REVERT: T 85 LYS cc_start: 0.7432 (OUTLIER) cc_final: 0.7058 (ptpp) REVERT: U 17 ARG cc_start: 0.6437 (tpp80) cc_final: 0.6126 (mtt-85) REVERT: U 21 ARG cc_start: 0.6055 (OUTLIER) cc_final: 0.5750 (mpt-90) REVERT: U 58 LYS cc_start: 0.4538 (OUTLIER) cc_final: 0.4070 (ttpp) REVERT: e 100 MET cc_start: 0.9091 (mtp) cc_final: 0.8847 (mtp) REVERT: f 111 ILE cc_start: 0.7530 (OUTLIER) cc_final: 0.7183 (mt) REVERT: f 133 ARG cc_start: 0.6344 (OUTLIER) cc_final: 0.6107 (ttm-80) REVERT: f 148 ARG cc_start: 0.6061 (mtp85) cc_final: 0.5719 (ttm170) REVERT: k 81 ASP cc_start: 0.8051 (m-30) cc_final: 0.7757 (m-30) REVERT: q 1 MET cc_start: 0.7637 (OUTLIER) cc_final: 0.6705 (tpt) REVERT: s 18 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7575 (mp0) REVERT: y 19 LYS cc_start: 0.8414 (OUTLIER) cc_final: 0.8160 (tttt) outliers start: 169 outliers final: 66 residues processed: 975 average time/residue: 2.6308 time to fit residues: 3545.6423 Evaluate side-chains 935 residues out of total 4572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 839 time to evaluate : 6.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 5 ILE Chi-restraints excluded: chain 4 residue 28 VAL Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain C residue 62 LYS Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain D residue 26 ARG Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 166 GLU Chi-restraints excluded: chain D residue 188 ARG Chi-restraints excluded: chain F residue 14 GLN Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain G residue 143 ARG Chi-restraints excluded: chain G residue 154 TYR Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain I residue 85 ARG Chi-restraints excluded: chain I residue 94 LEU Chi-restraints excluded: chain I residue 97 GLU Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain L residue 35 THR Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 54 ARG Chi-restraints excluded: chain L residue 76 GLU Chi-restraints excluded: chain L residue 94 ARG Chi-restraints excluded: chain L residue 123 LYS Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 53 ILE Chi-restraints excluded: chain M residue 75 MET Chi-restraints excluded: chain M residue 78 LYS Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain N residue 49 GLN Chi-restraints excluded: chain O residue 13 SER Chi-restraints excluded: chain Q residue 6 ARG Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain Q residue 55 ILE Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain S residue 20 GLU Chi-restraints excluded: chain S residue 56 GLN Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain T residue 53 GLU Chi-restraints excluded: chain T residue 85 LYS Chi-restraints excluded: chain U residue 14 VAL Chi-restraints excluded: chain U residue 21 ARG Chi-restraints excluded: chain U residue 36 GLU Chi-restraints excluded: chain U residue 58 LYS Chi-restraints excluded: chain U residue 60 LEU Chi-restraints excluded: chain c residue 182 ARG Chi-restraints excluded: chain d residue 17 GLU Chi-restraints excluded: chain d residue 39 ASP Chi-restraints excluded: chain d residue 73 VAL Chi-restraints excluded: chain d residue 95 SER Chi-restraints excluded: chain e residue 107 SER Chi-restraints excluded: chain f residue 35 THR Chi-restraints excluded: chain f residue 87 CYS Chi-restraints excluded: chain f residue 108 VAL Chi-restraints excluded: chain f residue 111 ILE Chi-restraints excluded: chain f residue 118 SER Chi-restraints excluded: chain f residue 133 ARG Chi-restraints excluded: chain f residue 152 LEU Chi-restraints excluded: chain g residue 41 VAL Chi-restraints excluded: chain g residue 43 VAL Chi-restraints excluded: chain g residue 47 ASP Chi-restraints excluded: chain g residue 127 THR Chi-restraints excluded: chain h residue 14 SER Chi-restraints excluded: chain i residue 1 MET Chi-restraints excluded: chain i residue 101 ILE Chi-restraints excluded: chain k residue 1 MET Chi-restraints excluded: chain k residue 54 GLN Chi-restraints excluded: chain l residue 1 MET Chi-restraints excluded: chain l residue 8 LYS Chi-restraints excluded: chain m residue 70 THR Chi-restraints excluded: chain n residue 40 ILE Chi-restraints excluded: chain n residue 49 VAL Chi-restraints excluded: chain q residue 1 MET Chi-restraints excluded: chain q residue 15 SER Chi-restraints excluded: chain q residue 29 THR Chi-restraints excluded: chain r residue 66 ILE Chi-restraints excluded: chain s residue 18 GLU Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain t residue 49 VAL Chi-restraints excluded: chain t residue 59 VAL Chi-restraints excluded: chain u residue 12 GLN Chi-restraints excluded: chain u residue 41 GLU Chi-restraints excluded: chain u residue 62 THR Chi-restraints excluded: chain u residue 65 VAL Chi-restraints excluded: chain y residue 19 LYS Chi-restraints excluded: chain z residue 23 THR Chi-restraints excluded: chain z residue 26 THR Chi-restraints excluded: chain z residue 27 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 981 random chunks: chunk 881 optimal weight: 0.9980 chunk 670 optimal weight: 9.9990 chunk 463 optimal weight: 20.0000 chunk 98 optimal weight: 10.0000 chunk 425 optimal weight: 10.0000 chunk 599 optimal weight: 10.0000 chunk 895 optimal weight: 6.9990 chunk 948 optimal weight: 7.9990 chunk 467 optimal weight: 20.0000 chunk 848 optimal weight: 20.0000 chunk 255 optimal weight: 10.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 81 ASN L 20 ASN ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 40 GLN Q 51 ASN T 52 ASN d 42 ASN e 165 HIS e 195 GLN f 81 GLN g 64 GLN g 111 HIS n 104 GLN s 48 GLN u 49 ASN w 20 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 152316 Z= 0.337 Angle : 0.847 20.204 227847 Z= 0.437 Chirality : 0.045 0.383 29017 Planarity : 0.008 0.152 12181 Dihedral : 23.294 174.618 76226 Min Nonbonded Distance : 1.778 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.29 % Favored : 96.58 % Rotamer: Outliers : 3.22 % Allowed : 15.66 % Favored : 81.12 % 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: 5472 helix: 1.07 (0.12), residues: 1868 sheet: -0.17 (0.15), residues: 1085 loop : -0.30 (0.12), residues: 2519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP c 248 HIS 0.012 0.002 HIS k 35 PHE 0.025 0.003 PHE F 8 TYR 0.030 0.003 TYR L 117 ARG 0.012 0.001 ARG z 40 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10944 Ramachandran restraints generated. 5472 Oldfield, 0 Emsley, 5472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10944 Ramachandran restraints generated. 5472 Oldfield, 0 Emsley, 5472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 993 residues out of total 4572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 846 time to evaluate : 6.980 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 46 LYS cc_start: 0.6913 (OUTLIER) cc_final: 0.6639 (mtpp) REVERT: B 16 PHE cc_start: 0.5486 (m-80) cc_final: 0.5208 (m-10) REVERT: B 44 GLU cc_start: 0.6113 (mt-10) cc_final: 0.5773 (tm-30) REVERT: B 56 GLU cc_start: 0.6856 (mm-30) cc_final: 0.6652 (mm-30) REVERT: B 59 LYS cc_start: 0.5730 (OUTLIER) cc_final: 0.5072 (tppp) REVERT: B 88 ASP cc_start: 0.5077 (m-30) cc_final: 0.4640 (t0) REVERT: B 100 MET cc_start: 0.7772 (mtt) cc_final: 0.7416 (mtp) REVERT: B 117 LEU cc_start: 0.5573 (tp) cc_final: 0.5341 (mt) REVERT: B 139 ARG cc_start: 0.5483 (OUTLIER) cc_final: 0.4754 (mtt180) REVERT: B 142 GLU cc_start: 0.6410 (tt0) cc_final: 0.6194 (tm-30) REVERT: B 145 GLU cc_start: 0.6740 (OUTLIER) cc_final: 0.6446 (tm-30) REVERT: B 161 LEU cc_start: 0.7783 (OUTLIER) cc_final: 0.7564 (mp) REVERT: B 207 ILE cc_start: 0.5995 (tp) cc_final: 0.5672 (OUTLIER) REVERT: C 45 LYS cc_start: 0.7758 (tttp) cc_final: 0.7476 (tptt) REVERT: C 58 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.8016 (mt-10) REVERT: C 62 LYS cc_start: 0.6268 (OUTLIER) cc_final: 0.5919 (mptp) REVERT: C 100 GLN cc_start: 0.7534 (tt0) cc_final: 0.7253 (tt0) REVERT: C 144 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7784 (mm) REVERT: C 206 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.7026 (tp30) REVERT: D 26 ARG cc_start: 0.7791 (OUTLIER) cc_final: 0.6533 (mtm-85) REVERT: D 161 LEU cc_start: 0.7927 (mp) cc_final: 0.7659 (mt) REVERT: D 183 LYS cc_start: 0.8122 (mtpt) cc_final: 0.7805 (mtpt) REVERT: D 187 GLU cc_start: 0.7339 (mm-30) cc_final: 0.6900 (tp30) REVERT: D 188 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.7133 (mmm160) REVERT: E 147 MET cc_start: 0.8441 (ttp) cc_final: 0.8219 (ttp) REVERT: F 14 GLN cc_start: 0.8052 (OUTLIER) cc_final: 0.7372 (mm-40) REVERT: F 17 GLN cc_start: 0.7513 (mp10) cc_final: 0.6924 (mp10) REVERT: F 29 ILE cc_start: 0.8177 (OUTLIER) cc_final: 0.7951 (mm) REVERT: F 36 ILE cc_start: 0.8531 (mm) cc_final: 0.8192 (mm) REVERT: G 143 ARG cc_start: 0.7550 (OUTLIER) cc_final: 0.7088 (ptp90) REVERT: G 154 TYR cc_start: 0.4337 (OUTLIER) cc_final: 0.3921 (m-80) REVERT: H 69 LYS cc_start: 0.7897 (mtpt) cc_final: 0.7614 (mtmm) REVERT: H 90 ASP cc_start: 0.7733 (OUTLIER) cc_final: 0.7499 (m-30) REVERT: H 117 ARG cc_start: 0.8835 (OUTLIER) cc_final: 0.8499 (mtt90) REVERT: I 46 MET cc_start: 0.6814 (tmm) cc_final: 0.6076 (tmt) REVERT: I 85 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.8198 (mtt-85) REVERT: I 97 GLU cc_start: 0.6941 (OUTLIER) cc_final: 0.6665 (tp30) REVERT: K 15 GLN cc_start: 0.6884 (mm-40) cc_final: 0.6111 (mm110) REVERT: L 54 ARG cc_start: 0.8323 (OUTLIER) cc_final: 0.7655 (ttm-80) REVERT: L 76 GLU cc_start: 0.7140 (OUTLIER) cc_final: 0.6598 (tm-30) REVERT: L 123 LYS cc_start: 0.5816 (OUTLIER) cc_final: 0.4832 (tptt) REVERT: M 53 ILE cc_start: 0.8235 (OUTLIER) cc_final: 0.7943 (mm) REVERT: M 75 MET cc_start: 0.7436 (ttp) cc_final: 0.6821 (tpp) REVERT: O 62 GLN cc_start: 0.8544 (mm110) cc_final: 0.8263 (tt0) REVERT: P 55 ASP cc_start: 0.7420 (m-30) cc_final: 0.7149 (p0) REVERT: P 76 LYS cc_start: 0.8078 (mtpp) cc_final: 0.7697 (mtmm) REVERT: R 48 ARG cc_start: 0.7603 (mtp85) cc_final: 0.7136 (mtt90) REVERT: S 20 GLU cc_start: 0.5972 (OUTLIER) cc_final: 0.5634 (tt0) REVERT: S 48 THR cc_start: 0.7481 (m) cc_final: 0.6748 (p) REVERT: S 56 GLN cc_start: 0.7872 (OUTLIER) cc_final: 0.7347 (pt0) REVERT: T 53 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7370 (tt0) REVERT: T 85 LYS cc_start: 0.7363 (OUTLIER) cc_final: 0.7023 (ptpp) REVERT: U 17 ARG cc_start: 0.6359 (tpp80) cc_final: 0.6071 (mtt-85) REVERT: U 21 ARG cc_start: 0.5964 (OUTLIER) cc_final: 0.5679 (mpt-90) REVERT: U 58 LYS cc_start: 0.4535 (OUTLIER) cc_final: 0.4261 (ttpt) REVERT: c 167 ARG cc_start: 0.7787 (ttp-170) cc_final: 0.7559 (ttp80) REVERT: d 7 LYS cc_start: 0.8816 (OUTLIER) cc_final: 0.8456 (ttpm) REVERT: f 148 ARG cc_start: 0.6020 (mtp85) cc_final: 0.5820 (ttt-90) REVERT: k 81 ASP cc_start: 0.8038 (m-30) cc_final: 0.7747 (m-30) REVERT: l 53 MET cc_start: 0.8785 (ptp) cc_final: 0.8559 (ptp) REVERT: r 1 MET cc_start: 0.6798 (OUTLIER) cc_final: 0.6454 (tmt) REVERT: s 18 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7482 (mp0) REVERT: s 48 GLN cc_start: 0.8615 (mt0) cc_final: 0.8403 (mt0) REVERT: y 19 LYS cc_start: 0.8422 (OUTLIER) cc_final: 0.8174 (tttt) outliers start: 147 outliers final: 72 residues processed: 938 average time/residue: 2.6699 time to fit residues: 3452.6557 Evaluate side-chains 927 residues out of total 4572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 823 time to evaluate : 6.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 10 LYS Chi-restraints excluded: chain 1 residue 46 LYS Chi-restraints excluded: chain 2 residue 52 LYS Chi-restraints excluded: chain 4 residue 27 THR Chi-restraints excluded: chain 4 residue 28 VAL Chi-restraints excluded: chain 4 residue 56 ARG Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain C residue 62 LYS Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 206 GLU Chi-restraints excluded: chain D residue 26 ARG Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 163 GLU Chi-restraints excluded: chain D residue 166 GLU Chi-restraints excluded: chain D residue 188 ARG Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain F residue 14 GLN Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain G residue 143 ARG Chi-restraints excluded: chain G residue 154 TYR Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 117 ARG Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 85 ARG Chi-restraints excluded: chain I residue 94 LEU Chi-restraints excluded: chain I residue 97 GLU Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 81 GLU Chi-restraints excluded: chain K residue 110 ILE Chi-restraints excluded: chain L residue 35 THR Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 54 ARG Chi-restraints excluded: chain L residue 76 GLU Chi-restraints excluded: chain L residue 94 ARG Chi-restraints excluded: chain L residue 123 LYS Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 53 ILE Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain O residue 13 SER Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain Q residue 55 ILE Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain S residue 20 GLU Chi-restraints excluded: chain S residue 56 GLN Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain T residue 53 GLU Chi-restraints excluded: chain T residue 85 LYS Chi-restraints excluded: chain U residue 14 VAL Chi-restraints excluded: chain U residue 21 ARG Chi-restraints excluded: chain U residue 36 GLU Chi-restraints excluded: chain U residue 58 LYS Chi-restraints excluded: chain U residue 60 LEU Chi-restraints excluded: chain c residue 182 ARG Chi-restraints excluded: chain d residue 7 LYS Chi-restraints excluded: chain d residue 17 GLU Chi-restraints excluded: chain d residue 39 ASP Chi-restraints excluded: chain d residue 73 VAL Chi-restraints excluded: chain d residue 95 SER Chi-restraints excluded: chain e residue 107 SER Chi-restraints excluded: chain f residue 17 MET Chi-restraints excluded: chain f residue 32 GLU Chi-restraints excluded: chain f residue 35 THR Chi-restraints excluded: chain f residue 64 LYS Chi-restraints excluded: chain f residue 108 VAL Chi-restraints excluded: chain f residue 118 SER Chi-restraints excluded: chain f residue 152 LEU Chi-restraints excluded: chain g residue 43 VAL Chi-restraints excluded: chain g residue 47 ASP Chi-restraints excluded: chain g residue 99 LYS Chi-restraints excluded: chain g residue 127 THR Chi-restraints excluded: chain h residue 14 SER Chi-restraints excluded: chain i residue 1 MET Chi-restraints excluded: chain i residue 101 ILE Chi-restraints excluded: chain k residue 54 GLN Chi-restraints excluded: chain l residue 8 LYS Chi-restraints excluded: chain l residue 30 SER Chi-restraints excluded: chain l residue 115 GLU Chi-restraints excluded: chain m residue 70 THR Chi-restraints excluded: chain n residue 40 ILE Chi-restraints excluded: chain n residue 49 VAL Chi-restraints excluded: chain q residue 15 SER Chi-restraints excluded: chain q residue 20 VAL Chi-restraints excluded: chain q residue 64 VAL Chi-restraints excluded: chain r residue 1 MET Chi-restraints excluded: chain s residue 18 GLU Chi-restraints excluded: chain t residue 49 VAL Chi-restraints excluded: chain t residue 59 VAL Chi-restraints excluded: chain u residue 12 GLN Chi-restraints excluded: chain u residue 41 GLU Chi-restraints excluded: chain u residue 62 THR Chi-restraints excluded: chain y residue 19 LYS Chi-restraints excluded: chain z residue 23 THR Chi-restraints excluded: chain z residue 26 THR Chi-restraints excluded: chain z residue 27 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 981 random chunks: chunk 789 optimal weight: 9.9990 chunk 538 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 chunk 706 optimal weight: 4.9990 chunk 391 optimal weight: 5.9990 chunk 809 optimal weight: 10.0000 chunk 655 optimal weight: 9.9990 chunk 1 optimal weight: 9.9990 chunk 484 optimal weight: 10.0000 chunk 851 optimal weight: 5.9990 chunk 239 optimal weight: 6.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 81 ASN L 20 ASN N 43 ASN O 40 GLN P 63 GLN Q 51 ASN T 52 ASN d 42 ASN e 195 GLN f 81 GLN g 64 GLN ** g 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 104 GLN u 49 ASN w 20 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 152316 Z= 0.322 Angle : 0.832 21.294 227847 Z= 0.432 Chirality : 0.044 0.383 29017 Planarity : 0.008 0.150 12181 Dihedral : 23.289 174.516 76220 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.33 % Favored : 96.55 % Rotamer: Outliers : 3.33 % Allowed : 15.86 % Favored : 80.81 % 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: 0.26 (0.11), residues: 5472 helix: 1.13 (0.12), residues: 1858 sheet: -0.19 (0.15), residues: 1096 loop : -0.29 (0.12), residues: 2518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP c 248 HIS 0.013 0.002 HIS k 35 PHE 0.027 0.003 PHE F 8 TYR 0.031 0.003 TYR L 117 ARG 0.014 0.001 ARG z 40 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10944 Ramachandran restraints generated. 5472 Oldfield, 0 Emsley, 5472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10944 Ramachandran restraints generated. 5472 Oldfield, 0 Emsley, 5472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 993 residues out of total 4572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 841 time to evaluate : 7.115 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 28 ARG cc_start: 0.6767 (OUTLIER) cc_final: 0.6329 (mmt180) REVERT: 1 46 LYS cc_start: 0.6896 (OUTLIER) cc_final: 0.6650 (mtpp) REVERT: B 16 PHE cc_start: 0.5514 (m-80) cc_final: 0.5253 (m-10) REVERT: B 88 ASP cc_start: 0.5072 (m-30) cc_final: 0.4647 (t0) REVERT: B 100 MET cc_start: 0.7818 (mtt) cc_final: 0.7480 (mtp) REVERT: B 139 ARG cc_start: 0.5504 (OUTLIER) cc_final: 0.4789 (mtt180) REVERT: B 145 GLU cc_start: 0.6763 (OUTLIER) cc_final: 0.6477 (tm-30) REVERT: B 161 LEU cc_start: 0.7797 (OUTLIER) cc_final: 0.7524 (mp) REVERT: B 207 ILE cc_start: 0.5912 (tp) cc_final: 0.5564 (OUTLIER) REVERT: C 45 LYS cc_start: 0.7750 (tttp) cc_final: 0.7471 (tptt) REVERT: C 62 LYS cc_start: 0.6262 (OUTLIER) cc_final: 0.5908 (mptp) REVERT: C 100 GLN cc_start: 0.7539 (tt0) cc_final: 0.7245 (tt0) REVERT: C 144 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7783 (mm) REVERT: D 161 LEU cc_start: 0.7957 (mp) cc_final: 0.7695 (mt) REVERT: D 183 LYS cc_start: 0.8137 (mtpt) cc_final: 0.7756 (mtpt) REVERT: D 187 GLU cc_start: 0.7291 (mm-30) cc_final: 0.7089 (mm-30) REVERT: D 188 ARG cc_start: 0.8122 (OUTLIER) cc_final: 0.7092 (mmm160) REVERT: F 14 GLN cc_start: 0.8072 (OUTLIER) cc_final: 0.7405 (mm-40) REVERT: F 17 GLN cc_start: 0.7508 (mp10) cc_final: 0.6925 (mp10) REVERT: F 36 ILE cc_start: 0.8535 (mm) cc_final: 0.8201 (mm) REVERT: G 143 ARG cc_start: 0.7539 (OUTLIER) cc_final: 0.7103 (ptp90) REVERT: G 154 TYR cc_start: 0.4284 (OUTLIER) cc_final: 0.3866 (m-80) REVERT: H 69 LYS cc_start: 0.7908 (mtpt) cc_final: 0.7618 (mtmm) REVERT: H 90 ASP cc_start: 0.7743 (OUTLIER) cc_final: 0.7502 (m-30) REVERT: I 46 MET cc_start: 0.6811 (tmm) cc_final: 0.6084 (tmt) REVERT: I 85 ARG cc_start: 0.8457 (OUTLIER) cc_final: 0.8195 (mtt-85) REVERT: I 97 GLU cc_start: 0.6943 (OUTLIER) cc_final: 0.6671 (tp30) REVERT: K 15 GLN cc_start: 0.6885 (mm-40) cc_final: 0.6096 (mm110) REVERT: L 54 ARG cc_start: 0.8300 (OUTLIER) cc_final: 0.7621 (ttm-80) REVERT: L 76 GLU cc_start: 0.7148 (OUTLIER) cc_final: 0.6645 (tm-30) REVERT: L 123 LYS cc_start: 0.5795 (OUTLIER) cc_final: 0.4797 (tptt) REVERT: M 53 ILE cc_start: 0.8138 (OUTLIER) cc_final: 0.7897 (mm) REVERT: M 75 MET cc_start: 0.7493 (OUTLIER) cc_final: 0.6829 (tpp) REVERT: O 62 GLN cc_start: 0.8547 (mm110) cc_final: 0.8263 (tt0) REVERT: P 55 ASP cc_start: 0.7424 (m-30) cc_final: 0.7163 (p0) REVERT: P 76 LYS cc_start: 0.8085 (mtpp) cc_final: 0.7708 (mtmm) REVERT: R 48 ARG cc_start: 0.7607 (mtp85) cc_final: 0.7140 (mtt90) REVERT: S 20 GLU cc_start: 0.6024 (OUTLIER) cc_final: 0.5687 (tt0) REVERT: S 48 THR cc_start: 0.7473 (m) cc_final: 0.6722 (p) REVERT: S 56 GLN cc_start: 0.7896 (OUTLIER) cc_final: 0.7367 (pt0) REVERT: T 53 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7382 (tt0) REVERT: T 85 LYS cc_start: 0.7395 (OUTLIER) cc_final: 0.6987 (ptpp) REVERT: U 17 ARG cc_start: 0.6366 (tpp80) cc_final: 0.6071 (mtt-85) REVERT: U 21 ARG cc_start: 0.5959 (OUTLIER) cc_final: 0.5659 (mpt-90) REVERT: U 29 LEU cc_start: 0.7515 (OUTLIER) cc_final: 0.7001 (mp) REVERT: U 58 LYS cc_start: 0.4550 (OUTLIER) cc_final: 0.4294 (ttpt) REVERT: c 167 ARG cc_start: 0.7785 (ttp-170) cc_final: 0.7561 (ttp80) REVERT: e 100 MET cc_start: 0.9098 (mtp) cc_final: 0.8800 (mtp) REVERT: f 133 ARG cc_start: 0.6284 (OUTLIER) cc_final: 0.6006 (ttm-80) REVERT: f 148 ARG cc_start: 0.6003 (mtp85) cc_final: 0.5696 (ttm170) REVERT: k 1 MET cc_start: 0.7511 (OUTLIER) cc_final: 0.6560 (ptt) REVERT: k 81 ASP cc_start: 0.8034 (m-30) cc_final: 0.7739 (m-30) REVERT: q 1 MET cc_start: 0.7594 (OUTLIER) cc_final: 0.6697 (tpt) REVERT: s 18 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7578 (mp0) REVERT: s 48 GLN cc_start: 0.8617 (mt0) cc_final: 0.8397 (mt0) REVERT: y 19 LYS cc_start: 0.8421 (OUTLIER) cc_final: 0.8177 (tttt) outliers start: 152 outliers final: 79 residues processed: 937 average time/residue: 2.6143 time to fit residues: 3380.2579 Evaluate side-chains 941 residues out of total 4572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 832 time to evaluate : 6.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 5 ILE Chi-restraints excluded: chain 0 residue 10 LYS Chi-restraints excluded: chain 0 residue 28 ARG Chi-restraints excluded: chain 1 residue 46 LYS Chi-restraints excluded: chain 2 residue 52 LYS Chi-restraints excluded: chain 3 residue 8 LYS Chi-restraints excluded: chain 3 residue 12 ARG Chi-restraints excluded: chain 4 residue 28 VAL Chi-restraints excluded: chain 4 residue 56 ARG Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain C residue 62 LYS Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 163 GLU Chi-restraints excluded: chain D residue 166 GLU Chi-restraints excluded: chain D residue 188 ARG Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain F residue 14 GLN Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain G residue 143 ARG Chi-restraints excluded: chain G residue 154 TYR Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain I residue 85 ARG Chi-restraints excluded: chain I residue 94 LEU Chi-restraints excluded: chain I residue 97 GLU Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 81 GLU Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 110 ILE Chi-restraints excluded: chain L residue 35 THR Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 54 ARG Chi-restraints excluded: chain L residue 76 GLU Chi-restraints excluded: chain L residue 94 ARG Chi-restraints excluded: chain L residue 123 LYS Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 53 ILE Chi-restraints excluded: chain M residue 75 MET Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain O residue 13 SER Chi-restraints excluded: chain O residue 14 GLU Chi-restraints excluded: chain Q residue 6 ARG Chi-restraints excluded: chain Q residue 55 ILE Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain S residue 20 GLU Chi-restraints excluded: chain S residue 56 GLN Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain T residue 53 GLU Chi-restraints excluded: chain T residue 85 LYS Chi-restraints excluded: chain U residue 14 VAL Chi-restraints excluded: chain U residue 21 ARG Chi-restraints excluded: chain U residue 29 LEU Chi-restraints excluded: chain U residue 36 GLU Chi-restraints excluded: chain U residue 58 LYS Chi-restraints excluded: chain U residue 60 LEU Chi-restraints excluded: chain c residue 182 ARG Chi-restraints excluded: chain d residue 17 GLU Chi-restraints excluded: chain d residue 39 ASP Chi-restraints excluded: chain d residue 73 VAL Chi-restraints excluded: chain d residue 95 SER Chi-restraints excluded: chain e residue 107 SER Chi-restraints excluded: chain f residue 17 MET Chi-restraints excluded: chain f residue 35 THR Chi-restraints excluded: chain f residue 108 VAL Chi-restraints excluded: chain f residue 118 SER Chi-restraints excluded: chain f residue 133 ARG Chi-restraints excluded: chain f residue 152 LEU Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 41 VAL Chi-restraints excluded: chain g residue 47 ASP Chi-restraints excluded: chain g residue 84 THR Chi-restraints excluded: chain g residue 127 THR Chi-restraints excluded: chain h residue 14 SER Chi-restraints excluded: chain i residue 1 MET Chi-restraints excluded: chain i residue 101 ILE Chi-restraints excluded: chain k residue 1 MET Chi-restraints excluded: chain k residue 54 GLN Chi-restraints excluded: chain l residue 1 MET Chi-restraints excluded: chain l residue 8 LYS Chi-restraints excluded: chain l residue 30 SER Chi-restraints excluded: chain l residue 115 GLU Chi-restraints excluded: chain m residue 70 THR Chi-restraints excluded: chain n residue 40 ILE Chi-restraints excluded: chain n residue 49 VAL Chi-restraints excluded: chain q residue 1 MET Chi-restraints excluded: chain q residue 15 SER Chi-restraints excluded: chain q residue 64 VAL Chi-restraints excluded: chain r residue 66 ILE Chi-restraints excluded: chain s residue 18 GLU Chi-restraints excluded: chain t residue 49 VAL Chi-restraints excluded: chain t residue 59 VAL Chi-restraints excluded: chain u residue 12 GLN Chi-restraints excluded: chain u residue 41 GLU Chi-restraints excluded: chain u residue 62 THR Chi-restraints excluded: chain y residue 19 LYS Chi-restraints excluded: chain z residue 23 THR Chi-restraints excluded: chain z residue 26 THR Chi-restraints excluded: chain z residue 27 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 981 random chunks: chunk 319 optimal weight: 9.9990 chunk 853 optimal weight: 0.5980 chunk 187 optimal weight: 20.0000 chunk 556 optimal weight: 20.0000 chunk 234 optimal weight: 10.0000 chunk 949 optimal weight: 20.0000 chunk 787 optimal weight: 0.9990 chunk 439 optimal weight: 20.0000 chunk 78 optimal weight: 10.0000 chunk 313 optimal weight: 10.0000 chunk 498 optimal weight: 20.0000 overall best weight: 6.3192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 81 ASN L 20 ASN O 40 GLN Q 51 ASN d 42 ASN e 195 GLN g 64 GLN n 104 GLN u 49 ASN w 20 HIS x 31 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 152316 Z= 0.303 Angle : 0.807 20.440 227847 Z= 0.421 Chirality : 0.043 0.386 29017 Planarity : 0.008 0.149 12181 Dihedral : 23.268 174.569 76216 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.27 % Favored : 96.60 % Rotamer: Outliers : 3.30 % Allowed : 16.06 % Favored : 80.64 % 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: 0.33 (0.11), residues: 5472 helix: 1.20 (0.12), residues: 1866 sheet: -0.16 (0.15), residues: 1091 loop : -0.25 (0.12), residues: 2515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 201 HIS 0.012 0.002 HIS k 35 PHE 0.026 0.002 PHE F 8 TYR 0.030 0.003 TYR L 117 ARG 0.012 0.001 ARG z 40 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10944 Ramachandran restraints generated. 5472 Oldfield, 0 Emsley, 5472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10944 Ramachandran restraints generated. 5472 Oldfield, 0 Emsley, 5472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 984 residues out of total 4572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 833 time to evaluate : 6.939 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 28 ARG cc_start: 0.6752 (OUTLIER) cc_final: 0.6311 (mmt180) REVERT: 1 46 LYS cc_start: 0.6905 (OUTLIER) cc_final: 0.6640 (mtpp) REVERT: B 16 PHE cc_start: 0.5531 (m-80) cc_final: 0.5265 (m-10) REVERT: B 88 ASP cc_start: 0.5016 (m-30) cc_final: 0.4607 (t0) REVERT: B 100 MET cc_start: 0.7811 (mtt) cc_final: 0.7472 (mtp) REVERT: B 139 ARG cc_start: 0.5499 (OUTLIER) cc_final: 0.4753 (mtt180) REVERT: B 145 GLU cc_start: 0.6735 (OUTLIER) cc_final: 0.6460 (tm-30) REVERT: B 161 LEU cc_start: 0.7792 (OUTLIER) cc_final: 0.7555 (mp) REVERT: C 45 LYS cc_start: 0.7789 (tttp) cc_final: 0.7509 (tptt) REVERT: C 58 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.8020 (mt-10) REVERT: C 62 LYS cc_start: 0.6253 (OUTLIER) cc_final: 0.5901 (mptp) REVERT: C 100 GLN cc_start: 0.7516 (tt0) cc_final: 0.7233 (tt0) REVERT: C 144 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7800 (mm) REVERT: D 161 LEU cc_start: 0.7897 (mp) cc_final: 0.7691 (mt) REVERT: D 183 LYS cc_start: 0.8128 (mtpt) cc_final: 0.7751 (mtpt) REVERT: D 187 GLU cc_start: 0.7300 (mm-30) cc_final: 0.7054 (mm-30) REVERT: D 188 ARG cc_start: 0.8116 (OUTLIER) cc_final: 0.6903 (mmm160) REVERT: E 147 MET cc_start: 0.8456 (ttp) cc_final: 0.7984 (ttp) REVERT: E 163 GLU cc_start: 0.7132 (OUTLIER) cc_final: 0.6851 (mt-10) REVERT: F 14 GLN cc_start: 0.8055 (OUTLIER) cc_final: 0.7416 (mm-40) REVERT: F 17 GLN cc_start: 0.7517 (mp10) cc_final: 0.6917 (mp10) REVERT: F 36 ILE cc_start: 0.8584 (mm) cc_final: 0.8235 (mm) REVERT: G 143 ARG cc_start: 0.7533 (OUTLIER) cc_final: 0.7067 (ptp90) REVERT: G 154 TYR cc_start: 0.4413 (OUTLIER) cc_final: 0.3957 (m-10) REVERT: H 69 LYS cc_start: 0.7901 (mtpt) cc_final: 0.7611 (mtmm) REVERT: H 90 ASP cc_start: 0.7724 (OUTLIER) cc_final: 0.7489 (m-30) REVERT: H 117 ARG cc_start: 0.8830 (OUTLIER) cc_final: 0.8497 (mtt90) REVERT: I 46 MET cc_start: 0.6811 (tmm) cc_final: 0.6079 (tmt) REVERT: I 85 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.8190 (mtt-85) REVERT: I 97 GLU cc_start: 0.6940 (OUTLIER) cc_final: 0.6671 (tp30) REVERT: K 15 GLN cc_start: 0.6886 (mm-40) cc_final: 0.6088 (mm110) REVERT: L 54 ARG cc_start: 0.8296 (OUTLIER) cc_final: 0.7615 (ttm-80) REVERT: L 76 GLU cc_start: 0.7122 (OUTLIER) cc_final: 0.6817 (tt0) REVERT: L 123 LYS cc_start: 0.5785 (OUTLIER) cc_final: 0.4776 (tptt) REVERT: M 53 ILE cc_start: 0.8122 (OUTLIER) cc_final: 0.7884 (mm) REVERT: M 75 MET cc_start: 0.7470 (OUTLIER) cc_final: 0.6819 (tpp) REVERT: O 62 GLN cc_start: 0.8547 (mm110) cc_final: 0.8263 (tt0) REVERT: P 76 LYS cc_start: 0.8059 (mtpp) cc_final: 0.7684 (mtmm) REVERT: R 48 ARG cc_start: 0.7591 (mtp85) cc_final: 0.7132 (mtt90) REVERT: S 20 GLU cc_start: 0.6058 (OUTLIER) cc_final: 0.5713 (tt0) REVERT: S 48 THR cc_start: 0.7441 (m) cc_final: 0.6699 (p) REVERT: S 56 GLN cc_start: 0.7880 (OUTLIER) cc_final: 0.7353 (pt0) REVERT: T 53 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7388 (tt0) REVERT: T 85 LYS cc_start: 0.7378 (OUTLIER) cc_final: 0.7043 (ptpp) REVERT: U 17 ARG cc_start: 0.6390 (tpp80) cc_final: 0.6091 (mtt-85) REVERT: U 21 ARG cc_start: 0.5965 (OUTLIER) cc_final: 0.5659 (mpt-90) REVERT: U 29 LEU cc_start: 0.7495 (OUTLIER) cc_final: 0.6989 (mp) REVERT: U 58 LYS cc_start: 0.4540 (OUTLIER) cc_final: 0.4293 (ttpt) REVERT: c 167 ARG cc_start: 0.7781 (ttp-170) cc_final: 0.7564 (ttp80) REVERT: d 7 LYS cc_start: 0.8803 (OUTLIER) cc_final: 0.8529 (ttpm) REVERT: f 80 ARG cc_start: 0.5889 (OUTLIER) cc_final: 0.4963 (mmt180) REVERT: f 133 ARG cc_start: 0.6281 (OUTLIER) cc_final: 0.6015 (ttm-80) REVERT: k 81 ASP cc_start: 0.8026 (m-30) cc_final: 0.7730 (m-30) REVERT: s 18 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7461 (mp0) REVERT: s 48 GLN cc_start: 0.8613 (mt0) cc_final: 0.8388 (mt0) REVERT: y 19 LYS cc_start: 0.8409 (OUTLIER) cc_final: 0.8171 (tttt) outliers start: 151 outliers final: 81 residues processed: 929 average time/residue: 2.6369 time to fit residues: 3391.9918 Evaluate side-chains 943 residues out of total 4572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 828 time to evaluate : 6.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 5 ILE Chi-restraints excluded: chain 0 residue 10 LYS Chi-restraints excluded: chain 0 residue 28 ARG Chi-restraints excluded: chain 1 residue 46 LYS Chi-restraints excluded: chain 2 residue 52 LYS Chi-restraints excluded: chain 3 residue 8 LYS Chi-restraints excluded: chain 4 residue 27 THR Chi-restraints excluded: chain 4 residue 28 VAL Chi-restraints excluded: chain 4 residue 32 LEU Chi-restraints excluded: chain 4 residue 56 ARG Chi-restraints excluded: chain 4 residue 57 VAL Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain C residue 62 LYS Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 206 GLU Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 163 GLU Chi-restraints excluded: chain D residue 166 GLU Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 188 ARG Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain F residue 14 GLN Chi-restraints excluded: chain G residue 143 ARG Chi-restraints excluded: chain G residue 154 TYR Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 117 ARG Chi-restraints excluded: chain I residue 85 ARG Chi-restraints excluded: chain I residue 94 LEU Chi-restraints excluded: chain I residue 97 GLU Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 81 GLU Chi-restraints excluded: chain K residue 110 ILE Chi-restraints excluded: chain L residue 35 THR Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 54 ARG Chi-restraints excluded: chain L residue 76 GLU Chi-restraints excluded: chain L residue 94 ARG Chi-restraints excluded: chain L residue 123 LYS Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 53 ILE Chi-restraints excluded: chain M residue 75 MET Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain O residue 13 SER Chi-restraints excluded: chain O residue 14 GLU Chi-restraints excluded: chain Q residue 6 ARG Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain Q residue 55 ILE Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain S residue 20 GLU Chi-restraints excluded: chain S residue 56 GLN Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain T residue 53 GLU Chi-restraints excluded: chain T residue 85 LYS Chi-restraints excluded: chain U residue 14 VAL Chi-restraints excluded: chain U residue 21 ARG Chi-restraints excluded: chain U residue 29 LEU Chi-restraints excluded: chain U residue 36 GLU Chi-restraints excluded: chain U residue 58 LYS Chi-restraints excluded: chain c residue 182 ARG Chi-restraints excluded: chain d residue 7 LYS Chi-restraints excluded: chain d residue 17 GLU Chi-restraints excluded: chain d residue 39 ASP Chi-restraints excluded: chain d residue 73 VAL Chi-restraints excluded: chain d residue 95 SER Chi-restraints excluded: chain e residue 107 SER Chi-restraints excluded: chain f residue 17 MET Chi-restraints excluded: chain f residue 32 GLU Chi-restraints excluded: chain f residue 35 THR Chi-restraints excluded: chain f residue 80 ARG Chi-restraints excluded: chain f residue 108 VAL Chi-restraints excluded: chain f residue 118 SER Chi-restraints excluded: chain f residue 133 ARG Chi-restraints excluded: chain f residue 152 LEU Chi-restraints excluded: chain g residue 127 THR Chi-restraints excluded: chain h residue 14 SER Chi-restraints excluded: chain i residue 1 MET Chi-restraints excluded: chain i residue 101 ILE Chi-restraints excluded: chain k residue 1 MET Chi-restraints excluded: chain k residue 54 GLN Chi-restraints excluded: chain l residue 1 MET Chi-restraints excluded: chain l residue 8 LYS Chi-restraints excluded: chain l residue 30 SER Chi-restraints excluded: chain l residue 115 GLU Chi-restraints excluded: chain m residue 70 THR Chi-restraints excluded: chain n residue 40 ILE Chi-restraints excluded: chain n residue 49 VAL Chi-restraints excluded: chain o residue 2 SER Chi-restraints excluded: chain q residue 15 SER Chi-restraints excluded: chain q residue 20 VAL Chi-restraints excluded: chain q residue 29 THR Chi-restraints excluded: chain q residue 64 VAL Chi-restraints excluded: chain s residue 18 GLU Chi-restraints excluded: chain t residue 49 VAL Chi-restraints excluded: chain t residue 59 VAL Chi-restraints excluded: chain u residue 12 GLN Chi-restraints excluded: chain u residue 41 GLU Chi-restraints excluded: chain u residue 62 THR Chi-restraints excluded: chain u residue 65 VAL Chi-restraints excluded: chain y residue 19 LYS Chi-restraints excluded: chain z residue 23 THR Chi-restraints excluded: chain z residue 26 THR Chi-restraints excluded: chain z residue 27 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 981 random chunks: chunk 915 optimal weight: 4.9990 chunk 106 optimal weight: 20.0000 chunk 540 optimal weight: 10.0000 chunk 693 optimal weight: 20.0000 chunk 537 optimal weight: 10.0000 chunk 798 optimal weight: 9.9990 chunk 530 optimal weight: 20.0000 chunk 945 optimal weight: 0.3980 chunk 591 optimal weight: 9.9990 chunk 576 optimal weight: 10.0000 chunk 436 optimal weight: 20.0000 overall best weight: 7.0790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 81 ASN L 20 ASN O 40 GLN Q 51 ASN d 42 ASN e 195 GLN g 64 GLN n 104 GLN u 49 ASN w 20 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 152316 Z= 0.334 Angle : 0.853 21.173 227847 Z= 0.440 Chirality : 0.045 0.385 29017 Planarity : 0.008 0.152 12181 Dihedral : 23.269 174.613 76214 Min Nonbonded Distance : 1.774 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.23 % Favored : 96.64 % Rotamer: Outliers : 3.43 % Allowed : 16.15 % Favored : 80.42 % 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: 0.28 (0.11), residues: 5472 helix: 1.15 (0.12), residues: 1862 sheet: -0.16 (0.15), residues: 1082 loop : -0.28 (0.12), residues: 2528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP c 248 HIS 0.014 0.002 HIS k 35 PHE 0.035 0.003 PHE B 91 TYR 0.035 0.003 TYR N 20 ARG 0.013 0.001 ARG z 40 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10944 Ramachandran restraints generated. 5472 Oldfield, 0 Emsley, 5472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10944 Ramachandran restraints generated. 5472 Oldfield, 0 Emsley, 5472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 993 residues out of total 4572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 836 time to evaluate : 6.911 Fit side-chains revert: symmetry clash REVERT: 0 28 ARG cc_start: 0.6778 (OUTLIER) cc_final: 0.6335 (mmt180) REVERT: 1 46 LYS cc_start: 0.6956 (OUTLIER) cc_final: 0.6736 (mtpp) REVERT: B 16 PHE cc_start: 0.5482 (m-80) cc_final: 0.5221 (m-10) REVERT: B 44 GLU cc_start: 0.6029 (mt-10) cc_final: 0.5757 (tm-30) REVERT: B 88 ASP cc_start: 0.4956 (m-30) cc_final: 0.4568 (t0) REVERT: B 100 MET cc_start: 0.7816 (mtt) cc_final: 0.7474 (mtp) REVERT: B 139 ARG cc_start: 0.5519 (OUTLIER) cc_final: 0.4804 (mtt180) REVERT: B 145 GLU cc_start: 0.6732 (OUTLIER) cc_final: 0.6483 (tm-30) REVERT: B 161 LEU cc_start: 0.7792 (OUTLIER) cc_final: 0.7521 (mp) REVERT: B 207 ILE cc_start: 0.5913 (OUTLIER) cc_final: 0.5668 (mt) REVERT: C 45 LYS cc_start: 0.7809 (tttp) cc_final: 0.7525 (tptt) REVERT: C 58 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.8013 (mt-10) REVERT: C 62 LYS cc_start: 0.6258 (OUTLIER) cc_final: 0.5903 (mptp) REVERT: C 100 GLN cc_start: 0.7519 (tt0) cc_final: 0.7240 (tt0) REVERT: C 144 LEU cc_start: 0.8161 (OUTLIER) cc_final: 0.7804 (mm) REVERT: D 161 LEU cc_start: 0.7901 (mp) cc_final: 0.7685 (mt) REVERT: D 183 LYS cc_start: 0.8133 (mtpt) cc_final: 0.7756 (mtpt) REVERT: D 187 GLU cc_start: 0.7319 (mm-30) cc_final: 0.7070 (mm-30) REVERT: D 188 ARG cc_start: 0.8119 (OUTLIER) cc_final: 0.7163 (mmm160) REVERT: E 163 GLU cc_start: 0.7123 (OUTLIER) cc_final: 0.6829 (mt-10) REVERT: F 14 GLN cc_start: 0.8060 (OUTLIER) cc_final: 0.7407 (mm-40) REVERT: F 17 GLN cc_start: 0.7514 (mp10) cc_final: 0.6898 (mp10) REVERT: G 143 ARG cc_start: 0.7537 (OUTLIER) cc_final: 0.7072 (ptp90) REVERT: G 154 TYR cc_start: 0.4366 (OUTLIER) cc_final: 0.3920 (m-10) REVERT: H 69 LYS cc_start: 0.7908 (mtpt) cc_final: 0.7615 (mtmm) REVERT: H 90 ASP cc_start: 0.7741 (OUTLIER) cc_final: 0.7500 (m-30) REVERT: H 117 ARG cc_start: 0.8831 (OUTLIER) cc_final: 0.8503 (mtt90) REVERT: I 46 MET cc_start: 0.6851 (tmm) cc_final: 0.6094 (tmt) REVERT: I 85 ARG cc_start: 0.8458 (OUTLIER) cc_final: 0.8195 (mtt-85) REVERT: I 97 GLU cc_start: 0.6944 (OUTLIER) cc_final: 0.6672 (tp30) REVERT: K 15 GLN cc_start: 0.6887 (mm-40) cc_final: 0.6227 (mm110) REVERT: L 54 ARG cc_start: 0.8325 (OUTLIER) cc_final: 0.7655 (ttm-80) REVERT: L 76 GLU cc_start: 0.7139 (OUTLIER) cc_final: 0.6884 (tt0) REVERT: L 123 LYS cc_start: 0.5691 (OUTLIER) cc_final: 0.4666 (tptt) REVERT: M 53 ILE cc_start: 0.8111 (OUTLIER) cc_final: 0.7846 (mm) REVERT: M 75 MET cc_start: 0.7494 (OUTLIER) cc_final: 0.6837 (tpp) REVERT: O 62 GLN cc_start: 0.8550 (mm110) cc_final: 0.8262 (tt0) REVERT: P 76 LYS cc_start: 0.8078 (mtpp) cc_final: 0.7703 (mtmm) REVERT: Q 50 ASN cc_start: 0.6978 (m-40) cc_final: 0.6718 (m110) REVERT: R 48 ARG cc_start: 0.7609 (mtp85) cc_final: 0.7145 (mtt90) REVERT: S 20 GLU cc_start: 0.6016 (OUTLIER) cc_final: 0.5683 (tt0) REVERT: S 48 THR cc_start: 0.7452 (m) cc_final: 0.6697 (p) REVERT: S 56 GLN cc_start: 0.7898 (OUTLIER) cc_final: 0.7364 (pt0) REVERT: T 53 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7399 (tt0) REVERT: T 85 LYS cc_start: 0.7368 (OUTLIER) cc_final: 0.7035 (ptpp) REVERT: U 17 ARG cc_start: 0.6371 (tpp80) cc_final: 0.6077 (mtt-85) REVERT: U 21 ARG cc_start: 0.5993 (OUTLIER) cc_final: 0.5693 (mpt-90) REVERT: U 29 LEU cc_start: 0.7513 (OUTLIER) cc_final: 0.6998 (mp) REVERT: U 58 LYS cc_start: 0.4583 (OUTLIER) cc_final: 0.4043 (tttm) REVERT: c 167 ARG cc_start: 0.7782 (ttp-170) cc_final: 0.7563 (ttp80) REVERT: d 7 LYS cc_start: 0.8804 (OUTLIER) cc_final: 0.8458 (ttpm) REVERT: f 80 ARG cc_start: 0.5911 (OUTLIER) cc_final: 0.4956 (mmt180) REVERT: f 133 ARG cc_start: 0.6297 (OUTLIER) cc_final: 0.6034 (ttm-80) REVERT: k 81 ASP cc_start: 0.8036 (m-30) cc_final: 0.7692 (m-30) REVERT: l 6 ARG cc_start: 0.8083 (ptm-80) cc_final: 0.7836 (ptm-80) REVERT: s 48 GLN cc_start: 0.8611 (mt0) cc_final: 0.8380 (mt0) REVERT: t 61 LYS cc_start: 0.7852 (OUTLIER) cc_final: 0.7412 (pttt) REVERT: y 19 LYS cc_start: 0.8423 (OUTLIER) cc_final: 0.8161 (tttt) outliers start: 157 outliers final: 92 residues processed: 937 average time/residue: 2.6298 time to fit residues: 3402.8430 Evaluate side-chains 958 residues out of total 4572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 831 time to evaluate : 6.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 5 ILE Chi-restraints excluded: chain 0 residue 10 LYS Chi-restraints excluded: chain 0 residue 28 ARG Chi-restraints excluded: chain 1 residue 46 LYS Chi-restraints excluded: chain 2 residue 52 LYS Chi-restraints excluded: chain 3 residue 8 LYS Chi-restraints excluded: chain 3 residue 12 ARG Chi-restraints excluded: chain 4 residue 27 THR Chi-restraints excluded: chain 4 residue 28 VAL Chi-restraints excluded: chain 4 residue 32 LEU Chi-restraints excluded: chain 4 residue 56 ARG Chi-restraints excluded: chain 4 residue 57 VAL Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain C residue 62 LYS Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 206 GLU Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 163 GLU Chi-restraints excluded: chain D residue 166 GLU Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 188 ARG Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain F residue 14 GLN Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain G residue 143 ARG Chi-restraints excluded: chain G residue 154 TYR Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 117 ARG Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain I residue 85 ARG Chi-restraints excluded: chain I residue 94 LEU Chi-restraints excluded: chain I residue 97 GLU Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 81 GLU Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 110 ILE Chi-restraints excluded: chain L residue 35 THR Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 54 ARG Chi-restraints excluded: chain L residue 76 GLU Chi-restraints excluded: chain L residue 94 ARG Chi-restraints excluded: chain L residue 123 LYS Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 53 ILE Chi-restraints excluded: chain M residue 75 MET Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain O residue 13 SER Chi-restraints excluded: chain O residue 14 GLU Chi-restraints excluded: chain Q residue 6 ARG Chi-restraints excluded: chain Q residue 55 ILE Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain S residue 20 GLU Chi-restraints excluded: chain S residue 56 GLN Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain T residue 53 GLU Chi-restraints excluded: chain T residue 85 LYS Chi-restraints excluded: chain U residue 14 VAL Chi-restraints excluded: chain U residue 21 ARG Chi-restraints excluded: chain U residue 29 LEU Chi-restraints excluded: chain U residue 36 GLU Chi-restraints excluded: chain U residue 58 LYS Chi-restraints excluded: chain c residue 182 ARG Chi-restraints excluded: chain d residue 7 LYS Chi-restraints excluded: chain d residue 17 GLU Chi-restraints excluded: chain d residue 39 ASP Chi-restraints excluded: chain d residue 73 VAL Chi-restraints excluded: chain d residue 95 SER Chi-restraints excluded: chain d residue 207 VAL Chi-restraints excluded: chain e residue 107 SER Chi-restraints excluded: chain f residue 17 MET Chi-restraints excluded: chain f residue 32 GLU Chi-restraints excluded: chain f residue 35 THR Chi-restraints excluded: chain f residue 80 ARG Chi-restraints excluded: chain f residue 108 VAL Chi-restraints excluded: chain f residue 118 SER Chi-restraints excluded: chain f residue 133 ARG Chi-restraints excluded: chain f residue 152 LEU Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 41 VAL Chi-restraints excluded: chain g residue 106 SER Chi-restraints excluded: chain g residue 127 THR Chi-restraints excluded: chain g residue 158 LYS Chi-restraints excluded: chain h residue 14 SER Chi-restraints excluded: chain i residue 1 MET Chi-restraints excluded: chain i residue 101 ILE Chi-restraints excluded: chain k residue 1 MET Chi-restraints excluded: chain k residue 54 GLN Chi-restraints excluded: chain l residue 1 MET Chi-restraints excluded: chain l residue 8 LYS Chi-restraints excluded: chain l residue 30 SER Chi-restraints excluded: chain l residue 115 GLU Chi-restraints excluded: chain m residue 70 THR Chi-restraints excluded: chain n residue 40 ILE Chi-restraints excluded: chain n residue 49 VAL Chi-restraints excluded: chain o residue 2 SER Chi-restraints excluded: chain q residue 15 SER Chi-restraints excluded: chain q residue 20 VAL Chi-restraints excluded: chain q residue 29 THR Chi-restraints excluded: chain q residue 64 VAL Chi-restraints excluded: chain r residue 66 ILE Chi-restraints excluded: chain t residue 49 VAL Chi-restraints excluded: chain t residue 59 VAL Chi-restraints excluded: chain t residue 61 LYS Chi-restraints excluded: chain t residue 93 VAL Chi-restraints excluded: chain u residue 12 GLN Chi-restraints excluded: chain u residue 41 GLU Chi-restraints excluded: chain u residue 58 SER Chi-restraints excluded: chain u residue 62 THR Chi-restraints excluded: chain u residue 65 VAL Chi-restraints excluded: chain y residue 19 LYS Chi-restraints excluded: chain z residue 23 THR Chi-restraints excluded: chain z residue 26 THR Chi-restraints excluded: chain z residue 27 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 981 random chunks: chunk 584 optimal weight: 10.0000 chunk 377 optimal weight: 10.0000 chunk 564 optimal weight: 10.0000 chunk 284 optimal weight: 9.9990 chunk 185 optimal weight: 1.9990 chunk 183 optimal weight: 5.9990 chunk 601 optimal weight: 8.9990 chunk 644 optimal weight: 10.0000 chunk 467 optimal weight: 20.0000 chunk 88 optimal weight: 10.0000 chunk 743 optimal weight: 4.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 81 ASN L 20 ASN O 40 GLN Q 51 ASN d 42 ASN e 195 GLN g 64 GLN n 104 GLN u 49 ASN w 20 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 152316 Z= 0.308 Angle : 0.814 21.028 227847 Z= 0.425 Chirality : 0.043 0.384 29017 Planarity : 0.008 0.150 12181 Dihedral : 23.269 174.684 76214 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.25 % Favored : 96.62 % Rotamer: Outliers : 3.26 % Allowed : 16.36 % Favored : 80.38 % 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: 0.31 (0.11), residues: 5472 helix: 1.19 (0.12), residues: 1862 sheet: -0.15 (0.15), residues: 1087 loop : -0.27 (0.12), residues: 2523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP c 248 HIS 0.013 0.002 HIS k 35 PHE 0.027 0.003 PHE F 8 TYR 0.038 0.003 TYR N 20 ARG 0.014 0.001 ARG z 40 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10944 Ramachandran restraints generated. 5472 Oldfield, 0 Emsley, 5472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10944 Ramachandran restraints generated. 5472 Oldfield, 0 Emsley, 5472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 984 residues out of total 4572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 835 time to evaluate : 6.075 Fit side-chains revert: symmetry clash REVERT: 0 28 ARG cc_start: 0.6774 (OUTLIER) cc_final: 0.6336 (mmt180) REVERT: 1 46 LYS cc_start: 0.6943 (OUTLIER) cc_final: 0.6721 (mtpp) REVERT: B 16 PHE cc_start: 0.5476 (m-80) cc_final: 0.5217 (m-10) REVERT: B 44 GLU cc_start: 0.6078 (mt-10) cc_final: 0.5821 (tm-30) REVERT: B 59 LYS cc_start: 0.6230 (ttmt) cc_final: 0.5818 (tttm) REVERT: B 88 ASP cc_start: 0.4950 (m-30) cc_final: 0.4570 (t0) REVERT: B 100 MET cc_start: 0.7817 (mtt) cc_final: 0.7472 (mtp) REVERT: B 139 ARG cc_start: 0.5492 (OUTLIER) cc_final: 0.4773 (mtt180) REVERT: B 145 GLU cc_start: 0.6723 (OUTLIER) cc_final: 0.6472 (tm-30) REVERT: B 161 LEU cc_start: 0.7790 (OUTLIER) cc_final: 0.7520 (mp) REVERT: B 207 ILE cc_start: 0.5900 (OUTLIER) cc_final: 0.5664 (mt) REVERT: C 45 LYS cc_start: 0.7788 (tttp) cc_final: 0.7502 (tptt) REVERT: C 58 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.8016 (mt-10) REVERT: C 62 LYS cc_start: 0.6249 (OUTLIER) cc_final: 0.5894 (mptp) REVERT: C 100 GLN cc_start: 0.7512 (tt0) cc_final: 0.7234 (tt0) REVERT: C 144 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7792 (mm) REVERT: D 161 LEU cc_start: 0.7889 (mp) cc_final: 0.7678 (mt) REVERT: D 183 LYS cc_start: 0.8131 (mtpt) cc_final: 0.7755 (mtpt) REVERT: D 187 GLU cc_start: 0.7314 (mm-30) cc_final: 0.7060 (mm-30) REVERT: D 188 ARG cc_start: 0.8110 (OUTLIER) cc_final: 0.7071 (mmm160) REVERT: E 147 MET cc_start: 0.8309 (ttp) cc_final: 0.7954 (ttp) REVERT: E 163 GLU cc_start: 0.7124 (OUTLIER) cc_final: 0.6847 (mt-10) REVERT: F 14 GLN cc_start: 0.8055 (OUTLIER) cc_final: 0.7410 (mm-40) REVERT: F 17 GLN cc_start: 0.7467 (mp10) cc_final: 0.6870 (mp10) REVERT: F 36 ILE cc_start: 0.8549 (mm) cc_final: 0.8208 (mm) REVERT: G 143 ARG cc_start: 0.7534 (OUTLIER) cc_final: 0.7069 (ptp90) REVERT: G 154 TYR cc_start: 0.4353 (OUTLIER) cc_final: 0.3908 (m-10) REVERT: H 69 LYS cc_start: 0.7924 (mtpt) cc_final: 0.7634 (mtmm) REVERT: H 90 ASP cc_start: 0.7739 (OUTLIER) cc_final: 0.7498 (m-30) REVERT: H 117 ARG cc_start: 0.8833 (OUTLIER) cc_final: 0.8505 (mtt90) REVERT: I 46 MET cc_start: 0.6852 (tmm) cc_final: 0.6097 (tmt) REVERT: I 85 ARG cc_start: 0.8456 (OUTLIER) cc_final: 0.8195 (mtt-85) REVERT: I 97 GLU cc_start: 0.6938 (OUTLIER) cc_final: 0.6668 (tp30) REVERT: K 15 GLN cc_start: 0.6883 (mm-40) cc_final: 0.6219 (mm110) REVERT: L 54 ARG cc_start: 0.8304 (OUTLIER) cc_final: 0.7630 (ttm-80) REVERT: L 76 GLU cc_start: 0.7112 (OUTLIER) cc_final: 0.6864 (tt0) REVERT: L 123 LYS cc_start: 0.5771 (OUTLIER) cc_final: 0.4762 (tptt) REVERT: M 53 ILE cc_start: 0.8135 (OUTLIER) cc_final: 0.7898 (mm) REVERT: M 75 MET cc_start: 0.7493 (OUTLIER) cc_final: 0.6834 (tpp) REVERT: O 62 GLN cc_start: 0.8550 (OUTLIER) cc_final: 0.8264 (tt0) REVERT: P 53 ASP cc_start: 0.8443 (t0) cc_final: 0.8200 (t0) REVERT: P 76 LYS cc_start: 0.8051 (mtpp) cc_final: 0.7677 (mtmm) REVERT: Q 50 ASN cc_start: 0.7006 (m-40) cc_final: 0.6746 (m110) REVERT: R 48 ARG cc_start: 0.7603 (mtp85) cc_final: 0.7140 (mtt90) REVERT: S 20 GLU cc_start: 0.6059 (OUTLIER) cc_final: 0.5710 (tt0) REVERT: S 48 THR cc_start: 0.7447 (m) cc_final: 0.6697 (p) REVERT: S 56 GLN cc_start: 0.7889 (OUTLIER) cc_final: 0.7353 (pt0) REVERT: T 53 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7390 (tt0) REVERT: T 85 LYS cc_start: 0.7369 (OUTLIER) cc_final: 0.7042 (ptpp) REVERT: U 17 ARG cc_start: 0.6370 (tpp80) cc_final: 0.6077 (mtt-85) REVERT: U 21 ARG cc_start: 0.5995 (OUTLIER) cc_final: 0.5689 (mpt-90) REVERT: U 58 LYS cc_start: 0.4572 (OUTLIER) cc_final: 0.4046 (tttm) REVERT: c 167 ARG cc_start: 0.7778 (ttp-170) cc_final: 0.7563 (ttp80) REVERT: d 7 LYS cc_start: 0.8811 (OUTLIER) cc_final: 0.8464 (ttpm) REVERT: f 80 ARG cc_start: 0.5887 (OUTLIER) cc_final: 0.4944 (mmt180) REVERT: f 133 ARG cc_start: 0.6290 (OUTLIER) cc_final: 0.6035 (ttm-80) REVERT: k 81 ASP cc_start: 0.8030 (m-30) cc_final: 0.7735 (m-30) REVERT: l 6 ARG cc_start: 0.8085 (ptm-80) cc_final: 0.7837 (ptm-80) REVERT: q 1 MET cc_start: 0.7569 (OUTLIER) cc_final: 0.6619 (tpp) REVERT: s 18 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7481 (mp0) REVERT: s 48 GLN cc_start: 0.8608 (mt0) cc_final: 0.8377 (mt0) REVERT: t 61 LYS cc_start: 0.7848 (OUTLIER) cc_final: 0.7409 (pttt) REVERT: y 19 LYS cc_start: 0.8419 (OUTLIER) cc_final: 0.8172 (tttt) outliers start: 149 outliers final: 92 residues processed: 932 average time/residue: 2.5596 time to fit residues: 3296.7925 Evaluate side-chains 955 residues out of total 4572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 826 time to evaluate : 6.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 10 LYS Chi-restraints excluded: chain 0 residue 28 ARG Chi-restraints excluded: chain 1 residue 46 LYS Chi-restraints excluded: chain 2 residue 52 LYS Chi-restraints excluded: chain 3 residue 8 LYS Chi-restraints excluded: chain 3 residue 12 ARG Chi-restraints excluded: chain 4 residue 27 THR Chi-restraints excluded: chain 4 residue 28 VAL Chi-restraints excluded: chain 4 residue 32 LEU Chi-restraints excluded: chain 4 residue 56 ARG Chi-restraints excluded: chain 4 residue 57 VAL Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain C residue 62 LYS Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 206 GLU Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 163 GLU Chi-restraints excluded: chain D residue 166 GLU Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 188 ARG Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain F residue 14 GLN Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain G residue 143 ARG Chi-restraints excluded: chain G residue 154 TYR Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 117 ARG Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain I residue 85 ARG Chi-restraints excluded: chain I residue 94 LEU Chi-restraints excluded: chain I residue 97 GLU Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 81 GLU Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 110 ILE Chi-restraints excluded: chain L residue 35 THR Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 54 ARG Chi-restraints excluded: chain L residue 76 GLU Chi-restraints excluded: chain L residue 94 ARG Chi-restraints excluded: chain L residue 108 LYS Chi-restraints excluded: chain L residue 123 LYS Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 53 ILE Chi-restraints excluded: chain M residue 75 MET Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain O residue 13 SER Chi-restraints excluded: chain O residue 14 GLU Chi-restraints excluded: chain O residue 62 GLN Chi-restraints excluded: chain Q residue 6 ARG Chi-restraints excluded: chain Q residue 55 ILE Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain S residue 20 GLU Chi-restraints excluded: chain S residue 56 GLN Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain T residue 53 GLU Chi-restraints excluded: chain T residue 85 LYS Chi-restraints excluded: chain U residue 14 VAL Chi-restraints excluded: chain U residue 21 ARG Chi-restraints excluded: chain U residue 36 GLU Chi-restraints excluded: chain U residue 58 LYS Chi-restraints excluded: chain c residue 182 ARG Chi-restraints excluded: chain d residue 7 LYS Chi-restraints excluded: chain d residue 17 GLU Chi-restraints excluded: chain d residue 39 ASP Chi-restraints excluded: chain d residue 73 VAL Chi-restraints excluded: chain d residue 95 SER Chi-restraints excluded: chain e residue 107 SER Chi-restraints excluded: chain f residue 17 MET Chi-restraints excluded: chain f residue 32 GLU Chi-restraints excluded: chain f residue 35 THR Chi-restraints excluded: chain f residue 80 ARG Chi-restraints excluded: chain f residue 108 VAL Chi-restraints excluded: chain f residue 118 SER Chi-restraints excluded: chain f residue 133 ARG Chi-restraints excluded: chain f residue 152 LEU Chi-restraints excluded: chain g residue 41 VAL Chi-restraints excluded: chain g residue 84 THR Chi-restraints excluded: chain g residue 106 SER Chi-restraints excluded: chain g residue 127 THR Chi-restraints excluded: chain h residue 14 SER Chi-restraints excluded: chain i residue 1 MET Chi-restraints excluded: chain i residue 101 ILE Chi-restraints excluded: chain k residue 1 MET Chi-restraints excluded: chain k residue 54 GLN Chi-restraints excluded: chain k residue 77 ILE Chi-restraints excluded: chain l residue 1 MET Chi-restraints excluded: chain l residue 8 LYS Chi-restraints excluded: chain l residue 30 SER Chi-restraints excluded: chain l residue 115 GLU Chi-restraints excluded: chain m residue 70 THR Chi-restraints excluded: chain n residue 40 ILE Chi-restraints excluded: chain n residue 49 VAL Chi-restraints excluded: chain o residue 2 SER Chi-restraints excluded: chain q residue 1 MET Chi-restraints excluded: chain q residue 15 SER Chi-restraints excluded: chain q residue 29 THR Chi-restraints excluded: chain q residue 64 VAL Chi-restraints excluded: chain r residue 66 ILE Chi-restraints excluded: chain s residue 18 GLU Chi-restraints excluded: chain s residue 93 LEU Chi-restraints excluded: chain t residue 49 VAL Chi-restraints excluded: chain t residue 59 VAL Chi-restraints excluded: chain t residue 61 LYS Chi-restraints excluded: chain t residue 93 VAL Chi-restraints excluded: chain u residue 12 GLN Chi-restraints excluded: chain u residue 41 GLU Chi-restraints excluded: chain u residue 58 SER Chi-restraints excluded: chain u residue 62 THR Chi-restraints excluded: chain u residue 65 VAL Chi-restraints excluded: chain y residue 19 LYS Chi-restraints excluded: chain z residue 23 THR Chi-restraints excluded: chain z residue 26 THR Chi-restraints excluded: chain z residue 27 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 981 random chunks: chunk 860 optimal weight: 4.9990 chunk 905 optimal weight: 20.0000 chunk 826 optimal weight: 0.5980 chunk 881 optimal weight: 0.2980 chunk 530 optimal weight: 20.0000 chunk 383 optimal weight: 10.0000 chunk 691 optimal weight: 30.0000 chunk 270 optimal weight: 10.0000 chunk 796 optimal weight: 0.0870 chunk 833 optimal weight: 8.9990 chunk 878 optimal weight: 10.0000 overall best weight: 2.9962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 ASN G 68 ASN K 81 ASN L 20 ASN O 40 GLN Q 51 ASN d 42 ASN e 165 HIS e 195 GLN g 64 GLN n 104 GLN u 49 ASN w 20 HIS x 31 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 152316 Z= 0.179 Angle : 0.659 15.240 227847 Z= 0.358 Chirality : 0.037 0.397 29017 Planarity : 0.006 0.138 12181 Dihedral : 23.160 175.669 76214 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.92 % Favored : 96.97 % Rotamer: Outliers : 2.34 % Allowed : 17.44 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.11), residues: 5472 helix: 1.62 (0.12), residues: 1868 sheet: 0.00 (0.15), residues: 1072 loop : -0.14 (0.12), residues: 2532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 201 HIS 0.008 0.001 HIS k 35 PHE 0.023 0.002 PHE F 8 TYR 0.033 0.002 TYR N 20 ARG 0.007 0.000 ARG U 47 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10944 Ramachandran restraints generated. 5472 Oldfield, 0 Emsley, 5472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10944 Ramachandran restraints generated. 5472 Oldfield, 0 Emsley, 5472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 970 residues out of total 4572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 863 time to evaluate : 6.275 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 46 LYS cc_start: 0.6790 (OUTLIER) cc_final: 0.6497 (mptt) REVERT: B 16 PHE cc_start: 0.5490 (m-80) cc_final: 0.5235 (m-10) REVERT: B 44 GLU cc_start: 0.5970 (mt-10) cc_final: 0.5709 (tm-30) REVERT: B 59 LYS cc_start: 0.6221 (ttmt) cc_final: 0.5742 (tttm) REVERT: B 88 ASP cc_start: 0.4957 (m-30) cc_final: 0.4559 (t0) REVERT: B 100 MET cc_start: 0.7803 (mtt) cc_final: 0.7460 (mtp) REVERT: B 139 ARG cc_start: 0.5456 (OUTLIER) cc_final: 0.5029 (mtp-110) REVERT: B 145 GLU cc_start: 0.6622 (OUTLIER) cc_final: 0.6409 (tm-30) REVERT: B 161 LEU cc_start: 0.7768 (OUTLIER) cc_final: 0.7558 (mp) REVERT: C 45 LYS cc_start: 0.7814 (tttp) cc_final: 0.7550 (tptt) REVERT: C 62 LYS cc_start: 0.6203 (OUTLIER) cc_final: 0.5849 (mptp) REVERT: C 144 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7728 (mm) REVERT: D 161 LEU cc_start: 0.7887 (mp) cc_final: 0.7650 (mt) REVERT: D 183 LYS cc_start: 0.8140 (mtpt) cc_final: 0.7781 (mtpt) REVERT: D 187 GLU cc_start: 0.7296 (mm-30) cc_final: 0.7080 (mm-30) REVERT: E 147 MET cc_start: 0.8448 (ttp) cc_final: 0.7968 (ttp) REVERT: E 163 GLU cc_start: 0.7216 (OUTLIER) cc_final: 0.6901 (mt-10) REVERT: F 14 GLN cc_start: 0.8002 (mm-40) cc_final: 0.7415 (mm-40) REVERT: F 17 GLN cc_start: 0.7482 (mp10) cc_final: 0.6867 (mp10) REVERT: G 77 SER cc_start: 0.7192 (m) cc_final: 0.6766 (p) REVERT: G 143 ARG cc_start: 0.7496 (OUTLIER) cc_final: 0.7151 (ptp90) REVERT: H 69 LYS cc_start: 0.7890 (mtpt) cc_final: 0.7596 (mtmm) REVERT: H 90 ASP cc_start: 0.7655 (OUTLIER) cc_final: 0.7451 (m-30) REVERT: I 46 MET cc_start: 0.6810 (tmm) cc_final: 0.6091 (tmt) REVERT: I 97 GLU cc_start: 0.6909 (OUTLIER) cc_final: 0.6643 (tp30) REVERT: J 14 ASP cc_start: 0.7840 (t0) cc_final: 0.7497 (t0) REVERT: K 15 GLN cc_start: 0.6914 (mm-40) cc_final: 0.6209 (mm110) REVERT: L 54 ARG cc_start: 0.8230 (OUTLIER) cc_final: 0.7503 (ttm-80) REVERT: L 76 GLU cc_start: 0.7040 (OUTLIER) cc_final: 0.6729 (tt0) REVERT: M 75 MET cc_start: 0.7457 (OUTLIER) cc_final: 0.6794 (tpp) REVERT: M 78 LYS cc_start: 0.7464 (ttpt) cc_final: 0.7195 (tmmt) REVERT: M 79 ARG cc_start: 0.7612 (ttt-90) cc_final: 0.7175 (ttt-90) REVERT: O 62 GLN cc_start: 0.8553 (OUTLIER) cc_final: 0.8263 (tt0) REVERT: P 76 LYS cc_start: 0.8034 (mtpp) cc_final: 0.7645 (mtmm) REVERT: R 48 ARG cc_start: 0.7547 (mtp85) cc_final: 0.7117 (mtt90) REVERT: S 48 THR cc_start: 0.7381 (m) cc_final: 0.6676 (p) REVERT: T 53 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7366 (tt0) REVERT: T 85 LYS cc_start: 0.7423 (OUTLIER) cc_final: 0.7006 (ptpp) REVERT: U 17 ARG cc_start: 0.6357 (tpp80) cc_final: 0.6100 (mtt-85) REVERT: U 29 LEU cc_start: 0.7416 (OUTLIER) cc_final: 0.6930 (mp) REVERT: U 31 GLU cc_start: 0.7221 (tp30) cc_final: 0.6628 (tt0) REVERT: c 146 MET cc_start: 0.9038 (mtp) cc_final: 0.8742 (mtp) REVERT: e 170 ARG cc_start: 0.7656 (mmt90) cc_final: 0.7373 (mmt90) REVERT: f 80 ARG cc_start: 0.5794 (OUTLIER) cc_final: 0.5001 (ttm170) REVERT: k 81 ASP cc_start: 0.7987 (m-30) cc_final: 0.7689 (m-30) REVERT: s 48 GLN cc_start: 0.8583 (mt0) cc_final: 0.8357 (mt0) REVERT: t 61 LYS cc_start: 0.7753 (OUTLIER) cc_final: 0.7311 (pttt) outliers start: 107 outliers final: 57 residues processed: 930 average time/residue: 2.6181 time to fit residues: 3377.6142 Evaluate side-chains 912 residues out of total 4572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 836 time to evaluate : 6.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 10 LYS Chi-restraints excluded: chain 1 residue 46 LYS Chi-restraints excluded: chain 4 residue 27 THR Chi-restraints excluded: chain 4 residue 28 VAL Chi-restraints excluded: chain 4 residue 32 LEU Chi-restraints excluded: chain 4 residue 56 ARG Chi-restraints excluded: chain 4 residue 57 VAL Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain C residue 62 LYS Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 163 GLU Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 143 ARG Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain I residue 94 LEU Chi-restraints excluded: chain I residue 97 GLU Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 81 GLU Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 110 ILE Chi-restraints excluded: chain L residue 35 THR Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 54 ARG Chi-restraints excluded: chain L residue 76 GLU Chi-restraints excluded: chain L residue 94 ARG Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 75 MET Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain O residue 13 SER Chi-restraints excluded: chain O residue 14 GLU Chi-restraints excluded: chain O residue 62 GLN Chi-restraints excluded: chain Q residue 6 ARG Chi-restraints excluded: chain Q residue 55 ILE Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain T residue 53 GLU Chi-restraints excluded: chain T residue 85 LYS Chi-restraints excluded: chain U residue 29 LEU Chi-restraints excluded: chain U residue 36 GLU Chi-restraints excluded: chain c residue 182 ARG Chi-restraints excluded: chain d residue 17 GLU Chi-restraints excluded: chain d residue 73 VAL Chi-restraints excluded: chain d residue 95 SER Chi-restraints excluded: chain f residue 17 MET Chi-restraints excluded: chain f residue 35 THR Chi-restraints excluded: chain f residue 80 ARG Chi-restraints excluded: chain f residue 118 SER Chi-restraints excluded: chain f residue 152 LEU Chi-restraints excluded: chain g residue 41 VAL Chi-restraints excluded: chain g residue 127 THR Chi-restraints excluded: chain g residue 134 LYS Chi-restraints excluded: chain g residue 158 LYS Chi-restraints excluded: chain h residue 14 SER Chi-restraints excluded: chain k residue 54 GLN Chi-restraints excluded: chain l residue 115 GLU Chi-restraints excluded: chain n residue 40 ILE Chi-restraints excluded: chain n residue 49 VAL Chi-restraints excluded: chain t residue 49 VAL Chi-restraints excluded: chain t residue 59 VAL Chi-restraints excluded: chain t residue 61 LYS Chi-restraints excluded: chain t residue 93 VAL Chi-restraints excluded: chain u residue 12 GLN Chi-restraints excluded: chain u residue 41 GLU Chi-restraints excluded: chain u residue 65 VAL Chi-restraints excluded: chain z residue 23 THR Chi-restraints excluded: chain z residue 26 THR Chi-restraints excluded: chain z residue 27 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 981 random chunks: chunk 578 optimal weight: 10.0000 chunk 931 optimal weight: 20.0000 chunk 568 optimal weight: 10.0000 chunk 442 optimal weight: 30.0000 chunk 647 optimal weight: 9.9990 chunk 977 optimal weight: 0.9980 chunk 899 optimal weight: 0.0570 chunk 778 optimal weight: 2.9990 chunk 80 optimal weight: 9.9990 chunk 601 optimal weight: 9.9990 chunk 477 optimal weight: 20.0000 overall best weight: 4.8104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 81 ASN O 40 GLN Q 51 ASN d 42 ASN e 115 GLN e 165 HIS e 195 GLN g 64 GLN n 104 GLN u 49 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 152316 Z= 0.246 Angle : 0.733 16.535 227847 Z= 0.390 Chirality : 0.040 0.388 29017 Planarity : 0.007 0.144 12181 Dihedral : 23.179 175.011 76204 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.18 % Favored : 96.71 % Rotamer: Outliers : 1.90 % Allowed : 17.98 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.11), residues: 5472 helix: 1.53 (0.12), residues: 1866 sheet: -0.07 (0.15), residues: 1077 loop : -0.15 (0.12), residues: 2529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 201 HIS 0.010 0.001 HIS k 35 PHE 0.025 0.002 PHE F 8 TYR 0.035 0.002 TYR N 20 ARG 0.009 0.001 ARG z 40 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10944 Ramachandran restraints generated. 5472 Oldfield, 0 Emsley, 5472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10944 Ramachandran restraints generated. 5472 Oldfield, 0 Emsley, 5472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 913 residues out of total 4572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 826 time to evaluate : 6.980 Fit side-chains revert: symmetry clash REVERT: 1 46 LYS cc_start: 0.6799 (OUTLIER) cc_final: 0.6538 (mtpp) REVERT: B 16 PHE cc_start: 0.5465 (m-80) cc_final: 0.5228 (m-10) REVERT: B 44 GLU cc_start: 0.5979 (mt-10) cc_final: 0.5740 (tm-30) REVERT: B 45 LYS cc_start: 0.6395 (mtpm) cc_final: 0.6184 (mtpm) REVERT: B 59 LYS cc_start: 0.6314 (ttmt) cc_final: 0.5820 (tttm) REVERT: B 88 ASP cc_start: 0.4966 (m-30) cc_final: 0.4562 (t0) REVERT: B 139 ARG cc_start: 0.5447 (OUTLIER) cc_final: 0.4719 (mtt180) REVERT: B 145 GLU cc_start: 0.6598 (OUTLIER) cc_final: 0.6380 (tm-30) REVERT: B 161 LEU cc_start: 0.7771 (OUTLIER) cc_final: 0.7550 (mp) REVERT: C 45 LYS cc_start: 0.7831 (tttp) cc_final: 0.7554 (tptt) REVERT: C 62 LYS cc_start: 0.6189 (OUTLIER) cc_final: 0.5831 (mptp) REVERT: C 144 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7767 (mm) REVERT: D 161 LEU cc_start: 0.7883 (mp) cc_final: 0.7647 (mt) REVERT: D 183 LYS cc_start: 0.8126 (mtpt) cc_final: 0.7763 (mtpt) REVERT: D 187 GLU cc_start: 0.7328 (mm-30) cc_final: 0.7067 (mm-30) REVERT: E 163 GLU cc_start: 0.7190 (OUTLIER) cc_final: 0.6903 (mt-10) REVERT: F 14 GLN cc_start: 0.8017 (mm-40) cc_final: 0.7423 (mm-40) REVERT: F 17 GLN cc_start: 0.7463 (mp10) cc_final: 0.6919 (mp10) REVERT: G 143 ARG cc_start: 0.7515 (OUTLIER) cc_final: 0.7157 (ptp90) REVERT: H 69 LYS cc_start: 0.7883 (mtpt) cc_final: 0.7585 (mtmm) REVERT: H 90 ASP cc_start: 0.7678 (OUTLIER) cc_final: 0.7454 (m-30) REVERT: I 46 MET cc_start: 0.6811 (tmm) cc_final: 0.6085 (tmt) REVERT: I 85 ARG cc_start: 0.8445 (OUTLIER) cc_final: 0.8175 (mtt-85) REVERT: I 97 GLU cc_start: 0.6931 (OUTLIER) cc_final: 0.6671 (tp30) REVERT: K 15 GLN cc_start: 0.6927 (mm-40) cc_final: 0.6211 (mm110) REVERT: L 54 ARG cc_start: 0.8270 (OUTLIER) cc_final: 0.7565 (ttm-80) REVERT: L 76 GLU cc_start: 0.7025 (OUTLIER) cc_final: 0.6789 (tt0) REVERT: M 75 MET cc_start: 0.7473 (OUTLIER) cc_final: 0.6815 (tpp) REVERT: M 78 LYS cc_start: 0.7472 (ttpt) cc_final: 0.7208 (tmmt) REVERT: M 79 ARG cc_start: 0.7603 (ttt-90) cc_final: 0.7192 (ttt-90) REVERT: O 62 GLN cc_start: 0.8566 (OUTLIER) cc_final: 0.8268 (tt0) REVERT: P 76 LYS cc_start: 0.8045 (mtpp) cc_final: 0.7659 (mtmm) REVERT: R 48 ARG cc_start: 0.7574 (mtp85) cc_final: 0.7141 (mtt90) REVERT: S 20 GLU cc_start: 0.6050 (OUTLIER) cc_final: 0.5704 (tt0) REVERT: S 48 THR cc_start: 0.7426 (m) cc_final: 0.6678 (p) REVERT: T 53 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7367 (tt0) REVERT: T 85 LYS cc_start: 0.7323 (OUTLIER) cc_final: 0.7004 (ptpp) REVERT: U 17 ARG cc_start: 0.6385 (tpp80) cc_final: 0.6120 (mtt-85) REVERT: U 29 LEU cc_start: 0.7482 (OUTLIER) cc_final: 0.6970 (mp) REVERT: U 31 GLU cc_start: 0.7290 (tp30) cc_final: 0.6669 (tt0) REVERT: f 80 ARG cc_start: 0.5794 (OUTLIER) cc_final: 0.5007 (ttm170) REVERT: h 1 MET cc_start: 0.6326 (ttm) cc_final: 0.6077 (ptp) REVERT: k 81 ASP cc_start: 0.8003 (m-30) cc_final: 0.7664 (m-30) REVERT: l 6 ARG cc_start: 0.8071 (ptm-80) cc_final: 0.7830 (ptm-80) REVERT: s 48 GLN cc_start: 0.8605 (mt0) cc_final: 0.8378 (mt0) REVERT: t 61 LYS cc_start: 0.7803 (OUTLIER) cc_final: 0.7353 (pttt) outliers start: 87 outliers final: 63 residues processed: 884 average time/residue: 2.6486 time to fit residues: 3232.6645 Evaluate side-chains 906 residues out of total 4572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 822 time to evaluate : 6.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 10 LYS Chi-restraints excluded: chain 1 residue 46 LYS Chi-restraints excluded: chain 4 residue 27 THR Chi-restraints excluded: chain 4 residue 28 VAL Chi-restraints excluded: chain 4 residue 32 LEU Chi-restraints excluded: chain 4 residue 56 ARG Chi-restraints excluded: chain 4 residue 57 VAL Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain C residue 62 LYS Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 163 GLU Chi-restraints excluded: chain D residue 166 GLU Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 143 ARG Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain I residue 85 ARG Chi-restraints excluded: chain I residue 94 LEU Chi-restraints excluded: chain I residue 97 GLU Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 81 GLU Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 110 ILE Chi-restraints excluded: chain L residue 35 THR Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 54 ARG Chi-restraints excluded: chain L residue 76 GLU Chi-restraints excluded: chain L residue 94 ARG Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 75 MET Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain O residue 13 SER Chi-restraints excluded: chain O residue 14 GLU Chi-restraints excluded: chain O residue 62 GLN Chi-restraints excluded: chain Q residue 6 ARG Chi-restraints excluded: chain Q residue 55 ILE Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain S residue 20 GLU Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain T residue 53 GLU Chi-restraints excluded: chain T residue 85 LYS Chi-restraints excluded: chain U residue 29 LEU Chi-restraints excluded: chain U residue 36 GLU Chi-restraints excluded: chain c residue 182 ARG Chi-restraints excluded: chain d residue 17 GLU Chi-restraints excluded: chain d residue 39 ASP Chi-restraints excluded: chain d residue 73 VAL Chi-restraints excluded: chain d residue 95 SER Chi-restraints excluded: chain f residue 17 MET Chi-restraints excluded: chain f residue 32 GLU Chi-restraints excluded: chain f residue 35 THR Chi-restraints excluded: chain f residue 80 ARG Chi-restraints excluded: chain f residue 118 SER Chi-restraints excluded: chain f residue 152 LEU Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 41 VAL Chi-restraints excluded: chain g residue 127 THR Chi-restraints excluded: chain g residue 134 LYS Chi-restraints excluded: chain g residue 158 LYS Chi-restraints excluded: chain h residue 14 SER Chi-restraints excluded: chain i residue 1 MET Chi-restraints excluded: chain k residue 54 GLN Chi-restraints excluded: chain l residue 115 GLU Chi-restraints excluded: chain n residue 40 ILE Chi-restraints excluded: chain n residue 49 VAL Chi-restraints excluded: chain t residue 49 VAL Chi-restraints excluded: chain t residue 59 VAL Chi-restraints excluded: chain t residue 61 LYS Chi-restraints excluded: chain t residue 93 VAL Chi-restraints excluded: chain u residue 12 GLN Chi-restraints excluded: chain u residue 41 GLU Chi-restraints excluded: chain u residue 65 VAL Chi-restraints excluded: chain z residue 23 THR Chi-restraints excluded: chain z residue 26 THR Chi-restraints excluded: chain z residue 27 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 981 random chunks: chunk 618 optimal weight: 20.0000 chunk 829 optimal weight: 0.5980 chunk 238 optimal weight: 4.9990 chunk 717 optimal weight: 10.0000 chunk 114 optimal weight: 10.0000 chunk 216 optimal weight: 5.9990 chunk 779 optimal weight: 5.9990 chunk 326 optimal weight: 7.9990 chunk 800 optimal weight: 6.9990 chunk 98 optimal weight: 10.0000 chunk 143 optimal weight: 10.0000 overall best weight: 4.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 61 ASN K 81 ASN O 40 GLN Q 51 ASN d 42 ASN e 165 HIS e 195 GLN g 64 GLN n 104 GLN u 49 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.152320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.117479 restraints weight = 123218.105| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 0.56 r_work: 0.3225 rms_B_bonded: 1.35 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 2.26 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 152316 Z= 0.250 Angle : 0.747 17.597 227847 Z= 0.395 Chirality : 0.041 0.391 29017 Planarity : 0.007 0.144 12181 Dihedral : 23.176 175.161 76204 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.16 % Favored : 96.73 % Rotamer: Outliers : 2.21 % Allowed : 17.76 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.11), residues: 5472 helix: 1.50 (0.12), residues: 1866 sheet: -0.08 (0.15), residues: 1077 loop : -0.15 (0.12), residues: 2529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 201 HIS 0.010 0.001 HIS k 35 PHE 0.025 0.002 PHE F 8 TYR 0.042 0.002 TYR N 20 ARG 0.009 0.001 ARG z 40 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 53861.96 seconds wall clock time: 933 minutes 43.09 seconds (56023.09 seconds total)