Starting phenix.real_space_refine on Mon Apr 15 10:33:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8whx_37551/04_2024/8whx_37551.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8whx_37551/04_2024/8whx_37551.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8whx_37551/04_2024/8whx_37551.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8whx_37551/04_2024/8whx_37551.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8whx_37551/04_2024/8whx_37551.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8whx_37551/04_2024/8whx_37551.pdb" } resolution = 2.8 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= 0.003 sd= 0.013 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: 5 Type Number sf(0) Gaussians P 4652 5.49 5 S 87 5.16 5 C 70971 2.51 5 N 26654 2.21 5 O 39999 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F GLU 19": "OE1" <-> "OE2" Residue "F GLU 43": "OE1" <-> "OE2" Residue "F GLU 56": "OE1" <-> "OE2" Residue "F GLU 83": "OE1" <-> "OE2" Residue "F TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 96": "OE1" <-> "OE2" Residue "F GLU 104": "OE1" <-> "OE2" Residue "G GLU 19": "OE1" <-> "OE2" Residue "G GLU 28": "OE1" <-> "OE2" Residue "G GLU 150": "OE1" <-> "OE2" Residue "G GLU 163": "OE1" <-> "OE2" Residue "G GLU 199": "OE1" <-> "OE2" Residue "H GLU 18": "OE1" <-> "OE2" Residue "H GLU 105": "OE1" <-> "OE2" Residue "M GLU 102": "OE1" <-> "OE2" Residue "N GLU 18": "OE1" <-> "OE2" Residue "N GLU 120": "OE1" <-> "OE2" Residue "O GLU 74": "OE1" <-> "OE2" Residue "O GLU 146": "OE1" <-> "OE2" Residue "Q GLU 38": "OE1" <-> "OE2" Residue "Q TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 49": "OE1" <-> "OE2" Residue "Q GLU 82": "OE1" <-> "OE2" Residue "Q GLU 101": "OE1" <-> "OE2" Residue "R GLU 12": "OE1" <-> "OE2" Residue "R GLU 90": "OE1" <-> "OE2" Residue "S GLU 33": "OE1" <-> "OE2" Residue "S GLU 63": "OE1" <-> "OE2" Residue "S GLU 70": "OE1" <-> "OE2" Residue "S GLU 101": "OE1" <-> "OE2" Residue "S GLU 111": "OE1" <-> "OE2" Residue "T GLU 56": "OE1" <-> "OE2" Residue "T GLU 89": "OE1" <-> "OE2" Residue "U GLU 25": "OE1" <-> "OE2" Residue "U GLU 30": "OE1" <-> "OE2" Residue "U GLU 63": "OE1" <-> "OE2" Residue "U GLU 66": "OE1" <-> "OE2" Residue "V GLU 38": "OE1" <-> "OE2" Residue "V GLU 52": "OE1" <-> "OE2" Residue "V GLU 69": "OE1" <-> "OE2" Residue "W GLU 18": "OE1" <-> "OE2" Residue "W GLU 25": "OE1" <-> "OE2" Residue "W GLU 47": "OE1" <-> "OE2" Residue "X GLU 36": "OE1" <-> "OE2" Residue "Z GLU 35": "OE1" <-> "OE2" Residue "2 GLU 9": "OE1" <-> "OE2" Residue "2 GLU 27": "OE1" <-> "OE2" Residue "2 GLU 28": "OE1" <-> "OE2" Residue "2 GLU 53": "OE1" <-> "OE2" Residue "2 GLU 65": "OE1" <-> "OE2" Residue "3 GLU 3": "OE1" <-> "OE2" Residue "3 GLU 55": "OE1" <-> "OE2" Residue "3 GLU 58": "OE1" <-> "OE2" Residue "8 GLU 34": "OE1" <-> "OE2" Residue "d GLU 91": "OE1" <-> "OE2" Residue "d GLU 104": "OE1" <-> "OE2" Residue "g GLU 16": "OE1" <-> "OE2" Residue "g GLU 24": "OE1" <-> "OE2" Residue "g ASP 33": "OD1" <-> "OD2" Residue "g GLU 51": "OE1" <-> "OE2" Residue "g GLU 57": "OE1" <-> "OE2" Residue "g GLU 68": "OE1" <-> "OE2" Residue "g GLU 83": "OE1" <-> "OE2" Residue "i GLU 38": "OE1" <-> "OE2" Residue "i GLU 43": "OE1" <-> "OE2" Residue "i GLU 71": "OE1" <-> "OE2" Residue "j GLU 34": "OE1" <-> "OE2" Residue "j GLU 56": "OE1" <-> "OE2" Residue "j GLU 113": "OE1" <-> "OE2" Residue "k GLU 16": "OE1" <-> "OE2" Residue "l GLU 77": "OE1" <-> "OE2" Residue "l GLU 85": "OE1" <-> "OE2" Residue "l GLU 103": "OE1" <-> "OE2" Residue "l GLU 115": "OE1" <-> "OE2" Residue "n GLU 32": "OE1" <-> "OE2" Residue "n GLU 61": "OE1" <-> "OE2" Residue "n GLU 67": "OE1" <-> "OE2" Residue "n GLU 73": "OE1" <-> "OE2" Residue "n GLU 83": "OE1" <-> "OE2" Residue "o GLU 92": "OE1" <-> "OE2" Residue "p GLU 26": "OE1" <-> "OE2" Residue "p GLU 83": "OE1" <-> "OE2" Residue "q GLU 45": "OE1" <-> "OE2" Residue "q GLU 54": "OE1" <-> "OE2" Residue "q GLU 90": "OE1" <-> "OE2" Residue "r GLU 14": "OE1" <-> "OE2" Residue "r GLU 39": "OE1" <-> "OE2" Residue "r GLU 92": "OE1" <-> "OE2" Residue "r GLU 95": "OE1" <-> "OE2" Residue "t GLU 64": "OE1" <-> "OE2" Residue "t GLU 73": "OE1" <-> "OE2" Residue "u GLU 49": "OE1" <-> "OE2" Residue "c GLU 82": "OE1" <-> "OE2" Residue "c GLU 133": "OE1" <-> "OE2" Residue "c GLU 140": "OE1" <-> "OE2" Residue "c GLU 145": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 142363 Number of models: 1 Model: "" Number of chains: 50 Chain: "E" Number of atoms: 2110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2110 Classifications: {'peptide': 275} Link IDs: {'PTRANS': 19, 'TRANS': 255} Chain: "F" Number of atoms: 1587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1587 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 8, 'TRANS': 205} Chain: "G" Number of atoms: 1569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1569 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "H" Number of atoms: 1436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1436 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 8, 'TRANS': 172} Chain: "I" Number of atoms: 1260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1260 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 11, 'TRANS': 153} Chain: "J" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 308 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 1, 'TRANS': 39} Chain: "M" Number of atoms: 1130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1130 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 10, 'TRANS': 135} Chain: "N" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "O" Number of atoms: 1078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1078 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 6, 'TRANS': 138} Chain: "Q" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 928 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 6, 'TRANS': 111} Chain: "R" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 941 Classifications: {'peptide': 124} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "S" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 907 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain: "T" Number of atoms: 988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 988 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "U" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 754 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 3, 'TRANS': 96} Chain: "V" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 864 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 8, 'TRANS': 104} Chain: "W" Number of atoms: 756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 756 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "X" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 703 Classifications: {'peptide': 92} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 88} Chain breaks: 1 Chain: "Z" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 574 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 4, 'TRANS': 72} Chain: "1" Number of atoms: 470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 470 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 4, 'TRANS': 58} Chain: "2" Number of atoms: 527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 527 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 1, 'TRANS': 61} Chain: "3" Number of atoms: 470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 470 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Chain: "5" Number of atoms: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 423 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 3, 'TRANS': 50} Chain: "6" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 405 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 4, 'TRANS': 44} Chain: "7" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 372 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "8" Number of atoms: 502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 502 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 1, 'TRANS': 61} Chain: "4" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 445 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 2, 'TRANS': 54} Chain breaks: 1 Chain: "A" Number of atoms: 64865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3020, 64865 Classifications: {'RNA': 3020} Modifications used: {'rna2p_pur': 293, 'rna2p_pyr': 148, 'rna3p_pur': 1437, 'rna3p_pyr': 1142} Link IDs: {'rna2p': 441, 'rna3p': 2578} Chain breaks: 3 Chain: "B" Number of atoms: 2502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 2502 Classifications: {'RNA': 117} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 7, 'rna3p_pur': 57, 'rna3p_pyr': 46} Link IDs: {'rna2p': 14, 'rna3p': 102} Chain: "a" Number of atoms: 32521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1515, 32521 Classifications: {'RNA': 1515} Modifications used: {'rna2p_pur': 111, 'rna2p_pyr': 85, 'rna3p_pur': 739, 'rna3p_pyr': 580} Link IDs: {'rna2p': 196, 'rna3p': 1318} Chain: "v" Number of atoms: 271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 271 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "d" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1656 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 5, 'TRANS': 201} Chain: "e" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1641 Classifications: {'peptide': 200} Link IDs: {'PTRANS': 11, 'TRANS': 188} Chain: "f" Number of atoms: 1223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1223 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 8, 'TRANS': 159} Chain: "g" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 771 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain: "h" Number of atoms: 1207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1207 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 8, 'TRANS': 144} Chain: "i" Number of atoms: 1010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1010 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "j" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 994 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 8, 'TRANS': 117} Chain: "k" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 784 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 7, 'TRANS': 90} Chain: "l" Number of atoms: 855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 855 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "m" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 958 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "n" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 935 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 3, 'TRANS': 112} Chain: "o" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 819 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 93} Chain: "p" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 720 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "q" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 891 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 8, 'TRANS': 104} Chain: "r" Number of atoms: 748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 748 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 5, 'TRANS': 88} Chain: "s" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 513 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 1, 'TRANS': 63} Chain: "t" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 662 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 4, 'TRANS': 77} Chain: "u" Number of atoms: 660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 660 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "c" Number of atoms: 1708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1708 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 7, 'TRANS': 209} Chain: "w" Number of atoms: 1004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1004 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 117} 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 Time building chain proxies: 52.90, per 1000 atoms: 0.37 Number of scatterers: 142363 At special positions: 0 Unit cell: (279.27, 258.94, 243.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 87 16.00 P 4652 15.00 O 39999 8.00 N 26654 7.00 C 70971 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 57.27 Conformation dependent library (CDL) restraints added in 5.4 seconds 10686 Ramachandran restraints generated. 5343 Oldfield, 0 Emsley, 5343 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9926 Finding SS restraints... Secondary structure from input PDB file: 178 helices and 66 sheets defined 37.6% alpha, 20.6% beta 1597 base pairs and 2406 stacking pairs defined. Time for finding SS restraints: 48.04 Creating SS restraints... Processing helix chain 'E' and resid 10 through 14 removed outlier: 3.661A pdb=" N ARG E 14 " --> pdb=" O PRO E 11 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 32 No H-bonds generated for 'chain 'E' and resid 30 through 32' Processing helix chain 'E' and resid 134 through 136 No H-bonds generated for 'chain 'E' and resid 134 through 136' Processing helix chain 'E' and resid 198 through 204 removed outlier: 4.339A pdb=" N SER E 202 " --> pdb=" O ALA E 199 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE E 204 " --> pdb=" O GLN E 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 215 removed outlier: 3.912A pdb=" N MET E 212 " --> pdb=" O LYS E 208 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 226 Processing helix chain 'E' and resid 262 through 266 removed outlier: 4.044A pdb=" N LYS E 266 " --> pdb=" O PRO E 263 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 46 Processing helix chain 'F' and resid 58 through 62 Processing helix chain 'F' and resid 63 through 74 Processing helix chain 'F' and resid 88 through 93 Processing helix chain 'F' and resid 102 through 106 Processing helix chain 'F' and resid 125 through 131 Processing helix chain 'G' and resid 21 through 26 Processing helix chain 'G' and resid 30 through 46 Processing helix chain 'G' and resid 103 through 121 removed outlier: 3.647A pdb=" N ASN G 121 " --> pdb=" O ASP G 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 149 Processing helix chain 'G' and resid 162 through 169 Processing helix chain 'G' and resid 179 through 183 removed outlier: 3.671A pdb=" N LEU G 183 " --> pdb=" O PRO G 180 " (cutoff:3.500A) Processing helix chain 'G' and resid 184 through 190 Processing helix chain 'G' and resid 198 through 210 removed outlier: 3.570A pdb=" N LYS G 210 " --> pdb=" O SER G 206 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 28 removed outlier: 3.759A pdb=" N ILE H 19 " --> pdb=" O TYR H 15 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N ARG H 20 " --> pdb=" O ARG H 16 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLU H 21 " --> pdb=" O GLU H 17 " (cutoff:3.500A) Processing helix chain 'H' and resid 31 through 35 removed outlier: 3.673A pdb=" N ILE H 35 " --> pdb=" O VAL H 32 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 53 Processing helix chain 'H' and resid 54 through 69 Processing helix chain 'H' and resid 99 through 113 removed outlier: 3.707A pdb=" N MET H 103 " --> pdb=" O ARG H 99 " (cutoff:3.500A) Processing helix chain 'H' and resid 169 through 181 Processing helix chain 'I' and resid 3 through 7 removed outlier: 3.636A pdb=" N GLN I 7 " --> pdb=" O ARG I 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 3 through 7' Processing helix chain 'I' and resid 59 through 82 removed outlier: 4.473A pdb=" N GLY I 67 " --> pdb=" O ARG I 63 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU I 68 " --> pdb=" O SER I 64 " (cutoff:3.500A) Processing helix chain 'I' and resid 138 through 151 Processing helix chain 'J' and resid 22 through 29 Processing helix chain 'M' and resid 24 through 38 Processing helix chain 'M' and resid 58 through 62 Processing helix chain 'M' and resid 67 through 72 Processing helix chain 'M' and resid 89 through 96 Processing helix chain 'M' and resid 96 through 107 removed outlier: 3.977A pdb=" N VAL M 100 " --> pdb=" O HIS M 96 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N VAL M 101 " --> pdb=" O PRO M 97 " (cutoff:3.500A) Processing helix chain 'M' and resid 112 through 120 removed outlier: 3.882A pdb=" N LYS M 120 " --> pdb=" O ARG M 116 " (cutoff:3.500A) Processing helix chain 'M' and resid 132 through 136 Processing helix chain 'N' and resid 104 through 109 removed outlier: 4.200A pdb=" N GLU N 108 " --> pdb=" O ARG N 104 " (cutoff:3.500A) Processing helix chain 'N' and resid 111 through 118 Processing helix chain 'O' and resid 80 through 87 Processing helix chain 'O' and resid 94 through 101 Processing helix chain 'O' and resid 130 through 140 Processing helix chain 'Q' and resid 13 through 32 Processing helix chain 'Q' and resid 38 through 57 Proline residue: Q 46 - end of helix removed outlier: 3.578A pdb=" N LYS Q 57 " --> pdb=" O THR Q 53 " (cutoff:3.500A) Processing helix chain 'Q' and resid 59 through 71 removed outlier: 4.043A pdb=" N LYS Q 69 " --> pdb=" O GLU Q 65 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ARG Q 71 " --> pdb=" O MET Q 67 " (cutoff:3.500A) Processing helix chain 'Q' and resid 72 through 82 Processing helix chain 'Q' and resid 82 through 87 Processing helix chain 'R' and resid 9 through 27 removed outlier: 3.702A pdb=" N LEU R 25 " --> pdb=" O ARG R 21 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS R 27 " --> pdb=" O ALA R 23 " (cutoff:3.500A) Processing helix chain 'R' and resid 67 through 72 Processing helix chain 'R' and resid 76 through 96 Processing helix chain 'R' and resid 111 through 123 Processing helix chain 'S' and resid 4 through 12 removed outlier: 4.130A pdb=" N ALA S 10 " --> pdb=" O PHE S 6 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N SER S 11 " --> pdb=" O VAL S 7 " (cutoff:3.500A) Processing helix chain 'S' and resid 52 through 55 removed outlier: 3.577A pdb=" N SER S 55 " --> pdb=" O GLY S 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 52 through 55' Processing helix chain 'S' and resid 96 through 102 removed outlier: 3.518A pdb=" N LEU S 102 " --> pdb=" O LEU S 99 " (cutoff:3.500A) Processing helix chain 'S' and resid 103 through 108 removed outlier: 3.501A pdb=" N LYS S 106 " --> pdb=" O ARG S 103 " (cutoff:3.500A) Processing helix chain 'T' and resid 6 through 21 removed outlier: 3.957A pdb=" N LYS T 13 " --> pdb=" O ASN T 9 " (cutoff:3.500A) Processing helix chain 'T' and resid 25 through 30 removed outlier: 3.703A pdb=" N ARG T 28 " --> pdb=" O ARG T 25 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER T 29 " --> pdb=" O GLY T 26 " (cutoff:3.500A) Processing helix chain 'T' and resid 31 through 71 removed outlier: 3.565A pdb=" N ARG T 51 " --> pdb=" O TYR T 47 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LYS T 54 " --> pdb=" O ARG T 50 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLY T 55 " --> pdb=" O ARG T 51 " (cutoff:3.500A) Processing helix chain 'T' and resid 75 through 87 Processing helix chain 'T' and resid 91 through 102 Processing helix chain 'T' and resid 102 through 117 Processing helix chain 'U' and resid 51 through 57 Processing helix chain 'V' and resid 20 through 29 removed outlier: 3.724A pdb=" N VAL V 27 " --> pdb=" O LYS V 23 " (cutoff:3.500A) Processing helix chain 'V' and resid 35 through 46 Processing helix chain 'V' and resid 50 through 68 Processing helix chain 'V' and resid 72 through 74 No H-bonds generated for 'chain 'V' and resid 72 through 74' Processing helix chain 'V' and resid 96 through 98 No H-bonds generated for 'chain 'V' and resid 96 through 98' Processing helix chain 'W' and resid 6 through 9 removed outlier: 4.069A pdb=" N ASP W 9 " --> pdb=" O ASP W 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 6 through 9' Processing helix chain 'W' and resid 17 through 26 removed outlier: 3.693A pdb=" N ASP W 26 " --> pdb=" O GLY W 22 " (cutoff:3.500A) Processing helix chain 'W' and resid 38 through 51 Processing helix chain 'W' and resid 93 through 97 Processing helix chain '1' and resid 53 through 58 Processing helix chain '2' and resid 6 through 11 Processing helix chain '2' and resid 14 through 39 Processing helix chain '2' and resid 44 through 67 removed outlier: 4.228A pdb=" N ARG 2 48 " --> pdb=" O ASN 2 44 " (cutoff:3.500A) Processing helix chain '3' and resid 16 through 27 Processing helix chain '3' and resid 40 through 50 Processing helix chain '5' and resid 9 through 18 Processing helix chain '5' and resid 43 through 49 Processing helix chain '7' and resid 11 through 20 Processing helix chain '7' and resid 20 through 27 removed outlier: 3.997A pdb=" N THR 7 27 " --> pdb=" O LEU 7 23 " (cutoff:3.500A) Processing helix chain '7' and resid 27 through 41 Processing helix chain '8' and resid 7 through 14 Processing helix chain '8' and resid 37 through 44 Processing helix chain '8' and resid 51 through 64 removed outlier: 4.540A pdb=" N SER 8 56 " --> pdb=" O ALA 8 52 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N ARG 8 57 " --> pdb=" O ALA 8 53 " (cutoff:3.500A) Processing helix chain '4' and resid 57 through 65 Processing helix chain 'v' and resid 3 through 24 removed outlier: 4.451A pdb=" N LYS v 7 " --> pdb=" O SER v 3 " (cutoff:3.500A) Processing helix chain 'v' and resid 24 through 32 Processing helix chain 'd' and resid 6 through 11 Processing helix chain 'd' and resid 27 through 46 Processing helix chain 'd' and resid 71 through 76 removed outlier: 3.787A pdb=" N VAL d 75 " --> pdb=" O ARG d 71 " (cutoff:3.500A) Processing helix chain 'd' and resid 80 through 92 Processing helix chain 'd' and resid 107 through 110 Processing helix chain 'd' and resid 111 through 126 removed outlier: 3.563A pdb=" N ASN d 125 " --> pdb=" O GLU d 121 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ARG d 126 " --> pdb=" O GLN d 122 " (cutoff:3.500A) Processing helix chain 'd' and resid 128 through 142 Processing helix chain 'd' and resid 156 through 160 Processing helix chain 'e' and resid 8 through 16 removed outlier: 3.611A pdb=" N SER e 12 " --> pdb=" O ALA e 8 " (cutoff:3.500A) Processing helix chain 'e' and resid 23 through 29 removed outlier: 3.946A pdb=" N GLU e 27 " --> pdb=" O ASP e 23 " (cutoff:3.500A) Processing helix chain 'e' and resid 44 through 60 Processing helix chain 'e' and resid 63 through 77 Processing helix chain 'e' and resid 80 through 91 Processing helix chain 'e' and resid 92 through 100 Processing helix chain 'e' and resid 105 through 115 Processing helix chain 'e' and resid 142 through 146 removed outlier: 4.373A pdb=" N ASN e 146 " --> pdb=" O LYS e 143 " (cutoff:3.500A) Processing helix chain 'e' and resid 147 through 155 Processing helix chain 'e' and resid 182 through 187 removed outlier: 4.647A pdb=" N ASP e 187 " --> pdb=" O ARG e 183 " (cutoff:3.500A) Processing helix chain 'e' and resid 191 through 200 removed outlier: 3.862A pdb=" N ILE e 195 " --> pdb=" O THR e 191 " (cutoff:3.500A) Processing helix chain 'f' and resid 80 through 95 Processing helix chain 'f' and resid 133 through 143 Processing helix chain 'f' and resid 157 through 170 Processing helix chain 'f' and resid 174 through 183 Processing helix chain 'f' and resid 185 through 190 Processing helix chain 'f' and resid 191 through 202 removed outlier: 3.666A pdb=" N ALA f 197 " --> pdb=" O GLY f 193 " (cutoff:3.500A) Processing helix chain 'g' and resid 15 through 17 No H-bonds generated for 'chain 'g' and resid 15 through 17' Processing helix chain 'g' and resid 18 through 27 Processing helix chain 'g' and resid 27 through 35 removed outlier: 4.265A pdb=" N GLY g 34 " --> pdb=" O ILE g 30 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLY g 35 " --> pdb=" O ARG g 31 " (cutoff:3.500A) Processing helix chain 'g' and resid 68 through 82 Processing helix chain 'h' and resid 20 through 31 removed outlier: 4.054A pdb=" N THR h 24 " --> pdb=" O SER h 20 " (cutoff:3.500A) Processing helix chain 'h' and resid 35 through 55 Processing helix chain 'h' and resid 57 through 70 removed outlier: 3.932A pdb=" N THR h 61 " --> pdb=" O ASP h 57 " (cutoff:3.500A) Processing helix chain 'h' and resid 92 through 110 Processing helix chain 'h' and resid 115 through 129 Processing helix chain 'h' and resid 132 through 148 Processing helix chain 'h' and resid 149 through 152 Processing helix chain 'i' and resid 5 through 20 Processing helix chain 'i' and resid 30 through 43 Processing helix chain 'i' and resid 115 through 122 Processing helix chain 'j' and resid 61 through 76 Proline residue: j 71 - end of helix Processing helix chain 'j' and resid 91 through 111 Processing helix chain 'j' and resid 114 through 121 Processing helix chain 'k' and resid 14 through 32 Processing helix chain 'k' and resid 80 through 88 Processing helix chain 'l' and resid 62 through 67 Processing helix chain 'l' and resid 68 through 85 Processing helix chain 'l' and resid 101 through 112 Processing helix chain 'm' and resid 3 through 11 Processing helix chain 'm' and resid 113 through 117 Processing helix chain 'n' and resid 14 through 20 Processing helix chain 'n' and resid 26 through 38 Processing helix chain 'n' and resid 49 through 64 Processing helix chain 'n' and resid 67 through 84 Processing helix chain 'n' and resid 86 through 94 Processing helix chain 'n' and resid 107 through 112 Processing helix chain 'o' and resid 3 through 21 removed outlier: 3.876A pdb=" N ASN o 10 " --> pdb=" O LYS o 6 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N GLU o 11 " --> pdb=" O ILE o 7 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLN o 12 " --> pdb=" O VAL o 8 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ARG o 13 " --> pdb=" O LYS o 9 " (cutoff:3.500A) Processing helix chain 'o' and resid 23 through 33 removed outlier: 3.953A pdb=" N LYS o 28 " --> pdb=" O ARG o 24 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ARG o 29 " --> pdb=" O ALA o 25 " (cutoff:3.500A) Processing helix chain 'o' and resid 43 through 51 Processing helix chain 'o' and resid 52 through 60 Proline residue: o 57 - end of helix Processing helix chain 'o' and resid 81 through 90 removed outlier: 3.518A pdb=" N ARG o 85 " --> pdb=" O ARG o 81 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU o 86 " --> pdb=" O VAL o 82 " (cutoff:3.500A) Processing helix chain 'p' and resid 4 through 16 Processing helix chain 'p' and resid 24 through 46 removed outlier: 3.830A pdb=" N VAL p 45 " --> pdb=" O GLU p 41 " (cutoff:3.500A) Processing helix chain 'p' and resid 49 through 74 Processing helix chain 'p' and resid 74 through 86 Processing helix chain 'q' and resid 52 through 63 Processing helix chain 'q' and resid 67 through 78 Processing helix chain 'q' and resid 78 through 85 Processing helix chain 'q' and resid 101 through 114 Processing helix chain 's' and resid 34 through 40 removed outlier: 3.755A pdb=" N LEU s 38 " --> pdb=" O ASP s 34 " (cutoff:3.500A) Processing helix chain 's' and resid 50 through 55 Processing helix chain 's' and resid 57 through 74 Processing helix chain 't' and resid 12 through 23 Processing helix chain 't' and resid 41 through 45 removed outlier: 3.746A pdb=" N ILE t 45 " --> pdb=" O PRO t 42 " (cutoff:3.500A) Processing helix chain 't' and resid 70 through 75 Processing helix chain 'u' and resid 4 through 42 Processing helix chain 'u' and resid 43 through 64 removed outlier: 3.643A pdb=" N ALA u 47 " --> pdb=" O ASP u 43 " (cutoff:3.500A) Processing helix chain 'u' and resid 68 through 86 Processing helix chain 'c' and resid 24 through 29 removed outlier: 4.754A pdb=" N ARG c 29 " --> pdb=" O LYS c 26 " (cutoff:3.500A) Processing helix chain 'c' and resid 42 through 63 removed outlier: 3.717A pdb=" N THR c 46 " --> pdb=" O ASP c 42 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LYS c 52 " --> pdb=" O THR c 48 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N HIS c 63 " --> pdb=" O GLU c 59 " (cutoff:3.500A) Processing helix chain 'c' and resid 73 through 76 Processing helix chain 'c' and resid 77 through 88 Processing helix chain 'c' and resid 103 through 124 removed outlier: 3.823A pdb=" N LYS c 109 " --> pdb=" O SER c 105 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ARG c 110 " --> pdb=" O THR c 106 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU c 111 " --> pdb=" O VAL c 107 " (cutoff:3.500A) Processing helix chain 'c' and resid 130 through 148 Processing helix chain 'c' and resid 169 through 180 removed outlier: 3.719A pdb=" N VAL c 173 " --> pdb=" O GLU c 169 " (cutoff:3.500A) Processing helix chain 'c' and resid 206 through 225 Processing helix chain 'w' and resid 13 through 23 Processing helix chain 'w' and resid 24 through 26 No H-bonds generated for 'chain 'w' and resid 24 through 26' Processing helix chain 'w' and resid 73 through 93 Processing helix chain 'w' and resid 95 through 100 Processing sheet with id=AA1, first strand: chain 'E' and resid 3 through 5 Processing sheet with id=AA2, first strand: chain 'E' and resid 34 through 35 Processing sheet with id=AA3, first strand: chain 'E' and resid 102 through 106 removed outlier: 6.652A pdb=" N ILE E 92 " --> pdb=" O ILE E 82 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ILE E 82 " --> pdb=" O ILE E 92 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LEU E 94 " --> pdb=" O ALA E 80 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 130 through 132 removed outlier: 6.029A pdb=" N LEU E 165 " --> pdb=" O ARG E 176 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ARG E 176 " --> pdb=" O LEU E 165 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY E 167 " --> pdb=" O ALA E 174 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ARG E 184 " --> pdb=" O ILE E 268 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N ILE E 268 " --> pdb=" O ARG E 184 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 145 through 146 removed outlier: 6.133A pdb=" N VAL E 145 " --> pdb=" O LYS E 154 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 5 through 17 removed outlier: 6.118A pdb=" N LYS F 10 " --> pdb=" O LYS F 30 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N LYS F 30 " --> pdb=" O LYS F 10 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY F 12 " --> pdb=" O VAL F 28 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL F 191 " --> pdb=" O VAL F 185 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N VAL F 185 " --> pdb=" O VAL F 191 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LEU F 193 " --> pdb=" O HIS F 183 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LYS F 181 " --> pdb=" O LYS F 195 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N THR F 176 " --> pdb=" O GLY F 116 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N GLY F 116 " --> pdb=" O THR F 176 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N GLN F 178 " --> pdb=" O VAL F 114 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N VAL F 114 " --> pdb=" O GLN F 178 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N THR F 117 " --> pdb=" O LEU F 205 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N LEU F 205 " --> pdb=" O THR F 117 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 80 through 85 removed outlier: 3.636A pdb=" N ARG F 38 " --> pdb=" O GLN F 51 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ALA F 53 " --> pdb=" O VAL F 36 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N VAL F 36 " --> pdb=" O ALA F 53 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 120 through 124 removed outlier: 3.603A pdb=" N GLY F 122 " --> pdb=" O MET F 170 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 14 through 20 removed outlier: 3.969A pdb=" N GLY G 16 " --> pdb=" O VAL G 7 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU G 3 " --> pdb=" O LEU G 20 " (cutoff:3.500A) removed outlier: 8.322A pdb=" N ILE G 124 " --> pdb=" O LYS G 4 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ASP G 6 " --> pdb=" O ILE G 124 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ALA G 126 " --> pdb=" O ASP G 6 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N HIS G 125 " --> pdb=" O PHE G 196 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N LEU G 155 " --> pdb=" O VAL G 195 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N SER G 197 " --> pdb=" O LEU G 155 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N VAL G 157 " --> pdb=" O SER G 197 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL G 154 " --> pdb=" O HIS G 176 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N ILE G 178 " --> pdb=" O VAL G 154 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N VAL G 156 " --> pdb=" O ILE G 178 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 73 through 76 removed outlier: 3.806A pdb=" N GLY H 93 " --> pdb=" O ARG H 75 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N VAL H 164 " --> pdb=" O VAL H 39 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N VAL H 41 " --> pdb=" O THR H 162 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N THR H 162 " --> pdb=" O VAL H 41 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N VAL H 43 " --> pdb=" O ASP H 160 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ASP H 160 " --> pdb=" O VAL H 43 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 16 through 20 Processing sheet with id=AB3, first strand: chain 'I' and resid 42 through 46 removed outlier: 3.753A pdb=" N SER I 42 " --> pdb=" O THR I 54 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 122 through 126 Processing sheet with id=AB5, first strand: chain 'I' and resid 96 through 100 removed outlier: 3.580A pdb=" N GLN I 98 " --> pdb=" O GLU I 105 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'J' and resid 18 through 19 removed outlier: 3.924A pdb=" N LEU J 3 " --> pdb=" O VAL J 19 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'M' and resid 122 through 124 removed outlier: 6.328A pdb=" N TYR M 16 " --> pdb=" O ILE M 55 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N ILE M 57 " --> pdb=" O TYR M 16 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ILE M 18 " --> pdb=" O ILE M 57 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N TRP M 15 " --> pdb=" O ILE M 138 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'M' and resid 73 through 77 Processing sheet with id=AB9, first strand: chain 'N' and resid 7 through 10 removed outlier: 3.501A pdb=" N VAL N 10 " --> pdb=" O LYS N 17 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N LYS N 17 " --> pdb=" O VAL N 10 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ALA N 16 " --> pdb=" O ALA N 46 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ALA N 46 " --> pdb=" O ALA N 16 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N GLU N 18 " --> pdb=" O LYS N 44 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL N 40 " --> pdb=" O ILE N 22 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N VAL N 24 " --> pdb=" O VAL N 38 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N VAL N 38 " --> pdb=" O VAL N 24 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LYS N 59 " --> pdb=" O ILE N 87 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ALA N 83 " --> pdb=" O VAL N 63 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N ALA N 84 " --> pdb=" O ARG N 7 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LYS N 9 " --> pdb=" O ALA N 84 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N ILE N 86 " --> pdb=" O LYS N 9 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'N' and resid 69 through 70 removed outlier: 6.597A pdb=" N THR S 57 " --> pdb=" O ARG S 49 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ARG S 49 " --> pdb=" O THR S 57 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N THR S 59 " --> pdb=" O ILE S 47 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N GLU S 63 " --> pdb=" O LYS S 43 " (cutoff:3.500A) removed outlier: 8.747A pdb=" N LYS S 43 " --> pdb=" O GLU S 63 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N THR S 24 " --> pdb=" O LEU S 86 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N HIS S 82 " --> pdb=" O HIS S 28 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N LYS S 30 " --> pdb=" O ILE S 80 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ILE S 80 " --> pdb=" O LYS S 30 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'O' and resid 76 through 79 removed outlier: 6.015A pdb=" N GLN O 76 " --> pdb=" O LYS O 111 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N LEU O 113 " --> pdb=" O GLN O 76 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N VAL O 78 " --> pdb=" O LEU O 113 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'O' and resid 91 through 93 removed outlier: 7.723A pdb=" N THR O 145 " --> pdb=" O VAL O 122 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N VAL O 124 " --> pdb=" O THR O 145 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'Q' and resid 33 through 37 removed outlier: 4.165A pdb=" N MET Q 110 " --> pdb=" O VAL Q 100 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'R' and resid 58 through 64 removed outlier: 6.015A pdb=" N THR R 59 " --> pdb=" O ASN R 53 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ASN R 53 " --> pdb=" O THR R 59 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ALA R 61 " --> pdb=" O LEU R 51 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N LEU R 38 " --> pdb=" O ASP R 103 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'S' and resid 89 through 90 removed outlier: 4.343A pdb=" N LYS S 110 " --> pdb=" O ASP S 90 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'U' and resid 12 through 16 removed outlier: 6.923A pdb=" N TYR U 4 " --> pdb=" O VAL U 42 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N VAL U 42 " --> pdb=" O TYR U 4 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ILE U 6 " --> pdb=" O ALA U 40 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'U' and resid 21 through 25 removed outlier: 6.527A pdb=" N LEU U 94 " --> pdb=" O HIS U 67 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N HIS U 67 " --> pdb=" O LEU U 94 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL U 96 " --> pdb=" O LEU U 65 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N THR U 61 " --> pdb=" O THR U 100 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'U' and resid 73 through 78 Processing sheet with id=AD1, first strand: chain 'V' and resid 9 through 17 removed outlier: 5.488A pdb=" N SER V 108 " --> pdb=" O TYR V 16 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N GLU V 115 " --> pdb=" O VAL V 78 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N VAL V 78 " --> pdb=" O GLU V 115 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'V' and resid 89 through 94 Processing sheet with id=AD3, first strand: chain 'W' and resid 11 through 14 removed outlier: 4.397A pdb=" N LYS W 80 " --> pdb=" O VAL W 33 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER W 56 " --> pdb=" O LYS W 85 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'W' and resid 66 through 69 Processing sheet with id=AD5, first strand: chain 'X' and resid 66 through 67 removed outlier: 7.002A pdb=" N LYS X 32 " --> pdb=" O ALA X 26 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N ALA X 26 " --> pdb=" O LYS X 32 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LEU X 34 " --> pdb=" O LEU X 24 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N THR X 8 " --> pdb=" O VAL X 74 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL X 73 " --> pdb=" O THR X 81 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'X' and resid 40 through 43 Processing sheet with id=AD7, first strand: chain 'X' and resid 83 through 87 Processing sheet with id=AD8, first strand: chain 'Z' and resid 22 through 23 removed outlier: 6.826A pdb=" N LEU Z 59 " --> pdb=" O LEU Z 37 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'Z' and resid 30 through 31 Processing sheet with id=AE1, first strand: chain '1' and resid 13 through 18 Processing sheet with id=AE2, first strand: chain '1' and resid 33 through 39 Processing sheet with id=AE3, first strand: chain '3' and resid 34 through 38 Processing sheet with id=AE4, first strand: chain '5' and resid 27 through 31 Processing sheet with id=AE5, first strand: chain '6' and resid 22 through 26 removed outlier: 3.523A pdb=" N THR 6 25 " --> pdb=" O ILE 6 11 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain '8' and resid 15 through 16 Processing sheet with id=AE7, first strand: chain '4' and resid 22 through 26 removed outlier: 7.588A pdb=" N ILE 4 33 " --> pdb=" O ASP 4 11 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N THR 4 13 " --> pdb=" O ILE 4 33 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'd' and resid 20 through 21 removed outlier: 3.561A pdb=" N ARG d 58 " --> pdb=" O ARG d 21 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASP d 53 " --> pdb=" O HIS d 68 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N VAL d 63 " --> pdb=" O GLN d 99 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N ASN d 101 " --> pdb=" O VAL d 63 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VAL d 65 " --> pdb=" O ASN d 101 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N LEU d 103 " --> pdb=" O VAL d 65 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ILE d 67 " --> pdb=" O LEU d 103 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'd' and resid 164 through 171 removed outlier: 3.617A pdb=" N LYS d 204 " --> pdb=" O ASP d 181 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N ASP d 181 " --> pdb=" O LYS d 204 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'e' and resid 123 through 124 removed outlier: 3.770A pdb=" N ASP e 136 " --> pdb=" O VAL e 177 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'f' and resid 37 through 49 removed outlier: 5.337A pdb=" N GLU f 38 " --> pdb=" O GLY f 65 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N GLY f 65 " --> pdb=" O GLU f 38 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N VAL f 40 " --> pdb=" O ILE f 63 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N ILE f 63 " --> pdb=" O VAL f 40 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N SER f 42 " --> pdb=" O LEU f 61 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'f' and resid 101 through 102 Processing sheet with id=AF4, first strand: chain 'f' and resid 110 through 114 removed outlier: 6.013A pdb=" N ILE f 131 " --> pdb=" O ALA f 150 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N SER f 152 " --> pdb=" O ILE f 131 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'g' and resid 37 through 47 removed outlier: 6.440A pdb=" N ASP g 38 " --> pdb=" O LYS g 66 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N LYS g 66 " --> pdb=" O ASP g 38 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N VAL g 40 " --> pdb=" O ASP g 64 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ASP g 64 " --> pdb=" O VAL g 40 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N ILE g 42 " --> pdb=" O VAL g 62 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N VAL g 62 " --> pdb=" O ILE g 42 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLY g 44 " --> pdb=" O TYR g 60 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N TYR g 60 " --> pdb=" O GLY g 44 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N ARG g 92 " --> pdb=" O PRO g 3 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N GLU g 5 " --> pdb=" O VAL g 90 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N VAL g 90 " --> pdb=" O GLU g 5 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N MET g 7 " --> pdb=" O THR g 88 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N THR g 88 " --> pdb=" O MET g 7 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE g 9 " --> pdb=" O LEU g 86 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'h' and resid 73 through 79 Processing sheet with id=AF7, first strand: chain 'i' and resid 25 through 28 removed outlier: 3.550A pdb=" N ASP i 48 " --> pdb=" O GLN i 63 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'i' and resid 76 through 79 Processing sheet with id=AF9, first strand: chain 'i' and resid 76 through 79 removed outlier: 5.914A pdb=" N VAL i 127 " --> pdb=" O SER i 107 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N SER i 107 " --> pdb=" O VAL i 127 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA i 129 " --> pdb=" O ILE i 105 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'j' and resid 26 through 32 removed outlier: 4.795A pdb=" N ILE j 26 " --> pdb=" O LEU j 41 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LEU j 41 " --> pdb=" O ILE j 26 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N THR j 28 " --> pdb=" O VAL j 39 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ASN j 49 " --> pdb=" O ALA j 85 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N LEU j 87 " --> pdb=" O ASN j 49 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'k' and resid 40 through 52 removed outlier: 6.263A pdb=" N LEU k 73 " --> pdb=" O PRO k 41 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N LYS k 71 " --> pdb=" O PRO k 43 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'k' and resid 40 through 52 removed outlier: 6.263A pdb=" N LEU k 73 " --> pdb=" O PRO k 41 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N LYS k 71 " --> pdb=" O PRO k 43 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'l' and resid 50 through 55 removed outlier: 6.973A pdb=" N GLY l 28 " --> pdb=" O ASP l 92 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N PHE l 94 " --> pdb=" O GLY l 28 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ALA l 30 " --> pdb=" O PHE l 94 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N LYS l 96 " --> pdb=" O ALA l 30 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N ILE l 32 " --> pdb=" O LYS l 96 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL l 91 " --> pdb=" O GLY l 117 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ILE l 119 " --> pdb=" O VAL l 91 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N VAL l 93 " --> pdb=" O ILE l 119 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N ASP l 121 " --> pdb=" O VAL l 93 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N VAL l 95 " --> pdb=" O ASP l 121 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'm' and resid 29 through 40 removed outlier: 5.950A pdb=" N CYS m 34 " --> pdb=" O LYS m 56 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LYS m 56 " --> pdb=" O CYS m 34 " (cutoff:3.500A) removed outlier: 10.014A pdb=" N TYR m 95 " --> pdb=" O GLU m 62 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N THR m 64 " --> pdb=" O TYR m 95 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N ILE m 97 " --> pdb=" O THR m 64 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N TYR m 66 " --> pdb=" O ILE m 97 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'o' and resid 73 through 74 Processing sheet with id=AG7, first strand: chain 'q' and resid 49 through 51 removed outlier: 5.956A pdb=" N VAL q 36 " --> pdb=" O VAL q 22 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N VAL q 22 " --> pdb=" O VAL q 36 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY q 38 " --> pdb=" O ILE q 20 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLN q 17 " --> pdb=" O LEU q 10 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N VAL q 3 " --> pdb=" O GLN q 65 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'r' and resid 22 through 32 removed outlier: 16.133A pdb=" N THR r 22 " --> pdb=" O ARG r 43 " (cutoff:3.500A) removed outlier: 12.297A pdb=" N ARG r 43 " --> pdb=" O THR r 22 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N ILE r 24 " --> pdb=" O GLU r 41 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N GLU r 41 " --> pdb=" O ILE r 24 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL r 37 " --> pdb=" O VAL r 28 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N ASP r 30 " --> pdb=" O THR r 35 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N THR r 35 " --> pdb=" O ASP r 30 " (cutoff:3.500A) removed outlier: 16.360A pdb=" N LYS r 86 " --> pdb=" O THR r 56 " (cutoff:3.500A) removed outlier: 13.618A pdb=" N LYS r 58 " --> pdb=" O LYS r 86 " (cutoff:3.500A) removed outlier: 9.547A pdb=" N TRP r 88 " --> pdb=" O LYS r 58 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N LYS r 60 " --> pdb=" O TRP r 88 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N LEU r 90 " --> pdb=" O LYS r 60 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N HIS r 62 " --> pdb=" O LEU r 90 " (cutoff:3.500A) removed outlier: 8.550A pdb=" N GLU r 92 " --> pdb=" O HIS r 62 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N ARG r 87 " --> pdb=" O THR r 79 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N SER r 75 " --> pdb=" O VAL r 91 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ILE r 93 " --> pdb=" O ARG r 73 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ARG r 73 " --> pdb=" O ILE r 93 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 't' and resid 31 through 33 removed outlier: 6.845A pdb=" N ILE t 31 " --> pdb=" O ALA t 50 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N HIS t 52 " --> pdb=" O ILE t 31 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N THR t 33 " --> pdb=" O HIS t 52 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'c' and resid 31 through 35 Processing sheet with id=AH2, first strand: chain 'c' and resid 91 through 92 removed outlier: 8.346A pdb=" N VAL c 92 " --> pdb=" O VAL c 67 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N PHE c 69 " --> pdb=" O VAL c 92 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N VAL c 161 " --> pdb=" O ILE c 184 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N ILE c 186 " --> pdb=" O VAL c 161 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N VAL c 163 " --> pdb=" O ILE c 186 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR c 198 " --> pdb=" O VAL c 183 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'w' and resid 4 through 6 removed outlier: 3.556A pdb=" N LEU w 40 " --> pdb=" O SER w 6 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ASP w 59 " --> pdb=" O LEU w 34 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ALA w 36 " --> pdb=" O ASN w 57 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ASN w 57 " --> pdb=" O ALA w 36 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N VAL w 38 " --> pdb=" O GLN w 55 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N GLN w 55 " --> pdb=" O VAL w 38 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N LEU w 40 " --> pdb=" O ILE w 53 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ILE w 53 " --> pdb=" O LEU w 40 " (cutoff:3.500A) 1865 hydrogen bonds defined for protein. 5247 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 4081 hydrogen bonds 6422 hydrogen bond angles 0 basepair planarities 1597 basepair parallelities 2406 stacking parallelities Total time for adding SS restraints: 246.49 Time building geometry restraints manager: 61.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 14132 1.31 - 1.44: 68714 1.44 - 1.57: 62643 1.57 - 1.69: 9298 1.69 - 1.82: 149 Bond restraints: 154936 Sorted by residual: bond pdb=" CG1 ILE c 31 " pdb=" CD1 ILE c 31 " ideal model delta sigma weight residual 1.513 1.301 0.212 3.90e-02 6.57e+02 2.95e+01 bond pdb=" O5' A a 698 " pdb=" C5' A a 698 " ideal model delta sigma weight residual 1.420 1.360 0.060 1.50e-02 4.44e+03 1.60e+01 bond pdb=" C4' A a 698 " pdb=" C3' A a 698 " ideal model delta sigma weight residual 1.521 1.478 0.043 1.50e-02 4.44e+03 8.37e+00 bond pdb=" C MET c 27 " pdb=" O MET c 27 " ideal model delta sigma weight residual 1.235 1.195 0.040 1.38e-02 5.25e+03 8.27e+00 bond pdb=" C ALA g 67 " pdb=" N GLU g 68 " ideal model delta sigma weight residual 1.329 1.284 0.045 1.60e-02 3.91e+03 7.92e+00 ... (remaining 154931 not shown) Histogram of bond angle deviations from ideal: 98.13 - 105.30: 22182 105.30 - 112.46: 89618 112.46 - 119.63: 52089 119.63 - 126.79: 56117 126.79 - 133.96: 12430 Bond angle restraints: 232436 Sorted by residual: angle pdb=" C ALA g 67 " pdb=" N GLU g 68 " pdb=" CA GLU g 68 " ideal model delta sigma weight residual 120.49 130.63 -10.14 1.42e+00 4.96e-01 5.09e+01 angle pdb=" C SER u 48 " pdb=" N GLU u 49 " pdb=" CA GLU u 49 " ideal model delta sigma weight residual 121.14 114.01 7.13 1.75e+00 3.27e-01 1.66e+01 angle pdb=" CA GLU 2 28 " pdb=" CB GLU 2 28 " pdb=" CG GLU 2 28 " ideal model delta sigma weight residual 114.10 121.94 -7.84 2.00e+00 2.50e-01 1.54e+01 angle pdb=" O3' A A1076 " pdb=" C3' A A1076 " pdb=" C2' A A1076 " ideal model delta sigma weight residual 113.70 107.98 5.72 1.50e+00 4.44e-01 1.45e+01 angle pdb=" C5' A a 698 " pdb=" C4' A a 698 " pdb=" C3' A a 698 " ideal model delta sigma weight residual 116.00 110.43 5.57 1.50e+00 4.44e-01 1.38e+01 ... (remaining 232431 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 86561 35.97 - 71.94: 11978 71.94 - 107.92: 1298 107.92 - 143.89: 41 143.89 - 179.86: 50 Dihedral angle restraints: 99928 sinusoidal: 84485 harmonic: 15443 Sorted by residual: dihedral pdb=" O4' C A1535 " pdb=" C1' C A1535 " pdb=" N1 C A1535 " pdb=" C2 C A1535 " ideal model delta sinusoidal sigma weight residual 200.00 20.19 179.81 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C A2025 " pdb=" C1' C A2025 " pdb=" N1 C A2025 " pdb=" C2 C A2025 " ideal model delta sinusoidal sigma weight residual -160.00 13.88 -173.88 1 1.50e+01 4.44e-03 8.51e+01 dihedral pdb=" O4' C A3046 " pdb=" C1' C A3046 " pdb=" N1 C A3046 " pdb=" C2 C A3046 " ideal model delta sinusoidal sigma weight residual -160.00 11.69 -171.69 1 1.50e+01 4.44e-03 8.49e+01 ... (remaining 99925 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 27163 0.061 - 0.122: 2266 0.122 - 0.182: 269 0.182 - 0.243: 36 0.243 - 0.304: 7 Chirality restraints: 29741 Sorted by residual: chirality pdb=" C3' A a 895 " pdb=" C4' A a 895 " pdb=" O3' A a 895 " pdb=" C2' A a 895 " both_signs ideal model delta sigma weight residual False -2.74 -2.44 -0.30 2.00e-01 2.50e+01 2.31e+00 chirality pdb=" C3' U a1482 " pdb=" C4' U a1482 " pdb=" O3' U a1482 " pdb=" C2' U a1482 " both_signs ideal model delta sigma weight residual False -2.74 -2.45 -0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" C1' G A 297 " pdb=" O4' G A 297 " pdb=" C2' G A 297 " pdb=" N9 G A 297 " both_signs ideal model delta sigma weight residual False 2.46 2.19 0.27 2.00e-01 2.50e+01 1.85e+00 ... (remaining 29738 not shown) Planarity restraints: 12205 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C B 62 " -0.010 2.00e-02 2.50e+03 2.85e-02 1.83e+01 pdb=" N1 C B 62 " 0.000 2.00e-02 2.50e+03 pdb=" C2 C B 62 " 0.071 2.00e-02 2.50e+03 pdb=" O2 C B 62 " -0.039 2.00e-02 2.50e+03 pdb=" N3 C B 62 " -0.008 2.00e-02 2.50e+03 pdb=" C4 C B 62 " 0.016 2.00e-02 2.50e+03 pdb=" N4 C B 62 " -0.016 2.00e-02 2.50e+03 pdb=" C5 C B 62 " -0.010 2.00e-02 2.50e+03 pdb=" C6 C B 62 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A A1098 " 0.041 2.00e-02 2.50e+03 1.88e-02 9.75e+00 pdb=" N9 A A1098 " -0.044 2.00e-02 2.50e+03 pdb=" C8 A A1098 " -0.003 2.00e-02 2.50e+03 pdb=" N7 A A1098 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A A1098 " 0.002 2.00e-02 2.50e+03 pdb=" C6 A A1098 " 0.006 2.00e-02 2.50e+03 pdb=" N6 A A1098 " 0.011 2.00e-02 2.50e+03 pdb=" N1 A A1098 " 0.002 2.00e-02 2.50e+03 pdb=" C2 A A1098 " -0.004 2.00e-02 2.50e+03 pdb=" N3 A A1098 " -0.006 2.00e-02 2.50e+03 pdb=" C4 A A1098 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG 1 41 " -0.048 5.00e-02 4.00e+02 7.34e-02 8.63e+00 pdb=" N PRO 1 42 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO 1 42 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO 1 42 " -0.040 5.00e-02 4.00e+02 ... (remaining 12202 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 5277 2.65 - 3.21: 117154 3.21 - 3.77: 296148 3.77 - 4.34: 391888 4.34 - 4.90: 514791 Nonbonded interactions: 1325258 Sorted by model distance: nonbonded pdb=" O6 G A 989 " pdb=" N2 G A 990 " model vdw 2.082 2.520 nonbonded pdb=" N GLU o 11 " pdb=" OE1 GLU o 11 " model vdw 2.104 2.520 nonbonded pdb=" OD1 ASP i 48 " pdb=" N TYR i 49 " model vdw 2.110 2.520 nonbonded pdb=" O2' U a 438 " pdb=" O2 U a 439 " model vdw 2.124 2.440 nonbonded pdb=" O2' A a 92 " pdb=" O5' C a 93 " model vdw 2.126 2.440 ... (remaining 1325253 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: 6.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.150 Extract box with map and model: 16.340 Check model and map are aligned: 1.530 Set scattering table: 0.970 Process input model: 498.460 Find NCS groups from input model: 2.610 Set up NCS constraints: 0.330 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:10.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 537.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.212 154936 Z= 0.254 Angle : 0.599 10.854 232436 Z= 0.316 Chirality : 0.036 0.304 29741 Planarity : 0.005 0.079 12205 Dihedral : 24.287 179.862 90002 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 4.39 % Allowed : 32.04 % Favored : 63.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.11), residues: 5343 helix: 1.25 (0.12), residues: 1791 sheet: -0.01 (0.16), residues: 1066 loop : -0.44 (0.12), residues: 2486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP w 96 HIS 0.006 0.001 HIS Q 77 PHE 0.028 0.002 PHE c 56 TYR 0.025 0.002 TYR c 198 ARG 0.016 0.000 ARG s 52 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10686 Ramachandran restraints generated. 5343 Oldfield, 0 Emsley, 5343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10686 Ramachandran restraints generated. 5343 Oldfield, 0 Emsley, 5343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 764 residues out of total 4467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 568 time to evaluate : 5.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 29 ARG cc_start: 0.8019 (ptm-80) cc_final: 0.7697 (ptt90) REVERT: e 71 TYR cc_start: 0.9380 (t80) cc_final: 0.9138 (t80) REVERT: e 98 TYR cc_start: 0.9135 (t80) cc_final: 0.8807 (t80) REVERT: f 79 LYS cc_start: 0.8835 (mmtm) cc_final: 0.8621 (mttt) REVERT: h 85 TYR cc_start: 0.7249 (OUTLIER) cc_final: 0.5500 (m-80) REVERT: j 120 LYS cc_start: 0.8875 (OUTLIER) cc_final: 0.8630 (mmtm) REVERT: s 19 LYS cc_start: 0.7580 (mmmt) cc_final: 0.6700 (tptt) REVERT: u 59 ASP cc_start: 0.8245 (p0) cc_final: 0.7935 (p0) REVERT: c 100 MET cc_start: 0.7784 (OUTLIER) cc_final: 0.7361 (mpp) outliers start: 196 outliers final: 162 residues processed: 737 average time/residue: 1.8537 time to fit residues: 2033.0861 Evaluate side-chains 700 residues out of total 4467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 535 time to evaluate : 5.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 257 THR Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 167 SER Chi-restraints excluded: chain F residue 191 VAL Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain G residue 3 LEU Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 63 LYS Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain H residue 125 SER Chi-restraints excluded: chain H residue 151 ASP Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain I residue 9 VAL Chi-restraints excluded: chain I residue 57 ASP Chi-restraints excluded: chain I residue 112 HIS Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 23 ASP Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 17 VAL Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 60 ASP Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 61 VAL Chi-restraints excluded: chain N residue 81 GLU Chi-restraints excluded: chain N residue 94 ARG Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain O residue 132 SER Chi-restraints excluded: chain O residue 135 GLU Chi-restraints excluded: chain Q residue 15 SER Chi-restraints excluded: chain Q residue 101 GLU Chi-restraints excluded: chain Q residue 116 VAL Chi-restraints excluded: chain R residue 12 GLU Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 47 ILE Chi-restraints excluded: chain R residue 116 LEU Chi-restraints excluded: chain S residue 18 THR Chi-restraints excluded: chain S residue 64 SER Chi-restraints excluded: chain S residue 69 VAL Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain T residue 16 THR Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain U residue 3 THR Chi-restraints excluded: chain U residue 7 VAL Chi-restraints excluded: chain U residue 24 VAL Chi-restraints excluded: chain U residue 36 SER Chi-restraints excluded: chain U residue 39 VAL Chi-restraints excluded: chain U residue 61 THR Chi-restraints excluded: chain V residue 11 THR Chi-restraints excluded: chain V residue 51 SER Chi-restraints excluded: chain V residue 88 THR Chi-restraints excluded: chain W residue 40 THR Chi-restraints excluded: chain W residue 69 THR Chi-restraints excluded: chain X residue 3 VAL Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain X residue 66 ILE Chi-restraints excluded: chain X residue 83 VAL Chi-restraints excluded: chain X residue 90 GLU Chi-restraints excluded: chain X residue 100 THR Chi-restraints excluded: chain Z residue 12 ASN Chi-restraints excluded: chain Z residue 38 VAL Chi-restraints excluded: chain Z residue 49 VAL Chi-restraints excluded: chain 1 residue 4 VAL Chi-restraints excluded: chain 1 residue 45 ASN Chi-restraints excluded: chain 2 residue 5 THR Chi-restraints excluded: chain 2 residue 63 GLU Chi-restraints excluded: chain 3 residue 7 THR Chi-restraints excluded: chain 3 residue 28 LEU Chi-restraints excluded: chain 5 residue 37 ARG Chi-restraints excluded: chain 6 residue 7 VAL Chi-restraints excluded: chain 6 residue 38 ILE Chi-restraints excluded: chain 6 residue 52 LYS Chi-restraints excluded: chain 7 residue 46 THR Chi-restraints excluded: chain 8 residue 6 THR Chi-restraints excluded: chain 8 residue 23 VAL Chi-restraints excluded: chain 8 residue 33 LEU Chi-restraints excluded: chain 4 residue 29 GLN Chi-restraints excluded: chain 4 residue 33 ILE Chi-restraints excluded: chain d residue 75 VAL Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain d residue 163 SER Chi-restraints excluded: chain d residue 191 THR Chi-restraints excluded: chain e residue 5 THR Chi-restraints excluded: chain e residue 59 SER Chi-restraints excluded: chain f residue 41 VAL Chi-restraints excluded: chain f residue 62 VAL Chi-restraints excluded: chain f residue 71 VAL Chi-restraints excluded: chain f residue 152 SER Chi-restraints excluded: chain f residue 188 ASP Chi-restraints excluded: chain g residue 8 VAL Chi-restraints excluded: chain g residue 10 LEU Chi-restraints excluded: chain g residue 18 THR Chi-restraints excluded: chain g residue 22 SER Chi-restraints excluded: chain g residue 38 ASP Chi-restraints excluded: chain g residue 65 VAL Chi-restraints excluded: chain h residue 24 THR Chi-restraints excluded: chain h residue 66 LEU Chi-restraints excluded: chain h residue 75 VAL Chi-restraints excluded: chain h residue 84 THR Chi-restraints excluded: chain h residue 85 TYR Chi-restraints excluded: chain i residue 51 THR Chi-restraints excluded: chain i residue 52 GLU Chi-restraints excluded: chain i residue 73 SER Chi-restraints excluded: chain i residue 115 ASP Chi-restraints excluded: chain i residue 131 VAL Chi-restraints excluded: chain j residue 28 THR Chi-restraints excluded: chain j residue 42 VAL Chi-restraints excluded: chain j residue 63 VAL Chi-restraints excluded: chain j residue 120 LYS Chi-restraints excluded: chain j residue 131 ILE Chi-restraints excluded: chain j residue 147 TYR Chi-restraints excluded: chain k residue 15 HIS Chi-restraints excluded: chain k residue 36 VAL Chi-restraints excluded: chain l residue 35 THR Chi-restraints excluded: chain l residue 37 ASN Chi-restraints excluded: chain l residue 91 VAL Chi-restraints excluded: chain l residue 100 SER Chi-restraints excluded: chain m residue 8 VAL Chi-restraints excluded: chain m residue 35 THR Chi-restraints excluded: chain m residue 63 VAL Chi-restraints excluded: chain m residue 64 THR Chi-restraints excluded: chain m residue 79 MET Chi-restraints excluded: chain m residue 104 THR Chi-restraints excluded: chain n residue 45 THR Chi-restraints excluded: chain o residue 23 ARG Chi-restraints excluded: chain o residue 60 LEU Chi-restraints excluded: chain p residue 4 THR Chi-restraints excluded: chain p residue 40 THR Chi-restraints excluded: chain p residue 73 VAL Chi-restraints excluded: chain p residue 82 ILE Chi-restraints excluded: chain q residue 13 ILE Chi-restraints excluded: chain q residue 86 LEU Chi-restraints excluded: chain q residue 92 THR Chi-restraints excluded: chain r residue 70 ILE Chi-restraints excluded: chain r residue 72 ASP Chi-restraints excluded: chain t residue 14 HIS Chi-restraints excluded: chain t residue 34 TRP Chi-restraints excluded: chain t residue 35 SER Chi-restraints excluded: chain t residue 48 THR Chi-restraints excluded: chain t residue 79 THR Chi-restraints excluded: chain u residue 30 THR Chi-restraints excluded: chain u residue 32 ILE Chi-restraints excluded: chain c residue 19 GLN Chi-restraints excluded: chain c residue 100 MET Chi-restraints excluded: chain c residue 105 SER Chi-restraints excluded: chain c residue 163 VAL Chi-restraints excluded: chain c residue 169 GLU Chi-restraints excluded: chain w residue 7 THR Chi-restraints excluded: chain w residue 92 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 987 random chunks: chunk 833 optimal weight: 9.9990 chunk 748 optimal weight: 20.0000 chunk 415 optimal weight: 10.0000 chunk 255 optimal weight: 20.0000 chunk 504 optimal weight: 50.0000 chunk 399 optimal weight: 10.0000 chunk 773 optimal weight: 9.9990 chunk 299 optimal weight: 10.0000 chunk 470 optimal weight: 10.0000 chunk 575 optimal weight: 10.0000 chunk 896 optimal weight: 40.0000 overall best weight: 9.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 99 GLN H 83 GLN R 56 ASN V 66 GLN Z 79 ASN ** 1 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 36 GLN d 145 ASN g 78 GLN ** h 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 49 GLN ** t 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 moved from start: 0.0532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.090 154936 Z= 0.410 Angle : 0.638 10.874 232436 Z= 0.329 Chirality : 0.041 0.320 29741 Planarity : 0.005 0.068 12205 Dihedral : 24.247 179.818 79553 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 6.47 % Allowed : 28.62 % Favored : 64.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.11), residues: 5343 helix: 1.23 (0.12), residues: 1811 sheet: -0.08 (0.16), residues: 1060 loop : -0.51 (0.12), residues: 2472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP w 96 HIS 0.005 0.001 HIS k 15 PHE 0.015 0.002 PHE t 74 TYR 0.015 0.002 TYR c 198 ARG 0.010 0.001 ARG s 52 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10686 Ramachandran restraints generated. 5343 Oldfield, 0 Emsley, 5343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10686 Ramachandran restraints generated. 5343 Oldfield, 0 Emsley, 5343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 863 residues out of total 4467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 289 poor density : 574 time to evaluate : 5.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 211 ARG cc_start: 0.9321 (OUTLIER) cc_final: 0.8457 (mtm180) REVERT: F 69 GLN cc_start: 0.9172 (OUTLIER) cc_final: 0.8813 (mt0) REVERT: F 86 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.9099 (mt) REVERT: F 174 ARG cc_start: 0.8889 (OUTLIER) cc_final: 0.8375 (ttt90) REVERT: I 98 GLN cc_start: 0.7483 (pp30) cc_final: 0.7274 (pm20) REVERT: T 28 ARG cc_start: 0.9118 (OUTLIER) cc_final: 0.8754 (mtt180) REVERT: T 59 LYS cc_start: 0.9263 (OUTLIER) cc_final: 0.9002 (ttmt) REVERT: T 120 ASP cc_start: 0.8520 (t0) cc_final: 0.8282 (t0) REVERT: 2 6 THR cc_start: 0.9127 (OUTLIER) cc_final: 0.8921 (t) REVERT: 6 19 LYS cc_start: 0.7945 (tptt) cc_final: 0.7608 (tptm) REVERT: 6 29 ARG cc_start: 0.8145 (ptm-80) cc_final: 0.7806 (ptt90) REVERT: 6 52 LYS cc_start: 0.8558 (tppt) cc_final: 0.8295 (ttmm) REVERT: d 82 GLU cc_start: 0.6702 (OUTLIER) cc_final: 0.6051 (mp0) REVERT: e 71 TYR cc_start: 0.9390 (t80) cc_final: 0.9187 (t80) REVERT: e 98 TYR cc_start: 0.9139 (t80) cc_final: 0.8882 (t80) REVERT: e 108 MET cc_start: 0.8894 (ttp) cc_final: 0.8591 (ttp) REVERT: f 77 LYS cc_start: 0.8348 (OUTLIER) cc_final: 0.7842 (pttm) REVERT: f 79 LYS cc_start: 0.8864 (mmtm) cc_final: 0.8646 (mttt) REVERT: f 91 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7665 (tm-30) REVERT: g 64 ASP cc_start: 0.8336 (OUTLIER) cc_final: 0.8117 (m-30) REVERT: g 74 GLU cc_start: 0.8732 (tp30) cc_final: 0.8145 (tp30) REVERT: g 78 GLN cc_start: 0.9030 (mt0) cc_final: 0.8737 (mt0) REVERT: h 66 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8827 (tp) REVERT: h 85 TYR cc_start: 0.7338 (OUTLIER) cc_final: 0.5476 (m-80) REVERT: h 110 GLN cc_start: 0.8911 (pm20) cc_final: 0.8495 (pm20) REVERT: j 66 GLN cc_start: 0.8542 (tm-30) cc_final: 0.8284 (tm-30) REVERT: j 82 ASP cc_start: 0.8372 (t70) cc_final: 0.7926 (t70) REVERT: n 108 ARG cc_start: 0.9376 (OUTLIER) cc_final: 0.7870 (mmm160) REVERT: p 9 LYS cc_start: 0.8868 (mtmm) cc_final: 0.8566 (mtmm) REVERT: p 44 LYS cc_start: 0.8803 (OUTLIER) cc_final: 0.8485 (mtpt) REVERT: r 95 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.8176 (pt0) REVERT: t 34 TRP cc_start: 0.8896 (OUTLIER) cc_final: 0.8270 (m-10) REVERT: t 73 GLU cc_start: 0.8612 (mm-30) cc_final: 0.8387 (mm-30) REVERT: u 59 ASP cc_start: 0.8259 (p0) cc_final: 0.7914 (p0) REVERT: c 27 MET cc_start: 0.7390 (mmp) cc_final: 0.7121 (mmp) REVERT: c 29 ARG cc_start: 0.7504 (OUTLIER) cc_final: 0.7205 (mtp-110) outliers start: 289 outliers final: 152 residues processed: 783 average time/residue: 1.9439 time to fit residues: 2238.2412 Evaluate side-chains 710 residues out of total 4467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 540 time to evaluate : 5.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 211 ARG Chi-restraints excluded: chain F residue 69 GLN Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 167 SER Chi-restraints excluded: chain F residue 174 ARG Chi-restraints excluded: chain F residue 191 VAL Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain G residue 3 LEU Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 63 LYS Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain H residue 25 GLN Chi-restraints excluded: chain H residue 80 SER Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 151 ASP Chi-restraints excluded: chain H residue 153 ILE Chi-restraints excluded: chain H residue 162 THR Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain I residue 57 ASP Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 112 HIS Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 17 VAL Chi-restraints excluded: chain M residue 22 ASP Chi-restraints excluded: chain M residue 129 ASP Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 81 GLU Chi-restraints excluded: chain N residue 90 ASP Chi-restraints excluded: chain O residue 15 GLU Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain O residue 132 SER Chi-restraints excluded: chain O residue 135 GLU Chi-restraints excluded: chain O residue 145 THR Chi-restraints excluded: chain Q residue 116 VAL Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 47 ILE Chi-restraints excluded: chain R residue 73 ILE Chi-restraints excluded: chain R residue 116 LEU Chi-restraints excluded: chain S residue 18 THR Chi-restraints excluded: chain S residue 69 VAL Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 101 GLU Chi-restraints excluded: chain T residue 28 ARG Chi-restraints excluded: chain T residue 59 LYS Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain U residue 39 VAL Chi-restraints excluded: chain U residue 47 ASN Chi-restraints excluded: chain V residue 51 SER Chi-restraints excluded: chain V residue 88 THR Chi-restraints excluded: chain W residue 9 ASP Chi-restraints excluded: chain W residue 10 ILE Chi-restraints excluded: chain W residue 40 THR Chi-restraints excluded: chain X residue 3 VAL Chi-restraints excluded: chain X residue 24 LEU Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain X residue 66 ILE Chi-restraints excluded: chain X residue 77 ASP Chi-restraints excluded: chain X residue 83 VAL Chi-restraints excluded: chain X residue 90 GLU Chi-restraints excluded: chain Z residue 38 VAL Chi-restraints excluded: chain Z residue 49 VAL Chi-restraints excluded: chain Z residue 57 ASP Chi-restraints excluded: chain 1 residue 45 ASN Chi-restraints excluded: chain 2 residue 5 THR Chi-restraints excluded: chain 2 residue 6 THR Chi-restraints excluded: chain 2 residue 27 GLU Chi-restraints excluded: chain 2 residue 53 GLU Chi-restraints excluded: chain 2 residue 58 TYR Chi-restraints excluded: chain 3 residue 28 LEU Chi-restraints excluded: chain 3 residue 38 GLU Chi-restraints excluded: chain 5 residue 51 LEU Chi-restraints excluded: chain 6 residue 7 VAL Chi-restraints excluded: chain 6 residue 38 ILE Chi-restraints excluded: chain 7 residue 46 THR Chi-restraints excluded: chain 8 residue 6 THR Chi-restraints excluded: chain 8 residue 23 VAL Chi-restraints excluded: chain 4 residue 33 ILE Chi-restraints excluded: chain d residue 75 VAL Chi-restraints excluded: chain d residue 82 GLU Chi-restraints excluded: chain d residue 139 SER Chi-restraints excluded: chain d residue 191 THR Chi-restraints excluded: chain d residue 192 THR Chi-restraints excluded: chain d residue 198 VAL Chi-restraints excluded: chain e residue 5 THR Chi-restraints excluded: chain e residue 139 ASP Chi-restraints excluded: chain e residue 169 VAL Chi-restraints excluded: chain e residue 186 ILE Chi-restraints excluded: chain f residue 37 ILE Chi-restraints excluded: chain f residue 41 VAL Chi-restraints excluded: chain f residue 62 VAL Chi-restraints excluded: chain f residue 77 LYS Chi-restraints excluded: chain f residue 91 GLU Chi-restraints excluded: chain f residue 101 LEU Chi-restraints excluded: chain f residue 104 SER Chi-restraints excluded: chain g residue 8 VAL Chi-restraints excluded: chain g residue 13 THR Chi-restraints excluded: chain g residue 38 ASP Chi-restraints excluded: chain g residue 64 ASP Chi-restraints excluded: chain g residue 65 VAL Chi-restraints excluded: chain h residue 24 THR Chi-restraints excluded: chain h residue 56 THR Chi-restraints excluded: chain h residue 66 LEU Chi-restraints excluded: chain h residue 75 VAL Chi-restraints excluded: chain h residue 85 TYR Chi-restraints excluded: chain i residue 4 THR Chi-restraints excluded: chain i residue 25 VAL Chi-restraints excluded: chain i residue 51 THR Chi-restraints excluded: chain i residue 115 ASP Chi-restraints excluded: chain i residue 131 VAL Chi-restraints excluded: chain j residue 28 THR Chi-restraints excluded: chain j residue 42 VAL Chi-restraints excluded: chain j residue 78 VAL Chi-restraints excluded: chain j residue 147 TYR Chi-restraints excluded: chain j residue 150 ARG Chi-restraints excluded: chain k residue 15 HIS Chi-restraints excluded: chain k residue 25 ILE Chi-restraints excluded: chain k residue 26 VAL Chi-restraints excluded: chain k residue 36 VAL Chi-restraints excluded: chain l residue 25 VAL Chi-restraints excluded: chain l residue 37 ASN Chi-restraints excluded: chain l residue 91 VAL Chi-restraints excluded: chain l residue 92 ASP Chi-restraints excluded: chain l residue 100 SER Chi-restraints excluded: chain l residue 110 GLN Chi-restraints excluded: chain m residue 9 ARG Chi-restraints excluded: chain m residue 63 VAL Chi-restraints excluded: chain m residue 64 THR Chi-restraints excluded: chain m residue 79 MET Chi-restraints excluded: chain m residue 104 THR Chi-restraints excluded: chain m residue 109 ASN Chi-restraints excluded: chain n residue 4 LEU Chi-restraints excluded: chain n residue 45 THR Chi-restraints excluded: chain n residue 49 THR Chi-restraints excluded: chain n residue 50 ASP Chi-restraints excluded: chain n residue 108 ARG Chi-restraints excluded: chain o residue 23 ARG Chi-restraints excluded: chain o residue 55 SER Chi-restraints excluded: chain o residue 66 VAL Chi-restraints excluded: chain p residue 44 LYS Chi-restraints excluded: chain p residue 82 ILE Chi-restraints excluded: chain q residue 86 LEU Chi-restraints excluded: chain q residue 92 THR Chi-restraints excluded: chain r residue 72 ASP Chi-restraints excluded: chain r residue 95 GLU Chi-restraints excluded: chain s residue 34 ASP Chi-restraints excluded: chain t residue 14 HIS Chi-restraints excluded: chain t residue 34 TRP Chi-restraints excluded: chain t residue 45 ILE Chi-restraints excluded: chain t residue 58 VAL Chi-restraints excluded: chain t residue 63 THR Chi-restraints excluded: chain t residue 79 THR Chi-restraints excluded: chain c residue 19 GLN Chi-restraints excluded: chain c residue 29 ARG Chi-restraints excluded: chain c residue 100 MET Chi-restraints excluded: chain c residue 147 SER Chi-restraints excluded: chain c residue 163 VAL Chi-restraints excluded: chain c residue 169 GLU Chi-restraints excluded: chain w residue 5 VAL Chi-restraints excluded: chain w residue 7 THR Chi-restraints excluded: chain w residue 41 THR Chi-restraints excluded: chain w residue 92 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 987 random chunks: chunk 498 optimal weight: 10.0000 chunk 278 optimal weight: 9.9990 chunk 745 optimal weight: 5.9990 chunk 610 optimal weight: 20.0000 chunk 247 optimal weight: 8.9990 chunk 897 optimal weight: 30.0000 chunk 970 optimal weight: 40.0000 chunk 799 optimal weight: 20.0000 chunk 890 optimal weight: 20.0000 chunk 306 optimal weight: 20.0000 chunk 720 optimal weight: 20.0000 overall best weight: 10.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 68 GLN H 83 GLN R 56 ASN V 66 GLN Z 79 ASN ** 1 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 145 ASN ** h 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 49 ASN k 56 HIS l 47 GLN o 12 GLN ** o 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 107 ASN ** c 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8865 moved from start: 0.0811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.089 154936 Z= 0.446 Angle : 0.664 12.120 232436 Z= 0.341 Chirality : 0.042 0.334 29741 Planarity : 0.005 0.069 12205 Dihedral : 24.213 179.816 79448 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 7.77 % Allowed : 27.72 % Favored : 64.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.11), residues: 5343 helix: 1.17 (0.12), residues: 1811 sheet: -0.17 (0.16), residues: 1065 loop : -0.59 (0.12), residues: 2467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP w 96 HIS 0.006 0.001 HIS k 15 PHE 0.017 0.002 PHE t 74 TYR 0.024 0.002 TYR d 23 ARG 0.009 0.001 ARG 4 25 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10686 Ramachandran restraints generated. 5343 Oldfield, 0 Emsley, 5343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10686 Ramachandran restraints generated. 5343 Oldfield, 0 Emsley, 5343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 919 residues out of total 4467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 347 poor density : 572 time to evaluate : 5.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 211 ARG cc_start: 0.9328 (OUTLIER) cc_final: 0.8508 (mtm180) REVERT: F 69 GLN cc_start: 0.9193 (OUTLIER) cc_final: 0.8825 (mt0) REVERT: F 86 LEU cc_start: 0.9288 (OUTLIER) cc_final: 0.9064 (mt) REVERT: F 94 GLU cc_start: 0.8042 (mp0) cc_final: 0.7822 (mp0) REVERT: H 13 GLN cc_start: 0.8452 (tp-100) cc_final: 0.8191 (tp-100) REVERT: H 14 ARG cc_start: 0.8323 (OUTLIER) cc_final: 0.7892 (ttt180) REVERT: J 1 MET cc_start: 0.6990 (OUTLIER) cc_final: 0.6758 (pmm) REVERT: R 24 ARG cc_start: 0.8959 (OUTLIER) cc_final: 0.8467 (ptp90) REVERT: R 71 ARG cc_start: 0.7475 (OUTLIER) cc_final: 0.6845 (ttt-90) REVERT: S 93 ARG cc_start: 0.9456 (OUTLIER) cc_final: 0.7885 (mtm-85) REVERT: T 28 ARG cc_start: 0.9099 (OUTLIER) cc_final: 0.8240 (mtt180) REVERT: T 59 LYS cc_start: 0.9223 (OUTLIER) cc_final: 0.8960 (ttmt) REVERT: T 120 ASP cc_start: 0.8548 (t0) cc_final: 0.8193 (t0) REVERT: W 70 ARG cc_start: 0.7427 (OUTLIER) cc_final: 0.7209 (ptt90) REVERT: 2 17 GLU cc_start: 0.8767 (pm20) cc_final: 0.8554 (pm20) REVERT: 2 23 ARG cc_start: 0.8336 (OUTLIER) cc_final: 0.7673 (ttp-170) REVERT: 6 27 LYS cc_start: 0.8819 (OUTLIER) cc_final: 0.8390 (pttp) REVERT: 6 29 ARG cc_start: 0.8221 (ptm-80) cc_final: 0.7874 (ptt90) REVERT: 6 32 ASP cc_start: 0.8577 (m-30) cc_final: 0.8301 (m-30) REVERT: 6 39 LYS cc_start: 0.8692 (OUTLIER) cc_final: 0.8332 (ttpp) REVERT: d 12 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8698 (tp) REVERT: d 107 ASN cc_start: 0.7373 (t0) cc_final: 0.7052 (t0) REVERT: e 98 TYR cc_start: 0.9150 (t80) cc_final: 0.8885 (t80) REVERT: e 108 MET cc_start: 0.8921 (OUTLIER) cc_final: 0.8707 (ttp) REVERT: f 77 LYS cc_start: 0.8331 (OUTLIER) cc_final: 0.7829 (pttm) REVERT: f 91 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7630 (tm-30) REVERT: g 64 ASP cc_start: 0.8335 (OUTLIER) cc_final: 0.8087 (m-30) REVERT: g 74 GLU cc_start: 0.8543 (tp30) cc_final: 0.8121 (tm-30) REVERT: g 78 GLN cc_start: 0.9049 (mt0) cc_final: 0.8565 (mt0) REVERT: h 85 TYR cc_start: 0.7643 (OUTLIER) cc_final: 0.5827 (m-80) REVERT: h 110 GLN cc_start: 0.8835 (pm20) cc_final: 0.8437 (mp10) REVERT: j 66 GLN cc_start: 0.8566 (tm-30) cc_final: 0.8234 (tm-30) REVERT: j 147 TYR cc_start: 0.7894 (OUTLIER) cc_final: 0.7363 (p90) REVERT: k 80 THR cc_start: 0.7908 (OUTLIER) cc_final: 0.7491 (p) REVERT: m 70 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7654 (mt-10) REVERT: n 12 ASP cc_start: 0.8113 (t0) cc_final: 0.7809 (t0) REVERT: n 108 ARG cc_start: 0.9377 (OUTLIER) cc_final: 0.7844 (mmm160) REVERT: o 11 GLU cc_start: 0.8538 (mp0) cc_final: 0.8261 (mp0) REVERT: o 90 ARG cc_start: 0.8961 (OUTLIER) cc_final: 0.8760 (mtm180) REVERT: r 95 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.8278 (pt0) REVERT: t 73 GLU cc_start: 0.8539 (mm-30) cc_final: 0.8277 (mm-30) REVERT: t 81 LYS cc_start: 0.8754 (OUTLIER) cc_final: 0.8535 (mmmm) REVERT: u 33 ARG cc_start: 0.8955 (OUTLIER) cc_final: 0.7873 (ttm-80) REVERT: u 59 ASP cc_start: 0.8279 (p0) cc_final: 0.7971 (p0) REVERT: c 19 GLN cc_start: 0.7773 (OUTLIER) cc_final: 0.7533 (mp-120) REVERT: c 100 MET cc_start: 0.8246 (OUTLIER) cc_final: 0.7937 (tpp) REVERT: c 137 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7945 (mp) outliers start: 347 outliers final: 187 residues processed: 830 average time/residue: 1.9183 time to fit residues: 2341.9420 Evaluate side-chains 762 residues out of total 4467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 218 poor density : 544 time to evaluate : 5.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 211 ARG Chi-restraints excluded: chain F residue 69 GLN Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 167 SER Chi-restraints excluded: chain F residue 191 VAL Chi-restraints excluded: chain G residue 3 LEU Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 63 LYS Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain H residue 14 ARG Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 80 SER Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 151 ASP Chi-restraints excluded: chain H residue 153 ILE Chi-restraints excluded: chain H residue 162 THR Chi-restraints excluded: chain I residue 57 ASP Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 112 HIS Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain M residue 17 VAL Chi-restraints excluded: chain M residue 22 ASP Chi-restraints excluded: chain M residue 129 ASP Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 81 GLU Chi-restraints excluded: chain N residue 90 ASP Chi-restraints excluded: chain N residue 120 GLU Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 15 GLU Chi-restraints excluded: chain O residue 32 THR Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain O residue 132 SER Chi-restraints excluded: chain O residue 135 GLU Chi-restraints excluded: chain O residue 145 THR Chi-restraints excluded: chain O residue 146 GLU Chi-restraints excluded: chain Q residue 101 GLU Chi-restraints excluded: chain Q residue 116 VAL Chi-restraints excluded: chain R residue 24 ARG Chi-restraints excluded: chain R residue 71 ARG Chi-restraints excluded: chain R residue 116 LEU Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 18 THR Chi-restraints excluded: chain S residue 69 VAL Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 93 ARG Chi-restraints excluded: chain S residue 101 GLU Chi-restraints excluded: chain T residue 16 THR Chi-restraints excluded: chain T residue 28 ARG Chi-restraints excluded: chain T residue 59 LYS Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain U residue 39 VAL Chi-restraints excluded: chain U residue 47 ASN Chi-restraints excluded: chain U residue 96 VAL Chi-restraints excluded: chain V residue 11 THR Chi-restraints excluded: chain V residue 51 SER Chi-restraints excluded: chain W residue 9 ASP Chi-restraints excluded: chain W residue 10 ILE Chi-restraints excluded: chain W residue 40 THR Chi-restraints excluded: chain W residue 69 THR Chi-restraints excluded: chain W residue 70 ARG Chi-restraints excluded: chain X residue 3 VAL Chi-restraints excluded: chain X residue 24 LEU Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain X residue 61 THR Chi-restraints excluded: chain X residue 66 ILE Chi-restraints excluded: chain X residue 77 ASP Chi-restraints excluded: chain X residue 83 VAL Chi-restraints excluded: chain X residue 90 GLU Chi-restraints excluded: chain X residue 100 THR Chi-restraints excluded: chain Z residue 38 VAL Chi-restraints excluded: chain Z residue 49 VAL Chi-restraints excluded: chain Z residue 57 ASP Chi-restraints excluded: chain 1 residue 45 ASN Chi-restraints excluded: chain 2 residue 5 THR Chi-restraints excluded: chain 2 residue 14 THR Chi-restraints excluded: chain 2 residue 23 ARG Chi-restraints excluded: chain 2 residue 27 GLU Chi-restraints excluded: chain 2 residue 53 GLU Chi-restraints excluded: chain 2 residue 58 TYR Chi-restraints excluded: chain 2 residue 63 GLU Chi-restraints excluded: chain 3 residue 5 LYS Chi-restraints excluded: chain 3 residue 7 THR Chi-restraints excluded: chain 3 residue 28 LEU Chi-restraints excluded: chain 3 residue 38 GLU Chi-restraints excluded: chain 5 residue 37 ARG Chi-restraints excluded: chain 5 residue 51 LEU Chi-restraints excluded: chain 6 residue 7 VAL Chi-restraints excluded: chain 6 residue 27 LYS Chi-restraints excluded: chain 6 residue 34 ASP Chi-restraints excluded: chain 6 residue 38 ILE Chi-restraints excluded: chain 6 residue 39 LYS Chi-restraints excluded: chain 7 residue 46 THR Chi-restraints excluded: chain 8 residue 6 THR Chi-restraints excluded: chain 8 residue 23 VAL Chi-restraints excluded: chain 4 residue 33 ILE Chi-restraints excluded: chain d residue 12 LEU Chi-restraints excluded: chain d residue 20 SER Chi-restraints excluded: chain d residue 75 VAL Chi-restraints excluded: chain d residue 81 THR Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain d residue 139 SER Chi-restraints excluded: chain d residue 191 THR Chi-restraints excluded: chain d residue 198 VAL Chi-restraints excluded: chain d residue 206 ASP Chi-restraints excluded: chain e residue 5 THR Chi-restraints excluded: chain e residue 91 SER Chi-restraints excluded: chain e residue 108 MET Chi-restraints excluded: chain e residue 133 SER Chi-restraints excluded: chain e residue 139 ASP Chi-restraints excluded: chain e residue 169 VAL Chi-restraints excluded: chain f residue 37 ILE Chi-restraints excluded: chain f residue 41 VAL Chi-restraints excluded: chain f residue 42 SER Chi-restraints excluded: chain f residue 62 VAL Chi-restraints excluded: chain f residue 77 LYS Chi-restraints excluded: chain f residue 91 GLU Chi-restraints excluded: chain f residue 101 LEU Chi-restraints excluded: chain g residue 8 VAL Chi-restraints excluded: chain g residue 13 THR Chi-restraints excluded: chain g residue 22 SER Chi-restraints excluded: chain g residue 38 ASP Chi-restraints excluded: chain g residue 64 ASP Chi-restraints excluded: chain g residue 65 VAL Chi-restraints excluded: chain h residue 4 LYS Chi-restraints excluded: chain h residue 56 THR Chi-restraints excluded: chain h residue 66 LEU Chi-restraints excluded: chain h residue 75 VAL Chi-restraints excluded: chain h residue 84 THR Chi-restraints excluded: chain h residue 85 TYR Chi-restraints excluded: chain i residue 4 THR Chi-restraints excluded: chain i residue 25 VAL Chi-restraints excluded: chain i residue 51 THR Chi-restraints excluded: chain i residue 81 SER Chi-restraints excluded: chain i residue 115 ASP Chi-restraints excluded: chain j residue 28 THR Chi-restraints excluded: chain j residue 42 VAL Chi-restraints excluded: chain j residue 73 VAL Chi-restraints excluded: chain j residue 88 ASP Chi-restraints excluded: chain j residue 147 TYR Chi-restraints excluded: chain j residue 150 ARG Chi-restraints excluded: chain k residue 15 HIS Chi-restraints excluded: chain k residue 25 ILE Chi-restraints excluded: chain k residue 26 VAL Chi-restraints excluded: chain k residue 36 VAL Chi-restraints excluded: chain k residue 40 VAL Chi-restraints excluded: chain k residue 80 THR Chi-restraints excluded: chain l residue 25 VAL Chi-restraints excluded: chain l residue 37 ASN Chi-restraints excluded: chain l residue 67 SER Chi-restraints excluded: chain l residue 91 VAL Chi-restraints excluded: chain l residue 92 ASP Chi-restraints excluded: chain l residue 100 SER Chi-restraints excluded: chain l residue 110 GLN Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain m residue 8 VAL Chi-restraints excluded: chain m residue 9 ARG Chi-restraints excluded: chain m residue 35 THR Chi-restraints excluded: chain m residue 40 THR Chi-restraints excluded: chain m residue 63 VAL Chi-restraints excluded: chain m residue 64 THR Chi-restraints excluded: chain m residue 70 GLU Chi-restraints excluded: chain m residue 79 MET Chi-restraints excluded: chain m residue 104 THR Chi-restraints excluded: chain m residue 109 ASN Chi-restraints excluded: chain n residue 4 LEU Chi-restraints excluded: chain n residue 33 ILE Chi-restraints excluded: chain n residue 45 THR Chi-restraints excluded: chain n residue 49 THR Chi-restraints excluded: chain n residue 50 ASP Chi-restraints excluded: chain n residue 60 ILE Chi-restraints excluded: chain n residue 80 ARG Chi-restraints excluded: chain n residue 108 ARG Chi-restraints excluded: chain o residue 23 ARG Chi-restraints excluded: chain o residue 48 LEU Chi-restraints excluded: chain o residue 60 LEU Chi-restraints excluded: chain o residue 66 VAL Chi-restraints excluded: chain o residue 90 ARG Chi-restraints excluded: chain p residue 44 LYS Chi-restraints excluded: chain p residue 73 VAL Chi-restraints excluded: chain p residue 82 ILE Chi-restraints excluded: chain q residue 48 LEU Chi-restraints excluded: chain q residue 86 LEU Chi-restraints excluded: chain q residue 92 THR Chi-restraints excluded: chain r residue 70 ILE Chi-restraints excluded: chain r residue 72 ASP Chi-restraints excluded: chain r residue 95 GLU Chi-restraints excluded: chain s residue 56 ASN Chi-restraints excluded: chain t residue 14 HIS Chi-restraints excluded: chain t residue 21 VAL Chi-restraints excluded: chain t residue 27 THR Chi-restraints excluded: chain t residue 48 THR Chi-restraints excluded: chain t residue 63 THR Chi-restraints excluded: chain t residue 79 THR Chi-restraints excluded: chain t residue 81 LYS Chi-restraints excluded: chain u residue 33 ARG Chi-restraints excluded: chain u residue 45 ASP Chi-restraints excluded: chain c residue 19 GLN Chi-restraints excluded: chain c residue 29 ARG Chi-restraints excluded: chain c residue 100 MET Chi-restraints excluded: chain c residue 137 LEU Chi-restraints excluded: chain c residue 163 VAL Chi-restraints excluded: chain c residue 169 GLU Chi-restraints excluded: chain w residue 5 VAL Chi-restraints excluded: chain w residue 7 THR Chi-restraints excluded: chain w residue 92 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 987 random chunks: chunk 887 optimal weight: 9.9990 chunk 675 optimal weight: 10.0000 chunk 466 optimal weight: 10.0000 chunk 99 optimal weight: 30.0000 chunk 428 optimal weight: 50.0000 chunk 602 optimal weight: 10.0000 chunk 901 optimal weight: 7.9990 chunk 954 optimal weight: 40.0000 chunk 470 optimal weight: 7.9990 chunk 854 optimal weight: 8.9990 chunk 257 optimal weight: 2.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 172 ASN G 68 GLN R 56 ASN V 66 GLN W 27 ASN Z 79 ASN ** 1 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 36 GLN ** h 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 56 HIS l 47 GLN q 107 ASN c 15 HIS ** c 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.0814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 154936 Z= 0.320 Angle : 0.604 13.357 232436 Z= 0.312 Chirality : 0.038 0.325 29741 Planarity : 0.005 0.119 12205 Dihedral : 24.191 179.925 79436 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 6.74 % Allowed : 29.31 % Favored : 63.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.11), residues: 5343 helix: 1.31 (0.12), residues: 1823 sheet: -0.10 (0.16), residues: 1039 loop : -0.55 (0.12), residues: 2481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP w 96 HIS 0.006 0.001 HIS k 15 PHE 0.016 0.002 PHE t 74 TYR 0.017 0.002 TYR d 23 ARG 0.007 0.000 ARG I 96 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10686 Ramachandran restraints generated. 5343 Oldfield, 0 Emsley, 5343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10686 Ramachandran restraints generated. 5343 Oldfield, 0 Emsley, 5343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 870 residues out of total 4467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 301 poor density : 569 time to evaluate : 5.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 211 ARG cc_start: 0.9303 (OUTLIER) cc_final: 0.8306 (mtm180) REVERT: F 86 LEU cc_start: 0.9316 (OUTLIER) cc_final: 0.9093 (mt) REVERT: H 13 GLN cc_start: 0.8432 (tp-100) cc_final: 0.8188 (tp-100) REVERT: R 24 ARG cc_start: 0.8921 (OUTLIER) cc_final: 0.8625 (ptp90) REVERT: S 93 ARG cc_start: 0.9416 (OUTLIER) cc_final: 0.8018 (mtm-85) REVERT: T 28 ARG cc_start: 0.9075 (OUTLIER) cc_final: 0.8697 (mtt180) REVERT: T 59 LYS cc_start: 0.9247 (OUTLIER) cc_final: 0.8972 (ttmt) REVERT: T 120 ASP cc_start: 0.8549 (t0) cc_final: 0.8216 (t0) REVERT: W 70 ARG cc_start: 0.7660 (OUTLIER) cc_final: 0.7432 (ptt90) REVERT: 2 23 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.7692 (ttp-170) REVERT: 6 29 ARG cc_start: 0.8171 (ptm-80) cc_final: 0.7841 (ptt90) REVERT: 6 39 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.8257 (ttpp) REVERT: d 107 ASN cc_start: 0.7333 (t0) cc_final: 0.7045 (t0) REVERT: e 98 TYR cc_start: 0.9143 (t80) cc_final: 0.8825 (t80) REVERT: e 108 MET cc_start: 0.8878 (OUTLIER) cc_final: 0.8640 (ttp) REVERT: f 77 LYS cc_start: 0.8350 (OUTLIER) cc_final: 0.7883 (pttm) REVERT: f 91 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7631 (tm-30) REVERT: g 43 TRP cc_start: 0.8571 (OUTLIER) cc_final: 0.7899 (p-90) REVERT: g 64 ASP cc_start: 0.8324 (OUTLIER) cc_final: 0.8110 (m-30) REVERT: g 74 GLU cc_start: 0.8451 (tp30) cc_final: 0.8125 (tm-30) REVERT: g 78 GLN cc_start: 0.9039 (mt0) cc_final: 0.8607 (mt0) REVERT: h 21 GLN cc_start: 0.7902 (mm-40) cc_final: 0.7641 (mm-40) REVERT: h 85 TYR cc_start: 0.7658 (OUTLIER) cc_final: 0.6001 (m-80) REVERT: h 110 GLN cc_start: 0.8802 (OUTLIER) cc_final: 0.8450 (mp10) REVERT: j 66 GLN cc_start: 0.8540 (tm-30) cc_final: 0.8171 (tm-30) REVERT: j 147 TYR cc_start: 0.7948 (OUTLIER) cc_final: 0.7507 (p90) REVERT: k 80 THR cc_start: 0.7792 (OUTLIER) cc_final: 0.7348 (p) REVERT: m 70 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7685 (mt-10) REVERT: n 41 LYS cc_start: 0.8529 (OUTLIER) cc_final: 0.8176 (ptmm) REVERT: n 80 ARG cc_start: 0.8852 (OUTLIER) cc_final: 0.8522 (ppp80) REVERT: n 108 ARG cc_start: 0.9358 (OUTLIER) cc_final: 0.7864 (mmm160) REVERT: o 11 GLU cc_start: 0.8604 (mp0) cc_final: 0.8274 (mp0) REVERT: r 89 ARG cc_start: 0.8752 (OUTLIER) cc_final: 0.8529 (ttp80) REVERT: r 95 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.8283 (pt0) REVERT: t 81 LYS cc_start: 0.8753 (OUTLIER) cc_final: 0.8537 (mmmm) REVERT: u 59 ASP cc_start: 0.8211 (p0) cc_final: 0.7903 (p0) REVERT: c 29 ARG cc_start: 0.7549 (OUTLIER) cc_final: 0.7327 (ttp80) REVERT: c 100 MET cc_start: 0.8291 (tpp) cc_final: 0.7972 (tpp) REVERT: c 137 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7907 (mp) outliers start: 301 outliers final: 164 residues processed: 785 average time/residue: 1.9434 time to fit residues: 2236.7389 Evaluate side-chains 739 residues out of total 4467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 548 time to evaluate : 5.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 211 ARG Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 191 VAL Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 63 LYS Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain H residue 34 GLN Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 151 ASP Chi-restraints excluded: chain H residue 153 ILE Chi-restraints excluded: chain H residue 162 THR Chi-restraints excluded: chain I residue 57 ASP Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 112 HIS Chi-restraints excluded: chain M residue 17 VAL Chi-restraints excluded: chain M residue 22 ASP Chi-restraints excluded: chain M residue 129 ASP Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 81 GLU Chi-restraints excluded: chain N residue 90 ASP Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 15 GLU Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain O residue 82 ASP Chi-restraints excluded: chain O residue 135 GLU Chi-restraints excluded: chain O residue 145 THR Chi-restraints excluded: chain Q residue 37 THR Chi-restraints excluded: chain Q residue 101 GLU Chi-restraints excluded: chain Q residue 116 VAL Chi-restraints excluded: chain R residue 24 ARG Chi-restraints excluded: chain R residue 116 LEU Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 18 THR Chi-restraints excluded: chain S residue 69 VAL Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 93 ARG Chi-restraints excluded: chain S residue 101 GLU Chi-restraints excluded: chain T residue 16 THR Chi-restraints excluded: chain T residue 28 ARG Chi-restraints excluded: chain T residue 59 LYS Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain U residue 47 ASN Chi-restraints excluded: chain U residue 96 VAL Chi-restraints excluded: chain V residue 11 THR Chi-restraints excluded: chain V residue 88 THR Chi-restraints excluded: chain W residue 9 ASP Chi-restraints excluded: chain W residue 10 ILE Chi-restraints excluded: chain W residue 26 ASP Chi-restraints excluded: chain W residue 37 SER Chi-restraints excluded: chain W residue 40 THR Chi-restraints excluded: chain W residue 70 ARG Chi-restraints excluded: chain X residue 3 VAL Chi-restraints excluded: chain X residue 24 LEU Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain X residue 66 ILE Chi-restraints excluded: chain X residue 77 ASP Chi-restraints excluded: chain X residue 83 VAL Chi-restraints excluded: chain X residue 90 GLU Chi-restraints excluded: chain Z residue 12 ASN Chi-restraints excluded: chain Z residue 38 VAL Chi-restraints excluded: chain Z residue 49 VAL Chi-restraints excluded: chain Z residue 57 ASP Chi-restraints excluded: chain 1 residue 4 VAL Chi-restraints excluded: chain 1 residue 45 ASN Chi-restraints excluded: chain 2 residue 5 THR Chi-restraints excluded: chain 2 residue 14 THR Chi-restraints excluded: chain 2 residue 23 ARG Chi-restraints excluded: chain 2 residue 27 GLU Chi-restraints excluded: chain 2 residue 53 GLU Chi-restraints excluded: chain 2 residue 58 TYR Chi-restraints excluded: chain 3 residue 28 LEU Chi-restraints excluded: chain 3 residue 38 GLU Chi-restraints excluded: chain 5 residue 37 ARG Chi-restraints excluded: chain 5 residue 51 LEU Chi-restraints excluded: chain 6 residue 7 VAL Chi-restraints excluded: chain 6 residue 27 LYS Chi-restraints excluded: chain 6 residue 34 ASP Chi-restraints excluded: chain 6 residue 39 LYS Chi-restraints excluded: chain 7 residue 46 THR Chi-restraints excluded: chain 8 residue 23 VAL Chi-restraints excluded: chain 4 residue 33 ILE Chi-restraints excluded: chain d residue 20 SER Chi-restraints excluded: chain d residue 75 VAL Chi-restraints excluded: chain d residue 133 MET Chi-restraints excluded: chain d residue 139 SER Chi-restraints excluded: chain d residue 163 SER Chi-restraints excluded: chain d residue 191 THR Chi-restraints excluded: chain d residue 198 VAL Chi-restraints excluded: chain e residue 5 THR Chi-restraints excluded: chain e residue 108 MET Chi-restraints excluded: chain e residue 133 SER Chi-restraints excluded: chain e residue 139 ASP Chi-restraints excluded: chain e residue 169 VAL Chi-restraints excluded: chain f residue 37 ILE Chi-restraints excluded: chain f residue 41 VAL Chi-restraints excluded: chain f residue 42 SER Chi-restraints excluded: chain f residue 62 VAL Chi-restraints excluded: chain f residue 77 LYS Chi-restraints excluded: chain f residue 91 GLU Chi-restraints excluded: chain f residue 101 LEU Chi-restraints excluded: chain f residue 196 LYS Chi-restraints excluded: chain g residue 8 VAL Chi-restraints excluded: chain g residue 10 LEU Chi-restraints excluded: chain g residue 13 THR Chi-restraints excluded: chain g residue 18 THR Chi-restraints excluded: chain g residue 38 ASP Chi-restraints excluded: chain g residue 43 TRP Chi-restraints excluded: chain g residue 64 ASP Chi-restraints excluded: chain g residue 65 VAL Chi-restraints excluded: chain h residue 4 LYS Chi-restraints excluded: chain h residue 56 THR Chi-restraints excluded: chain h residue 66 LEU Chi-restraints excluded: chain h residue 75 VAL Chi-restraints excluded: chain h residue 84 THR Chi-restraints excluded: chain h residue 85 TYR Chi-restraints excluded: chain h residue 110 GLN Chi-restraints excluded: chain i residue 25 VAL Chi-restraints excluded: chain i residue 51 THR Chi-restraints excluded: chain i residue 115 ASP Chi-restraints excluded: chain j residue 28 THR Chi-restraints excluded: chain j residue 42 VAL Chi-restraints excluded: chain j residue 88 ASP Chi-restraints excluded: chain j residue 147 TYR Chi-restraints excluded: chain j residue 150 ARG Chi-restraints excluded: chain k residue 15 HIS Chi-restraints excluded: chain k residue 25 ILE Chi-restraints excluded: chain k residue 26 VAL Chi-restraints excluded: chain k residue 36 VAL Chi-restraints excluded: chain k residue 40 VAL Chi-restraints excluded: chain k residue 80 THR Chi-restraints excluded: chain l residue 25 VAL Chi-restraints excluded: chain l residue 37 ASN Chi-restraints excluded: chain l residue 67 SER Chi-restraints excluded: chain l residue 91 VAL Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain m residue 9 ARG Chi-restraints excluded: chain m residue 63 VAL Chi-restraints excluded: chain m residue 64 THR Chi-restraints excluded: chain m residue 70 GLU Chi-restraints excluded: chain m residue 79 MET Chi-restraints excluded: chain m residue 104 THR Chi-restraints excluded: chain m residue 109 ASN Chi-restraints excluded: chain n residue 4 LEU Chi-restraints excluded: chain n residue 41 LYS Chi-restraints excluded: chain n residue 45 THR Chi-restraints excluded: chain n residue 46 LYS Chi-restraints excluded: chain n residue 49 THR Chi-restraints excluded: chain n residue 50 ASP Chi-restraints excluded: chain n residue 80 ARG Chi-restraints excluded: chain n residue 90 LEU Chi-restraints excluded: chain n residue 108 ARG Chi-restraints excluded: chain o residue 23 ARG Chi-restraints excluded: chain o residue 48 LEU Chi-restraints excluded: chain o residue 60 LEU Chi-restraints excluded: chain o residue 66 VAL Chi-restraints excluded: chain p residue 44 LYS Chi-restraints excluded: chain q residue 48 LEU Chi-restraints excluded: chain q residue 86 LEU Chi-restraints excluded: chain q residue 92 THR Chi-restraints excluded: chain r residue 72 ASP Chi-restraints excluded: chain r residue 89 ARG Chi-restraints excluded: chain r residue 95 GLU Chi-restraints excluded: chain s residue 34 ASP Chi-restraints excluded: chain t residue 14 HIS Chi-restraints excluded: chain t residue 30 VAL Chi-restraints excluded: chain t residue 63 THR Chi-restraints excluded: chain t residue 79 THR Chi-restraints excluded: chain t residue 81 LYS Chi-restraints excluded: chain u residue 45 ASP Chi-restraints excluded: chain c residue 29 ARG Chi-restraints excluded: chain c residue 137 LEU Chi-restraints excluded: chain c residue 147 SER Chi-restraints excluded: chain c residue 163 VAL Chi-restraints excluded: chain c residue 166 THR Chi-restraints excluded: chain c residue 169 GLU Chi-restraints excluded: chain c residue 192 ASP Chi-restraints excluded: chain c residue 197 ASP Chi-restraints excluded: chain w residue 5 VAL Chi-restraints excluded: chain w residue 7 THR Chi-restraints excluded: chain w residue 92 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 987 random chunks: chunk 794 optimal weight: 9.9990 chunk 541 optimal weight: 60.0000 chunk 13 optimal weight: 0.3980 chunk 710 optimal weight: 20.0000 chunk 393 optimal weight: 30.0000 chunk 814 optimal weight: 9.9990 chunk 659 optimal weight: 20.0000 chunk 1 optimal weight: 4.9990 chunk 487 optimal weight: 10.0000 chunk 856 optimal weight: 2.9990 chunk 240 optimal weight: 30.0000 overall best weight: 5.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 99 GLN F 172 ASN G 68 GLN R 56 ASN V 66 GLN W 27 ASN Z 79 ASN ** 1 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 36 GLN ** d 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 107 ASN s 59 GLN c 77 GLN ** c 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.0869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 154936 Z= 0.248 Angle : 0.571 11.749 232436 Z= 0.295 Chirality : 0.036 0.321 29741 Planarity : 0.004 0.075 12205 Dihedral : 24.142 179.866 79417 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 6.14 % Allowed : 29.71 % Favored : 64.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.11), residues: 5343 helix: 1.48 (0.12), residues: 1823 sheet: -0.03 (0.16), residues: 1045 loop : -0.47 (0.12), residues: 2475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP w 96 HIS 0.006 0.001 HIS k 15 PHE 0.014 0.001 PHE 2 30 TYR 0.020 0.001 TYR e 71 ARG 0.009 0.000 ARG s 52 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10686 Ramachandran restraints generated. 5343 Oldfield, 0 Emsley, 5343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10686 Ramachandran restraints generated. 5343 Oldfield, 0 Emsley, 5343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 862 residues out of total 4467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 274 poor density : 588 time to evaluate : 5.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 188 ARG cc_start: 0.8966 (OUTLIER) cc_final: 0.8055 (mtp85) REVERT: E 211 ARG cc_start: 0.9309 (OUTLIER) cc_final: 0.8260 (mtt180) REVERT: F 69 GLN cc_start: 0.9112 (OUTLIER) cc_final: 0.8780 (mt0) REVERT: F 86 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.9107 (mt) REVERT: G 13 LYS cc_start: 0.8542 (OUTLIER) cc_final: 0.8250 (pptt) REVERT: H 13 GLN cc_start: 0.8414 (tp-100) cc_final: 0.8142 (tp-100) REVERT: H 182 PHE cc_start: 0.8490 (m-80) cc_final: 0.8278 (m-80) REVERT: R 24 ARG cc_start: 0.8902 (OUTLIER) cc_final: 0.8613 (ptp90) REVERT: R 71 ARG cc_start: 0.7425 (OUTLIER) cc_final: 0.6736 (ttt-90) REVERT: S 93 ARG cc_start: 0.9399 (OUTLIER) cc_final: 0.8193 (mtm-85) REVERT: T 28 ARG cc_start: 0.9070 (OUTLIER) cc_final: 0.8691 (mtt180) REVERT: T 59 LYS cc_start: 0.9248 (OUTLIER) cc_final: 0.8975 (ttmt) REVERT: T 120 ASP cc_start: 0.8544 (t0) cc_final: 0.8203 (t0) REVERT: W 70 ARG cc_start: 0.7609 (OUTLIER) cc_final: 0.7390 (ptt90) REVERT: 2 23 ARG cc_start: 0.8320 (OUTLIER) cc_final: 0.7669 (ttp-170) REVERT: 6 29 ARG cc_start: 0.8101 (ptm-80) cc_final: 0.7794 (ptt90) REVERT: 6 39 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8344 (ttpp) REVERT: d 12 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8672 (tp) REVERT: e 98 TYR cc_start: 0.9115 (t80) cc_final: 0.8846 (t80) REVERT: f 77 LYS cc_start: 0.8422 (OUTLIER) cc_final: 0.7984 (pttm) REVERT: f 91 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7447 (tm-30) REVERT: g 43 TRP cc_start: 0.8563 (OUTLIER) cc_final: 0.7923 (p-90) REVERT: g 66 LYS cc_start: 0.9060 (ttmm) cc_final: 0.8799 (tppp) REVERT: g 78 GLN cc_start: 0.9043 (mt0) cc_final: 0.8540 (mt0) REVERT: h 66 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8832 (tt) REVERT: h 85 TYR cc_start: 0.7646 (OUTLIER) cc_final: 0.6075 (m-80) REVERT: h 110 GLN cc_start: 0.8714 (OUTLIER) cc_final: 0.8361 (mp10) REVERT: j 66 GLN cc_start: 0.8550 (tm-30) cc_final: 0.8151 (tm-30) REVERT: j 147 TYR cc_start: 0.7959 (OUTLIER) cc_final: 0.7581 (p90) REVERT: k 80 THR cc_start: 0.7915 (OUTLIER) cc_final: 0.7502 (p) REVERT: l 114 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8813 (mm) REVERT: m 70 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7615 (mt-10) REVERT: n 41 LYS cc_start: 0.8477 (OUTLIER) cc_final: 0.8086 (ptmm) REVERT: n 80 ARG cc_start: 0.8859 (OUTLIER) cc_final: 0.8275 (tmm-80) REVERT: n 108 ARG cc_start: 0.9332 (OUTLIER) cc_final: 0.7890 (mmm160) REVERT: o 11 GLU cc_start: 0.8663 (mp0) cc_final: 0.8276 (mp0) REVERT: o 90 ARG cc_start: 0.8948 (OUTLIER) cc_final: 0.8168 (mtm-85) REVERT: q 99 LYS cc_start: 0.9128 (tppp) cc_final: 0.8499 (mmpt) REVERT: r 89 ARG cc_start: 0.8786 (OUTLIER) cc_final: 0.8530 (ttp80) REVERT: s 18 ARG cc_start: 0.6995 (mtm-85) cc_final: 0.6607 (mpp-170) REVERT: t 73 GLU cc_start: 0.8565 (mm-30) cc_final: 0.8263 (mm-30) REVERT: u 59 ASP cc_start: 0.8159 (p0) cc_final: 0.7859 (p0) REVERT: c 29 ARG cc_start: 0.7583 (OUTLIER) cc_final: 0.7345 (ttp80) REVERT: c 74 LYS cc_start: 0.8365 (ptmt) cc_final: 0.8017 (mmtp) REVERT: c 100 MET cc_start: 0.8362 (tpp) cc_final: 0.8065 (tpp) REVERT: w 109 ARG cc_start: 0.5021 (OUTLIER) cc_final: 0.4537 (ttp-110) outliers start: 274 outliers final: 149 residues processed: 787 average time/residue: 1.9628 time to fit residues: 2263.5705 Evaluate side-chains 730 residues out of total 4467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 550 time to evaluate : 5.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 188 ARG Chi-restraints excluded: chain E residue 211 ARG Chi-restraints excluded: chain F residue 69 GLN Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 191 VAL Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 63 LYS Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain H residue 34 GLN Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 162 THR Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 17 VAL Chi-restraints excluded: chain M residue 129 ASP Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 81 GLU Chi-restraints excluded: chain N residue 90 ASP Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 15 GLU Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain O residue 82 ASP Chi-restraints excluded: chain O residue 125 THR Chi-restraints excluded: chain O residue 132 SER Chi-restraints excluded: chain O residue 135 GLU Chi-restraints excluded: chain O residue 145 THR Chi-restraints excluded: chain Q residue 101 GLU Chi-restraints excluded: chain Q residue 116 VAL Chi-restraints excluded: chain R residue 24 ARG Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 71 ARG Chi-restraints excluded: chain R residue 88 ILE Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 18 THR Chi-restraints excluded: chain S residue 69 VAL Chi-restraints excluded: chain S residue 93 ARG Chi-restraints excluded: chain T residue 28 ARG Chi-restraints excluded: chain T residue 59 LYS Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain U residue 47 ASN Chi-restraints excluded: chain U residue 96 VAL Chi-restraints excluded: chain V residue 11 THR Chi-restraints excluded: chain V residue 88 THR Chi-restraints excluded: chain W residue 9 ASP Chi-restraints excluded: chain W residue 37 SER Chi-restraints excluded: chain W residue 40 THR Chi-restraints excluded: chain W residue 70 ARG Chi-restraints excluded: chain X residue 3 VAL Chi-restraints excluded: chain X residue 24 LEU Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain X residue 77 ASP Chi-restraints excluded: chain X residue 83 VAL Chi-restraints excluded: chain X residue 90 GLU Chi-restraints excluded: chain X residue 100 THR Chi-restraints excluded: chain Z residue 12 ASN Chi-restraints excluded: chain Z residue 49 VAL Chi-restraints excluded: chain 1 residue 45 ASN Chi-restraints excluded: chain 2 residue 23 ARG Chi-restraints excluded: chain 2 residue 27 GLU Chi-restraints excluded: chain 3 residue 7 THR Chi-restraints excluded: chain 3 residue 28 LEU Chi-restraints excluded: chain 3 residue 34 SER Chi-restraints excluded: chain 3 residue 38 GLU Chi-restraints excluded: chain 5 residue 37 ARG Chi-restraints excluded: chain 6 residue 7 VAL Chi-restraints excluded: chain 6 residue 27 LYS Chi-restraints excluded: chain 6 residue 39 LYS Chi-restraints excluded: chain 7 residue 46 THR Chi-restraints excluded: chain 8 residue 23 VAL Chi-restraints excluded: chain 4 residue 33 ILE Chi-restraints excluded: chain 4 residue 38 CYS Chi-restraints excluded: chain d residue 12 LEU Chi-restraints excluded: chain d residue 20 SER Chi-restraints excluded: chain d residue 75 VAL Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain d residue 137 ILE Chi-restraints excluded: chain d residue 139 SER Chi-restraints excluded: chain d residue 163 SER Chi-restraints excluded: chain d residue 198 VAL Chi-restraints excluded: chain e residue 5 THR Chi-restraints excluded: chain e residue 133 SER Chi-restraints excluded: chain e residue 139 ASP Chi-restraints excluded: chain f residue 37 ILE Chi-restraints excluded: chain f residue 41 VAL Chi-restraints excluded: chain f residue 42 SER Chi-restraints excluded: chain f residue 62 VAL Chi-restraints excluded: chain f residue 77 LYS Chi-restraints excluded: chain f residue 91 GLU Chi-restraints excluded: chain f residue 196 LYS Chi-restraints excluded: chain g residue 8 VAL Chi-restraints excluded: chain g residue 10 LEU Chi-restraints excluded: chain g residue 13 THR Chi-restraints excluded: chain g residue 18 THR Chi-restraints excluded: chain g residue 38 ASP Chi-restraints excluded: chain g residue 43 TRP Chi-restraints excluded: chain g residue 65 VAL Chi-restraints excluded: chain h residue 4 LYS Chi-restraints excluded: chain h residue 56 THR Chi-restraints excluded: chain h residue 66 LEU Chi-restraints excluded: chain h residue 85 TYR Chi-restraints excluded: chain h residue 89 VAL Chi-restraints excluded: chain h residue 110 GLN Chi-restraints excluded: chain i residue 4 THR Chi-restraints excluded: chain i residue 25 VAL Chi-restraints excluded: chain i residue 51 THR Chi-restraints excluded: chain i residue 81 SER Chi-restraints excluded: chain i residue 115 ASP Chi-restraints excluded: chain j residue 42 VAL Chi-restraints excluded: chain j residue 88 ASP Chi-restraints excluded: chain j residue 147 TYR Chi-restraints excluded: chain k residue 25 ILE Chi-restraints excluded: chain k residue 26 VAL Chi-restraints excluded: chain k residue 36 VAL Chi-restraints excluded: chain k residue 80 THR Chi-restraints excluded: chain l residue 25 VAL Chi-restraints excluded: chain l residue 37 ASN Chi-restraints excluded: chain l residue 67 SER Chi-restraints excluded: chain l residue 91 VAL Chi-restraints excluded: chain l residue 110 GLN Chi-restraints excluded: chain l residue 114 LEU Chi-restraints excluded: chain m residue 9 ARG Chi-restraints excluded: chain m residue 63 VAL Chi-restraints excluded: chain m residue 64 THR Chi-restraints excluded: chain m residue 70 GLU Chi-restraints excluded: chain m residue 79 MET Chi-restraints excluded: chain m residue 104 THR Chi-restraints excluded: chain m residue 107 VAL Chi-restraints excluded: chain m residue 109 ASN Chi-restraints excluded: chain n residue 41 LYS Chi-restraints excluded: chain n residue 45 THR Chi-restraints excluded: chain n residue 46 LYS Chi-restraints excluded: chain n residue 49 THR Chi-restraints excluded: chain n residue 50 ASP Chi-restraints excluded: chain n residue 80 ARG Chi-restraints excluded: chain n residue 90 LEU Chi-restraints excluded: chain n residue 108 ARG Chi-restraints excluded: chain o residue 23 ARG Chi-restraints excluded: chain o residue 48 LEU Chi-restraints excluded: chain o residue 55 SER Chi-restraints excluded: chain o residue 60 LEU Chi-restraints excluded: chain o residue 66 VAL Chi-restraints excluded: chain o residue 90 ARG Chi-restraints excluded: chain p residue 44 LYS Chi-restraints excluded: chain p residue 73 VAL Chi-restraints excluded: chain p residue 82 ILE Chi-restraints excluded: chain q residue 48 LEU Chi-restraints excluded: chain q residue 86 LEU Chi-restraints excluded: chain q residue 92 THR Chi-restraints excluded: chain r residue 65 ASN Chi-restraints excluded: chain r residue 72 ASP Chi-restraints excluded: chain r residue 89 ARG Chi-restraints excluded: chain s residue 34 ASP Chi-restraints excluded: chain t residue 14 HIS Chi-restraints excluded: chain t residue 45 ILE Chi-restraints excluded: chain t residue 63 THR Chi-restraints excluded: chain t residue 79 THR Chi-restraints excluded: chain u residue 45 ASP Chi-restraints excluded: chain c residue 29 ARG Chi-restraints excluded: chain c residue 163 VAL Chi-restraints excluded: chain c residue 166 THR Chi-restraints excluded: chain c residue 169 GLU Chi-restraints excluded: chain c residue 197 ASP Chi-restraints excluded: chain w residue 5 VAL Chi-restraints excluded: chain w residue 7 THR Chi-restraints excluded: chain w residue 92 ILE Chi-restraints excluded: chain w residue 109 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 987 random chunks: chunk 320 optimal weight: 10.0000 chunk 859 optimal weight: 4.9990 chunk 188 optimal weight: 8.9990 chunk 560 optimal weight: 10.0000 chunk 235 optimal weight: 8.9990 chunk 954 optimal weight: 40.0000 chunk 792 optimal weight: 1.9990 chunk 442 optimal weight: 30.0000 chunk 79 optimal weight: 4.9990 chunk 315 optimal weight: 40.0000 chunk 501 optimal weight: 20.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 99 GLN F 172 ASN R 56 ASN V 66 GLN W 27 ASN Z 79 ASN ** 1 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 12 ASN 5 36 GLN 4 15 GLN ** d 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 107 ASN ** h 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 56 HIS l 47 GLN l 84 GLN q 107 ASN c 77 GLN ** c 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.0944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 154936 Z= 0.261 Angle : 0.572 11.202 232436 Z= 0.296 Chirality : 0.036 0.322 29741 Planarity : 0.004 0.067 12205 Dihedral : 24.090 179.931 79397 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 6.29 % Allowed : 30.09 % Favored : 63.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.12), residues: 5343 helix: 1.52 (0.12), residues: 1821 sheet: 0.00 (0.16), residues: 1043 loop : -0.46 (0.12), residues: 2479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP w 96 HIS 0.004 0.001 HIS t 14 PHE 0.018 0.001 PHE I 106 TYR 0.019 0.001 TYR e 71 ARG 0.011 0.000 ARG s 52 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10686 Ramachandran restraints generated. 5343 Oldfield, 0 Emsley, 5343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10686 Ramachandran restraints generated. 5343 Oldfield, 0 Emsley, 5343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 863 residues out of total 4467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 281 poor density : 582 time to evaluate : 5.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 188 ARG cc_start: 0.8966 (OUTLIER) cc_final: 0.8051 (mtp85) REVERT: E 211 ARG cc_start: 0.9308 (OUTLIER) cc_final: 0.8217 (mtt180) REVERT: F 69 GLN cc_start: 0.9116 (OUTLIER) cc_final: 0.8774 (mt0) REVERT: F 86 LEU cc_start: 0.9326 (OUTLIER) cc_final: 0.9111 (mt) REVERT: H 13 GLN cc_start: 0.8408 (tp-100) cc_final: 0.8135 (tp-100) REVERT: R 24 ARG cc_start: 0.8928 (OUTLIER) cc_final: 0.8662 (ptp90) REVERT: R 71 ARG cc_start: 0.7426 (OUTLIER) cc_final: 0.6735 (ttt-90) REVERT: R 93 LYS cc_start: 0.8559 (tppp) cc_final: 0.8313 (ttmm) REVERT: S 93 ARG cc_start: 0.9401 (OUTLIER) cc_final: 0.8134 (mtm-85) REVERT: T 28 ARG cc_start: 0.9108 (OUTLIER) cc_final: 0.8732 (mtt90) REVERT: T 59 LYS cc_start: 0.9246 (OUTLIER) cc_final: 0.8977 (ttmt) REVERT: T 120 ASP cc_start: 0.8547 (t0) cc_final: 0.8201 (t0) REVERT: W 70 ARG cc_start: 0.7607 (OUTLIER) cc_final: 0.7391 (ptt90) REVERT: 2 23 ARG cc_start: 0.8319 (OUTLIER) cc_final: 0.7725 (ttp-170) REVERT: 6 29 ARG cc_start: 0.8090 (ptm-80) cc_final: 0.7795 (ptt90) REVERT: 6 39 LYS cc_start: 0.8647 (OUTLIER) cc_final: 0.8353 (ttpp) REVERT: 4 15 GLN cc_start: 0.7342 (OUTLIER) cc_final: 0.6914 (mm-40) REVERT: d 12 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8677 (tp) REVERT: e 98 TYR cc_start: 0.9106 (t80) cc_final: 0.8822 (t80) REVERT: f 70 MET cc_start: 0.8145 (tpp) cc_final: 0.7533 (mmt) REVERT: f 77 LYS cc_start: 0.8405 (OUTLIER) cc_final: 0.7955 (pttm) REVERT: f 91 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.7448 (tm-30) REVERT: g 43 TRP cc_start: 0.8555 (OUTLIER) cc_final: 0.7905 (p-90) REVERT: g 66 LYS cc_start: 0.9069 (ttmm) cc_final: 0.8765 (tppp) REVERT: g 74 GLU cc_start: 0.8550 (tm-30) cc_final: 0.8211 (tm-30) REVERT: g 78 GLN cc_start: 0.8796 (mt0) cc_final: 0.8595 (mt0) REVERT: h 66 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8842 (tt) REVERT: h 110 GLN cc_start: 0.8712 (OUTLIER) cc_final: 0.8358 (mp10) REVERT: j 66 GLN cc_start: 0.8541 (tm-30) cc_final: 0.8126 (tm-30) REVERT: j 81 PHE cc_start: 0.8987 (m-80) cc_final: 0.8564 (m-80) REVERT: j 147 TYR cc_start: 0.7901 (OUTLIER) cc_final: 0.7572 (p90) REVERT: k 60 ASP cc_start: 0.8762 (m-30) cc_final: 0.8485 (m-30) REVERT: k 80 THR cc_start: 0.7981 (OUTLIER) cc_final: 0.7569 (p) REVERT: l 90 LYS cc_start: 0.8651 (tptp) cc_final: 0.7644 (tmtt) REVERT: l 114 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8861 (mm) REVERT: m 70 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7600 (mt-10) REVERT: m 75 GLN cc_start: 0.8098 (OUTLIER) cc_final: 0.7776 (mp10) REVERT: n 41 LYS cc_start: 0.8380 (OUTLIER) cc_final: 0.8009 (ptmm) REVERT: n 80 ARG cc_start: 0.8841 (OUTLIER) cc_final: 0.8351 (tmm-80) REVERT: n 108 ARG cc_start: 0.9337 (OUTLIER) cc_final: 0.7916 (mmm160) REVERT: o 11 GLU cc_start: 0.8700 (mp0) cc_final: 0.8224 (mp0) REVERT: o 62 ASN cc_start: 0.8311 (OUTLIER) cc_final: 0.7844 (p0) REVERT: q 99 LYS cc_start: 0.9088 (tppp) cc_final: 0.8467 (mmpt) REVERT: t 73 GLU cc_start: 0.8406 (mm-30) cc_final: 0.8109 (mm-30) REVERT: t 81 LYS cc_start: 0.8770 (OUTLIER) cc_final: 0.8570 (mmmm) REVERT: u 59 ASP cc_start: 0.8173 (p0) cc_final: 0.7872 (p0) REVERT: c 29 ARG cc_start: 0.7556 (OUTLIER) cc_final: 0.7343 (ttp80) REVERT: c 74 LYS cc_start: 0.8405 (ptmt) cc_final: 0.8068 (mmtp) REVERT: c 100 MET cc_start: 0.8350 (tpp) cc_final: 0.7951 (tpp) REVERT: c 135 LEU cc_start: 0.5512 (OUTLIER) cc_final: 0.5219 (pp) REVERT: w 109 ARG cc_start: 0.5025 (OUTLIER) cc_final: 0.4565 (ttp-110) outliers start: 281 outliers final: 170 residues processed: 793 average time/residue: 1.9667 time to fit residues: 2275.4969 Evaluate side-chains 756 residues out of total 4467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 554 time to evaluate : 5.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 188 ARG Chi-restraints excluded: chain E residue 211 ARG Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 69 GLN Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 191 VAL Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 63 LYS Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain H residue 34 GLN Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 151 ASP Chi-restraints excluded: chain H residue 153 ILE Chi-restraints excluded: chain H residue 162 THR Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain M residue 12 THR Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 17 VAL Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 22 ASP Chi-restraints excluded: chain M residue 129 ASP Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 81 GLU Chi-restraints excluded: chain N residue 90 ASP Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 15 GLU Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain O residue 82 ASP Chi-restraints excluded: chain O residue 125 THR Chi-restraints excluded: chain O residue 132 SER Chi-restraints excluded: chain O residue 135 GLU Chi-restraints excluded: chain O residue 145 THR Chi-restraints excluded: chain Q residue 101 GLU Chi-restraints excluded: chain Q residue 116 VAL Chi-restraints excluded: chain R residue 24 ARG Chi-restraints excluded: chain R residue 71 ARG Chi-restraints excluded: chain R residue 88 ILE Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 18 THR Chi-restraints excluded: chain S residue 69 VAL Chi-restraints excluded: chain S residue 93 ARG Chi-restraints excluded: chain S residue 101 GLU Chi-restraints excluded: chain T residue 28 ARG Chi-restraints excluded: chain T residue 59 LYS Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain U residue 47 ASN Chi-restraints excluded: chain U residue 96 VAL Chi-restraints excluded: chain V residue 11 THR Chi-restraints excluded: chain V residue 88 THR Chi-restraints excluded: chain W residue 9 ASP Chi-restraints excluded: chain W residue 10 ILE Chi-restraints excluded: chain W residue 37 SER Chi-restraints excluded: chain W residue 40 THR Chi-restraints excluded: chain W residue 70 ARG Chi-restraints excluded: chain X residue 3 VAL Chi-restraints excluded: chain X residue 24 LEU Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain X residue 61 THR Chi-restraints excluded: chain X residue 66 ILE Chi-restraints excluded: chain X residue 77 ASP Chi-restraints excluded: chain X residue 83 VAL Chi-restraints excluded: chain X residue 90 GLU Chi-restraints excluded: chain X residue 100 THR Chi-restraints excluded: chain Z residue 12 ASN Chi-restraints excluded: chain Z residue 38 VAL Chi-restraints excluded: chain Z residue 49 VAL Chi-restraints excluded: chain 1 residue 4 VAL Chi-restraints excluded: chain 1 residue 45 ASN Chi-restraints excluded: chain 2 residue 23 ARG Chi-restraints excluded: chain 2 residue 27 GLU Chi-restraints excluded: chain 2 residue 53 GLU Chi-restraints excluded: chain 3 residue 7 THR Chi-restraints excluded: chain 3 residue 28 LEU Chi-restraints excluded: chain 3 residue 34 SER Chi-restraints excluded: chain 3 residue 38 GLU Chi-restraints excluded: chain 5 residue 37 ARG Chi-restraints excluded: chain 5 residue 51 LEU Chi-restraints excluded: chain 6 residue 7 VAL Chi-restraints excluded: chain 6 residue 27 LYS Chi-restraints excluded: chain 6 residue 34 ASP Chi-restraints excluded: chain 6 residue 39 LYS Chi-restraints excluded: chain 7 residue 46 THR Chi-restraints excluded: chain 8 residue 23 VAL Chi-restraints excluded: chain 4 residue 15 GLN Chi-restraints excluded: chain 4 residue 33 ILE Chi-restraints excluded: chain 4 residue 38 CYS Chi-restraints excluded: chain d residue 12 LEU Chi-restraints excluded: chain d residue 20 SER Chi-restraints excluded: chain d residue 75 VAL Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain d residue 137 ILE Chi-restraints excluded: chain d residue 139 SER Chi-restraints excluded: chain d residue 163 SER Chi-restraints excluded: chain d residue 191 THR Chi-restraints excluded: chain d residue 198 VAL Chi-restraints excluded: chain e residue 91 SER Chi-restraints excluded: chain e residue 133 SER Chi-restraints excluded: chain e residue 139 ASP Chi-restraints excluded: chain f residue 37 ILE Chi-restraints excluded: chain f residue 62 VAL Chi-restraints excluded: chain f residue 77 LYS Chi-restraints excluded: chain f residue 91 GLU Chi-restraints excluded: chain f residue 101 LEU Chi-restraints excluded: chain f residue 173 GLN Chi-restraints excluded: chain f residue 196 LYS Chi-restraints excluded: chain g residue 8 VAL Chi-restraints excluded: chain g residue 10 LEU Chi-restraints excluded: chain g residue 13 THR Chi-restraints excluded: chain g residue 18 THR Chi-restraints excluded: chain g residue 22 SER Chi-restraints excluded: chain g residue 38 ASP Chi-restraints excluded: chain g residue 43 TRP Chi-restraints excluded: chain g residue 65 VAL Chi-restraints excluded: chain h residue 4 LYS Chi-restraints excluded: chain h residue 56 THR Chi-restraints excluded: chain h residue 66 LEU Chi-restraints excluded: chain h residue 84 THR Chi-restraints excluded: chain h residue 110 GLN Chi-restraints excluded: chain i residue 4 THR Chi-restraints excluded: chain i residue 25 VAL Chi-restraints excluded: chain i residue 51 THR Chi-restraints excluded: chain i residue 81 SER Chi-restraints excluded: chain i residue 115 ASP Chi-restraints excluded: chain j residue 42 VAL Chi-restraints excluded: chain j residue 88 ASP Chi-restraints excluded: chain j residue 147 TYR Chi-restraints excluded: chain k residue 25 ILE Chi-restraints excluded: chain k residue 26 VAL Chi-restraints excluded: chain k residue 80 THR Chi-restraints excluded: chain l residue 25 VAL Chi-restraints excluded: chain l residue 37 ASN Chi-restraints excluded: chain l residue 67 SER Chi-restraints excluded: chain l residue 91 VAL Chi-restraints excluded: chain l residue 110 GLN Chi-restraints excluded: chain l residue 114 LEU Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain m residue 9 ARG Chi-restraints excluded: chain m residue 35 THR Chi-restraints excluded: chain m residue 63 VAL Chi-restraints excluded: chain m residue 64 THR Chi-restraints excluded: chain m residue 70 GLU Chi-restraints excluded: chain m residue 75 GLN Chi-restraints excluded: chain m residue 79 MET Chi-restraints excluded: chain m residue 104 THR Chi-restraints excluded: chain m residue 107 VAL Chi-restraints excluded: chain m residue 109 ASN Chi-restraints excluded: chain n residue 4 LEU Chi-restraints excluded: chain n residue 41 LYS Chi-restraints excluded: chain n residue 45 THR Chi-restraints excluded: chain n residue 46 LYS Chi-restraints excluded: chain n residue 49 THR Chi-restraints excluded: chain n residue 50 ASP Chi-restraints excluded: chain n residue 80 ARG Chi-restraints excluded: chain n residue 108 ARG Chi-restraints excluded: chain o residue 23 ARG Chi-restraints excluded: chain o residue 48 LEU Chi-restraints excluded: chain o residue 55 SER Chi-restraints excluded: chain o residue 60 LEU Chi-restraints excluded: chain o residue 62 ASN Chi-restraints excluded: chain o residue 66 VAL Chi-restraints excluded: chain p residue 44 LYS Chi-restraints excluded: chain p residue 73 VAL Chi-restraints excluded: chain p residue 82 ILE Chi-restraints excluded: chain q residue 48 LEU Chi-restraints excluded: chain q residue 86 LEU Chi-restraints excluded: chain q residue 92 THR Chi-restraints excluded: chain r residue 65 ASN Chi-restraints excluded: chain r residue 72 ASP Chi-restraints excluded: chain s residue 34 ASP Chi-restraints excluded: chain t residue 14 HIS Chi-restraints excluded: chain t residue 30 VAL Chi-restraints excluded: chain t residue 45 ILE Chi-restraints excluded: chain t residue 63 THR Chi-restraints excluded: chain t residue 79 THR Chi-restraints excluded: chain t residue 81 LYS Chi-restraints excluded: chain u residue 45 ASP Chi-restraints excluded: chain c residue 29 ARG Chi-restraints excluded: chain c residue 114 LEU Chi-restraints excluded: chain c residue 135 LEU Chi-restraints excluded: chain c residue 163 VAL Chi-restraints excluded: chain c residue 166 THR Chi-restraints excluded: chain c residue 169 GLU Chi-restraints excluded: chain c residue 192 ASP Chi-restraints excluded: chain c residue 197 ASP Chi-restraints excluded: chain w residue 5 VAL Chi-restraints excluded: chain w residue 7 THR Chi-restraints excluded: chain w residue 92 ILE Chi-restraints excluded: chain w residue 109 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 987 random chunks: chunk 920 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 544 optimal weight: 40.0000 chunk 697 optimal weight: 10.0000 chunk 540 optimal weight: 50.0000 chunk 803 optimal weight: 20.0000 chunk 533 optimal weight: 10.0000 chunk 951 optimal weight: 9.9990 chunk 595 optimal weight: 10.0000 chunk 579 optimal weight: 10.0000 chunk 439 optimal weight: 20.0000 overall best weight: 7.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 99 GLN F 172 ASN R 56 ASN R 86 GLN V 66 GLN W 27 ASN Z 79 ASN ** 1 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 15 GLN ** d 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 107 ASN ** h 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 47 GLN l 84 GLN q 107 ASN t 14 HIS c 77 GLN ** c 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.0976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 154936 Z= 0.319 Angle : 0.598 11.502 232436 Z= 0.308 Chirality : 0.037 0.324 29741 Planarity : 0.005 0.086 12205 Dihedral : 24.077 179.983 79391 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 6.14 % Allowed : 30.59 % Favored : 63.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.12), residues: 5343 helix: 1.47 (0.12), residues: 1819 sheet: -0.04 (0.16), residues: 1069 loop : -0.47 (0.12), residues: 2455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP w 96 HIS 0.007 0.001 HIS k 15 PHE 0.015 0.002 PHE 2 30 TYR 0.021 0.002 TYR e 71 ARG 0.017 0.000 ARG s 52 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10686 Ramachandran restraints generated. 5343 Oldfield, 0 Emsley, 5343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10686 Ramachandran restraints generated. 5343 Oldfield, 0 Emsley, 5343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 853 residues out of total 4467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 274 poor density : 579 time to evaluate : 5.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 168 LYS cc_start: 0.9134 (OUTLIER) cc_final: 0.8855 (mttt) REVERT: E 188 ARG cc_start: 0.8972 (OUTLIER) cc_final: 0.8068 (mtp85) REVERT: E 211 ARG cc_start: 0.9309 (OUTLIER) cc_final: 0.8318 (mtt180) REVERT: F 69 GLN cc_start: 0.9140 (OUTLIER) cc_final: 0.8794 (mt0) REVERT: F 86 LEU cc_start: 0.9345 (OUTLIER) cc_final: 0.9126 (mt) REVERT: F 174 ARG cc_start: 0.8870 (OUTLIER) cc_final: 0.8613 (ttt90) REVERT: H 13 GLN cc_start: 0.8415 (tp-100) cc_final: 0.8144 (tp-100) REVERT: R 24 ARG cc_start: 0.8899 (OUTLIER) cc_final: 0.8607 (ptp90) REVERT: R 71 ARG cc_start: 0.7422 (OUTLIER) cc_final: 0.6776 (ttt-90) REVERT: R 93 LYS cc_start: 0.8579 (tppp) cc_final: 0.8341 (ttmm) REVERT: S 93 ARG cc_start: 0.9410 (OUTLIER) cc_final: 0.8085 (mtm-85) REVERT: T 28 ARG cc_start: 0.9116 (OUTLIER) cc_final: 0.8756 (mtt180) REVERT: T 59 LYS cc_start: 0.9249 (OUTLIER) cc_final: 0.8973 (ttmt) REVERT: T 120 ASP cc_start: 0.8572 (t0) cc_final: 0.8225 (t0) REVERT: W 70 ARG cc_start: 0.7639 (OUTLIER) cc_final: 0.7411 (ptt90) REVERT: 2 23 ARG cc_start: 0.8336 (OUTLIER) cc_final: 0.7680 (ttp-170) REVERT: 6 22 ASN cc_start: 0.8769 (m-40) cc_final: 0.8297 (t0) REVERT: 6 29 ARG cc_start: 0.8126 (ptm-80) cc_final: 0.7825 (ptt90) REVERT: 6 39 LYS cc_start: 0.8653 (OUTLIER) cc_final: 0.8367 (ttpp) REVERT: 4 1 MET cc_start: 0.3652 (tpt) cc_final: 0.3343 (tpt) REVERT: 4 15 GLN cc_start: 0.7643 (OUTLIER) cc_final: 0.7354 (mm-40) REVERT: d 12 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8694 (tp) REVERT: e 98 TYR cc_start: 0.9106 (t80) cc_final: 0.8824 (t80) REVERT: e 200 SER cc_start: 0.8823 (OUTLIER) cc_final: 0.8579 (t) REVERT: f 70 MET cc_start: 0.8130 (tpp) cc_final: 0.7508 (mmt) REVERT: f 77 LYS cc_start: 0.8396 (OUTLIER) cc_final: 0.7939 (pttm) REVERT: f 91 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7597 (tm-30) REVERT: g 43 TRP cc_start: 0.8555 (OUTLIER) cc_final: 0.7914 (p-90) REVERT: g 66 LYS cc_start: 0.9074 (ttmm) cc_final: 0.8773 (tppp) REVERT: g 74 GLU cc_start: 0.8497 (tm-30) cc_final: 0.8269 (tm-30) REVERT: h 66 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8820 (tt) REVERT: h 110 GLN cc_start: 0.8722 (OUTLIER) cc_final: 0.8356 (mp10) REVERT: h 126 ASP cc_start: 0.8785 (m-30) cc_final: 0.8570 (m-30) REVERT: h 143 LYS cc_start: 0.9304 (OUTLIER) cc_final: 0.8907 (ttpt) REVERT: j 66 GLN cc_start: 0.8545 (tm-30) cc_final: 0.8127 (tm-30) REVERT: j 81 PHE cc_start: 0.8997 (m-80) cc_final: 0.8581 (m-80) REVERT: j 147 TYR cc_start: 0.7911 (OUTLIER) cc_final: 0.7451 (p90) REVERT: k 80 THR cc_start: 0.7995 (OUTLIER) cc_final: 0.7580 (p) REVERT: l 114 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8810 (mm) REVERT: m 70 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7601 (mt-10) REVERT: n 41 LYS cc_start: 0.8360 (OUTLIER) cc_final: 0.7969 (ptmm) REVERT: n 80 ARG cc_start: 0.8847 (OUTLIER) cc_final: 0.8483 (tmm-80) REVERT: n 108 ARG cc_start: 0.9355 (OUTLIER) cc_final: 0.7898 (mmm160) REVERT: o 11 GLU cc_start: 0.8729 (mp0) cc_final: 0.8237 (mp0) REVERT: o 62 ASN cc_start: 0.8333 (OUTLIER) cc_final: 0.7861 (p0) REVERT: q 99 LYS cc_start: 0.9055 (tppp) cc_final: 0.8531 (mmpt) REVERT: t 73 GLU cc_start: 0.8365 (mm-30) cc_final: 0.8134 (mm-30) REVERT: u 59 ASP cc_start: 0.8198 (p0) cc_final: 0.7900 (p0) REVERT: c 74 LYS cc_start: 0.8414 (ptmt) cc_final: 0.8095 (mmtp) REVERT: c 100 MET cc_start: 0.8374 (OUTLIER) cc_final: 0.7990 (tpp) REVERT: c 120 MET cc_start: 0.4077 (tmm) cc_final: 0.3378 (pp-130) REVERT: w 109 ARG cc_start: 0.5029 (OUTLIER) cc_final: 0.4608 (ttp-110) outliers start: 274 outliers final: 174 residues processed: 780 average time/residue: 1.9746 time to fit residues: 2269.9606 Evaluate side-chains 760 residues out of total 4467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 207 poor density : 553 time to evaluate : 5.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 168 LYS Chi-restraints excluded: chain E residue 188 ARG Chi-restraints excluded: chain E residue 211 ARG Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 69 GLN Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 174 ARG Chi-restraints excluded: chain F residue 191 VAL Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 63 LYS Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain H residue 34 GLN Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 151 ASP Chi-restraints excluded: chain H residue 153 ILE Chi-restraints excluded: chain H residue 162 THR Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain M residue 12 THR Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 17 VAL Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 22 ASP Chi-restraints excluded: chain M residue 129 ASP Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 81 GLU Chi-restraints excluded: chain N residue 90 ASP Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 15 GLU Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain O residue 125 THR Chi-restraints excluded: chain O residue 132 SER Chi-restraints excluded: chain O residue 135 GLU Chi-restraints excluded: chain O residue 145 THR Chi-restraints excluded: chain Q residue 37 THR Chi-restraints excluded: chain Q residue 101 GLU Chi-restraints excluded: chain Q residue 116 VAL Chi-restraints excluded: chain R residue 24 ARG Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 71 ARG Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 18 THR Chi-restraints excluded: chain S residue 69 VAL Chi-restraints excluded: chain S residue 93 ARG Chi-restraints excluded: chain S residue 101 GLU Chi-restraints excluded: chain T residue 28 ARG Chi-restraints excluded: chain T residue 59 LYS Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain U residue 47 ASN Chi-restraints excluded: chain U residue 96 VAL Chi-restraints excluded: chain V residue 11 THR Chi-restraints excluded: chain V residue 88 THR Chi-restraints excluded: chain W residue 9 ASP Chi-restraints excluded: chain W residue 10 ILE Chi-restraints excluded: chain W residue 37 SER Chi-restraints excluded: chain W residue 40 THR Chi-restraints excluded: chain W residue 69 THR Chi-restraints excluded: chain W residue 70 ARG Chi-restraints excluded: chain X residue 3 VAL Chi-restraints excluded: chain X residue 24 LEU Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain X residue 66 ILE Chi-restraints excluded: chain X residue 77 ASP Chi-restraints excluded: chain X residue 83 VAL Chi-restraints excluded: chain X residue 90 GLU Chi-restraints excluded: chain X residue 100 THR Chi-restraints excluded: chain Z residue 12 ASN Chi-restraints excluded: chain Z residue 38 VAL Chi-restraints excluded: chain Z residue 49 VAL Chi-restraints excluded: chain 1 residue 4 VAL Chi-restraints excluded: chain 1 residue 45 ASN Chi-restraints excluded: chain 2 residue 5 THR Chi-restraints excluded: chain 2 residue 23 ARG Chi-restraints excluded: chain 2 residue 27 GLU Chi-restraints excluded: chain 2 residue 53 GLU Chi-restraints excluded: chain 3 residue 7 THR Chi-restraints excluded: chain 3 residue 28 LEU Chi-restraints excluded: chain 3 residue 34 SER Chi-restraints excluded: chain 3 residue 38 GLU Chi-restraints excluded: chain 5 residue 37 ARG Chi-restraints excluded: chain 5 residue 51 LEU Chi-restraints excluded: chain 6 residue 7 VAL Chi-restraints excluded: chain 6 residue 27 LYS Chi-restraints excluded: chain 6 residue 38 ILE Chi-restraints excluded: chain 6 residue 39 LYS Chi-restraints excluded: chain 7 residue 46 THR Chi-restraints excluded: chain 8 residue 23 VAL Chi-restraints excluded: chain 4 residue 15 GLN Chi-restraints excluded: chain 4 residue 38 CYS Chi-restraints excluded: chain d residue 12 LEU Chi-restraints excluded: chain d residue 20 SER Chi-restraints excluded: chain d residue 75 VAL Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain d residue 137 ILE Chi-restraints excluded: chain d residue 139 SER Chi-restraints excluded: chain d residue 163 SER Chi-restraints excluded: chain d residue 191 THR Chi-restraints excluded: chain d residue 198 VAL Chi-restraints excluded: chain e residue 5 THR Chi-restraints excluded: chain e residue 91 SER Chi-restraints excluded: chain e residue 133 SER Chi-restraints excluded: chain e residue 139 ASP Chi-restraints excluded: chain e residue 200 SER Chi-restraints excluded: chain f residue 37 ILE Chi-restraints excluded: chain f residue 42 SER Chi-restraints excluded: chain f residue 62 VAL Chi-restraints excluded: chain f residue 77 LYS Chi-restraints excluded: chain f residue 91 GLU Chi-restraints excluded: chain f residue 173 GLN Chi-restraints excluded: chain f residue 196 LYS Chi-restraints excluded: chain g residue 10 LEU Chi-restraints excluded: chain g residue 13 THR Chi-restraints excluded: chain g residue 18 THR Chi-restraints excluded: chain g residue 22 SER Chi-restraints excluded: chain g residue 38 ASP Chi-restraints excluded: chain g residue 43 TRP Chi-restraints excluded: chain g residue 65 VAL Chi-restraints excluded: chain h residue 4 LYS Chi-restraints excluded: chain h residue 56 THR Chi-restraints excluded: chain h residue 66 LEU Chi-restraints excluded: chain h residue 84 THR Chi-restraints excluded: chain h residue 110 GLN Chi-restraints excluded: chain h residue 143 LYS Chi-restraints excluded: chain i residue 4 THR Chi-restraints excluded: chain i residue 25 VAL Chi-restraints excluded: chain i residue 51 THR Chi-restraints excluded: chain i residue 81 SER Chi-restraints excluded: chain i residue 115 ASP Chi-restraints excluded: chain j residue 28 THR Chi-restraints excluded: chain j residue 42 VAL Chi-restraints excluded: chain j residue 88 ASP Chi-restraints excluded: chain j residue 147 TYR Chi-restraints excluded: chain k residue 25 ILE Chi-restraints excluded: chain k residue 26 VAL Chi-restraints excluded: chain k residue 36 VAL Chi-restraints excluded: chain k residue 80 THR Chi-restraints excluded: chain l residue 25 VAL Chi-restraints excluded: chain l residue 37 ASN Chi-restraints excluded: chain l residue 67 SER Chi-restraints excluded: chain l residue 91 VAL Chi-restraints excluded: chain l residue 92 ASP Chi-restraints excluded: chain l residue 110 GLN Chi-restraints excluded: chain l residue 114 LEU Chi-restraints excluded: chain m residue 9 ARG Chi-restraints excluded: chain m residue 35 THR Chi-restraints excluded: chain m residue 63 VAL Chi-restraints excluded: chain m residue 64 THR Chi-restraints excluded: chain m residue 70 GLU Chi-restraints excluded: chain m residue 79 MET Chi-restraints excluded: chain m residue 104 THR Chi-restraints excluded: chain m residue 107 VAL Chi-restraints excluded: chain m residue 109 ASN Chi-restraints excluded: chain n residue 41 LYS Chi-restraints excluded: chain n residue 45 THR Chi-restraints excluded: chain n residue 46 LYS Chi-restraints excluded: chain n residue 49 THR Chi-restraints excluded: chain n residue 50 ASP Chi-restraints excluded: chain n residue 80 ARG Chi-restraints excluded: chain n residue 108 ARG Chi-restraints excluded: chain o residue 23 ARG Chi-restraints excluded: chain o residue 48 LEU Chi-restraints excluded: chain o residue 55 SER Chi-restraints excluded: chain o residue 60 LEU Chi-restraints excluded: chain o residue 62 ASN Chi-restraints excluded: chain o residue 66 VAL Chi-restraints excluded: chain p residue 44 LYS Chi-restraints excluded: chain p residue 73 VAL Chi-restraints excluded: chain p residue 82 ILE Chi-restraints excluded: chain q residue 48 LEU Chi-restraints excluded: chain q residue 86 LEU Chi-restraints excluded: chain q residue 92 THR Chi-restraints excluded: chain r residue 65 ASN Chi-restraints excluded: chain r residue 72 ASP Chi-restraints excluded: chain s residue 34 ASP Chi-restraints excluded: chain t residue 14 HIS Chi-restraints excluded: chain t residue 21 VAL Chi-restraints excluded: chain t residue 30 VAL Chi-restraints excluded: chain t residue 45 ILE Chi-restraints excluded: chain t residue 63 THR Chi-restraints excluded: chain t residue 79 THR Chi-restraints excluded: chain u residue 45 ASP Chi-restraints excluded: chain c residue 100 MET Chi-restraints excluded: chain c residue 153 ASP Chi-restraints excluded: chain c residue 163 VAL Chi-restraints excluded: chain c residue 166 THR Chi-restraints excluded: chain c residue 169 GLU Chi-restraints excluded: chain c residue 192 ASP Chi-restraints excluded: chain c residue 197 ASP Chi-restraints excluded: chain w residue 5 VAL Chi-restraints excluded: chain w residue 7 THR Chi-restraints excluded: chain w residue 92 ILE Chi-restraints excluded: chain w residue 109 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 987 random chunks: chunk 588 optimal weight: 20.0000 chunk 379 optimal weight: 50.0000 chunk 568 optimal weight: 10.0000 chunk 286 optimal weight: 10.0000 chunk 186 optimal weight: 10.0000 chunk 184 optimal weight: 8.9990 chunk 604 optimal weight: 10.0000 chunk 648 optimal weight: 10.0000 chunk 470 optimal weight: 10.0000 chunk 88 optimal weight: 40.0000 chunk 747 optimal weight: 30.0000 overall best weight: 9.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 99 GLN F 172 ASN R 56 ASN V 66 GLN W 27 ASN Z 79 ASN ** 1 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 36 GLN 4 15 GLN ** d 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 107 ASN g 78 GLN ** h 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 84 GLN q 50 GLN q 107 ASN ** t 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8860 moved from start: 0.1072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.081 154936 Z= 0.403 Angle : 0.643 12.567 232436 Z= 0.331 Chirality : 0.040 0.331 29741 Planarity : 0.005 0.093 12205 Dihedral : 24.102 179.962 79388 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 6.16 % Allowed : 30.79 % Favored : 63.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.11), residues: 5343 helix: 1.37 (0.12), residues: 1813 sheet: -0.02 (0.16), residues: 1056 loop : -0.55 (0.12), residues: 2474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP w 96 HIS 0.006 0.001 HIS k 15 PHE 0.017 0.002 PHE 2 30 TYR 0.023 0.002 TYR e 71 ARG 0.018 0.001 ARG s 52 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10686 Ramachandran restraints generated. 5343 Oldfield, 0 Emsley, 5343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10686 Ramachandran restraints generated. 5343 Oldfield, 0 Emsley, 5343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 846 residues out of total 4467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 275 poor density : 571 time to evaluate : 5.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 168 LYS cc_start: 0.9129 (OUTLIER) cc_final: 0.8793 (mttt) REVERT: E 188 ARG cc_start: 0.8952 (OUTLIER) cc_final: 0.8024 (mtp85) REVERT: E 211 ARG cc_start: 0.9326 (OUTLIER) cc_final: 0.8491 (mtm180) REVERT: E 273 ARG cc_start: 0.7611 (OUTLIER) cc_final: 0.6847 (mtm-85) REVERT: F 69 GLN cc_start: 0.9190 (OUTLIER) cc_final: 0.8808 (mt0) REVERT: F 86 LEU cc_start: 0.9347 (OUTLIER) cc_final: 0.9111 (mt) REVERT: H 13 GLN cc_start: 0.8415 (tp-100) cc_final: 0.8137 (tp-100) REVERT: I 88 MET cc_start: 0.7351 (mmm) cc_final: 0.6968 (tpp) REVERT: R 24 ARG cc_start: 0.8920 (OUTLIER) cc_final: 0.8581 (ptp90) REVERT: R 71 ARG cc_start: 0.7510 (OUTLIER) cc_final: 0.6841 (ttt-90) REVERT: R 93 LYS cc_start: 0.8624 (tppp) cc_final: 0.8391 (ttmm) REVERT: S 93 ARG cc_start: 0.9443 (OUTLIER) cc_final: 0.7979 (mtm-85) REVERT: T 28 ARG cc_start: 0.9137 (OUTLIER) cc_final: 0.8766 (mtt180) REVERT: T 59 LYS cc_start: 0.9264 (OUTLIER) cc_final: 0.9002 (ttmt) REVERT: T 120 ASP cc_start: 0.8603 (t0) cc_final: 0.8264 (t0) REVERT: W 70 ARG cc_start: 0.7623 (OUTLIER) cc_final: 0.7376 (ptt90) REVERT: 2 23 ARG cc_start: 0.8320 (OUTLIER) cc_final: 0.7669 (ttp-170) REVERT: 6 29 ARG cc_start: 0.8182 (ptm-80) cc_final: 0.7878 (ptt90) REVERT: 6 39 LYS cc_start: 0.8581 (OUTLIER) cc_final: 0.8204 (ttpp) REVERT: 4 1 MET cc_start: 0.3939 (tpt) cc_final: 0.3684 (tpt) REVERT: 4 15 GLN cc_start: 0.7764 (OUTLIER) cc_final: 0.7388 (mm-40) REVERT: d 12 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8708 (tp) REVERT: e 98 TYR cc_start: 0.9106 (t80) cc_final: 0.8824 (t80) REVERT: e 200 SER cc_start: 0.8832 (OUTLIER) cc_final: 0.8577 (t) REVERT: f 70 MET cc_start: 0.8154 (tpp) cc_final: 0.7488 (mmt) REVERT: f 77 LYS cc_start: 0.8418 (OUTLIER) cc_final: 0.7957 (pttm) REVERT: f 91 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.7472 (tm-30) REVERT: g 43 TRP cc_start: 0.8543 (OUTLIER) cc_final: 0.7884 (p-90) REVERT: g 74 GLU cc_start: 0.8560 (tm-30) cc_final: 0.8290 (tm-30) REVERT: h 66 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8835 (tt) REVERT: h 143 LYS cc_start: 0.9299 (OUTLIER) cc_final: 0.8902 (ttpt) REVERT: j 66 GLN cc_start: 0.8544 (tm-30) cc_final: 0.8120 (tm-30) REVERT: j 147 TYR cc_start: 0.7891 (OUTLIER) cc_final: 0.7328 (p90) REVERT: k 80 THR cc_start: 0.8003 (OUTLIER) cc_final: 0.7576 (p) REVERT: l 114 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8847 (mm) REVERT: m 70 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7668 (mt-10) REVERT: n 41 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.7934 (ptmm) REVERT: n 108 ARG cc_start: 0.9379 (OUTLIER) cc_final: 0.7873 (mmm160) REVERT: o 11 GLU cc_start: 0.8769 (mp0) cc_final: 0.8288 (mp0) REVERT: o 62 ASN cc_start: 0.8324 (OUTLIER) cc_final: 0.7867 (p0) REVERT: q 96 LYS cc_start: 0.8967 (tptm) cc_final: 0.8744 (tptm) REVERT: q 99 LYS cc_start: 0.9060 (tppp) cc_final: 0.8589 (mmpt) REVERT: r 95 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.8342 (pt0) REVERT: t 22 GLN cc_start: 0.8204 (mm-40) cc_final: 0.7908 (mm-40) REVERT: u 59 ASP cc_start: 0.8240 (p0) cc_final: 0.7940 (p0) REVERT: c 74 LYS cc_start: 0.8449 (ptmt) cc_final: 0.8152 (mmtp) REVERT: c 100 MET cc_start: 0.8381 (OUTLIER) cc_final: 0.7972 (tpp) REVERT: c 120 MET cc_start: 0.4228 (tmm) cc_final: 0.3647 (pp-130) REVERT: c 131 LYS cc_start: 0.5390 (OUTLIER) cc_final: 0.5129 (ttmt) REVERT: c 135 LEU cc_start: 0.5757 (OUTLIER) cc_final: 0.5422 (pp) REVERT: c 153 ASP cc_start: 0.8869 (OUTLIER) cc_final: 0.8071 (p0) REVERT: c 154 MET cc_start: 0.6668 (mpp) cc_final: 0.5955 (mpp) REVERT: w 109 ARG cc_start: 0.5112 (OUTLIER) cc_final: 0.4693 (ttp-110) outliers start: 275 outliers final: 183 residues processed: 786 average time/residue: 1.9027 time to fit residues: 2206.0738 Evaluate side-chains 774 residues out of total 4467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 218 poor density : 556 time to evaluate : 5.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 168 LYS Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 188 ARG Chi-restraints excluded: chain E residue 211 ARG Chi-restraints excluded: chain E residue 273 ARG Chi-restraints excluded: chain F residue 69 GLN Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 191 VAL Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 63 LYS Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain H residue 34 GLN Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 151 ASP Chi-restraints excluded: chain H residue 153 ILE Chi-restraints excluded: chain H residue 162 THR Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 17 VAL Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 22 ASP Chi-restraints excluded: chain M residue 129 ASP Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 81 GLU Chi-restraints excluded: chain N residue 90 ASP Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 15 GLU Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain O residue 125 THR Chi-restraints excluded: chain O residue 132 SER Chi-restraints excluded: chain O residue 135 GLU Chi-restraints excluded: chain O residue 145 THR Chi-restraints excluded: chain Q residue 37 THR Chi-restraints excluded: chain Q residue 74 ASP Chi-restraints excluded: chain Q residue 101 GLU Chi-restraints excluded: chain Q residue 116 VAL Chi-restraints excluded: chain R residue 24 ARG Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 71 ARG Chi-restraints excluded: chain R residue 88 ILE Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 18 THR Chi-restraints excluded: chain S residue 69 VAL Chi-restraints excluded: chain S residue 93 ARG Chi-restraints excluded: chain S residue 101 GLU Chi-restraints excluded: chain T residue 16 THR Chi-restraints excluded: chain T residue 28 ARG Chi-restraints excluded: chain T residue 59 LYS Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain U residue 47 ASN Chi-restraints excluded: chain U residue 96 VAL Chi-restraints excluded: chain V residue 11 THR Chi-restraints excluded: chain V residue 88 THR Chi-restraints excluded: chain W residue 9 ASP Chi-restraints excluded: chain W residue 10 ILE Chi-restraints excluded: chain W residue 37 SER Chi-restraints excluded: chain W residue 40 THR Chi-restraints excluded: chain W residue 69 THR Chi-restraints excluded: chain W residue 70 ARG Chi-restraints excluded: chain X residue 3 VAL Chi-restraints excluded: chain X residue 24 LEU Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain X residue 59 ILE Chi-restraints excluded: chain X residue 66 ILE Chi-restraints excluded: chain X residue 77 ASP Chi-restraints excluded: chain X residue 83 VAL Chi-restraints excluded: chain X residue 90 GLU Chi-restraints excluded: chain X residue 100 THR Chi-restraints excluded: chain Z residue 12 ASN Chi-restraints excluded: chain Z residue 38 VAL Chi-restraints excluded: chain Z residue 49 VAL Chi-restraints excluded: chain 1 residue 4 VAL Chi-restraints excluded: chain 1 residue 45 ASN Chi-restraints excluded: chain 2 residue 5 THR Chi-restraints excluded: chain 2 residue 23 ARG Chi-restraints excluded: chain 2 residue 27 GLU Chi-restraints excluded: chain 2 residue 53 GLU Chi-restraints excluded: chain 3 residue 7 THR Chi-restraints excluded: chain 3 residue 28 LEU Chi-restraints excluded: chain 3 residue 34 SER Chi-restraints excluded: chain 3 residue 38 GLU Chi-restraints excluded: chain 5 residue 37 ARG Chi-restraints excluded: chain 5 residue 51 LEU Chi-restraints excluded: chain 6 residue 7 VAL Chi-restraints excluded: chain 6 residue 13 LEU Chi-restraints excluded: chain 6 residue 34 ASP Chi-restraints excluded: chain 6 residue 38 ILE Chi-restraints excluded: chain 6 residue 39 LYS Chi-restraints excluded: chain 7 residue 46 THR Chi-restraints excluded: chain 8 residue 23 VAL Chi-restraints excluded: chain 8 residue 33 LEU Chi-restraints excluded: chain 4 residue 15 GLN Chi-restraints excluded: chain d residue 12 LEU Chi-restraints excluded: chain d residue 20 SER Chi-restraints excluded: chain d residue 75 VAL Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain d residue 137 ILE Chi-restraints excluded: chain d residue 139 SER Chi-restraints excluded: chain d residue 163 SER Chi-restraints excluded: chain d residue 191 THR Chi-restraints excluded: chain d residue 198 VAL Chi-restraints excluded: chain e residue 5 THR Chi-restraints excluded: chain e residue 91 SER Chi-restraints excluded: chain e residue 133 SER Chi-restraints excluded: chain e residue 139 ASP Chi-restraints excluded: chain e residue 186 ILE Chi-restraints excluded: chain e residue 200 SER Chi-restraints excluded: chain f residue 37 ILE Chi-restraints excluded: chain f residue 42 SER Chi-restraints excluded: chain f residue 62 VAL Chi-restraints excluded: chain f residue 77 LYS Chi-restraints excluded: chain f residue 91 GLU Chi-restraints excluded: chain f residue 173 GLN Chi-restraints excluded: chain f residue 196 LYS Chi-restraints excluded: chain g residue 10 LEU Chi-restraints excluded: chain g residue 13 THR Chi-restraints excluded: chain g residue 18 THR Chi-restraints excluded: chain g residue 22 SER Chi-restraints excluded: chain g residue 38 ASP Chi-restraints excluded: chain g residue 43 TRP Chi-restraints excluded: chain g residue 65 VAL Chi-restraints excluded: chain h residue 4 LYS Chi-restraints excluded: chain h residue 56 THR Chi-restraints excluded: chain h residue 66 LEU Chi-restraints excluded: chain h residue 84 THR Chi-restraints excluded: chain h residue 89 VAL Chi-restraints excluded: chain h residue 110 GLN Chi-restraints excluded: chain h residue 143 LYS Chi-restraints excluded: chain i residue 4 THR Chi-restraints excluded: chain i residue 25 VAL Chi-restraints excluded: chain i residue 51 THR Chi-restraints excluded: chain i residue 81 SER Chi-restraints excluded: chain i residue 115 ASP Chi-restraints excluded: chain j residue 28 THR Chi-restraints excluded: chain j residue 42 VAL Chi-restraints excluded: chain j residue 88 ASP Chi-restraints excluded: chain j residue 147 TYR Chi-restraints excluded: chain k residue 25 ILE Chi-restraints excluded: chain k residue 26 VAL Chi-restraints excluded: chain k residue 36 VAL Chi-restraints excluded: chain k residue 40 VAL Chi-restraints excluded: chain k residue 80 THR Chi-restraints excluded: chain l residue 25 VAL Chi-restraints excluded: chain l residue 37 ASN Chi-restraints excluded: chain l residue 67 SER Chi-restraints excluded: chain l residue 91 VAL Chi-restraints excluded: chain l residue 92 ASP Chi-restraints excluded: chain l residue 110 GLN Chi-restraints excluded: chain l residue 114 LEU Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain m residue 9 ARG Chi-restraints excluded: chain m residue 35 THR Chi-restraints excluded: chain m residue 63 VAL Chi-restraints excluded: chain m residue 64 THR Chi-restraints excluded: chain m residue 70 GLU Chi-restraints excluded: chain m residue 79 MET Chi-restraints excluded: chain m residue 104 THR Chi-restraints excluded: chain m residue 107 VAL Chi-restraints excluded: chain m residue 109 ASN Chi-restraints excluded: chain n residue 41 LYS Chi-restraints excluded: chain n residue 45 THR Chi-restraints excluded: chain n residue 46 LYS Chi-restraints excluded: chain n residue 49 THR Chi-restraints excluded: chain n residue 50 ASP Chi-restraints excluded: chain n residue 108 ARG Chi-restraints excluded: chain o residue 23 ARG Chi-restraints excluded: chain o residue 48 LEU Chi-restraints excluded: chain o residue 55 SER Chi-restraints excluded: chain o residue 60 LEU Chi-restraints excluded: chain o residue 62 ASN Chi-restraints excluded: chain o residue 66 VAL Chi-restraints excluded: chain p residue 44 LYS Chi-restraints excluded: chain p residue 57 LEU Chi-restraints excluded: chain p residue 73 VAL Chi-restraints excluded: chain p residue 82 ILE Chi-restraints excluded: chain q residue 21 ILE Chi-restraints excluded: chain q residue 48 LEU Chi-restraints excluded: chain q residue 86 LEU Chi-restraints excluded: chain q residue 92 THR Chi-restraints excluded: chain r residue 65 ASN Chi-restraints excluded: chain r residue 72 ASP Chi-restraints excluded: chain r residue 95 GLU Chi-restraints excluded: chain s residue 34 ASP Chi-restraints excluded: chain t residue 14 HIS Chi-restraints excluded: chain t residue 21 VAL Chi-restraints excluded: chain t residue 30 VAL Chi-restraints excluded: chain t residue 45 ILE Chi-restraints excluded: chain t residue 79 THR Chi-restraints excluded: chain u residue 45 ASP Chi-restraints excluded: chain c residue 100 MET Chi-restraints excluded: chain c residue 131 LYS Chi-restraints excluded: chain c residue 135 LEU Chi-restraints excluded: chain c residue 153 ASP Chi-restraints excluded: chain c residue 163 VAL Chi-restraints excluded: chain c residue 166 THR Chi-restraints excluded: chain c residue 169 GLU Chi-restraints excluded: chain c residue 192 ASP Chi-restraints excluded: chain c residue 197 ASP Chi-restraints excluded: chain w residue 5 VAL Chi-restraints excluded: chain w residue 7 THR Chi-restraints excluded: chain w residue 92 ILE Chi-restraints excluded: chain w residue 109 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 987 random chunks: chunk 865 optimal weight: 7.9990 chunk 911 optimal weight: 0.2980 chunk 831 optimal weight: 8.9990 chunk 886 optimal weight: 20.0000 chunk 533 optimal weight: 10.0000 chunk 386 optimal weight: 20.0000 chunk 696 optimal weight: 20.0000 chunk 272 optimal weight: 7.9990 chunk 801 optimal weight: 10.0000 chunk 838 optimal weight: 5.9990 chunk 883 optimal weight: 4.9990 overall best weight: 5.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 99 GLN F 172 ASN H 58 ASN R 56 ASN V 66 GLN W 27 ASN Z 79 ASN ** 1 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 36 GLN 4 15 GLN ** d 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 107 ASN e 121 ASN ** h 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 84 GLN q 107 ASN ** c 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 moved from start: 0.1055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 154936 Z= 0.245 Angle : 0.591 9.825 232436 Z= 0.307 Chirality : 0.036 0.324 29741 Planarity : 0.005 0.100 12205 Dihedral : 24.143 179.996 79388 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 5.28 % Allowed : 31.91 % Favored : 62.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.12), residues: 5343 helix: 1.45 (0.12), residues: 1819 sheet: -0.06 (0.16), residues: 1058 loop : -0.49 (0.12), residues: 2466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP w 96 HIS 0.006 0.001 HIS H 146 PHE 0.015 0.001 PHE t 74 TYR 0.024 0.001 TYR e 71 ARG 0.019 0.000 ARG s 52 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10686 Ramachandran restraints generated. 5343 Oldfield, 0 Emsley, 5343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10686 Ramachandran restraints generated. 5343 Oldfield, 0 Emsley, 5343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 807 residues out of total 4467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 236 poor density : 571 time to evaluate : 5.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 188 ARG cc_start: 0.8965 (OUTLIER) cc_final: 0.8071 (mtp85) REVERT: E 211 ARG cc_start: 0.9284 (OUTLIER) cc_final: 0.8401 (mtm180) REVERT: E 273 ARG cc_start: 0.7617 (OUTLIER) cc_final: 0.6852 (mtm-85) REVERT: F 69 GLN cc_start: 0.9131 (OUTLIER) cc_final: 0.8765 (mt0) REVERT: F 86 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.9114 (mt) REVERT: H 13 GLN cc_start: 0.8409 (tp-100) cc_final: 0.8144 (tp-100) REVERT: R 24 ARG cc_start: 0.8896 (OUTLIER) cc_final: 0.8589 (ptp90) REVERT: R 71 ARG cc_start: 0.7477 (OUTLIER) cc_final: 0.6747 (ttt-90) REVERT: R 93 LYS cc_start: 0.8595 (tppp) cc_final: 0.8392 (ttmm) REVERT: S 93 ARG cc_start: 0.9404 (OUTLIER) cc_final: 0.8094 (mtm-85) REVERT: T 28 ARG cc_start: 0.9068 (OUTLIER) cc_final: 0.8688 (mtt180) REVERT: T 59 LYS cc_start: 0.9244 (OUTLIER) cc_final: 0.8973 (ttmt) REVERT: T 120 ASP cc_start: 0.8568 (t0) cc_final: 0.8234 (t0) REVERT: W 70 ARG cc_start: 0.7614 (OUTLIER) cc_final: 0.7385 (ptt90) REVERT: 2 23 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.7678 (ttp-170) REVERT: 6 22 ASN cc_start: 0.8715 (m-40) cc_final: 0.8334 (t0) REVERT: 6 29 ARG cc_start: 0.8139 (ptm-80) cc_final: 0.7852 (ptt90) REVERT: 6 39 LYS cc_start: 0.8605 (OUTLIER) cc_final: 0.8326 (ttpp) REVERT: 4 1 MET cc_start: 0.3842 (tpt) cc_final: 0.3601 (tpt) REVERT: 4 15 GLN cc_start: 0.7806 (OUTLIER) cc_final: 0.7393 (mm-40) REVERT: d 12 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8672 (tp) REVERT: e 98 TYR cc_start: 0.9098 (t80) cc_final: 0.8812 (t80) REVERT: e 200 SER cc_start: 0.8810 (OUTLIER) cc_final: 0.8562 (t) REVERT: f 70 MET cc_start: 0.8157 (tpp) cc_final: 0.7486 (mmt) REVERT: f 91 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.7456 (tm-30) REVERT: g 43 TRP cc_start: 0.8549 (OUTLIER) cc_final: 0.7912 (p-90) REVERT: g 64 ASP cc_start: 0.8313 (OUTLIER) cc_final: 0.8099 (m-30) REVERT: h 66 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8827 (tt) REVERT: h 110 GLN cc_start: 0.8777 (OUTLIER) cc_final: 0.8384 (mp10) REVERT: h 126 ASP cc_start: 0.8773 (m-30) cc_final: 0.8541 (m-30) REVERT: h 143 LYS cc_start: 0.9296 (OUTLIER) cc_final: 0.8917 (ttpt) REVERT: j 66 GLN cc_start: 0.8515 (tm-30) cc_final: 0.8120 (tm-30) REVERT: j 147 TYR cc_start: 0.7880 (OUTLIER) cc_final: 0.7276 (p90) REVERT: k 80 THR cc_start: 0.7999 (OUTLIER) cc_final: 0.7583 (p) REVERT: l 114 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8853 (mm) REVERT: m 70 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7601 (mt-10) REVERT: n 41 LYS cc_start: 0.8329 (OUTLIER) cc_final: 0.7937 (ptmm) REVERT: n 108 ARG cc_start: 0.9345 (OUTLIER) cc_final: 0.7854 (mmm160) REVERT: o 11 GLU cc_start: 0.8768 (mp0) cc_final: 0.8269 (mp0) REVERT: q 96 LYS cc_start: 0.8953 (tptm) cc_final: 0.8696 (tptm) REVERT: q 99 LYS cc_start: 0.9039 (tppp) cc_final: 0.8580 (mmpt) REVERT: r 95 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.8290 (pt0) REVERT: t 19 VAL cc_start: 0.8022 (p) cc_final: 0.7698 (t) REVERT: t 22 GLN cc_start: 0.8044 (mm-40) cc_final: 0.7843 (mm-40) REVERT: t 73 GLU cc_start: 0.8569 (mm-30) cc_final: 0.8187 (mm-30) REVERT: u 43 ASP cc_start: 0.8587 (OUTLIER) cc_final: 0.7964 (p0) REVERT: u 59 ASP cc_start: 0.8137 (p0) cc_final: 0.7827 (p0) REVERT: c 74 LYS cc_start: 0.8439 (ptmt) cc_final: 0.8144 (mmtp) REVERT: c 100 MET cc_start: 0.8379 (OUTLIER) cc_final: 0.8003 (tpp) REVERT: c 135 LEU cc_start: 0.5758 (OUTLIER) cc_final: 0.5446 (pp) REVERT: w 109 ARG cc_start: 0.5057 (OUTLIER) cc_final: 0.4653 (ttp-110) outliers start: 236 outliers final: 171 residues processed: 745 average time/residue: 1.9061 time to fit residues: 2098.4187 Evaluate side-chains 757 residues out of total 4467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 553 time to evaluate : 5.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 188 ARG Chi-restraints excluded: chain E residue 211 ARG Chi-restraints excluded: chain E residue 273 ARG Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 69 GLN Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 191 VAL Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 63 LYS Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain H residue 34 GLN Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 151 ASP Chi-restraints excluded: chain H residue 153 ILE Chi-restraints excluded: chain H residue 162 THR Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 17 VAL Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 22 ASP Chi-restraints excluded: chain M residue 129 ASP Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 81 GLU Chi-restraints excluded: chain N residue 90 ASP Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 15 GLU Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain O residue 125 THR Chi-restraints excluded: chain O residue 132 SER Chi-restraints excluded: chain O residue 135 GLU Chi-restraints excluded: chain O residue 145 THR Chi-restraints excluded: chain Q residue 37 THR Chi-restraints excluded: chain Q residue 74 ASP Chi-restraints excluded: chain Q residue 101 GLU Chi-restraints excluded: chain Q residue 116 VAL Chi-restraints excluded: chain R residue 24 ARG Chi-restraints excluded: chain R residue 71 ARG Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 18 THR Chi-restraints excluded: chain S residue 69 VAL Chi-restraints excluded: chain S residue 93 ARG Chi-restraints excluded: chain S residue 101 GLU Chi-restraints excluded: chain T residue 28 ARG Chi-restraints excluded: chain T residue 59 LYS Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain U residue 47 ASN Chi-restraints excluded: chain U residue 96 VAL Chi-restraints excluded: chain V residue 11 THR Chi-restraints excluded: chain V residue 88 THR Chi-restraints excluded: chain W residue 9 ASP Chi-restraints excluded: chain W residue 10 ILE Chi-restraints excluded: chain W residue 40 THR Chi-restraints excluded: chain W residue 70 ARG Chi-restraints excluded: chain X residue 3 VAL Chi-restraints excluded: chain X residue 24 LEU Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain X residue 59 ILE Chi-restraints excluded: chain X residue 66 ILE Chi-restraints excluded: chain X residue 77 ASP Chi-restraints excluded: chain X residue 83 VAL Chi-restraints excluded: chain X residue 90 GLU Chi-restraints excluded: chain X residue 100 THR Chi-restraints excluded: chain Z residue 12 ASN Chi-restraints excluded: chain Z residue 38 VAL Chi-restraints excluded: chain Z residue 49 VAL Chi-restraints excluded: chain 1 residue 45 ASN Chi-restraints excluded: chain 2 residue 5 THR Chi-restraints excluded: chain 2 residue 23 ARG Chi-restraints excluded: chain 2 residue 27 GLU Chi-restraints excluded: chain 2 residue 53 GLU Chi-restraints excluded: chain 3 residue 7 THR Chi-restraints excluded: chain 3 residue 28 LEU Chi-restraints excluded: chain 3 residue 34 SER Chi-restraints excluded: chain 3 residue 38 GLU Chi-restraints excluded: chain 5 residue 13 THR Chi-restraints excluded: chain 5 residue 32 VAL Chi-restraints excluded: chain 5 residue 37 ARG Chi-restraints excluded: chain 5 residue 51 LEU Chi-restraints excluded: chain 6 residue 7 VAL Chi-restraints excluded: chain 6 residue 34 ASP Chi-restraints excluded: chain 6 residue 38 ILE Chi-restraints excluded: chain 6 residue 39 LYS Chi-restraints excluded: chain 7 residue 46 THR Chi-restraints excluded: chain 8 residue 23 VAL Chi-restraints excluded: chain 4 residue 15 GLN Chi-restraints excluded: chain d residue 12 LEU Chi-restraints excluded: chain d residue 20 SER Chi-restraints excluded: chain d residue 75 VAL Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain d residue 137 ILE Chi-restraints excluded: chain d residue 139 SER Chi-restraints excluded: chain d residue 198 VAL Chi-restraints excluded: chain e residue 5 THR Chi-restraints excluded: chain e residue 91 SER Chi-restraints excluded: chain e residue 133 SER Chi-restraints excluded: chain e residue 139 ASP Chi-restraints excluded: chain e residue 186 ILE Chi-restraints excluded: chain e residue 198 LEU Chi-restraints excluded: chain e residue 200 SER Chi-restraints excluded: chain f residue 37 ILE Chi-restraints excluded: chain f residue 42 SER Chi-restraints excluded: chain f residue 62 VAL Chi-restraints excluded: chain f residue 91 GLU Chi-restraints excluded: chain f residue 96 PHE Chi-restraints excluded: chain f residue 173 GLN Chi-restraints excluded: chain f residue 196 LYS Chi-restraints excluded: chain g residue 10 LEU Chi-restraints excluded: chain g residue 13 THR Chi-restraints excluded: chain g residue 18 THR Chi-restraints excluded: chain g residue 22 SER Chi-restraints excluded: chain g residue 38 ASP Chi-restraints excluded: chain g residue 43 TRP Chi-restraints excluded: chain g residue 64 ASP Chi-restraints excluded: chain g residue 65 VAL Chi-restraints excluded: chain h residue 4 LYS Chi-restraints excluded: chain h residue 56 THR Chi-restraints excluded: chain h residue 66 LEU Chi-restraints excluded: chain h residue 84 THR Chi-restraints excluded: chain h residue 110 GLN Chi-restraints excluded: chain h residue 143 LYS Chi-restraints excluded: chain i residue 4 THR Chi-restraints excluded: chain i residue 25 VAL Chi-restraints excluded: chain i residue 51 THR Chi-restraints excluded: chain i residue 81 SER Chi-restraints excluded: chain i residue 115 ASP Chi-restraints excluded: chain j residue 28 THR Chi-restraints excluded: chain j residue 42 VAL Chi-restraints excluded: chain j residue 88 ASP Chi-restraints excluded: chain j residue 147 TYR Chi-restraints excluded: chain k residue 25 ILE Chi-restraints excluded: chain k residue 26 VAL Chi-restraints excluded: chain k residue 36 VAL Chi-restraints excluded: chain k residue 40 VAL Chi-restraints excluded: chain k residue 54 SER Chi-restraints excluded: chain k residue 80 THR Chi-restraints excluded: chain l residue 25 VAL Chi-restraints excluded: chain l residue 37 ASN Chi-restraints excluded: chain l residue 67 SER Chi-restraints excluded: chain l residue 84 GLN Chi-restraints excluded: chain l residue 91 VAL Chi-restraints excluded: chain l residue 92 ASP Chi-restraints excluded: chain l residue 110 GLN Chi-restraints excluded: chain l residue 114 LEU Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain m residue 9 ARG Chi-restraints excluded: chain m residue 35 THR Chi-restraints excluded: chain m residue 63 VAL Chi-restraints excluded: chain m residue 64 THR Chi-restraints excluded: chain m residue 70 GLU Chi-restraints excluded: chain m residue 79 MET Chi-restraints excluded: chain m residue 104 THR Chi-restraints excluded: chain m residue 107 VAL Chi-restraints excluded: chain m residue 109 ASN Chi-restraints excluded: chain n residue 41 LYS Chi-restraints excluded: chain n residue 45 THR Chi-restraints excluded: chain n residue 46 LYS Chi-restraints excluded: chain n residue 49 THR Chi-restraints excluded: chain n residue 108 ARG Chi-restraints excluded: chain o residue 23 ARG Chi-restraints excluded: chain o residue 48 LEU Chi-restraints excluded: chain o residue 55 SER Chi-restraints excluded: chain o residue 60 LEU Chi-restraints excluded: chain o residue 66 VAL Chi-restraints excluded: chain p residue 44 LYS Chi-restraints excluded: chain p residue 73 VAL Chi-restraints excluded: chain p residue 82 ILE Chi-restraints excluded: chain q residue 21 ILE Chi-restraints excluded: chain q residue 48 LEU Chi-restraints excluded: chain q residue 86 LEU Chi-restraints excluded: chain q residue 92 THR Chi-restraints excluded: chain r residue 65 ASN Chi-restraints excluded: chain r residue 72 ASP Chi-restraints excluded: chain r residue 95 GLU Chi-restraints excluded: chain s residue 34 ASP Chi-restraints excluded: chain t residue 14 HIS Chi-restraints excluded: chain t residue 30 VAL Chi-restraints excluded: chain t residue 45 ILE Chi-restraints excluded: chain t residue 79 THR Chi-restraints excluded: chain u residue 43 ASP Chi-restraints excluded: chain c residue 100 MET Chi-restraints excluded: chain c residue 135 LEU Chi-restraints excluded: chain c residue 153 ASP Chi-restraints excluded: chain c residue 163 VAL Chi-restraints excluded: chain c residue 169 GLU Chi-restraints excluded: chain c residue 192 ASP Chi-restraints excluded: chain c residue 197 ASP Chi-restraints excluded: chain w residue 5 VAL Chi-restraints excluded: chain w residue 7 THR Chi-restraints excluded: chain w residue 92 ILE Chi-restraints excluded: chain w residue 109 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 987 random chunks: chunk 582 optimal weight: 30.0000 chunk 937 optimal weight: 10.0000 chunk 572 optimal weight: 10.0000 chunk 444 optimal weight: 20.0000 chunk 651 optimal weight: 20.0000 chunk 983 optimal weight: 10.0000 chunk 905 optimal weight: 20.0000 chunk 783 optimal weight: 20.0000 chunk 81 optimal weight: 7.9990 chunk 604 optimal weight: 20.0000 chunk 480 optimal weight: 20.0000 overall best weight: 11.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 99 GLN F 172 ASN H 70 GLN R 56 ASN V 66 GLN W 27 ASN W 58 ASN Z 79 ASN ** 1 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 15 GLN ** d 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 107 ASN ** f 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 47 GLN l 84 GLN q 107 ASN ** t 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8869 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.091 154936 Z= 0.471 Angle : 0.681 12.281 232436 Z= 0.349 Chirality : 0.043 0.332 29741 Planarity : 0.005 0.106 12205 Dihedral : 24.109 179.881 79388 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 5.17 % Allowed : 31.91 % Favored : 62.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.11), residues: 5343 helix: 1.28 (0.12), residues: 1822 sheet: -0.12 (0.16), residues: 1084 loop : -0.61 (0.12), residues: 2437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP w 96 HIS 0.007 0.001 HIS k 15 PHE 0.027 0.002 PHE c 30 TYR 0.028 0.002 TYR e 71 ARG 0.020 0.001 ARG s 52 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10686 Ramachandran restraints generated. 5343 Oldfield, 0 Emsley, 5343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10686 Ramachandran restraints generated. 5343 Oldfield, 0 Emsley, 5343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 789 residues out of total 4467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 231 poor density : 558 time to evaluate : 5.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 188 ARG cc_start: 0.8982 (OUTLIER) cc_final: 0.8077 (mtp85) REVERT: E 211 ARG cc_start: 0.9328 (OUTLIER) cc_final: 0.8493 (mtt180) REVERT: E 273 ARG cc_start: 0.7584 (OUTLIER) cc_final: 0.6832 (mtm-85) REVERT: F 69 GLN cc_start: 0.9205 (OUTLIER) cc_final: 0.8806 (mt0) REVERT: H 13 GLN cc_start: 0.8399 (tp-100) cc_final: 0.8139 (tp-100) REVERT: R 24 ARG cc_start: 0.8934 (OUTLIER) cc_final: 0.8591 (ptp90) REVERT: R 71 ARG cc_start: 0.7621 (OUTLIER) cc_final: 0.6948 (ttt-90) REVERT: R 93 LYS cc_start: 0.8599 (tppp) cc_final: 0.8393 (ttmm) REVERT: S 93 ARG cc_start: 0.9453 (OUTLIER) cc_final: 0.7996 (mtm-85) REVERT: T 28 ARG cc_start: 0.9112 (OUTLIER) cc_final: 0.8737 (mtt180) REVERT: T 59 LYS cc_start: 0.9226 (OUTLIER) cc_final: 0.8961 (ttmt) REVERT: T 120 ASP cc_start: 0.8598 (t0) cc_final: 0.8253 (t0) REVERT: W 70 ARG cc_start: 0.7632 (OUTLIER) cc_final: 0.7382 (ptt90) REVERT: 2 23 ARG cc_start: 0.8336 (OUTLIER) cc_final: 0.7673 (ttp-170) REVERT: 6 29 ARG cc_start: 0.8182 (ptm-80) cc_final: 0.7887 (ptt90) REVERT: 6 39 LYS cc_start: 0.8598 (OUTLIER) cc_final: 0.8211 (ttpp) REVERT: 4 15 GLN cc_start: 0.7822 (OUTLIER) cc_final: 0.7411 (mm-40) REVERT: 4 33 ILE cc_start: 0.6733 (mm) cc_final: 0.6497 (mm) REVERT: d 12 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8712 (tp) REVERT: e 200 SER cc_start: 0.8844 (OUTLIER) cc_final: 0.8593 (t) REVERT: f 70 MET cc_start: 0.8107 (tpp) cc_final: 0.7470 (mmt) REVERT: f 91 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7581 (tt0) REVERT: g 43 TRP cc_start: 0.8534 (OUTLIER) cc_final: 0.7866 (p-90) REVERT: g 64 ASP cc_start: 0.8335 (OUTLIER) cc_final: 0.8122 (m-30) REVERT: h 66 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8837 (tt) REVERT: h 126 ASP cc_start: 0.8796 (m-30) cc_final: 0.8561 (m-30) REVERT: h 143 LYS cc_start: 0.9302 (OUTLIER) cc_final: 0.8923 (ttpt) REVERT: j 61 ASN cc_start: 0.8547 (t0) cc_final: 0.8333 (t0) REVERT: j 66 GLN cc_start: 0.8522 (tm-30) cc_final: 0.8119 (tm-30) REVERT: j 147 TYR cc_start: 0.7993 (OUTLIER) cc_final: 0.7366 (p90) REVERT: k 80 THR cc_start: 0.7991 (OUTLIER) cc_final: 0.7557 (p) REVERT: l 114 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8909 (mm) REVERT: m 70 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7664 (mt-10) REVERT: n 41 LYS cc_start: 0.8360 (OUTLIER) cc_final: 0.7990 (ptmm) REVERT: n 108 ARG cc_start: 0.9388 (OUTLIER) cc_final: 0.7847 (mmm160) REVERT: o 11 GLU cc_start: 0.8739 (mp0) cc_final: 0.8257 (mp0) REVERT: q 96 LYS cc_start: 0.8996 (tptm) cc_final: 0.8728 (tptm) REVERT: q 99 LYS cc_start: 0.9026 (tppp) cc_final: 0.8572 (mmpt) REVERT: q 102 LYS cc_start: 0.8927 (tttp) cc_final: 0.8394 (tttm) REVERT: t 22 GLN cc_start: 0.8057 (mm-40) cc_final: 0.7826 (mm-40) REVERT: t 23 ASN cc_start: 0.8474 (p0) cc_final: 0.8045 (OUTLIER) REVERT: t 73 GLU cc_start: 0.8637 (mm-30) cc_final: 0.8354 (mm-30) REVERT: u 43 ASP cc_start: 0.8607 (OUTLIER) cc_final: 0.8004 (p0) REVERT: u 59 ASP cc_start: 0.8278 (p0) cc_final: 0.7983 (p0) REVERT: c 74 LYS cc_start: 0.8484 (ptmt) cc_final: 0.8214 (mmtp) REVERT: c 100 MET cc_start: 0.8406 (OUTLIER) cc_final: 0.8014 (tpp) REVERT: c 120 MET cc_start: 0.4192 (tmm) cc_final: 0.3515 (pp-130) REVERT: c 135 LEU cc_start: 0.5815 (OUTLIER) cc_final: 0.5476 (pp) REVERT: c 153 ASP cc_start: 0.8897 (OUTLIER) cc_final: 0.8061 (p0) REVERT: w 109 ARG cc_start: 0.5157 (OUTLIER) cc_final: 0.4738 (ttp-110) outliers start: 231 outliers final: 171 residues processed: 732 average time/residue: 1.9188 time to fit residues: 2086.7357 Evaluate side-chains 751 residues out of total 4467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 550 time to evaluate : 5.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 188 ARG Chi-restraints excluded: chain E residue 211 ARG Chi-restraints excluded: chain E residue 273 ARG Chi-restraints excluded: chain F residue 69 GLN Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 191 VAL Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 63 LYS Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain H residue 34 GLN Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 151 ASP Chi-restraints excluded: chain H residue 153 ILE Chi-restraints excluded: chain H residue 162 THR Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 17 VAL Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 22 ASP Chi-restraints excluded: chain M residue 129 ASP Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 81 GLU Chi-restraints excluded: chain N residue 90 ASP Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 15 GLU Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain O residue 125 THR Chi-restraints excluded: chain O residue 132 SER Chi-restraints excluded: chain O residue 135 GLU Chi-restraints excluded: chain O residue 145 THR Chi-restraints excluded: chain Q residue 37 THR Chi-restraints excluded: chain Q residue 74 ASP Chi-restraints excluded: chain Q residue 101 GLU Chi-restraints excluded: chain Q residue 116 VAL Chi-restraints excluded: chain R residue 24 ARG Chi-restraints excluded: chain R residue 71 ARG Chi-restraints excluded: chain R residue 88 ILE Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 18 THR Chi-restraints excluded: chain S residue 69 VAL Chi-restraints excluded: chain S residue 93 ARG Chi-restraints excluded: chain S residue 101 GLU Chi-restraints excluded: chain T residue 16 THR Chi-restraints excluded: chain T residue 28 ARG Chi-restraints excluded: chain T residue 59 LYS Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain U residue 47 ASN Chi-restraints excluded: chain U residue 96 VAL Chi-restraints excluded: chain V residue 11 THR Chi-restraints excluded: chain V residue 88 THR Chi-restraints excluded: chain W residue 9 ASP Chi-restraints excluded: chain W residue 10 ILE Chi-restraints excluded: chain W residue 40 THR Chi-restraints excluded: chain W residue 70 ARG Chi-restraints excluded: chain X residue 3 VAL Chi-restraints excluded: chain X residue 24 LEU Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain X residue 66 ILE Chi-restraints excluded: chain X residue 77 ASP Chi-restraints excluded: chain X residue 83 VAL Chi-restraints excluded: chain X residue 90 GLU Chi-restraints excluded: chain X residue 100 THR Chi-restraints excluded: chain Z residue 12 ASN Chi-restraints excluded: chain Z residue 38 VAL Chi-restraints excluded: chain Z residue 49 VAL Chi-restraints excluded: chain 1 residue 45 ASN Chi-restraints excluded: chain 2 residue 5 THR Chi-restraints excluded: chain 2 residue 14 THR Chi-restraints excluded: chain 2 residue 23 ARG Chi-restraints excluded: chain 2 residue 27 GLU Chi-restraints excluded: chain 2 residue 53 GLU Chi-restraints excluded: chain 3 residue 7 THR Chi-restraints excluded: chain 3 residue 28 LEU Chi-restraints excluded: chain 3 residue 34 SER Chi-restraints excluded: chain 3 residue 38 GLU Chi-restraints excluded: chain 5 residue 13 THR Chi-restraints excluded: chain 5 residue 32 VAL Chi-restraints excluded: chain 5 residue 37 ARG Chi-restraints excluded: chain 5 residue 51 LEU Chi-restraints excluded: chain 6 residue 7 VAL Chi-restraints excluded: chain 6 residue 13 LEU Chi-restraints excluded: chain 6 residue 34 ASP Chi-restraints excluded: chain 6 residue 38 ILE Chi-restraints excluded: chain 6 residue 39 LYS Chi-restraints excluded: chain 7 residue 46 THR Chi-restraints excluded: chain 8 residue 23 VAL Chi-restraints excluded: chain 4 residue 15 GLN Chi-restraints excluded: chain d residue 12 LEU Chi-restraints excluded: chain d residue 20 SER Chi-restraints excluded: chain d residue 75 VAL Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain d residue 139 SER Chi-restraints excluded: chain d residue 198 VAL Chi-restraints excluded: chain e residue 5 THR Chi-restraints excluded: chain e residue 91 SER Chi-restraints excluded: chain e residue 133 SER Chi-restraints excluded: chain e residue 139 ASP Chi-restraints excluded: chain e residue 186 ILE Chi-restraints excluded: chain e residue 200 SER Chi-restraints excluded: chain f residue 37 ILE Chi-restraints excluded: chain f residue 41 VAL Chi-restraints excluded: chain f residue 42 SER Chi-restraints excluded: chain f residue 62 VAL Chi-restraints excluded: chain f residue 91 GLU Chi-restraints excluded: chain f residue 173 GLN Chi-restraints excluded: chain g residue 10 LEU Chi-restraints excluded: chain g residue 13 THR Chi-restraints excluded: chain g residue 18 THR Chi-restraints excluded: chain g residue 22 SER Chi-restraints excluded: chain g residue 27 LEU Chi-restraints excluded: chain g residue 38 ASP Chi-restraints excluded: chain g residue 43 TRP Chi-restraints excluded: chain g residue 64 ASP Chi-restraints excluded: chain g residue 65 VAL Chi-restraints excluded: chain h residue 56 THR Chi-restraints excluded: chain h residue 66 LEU Chi-restraints excluded: chain h residue 84 THR Chi-restraints excluded: chain h residue 110 GLN Chi-restraints excluded: chain h residue 143 LYS Chi-restraints excluded: chain i residue 4 THR Chi-restraints excluded: chain i residue 25 VAL Chi-restraints excluded: chain i residue 51 THR Chi-restraints excluded: chain i residue 81 SER Chi-restraints excluded: chain i residue 115 ASP Chi-restraints excluded: chain j residue 28 THR Chi-restraints excluded: chain j residue 42 VAL Chi-restraints excluded: chain j residue 88 ASP Chi-restraints excluded: chain j residue 147 TYR Chi-restraints excluded: chain k residue 25 ILE Chi-restraints excluded: chain k residue 26 VAL Chi-restraints excluded: chain k residue 36 VAL Chi-restraints excluded: chain k residue 40 VAL Chi-restraints excluded: chain k residue 54 SER Chi-restraints excluded: chain k residue 80 THR Chi-restraints excluded: chain l residue 25 VAL Chi-restraints excluded: chain l residue 37 ASN Chi-restraints excluded: chain l residue 67 SER Chi-restraints excluded: chain l residue 91 VAL Chi-restraints excluded: chain l residue 92 ASP Chi-restraints excluded: chain l residue 110 GLN Chi-restraints excluded: chain l residue 114 LEU Chi-restraints excluded: chain m residue 9 ARG Chi-restraints excluded: chain m residue 35 THR Chi-restraints excluded: chain m residue 63 VAL Chi-restraints excluded: chain m residue 64 THR Chi-restraints excluded: chain m residue 70 GLU Chi-restraints excluded: chain m residue 79 MET Chi-restraints excluded: chain m residue 104 THR Chi-restraints excluded: chain m residue 107 VAL Chi-restraints excluded: chain m residue 109 ASN Chi-restraints excluded: chain n residue 41 LYS Chi-restraints excluded: chain n residue 45 THR Chi-restraints excluded: chain n residue 46 LYS Chi-restraints excluded: chain n residue 49 THR Chi-restraints excluded: chain n residue 108 ARG Chi-restraints excluded: chain o residue 23 ARG Chi-restraints excluded: chain o residue 48 LEU Chi-restraints excluded: chain o residue 55 SER Chi-restraints excluded: chain o residue 60 LEU Chi-restraints excluded: chain o residue 66 VAL Chi-restraints excluded: chain p residue 44 LYS Chi-restraints excluded: chain p residue 73 VAL Chi-restraints excluded: chain p residue 82 ILE Chi-restraints excluded: chain q residue 21 ILE Chi-restraints excluded: chain q residue 48 LEU Chi-restraints excluded: chain q residue 86 LEU Chi-restraints excluded: chain q residue 92 THR Chi-restraints excluded: chain r residue 65 ASN Chi-restraints excluded: chain r residue 70 ILE Chi-restraints excluded: chain r residue 72 ASP Chi-restraints excluded: chain s residue 34 ASP Chi-restraints excluded: chain t residue 14 HIS Chi-restraints excluded: chain t residue 27 THR Chi-restraints excluded: chain t residue 30 VAL Chi-restraints excluded: chain t residue 45 ILE Chi-restraints excluded: chain t residue 48 THR Chi-restraints excluded: chain t residue 79 THR Chi-restraints excluded: chain u residue 43 ASP Chi-restraints excluded: chain c residue 100 MET Chi-restraints excluded: chain c residue 135 LEU Chi-restraints excluded: chain c residue 153 ASP Chi-restraints excluded: chain c residue 163 VAL Chi-restraints excluded: chain c residue 169 GLU Chi-restraints excluded: chain c residue 192 ASP Chi-restraints excluded: chain c residue 197 ASP Chi-restraints excluded: chain w residue 5 VAL Chi-restraints excluded: chain w residue 7 THR Chi-restraints excluded: chain w residue 92 ILE Chi-restraints excluded: chain w residue 109 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 987 random chunks: chunk 621 optimal weight: 10.0000 chunk 834 optimal weight: 1.9990 chunk 239 optimal weight: 20.0000 chunk 721 optimal weight: 20.0000 chunk 115 optimal weight: 0.9990 chunk 217 optimal weight: 1.9990 chunk 784 optimal weight: 8.9990 chunk 328 optimal weight: 10.0000 chunk 805 optimal weight: 6.9990 chunk 99 optimal weight: 30.0000 chunk 144 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 99 GLN F 172 ASN G 68 GLN R 56 ASN V 66 GLN ** W 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 58 ASN Z 79 ASN ** 1 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 107 ASN g 78 GLN ** h 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 84 GLN q 107 ASN ** c 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.054380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.039729 restraints weight = 673719.447| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 1.37 r_work: 0.2715 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2629 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8889 moved from start: 0.1125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.256 154936 Z= 0.206 Angle : 0.591 13.105 232436 Z= 0.307 Chirality : 0.036 0.322 29741 Planarity : 0.005 0.105 12205 Dihedral : 24.182 179.823 79388 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 4.52 % Allowed : 32.65 % Favored : 62.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.11), residues: 5343 helix: 1.39 (0.12), residues: 1829 sheet: -0.10 (0.16), residues: 1059 loop : -0.52 (0.12), residues: 2455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP w 96 HIS 0.004 0.001 HIS k 15 PHE 0.015 0.001 PHE 2 30 TYR 0.025 0.001 TYR e 71 ARG 0.020 0.000 ARG s 52 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 35811.96 seconds wall clock time: 628 minutes 50.33 seconds (37730.33 seconds total)