Starting phenix.real_space_refine on Tue Feb 20 23:20:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zod_14846/02_2024/7zod_14846.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zod_14846/02_2024/7zod_14846.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zod_14846/02_2024/7zod_14846.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zod_14846/02_2024/7zod_14846.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zod_14846/02_2024/7zod_14846.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zod_14846/02_2024/7zod_14846.pdb" } resolution = 2.56 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.016 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 3096 5.49 5 S 75 5.16 5 C 44847 2.51 5 N 16908 2.21 5 O 25776 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "0 ARG 3": "NH1" <-> "NH2" Residue "0 ARG 11": "NH1" <-> "NH2" Residue "0 ARG 18": "NH1" <-> "NH2" Residue "0 ARG 37": "NH1" <-> "NH2" Residue "0 ARG 50": "NH1" <-> "NH2" Residue "0 ARG 57": "NH1" <-> "NH2" Residue "0 ARG 74": "NH1" <-> "NH2" Residue "1 GLU 5": "OE1" <-> "OE2" Residue "1 GLU 12": "OE1" <-> "OE2" Residue "1 GLU 13": "OE1" <-> "OE2" Residue "1 GLU 24": "OE1" <-> "OE2" Residue "1 ARG 29": "NH1" <-> "NH2" Residue "1 ARG 47": "NH1" <-> "NH2" Residue "1 ARG 52": "NH1" <-> "NH2" Residue "1 GLU 59": "OE1" <-> "OE2" Residue "2 ARG 11": "NH1" <-> "NH2" Residue "2 ARG 30": "NH1" <-> "NH2" Residue "2 ARG 45": "NH1" <-> "NH2" Residue "3 ARG 10": "NH1" <-> "NH2" Residue "3 ARG 16": "NH1" <-> "NH2" Residue "3 ARG 52": "NH1" <-> "NH2" Residue "4 GLU 35": "OE1" <-> "OE2" Residue "4 ARG 44": "NH1" <-> "NH2" Residue "4 GLU 51": "OE1" <-> "OE2" Residue "6 ARG 3": "NH1" <-> "NH2" Residue "6 ARG 12": "NH1" <-> "NH2" Residue "6 ARG 14": "NH1" <-> "NH2" Residue "6 ARG 19": "NH1" <-> "NH2" Residue "6 ARG 21": "NH1" <-> "NH2" Residue "6 ARG 33": "NH1" <-> "NH2" Residue "6 ARG 41": "NH1" <-> "NH2" Residue "7 ARG 13": "NH1" <-> "NH2" Residue "7 ARG 30": "NH1" <-> "NH2" Residue "7 ARG 40": "NH1" <-> "NH2" Residue "7 ARG 42": "NH1" <-> "NH2" Residue "8 ARG 24": "NH1" <-> "NH2" Residue "c GLU 23": "OE1" <-> "OE2" Residue "c ARG 52": "NH1" <-> "NH2" Residue "c ARG 63": "NH1" <-> "NH2" Residue "c ARG 80": "NH1" <-> "NH2" Residue "c GLU 82": "OE1" <-> "OE2" Residue "c ARG 133": "NH1" <-> "NH2" Residue "c GLU 145": "OE1" <-> "OE2" Residue "c ARG 167": "NH1" <-> "NH2" Residue "c ARG 177": "NH1" <-> "NH2" Residue "c ARG 182": "NH1" <-> "NH2" Residue "c ARG 189": "NH1" <-> "NH2" Residue "c GLU 199": "OE1" <-> "OE2" Residue "c ARG 203": "NH1" <-> "NH2" Residue "c ARG 212": "NH1" <-> "NH2" Residue "c GLU 236": "OE1" <-> "OE2" Residue "d ARG 13": "NH1" <-> "NH2" Residue "d GLU 30": "OE1" <-> "OE2" Residue "d ARG 33": "NH1" <-> "NH2" Residue "d ARG 59": "NH1" <-> "NH2" Residue "d GLU 64": "OE1" <-> "OE2" Residue "d ARG 77": "NH1" <-> "NH2" Residue "d ARG 83": "NH1" <-> "NH2" Residue "d GLU 86": "OE1" <-> "OE2" Residue "d GLU 89": "OE1" <-> "OE2" Residue "d ARG 169": "NH1" <-> "NH2" Residue "d ARG 184": "NH1" <-> "NH2" Residue "e GLU 16": "OE1" <-> "OE2" Residue "e ARG 21": "NH1" <-> "NH2" Residue "e ARG 44": "NH1" <-> "NH2" Residue "e ARG 49": "NH1" <-> "NH2" Residue "e GLU 51": "OE1" <-> "OE2" Residue "e ARG 61": "NH1" <-> "NH2" Residue "e ARG 67": "NH1" <-> "NH2" Residue "e ARG 88": "NH1" <-> "NH2" Residue "e ARG 102": "NH1" <-> "NH2" Residue "e GLU 111": "OE1" <-> "OE2" Residue "e GLU 122": "OE1" <-> "OE2" Residue "e GLU 127": "OE1" <-> "OE2" Residue "e GLU 144": "OE1" <-> "OE2" Residue "e GLU 155": "OE1" <-> "OE2" Residue "e ARG 162": "NH1" <-> "NH2" Residue "e ARG 170": "NH1" <-> "NH2" Residue "e GLU 197": "OE1" <-> "OE2" Residue "f ARG 71": "NH1" <-> "NH2" Residue "f ARG 80": "NH1" <-> "NH2" Residue "f ARG 92": "NH1" <-> "NH2" Residue "f GLU 94": "OE1" <-> "OE2" Residue "f GLU 98": "OE1" <-> "OE2" Residue "f GLU 101": "OE1" <-> "OE2" Residue "f ARG 102": "NH1" <-> "NH2" Residue "f ARG 110": "NH1" <-> "NH2" Residue "f ARG 112": "NH1" <-> "NH2" Residue "f ARG 115": "NH1" <-> "NH2" Residue "f ARG 133": "NH1" <-> "NH2" Residue "g ARG 3": "NH1" <-> "NH2" Residue "g GLU 32": "OE1" <-> "OE2" Residue "g GLU 81": "OE1" <-> "OE2" Residue "g GLU 124": "OE1" <-> "OE2" Residue "g GLU 130": "OE1" <-> "OE2" Residue "g ARG 153": "NH1" <-> "NH2" Residue "g ARG 163": "NH1" <-> "NH2" Residue "g ARG 170": "NH1" <-> "NH2" Residue "h ARG 27": "NH1" <-> "NH2" Residue "j GLU 9": "OE1" <-> "OE2" Residue "j ARG 13": "NH1" <-> "NH2" Residue "j ARG 37": "NH1" <-> "NH2" Residue "j GLU 91": "OE1" <-> "OE2" Residue "j ARG 96": "NH1" <-> "NH2" Residue "j GLU 102": "OE1" <-> "OE2" Residue "j ARG 120": "NH1" <-> "NH2" Residue "k GLU 4": "OE1" <-> "OE2" Residue "k GLU 45": "OE1" <-> "OE2" Residue "k GLU 110": "OE1" <-> "OE2" Residue "k PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 10": "OE1" <-> "OE2" Residue "l ARG 21": "NH1" <-> "NH2" Residue "l ARG 33": "NH1" <-> "NH2" Residue "l ARG 41": "NH1" <-> "NH2" Residue "l ARG 47": "NH1" <-> "NH2" Residue "l ARG 60": "NH1" <-> "NH2" Residue "l ARG 78": "NH1" <-> "NH2" Residue "l GLU 86": "OE1" <-> "OE2" Residue "l ARG 126": "NH1" <-> "NH2" Residue "m ARG 10": "NH1" <-> "NH2" Residue "m ARG 18": "NH1" <-> "NH2" Residue "m ARG 40": "NH1" <-> "NH2" Residue "m ARG 44": "NH1" <-> "NH2" Residue "m ARG 50": "NH1" <-> "NH2" Residue "m ARG 55": "NH1" <-> "NH2" Residue "m ARG 59": "NH1" <-> "NH2" Residue "m GLU 104": "OE1" <-> "OE2" Residue "m GLU 110": "OE1" <-> "OE2" Residue "m GLU 111": "OE1" <-> "OE2" Residue "m ARG 114": "NH1" <-> "NH2" Residue "n ARG 8": "NH1" <-> "NH2" Residue "n ARG 12": "NH1" <-> "NH2" Residue "n ARG 17": "NH1" <-> "NH2" Residue "n ARG 22": "NH1" <-> "NH2" Residue "n GLU 43": "OE1" <-> "OE2" Residue "n ARG 46": "NH1" <-> "NH2" Residue "n GLU 49": "OE1" <-> "OE2" Residue "n ARG 63": "NH1" <-> "NH2" Residue "n ARG 64": "NH1" <-> "NH2" Residue "n ARG 69": "NH1" <-> "NH2" Residue "n ARG 71": "NH1" <-> "NH2" Residue "n ARG 96": "NH1" <-> "NH2" Residue "n ARG 118": "NH1" <-> "NH2" Residue "n GLU 120": "OE1" <-> "OE2" Residue "o ARG 10": "NH1" <-> "NH2" Residue "o ARG 16": "NH1" <-> "NH2" Residue "o GLU 20": "OE1" <-> "OE2" Residue "o ARG 25": "NH1" <-> "NH2" Residue "o GLU 80": "OE1" <-> "OE2" Residue "o ARG 81": "NH1" <-> "NH2" Residue "o ARG 94": "NH1" <-> "NH2" Residue "o ARG 102": "NH1" <-> "NH2" Residue "o ARG 111": "NH1" <-> "NH2" Residue "o GLU 112": "OE1" <-> "OE2" Residue "p ARG 21": "NH1" <-> "NH2" Residue "p ARG 39": "NH1" <-> "NH2" Residue "p GLU 44": "OE1" <-> "OE2" Residue "p ARG 51": "NH1" <-> "NH2" Residue "p ARG 62": "NH1" <-> "NH2" Residue "p ARG 89": "NH1" <-> "NH2" Residue "p ARG 101": "NH1" <-> "NH2" Residue "p GLU 102": "OE1" <-> "OE2" Residue "p ARG 109": "NH1" <-> "NH2" Residue "q ARG 3": "NH1" <-> "NH2" Residue "q ARG 6": "NH1" <-> "NH2" Residue "q ARG 13": "NH1" <-> "NH2" Residue "q ARG 33": "NH1" <-> "NH2" Residue "q ARG 48": "NH1" <-> "NH2" Residue "q ARG 70": "NH1" <-> "NH2" Residue "q GLU 89": "OE1" <-> "OE2" Residue "q GLU 111": "OE1" <-> "OE2" Residue "r ARG 21": "NH1" <-> "NH2" Residue "r GLU 23": "OE1" <-> "OE2" Residue "r GLU 34": "OE1" <-> "OE2" Residue "r GLU 37": "OE1" <-> "OE2" Residue "r GLU 45": "OE1" <-> "OE2" Residue "r GLU 46": "OE1" <-> "OE2" Residue "r ARG 68": "NH1" <-> "NH2" Residue "r GLU 70": "OE1" <-> "OE2" Residue "r ARG 78": "NH1" <-> "NH2" Residue "r ARG 79": "NH1" <-> "NH2" Residue "r ARG 84": "NH1" <-> "NH2" Residue "s PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s GLU 78": "OE1" <-> "OE2" Residue "s ARG 84": "NH1" <-> "NH2" Residue "s ARG 88": "NH1" <-> "NH2" Residue "s ARG 95": "NH1" <-> "NH2" Residue "t GLU 4": "OE1" <-> "OE2" Residue "t GLU 5": "OE1" <-> "OE2" Residue "t ARG 12": "NH1" <-> "NH2" Residue "t GLU 18": "OE1" <-> "OE2" Residue "t GLU 42": "OE1" <-> "OE2" Residue "t GLU 54": "OE1" <-> "OE2" Residue "t ARG 77": "NH1" <-> "NH2" Residue "t ARG 80": "NH1" <-> "NH2" Residue "u ARG 6": "NH1" <-> "NH2" Residue "u ARG 7": "NH1" <-> "NH2" Residue "u GLU 10": "OE1" <-> "OE2" Residue "u ARG 82": "NH1" <-> "NH2" Residue "u ARG 86": "NH1" <-> "NH2" Residue "u ARG 94": "NH1" <-> "NH2" Residue "w GLU 35": "OE1" <-> "OE2" Residue "w GLU 59": "OE1" <-> "OE2" Residue "y ARG 11": "NH1" <-> "NH2" Residue "y GLU 29": "OE1" <-> "OE2" Residue "y GLU 83": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 90702 Number of models: 1 Model: "" Number of chains: 31 Chain: "0" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "1" Number of atoms: 495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 495 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "2" Number of atoms: 439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 439 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 2, 'TRANS': 54} Chain: "3" Number of atoms: 434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 434 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 1, 'TRANS': 53} Chain: "4" Number of atoms: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 409 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "6" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "7" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 504 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "8" Number of atoms: 301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 301 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "a" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 2529 Classifications: {'RNA': 118} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 5, 'rna3p_pur': 55, 'rna3p_pyr': 49} Link IDs: {'rna2p': 14, 'rna3p': 103} Chain: "b" Number of atoms: 62281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2901, 62281 Classifications: {'RNA': 2901} Modifications used: {'rna2p_pur': 284, 'rna2p_pyr': 164, 'rna3p_pur': 1391, 'rna3p_pyr': 1062} Link IDs: {'rna2p': 448, 'rna3p': 2452} Chain: "c" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2082 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "d" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1565 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 202} Chain: "e" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "f" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1410 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "g" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1323 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "h" Number of atoms: 287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 287 Classifications: {'peptide': 39} Link IDs: {'PTRANS': 2, 'TRANS': 36} Chain: "j" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "k" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "l" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1043 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 4, 'TRANS': 138} Chain: "m" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1074 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "n" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 960 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "o" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 892 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "p" Number of atoms: 908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 908 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 3, 'TRANS': 109} Chain: "q" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "r" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 810 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 1, 'TRANS': 100} Chain: "s" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 845 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 2, 'TRANS': 106} Chain: "t" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 793 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 1, 'TRANS': 99} Chain: "u" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 779 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "v" Number of atoms: 1646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1646 Classifications: {'RNA': 77} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 8, 'rna3p_pur': 35, 'rna3p_pyr': 29} Link IDs: {'rna2p': 13, 'rna3p': 63} Chain: "w" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "y" Number of atoms: 572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 572 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Time building chain proxies: 36.19, per 1000 atoms: 0.40 Number of scatterers: 90702 At special positions: 0 Unit cell: (201.663, 210.199, 221.936, 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 75 16.00 P 3096 15.00 O 25776 8.00 N 16908 7.00 C 44847 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS 8 14 " - pdb=" SG CYS 8 27 " distance=2.04 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: 37.54 Conformation dependent library (CDL) restraints added in 3.8 seconds 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5670 Finding SS restraints... Secondary structure from input PDB file: 86 helices and 47 sheets defined 29.3% alpha, 21.6% beta 1003 base pairs and 1605 stacking pairs defined. Time for finding SS restraints: 37.17 Creating SS restraints... Processing helix chain '0' and resid 53 through 63 Processing helix chain '0' and resid 63 through 74 Processing helix chain '1' and resid 11 through 35 Processing helix chain '1' and resid 41 through 61 Processing helix chain '2' and resid 17 through 28 Processing helix chain '2' and resid 41 through 51 removed outlier: 3.721A pdb=" N VAL 2 51 " --> pdb=" O MET 2 47 " (cutoff:3.500A) Processing helix chain '3' and resid 9 through 18 Processing helix chain '6' and resid 8 through 17 Processing helix chain '6' and resid 17 through 24 removed outlier: 4.378A pdb=" N THR 6 24 " --> pdb=" O ALA 6 20 " (cutoff:3.500A) Processing helix chain '6' and resid 24 through 38 Processing helix chain '7' and resid 7 through 12 removed outlier: 3.528A pdb=" N LYS 7 12 " --> pdb=" O ARG 7 8 " (cutoff:3.500A) Processing helix chain '7' and resid 37 through 44 Processing helix chain '7' and resid 51 through 62 removed outlier: 4.474A pdb=" N GLY 7 56 " --> pdb=" O LYS 7 52 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N LEU 7 57 " --> pdb=" O GLY 7 53 " (cutoff:3.500A) Processing helix chain '8' and resid 30 through 33 Processing helix chain 'c' and resid 30 through 32 No H-bonds generated for 'chain 'c' and resid 30 through 32' Processing helix chain 'c' and resid 197 through 203 removed outlier: 4.270A pdb=" N MET c 201 " --> pdb=" O ALA c 198 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG c 203 " --> pdb=" O HIS c 200 " (cutoff:3.500A) Processing helix chain 'c' and resid 207 through 213 removed outlier: 3.829A pdb=" N ALA c 211 " --> pdb=" O LYS c 207 " (cutoff:3.500A) Processing helix chain 'c' and resid 221 through 225 Processing helix chain 'd' and resid 39 through 44 Processing helix chain 'd' and resid 56 through 60 Processing helix chain 'd' and resid 61 through 72 removed outlier: 3.880A pdb=" N ALA d 71 " --> pdb=" O HIS d 67 " (cutoff:3.500A) Processing helix chain 'd' and resid 97 through 102 Processing helix chain 'd' and resid 120 through 126 Processing helix chain 'e' and resid 15 through 20 Processing helix chain 'e' and resid 24 through 40 removed outlier: 3.755A pdb=" N ARG e 40 " --> pdb=" O ALA e 36 " (cutoff:3.500A) Processing helix chain 'e' and resid 97 through 115 Processing helix chain 'e' and resid 130 through 142 removed outlier: 3.512A pdb=" N LEU e 134 " --> pdb=" O LYS e 130 " (cutoff:3.500A) Processing helix chain 'e' and resid 154 through 162 Processing helix chain 'e' and resid 176 through 183 removed outlier: 3.550A pdb=" N ILE e 181 " --> pdb=" O PRO e 177 " (cutoff:3.500A) Processing helix chain 'e' and resid 190 through 201 Processing helix chain 'f' and resid 3 through 12 Processing helix chain 'f' and resid 12 through 21 Processing helix chain 'f' and resid 24 through 28 removed outlier: 3.528A pdb=" N VAL f 28 " --> pdb=" O VAL f 25 " (cutoff:3.500A) Processing helix chain 'f' and resid 40 through 45 removed outlier: 3.533A pdb=" N ALA f 43 " --> pdb=" O VAL f 40 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ILE f 44 " --> pdb=" O GLY f 41 " (cutoff:3.500A) Processing helix chain 'f' and resid 47 through 61 Processing helix chain 'f' and resid 93 through 105 Processing helix chain 'f' and resid 107 through 111 Processing helix chain 'f' and resid 162 through 173 removed outlier: 3.633A pdb=" N GLY f 166 " --> pdb=" O SER f 162 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N PHE f 173 " --> pdb=" O LEU f 169 " (cutoff:3.500A) Processing helix chain 'g' and resid 60 through 80 removed outlier: 3.635A pdb=" N THR g 80 " --> pdb=" O VAL g 76 " (cutoff:3.500A) Processing helix chain 'g' and resid 137 through 150 Processing helix chain 'h' and resid 30 through 34 Processing helix chain 'j' and resid 24 through 38 removed outlier: 3.818A pdb=" N GLU j 31 " --> pdb=" O ARG j 27 " (cutoff:3.500A) Processing helix chain 'j' and resid 58 through 62 removed outlier: 3.543A pdb=" N VAL j 62 " --> pdb=" O ALA j 59 " (cutoff:3.500A) Processing helix chain 'j' and resid 67 through 72 Processing helix chain 'j' and resid 89 through 96 Processing helix chain 'j' and resid 97 through 109 removed outlier: 4.216A pdb=" N ILE j 101 " --> pdb=" O PRO j 97 " (cutoff:3.500A) Processing helix chain 'j' and resid 112 through 120 Processing helix chain 'k' and resid 104 through 108 Processing helix chain 'k' and resid 112 through 119 Processing helix chain 'l' and resid 56 through 61 removed outlier: 3.541A pdb=" N LEU l 61 " --> pdb=" O LEU l 57 " (cutoff:3.500A) Processing helix chain 'l' and resid 70 through 72 No H-bonds generated for 'chain 'l' and resid 70 through 72' Processing helix chain 'l' and resid 80 through 86 removed outlier: 4.024A pdb=" N ALA l 83 " --> pdb=" O SER l 80 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL l 85 " --> pdb=" O LEU l 82 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N GLU l 86 " --> pdb=" O ALA l 83 " (cutoff:3.500A) Processing helix chain 'l' and resid 91 through 98 Processing helix chain 'l' and resid 128 through 138 Processing helix chain 'm' and resid 43 through 58 Processing helix chain 'm' and resid 109 through 122 removed outlier: 3.507A pdb=" N ALA m 122 " --> pdb=" O LYS m 118 " (cutoff:3.500A) Processing helix chain 'n' and resid 13 through 32 Processing helix chain 'n' and resid 44 through 56 Proline residue: n 50 - end of helix Processing helix chain 'n' and resid 59 through 70 Processing helix chain 'n' and resid 72 through 82 Processing helix chain 'n' and resid 82 through 87 Processing helix chain 'o' and resid 3 through 16 removed outlier: 4.035A pdb=" N ARG o 13 " --> pdb=" O ARG o 9 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ALA o 14 " --> pdb=" O ARG o 10 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG o 16 " --> pdb=" O THR o 12 " (cutoff:3.500A) Processing helix chain 'o' and resid 55 through 60 removed outlier: 4.129A pdb=" N GLU o 60 " --> pdb=" O LYS o 56 " (cutoff:3.500A) Processing helix chain 'o' and resid 67 through 85 Processing helix chain 'o' and resid 101 through 115 removed outlier: 3.747A pdb=" N LEU o 115 " --> pdb=" O ARG o 111 " (cutoff:3.500A) Processing helix chain 'p' and resid 3 through 11 Processing helix chain 'p' and resid 53 through 56 Processing helix chain 'p' and resid 97 through 103 Processing helix chain 'p' and resid 104 through 109 removed outlier: 3.888A pdb=" N ARG p 109 " --> pdb=" O LYS p 106 " (cutoff:3.500A) Processing helix chain 'q' and resid 6 through 20 removed outlier: 3.816A pdb=" N GLN q 20 " --> pdb=" O LYS q 16 " (cutoff:3.500A) Processing helix chain 'q' and resid 26 through 31 removed outlier: 3.630A pdb=" N ARG q 30 " --> pdb=" O GLY q 26 " (cutoff:3.500A) Processing helix chain 'q' and resid 31 through 72 removed outlier: 3.731A pdb=" N GLN q 37 " --> pdb=" O ARG q 33 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LYS q 54 " --> pdb=" O ARG q 50 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG q 55 " --> pdb=" O ARG q 51 " (cutoff:3.500A) Processing helix chain 'q' and resid 75 through 86 Processing helix chain 'q' and resid 91 through 102 Processing helix chain 'q' and resid 102 through 118 Processing helix chain 's' and resid 13 through 22 removed outlier: 3.775A pdb=" N VAL s 20 " --> pdb=" O LYS s 16 " (cutoff:3.500A) Processing helix chain 's' and resid 28 through 38 removed outlier: 3.501A pdb=" N TYR s 38 " --> pdb=" O ASP s 34 " (cutoff:3.500A) Processing helix chain 's' and resid 41 through 61 removed outlier: 3.989A pdb=" N VAL s 45 " --> pdb=" O LYS s 41 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU s 46 " --> pdb=" O LYS s 42 " (cutoff:3.500A) Processing helix chain 's' and resid 65 through 69 Processing helix chain 's' and resid 89 through 91 No H-bonds generated for 'chain 's' and resid 89 through 91' Processing helix chain 't' and resid 3 through 10 Processing helix chain 't' and resid 18 through 28 Processing helix chain 't' and resid 39 through 52 Processing helix chain 'w' and resid 13 through 23 Processing helix chain 'w' and resid 44 through 51 Processing helix chain 'w' and resid 53 through 58 Processing sheet with id=AA1, first strand: chain '0' and resid 13 through 18 Processing sheet with id=AA2, first strand: chain '0' and resid 33 through 40 removed outlier: 3.570A pdb=" N ARG 0 45 " --> pdb=" O VAL 0 40 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '2' and resid 35 through 38 Processing sheet with id=AA4, first strand: chain '3' and resid 29 through 30 Processing sheet with id=AA5, first strand: chain '3' and resid 48 through 49 Processing sheet with id=AA6, first strand: chain '4' and resid 20 through 25 Processing sheet with id=AA7, first strand: chain '7' and resid 15 through 16 Processing sheet with id=AA8, first strand: chain '8' and resid 2 through 4 removed outlier: 6.062A pdb=" N LYS 8 2 " --> pdb=" O ARG 8 36 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N ILE 8 23 " --> pdb=" O GLN 8 37 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'c' and resid 3 through 5 Processing sheet with id=AB1, first strand: chain 'c' and resid 34 through 36 Processing sheet with id=AB2, first strand: chain 'c' and resid 100 through 105 removed outlier: 6.383A pdb=" N LEU c 95 " --> pdb=" O VAL c 78 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N VAL c 78 " --> pdb=" O LEU c 95 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'c' and resid 129 through 131 removed outlier: 6.245A pdb=" N ILE c 164 " --> pdb=" O ARG c 175 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ARG c 175 " --> pdb=" O ILE c 164 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA c 166 " --> pdb=" O THR c 173 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N LYS c 183 " --> pdb=" O ILE c 267 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ILE c 267 " --> pdb=" O LYS c 183 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'c' and resid 144 through 145 removed outlier: 6.054A pdb=" N VAL c 144 " --> pdb=" O GLN c 153 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'd' and resid 169 through 175 removed outlier: 5.330A pdb=" N THR d 171 " --> pdb=" O GLY d 111 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N GLY d 111 " --> pdb=" O THR d 171 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N GLN d 173 " --> pdb=" O VAL d 109 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N VAL d 109 " --> pdb=" O GLN d 173 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N THR d 112 " --> pdb=" O ASP d 200 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N ASP d 200 " --> pdb=" O THR d 112 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N LYS d 8 " --> pdb=" O GLU d 28 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLU d 28 " --> pdb=" O LYS d 8 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY d 10 " --> pdb=" O VAL d 26 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N LYS d 190 " --> pdb=" O VAL d 177 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL d 177 " --> pdb=" O LYS d 190 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'd' and resid 80 through 83 removed outlier: 6.586A pdb=" N ALA d 47 " --> pdb=" O VAL d 37 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N VAL d 37 " --> pdb=" O ALA d 47 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N GLN d 49 " --> pdb=" O THR d 35 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'd' and resid 117 through 119 Processing sheet with id=AB8, first strand: chain 'e' and resid 2 through 3 Processing sheet with id=AB9, first strand: chain 'e' and resid 118 through 121 Processing sheet with id=AC1, first strand: chain 'f' and resid 66 through 69 removed outlier: 3.880A pdb=" N GLY f 86 " --> pdb=" O THR f 68 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N THR f 157 " --> pdb=" O GLU f 32 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ILE f 34 " --> pdb=" O THR f 155 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N THR f 155 " --> pdb=" O ILE f 34 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N LEU f 36 " --> pdb=" O ASP f 153 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ASP f 153 " --> pdb=" O LEU f 36 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU f 152 " --> pdb=" O VAL f 132 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'g' and resid 9 through 10 Processing sheet with id=AC3, first strand: chain 'g' and resid 16 through 20 Processing sheet with id=AC4, first strand: chain 'g' and resid 122 through 124 removed outlier: 3.604A pdb=" N VAL g 90 " --> pdb=" O GLY g 161 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'g' and resid 96 through 99 removed outlier: 3.694A pdb=" N VAL g 113 " --> pdb=" O LEU g 105 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'h' and resid 18 through 20 Processing sheet with id=AC7, first strand: chain 'j' and resid 122 through 124 removed outlier: 6.815A pdb=" N TRP j 15 " --> pdb=" O GLN j 138 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'j' and resid 73 through 77 Processing sheet with id=AC9, first strand: chain 'k' and resid 7 through 10 removed outlier: 3.659A pdb=" N VAL k 10 " --> pdb=" O ARG k 17 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ARG k 17 " --> pdb=" O VAL k 10 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N GLU k 45 " --> pdb=" O ARG k 17 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL k 19 " --> pdb=" O ILE k 43 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ILE k 43 " --> pdb=" O VAL k 19 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N CYS k 21 " --> pdb=" O ILE k 41 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ILE k 41 " --> pdb=" O CYS k 21 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N LYS k 23 " --> pdb=" O ILE k 39 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N ILE k 39 " --> pdb=" O LYS k 23 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS k 59 " --> pdb=" O LEU k 87 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ALA k 83 " --> pdb=" O VAL k 63 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N CYS k 84 " --> pdb=" O MET k 7 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ASN k 9 " --> pdb=" O CYS k 84 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N LEU k 86 " --> pdb=" O ASN k 9 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'k' and resid 69 through 70 removed outlier: 3.570A pdb=" N ALA p 49 " --> pdb=" O THR p 60 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ARG p 62 " --> pdb=" O VAL p 47 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N VAL p 47 " --> pdb=" O ARG p 62 " (cutoff:3.500A) removed outlier: 8.600A pdb=" N ILE p 64 " --> pdb=" O GLY p 45 " (cutoff:3.500A) removed outlier: 8.710A pdb=" N GLY p 45 " --> pdb=" O ILE p 64 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N THR p 25 " --> pdb=" O VAL p 86 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N VAL p 86 " --> pdb=" O THR p 25 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N GLU p 27 " --> pdb=" O ILE p 84 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ILE p 84 " --> pdb=" O GLU p 27 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N LYS p 29 " --> pdb=" O ASP p 82 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'l' and resid 74 through 78 Processing sheet with id=AD3, first strand: chain 'l' and resid 89 through 90 Processing sheet with id=AD4, first strand: chain 'm' and resid 62 through 65 removed outlier: 6.131A pdb=" N VAL m 101 " --> pdb=" O ALA m 35 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ALA m 35 " --> pdb=" O VAL m 101 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N TYR m 103 " --> pdb=" O LEU m 33 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'm' and resid 39 through 42 removed outlier: 3.651A pdb=" N ASN m 88 " --> pdb=" O GLU m 75 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ILE m 73 " --> pdb=" O GLU m 90 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N TRP m 92 " --> pdb=" O LYS m 71 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N LYS m 71 " --> pdb=" O TRP m 92 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'n' and resid 33 through 37 removed outlier: 5.688A pdb=" N MET n 110 " --> pdb=" O CYS n 100 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'o' and resid 47 through 52 removed outlier: 6.622A pdb=" N VAL o 39 " --> pdb=" O LEU o 48 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ALA o 50 " --> pdb=" O ALA o 37 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ALA o 37 " --> pdb=" O ALA o 50 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N SER o 52 " --> pdb=" O ILE o 35 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ILE o 35 " --> pdb=" O SER o 52 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'r' and resid 11 through 14 removed outlier: 3.547A pdb=" N MET r 40 " --> pdb=" O VAL r 4 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N GLN r 6 " --> pdb=" O VAL r 38 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N VAL r 38 " --> pdb=" O GLN r 6 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'r' and resid 19 through 23 removed outlier: 6.742A pdb=" N PHE r 93 " --> pdb=" O HIS r 66 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N HIS r 66 " --> pdb=" O PHE r 93 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ASP r 95 " --> pdb=" O VAL r 64 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LYS r 60 " --> pdb=" O THR r 99 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'r' and resid 72 through 78 removed outlier: 4.076A pdb=" N TYR r 83 " --> pdb=" O ARG r 78 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 's' and resid 3 through 10 removed outlier: 5.517A pdb=" N ILE s 4 " --> pdb=" O VAL s 107 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N VAL s 107 " --> pdb=" O ILE s 4 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N LYS s 6 " --> pdb=" O VAL s 105 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N VAL s 105 " --> pdb=" O LYS s 6 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N ARG s 8 " --> pdb=" O ILE s 103 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ILE s 103 " --> pdb=" O ARG s 8 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N SER s 108 " --> pdb=" O VAL s 71 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N VAL s 71 " --> pdb=" O SER s 108 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 's' and resid 82 through 87 Processing sheet with id=AE4, first strand: chain 't' and resid 11 through 14 removed outlier: 3.839A pdb=" N LYS t 89 " --> pdb=" O VAL t 34 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N TRP t 88 " --> pdb=" O VAL t 62 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N VAL t 62 " --> pdb=" O TRP t 88 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N LYS t 90 " --> pdb=" O THR t 60 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N THR t 60 " --> pdb=" O LYS t 90 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N TYR t 92 " --> pdb=" O VAL t 58 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N VAL t 58 " --> pdb=" O TYR t 92 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N THR t 94 " --> pdb=" O GLU t 56 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 't' and resid 67 through 72 Processing sheet with id=AE6, first strand: chain 'u' and resid 65 through 66 removed outlier: 3.763A pdb=" N LYS u 33 " --> pdb=" O LEU u 29 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN u 27 " --> pdb=" O ILE u 35 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'u' and resid 41 through 45 Processing sheet with id=AE8, first strand: chain 'u' and resid 83 through 88 Processing sheet with id=AE9, first strand: chain 'w' and resid 3 through 8 removed outlier: 7.858A pdb=" N ASN w 5 " --> pdb=" O ASP w 43 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ASP w 43 " --> pdb=" O ASN w 5 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N GLN w 87 " --> pdb=" O LYS w 25 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE w 89 " --> pdb=" O PRO w 27 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASP w 76 " --> pdb=" O ASP w 90 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N VAL w 92 " --> pdb=" O ALA w 74 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N ALA w 74 " --> pdb=" O VAL w 92 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'y' and resid 22 through 23 removed outlier: 7.007A pdb=" N LEU y 59 " --> pdb=" O ILE y 37 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'y' and resid 30 through 31 934 hydrogen bonds defined for protein. 2529 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2531 hydrogen bonds 3936 hydrogen bond angles 0 basepair planarities 1003 basepair parallelities 1605 stacking parallelities Total time for adding SS restraints: 148.54 Time building geometry restraints manager: 40.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 16190 1.33 - 1.46: 43380 1.46 - 1.59: 35412 1.59 - 1.72: 3879 1.72 - 1.85: 137 Bond restraints: 98998 Sorted by residual: bond pdb=" C ARG l 60 " pdb=" N LEU l 61 " ideal model delta sigma weight residual 1.331 1.230 0.101 2.07e-02 2.33e+03 2.37e+01 bond pdb=" O3' G b2330 " pdb=" P G b2331 " ideal model delta sigma weight residual 1.607 1.674 -0.067 1.50e-02 4.44e+03 2.00e+01 bond pdb=" O3' A b2119 " pdb=" P G b2120 " ideal model delta sigma weight residual 1.607 1.667 -0.060 1.50e-02 4.44e+03 1.60e+01 bond pdb=" O3' U b 895 " pdb=" P A b 896 " ideal model delta sigma weight residual 1.607 1.665 -0.058 1.50e-02 4.44e+03 1.51e+01 bond pdb=" N ILE 7 32 " pdb=" CA ILE 7 32 " ideal model delta sigma weight residual 1.459 1.506 -0.047 1.25e-02 6.40e+03 1.44e+01 ... (remaining 98993 not shown) Histogram of bond angle deviations from ideal: 96.91 - 104.37: 13178 104.37 - 111.82: 54753 111.82 - 119.28: 34287 119.28 - 126.74: 38379 126.74 - 134.20: 8426 Bond angle restraints: 149023 Sorted by residual: angle pdb=" O3' G b2133 " pdb=" C3' G b2133 " pdb=" C2' G b2133 " ideal model delta sigma weight residual 113.70 128.07 -14.37 1.50e+00 4.44e-01 9.18e+01 angle pdb=" O3' U b 895 " pdb=" C3' U b 895 " pdb=" C2' U b 895 " ideal model delta sigma weight residual 109.50 122.36 -12.86 1.50e+00 4.44e-01 7.35e+01 angle pdb=" C4' G b2157 " pdb=" C3' G b2157 " pdb=" O3' G b2157 " ideal model delta sigma weight residual 109.40 121.04 -11.64 1.50e+00 4.44e-01 6.02e+01 angle pdb=" O3' U b2139 " pdb=" C3' U b2139 " pdb=" C2' U b2139 " ideal model delta sigma weight residual 109.50 119.95 -10.45 1.50e+00 4.44e-01 4.85e+01 angle pdb=" O3' U b2118 " pdb=" C3' U b2118 " pdb=" C2' U b2118 " ideal model delta sigma weight residual 109.50 119.73 -10.23 1.50e+00 4.44e-01 4.65e+01 ... (remaining 149018 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 54729 35.99 - 71.99: 7898 71.99 - 107.98: 817 107.98 - 143.98: 21 143.98 - 179.97: 30 Dihedral angle restraints: 63495 sinusoidal: 54683 harmonic: 8812 Sorted by residual: dihedral pdb=" O4' U b 99 " pdb=" C1' U b 99 " pdb=" N1 U b 99 " pdb=" C2 U b 99 " ideal model delta sinusoidal sigma weight residual 200.00 27.81 172.19 1 1.50e+01 4.44e-03 8.49e+01 dihedral pdb=" O4' U b2155 " pdb=" C1' U b2155 " pdb=" N1 U b2155 " pdb=" C2 U b2155 " ideal model delta sinusoidal sigma weight residual 200.00 35.96 164.04 1 1.50e+01 4.44e-03 8.37e+01 dihedral pdb=" O4' U b2884 " pdb=" C1' U b2884 " pdb=" N1 U b2884 " pdb=" C2 U b2884 " ideal model delta sinusoidal sigma weight residual 200.00 43.17 156.83 1 1.50e+01 4.44e-03 8.19e+01 ... (remaining 63492 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.206: 18901 0.206 - 0.412: 263 0.412 - 0.618: 4 0.618 - 0.824: 5 0.824 - 1.030: 1 Chirality restraints: 19174 Sorted by residual: chirality pdb=" C3' G b2133 " pdb=" C4' G b2133 " pdb=" O3' G b2133 " pdb=" C2' G b2133 " both_signs ideal model delta sigma weight residual False -2.48 -1.45 -1.03 2.00e-01 2.50e+01 2.65e+01 chirality pdb=" C3' U b 895 " pdb=" C4' U b 895 " pdb=" O3' U b 895 " pdb=" C2' U b 895 " both_signs ideal model delta sigma weight residual False -2.74 -2.06 -0.68 2.00e-01 2.50e+01 1.16e+01 chirality pdb=" CA VAL r 51 " pdb=" N VAL r 51 " pdb=" C VAL r 51 " pdb=" CB VAL r 51 " both_signs ideal model delta sigma weight residual False 2.44 1.79 0.65 2.00e-01 2.50e+01 1.06e+01 ... (remaining 19171 not shown) Planarity restraints: 7331 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A b1328 " 0.050 2.00e-02 2.50e+03 2.25e-02 1.40e+01 pdb=" N9 A b1328 " -0.051 2.00e-02 2.50e+03 pdb=" C8 A b1328 " -0.002 2.00e-02 2.50e+03 pdb=" N7 A b1328 " 0.002 2.00e-02 2.50e+03 pdb=" C5 A b1328 " -0.005 2.00e-02 2.50e+03 pdb=" C6 A b1328 " 0.005 2.00e-02 2.50e+03 pdb=" N6 A b1328 " 0.016 2.00e-02 2.50e+03 pdb=" N1 A b1328 " 0.002 2.00e-02 2.50e+03 pdb=" C2 A b1328 " 0.002 2.00e-02 2.50e+03 pdb=" N3 A b1328 " -0.008 2.00e-02 2.50e+03 pdb=" C4 A b1328 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A b 727 " 0.046 2.00e-02 2.50e+03 2.14e-02 1.26e+01 pdb=" N9 A b 727 " -0.051 2.00e-02 2.50e+03 pdb=" C8 A b 727 " -0.002 2.00e-02 2.50e+03 pdb=" N7 A b 727 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A b 727 " 0.001 2.00e-02 2.50e+03 pdb=" C6 A b 727 " 0.006 2.00e-02 2.50e+03 pdb=" N6 A b 727 " 0.012 2.00e-02 2.50e+03 pdb=" N1 A b 727 " 0.003 2.00e-02 2.50e+03 pdb=" C2 A b 727 " -0.004 2.00e-02 2.50e+03 pdb=" N3 A b 727 " -0.006 2.00e-02 2.50e+03 pdb=" C4 A b 727 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS 7 31 " -0.017 2.00e-02 2.50e+03 3.47e-02 1.20e+01 pdb=" C HIS 7 31 " 0.060 2.00e-02 2.50e+03 pdb=" O HIS 7 31 " -0.023 2.00e-02 2.50e+03 pdb=" N ILE 7 32 " -0.020 2.00e-02 2.50e+03 ... (remaining 7328 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.45: 286 2.45 - 3.06: 54026 3.06 - 3.67: 171178 3.67 - 4.29: 270959 4.29 - 4.90: 359564 Nonbonded interactions: 856013 Sorted by model distance: nonbonded pdb=" O4 U b 62 " pdb=" N6 A b 63 " model vdw 1.835 2.520 nonbonded pdb=" OP1 G b1666 " pdb=" NZ LYS k 66 " model vdw 2.064 2.520 nonbonded pdb=" O LYS u 97 " pdb=" OG SER u 98 " model vdw 2.095 2.440 nonbonded pdb=" OD1 ASP h 7 " pdb=" N LYS h 8 " model vdw 2.098 2.520 nonbonded pdb=" O2' A b1494 " pdb=" O5' A b1495 " model vdw 2.098 2.440 ... (remaining 856008 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: 2.860 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: 0.100 Extract box with map and model: 15.590 Check model and map are aligned: 1.090 Set scattering table: 0.670 Process input model: 328.130 Find NCS groups from input model: 1.590 Set up NCS constraints: 0.250 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: 0.020 Load rotamer database and sin/cos tables:11.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 362.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6286 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 : 0.010 0.101 98998 Z= 0.631 Angle : 0.862 14.375 149023 Z= 0.492 Chirality : 0.064 1.030 19174 Planarity : 0.005 0.060 7331 Dihedral : 24.536 179.969 57822 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.08 % Favored : 93.62 % Rotamer: Outliers : 3.44 % Allowed : 42.60 % Favored : 53.96 % Cbeta Deviations : 0.14 % 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: -1.02 (0.15), residues: 3057 helix: 0.37 (0.18), residues: 787 sheet: -0.59 (0.19), residues: 701 loop : -1.23 (0.15), residues: 1569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP m 92 HIS 0.013 0.003 HIS e 92 PHE 0.047 0.003 PHE h 29 TYR 0.043 0.003 TYR t 92 ARG 0.025 0.002 ARG 3 52 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 703 residues out of total 2526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 616 time to evaluate : 3.755 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 25 THR cc_start: 0.7858 (m) cc_final: 0.7545 (t) REVERT: 0 60 ASP cc_start: 0.6128 (p0) cc_final: 0.5383 (m-30) REVERT: 0 72 ARG cc_start: 0.7047 (mtm-85) cc_final: 0.6579 (mtm-85) REVERT: 1 27 ASN cc_start: 0.7107 (m-40) cc_final: 0.6869 (m-40) REVERT: 2 6 LYS cc_start: 0.7921 (mtpp) cc_final: 0.7605 (mmtt) REVERT: 2 45 ARG cc_start: 0.7575 (mmt180) cc_final: 0.7321 (mmt180) REVERT: 3 9 THR cc_start: 0.6501 (m) cc_final: 0.6244 (p) REVERT: 3 37 LYS cc_start: 0.7164 (mtmm) cc_final: 0.6953 (mtpt) REVERT: 4 26 ASN cc_start: 0.7505 (t0) cc_final: 0.7111 (t0) REVERT: 4 37 LYS cc_start: 0.6793 (mttp) cc_final: 0.6548 (mmmm) REVERT: 4 38 LYS cc_start: 0.7737 (mttm) cc_final: 0.7300 (mmmm) REVERT: 4 40 ASP cc_start: 0.7905 (t0) cc_final: 0.7636 (t0) REVERT: 6 1 MET cc_start: 0.6868 (mpp) cc_final: 0.6261 (mpp) REVERT: 8 9 LYS cc_start: 0.7762 (mtmm) cc_final: 0.7545 (mtpp) REVERT: 8 18 LYS cc_start: 0.7350 (OUTLIER) cc_final: 0.6933 (tttm) REVERT: 8 26 ILE cc_start: 0.7676 (pt) cc_final: 0.7463 (pp) REVERT: c 4 VAL cc_start: 0.7700 (m) cc_final: 0.7487 (t) REVERT: c 35 GLU cc_start: 0.7662 (pt0) cc_final: 0.7386 (pt0) REVERT: c 125 LYS cc_start: 0.7076 (ptmm) cc_final: 0.6854 (ptmm) REVERT: c 146 MET cc_start: 0.7380 (mtm) cc_final: 0.7011 (mtp) REVERT: c 161 TYR cc_start: 0.7789 (p90) cc_final: 0.7575 (p90) REVERT: c 163 GLN cc_start: 0.7378 (mt0) cc_final: 0.7137 (mt0) REVERT: c 168 ASP cc_start: 0.4204 (OUTLIER) cc_final: 0.3850 (p0) REVERT: c 183 LYS cc_start: 0.7262 (ttpp) cc_final: 0.6654 (mttt) REVERT: c 269 ARG cc_start: 0.6651 (ttp80) cc_final: 0.5888 (ttp80) REVERT: d 1 MET cc_start: 0.5237 (ttm) cc_final: 0.4592 (tmm) REVERT: d 7 LYS cc_start: 0.7144 (ttpp) cc_final: 0.6607 (ttmm) REVERT: d 29 VAL cc_start: 0.7434 (m) cc_final: 0.7170 (t) REVERT: d 64 GLU cc_start: 0.5727 (mt-10) cc_final: 0.4993 (mm-30) REVERT: d 74 GLU cc_start: 0.7447 (tp30) cc_final: 0.6857 (tm-30) REVERT: d 103 ASP cc_start: 0.6203 (OUTLIER) cc_final: 0.5510 (m-30) REVERT: d 128 ARG cc_start: 0.5880 (mtp180) cc_final: 0.5094 (mmp80) REVERT: d 157 LYS cc_start: 0.7625 (tppp) cc_final: 0.7124 (mmtm) REVERT: d 185 ASN cc_start: 0.7005 (m-40) cc_final: 0.6614 (m110) REVERT: e 25 GLU cc_start: 0.7276 (tt0) cc_final: 0.6746 (tt0) REVERT: e 141 MET cc_start: 0.6462 (mtp) cc_final: 0.6224 (mtp) REVERT: e 144 GLU cc_start: 0.6056 (pm20) cc_final: 0.5783 (pm20) REVERT: e 150 THR cc_start: 0.7423 (p) cc_final: 0.7115 (m) REVERT: e 155 GLU cc_start: 0.6091 (tm-30) cc_final: 0.5833 (tm-30) REVERT: e 194 LYS cc_start: 0.5201 (mmmt) cc_final: 0.4973 (mmtm) REVERT: f 3 LYS cc_start: 0.4891 (ptmm) cc_final: 0.4660 (mmpt) REVERT: f 26 MET cc_start: 0.5125 (ptm) cc_final: 0.4925 (ptm) REVERT: f 44 ILE cc_start: 0.5071 (OUTLIER) cc_final: 0.4682 (mp) REVERT: f 49 LEU cc_start: 0.4444 (pt) cc_final: 0.4140 (mt) REVERT: f 64 LYS cc_start: 0.2437 (mptp) cc_final: 0.2189 (tttm) REVERT: f 113 ASP cc_start: 0.4869 (t70) cc_final: 0.4642 (p0) REVERT: f 125 ARG cc_start: 0.5560 (mtt-85) cc_final: 0.4991 (mtp180) REVERT: f 130 MET cc_start: 0.5782 (mtp) cc_final: 0.5509 (mtp) REVERT: f 150 ARG cc_start: 0.4756 (mtt90) cc_final: 0.4541 (ptp90) REVERT: f 154 ILE cc_start: 0.6235 (mm) cc_final: 0.5621 (mt) REVERT: g 32 GLU cc_start: 0.6367 (OUTLIER) cc_final: 0.5436 (tm-30) REVERT: g 36 THR cc_start: 0.7203 (OUTLIER) cc_final: 0.6702 (m) REVERT: g 74 SER cc_start: 0.6396 (m) cc_final: 0.6118 (t) REVERT: g 139 GLN cc_start: 0.6153 (tm-30) cc_final: 0.5756 (tt0) REVERT: g 151 TYR cc_start: 0.7083 (m-80) cc_final: 0.6854 (m-80) REVERT: g 171 THR cc_start: 0.7511 (p) cc_final: 0.7291 (t) REVERT: j 2 LYS cc_start: 0.7352 (mmmt) cc_final: 0.6700 (mtmt) REVERT: j 53 TYR cc_start: 0.7647 (m-80) cc_final: 0.7442 (m-80) REVERT: j 85 LYS cc_start: 0.6714 (mttm) cc_final: 0.6099 (mmmt) REVERT: j 91 GLU cc_start: 0.6844 (mt-10) cc_final: 0.6428 (mt-10) REVERT: j 98 GLU cc_start: 0.6896 (OUTLIER) cc_final: 0.6609 (mp0) REVERT: j 106 LYS cc_start: 0.6691 (tttp) cc_final: 0.6047 (tppt) REVERT: j 128 ASN cc_start: 0.7085 (t0) cc_final: 0.6778 (t0) REVERT: j 136 GLN cc_start: 0.7656 (mt0) cc_final: 0.7094 (mt0) REVERT: k 53 LYS cc_start: 0.6476 (mmpt) cc_final: 0.5657 (mppt) REVERT: k 98 ARG cc_start: 0.5594 (mtt180) cc_final: 0.5244 (mtm110) REVERT: k 100 PHE cc_start: 0.8090 (m-80) cc_final: 0.7821 (m-80) REVERT: k 114 LYS cc_start: 0.6019 (mtpp) cc_final: 0.5512 (tppt) REVERT: l 2 ARG cc_start: 0.6813 (mmt180) cc_final: 0.6496 (mmt180) REVERT: l 106 GLU cc_start: 0.7352 (pt0) cc_final: 0.7123 (pt0) REVERT: l 123 ARG cc_start: 0.7046 (tpp80) cc_final: 0.6497 (tpp80) REVERT: m 118 LYS cc_start: 0.7060 (ttpp) cc_final: 0.5973 (tmtm) REVERT: m 127 LYS cc_start: 0.6665 (mtpp) cc_final: 0.5747 (mmtt) REVERT: n 15 SER cc_start: 0.7172 (OUTLIER) cc_final: 0.6913 (m) REVERT: n 35 LYS cc_start: 0.7775 (tttt) cc_final: 0.7481 (tttm) REVERT: n 114 GLU cc_start: 0.7862 (pt0) cc_final: 0.7602 (pt0) REVERT: o 38 GLN cc_start: 0.7948 (mt0) cc_final: 0.7482 (mt0) REVERT: o 55 GLU cc_start: 0.6614 (mt-10) cc_final: 0.6088 (mt-10) REVERT: p 6 LYS cc_start: 0.6800 (ttmm) cc_final: 0.6328 (mttp) REVERT: p 89 ARG cc_start: 0.6509 (mtm-85) cc_final: 0.5537 (mtt-85) REVERT: q 71 GLN cc_start: 0.6672 (mt0) cc_final: 0.5837 (mm-40) REVERT: q 85 LYS cc_start: 0.6120 (mtmt) cc_final: 0.5783 (mttp) REVERT: q 107 THR cc_start: 0.7298 (m) cc_final: 0.6965 (t) REVERT: r 51 VAL cc_start: 0.4560 (OUTLIER) cc_final: 0.4259 (t) REVERT: r 55 ASP cc_start: 0.5895 (OUTLIER) cc_final: 0.5641 (p0) REVERT: s 2 GLU cc_start: 0.6988 (mt-10) cc_final: 0.6782 (mt-10) REVERT: s 28 LYS cc_start: 0.7035 (mttp) cc_final: 0.6548 (mttm) REVERT: s 70 LYS cc_start: 0.7372 (mttp) cc_final: 0.6938 (mtmm) REVERT: s 73 LYS cc_start: 0.7385 (mtmm) cc_final: 0.7182 (ttmt) REVERT: s 92 ARG cc_start: 0.6171 (mtp-110) cc_final: 0.5150 (ttp-170) REVERT: t 49 LYS cc_start: 0.6917 (tttm) cc_final: 0.6684 (tttp) REVERT: t 56 GLU cc_start: 0.6947 (mm-30) cc_final: 0.6651 (tt0) REVERT: t 85 ARG cc_start: 0.6246 (mmm-85) cc_final: 0.6009 (mtt90) REVERT: u 10 GLU cc_start: 0.6340 (mm-30) cc_final: 0.5603 (tp30) REVERT: u 24 LYS cc_start: 0.6485 (ttmm) cc_final: 0.5473 (tmmt) REVERT: u 36 VAL cc_start: 0.6829 (m) cc_final: 0.6240 (t) REVERT: u 46 GLN cc_start: 0.6876 (mm-40) cc_final: 0.6664 (mm-40) REVERT: u 62 GLU cc_start: 0.6484 (pm20) cc_final: 0.6127 (pt0) REVERT: w 1 MET cc_start: 0.4588 (ppp) cc_final: 0.4008 (mmt) REVERT: w 41 GLU cc_start: 0.7274 (mt-10) cc_final: 0.6909 (mt-10) REVERT: w 46 LYS cc_start: 0.6844 (mmtp) cc_final: 0.6604 (mtpp) REVERT: w 48 MET cc_start: 0.6727 (tpt) cc_final: 0.6264 (tmm) REVERT: w 53 LYS cc_start: 0.6276 (mttm) cc_final: 0.5444 (mmtt) REVERT: y 11 ARG cc_start: 0.6302 (ptm160) cc_final: 0.6043 (ptm160) REVERT: y 68 LYS cc_start: 0.7658 (tttm) cc_final: 0.7454 (tptp) REVERT: y 70 GLU cc_start: 0.6888 (tt0) cc_final: 0.6562 (mt-10) REVERT: y 83 GLU cc_start: 0.6773 (mt-10) cc_final: 0.6166 (mm-30) outliers start: 87 outliers final: 13 residues processed: 671 average time/residue: 1.9668 time to fit residues: 1729.8302 Evaluate side-chains 487 residues out of total 2526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 464 time to evaluate : 3.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 66 THR Chi-restraints excluded: chain 8 residue 18 LYS Chi-restraints excluded: chain c residue 168 ASP Chi-restraints excluded: chain d residue 103 ASP Chi-restraints excluded: chain d residue 151 THR Chi-restraints excluded: chain f residue 44 ILE Chi-restraints excluded: chain f residue 91 LEU Chi-restraints excluded: chain g residue 32 GLU Chi-restraints excluded: chain g residue 36 THR Chi-restraints excluded: chain g residue 81 GLU Chi-restraints excluded: chain h residue 15 LEU Chi-restraints excluded: chain j residue 98 GLU Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain m residue 7 THR Chi-restraints excluded: chain n residue 15 SER Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain o residue 24 THR Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain r residue 51 VAL Chi-restraints excluded: chain r residue 55 ASP Chi-restraints excluded: chain w residue 72 VAL Chi-restraints excluded: chain y residue 41 ARG Chi-restraints excluded: chain y residue 43 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 607 random chunks: chunk 512 optimal weight: 0.9980 chunk 460 optimal weight: 0.9980 chunk 255 optimal weight: 2.9990 chunk 157 optimal weight: 40.0000 chunk 310 optimal weight: 5.9990 chunk 245 optimal weight: 5.9990 chunk 475 optimal weight: 0.7980 chunk 184 optimal weight: 6.9990 chunk 289 optimal weight: 6.9990 chunk 354 optimal weight: 5.9990 chunk 551 optimal weight: 4.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 20 HIS 6 29 GLN 7 28 ASN c 200 HIS c 243 HIS c 260 ASN d 126 ASN d 173 GLN e 156 ASN g 104 ASN g 115 HIS j 47 HIS ** j 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 138 GLN l 54 GLN m 45 GLN ** p 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 75 GLN q 20 GLN q 37 GLN q 56 GLN q 66 ASN t 59 ASN u 53 ASN ** u 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 75 GLN y 46 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6492 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 98998 Z= 0.192 Angle : 0.616 9.788 149023 Z= 0.325 Chirality : 0.037 0.324 19174 Planarity : 0.005 0.053 7331 Dihedral : 24.291 179.365 51766 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.42 % Favored : 95.42 % Rotamer: Outliers : 7.17 % Allowed : 32.82 % Favored : 60.02 % 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: -0.65 (0.15), residues: 3057 helix: 0.76 (0.18), residues: 805 sheet: -0.37 (0.19), residues: 688 loop : -1.07 (0.15), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP c 213 HIS 0.010 0.002 HIS r 89 PHE 0.019 0.002 PHE m 68 TYR 0.015 0.002 TYR n 112 ARG 0.010 0.001 ARG g 95 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 667 residues out of total 2526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 486 time to evaluate : 3.751 Fit side-chains revert: symmetry clash REVERT: 0 43 GLU cc_start: 0.7515 (pt0) cc_final: 0.7217 (pt0) REVERT: 0 60 ASP cc_start: 0.6640 (p0) cc_final: 0.5863 (m-30) REVERT: 0 72 ARG cc_start: 0.7285 (mtm-85) cc_final: 0.6873 (mtm-85) REVERT: 1 39 GLN cc_start: 0.8043 (OUTLIER) cc_final: 0.7733 (tt0) REVERT: 1 44 LYS cc_start: 0.6510 (tttt) cc_final: 0.6261 (ttmt) REVERT: 2 6 LYS cc_start: 0.8286 (mtpp) cc_final: 0.7931 (mmtt) REVERT: 3 9 THR cc_start: 0.6892 (m) cc_final: 0.6559 (p) REVERT: 3 12 LYS cc_start: 0.6555 (OUTLIER) cc_final: 0.5922 (mmtm) REVERT: 3 15 MET cc_start: 0.8348 (mtm) cc_final: 0.8137 (mtm) REVERT: 4 37 LYS cc_start: 0.7084 (OUTLIER) cc_final: 0.6514 (mmmt) REVERT: 4 38 LYS cc_start: 0.7850 (mttm) cc_final: 0.7409 (mmmm) REVERT: 4 50 LYS cc_start: 0.6416 (mmtp) cc_final: 0.6204 (mmtt) REVERT: 6 1 MET cc_start: 0.7012 (OUTLIER) cc_final: 0.6425 (mpp) REVERT: 7 19 LYS cc_start: 0.7494 (OUTLIER) cc_final: 0.7283 (pttt) REVERT: 7 59 ILE cc_start: 0.7077 (mm) cc_final: 0.6824 (mt) REVERT: 8 1 MET cc_start: 0.7814 (tpp) cc_final: 0.7542 (tpp) REVERT: 8 12 ARG cc_start: 0.5613 (mtm110) cc_final: 0.5062 (ptt-90) REVERT: 8 15 LYS cc_start: 0.6811 (ttmm) cc_final: 0.5852 (tttp) REVERT: c 3 VAL cc_start: 0.7598 (m) cc_final: 0.7296 (t) REVERT: c 5 LYS cc_start: 0.6822 (tttp) cc_final: 0.6488 (tttp) REVERT: c 7 LYS cc_start: 0.7647 (OUTLIER) cc_final: 0.7318 (mttp) REVERT: c 74 ILE cc_start: 0.6978 (OUTLIER) cc_final: 0.6777 (mm) REVERT: c 118 SER cc_start: 0.8629 (t) cc_final: 0.7985 (t) REVERT: c 125 LYS cc_start: 0.7352 (ptmm) cc_final: 0.7006 (pttt) REVERT: c 146 MET cc_start: 0.7837 (mtm) cc_final: 0.7439 (mtp) REVERT: c 163 GLN cc_start: 0.7290 (mt0) cc_final: 0.7038 (mt0) REVERT: c 183 LYS cc_start: 0.7367 (ttpp) cc_final: 0.6876 (mttt) REVERT: c 265 LYS cc_start: 0.7612 (OUTLIER) cc_final: 0.7401 (pttm) REVERT: c 269 ARG cc_start: 0.6418 (ttp80) cc_final: 0.6026 (ttt90) REVERT: c 270 ARG cc_start: 0.7330 (ttt-90) cc_final: 0.5271 (mmm160) REVERT: d 1 MET cc_start: 0.5310 (ttm) cc_final: 0.4677 (tmm) REVERT: d 7 LYS cc_start: 0.7534 (ttpp) cc_final: 0.6975 (ttmm) REVERT: d 74 GLU cc_start: 0.7338 (tp30) cc_final: 0.7125 (mm-30) REVERT: d 103 ASP cc_start: 0.6330 (OUTLIER) cc_final: 0.5662 (m-30) REVERT: d 128 ARG cc_start: 0.5836 (mtp180) cc_final: 0.5270 (mmp80) REVERT: d 139 SER cc_start: 0.7717 (OUTLIER) cc_final: 0.7169 (p) REVERT: d 165 MET cc_start: 0.7633 (ttp) cc_final: 0.7336 (ttp) REVERT: d 183 GLU cc_start: 0.6531 (pm20) cc_final: 0.5866 (pt0) REVERT: d 184 ARG cc_start: 0.6775 (OUTLIER) cc_final: 0.6506 (mtm180) REVERT: d 185 ASN cc_start: 0.7249 (m-40) cc_final: 0.6699 (m-40) REVERT: d 202 ILE cc_start: 0.8137 (mt) cc_final: 0.7831 (mm) REVERT: e 25 GLU cc_start: 0.7443 (tt0) cc_final: 0.7083 (tt0) REVERT: e 61 ARG cc_start: 0.5891 (mtp180) cc_final: 0.5661 (ptm-80) REVERT: e 141 MET cc_start: 0.6386 (mtp) cc_final: 0.5923 (mtp) REVERT: e 144 GLU cc_start: 0.6479 (pm20) cc_final: 0.6172 (pm20) REVERT: e 150 THR cc_start: 0.7233 (p) cc_final: 0.6834 (m) REVERT: e 165 HIS cc_start: 0.3126 (OUTLIER) cc_final: 0.2440 (m-70) REVERT: e 194 LYS cc_start: 0.5559 (mmmt) cc_final: 0.5275 (mmtm) REVERT: e 197 GLU cc_start: 0.6604 (tt0) cc_final: 0.6032 (mt-10) REVERT: f 3 LYS cc_start: 0.5255 (ptmm) cc_final: 0.4873 (mmpt) REVERT: f 44 ILE cc_start: 0.4999 (OUTLIER) cc_final: 0.4686 (mp) REVERT: f 49 LEU cc_start: 0.4380 (pt) cc_final: 0.4109 (mt) REVERT: f 64 LYS cc_start: 0.3032 (mptp) cc_final: 0.2779 (tttm) REVERT: f 80 ARG cc_start: 0.5497 (ttm110) cc_final: 0.4696 (tpp80) REVERT: f 111 ILE cc_start: 0.6276 (pp) cc_final: 0.5912 (mt) REVERT: f 117 LEU cc_start: 0.5346 (OUTLIER) cc_final: 0.5072 (mp) REVERT: f 125 ARG cc_start: 0.5210 (mtt-85) cc_final: 0.4797 (mtp85) REVERT: f 148 ARG cc_start: 0.5611 (mmm-85) cc_final: 0.4994 (ttm110) REVERT: g 36 THR cc_start: 0.7140 (OUTLIER) cc_final: 0.6771 (p) REVERT: g 75 MET cc_start: 0.6723 (OUTLIER) cc_final: 0.6473 (mtt) REVERT: g 139 GLN cc_start: 0.6606 (tm-30) cc_final: 0.6071 (tt0) REVERT: g 153 ARG cc_start: 0.7237 (ptp90) cc_final: 0.6289 (mtt90) REVERT: g 169 VAL cc_start: 0.6549 (OUTLIER) cc_final: 0.6314 (p) REVERT: h 15 LEU cc_start: 0.5176 (OUTLIER) cc_final: 0.4670 (pp) REVERT: j 2 LYS cc_start: 0.7118 (mmmt) cc_final: 0.6637 (mtmt) REVERT: j 91 GLU cc_start: 0.6863 (mt-10) cc_final: 0.6505 (mt-10) REVERT: j 95 ARG cc_start: 0.6711 (mpt180) cc_final: 0.6294 (mpt-90) REVERT: j 98 GLU cc_start: 0.7237 (OUTLIER) cc_final: 0.7009 (mp0) REVERT: j 106 LYS cc_start: 0.7143 (tttp) cc_final: 0.6296 (ttpt) REVERT: j 138 GLN cc_start: 0.7742 (pt0) cc_final: 0.7432 (pt0) REVERT: k 20 MET cc_start: 0.8321 (ttm) cc_final: 0.8058 (ttp) REVERT: k 53 LYS cc_start: 0.6878 (mmpt) cc_final: 0.5901 (mppt) REVERT: k 98 ARG cc_start: 0.5772 (mtt180) cc_final: 0.5220 (mtm110) REVERT: k 114 LYS cc_start: 0.6332 (mtpp) cc_final: 0.5401 (tppt) REVERT: l 2 ARG cc_start: 0.7565 (mmt180) cc_final: 0.6814 (mmt180) REVERT: l 55 MET cc_start: 0.7796 (tpp) cc_final: 0.7569 (tpp) REVERT: l 106 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7338 (pt0) REVERT: l 123 ARG cc_start: 0.7403 (tpp80) cc_final: 0.6892 (tpp80) REVERT: m 1 MET cc_start: 0.6419 (OUTLIER) cc_final: 0.5890 (tpp) REVERT: m 78 LEU cc_start: 0.8047 (tp) cc_final: 0.7766 (tp) REVERT: m 118 LYS cc_start: 0.7169 (ttpp) cc_final: 0.5971 (tmtm) REVERT: m 127 LYS cc_start: 0.6898 (mtpp) cc_final: 0.5890 (mmtt) REVERT: n 35 LYS cc_start: 0.8066 (tttt) cc_final: 0.7639 (tttm) REVERT: n 82 GLU cc_start: 0.7147 (mt-10) cc_final: 0.6926 (mt-10) REVERT: n 114 GLU cc_start: 0.8143 (pt0) cc_final: 0.7739 (pt0) REVERT: o 5 SER cc_start: 0.7741 (OUTLIER) cc_final: 0.7355 (p) REVERT: o 9 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.7750 (tmm160) REVERT: o 54 VAL cc_start: 0.6986 (OUTLIER) cc_final: 0.6778 (m) REVERT: o 55 GLU cc_start: 0.6734 (mt-10) cc_final: 0.6194 (mt-10) REVERT: o 62 LEU cc_start: 0.7211 (OUTLIER) cc_final: 0.6904 (mm) REVERT: p 6 LYS cc_start: 0.6858 (ttmm) cc_final: 0.6574 (mtmt) REVERT: p 11 GLU cc_start: 0.7208 (pt0) cc_final: 0.6827 (pt0) REVERT: p 71 GLU cc_start: 0.8577 (mt-10) cc_final: 0.8353 (mt-10) REVERT: p 89 ARG cc_start: 0.6614 (mtm-85) cc_final: 0.5686 (mtt-85) REVERT: q 71 GLN cc_start: 0.6459 (OUTLIER) cc_final: 0.5653 (mm110) REVERT: q 85 LYS cc_start: 0.6590 (mtmt) cc_final: 0.6140 (mttp) REVERT: q 89 GLU cc_start: 0.7456 (OUTLIER) cc_final: 0.7133 (mt-10) REVERT: r 60 LYS cc_start: 0.7215 (mptp) cc_final: 0.6895 (mptm) REVERT: s 28 LYS cc_start: 0.7291 (mttp) cc_final: 0.6794 (mttm) REVERT: s 33 LEU cc_start: 0.6858 (OUTLIER) cc_final: 0.6627 (mp) REVERT: s 66 ILE cc_start: 0.6869 (OUTLIER) cc_final: 0.5943 (mm) REVERT: s 70 LYS cc_start: 0.7470 (mttp) cc_final: 0.7100 (mtmm) REVERT: s 73 LYS cc_start: 0.7569 (mtmm) cc_final: 0.7321 (ttmt) REVERT: s 92 ARG cc_start: 0.6325 (mtp-110) cc_final: 0.5350 (ttp-170) REVERT: t 6 ARG cc_start: 0.6404 (OUTLIER) cc_final: 0.5945 (tpt-90) REVERT: t 25 GLU cc_start: 0.7177 (OUTLIER) cc_final: 0.6959 (pt0) REVERT: t 49 LYS cc_start: 0.7267 (tttm) cc_final: 0.6966 (tttp) REVERT: t 56 GLU cc_start: 0.7269 (mm-30) cc_final: 0.7065 (tt0) REVERT: u 10 GLU cc_start: 0.6706 (mm-30) cc_final: 0.5788 (tp30) REVERT: u 21 LYS cc_start: 0.7821 (OUTLIER) cc_final: 0.7521 (mttt) REVERT: u 24 LYS cc_start: 0.7081 (ttmm) cc_final: 0.6174 (tmmt) REVERT: u 46 GLN cc_start: 0.7289 (mm-40) cc_final: 0.7069 (mm-40) REVERT: w 1 MET cc_start: 0.4856 (ppp) cc_final: 0.4275 (mmt) REVERT: w 24 ASN cc_start: 0.7099 (t0) cc_final: 0.5910 (m-40) REVERT: w 41 GLU cc_start: 0.7487 (mt-10) cc_final: 0.7139 (mt-10) REVERT: w 46 LYS cc_start: 0.6952 (mmtp) cc_final: 0.6409 (mtpp) REVERT: w 53 LYS cc_start: 0.6013 (mttm) cc_final: 0.5248 (mmtt) REVERT: y 11 ARG cc_start: 0.6300 (ptm160) cc_final: 0.6065 (ptm160) REVERT: y 17 GLU cc_start: 0.6962 (pt0) cc_final: 0.6501 (pt0) REVERT: y 51 VAL cc_start: 0.7501 (OUTLIER) cc_final: 0.7021 (t) REVERT: y 62 LYS cc_start: 0.7939 (mtmt) cc_final: 0.7737 (mtpp) REVERT: y 68 LYS cc_start: 0.7942 (tttm) cc_final: 0.7397 (tptt) REVERT: y 70 GLU cc_start: 0.7356 (tt0) cc_final: 0.7108 (mt-10) REVERT: y 83 GLU cc_start: 0.7028 (mt-10) cc_final: 0.6249 (mm-30) outliers start: 181 outliers final: 59 residues processed: 620 average time/residue: 1.9520 time to fit residues: 1598.8791 Evaluate side-chains 540 residues out of total 2526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 448 time to evaluate : 3.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 2 SER Chi-restraints excluded: chain 0 residue 66 THR Chi-restraints excluded: chain 1 residue 11 VAL Chi-restraints excluded: chain 1 residue 39 GLN Chi-restraints excluded: chain 1 residue 58 ASN Chi-restraints excluded: chain 2 residue 36 VAL Chi-restraints excluded: chain 2 residue 41 THR Chi-restraints excluded: chain 3 residue 12 LYS Chi-restraints excluded: chain 3 residue 27 SER Chi-restraints excluded: chain 4 residue 5 ILE Chi-restraints excluded: chain 4 residue 17 THR Chi-restraints excluded: chain 4 residue 37 LYS Chi-restraints excluded: chain 4 residue 42 VAL Chi-restraints excluded: chain 4 residue 43 VAL Chi-restraints excluded: chain 6 residue 1 MET Chi-restraints excluded: chain 7 residue 6 THR Chi-restraints excluded: chain 7 residue 19 LYS Chi-restraints excluded: chain 8 residue 10 LEU Chi-restraints excluded: chain c residue 7 LYS Chi-restraints excluded: chain c residue 20 VAL Chi-restraints excluded: chain c residue 74 ILE Chi-restraints excluded: chain c residue 162 VAL Chi-restraints excluded: chain c residue 220 VAL Chi-restraints excluded: chain c residue 265 LYS Chi-restraints excluded: chain c residue 272 SER Chi-restraints excluded: chain d residue 2 ILE Chi-restraints excluded: chain d residue 29 VAL Chi-restraints excluded: chain d residue 40 LEU Chi-restraints excluded: chain d residue 103 ASP Chi-restraints excluded: chain d residue 139 SER Chi-restraints excluded: chain d residue 184 ARG Chi-restraints excluded: chain e residue 4 VAL Chi-restraints excluded: chain e residue 165 HIS Chi-restraints excluded: chain f residue 24 SER Chi-restraints excluded: chain f residue 35 THR Chi-restraints excluded: chain f residue 44 ILE Chi-restraints excluded: chain f residue 104 ILE Chi-restraints excluded: chain f residue 108 VAL Chi-restraints excluded: chain f residue 117 LEU Chi-restraints excluded: chain f residue 142 ASP Chi-restraints excluded: chain f residue 146 VAL Chi-restraints excluded: chain g residue 17 VAL Chi-restraints excluded: chain g residue 36 THR Chi-restraints excluded: chain g residue 75 MET Chi-restraints excluded: chain g residue 81 GLU Chi-restraints excluded: chain g residue 90 VAL Chi-restraints excluded: chain g residue 169 VAL Chi-restraints excluded: chain h residue 3 VAL Chi-restraints excluded: chain h residue 9 VAL Chi-restraints excluded: chain h residue 15 LEU Chi-restraints excluded: chain h residue 25 TYR Chi-restraints excluded: chain j residue 98 GLU Chi-restraints excluded: chain j residue 131 ASN Chi-restraints excluded: chain k residue 35 VAL Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 80 ASP Chi-restraints excluded: chain l residue 106 GLU Chi-restraints excluded: chain l residue 117 THR Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain m residue 1 MET Chi-restraints excluded: chain m residue 5 LYS Chi-restraints excluded: chain m residue 7 THR Chi-restraints excluded: chain m residue 30 SER Chi-restraints excluded: chain m residue 135 VAL Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain n residue 70 THR Chi-restraints excluded: chain o residue 5 SER Chi-restraints excluded: chain o residue 9 ARG Chi-restraints excluded: chain o residue 24 THR Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain o residue 49 VAL Chi-restraints excluded: chain o residue 54 VAL Chi-restraints excluded: chain o residue 62 LEU Chi-restraints excluded: chain p residue 46 VAL Chi-restraints excluded: chain q residue 71 GLN Chi-restraints excluded: chain q residue 89 GLU Chi-restraints excluded: chain r residue 34 GLU Chi-restraints excluded: chain r residue 47 VAL Chi-restraints excluded: chain s residue 33 LEU Chi-restraints excluded: chain s residue 66 ILE Chi-restraints excluded: chain s residue 101 SER Chi-restraints excluded: chain t residue 6 ARG Chi-restraints excluded: chain t residue 25 GLU Chi-restraints excluded: chain t residue 67 VAL Chi-restraints excluded: chain t residue 69 GLN Chi-restraints excluded: chain u residue 21 LYS Chi-restraints excluded: chain u residue 39 ILE Chi-restraints excluded: chain u residue 41 LEU Chi-restraints excluded: chain u residue 68 SER Chi-restraints excluded: chain w residue 72 VAL Chi-restraints excluded: chain y residue 43 THR Chi-restraints excluded: chain y residue 51 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 607 random chunks: chunk 306 optimal weight: 8.9990 chunk 171 optimal weight: 10.0000 chunk 458 optimal weight: 9.9990 chunk 375 optimal weight: 0.5980 chunk 152 optimal weight: 10.0000 chunk 552 optimal weight: 5.9990 chunk 596 optimal weight: 20.0000 chunk 491 optimal weight: 3.9990 chunk 547 optimal weight: 10.0000 chunk 188 optimal weight: 10.0000 chunk 443 optimal weight: 4.9990 overall best weight: 4.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 38 GLN 3 5 GLN 6 29 GLN c 25 HIS c 260 ASN d 49 GLN d 126 ASN e 30 GLN f 63 GLN g 128 GLN j 128 ASN k 88 ASN o 34 HIS ** o 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 66 ASN q 56 GLN r 43 ASN r 86 GLN s 31 GLN t 59 ASN u 54 GLN w 12 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6590 moved from start: 0.3632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 98998 Z= 0.330 Angle : 0.728 11.075 149023 Z= 0.380 Chirality : 0.043 0.349 19174 Planarity : 0.006 0.082 7331 Dihedral : 24.360 179.549 51745 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.17 % Favored : 94.67 % Rotamer: Outliers : 8.55 % Allowed : 27.99 % Favored : 63.46 % 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: -0.68 (0.15), residues: 3057 helix: 0.60 (0.18), residues: 810 sheet: -0.43 (0.19), residues: 705 loop : -0.99 (0.15), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP c 213 HIS 0.014 0.002 HIS r 89 PHE 0.028 0.003 PHE h 29 TYR 0.020 0.002 TYR q 32 ARG 0.009 0.001 ARG t 77 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 687 residues out of total 2526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 216 poor density : 471 time to evaluate : 3.819 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 60 ASP cc_start: 0.6407 (p0) cc_final: 0.5855 (m-30) REVERT: 0 62 LYS cc_start: 0.7389 (OUTLIER) cc_final: 0.7147 (mtmm) REVERT: 0 76 GLU cc_start: 0.5564 (OUTLIER) cc_final: 0.5088 (tp30) REVERT: 1 4 LYS cc_start: 0.4788 (OUTLIER) cc_final: 0.4084 (ttmt) REVERT: 1 24 GLU cc_start: 0.6201 (tp30) cc_final: 0.5506 (tp30) REVERT: 1 44 LYS cc_start: 0.6492 (OUTLIER) cc_final: 0.5852 (ttmt) REVERT: 1 59 GLU cc_start: 0.6915 (OUTLIER) cc_final: 0.6556 (mt-10) REVERT: 2 19 LYS cc_start: 0.7271 (OUTLIER) cc_final: 0.7016 (tttm) REVERT: 3 9 THR cc_start: 0.7208 (m) cc_final: 0.6784 (p) REVERT: 3 12 LYS cc_start: 0.6862 (OUTLIER) cc_final: 0.6244 (mmtm) REVERT: 3 15 MET cc_start: 0.8236 (mtm) cc_final: 0.8029 (mtm) REVERT: 4 30 LYS cc_start: 0.6450 (OUTLIER) cc_final: 0.5970 (ptmt) REVERT: 4 37 LYS cc_start: 0.7325 (OUTLIER) cc_final: 0.7002 (mttp) REVERT: 4 45 GLN cc_start: 0.7142 (mm110) cc_final: 0.6512 (mm110) REVERT: 6 1 MET cc_start: 0.7227 (mpp) cc_final: 0.6660 (mpp) REVERT: 8 13 ASN cc_start: 0.7192 (m110) cc_final: 0.6938 (m-40) REVERT: 8 15 LYS cc_start: 0.6784 (ttmm) cc_final: 0.5897 (tttp) REVERT: c 5 LYS cc_start: 0.7150 (tttp) cc_final: 0.6632 (tptp) REVERT: c 7 LYS cc_start: 0.7990 (OUTLIER) cc_final: 0.7614 (mttt) REVERT: c 74 ILE cc_start: 0.7065 (OUTLIER) cc_final: 0.6778 (mm) REVERT: c 79 GLU cc_start: 0.7086 (OUTLIER) cc_final: 0.6583 (mt-10) REVERT: c 87 ARG cc_start: 0.6808 (OUTLIER) cc_final: 0.6210 (mtt-85) REVERT: c 110 LEU cc_start: 0.7255 (OUTLIER) cc_final: 0.6994 (tp) REVERT: c 125 LYS cc_start: 0.7327 (ptmm) cc_final: 0.6971 (pttt) REVERT: c 146 MET cc_start: 0.7809 (mtm) cc_final: 0.7495 (mtp) REVERT: c 163 GLN cc_start: 0.7435 (OUTLIER) cc_final: 0.7180 (mt0) REVERT: c 183 LYS cc_start: 0.7497 (OUTLIER) cc_final: 0.6955 (mttt) REVERT: c 265 LYS cc_start: 0.7936 (OUTLIER) cc_final: 0.7722 (pttm) REVERT: c 269 ARG cc_start: 0.6875 (ttp80) cc_final: 0.6262 (ttt90) REVERT: d 1 MET cc_start: 0.5548 (ttm) cc_final: 0.5244 (ttm) REVERT: d 7 LYS cc_start: 0.7853 (ttpp) cc_final: 0.7304 (ttmm) REVERT: d 13 ARG cc_start: 0.8079 (OUTLIER) cc_final: 0.6507 (ptt180) REVERT: d 40 LEU cc_start: 0.7855 (OUTLIER) cc_final: 0.7646 (mp) REVERT: d 48 ILE cc_start: 0.7507 (OUTLIER) cc_final: 0.7209 (pp) REVERT: d 64 GLU cc_start: 0.6366 (mt-10) cc_final: 0.5355 (mm-30) REVERT: d 74 GLU cc_start: 0.7256 (tp30) cc_final: 0.6994 (mm-30) REVERT: d 103 ASP cc_start: 0.6403 (OUTLIER) cc_final: 0.5702 (m-30) REVERT: d 128 ARG cc_start: 0.5521 (mtp180) cc_final: 0.5101 (mmp80) REVERT: d 183 GLU cc_start: 0.6308 (pm20) cc_final: 0.5668 (pt0) REVERT: d 184 ARG cc_start: 0.6982 (OUTLIER) cc_final: 0.6757 (mtm180) REVERT: d 202 ILE cc_start: 0.7920 (mt) cc_final: 0.7684 (mm) REVERT: e 13 THR cc_start: 0.7311 (OUTLIER) cc_final: 0.7014 (m) REVERT: e 21 ARG cc_start: 0.6597 (OUTLIER) cc_final: 0.5972 (mtp85) REVERT: e 25 GLU cc_start: 0.7466 (tt0) cc_final: 0.7113 (tt0) REVERT: e 61 ARG cc_start: 0.6622 (mtp180) cc_final: 0.6322 (ptm-80) REVERT: e 137 LYS cc_start: 0.6785 (tttt) cc_final: 0.6556 (tttt) REVERT: e 139 LYS cc_start: 0.7241 (tttp) cc_final: 0.6671 (ttmp) REVERT: e 141 MET cc_start: 0.6586 (mtp) cc_final: 0.5972 (mtp) REVERT: e 194 LYS cc_start: 0.5724 (mmmt) cc_final: 0.5345 (mmtm) REVERT: e 197 GLU cc_start: 0.6693 (tt0) cc_final: 0.6210 (mt-10) REVERT: f 3 LYS cc_start: 0.5417 (ptmm) cc_final: 0.4884 (mmpt) REVERT: f 49 LEU cc_start: 0.4465 (pt) cc_final: 0.4033 (mt) REVERT: f 64 LYS cc_start: 0.3051 (mptp) cc_final: 0.2707 (tttm) REVERT: f 88 LYS cc_start: 0.6448 (OUTLIER) cc_final: 0.6035 (tttt) REVERT: f 117 LEU cc_start: 0.5323 (OUTLIER) cc_final: 0.5025 (mp) REVERT: f 125 ARG cc_start: 0.5217 (mtt-85) cc_final: 0.4678 (mtp85) REVERT: f 150 ARG cc_start: 0.4705 (mtt90) cc_final: 0.4385 (ptp90) REVERT: g 36 THR cc_start: 0.7161 (OUTLIER) cc_final: 0.6772 (m) REVERT: g 121 ILE cc_start: 0.7181 (mm) cc_final: 0.6876 (mp) REVERT: g 153 ARG cc_start: 0.7364 (ptp90) cc_final: 0.6574 (mtt90) REVERT: g 177 LYS cc_start: 0.2007 (OUTLIER) cc_final: 0.1765 (pttp) REVERT: h 15 LEU cc_start: 0.5490 (OUTLIER) cc_final: 0.5031 (pp) REVERT: j 2 LYS cc_start: 0.7219 (mmmt) cc_final: 0.6631 (mtmt) REVERT: j 43 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7074 (pm20) REVERT: j 61 LYS cc_start: 0.7220 (OUTLIER) cc_final: 0.6539 (mmtt) REVERT: j 98 GLU cc_start: 0.7308 (OUTLIER) cc_final: 0.7048 (mp0) REVERT: j 106 LYS cc_start: 0.7541 (tttp) cc_final: 0.6598 (ttpt) REVERT: k 53 LYS cc_start: 0.6931 (mmpt) cc_final: 0.5792 (mppt) REVERT: k 98 ARG cc_start: 0.5607 (mtt180) cc_final: 0.4932 (mtm110) REVERT: l 55 MET cc_start: 0.8007 (tpp) cc_final: 0.7759 (tpp) REVERT: l 106 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7137 (pm20) REVERT: l 123 ARG cc_start: 0.7810 (tpp80) cc_final: 0.7164 (tpp80) REVERT: m 6 ARG cc_start: 0.7312 (OUTLIER) cc_final: 0.6606 (mtp85) REVERT: m 118 LYS cc_start: 0.7039 (ttpp) cc_final: 0.6657 (ttmm) REVERT: m 126 ILE cc_start: 0.7505 (OUTLIER) cc_final: 0.7222 (mm) REVERT: m 127 LYS cc_start: 0.7031 (mtpp) cc_final: 0.6807 (mtpp) REVERT: n 18 GLN cc_start: 0.6810 (OUTLIER) cc_final: 0.6422 (tt0) REVERT: n 35 LYS cc_start: 0.7981 (tttt) cc_final: 0.7506 (tttm) REVERT: n 114 GLU cc_start: 0.8152 (pt0) cc_final: 0.7787 (pt0) REVERT: o 10 ARG cc_start: 0.7389 (OUTLIER) cc_final: 0.5680 (mtp180) REVERT: o 55 GLU cc_start: 0.6463 (mt-10) cc_final: 0.6081 (mt-10) REVERT: p 7 GLN cc_start: 0.7044 (OUTLIER) cc_final: 0.6508 (pp30) REVERT: p 11 GLU cc_start: 0.7292 (pt0) cc_final: 0.6777 (pt0) REVERT: p 89 ARG cc_start: 0.6815 (mtm-85) cc_final: 0.5816 (mtt-85) REVERT: p 102 GLU cc_start: 0.6797 (mm-30) cc_final: 0.6387 (mp0) REVERT: p 112 GLU cc_start: 0.6992 (tt0) cc_final: 0.6360 (tt0) REVERT: q 71 GLN cc_start: 0.6528 (OUTLIER) cc_final: 0.6130 (mm110) REVERT: q 85 LYS cc_start: 0.7399 (mtmt) cc_final: 0.6792 (mttt) REVERT: q 89 GLU cc_start: 0.7478 (OUTLIER) cc_final: 0.7049 (mt-10) REVERT: r 13 ARG cc_start: 0.8460 (ttp80) cc_final: 0.8001 (ttp80) REVERT: r 26 ASP cc_start: 0.6891 (OUTLIER) cc_final: 0.6602 (t0) REVERT: r 34 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.6983 (mp0) REVERT: r 60 LYS cc_start: 0.7486 (mptp) cc_final: 0.7228 (mttm) REVERT: r 70 GLU cc_start: 0.6891 (tt0) cc_final: 0.6120 (tp30) REVERT: s 2 GLU cc_start: 0.7277 (mt-10) cc_final: 0.7017 (mt-10) REVERT: s 28 LYS cc_start: 0.7301 (mttp) cc_final: 0.6845 (mttm) REVERT: s 70 LYS cc_start: 0.7497 (mttp) cc_final: 0.7195 (mtmm) REVERT: s 73 LYS cc_start: 0.7579 (mtmm) cc_final: 0.7377 (mtpt) REVERT: s 92 ARG cc_start: 0.6635 (mtp-110) cc_final: 0.5481 (mtm110) REVERT: s 95 ARG cc_start: 0.6791 (tpp80) cc_final: 0.5002 (ppt90) REVERT: s 109 ASP cc_start: 0.6449 (OUTLIER) cc_final: 0.5518 (p0) REVERT: t 1 MET cc_start: 0.6754 (tpp) cc_final: 0.6494 (tpp) REVERT: t 4 GLU cc_start: 0.6653 (OUTLIER) cc_final: 0.6427 (tp30) REVERT: t 25 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.7247 (pt0) REVERT: t 26 LYS cc_start: 0.6728 (tppp) cc_final: 0.6436 (mmtp) REVERT: t 32 LEU cc_start: 0.7763 (OUTLIER) cc_final: 0.7382 (pp) REVERT: t 49 LYS cc_start: 0.7211 (tttm) cc_final: 0.6614 (tttp) REVERT: t 54 GLU cc_start: 0.5536 (pm20) cc_final: 0.5204 (mm-30) REVERT: t 56 GLU cc_start: 0.7501 (mm-30) cc_final: 0.7249 (tt0) REVERT: u 10 GLU cc_start: 0.7109 (mm-30) cc_final: 0.6227 (tp30) REVERT: u 21 LYS cc_start: 0.8096 (OUTLIER) cc_final: 0.7634 (mmmm) REVERT: u 24 LYS cc_start: 0.7472 (ttmm) cc_final: 0.6435 (ttpp) REVERT: u 46 GLN cc_start: 0.7450 (mm-40) cc_final: 0.7137 (mm-40) REVERT: w 1 MET cc_start: 0.4933 (ppp) cc_final: 0.4267 (mmt) REVERT: w 24 ASN cc_start: 0.7560 (t0) cc_final: 0.6414 (m-40) REVERT: w 41 GLU cc_start: 0.7337 (mt-10) cc_final: 0.7128 (mt-10) REVERT: w 53 LYS cc_start: 0.5969 (mttm) cc_final: 0.5215 (mmtt) REVERT: y 11 ARG cc_start: 0.6468 (ptm160) cc_final: 0.6130 (ptt-90) REVERT: y 17 GLU cc_start: 0.7229 (OUTLIER) cc_final: 0.6542 (pp20) REVERT: y 62 LYS cc_start: 0.8014 (mtmt) cc_final: 0.7803 (mtpp) REVERT: y 68 LYS cc_start: 0.7974 (OUTLIER) cc_final: 0.7537 (tptt) outliers start: 216 outliers final: 91 residues processed: 613 average time/residue: 1.9848 time to fit residues: 1595.5540 Evaluate side-chains 591 residues out of total 2526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 451 time to evaluate : 3.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 2 SER Chi-restraints excluded: chain 0 residue 25 THR Chi-restraints excluded: chain 0 residue 62 LYS Chi-restraints excluded: chain 0 residue 66 THR Chi-restraints excluded: chain 0 residue 76 GLU Chi-restraints excluded: chain 1 residue 4 LYS Chi-restraints excluded: chain 1 residue 44 LYS Chi-restraints excluded: chain 1 residue 58 ASN Chi-restraints excluded: chain 1 residue 59 GLU Chi-restraints excluded: chain 2 residue 19 LYS Chi-restraints excluded: chain 2 residue 36 VAL Chi-restraints excluded: chain 3 residue 12 LYS Chi-restraints excluded: chain 4 residue 5 ILE Chi-restraints excluded: chain 4 residue 17 THR Chi-restraints excluded: chain 4 residue 30 LYS Chi-restraints excluded: chain 4 residue 37 LYS Chi-restraints excluded: chain 4 residue 42 VAL Chi-restraints excluded: chain 4 residue 43 VAL Chi-restraints excluded: chain 7 residue 6 THR Chi-restraints excluded: chain 7 residue 52 LYS Chi-restraints excluded: chain 8 residue 10 LEU Chi-restraints excluded: chain 8 residue 32 LYS Chi-restraints excluded: chain c residue 7 LYS Chi-restraints excluded: chain c residue 20 VAL Chi-restraints excluded: chain c residue 74 ILE Chi-restraints excluded: chain c residue 79 GLU Chi-restraints excluded: chain c residue 87 ARG Chi-restraints excluded: chain c residue 110 LEU Chi-restraints excluded: chain c residue 118 SER Chi-restraints excluded: chain c residue 120 VAL Chi-restraints excluded: chain c residue 132 MET Chi-restraints excluded: chain c residue 162 VAL Chi-restraints excluded: chain c residue 163 GLN Chi-restraints excluded: chain c residue 183 LYS Chi-restraints excluded: chain c residue 265 LYS Chi-restraints excluded: chain c residue 272 SER Chi-restraints excluded: chain d residue 13 ARG Chi-restraints excluded: chain d residue 29 VAL Chi-restraints excluded: chain d residue 40 LEU Chi-restraints excluded: chain d residue 48 ILE Chi-restraints excluded: chain d residue 95 SER Chi-restraints excluded: chain d residue 103 ASP Chi-restraints excluded: chain d residue 131 ASP Chi-restraints excluded: chain d residue 151 THR Chi-restraints excluded: chain d residue 175 LEU Chi-restraints excluded: chain d residue 184 ARG Chi-restraints excluded: chain e residue 4 VAL Chi-restraints excluded: chain e residue 10 SER Chi-restraints excluded: chain e residue 13 THR Chi-restraints excluded: chain e residue 21 ARG Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain e residue 95 LYS Chi-restraints excluded: chain e residue 119 ILE Chi-restraints excluded: chain e residue 173 THR Chi-restraints excluded: chain f residue 26 MET Chi-restraints excluded: chain f residue 35 THR Chi-restraints excluded: chain f residue 88 LYS Chi-restraints excluded: chain f residue 104 ILE Chi-restraints excluded: chain f residue 108 VAL Chi-restraints excluded: chain f residue 117 LEU Chi-restraints excluded: chain f residue 132 VAL Chi-restraints excluded: chain f residue 142 ASP Chi-restraints excluded: chain f residue 146 VAL Chi-restraints excluded: chain g residue 11 VAL Chi-restraints excluded: chain g residue 17 VAL Chi-restraints excluded: chain g residue 36 THR Chi-restraints excluded: chain g residue 51 THR Chi-restraints excluded: chain g residue 81 GLU Chi-restraints excluded: chain g residue 90 VAL Chi-restraints excluded: chain g residue 99 LYS Chi-restraints excluded: chain g residue 107 LEU Chi-restraints excluded: chain g residue 177 LYS Chi-restraints excluded: chain h residue 3 VAL Chi-restraints excluded: chain h residue 9 VAL Chi-restraints excluded: chain h residue 15 LEU Chi-restraints excluded: chain h residue 22 LYS Chi-restraints excluded: chain h residue 37 VAL Chi-restraints excluded: chain j residue 11 VAL Chi-restraints excluded: chain j residue 43 GLU Chi-restraints excluded: chain j residue 61 LYS Chi-restraints excluded: chain j residue 62 VAL Chi-restraints excluded: chain j residue 64 VAL Chi-restraints excluded: chain j residue 98 GLU Chi-restraints excluded: chain j residue 131 ASN Chi-restraints excluded: chain k residue 35 VAL Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 80 ASP Chi-restraints excluded: chain k residue 88 ASN Chi-restraints excluded: chain l residue 95 LEU Chi-restraints excluded: chain l residue 106 GLU Chi-restraints excluded: chain l residue 117 THR Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain m residue 6 ARG Chi-restraints excluded: chain m residue 7 THR Chi-restraints excluded: chain m residue 30 SER Chi-restraints excluded: chain m residue 104 GLU Chi-restraints excluded: chain m residue 126 ILE Chi-restraints excluded: chain m residue 129 THR Chi-restraints excluded: chain n residue 14 SER Chi-restraints excluded: chain n residue 18 GLN Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain n residue 70 THR Chi-restraints excluded: chain o residue 10 ARG Chi-restraints excluded: chain o residue 24 THR Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain o residue 48 LEU Chi-restraints excluded: chain o residue 49 VAL Chi-restraints excluded: chain o residue 54 VAL Chi-restraints excluded: chain o residue 62 LEU Chi-restraints excluded: chain o residue 67 ASN Chi-restraints excluded: chain p residue 7 GLN Chi-restraints excluded: chain p residue 70 VAL Chi-restraints excluded: chain q residue 58 ARG Chi-restraints excluded: chain q residue 71 GLN Chi-restraints excluded: chain q residue 84 LYS Chi-restraints excluded: chain q residue 89 GLU Chi-restraints excluded: chain r residue 26 ASP Chi-restraints excluded: chain r residue 34 GLU Chi-restraints excluded: chain r residue 45 GLU Chi-restraints excluded: chain r residue 47 VAL Chi-restraints excluded: chain r residue 85 LYS Chi-restraints excluded: chain s residue 101 SER Chi-restraints excluded: chain s residue 109 ASP Chi-restraints excluded: chain t residue 4 GLU Chi-restraints excluded: chain t residue 25 GLU Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain t residue 36 LYS Chi-restraints excluded: chain t residue 50 LEU Chi-restraints excluded: chain t residue 67 VAL Chi-restraints excluded: chain t residue 69 GLN Chi-restraints excluded: chain t residue 100 ASN Chi-restraints excluded: chain u residue 21 LYS Chi-restraints excluded: chain u residue 68 SER Chi-restraints excluded: chain w residue 72 VAL Chi-restraints excluded: chain y residue 17 GLU Chi-restraints excluded: chain y residue 19 LYS Chi-restraints excluded: chain y residue 43 THR Chi-restraints excluded: chain y residue 51 VAL Chi-restraints excluded: chain y residue 68 LYS Chi-restraints excluded: chain y residue 72 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 607 random chunks: chunk 545 optimal weight: 8.9990 chunk 415 optimal weight: 1.9990 chunk 286 optimal weight: 10.0000 chunk 61 optimal weight: 10.0000 chunk 263 optimal weight: 40.0000 chunk 370 optimal weight: 5.9990 chunk 554 optimal weight: 0.6980 chunk 586 optimal weight: 30.0000 chunk 289 optimal weight: 10.0000 chunk 525 optimal weight: 8.9990 chunk 158 optimal weight: 50.0000 overall best weight: 5.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 5 GLN 6 29 GLN c 260 ASN d 173 GLN d 185 ASN e 94 GLN f 63 GLN g 104 ASN ** j 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 128 ASN ** p 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 56 GLN r 86 GLN s 31 GLN t 59 ASN t 99 GLN ** u 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6594 moved from start: 0.3836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 98998 Z= 0.337 Angle : 0.710 11.152 149023 Z= 0.370 Chirality : 0.043 0.350 19174 Planarity : 0.006 0.086 7331 Dihedral : 24.300 179.371 51743 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.78 % Favored : 95.06 % Rotamer: Outliers : 8.08 % Allowed : 27.16 % Favored : 64.77 % 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: -0.64 (0.15), residues: 3057 helix: 0.59 (0.18), residues: 809 sheet: -0.36 (0.19), residues: 710 loop : -0.95 (0.15), residues: 1538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP c 213 HIS 0.012 0.002 HIS r 89 PHE 0.023 0.002 PHE h 29 TYR 0.019 0.002 TYR q 32 ARG 0.008 0.001 ARG 4 44 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 684 residues out of total 2526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 480 time to evaluate : 4.401 Fit side-chains revert: symmetry clash REVERT: 0 60 ASP cc_start: 0.6289 (p0) cc_final: 0.5974 (m-30) REVERT: 0 62 LYS cc_start: 0.7386 (OUTLIER) cc_final: 0.6815 (mtmm) REVERT: 0 72 ARG cc_start: 0.7028 (mtm-85) cc_final: 0.6707 (mtm-85) REVERT: 1 4 LYS cc_start: 0.5046 (OUTLIER) cc_final: 0.4264 (ttmt) REVERT: 1 13 GLU cc_start: 0.6436 (pt0) cc_final: 0.6028 (pt0) REVERT: 1 24 GLU cc_start: 0.6218 (tp30) cc_final: 0.5526 (tp30) REVERT: 1 44 LYS cc_start: 0.6430 (OUTLIER) cc_final: 0.5805 (ttmt) REVERT: 1 59 GLU cc_start: 0.6737 (OUTLIER) cc_final: 0.6426 (mt-10) REVERT: 2 19 LYS cc_start: 0.7292 (OUTLIER) cc_final: 0.7035 (tttm) REVERT: 2 39 GLU cc_start: 0.7761 (pm20) cc_final: 0.7383 (pt0) REVERT: 2 56 LYS cc_start: 0.7564 (OUTLIER) cc_final: 0.7044 (ttpp) REVERT: 3 9 THR cc_start: 0.7160 (m) cc_final: 0.6741 (p) REVERT: 3 12 LYS cc_start: 0.6748 (OUTLIER) cc_final: 0.6097 (mmtm) REVERT: 4 7 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7506 (pm20) REVERT: 4 37 LYS cc_start: 0.7462 (OUTLIER) cc_final: 0.7125 (mttp) REVERT: 4 44 ARG cc_start: 0.6481 (OUTLIER) cc_final: 0.5870 (mmm160) REVERT: 4 45 GLN cc_start: 0.7167 (mm110) cc_final: 0.6547 (mm110) REVERT: 6 1 MET cc_start: 0.7222 (OUTLIER) cc_final: 0.6751 (mpp) REVERT: 8 12 ARG cc_start: 0.5703 (mtm110) cc_final: 0.5407 (ptt-90) REVERT: 8 13 ASN cc_start: 0.7099 (m110) cc_final: 0.6761 (m-40) REVERT: 8 15 LYS cc_start: 0.7021 (ttmm) cc_final: 0.6066 (tttp) REVERT: c 5 LYS cc_start: 0.7023 (tttp) cc_final: 0.6477 (tptp) REVERT: c 7 LYS cc_start: 0.7949 (OUTLIER) cc_final: 0.7597 (mttt) REVERT: c 74 ILE cc_start: 0.7008 (OUTLIER) cc_final: 0.6738 (mm) REVERT: c 79 GLU cc_start: 0.7118 (OUTLIER) cc_final: 0.6633 (mt-10) REVERT: c 87 ARG cc_start: 0.6949 (OUTLIER) cc_final: 0.5658 (mtm-85) REVERT: c 125 LYS cc_start: 0.7400 (ptmm) cc_final: 0.7101 (pttt) REVERT: c 146 MET cc_start: 0.7829 (mtm) cc_final: 0.7543 (mtp) REVERT: c 163 GLN cc_start: 0.7383 (mt0) cc_final: 0.7144 (mt0) REVERT: c 183 LYS cc_start: 0.7421 (OUTLIER) cc_final: 0.6920 (mttm) REVERT: c 265 LYS cc_start: 0.8011 (OUTLIER) cc_final: 0.7736 (pttm) REVERT: c 269 ARG cc_start: 0.6765 (ttp80) cc_final: 0.6234 (ttt90) REVERT: d 1 MET cc_start: 0.5548 (ttm) cc_final: 0.5058 (ttm) REVERT: d 7 LYS cc_start: 0.7842 (ttpp) cc_final: 0.7310 (ttmm) REVERT: d 13 ARG cc_start: 0.8098 (OUTLIER) cc_final: 0.6491 (ptt180) REVERT: d 64 GLU cc_start: 0.6303 (mt-10) cc_final: 0.5405 (mm-30) REVERT: d 74 GLU cc_start: 0.7381 (tp30) cc_final: 0.7140 (mm-30) REVERT: d 103 ASP cc_start: 0.6238 (OUTLIER) cc_final: 0.5688 (m-30) REVERT: d 128 ARG cc_start: 0.5451 (OUTLIER) cc_final: 0.5135 (mtp85) REVERT: d 157 LYS cc_start: 0.7911 (OUTLIER) cc_final: 0.7201 (tttp) REVERT: d 183 GLU cc_start: 0.6459 (pm20) cc_final: 0.5775 (pt0) REVERT: d 202 ILE cc_start: 0.8018 (mt) cc_final: 0.7736 (mm) REVERT: e 13 THR cc_start: 0.7304 (OUTLIER) cc_final: 0.7057 (m) REVERT: e 21 ARG cc_start: 0.6583 (mtp85) cc_final: 0.6019 (mtp85) REVERT: e 25 GLU cc_start: 0.7549 (tt0) cc_final: 0.7192 (tt0) REVERT: e 61 ARG cc_start: 0.6589 (mtp180) cc_final: 0.6354 (ptm-80) REVERT: e 139 LYS cc_start: 0.7264 (tttp) cc_final: 0.6612 (ttmp) REVERT: e 194 LYS cc_start: 0.5715 (mmmt) cc_final: 0.5324 (mmtm) REVERT: e 197 GLU cc_start: 0.6805 (tt0) cc_final: 0.6458 (mt-10) REVERT: f 3 LYS cc_start: 0.5291 (ptmm) cc_final: 0.4793 (mmpt) REVERT: f 38 MET cc_start: 0.6596 (ptp) cc_final: 0.6306 (ptm) REVERT: f 49 LEU cc_start: 0.4534 (pt) cc_final: 0.4139 (mt) REVERT: f 64 LYS cc_start: 0.3245 (mptp) cc_final: 0.2847 (tttm) REVERT: f 67 ILE cc_start: 0.7896 (OUTLIER) cc_final: 0.7576 (mm) REVERT: f 88 LYS cc_start: 0.6407 (OUTLIER) cc_final: 0.6022 (tttt) REVERT: f 125 ARG cc_start: 0.4979 (mtt-85) cc_final: 0.4719 (mtp85) REVERT: f 141 ILE cc_start: 0.5317 (OUTLIER) cc_final: 0.4625 (pt) REVERT: f 142 ASP cc_start: 0.3432 (OUTLIER) cc_final: 0.3028 (p0) REVERT: f 150 ARG cc_start: 0.4522 (mtt90) cc_final: 0.4204 (mtm110) REVERT: g 121 ILE cc_start: 0.7176 (mm) cc_final: 0.6840 (mp) REVERT: g 153 ARG cc_start: 0.7253 (ptp90) cc_final: 0.6509 (mtt90) REVERT: g 169 VAL cc_start: 0.6492 (OUTLIER) cc_final: 0.6199 (p) REVERT: h 15 LEU cc_start: 0.5307 (OUTLIER) cc_final: 0.4962 (pp) REVERT: j 2 LYS cc_start: 0.7436 (mmmt) cc_final: 0.6779 (mtmt) REVERT: j 43 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7030 (pm20) REVERT: j 61 LYS cc_start: 0.7246 (OUTLIER) cc_final: 0.6536 (mmtt) REVERT: j 95 ARG cc_start: 0.6784 (OUTLIER) cc_final: 0.5501 (ttp-110) REVERT: j 98 GLU cc_start: 0.7260 (OUTLIER) cc_final: 0.7012 (mp0) REVERT: j 106 LYS cc_start: 0.7524 (tttp) cc_final: 0.6590 (ttpt) REVERT: k 4 GLU cc_start: 0.7564 (mt-10) cc_final: 0.7077 (mt-10) REVERT: k 53 LYS cc_start: 0.6929 (mmpt) cc_final: 0.5899 (mppt) REVERT: k 98 ARG cc_start: 0.5568 (mtt180) cc_final: 0.4942 (mtm180) REVERT: k 114 LYS cc_start: 0.6397 (mtpp) cc_final: 0.5693 (tppt) REVERT: l 55 MET cc_start: 0.7982 (tpp) cc_final: 0.7696 (tpp) REVERT: l 106 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7188 (pm20) REVERT: l 123 ARG cc_start: 0.7731 (tpp80) cc_final: 0.7158 (tpp80) REVERT: m 6 ARG cc_start: 0.7283 (OUTLIER) cc_final: 0.6625 (mtp85) REVERT: m 81 ARG cc_start: 0.7186 (OUTLIER) cc_final: 0.6247 (mmt-90) REVERT: m 126 ILE cc_start: 0.7520 (OUTLIER) cc_final: 0.7180 (mm) REVERT: m 127 LYS cc_start: 0.6973 (OUTLIER) cc_final: 0.6604 (mtpp) REVERT: n 18 GLN cc_start: 0.6795 (OUTLIER) cc_final: 0.6385 (tt0) REVERT: o 10 ARG cc_start: 0.7405 (OUTLIER) cc_final: 0.5730 (mtp180) REVERT: o 55 GLU cc_start: 0.6609 (mt-10) cc_final: 0.6169 (mt-10) REVERT: o 62 LEU cc_start: 0.7210 (OUTLIER) cc_final: 0.6997 (mp) REVERT: p 7 GLN cc_start: 0.6959 (OUTLIER) cc_final: 0.6434 (pp30) REVERT: p 11 GLU cc_start: 0.7440 (pt0) cc_final: 0.7003 (pt0) REVERT: p 89 ARG cc_start: 0.6808 (mtm-85) cc_final: 0.5820 (mtt-85) REVERT: p 102 GLU cc_start: 0.7047 (mm-30) cc_final: 0.6358 (mp0) REVERT: p 112 GLU cc_start: 0.7172 (tt0) cc_final: 0.6467 (tt0) REVERT: q 58 ARG cc_start: 0.8094 (OUTLIER) cc_final: 0.7188 (ttt-90) REVERT: q 85 LYS cc_start: 0.7381 (mtmt) cc_final: 0.6845 (mttt) REVERT: q 89 GLU cc_start: 0.7427 (OUTLIER) cc_final: 0.6988 (mt-10) REVERT: r 26 ASP cc_start: 0.6738 (OUTLIER) cc_final: 0.6493 (t0) REVERT: r 34 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.6950 (mp0) REVERT: r 45 GLU cc_start: 0.6161 (OUTLIER) cc_final: 0.5692 (pt0) REVERT: r 60 LYS cc_start: 0.7542 (mptp) cc_final: 0.7315 (mttp) REVERT: r 70 GLU cc_start: 0.6964 (tt0) cc_final: 0.6175 (tp30) REVERT: s 2 GLU cc_start: 0.7342 (mt-10) cc_final: 0.7044 (mt-10) REVERT: s 28 LYS cc_start: 0.7370 (mttp) cc_final: 0.6983 (mttm) REVERT: s 34 ASP cc_start: 0.6462 (m-30) cc_final: 0.6253 (m-30) REVERT: s 70 LYS cc_start: 0.7498 (mttp) cc_final: 0.7171 (mtmm) REVERT: s 92 ARG cc_start: 0.6543 (mtp-110) cc_final: 0.5333 (mtm110) REVERT: s 95 ARG cc_start: 0.6760 (tpp80) cc_final: 0.4878 (ppt90) REVERT: s 109 ASP cc_start: 0.6454 (p0) cc_final: 0.5499 (p0) REVERT: t 4 GLU cc_start: 0.6705 (OUTLIER) cc_final: 0.6505 (tp30) REVERT: t 25 GLU cc_start: 0.7534 (OUTLIER) cc_final: 0.7252 (pt0) REVERT: t 26 LYS cc_start: 0.6807 (tppp) cc_final: 0.6520 (mmtp) REVERT: t 32 LEU cc_start: 0.7679 (OUTLIER) cc_final: 0.7306 (pp) REVERT: t 54 GLU cc_start: 0.5569 (pm20) cc_final: 0.5194 (mm-30) REVERT: t 56 GLU cc_start: 0.7528 (mm-30) cc_final: 0.7273 (tt0) REVERT: u 10 GLU cc_start: 0.7143 (mm-30) cc_final: 0.6372 (tp30) REVERT: u 21 LYS cc_start: 0.8245 (OUTLIER) cc_final: 0.7803 (mmmm) REVERT: u 24 LYS cc_start: 0.7298 (ttmm) cc_final: 0.6444 (ttpp) REVERT: u 37 GLU cc_start: 0.6739 (tp30) cc_final: 0.6485 (tp30) REVERT: u 46 GLN cc_start: 0.7383 (mm-40) cc_final: 0.7031 (mm-40) REVERT: u 62 GLU cc_start: 0.7406 (OUTLIER) cc_final: 0.6912 (pm20) REVERT: u 88 GLU cc_start: 0.7240 (OUTLIER) cc_final: 0.6653 (pt0) REVERT: w 1 MET cc_start: 0.4979 (ppp) cc_final: 0.4182 (mmt) REVERT: w 34 LYS cc_start: 0.5801 (tppp) cc_final: 0.5127 (ttmm) REVERT: w 41 GLU cc_start: 0.7283 (mt-10) cc_final: 0.7026 (mt-10) REVERT: w 53 LYS cc_start: 0.6125 (mttm) cc_final: 0.5335 (mmtt) REVERT: w 68 LYS cc_start: 0.6050 (ttmt) cc_final: 0.5249 (tptt) REVERT: y 11 ARG cc_start: 0.6556 (ptm160) cc_final: 0.6251 (ptt-90) REVERT: y 62 LYS cc_start: 0.8037 (mtmt) cc_final: 0.7835 (mtpp) REVERT: y 68 LYS cc_start: 0.7989 (OUTLIER) cc_final: 0.7496 (tptt) outliers start: 204 outliers final: 95 residues processed: 613 average time/residue: 1.9760 time to fit residues: 1591.6836 Evaluate side-chains 607 residues out of total 2526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 459 time to evaluate : 3.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 2 SER Chi-restraints excluded: chain 0 residue 25 THR Chi-restraints excluded: chain 0 residue 35 SER Chi-restraints excluded: chain 0 residue 56 MET Chi-restraints excluded: chain 0 residue 62 LYS Chi-restraints excluded: chain 0 residue 66 THR Chi-restraints excluded: chain 1 residue 4 LYS Chi-restraints excluded: chain 1 residue 44 LYS Chi-restraints excluded: chain 1 residue 58 ASN Chi-restraints excluded: chain 1 residue 59 GLU Chi-restraints excluded: chain 2 residue 19 LYS Chi-restraints excluded: chain 2 residue 36 VAL Chi-restraints excluded: chain 2 residue 56 LYS Chi-restraints excluded: chain 3 residue 12 LYS Chi-restraints excluded: chain 4 residue 5 ILE Chi-restraints excluded: chain 4 residue 7 GLU Chi-restraints excluded: chain 4 residue 17 THR Chi-restraints excluded: chain 4 residue 37 LYS Chi-restraints excluded: chain 4 residue 42 VAL Chi-restraints excluded: chain 4 residue 43 VAL Chi-restraints excluded: chain 4 residue 44 ARG Chi-restraints excluded: chain 6 residue 1 MET Chi-restraints excluded: chain 7 residue 52 LYS Chi-restraints excluded: chain 8 residue 10 LEU Chi-restraints excluded: chain 8 residue 17 VAL Chi-restraints excluded: chain 8 residue 32 LYS Chi-restraints excluded: chain c residue 7 LYS Chi-restraints excluded: chain c residue 20 VAL Chi-restraints excluded: chain c residue 74 ILE Chi-restraints excluded: chain c residue 79 GLU Chi-restraints excluded: chain c residue 87 ARG Chi-restraints excluded: chain c residue 116 ILE Chi-restraints excluded: chain c residue 118 SER Chi-restraints excluded: chain c residue 132 MET Chi-restraints excluded: chain c residue 162 VAL Chi-restraints excluded: chain c residue 183 LYS Chi-restraints excluded: chain c residue 265 LYS Chi-restraints excluded: chain c residue 272 SER Chi-restraints excluded: chain d residue 13 ARG Chi-restraints excluded: chain d residue 29 VAL Chi-restraints excluded: chain d residue 103 ASP Chi-restraints excluded: chain d residue 128 ARG Chi-restraints excluded: chain d residue 151 THR Chi-restraints excluded: chain d residue 157 LYS Chi-restraints excluded: chain d residue 175 LEU Chi-restraints excluded: chain e residue 4 VAL Chi-restraints excluded: chain e residue 10 SER Chi-restraints excluded: chain e residue 13 THR Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain e residue 95 LYS Chi-restraints excluded: chain f residue 16 LEU Chi-restraints excluded: chain f residue 26 MET Chi-restraints excluded: chain f residue 35 THR Chi-restraints excluded: chain f residue 67 ILE Chi-restraints excluded: chain f residue 72 LYS Chi-restraints excluded: chain f residue 88 LYS Chi-restraints excluded: chain f residue 104 ILE Chi-restraints excluded: chain f residue 108 VAL Chi-restraints excluded: chain f residue 117 LEU Chi-restraints excluded: chain f residue 132 VAL Chi-restraints excluded: chain f residue 141 ILE Chi-restraints excluded: chain f residue 142 ASP Chi-restraints excluded: chain f residue 155 THR Chi-restraints excluded: chain f residue 170 LEU Chi-restraints excluded: chain g residue 11 VAL Chi-restraints excluded: chain g residue 17 VAL Chi-restraints excluded: chain g residue 49 THR Chi-restraints excluded: chain g residue 81 GLU Chi-restraints excluded: chain g residue 90 VAL Chi-restraints excluded: chain g residue 99 LYS Chi-restraints excluded: chain g residue 107 LEU Chi-restraints excluded: chain g residue 169 VAL Chi-restraints excluded: chain h residue 3 VAL Chi-restraints excluded: chain h residue 9 VAL Chi-restraints excluded: chain h residue 15 LEU Chi-restraints excluded: chain h residue 22 LYS Chi-restraints excluded: chain h residue 37 VAL Chi-restraints excluded: chain j residue 10 THR Chi-restraints excluded: chain j residue 11 VAL Chi-restraints excluded: chain j residue 43 GLU Chi-restraints excluded: chain j residue 61 LYS Chi-restraints excluded: chain j residue 62 VAL Chi-restraints excluded: chain j residue 64 VAL Chi-restraints excluded: chain j residue 95 ARG Chi-restraints excluded: chain j residue 98 GLU Chi-restraints excluded: chain j residue 131 ASN Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 87 LEU Chi-restraints excluded: chain l residue 104 GLN Chi-restraints excluded: chain l residue 106 GLU Chi-restraints excluded: chain l residue 117 THR Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain m residue 5 LYS Chi-restraints excluded: chain m residue 6 ARG Chi-restraints excluded: chain m residue 7 THR Chi-restraints excluded: chain m residue 30 SER Chi-restraints excluded: chain m residue 78 LEU Chi-restraints excluded: chain m residue 81 ARG Chi-restraints excluded: chain m residue 104 GLU Chi-restraints excluded: chain m residue 126 ILE Chi-restraints excluded: chain m residue 127 LYS Chi-restraints excluded: chain m residue 129 THR Chi-restraints excluded: chain n residue 14 SER Chi-restraints excluded: chain n residue 18 GLN Chi-restraints excluded: chain n residue 48 VAL Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain n residue 70 THR Chi-restraints excluded: chain o residue 10 ARG Chi-restraints excluded: chain o residue 24 THR Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain o residue 48 LEU Chi-restraints excluded: chain o residue 49 VAL Chi-restraints excluded: chain o residue 54 VAL Chi-restraints excluded: chain o residue 62 LEU Chi-restraints excluded: chain o residue 67 ASN Chi-restraints excluded: chain p residue 7 GLN Chi-restraints excluded: chain p residue 46 VAL Chi-restraints excluded: chain p residue 63 LYS Chi-restraints excluded: chain p residue 70 VAL Chi-restraints excluded: chain q residue 58 ARG Chi-restraints excluded: chain q residue 89 GLU Chi-restraints excluded: chain r residue 26 ASP Chi-restraints excluded: chain r residue 34 GLU Chi-restraints excluded: chain r residue 45 GLU Chi-restraints excluded: chain r residue 47 VAL Chi-restraints excluded: chain r residue 85 LYS Chi-restraints excluded: chain s residue 33 LEU Chi-restraints excluded: chain s residue 66 ILE Chi-restraints excluded: chain s residue 101 SER Chi-restraints excluded: chain t residue 4 GLU Chi-restraints excluded: chain t residue 6 ARG Chi-restraints excluded: chain t residue 25 GLU Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain t residue 50 LEU Chi-restraints excluded: chain t residue 55 VAL Chi-restraints excluded: chain t residue 67 VAL Chi-restraints excluded: chain t residue 69 GLN Chi-restraints excluded: chain t residue 100 ASN Chi-restraints excluded: chain u residue 21 LYS Chi-restraints excluded: chain u residue 62 GLU Chi-restraints excluded: chain u residue 68 SER Chi-restraints excluded: chain u residue 88 GLU Chi-restraints excluded: chain w residue 72 VAL Chi-restraints excluded: chain y residue 17 GLU Chi-restraints excluded: chain y residue 19 LYS Chi-restraints excluded: chain y residue 43 THR Chi-restraints excluded: chain y residue 51 VAL Chi-restraints excluded: chain y residue 68 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 607 random chunks: chunk 488 optimal weight: 9.9990 chunk 333 optimal weight: 10.0000 chunk 8 optimal weight: 7.9990 chunk 436 optimal weight: 9.9990 chunk 242 optimal weight: 10.0000 chunk 500 optimal weight: 0.9990 chunk 405 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 299 optimal weight: 10.0000 chunk 526 optimal weight: 5.9990 chunk 148 optimal weight: 8.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 5 GLN 6 29 GLN e 46 GLN g 104 ASN ** j 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 128 ASN ** k 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 3 GLN m 60 GLN q 56 GLN r 86 GLN s 31 GLN t 59 ASN ** u 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6602 moved from start: 0.4075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 98998 Z= 0.355 Angle : 0.737 11.512 149023 Z= 0.383 Chirality : 0.045 0.369 19174 Planarity : 0.006 0.090 7331 Dihedral : 24.301 179.565 51742 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.23 % Favored : 94.64 % Rotamer: Outliers : 8.71 % Allowed : 25.85 % Favored : 65.44 % 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: -0.69 (0.15), residues: 3057 helix: 0.54 (0.18), residues: 801 sheet: -0.35 (0.19), residues: 714 loop : -1.00 (0.15), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP c 213 HIS 0.012 0.002 HIS r 89 PHE 0.023 0.003 PHE h 29 TYR 0.018 0.003 TYR q 32 ARG 0.015 0.001 ARG d 184 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 707 residues out of total 2526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 220 poor density : 487 time to evaluate : 3.917 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 62 LYS cc_start: 0.7480 (OUTLIER) cc_final: 0.7084 (mmmt) REVERT: 0 72 ARG cc_start: 0.6989 (mtm-85) cc_final: 0.6751 (mtm-85) REVERT: 0 76 GLU cc_start: 0.5850 (OUTLIER) cc_final: 0.5540 (tt0) REVERT: 1 4 LYS cc_start: 0.4998 (OUTLIER) cc_final: 0.4146 (ttmt) REVERT: 1 24 GLU cc_start: 0.6237 (tp30) cc_final: 0.5530 (tp30) REVERT: 1 44 LYS cc_start: 0.6415 (OUTLIER) cc_final: 0.5817 (ttmt) REVERT: 1 59 GLU cc_start: 0.6755 (OUTLIER) cc_final: 0.6463 (mt-10) REVERT: 2 19 LYS cc_start: 0.7279 (OUTLIER) cc_final: 0.7015 (tttm) REVERT: 2 47 MET cc_start: 0.7892 (mtt) cc_final: 0.7690 (mtm) REVERT: 2 56 LYS cc_start: 0.7549 (OUTLIER) cc_final: 0.7046 (ttpp) REVERT: 3 9 THR cc_start: 0.7379 (m) cc_final: 0.6916 (p) REVERT: 4 24 THR cc_start: 0.7731 (p) cc_final: 0.7515 (p) REVERT: 4 30 LYS cc_start: 0.6203 (OUTLIER) cc_final: 0.5742 (ptmt) REVERT: 4 37 LYS cc_start: 0.7491 (OUTLIER) cc_final: 0.7225 (mttp) REVERT: 4 44 ARG cc_start: 0.6516 (OUTLIER) cc_final: 0.5925 (mmm160) REVERT: 4 45 GLN cc_start: 0.7161 (mm110) cc_final: 0.6564 (mm110) REVERT: 6 1 MET cc_start: 0.7304 (OUTLIER) cc_final: 0.6795 (mpp) REVERT: 8 12 ARG cc_start: 0.5780 (mtm110) cc_final: 0.5476 (ptt-90) REVERT: 8 13 ASN cc_start: 0.6975 (m110) cc_final: 0.6665 (m-40) REVERT: 8 15 LYS cc_start: 0.7035 (ttmm) cc_final: 0.6127 (tttp) REVERT: c 5 LYS cc_start: 0.7215 (tttp) cc_final: 0.6680 (tptp) REVERT: c 7 LYS cc_start: 0.7960 (OUTLIER) cc_final: 0.7591 (mttt) REVERT: c 74 ILE cc_start: 0.6916 (OUTLIER) cc_final: 0.6664 (mm) REVERT: c 79 GLU cc_start: 0.7136 (OUTLIER) cc_final: 0.6634 (mt-10) REVERT: c 87 ARG cc_start: 0.7019 (OUTLIER) cc_final: 0.5548 (mtm-85) REVERT: c 110 LEU cc_start: 0.7250 (OUTLIER) cc_final: 0.6984 (tp) REVERT: c 125 LYS cc_start: 0.7405 (ptmm) cc_final: 0.7067 (pttt) REVERT: c 146 MET cc_start: 0.7825 (mtm) cc_final: 0.7519 (mtp) REVERT: c 163 GLN cc_start: 0.7400 (OUTLIER) cc_final: 0.7163 (mt0) REVERT: c 183 LYS cc_start: 0.7467 (OUTLIER) cc_final: 0.6993 (mttm) REVERT: c 199 GLU cc_start: 0.7628 (mt-10) cc_final: 0.6327 (pm20) REVERT: c 265 LYS cc_start: 0.8016 (OUTLIER) cc_final: 0.7763 (pttm) REVERT: c 269 ARG cc_start: 0.6788 (ttp80) cc_final: 0.6305 (ttt90) REVERT: d 1 MET cc_start: 0.5345 (ttm) cc_final: 0.4864 (ttm) REVERT: d 7 LYS cc_start: 0.7893 (ttpp) cc_final: 0.7388 (ttmm) REVERT: d 13 ARG cc_start: 0.8107 (OUTLIER) cc_final: 0.6593 (ptt180) REVERT: d 40 LEU cc_start: 0.7984 (mp) cc_final: 0.7751 (mp) REVERT: d 48 ILE cc_start: 0.7605 (OUTLIER) cc_final: 0.7318 (pp) REVERT: d 64 GLU cc_start: 0.6402 (mt-10) cc_final: 0.6035 (mt-10) REVERT: d 99 GLU cc_start: 0.7256 (OUTLIER) cc_final: 0.6703 (tp30) REVERT: d 183 GLU cc_start: 0.6344 (pm20) cc_final: 0.5817 (pt0) REVERT: d 202 ILE cc_start: 0.8000 (mt) cc_final: 0.7716 (mm) REVERT: d 204 LYS cc_start: 0.7856 (OUTLIER) cc_final: 0.7008 (mtpt) REVERT: e 21 ARG cc_start: 0.6642 (OUTLIER) cc_final: 0.6054 (mtp85) REVERT: e 22 ASP cc_start: 0.7205 (p0) cc_final: 0.6876 (p0) REVERT: e 25 GLU cc_start: 0.7529 (tt0) cc_final: 0.7286 (tt0) REVERT: e 61 ARG cc_start: 0.6603 (mtp180) cc_final: 0.6334 (ptm-80) REVERT: e 139 LYS cc_start: 0.7155 (tttp) cc_final: 0.6835 (tttp) REVERT: e 194 LYS cc_start: 0.5711 (mmmt) cc_final: 0.5342 (mmtm) REVERT: e 197 GLU cc_start: 0.6702 (tt0) cc_final: 0.6402 (mt-10) REVERT: f 3 LYS cc_start: 0.5419 (ptmm) cc_final: 0.4728 (mmpt) REVERT: f 21 ASN cc_start: 0.5852 (OUTLIER) cc_final: 0.5467 (t0) REVERT: f 49 LEU cc_start: 0.4663 (OUTLIER) cc_final: 0.4227 (mt) REVERT: f 64 LYS cc_start: 0.3320 (mptp) cc_final: 0.2861 (tttm) REVERT: f 67 ILE cc_start: 0.7938 (OUTLIER) cc_final: 0.7620 (mm) REVERT: f 88 LYS cc_start: 0.6538 (OUTLIER) cc_final: 0.6135 (tttt) REVERT: f 141 ILE cc_start: 0.5346 (OUTLIER) cc_final: 0.4840 (pp) REVERT: g 25 THR cc_start: 0.6510 (m) cc_final: 0.6121 (t) REVERT: g 153 ARG cc_start: 0.7271 (ptp90) cc_final: 0.6585 (mtt90) REVERT: g 169 VAL cc_start: 0.6493 (OUTLIER) cc_final: 0.6086 (p) REVERT: h 15 LEU cc_start: 0.5257 (OUTLIER) cc_final: 0.4935 (pp) REVERT: j 2 LYS cc_start: 0.7525 (mmmt) cc_final: 0.7242 (mptm) REVERT: j 12 LYS cc_start: 0.7209 (tppt) cc_final: 0.6043 (tttm) REVERT: j 43 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7014 (pm20) REVERT: j 95 ARG cc_start: 0.6712 (OUTLIER) cc_final: 0.5482 (ttp-110) REVERT: j 98 GLU cc_start: 0.7257 (OUTLIER) cc_final: 0.6970 (mp0) REVERT: j 106 LYS cc_start: 0.7509 (tttp) cc_final: 0.6576 (ttpt) REVERT: k 4 GLU cc_start: 0.7683 (mt-10) cc_final: 0.7171 (mt-10) REVERT: k 53 LYS cc_start: 0.6850 (mmpt) cc_final: 0.5834 (mppt) REVERT: k 98 ARG cc_start: 0.5538 (mtt180) cc_final: 0.4866 (mtm180) REVERT: k 114 LYS cc_start: 0.6527 (mtpp) cc_final: 0.6322 (mmmt) REVERT: l 106 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7123 (pm20) REVERT: l 123 ARG cc_start: 0.7719 (tpp80) cc_final: 0.7187 (tpp80) REVERT: m 6 ARG cc_start: 0.7142 (OUTLIER) cc_final: 0.6560 (mtp85) REVERT: m 81 ARG cc_start: 0.7190 (OUTLIER) cc_final: 0.6607 (mmt-90) REVERT: m 126 ILE cc_start: 0.7454 (OUTLIER) cc_final: 0.7127 (mm) REVERT: m 127 LYS cc_start: 0.7130 (OUTLIER) cc_final: 0.6831 (mtpp) REVERT: m 133 LYS cc_start: 0.7477 (tttm) cc_final: 0.7133 (ptmm) REVERT: n 18 GLN cc_start: 0.6797 (OUTLIER) cc_final: 0.6383 (tt0) REVERT: o 10 ARG cc_start: 0.7397 (OUTLIER) cc_final: 0.5753 (mtp180) REVERT: o 16 ARG cc_start: 0.5825 (OUTLIER) cc_final: 0.5432 (mmt-90) REVERT: o 20 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7374 (pp20) REVERT: o 55 GLU cc_start: 0.6524 (mt-10) cc_final: 0.6189 (mt-10) REVERT: o 62 LEU cc_start: 0.7335 (OUTLIER) cc_final: 0.7088 (mp) REVERT: p 11 GLU cc_start: 0.7334 (pt0) cc_final: 0.6990 (pt0) REVERT: p 89 ARG cc_start: 0.6818 (mtm-85) cc_final: 0.5813 (mtt-85) REVERT: p 102 GLU cc_start: 0.6974 (mm-30) cc_final: 0.6331 (mp0) REVERT: p 112 GLU cc_start: 0.7000 (tt0) cc_final: 0.6317 (tt0) REVERT: q 58 ARG cc_start: 0.8137 (OUTLIER) cc_final: 0.7214 (ttt-90) REVERT: q 85 LYS cc_start: 0.7440 (mtmt) cc_final: 0.6871 (mttt) REVERT: q 89 GLU cc_start: 0.7413 (OUTLIER) cc_final: 0.6943 (mt-10) REVERT: r 13 ARG cc_start: 0.8434 (ttp80) cc_final: 0.7960 (ttp80) REVERT: r 26 ASP cc_start: 0.6744 (OUTLIER) cc_final: 0.6453 (t0) REVERT: r 34 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.7002 (mp0) REVERT: r 37 GLU cc_start: 0.7360 (mt-10) cc_final: 0.7012 (pt0) REVERT: r 46 GLU cc_start: 0.7067 (mp0) cc_final: 0.6718 (mp0) REVERT: r 60 LYS cc_start: 0.7690 (mptp) cc_final: 0.7398 (mttp) REVERT: r 70 GLU cc_start: 0.7011 (tt0) cc_final: 0.6224 (tp30) REVERT: s 2 GLU cc_start: 0.7426 (mt-10) cc_final: 0.7153 (mt-10) REVERT: s 28 LYS cc_start: 0.7368 (mttp) cc_final: 0.6959 (mttm) REVERT: s 34 ASP cc_start: 0.6380 (m-30) cc_final: 0.6154 (m-30) REVERT: s 70 LYS cc_start: 0.7583 (mttp) cc_final: 0.7275 (mtmm) REVERT: s 95 ARG cc_start: 0.6947 (tpp80) cc_final: 0.5085 (ppt90) REVERT: s 109 ASP cc_start: 0.6532 (p0) cc_final: 0.5576 (p0) REVERT: t 25 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.7323 (pt0) REVERT: t 26 LYS cc_start: 0.6907 (tppp) cc_final: 0.6590 (mmtp) REVERT: t 32 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7399 (pp) REVERT: t 54 GLU cc_start: 0.5630 (pm20) cc_final: 0.5263 (mm-30) REVERT: t 56 GLU cc_start: 0.7522 (mm-30) cc_final: 0.7109 (tt0) REVERT: u 10 GLU cc_start: 0.7143 (mm-30) cc_final: 0.6443 (tp30) REVERT: u 21 LYS cc_start: 0.8236 (OUTLIER) cc_final: 0.7809 (mmmm) REVERT: u 22 ARG cc_start: 0.7747 (mtm-85) cc_final: 0.7499 (mtp180) REVERT: u 24 LYS cc_start: 0.7207 (ttmm) cc_final: 0.6310 (ttpp) REVERT: u 37 GLU cc_start: 0.6950 (tp30) cc_final: 0.6510 (mm-30) REVERT: u 46 GLN cc_start: 0.7406 (mm-40) cc_final: 0.7067 (mm-40) REVERT: u 79 LYS cc_start: 0.7367 (mttm) cc_final: 0.7024 (mptp) REVERT: w 25 LYS cc_start: 0.7167 (mtpt) cc_final: 0.6640 (mtpp) REVERT: w 34 LYS cc_start: 0.5798 (tppp) cc_final: 0.5163 (ptmt) REVERT: w 41 GLU cc_start: 0.7275 (mt-10) cc_final: 0.7053 (mt-10) REVERT: w 53 LYS cc_start: 0.6412 (mttm) cc_final: 0.5503 (mmtt) REVERT: w 68 LYS cc_start: 0.5991 (ttmt) cc_final: 0.5193 (tptt) REVERT: y 11 ARG cc_start: 0.6393 (ptm160) cc_final: 0.6087 (ptt-90) REVERT: y 44 LYS cc_start: 0.7131 (ttmm) cc_final: 0.6775 (ttmt) REVERT: y 62 LYS cc_start: 0.8070 (mtmt) cc_final: 0.7782 (mtpp) REVERT: y 68 LYS cc_start: 0.7995 (OUTLIER) cc_final: 0.7328 (tptp) REVERT: y 70 GLU cc_start: 0.7947 (mt-10) cc_final: 0.6546 (mp0) outliers start: 220 outliers final: 115 residues processed: 631 average time/residue: 2.0209 time to fit residues: 1672.7125 Evaluate side-chains 636 residues out of total 2526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 469 time to evaluate : 3.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 2 SER Chi-restraints excluded: chain 0 residue 35 SER Chi-restraints excluded: chain 0 residue 56 MET Chi-restraints excluded: chain 0 residue 62 LYS Chi-restraints excluded: chain 0 residue 66 THR Chi-restraints excluded: chain 0 residue 76 GLU Chi-restraints excluded: chain 1 residue 4 LYS Chi-restraints excluded: chain 1 residue 44 LYS Chi-restraints excluded: chain 1 residue 58 ASN Chi-restraints excluded: chain 1 residue 59 GLU Chi-restraints excluded: chain 2 residue 19 LYS Chi-restraints excluded: chain 2 residue 36 VAL Chi-restraints excluded: chain 2 residue 56 LYS Chi-restraints excluded: chain 4 residue 5 ILE Chi-restraints excluded: chain 4 residue 17 THR Chi-restraints excluded: chain 4 residue 28 ARG Chi-restraints excluded: chain 4 residue 30 LYS Chi-restraints excluded: chain 4 residue 37 LYS Chi-restraints excluded: chain 4 residue 42 VAL Chi-restraints excluded: chain 4 residue 43 VAL Chi-restraints excluded: chain 4 residue 44 ARG Chi-restraints excluded: chain 6 residue 1 MET Chi-restraints excluded: chain 7 residue 19 LYS Chi-restraints excluded: chain 7 residue 52 LYS Chi-restraints excluded: chain 8 residue 10 LEU Chi-restraints excluded: chain 8 residue 17 VAL Chi-restraints excluded: chain 8 residue 32 LYS Chi-restraints excluded: chain c residue 7 LYS Chi-restraints excluded: chain c residue 20 VAL Chi-restraints excluded: chain c residue 74 ILE Chi-restraints excluded: chain c residue 79 GLU Chi-restraints excluded: chain c residue 87 ARG Chi-restraints excluded: chain c residue 110 LEU Chi-restraints excluded: chain c residue 116 ILE Chi-restraints excluded: chain c residue 118 SER Chi-restraints excluded: chain c residue 120 VAL Chi-restraints excluded: chain c residue 132 MET Chi-restraints excluded: chain c residue 162 VAL Chi-restraints excluded: chain c residue 163 GLN Chi-restraints excluded: chain c residue 183 LYS Chi-restraints excluded: chain c residue 265 LYS Chi-restraints excluded: chain c residue 272 SER Chi-restraints excluded: chain d residue 13 ARG Chi-restraints excluded: chain d residue 29 VAL Chi-restraints excluded: chain d residue 48 ILE Chi-restraints excluded: chain d residue 99 GLU Chi-restraints excluded: chain d residue 151 THR Chi-restraints excluded: chain d residue 175 LEU Chi-restraints excluded: chain d residue 179 ARG Chi-restraints excluded: chain d residue 204 LYS Chi-restraints excluded: chain e residue 4 VAL Chi-restraints excluded: chain e residue 10 SER Chi-restraints excluded: chain e residue 21 ARG Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain e residue 95 LYS Chi-restraints excluded: chain e residue 119 ILE Chi-restraints excluded: chain e residue 122 GLU Chi-restraints excluded: chain e residue 166 LYS Chi-restraints excluded: chain e residue 173 THR Chi-restraints excluded: chain f residue 16 LEU Chi-restraints excluded: chain f residue 21 ASN Chi-restraints excluded: chain f residue 26 MET Chi-restraints excluded: chain f residue 28 VAL Chi-restraints excluded: chain f residue 35 THR Chi-restraints excluded: chain f residue 49 LEU Chi-restraints excluded: chain f residue 67 ILE Chi-restraints excluded: chain f residue 72 LYS Chi-restraints excluded: chain f residue 88 LYS Chi-restraints excluded: chain f residue 104 ILE Chi-restraints excluded: chain f residue 108 VAL Chi-restraints excluded: chain f residue 117 LEU Chi-restraints excluded: chain f residue 132 VAL Chi-restraints excluded: chain f residue 141 ILE Chi-restraints excluded: chain f residue 170 LEU Chi-restraints excluded: chain g residue 11 VAL Chi-restraints excluded: chain g residue 17 VAL Chi-restraints excluded: chain g residue 49 THR Chi-restraints excluded: chain g residue 51 THR Chi-restraints excluded: chain g residue 81 GLU Chi-restraints excluded: chain g residue 90 VAL Chi-restraints excluded: chain g residue 99 LYS Chi-restraints excluded: chain g residue 107 LEU Chi-restraints excluded: chain g residue 169 VAL Chi-restraints excluded: chain h residue 3 VAL Chi-restraints excluded: chain h residue 9 VAL Chi-restraints excluded: chain h residue 15 LEU Chi-restraints excluded: chain h residue 22 LYS Chi-restraints excluded: chain h residue 37 VAL Chi-restraints excluded: chain j residue 1 MET Chi-restraints excluded: chain j residue 5 THR Chi-restraints excluded: chain j residue 10 THR Chi-restraints excluded: chain j residue 11 VAL Chi-restraints excluded: chain j residue 43 GLU Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 62 VAL Chi-restraints excluded: chain j residue 64 VAL Chi-restraints excluded: chain j residue 95 ARG Chi-restraints excluded: chain j residue 98 GLU Chi-restraints excluded: chain j residue 131 ASN Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain l residue 104 GLN Chi-restraints excluded: chain l residue 106 GLU Chi-restraints excluded: chain l residue 117 THR Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain m residue 6 ARG Chi-restraints excluded: chain m residue 7 THR Chi-restraints excluded: chain m residue 30 SER Chi-restraints excluded: chain m residue 81 ARG Chi-restraints excluded: chain m residue 104 GLU Chi-restraints excluded: chain m residue 126 ILE Chi-restraints excluded: chain m residue 127 LYS Chi-restraints excluded: chain m residue 129 THR Chi-restraints excluded: chain n residue 14 SER Chi-restraints excluded: chain n residue 18 GLN Chi-restraints excluded: chain n residue 35 LYS Chi-restraints excluded: chain n residue 48 VAL Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain n residue 70 THR Chi-restraints excluded: chain o residue 9 ARG Chi-restraints excluded: chain o residue 10 ARG Chi-restraints excluded: chain o residue 16 ARG Chi-restraints excluded: chain o residue 20 GLU Chi-restraints excluded: chain o residue 24 THR Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain o residue 48 LEU Chi-restraints excluded: chain o residue 49 VAL Chi-restraints excluded: chain o residue 54 VAL Chi-restraints excluded: chain o residue 62 LEU Chi-restraints excluded: chain o residue 67 ASN Chi-restraints excluded: chain p residue 7 GLN Chi-restraints excluded: chain p residue 46 VAL Chi-restraints excluded: chain p residue 63 LYS Chi-restraints excluded: chain p residue 70 VAL Chi-restraints excluded: chain p residue 110 ILE Chi-restraints excluded: chain q residue 6 ARG Chi-restraints excluded: chain q residue 41 LYS Chi-restraints excluded: chain q residue 58 ARG Chi-restraints excluded: chain q residue 89 GLU Chi-restraints excluded: chain r residue 26 ASP Chi-restraints excluded: chain r residue 34 GLU Chi-restraints excluded: chain r residue 45 GLU Chi-restraints excluded: chain r residue 47 VAL Chi-restraints excluded: chain r residue 85 LYS Chi-restraints excluded: chain s residue 33 LEU Chi-restraints excluded: chain s residue 66 ILE Chi-restraints excluded: chain s residue 101 SER Chi-restraints excluded: chain t residue 6 ARG Chi-restraints excluded: chain t residue 25 GLU Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain t residue 36 LYS Chi-restraints excluded: chain t residue 50 LEU Chi-restraints excluded: chain t residue 55 VAL Chi-restraints excluded: chain t residue 67 VAL Chi-restraints excluded: chain t residue 69 GLN Chi-restraints excluded: chain t residue 100 ASN Chi-restraints excluded: chain u residue 21 LYS Chi-restraints excluded: chain u residue 27 ASN Chi-restraints excluded: chain u residue 30 SER Chi-restraints excluded: chain u residue 68 SER Chi-restraints excluded: chain u residue 88 GLU Chi-restraints excluded: chain w residue 72 VAL Chi-restraints excluded: chain y residue 17 GLU Chi-restraints excluded: chain y residue 19 LYS Chi-restraints excluded: chain y residue 43 THR Chi-restraints excluded: chain y residue 51 VAL Chi-restraints excluded: chain y residue 68 LYS Chi-restraints excluded: chain y residue 72 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 607 random chunks: chunk 197 optimal weight: 10.0000 chunk 528 optimal weight: 0.9980 chunk 115 optimal weight: 10.0000 chunk 344 optimal weight: 2.9990 chunk 144 optimal weight: 10.0000 chunk 587 optimal weight: 20.0000 chunk 487 optimal weight: 4.9990 chunk 271 optimal weight: 10.0000 chunk 48 optimal weight: 10.0000 chunk 194 optimal weight: 10.0000 chunk 308 optimal weight: 8.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 5 GLN 6 29 GLN d 173 GLN g 104 ASN ** j 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 128 ASN k 88 ASN m 3 GLN q 56 GLN r 86 GLN s 31 GLN t 59 ASN ** u 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6600 moved from start: 0.4153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 98998 Z= 0.352 Angle : 0.726 11.735 149023 Z= 0.377 Chirality : 0.044 0.360 19174 Planarity : 0.006 0.092 7331 Dihedral : 24.267 179.674 51740 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.94 % Favored : 94.93 % Rotamer: Outliers : 8.35 % Allowed : 25.77 % Favored : 65.87 % 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: -0.70 (0.15), residues: 3057 helix: 0.50 (0.18), residues: 808 sheet: -0.36 (0.19), residues: 705 loop : -0.99 (0.15), residues: 1544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP c 213 HIS 0.010 0.002 HIS r 89 PHE 0.020 0.002 PHE q 36 TYR 0.019 0.002 TYR q 32 ARG 0.013 0.001 ARG d 184 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 683 residues out of total 2526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 211 poor density : 472 time to evaluate : 3.829 Fit side-chains revert: symmetry clash REVERT: 0 62 LYS cc_start: 0.7296 (OUTLIER) cc_final: 0.6919 (mtmm) REVERT: 0 72 ARG cc_start: 0.6924 (mtm-85) cc_final: 0.6695 (mtm-85) REVERT: 0 76 GLU cc_start: 0.5808 (OUTLIER) cc_final: 0.5377 (tt0) REVERT: 1 4 LYS cc_start: 0.4841 (OUTLIER) cc_final: 0.4026 (ttmt) REVERT: 1 24 GLU cc_start: 0.6310 (tp30) cc_final: 0.5596 (tp30) REVERT: 1 44 LYS cc_start: 0.6394 (OUTLIER) cc_final: 0.5791 (ttmt) REVERT: 1 59 GLU cc_start: 0.6781 (OUTLIER) cc_final: 0.6483 (mt-10) REVERT: 2 19 LYS cc_start: 0.7294 (OUTLIER) cc_final: 0.7040 (tttm) REVERT: 2 39 GLU cc_start: 0.7450 (pm20) cc_final: 0.6757 (pm20) REVERT: 2 56 LYS cc_start: 0.7518 (OUTLIER) cc_final: 0.7017 (ttpp) REVERT: 3 9 THR cc_start: 0.7263 (m) cc_final: 0.6797 (p) REVERT: 3 15 MET cc_start: 0.8233 (mtm) cc_final: 0.7985 (mtm) REVERT: 4 24 THR cc_start: 0.7653 (p) cc_final: 0.7422 (p) REVERT: 4 30 LYS cc_start: 0.6275 (OUTLIER) cc_final: 0.5697 (ptmt) REVERT: 4 37 LYS cc_start: 0.7496 (OUTLIER) cc_final: 0.7232 (mttp) REVERT: 4 44 ARG cc_start: 0.6472 (OUTLIER) cc_final: 0.5857 (mmm160) REVERT: 4 45 GLN cc_start: 0.7073 (mm110) cc_final: 0.6500 (mm110) REVERT: 6 1 MET cc_start: 0.7192 (OUTLIER) cc_final: 0.6739 (mpp) REVERT: 8 12 ARG cc_start: 0.5601 (mtm110) cc_final: 0.5228 (ptt-90) REVERT: 8 15 LYS cc_start: 0.6951 (ttmm) cc_final: 0.6067 (tttp) REVERT: c 5 LYS cc_start: 0.7108 (tttp) cc_final: 0.6557 (tptp) REVERT: c 7 LYS cc_start: 0.7952 (OUTLIER) cc_final: 0.7605 (mttt) REVERT: c 74 ILE cc_start: 0.6935 (OUTLIER) cc_final: 0.6695 (mm) REVERT: c 79 GLU cc_start: 0.7104 (OUTLIER) cc_final: 0.6646 (mt-10) REVERT: c 87 ARG cc_start: 0.7219 (OUTLIER) cc_final: 0.5597 (mtm-85) REVERT: c 108 LYS cc_start: 0.7281 (OUTLIER) cc_final: 0.6715 (ttmt) REVERT: c 110 LEU cc_start: 0.7306 (OUTLIER) cc_final: 0.7023 (tp) REVERT: c 125 LYS cc_start: 0.7366 (ptmm) cc_final: 0.7004 (pttt) REVERT: c 146 MET cc_start: 0.7819 (mtm) cc_final: 0.7503 (mtp) REVERT: c 163 GLN cc_start: 0.7388 (mt0) cc_final: 0.7178 (mt0) REVERT: c 183 LYS cc_start: 0.7475 (OUTLIER) cc_final: 0.6948 (mttm) REVERT: c 236 GLU cc_start: 0.7698 (mm-30) cc_final: 0.7273 (mm-30) REVERT: c 265 LYS cc_start: 0.8030 (OUTLIER) cc_final: 0.7791 (pttm) REVERT: c 269 ARG cc_start: 0.6762 (ttp80) cc_final: 0.6296 (ttt90) REVERT: d 1 MET cc_start: 0.5548 (ttm) cc_final: 0.5079 (ttm) REVERT: d 7 LYS cc_start: 0.7917 (ttpp) cc_final: 0.7439 (ttmm) REVERT: d 13 ARG cc_start: 0.8100 (OUTLIER) cc_final: 0.6523 (ptt180) REVERT: d 40 LEU cc_start: 0.8042 (mp) cc_final: 0.7809 (mp) REVERT: d 48 ILE cc_start: 0.7552 (OUTLIER) cc_final: 0.7278 (pp) REVERT: d 64 GLU cc_start: 0.6424 (mt-10) cc_final: 0.6030 (mt-10) REVERT: d 157 LYS cc_start: 0.7927 (OUTLIER) cc_final: 0.7112 (tptp) REVERT: d 183 GLU cc_start: 0.6402 (pm20) cc_final: 0.5896 (pt0) REVERT: d 202 ILE cc_start: 0.8021 (mt) cc_final: 0.7714 (mm) REVERT: d 204 LYS cc_start: 0.7875 (OUTLIER) cc_final: 0.7011 (mtpt) REVERT: e 21 ARG cc_start: 0.6633 (mtp85) cc_final: 0.6026 (mtp85) REVERT: e 22 ASP cc_start: 0.7234 (p0) cc_final: 0.6876 (p0) REVERT: e 25 GLU cc_start: 0.7522 (tt0) cc_final: 0.7153 (tt0) REVERT: e 61 ARG cc_start: 0.6590 (mtp180) cc_final: 0.6336 (ptm-80) REVERT: e 139 LYS cc_start: 0.7129 (tttp) cc_final: 0.6475 (ttmp) REVERT: e 194 LYS cc_start: 0.5719 (mmmt) cc_final: 0.5358 (mmtm) REVERT: e 197 GLU cc_start: 0.6686 (tt0) cc_final: 0.6425 (mt-10) REVERT: f 3 LYS cc_start: 0.5448 (ptmm) cc_final: 0.5237 (ttmt) REVERT: f 21 ASN cc_start: 0.5788 (OUTLIER) cc_final: 0.5409 (t0) REVERT: f 64 LYS cc_start: 0.3306 (mptp) cc_final: 0.2834 (tttm) REVERT: f 67 ILE cc_start: 0.7852 (OUTLIER) cc_final: 0.7478 (mm) REVERT: f 88 LYS cc_start: 0.6244 (OUTLIER) cc_final: 0.5532 (tttt) REVERT: f 141 ILE cc_start: 0.5419 (OUTLIER) cc_final: 0.4919 (pp) REVERT: g 25 THR cc_start: 0.6544 (m) cc_final: 0.5988 (t) REVERT: g 36 THR cc_start: 0.6699 (t) cc_final: 0.6353 (m) REVERT: g 81 GLU cc_start: 0.5852 (OUTLIER) cc_final: 0.4720 (tm-30) REVERT: g 153 ARG cc_start: 0.7264 (ptp90) cc_final: 0.6464 (mtt90) REVERT: g 158 LYS cc_start: 0.6634 (mttm) cc_final: 0.6423 (mttp) REVERT: g 169 VAL cc_start: 0.6406 (OUTLIER) cc_final: 0.6047 (p) REVERT: h 15 LEU cc_start: 0.5183 (OUTLIER) cc_final: 0.4903 (pp) REVERT: j 2 LYS cc_start: 0.7506 (mmmt) cc_final: 0.6819 (mtmt) REVERT: j 12 LYS cc_start: 0.7192 (tppt) cc_final: 0.6036 (tttm) REVERT: j 43 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.6969 (pm20) REVERT: j 95 ARG cc_start: 0.6816 (OUTLIER) cc_final: 0.5518 (ttp-110) REVERT: j 98 GLU cc_start: 0.7313 (OUTLIER) cc_final: 0.7007 (mp0) REVERT: j 106 LYS cc_start: 0.7531 (tttp) cc_final: 0.6607 (ttpt) REVERT: j 138 GLN cc_start: 0.7854 (OUTLIER) cc_final: 0.7557 (pt0) REVERT: k 4 GLU cc_start: 0.7716 (mt-10) cc_final: 0.7234 (mt-10) REVERT: k 7 MET cc_start: 0.8020 (OUTLIER) cc_final: 0.6992 (mmm) REVERT: k 53 LYS cc_start: 0.6883 (mmpt) cc_final: 0.5851 (mppt) REVERT: k 98 ARG cc_start: 0.5546 (mtt180) cc_final: 0.4876 (mtm180) REVERT: k 114 LYS cc_start: 0.6687 (mtpp) cc_final: 0.6318 (mmmt) REVERT: l 29 LYS cc_start: 0.6383 (OUTLIER) cc_final: 0.5700 (tttp) REVERT: l 55 MET cc_start: 0.8054 (tpp) cc_final: 0.7827 (tpp) REVERT: l 69 ARG cc_start: 0.6925 (OUTLIER) cc_final: 0.6105 (ttt-90) REVERT: l 106 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.7120 (pm20) REVERT: m 81 ARG cc_start: 0.7153 (OUTLIER) cc_final: 0.6527 (mmt-90) REVERT: m 126 ILE cc_start: 0.7429 (OUTLIER) cc_final: 0.7041 (mm) REVERT: m 127 LYS cc_start: 0.6881 (OUTLIER) cc_final: 0.6437 (mtpp) REVERT: m 133 LYS cc_start: 0.7471 (tttm) cc_final: 0.7120 (ptmm) REVERT: n 18 GLN cc_start: 0.6794 (OUTLIER) cc_final: 0.6383 (tt0) REVERT: o 3 LYS cc_start: 0.5763 (OUTLIER) cc_final: 0.5475 (tttp) REVERT: o 10 ARG cc_start: 0.7412 (OUTLIER) cc_final: 0.5780 (mtp180) REVERT: o 16 ARG cc_start: 0.5817 (OUTLIER) cc_final: 0.5374 (mmt-90) REVERT: o 55 GLU cc_start: 0.6519 (mt-10) cc_final: 0.6193 (mt-10) REVERT: o 62 LEU cc_start: 0.7282 (OUTLIER) cc_final: 0.7047 (mp) REVERT: p 7 GLN cc_start: 0.6666 (OUTLIER) cc_final: 0.6159 (pp30) REVERT: p 11 GLU cc_start: 0.7291 (pt0) cc_final: 0.6989 (pt0) REVERT: p 89 ARG cc_start: 0.6765 (mtm-85) cc_final: 0.5753 (mtt-85) REVERT: p 102 GLU cc_start: 0.6715 (mm-30) cc_final: 0.6387 (mp0) REVERT: p 112 GLU cc_start: 0.6982 (tt0) cc_final: 0.6311 (tt0) REVERT: q 58 ARG cc_start: 0.8113 (OUTLIER) cc_final: 0.7186 (ttt-90) REVERT: q 85 LYS cc_start: 0.7429 (mtmt) cc_final: 0.6876 (mttt) REVERT: r 13 ARG cc_start: 0.8432 (ttp80) cc_final: 0.7972 (ttp80) REVERT: r 26 ASP cc_start: 0.6642 (OUTLIER) cc_final: 0.6378 (t0) REVERT: r 34 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7033 (mp0) REVERT: r 37 GLU cc_start: 0.7394 (mt-10) cc_final: 0.7091 (pt0) REVERT: r 45 GLU cc_start: 0.6228 (OUTLIER) cc_final: 0.5966 (pt0) REVERT: r 60 LYS cc_start: 0.7579 (mptp) cc_final: 0.7290 (mttp) REVERT: r 70 GLU cc_start: 0.7020 (tt0) cc_final: 0.6209 (tp30) REVERT: s 22 ASP cc_start: 0.7356 (OUTLIER) cc_final: 0.6801 (m-30) REVERT: s 28 LYS cc_start: 0.7380 (mttp) cc_final: 0.6978 (mttm) REVERT: s 34 ASP cc_start: 0.6447 (m-30) cc_final: 0.6196 (m-30) REVERT: s 70 LYS cc_start: 0.7456 (mttp) cc_final: 0.7134 (mtmm) REVERT: s 92 ARG cc_start: 0.6612 (mtp-110) cc_final: 0.5412 (mtm110) REVERT: s 95 ARG cc_start: 0.7000 (tpp80) cc_final: 0.5110 (ppt90) REVERT: s 109 ASP cc_start: 0.6542 (p0) cc_final: 0.5552 (p0) REVERT: t 25 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.7314 (pt0) REVERT: t 26 LYS cc_start: 0.6779 (tppp) cc_final: 0.6451 (mmtp) REVERT: t 32 LEU cc_start: 0.7685 (OUTLIER) cc_final: 0.7310 (pp) REVERT: t 49 LYS cc_start: 0.7229 (ttmm) cc_final: 0.6686 (tttp) REVERT: t 54 GLU cc_start: 0.5636 (pm20) cc_final: 0.5257 (mm-30) REVERT: t 56 GLU cc_start: 0.7382 (mm-30) cc_final: 0.7152 (tt0) REVERT: u 10 GLU cc_start: 0.7129 (mm-30) cc_final: 0.6483 (tp30) REVERT: u 21 LYS cc_start: 0.8329 (OUTLIER) cc_final: 0.7916 (mmmm) REVERT: u 22 ARG cc_start: 0.7762 (mtm-85) cc_final: 0.7530 (mtp180) REVERT: u 24 LYS cc_start: 0.7273 (ttmm) cc_final: 0.6360 (ttpp) REVERT: u 37 GLU cc_start: 0.6983 (tp30) cc_final: 0.6577 (mm-30) REVERT: u 46 GLN cc_start: 0.7406 (mm-40) cc_final: 0.7022 (mm-40) REVERT: u 62 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.6918 (pm20) REVERT: u 79 LYS cc_start: 0.7339 (OUTLIER) cc_final: 0.7007 (mptp) REVERT: w 25 LYS cc_start: 0.7182 (mtpt) cc_final: 0.6610 (mtpp) REVERT: w 34 LYS cc_start: 0.5792 (tppp) cc_final: 0.5127 (ptmt) REVERT: w 41 GLU cc_start: 0.7294 (mt-10) cc_final: 0.7056 (mt-10) REVERT: w 53 LYS cc_start: 0.6514 (mttm) cc_final: 0.5493 (mmtt) REVERT: w 68 LYS cc_start: 0.5872 (ttmt) cc_final: 0.5125 (tptt) REVERT: y 62 LYS cc_start: 0.8098 (mtmt) cc_final: 0.7791 (mtpp) REVERT: y 68 LYS cc_start: 0.7991 (OUTLIER) cc_final: 0.7707 (tptp) outliers start: 211 outliers final: 115 residues processed: 614 average time/residue: 2.0103 time to fit residues: 1616.7278 Evaluate side-chains 643 residues out of total 2526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 470 time to evaluate : 3.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 2 SER Chi-restraints excluded: chain 0 residue 25 THR Chi-restraints excluded: chain 0 residue 35 SER Chi-restraints excluded: chain 0 residue 56 MET Chi-restraints excluded: chain 0 residue 62 LYS Chi-restraints excluded: chain 0 residue 66 THR Chi-restraints excluded: chain 0 residue 76 GLU Chi-restraints excluded: chain 1 residue 4 LYS Chi-restraints excluded: chain 1 residue 38 GLN Chi-restraints excluded: chain 1 residue 44 LYS Chi-restraints excluded: chain 1 residue 58 ASN Chi-restraints excluded: chain 1 residue 59 GLU Chi-restraints excluded: chain 2 residue 7 ILE Chi-restraints excluded: chain 2 residue 19 LYS Chi-restraints excluded: chain 2 residue 36 VAL Chi-restraints excluded: chain 2 residue 56 LYS Chi-restraints excluded: chain 4 residue 5 ILE Chi-restraints excluded: chain 4 residue 17 THR Chi-restraints excluded: chain 4 residue 30 LYS Chi-restraints excluded: chain 4 residue 37 LYS Chi-restraints excluded: chain 4 residue 42 VAL Chi-restraints excluded: chain 4 residue 43 VAL Chi-restraints excluded: chain 4 residue 44 ARG Chi-restraints excluded: chain 6 residue 1 MET Chi-restraints excluded: chain 7 residue 19 LYS Chi-restraints excluded: chain 7 residue 52 LYS Chi-restraints excluded: chain 8 residue 10 LEU Chi-restraints excluded: chain 8 residue 17 VAL Chi-restraints excluded: chain 8 residue 32 LYS Chi-restraints excluded: chain c residue 7 LYS Chi-restraints excluded: chain c residue 20 VAL Chi-restraints excluded: chain c residue 74 ILE Chi-restraints excluded: chain c residue 79 GLU Chi-restraints excluded: chain c residue 87 ARG Chi-restraints excluded: chain c residue 108 LYS Chi-restraints excluded: chain c residue 110 LEU Chi-restraints excluded: chain c residue 116 ILE Chi-restraints excluded: chain c residue 118 SER Chi-restraints excluded: chain c residue 132 MET Chi-restraints excluded: chain c residue 162 VAL Chi-restraints excluded: chain c residue 183 LYS Chi-restraints excluded: chain c residue 265 LYS Chi-restraints excluded: chain d residue 13 ARG Chi-restraints excluded: chain d residue 29 VAL Chi-restraints excluded: chain d residue 48 ILE Chi-restraints excluded: chain d residue 131 ASP Chi-restraints excluded: chain d residue 151 THR Chi-restraints excluded: chain d residue 157 LYS Chi-restraints excluded: chain d residue 175 LEU Chi-restraints excluded: chain d residue 179 ARG Chi-restraints excluded: chain d residue 204 LYS Chi-restraints excluded: chain e residue 10 SER Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain e residue 95 LYS Chi-restraints excluded: chain e residue 119 ILE Chi-restraints excluded: chain e residue 122 GLU Chi-restraints excluded: chain e residue 166 LYS Chi-restraints excluded: chain e residue 173 THR Chi-restraints excluded: chain f residue 16 LEU Chi-restraints excluded: chain f residue 21 ASN Chi-restraints excluded: chain f residue 26 MET Chi-restraints excluded: chain f residue 35 THR Chi-restraints excluded: chain f residue 67 ILE Chi-restraints excluded: chain f residue 72 LYS Chi-restraints excluded: chain f residue 88 LYS Chi-restraints excluded: chain f residue 104 ILE Chi-restraints excluded: chain f residue 108 VAL Chi-restraints excluded: chain f residue 117 LEU Chi-restraints excluded: chain f residue 132 VAL Chi-restraints excluded: chain f residue 141 ILE Chi-restraints excluded: chain f residue 170 LEU Chi-restraints excluded: chain g residue 11 VAL Chi-restraints excluded: chain g residue 17 VAL Chi-restraints excluded: chain g residue 49 THR Chi-restraints excluded: chain g residue 81 GLU Chi-restraints excluded: chain g residue 90 VAL Chi-restraints excluded: chain g residue 99 LYS Chi-restraints excluded: chain g residue 107 LEU Chi-restraints excluded: chain g residue 113 VAL Chi-restraints excluded: chain g residue 169 VAL Chi-restraints excluded: chain h residue 3 VAL Chi-restraints excluded: chain h residue 9 VAL Chi-restraints excluded: chain h residue 15 LEU Chi-restraints excluded: chain h residue 22 LYS Chi-restraints excluded: chain h residue 37 VAL Chi-restraints excluded: chain j residue 1 MET Chi-restraints excluded: chain j residue 5 THR Chi-restraints excluded: chain j residue 10 THR Chi-restraints excluded: chain j residue 11 VAL Chi-restraints excluded: chain j residue 43 GLU Chi-restraints excluded: chain j residue 62 VAL Chi-restraints excluded: chain j residue 64 VAL Chi-restraints excluded: chain j residue 95 ARG Chi-restraints excluded: chain j residue 98 GLU Chi-restraints excluded: chain j residue 131 ASN Chi-restraints excluded: chain j residue 138 GLN Chi-restraints excluded: chain k residue 7 MET Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 88 ASN Chi-restraints excluded: chain l residue 29 LYS Chi-restraints excluded: chain l residue 69 ARG Chi-restraints excluded: chain l residue 104 GLN Chi-restraints excluded: chain l residue 106 GLU Chi-restraints excluded: chain l residue 117 THR Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain m residue 5 LYS Chi-restraints excluded: chain m residue 7 THR Chi-restraints excluded: chain m residue 30 SER Chi-restraints excluded: chain m residue 78 LEU Chi-restraints excluded: chain m residue 81 ARG Chi-restraints excluded: chain m residue 104 GLU Chi-restraints excluded: chain m residue 126 ILE Chi-restraints excluded: chain m residue 127 LYS Chi-restraints excluded: chain m residue 129 THR Chi-restraints excluded: chain n residue 14 SER Chi-restraints excluded: chain n residue 18 GLN Chi-restraints excluded: chain n residue 35 LYS Chi-restraints excluded: chain n residue 48 VAL Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain n residue 70 THR Chi-restraints excluded: chain n residue 74 GLU Chi-restraints excluded: chain o residue 3 LYS Chi-restraints excluded: chain o residue 9 ARG Chi-restraints excluded: chain o residue 10 ARG Chi-restraints excluded: chain o residue 16 ARG Chi-restraints excluded: chain o residue 24 THR Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain o residue 48 LEU Chi-restraints excluded: chain o residue 49 VAL Chi-restraints excluded: chain o residue 54 VAL Chi-restraints excluded: chain o residue 62 LEU Chi-restraints excluded: chain p residue 7 GLN Chi-restraints excluded: chain p residue 46 VAL Chi-restraints excluded: chain p residue 63 LYS Chi-restraints excluded: chain p residue 70 VAL Chi-restraints excluded: chain p residue 76 THR Chi-restraints excluded: chain q residue 6 ARG Chi-restraints excluded: chain q residue 58 ARG Chi-restraints excluded: chain q residue 84 LYS Chi-restraints excluded: chain r residue 26 ASP Chi-restraints excluded: chain r residue 34 GLU Chi-restraints excluded: chain r residue 45 GLU Chi-restraints excluded: chain r residue 47 VAL Chi-restraints excluded: chain s residue 22 ASP Chi-restraints excluded: chain s residue 33 LEU Chi-restraints excluded: chain s residue 66 ILE Chi-restraints excluded: chain s residue 101 SER Chi-restraints excluded: chain s residue 106 VAL Chi-restraints excluded: chain t residue 4 GLU Chi-restraints excluded: chain t residue 6 ARG Chi-restraints excluded: chain t residue 25 GLU Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain t residue 36 LYS Chi-restraints excluded: chain t residue 50 LEU Chi-restraints excluded: chain t residue 55 VAL Chi-restraints excluded: chain t residue 67 VAL Chi-restraints excluded: chain t residue 69 GLN Chi-restraints excluded: chain t residue 100 ASN Chi-restraints excluded: chain u residue 17 LYS Chi-restraints excluded: chain u residue 21 LYS Chi-restraints excluded: chain u residue 27 ASN Chi-restraints excluded: chain u residue 30 SER Chi-restraints excluded: chain u residue 62 GLU Chi-restraints excluded: chain u residue 68 SER Chi-restraints excluded: chain u residue 79 LYS Chi-restraints excluded: chain u residue 88 GLU Chi-restraints excluded: chain w residue 72 VAL Chi-restraints excluded: chain y residue 17 GLU Chi-restraints excluded: chain y residue 19 LYS Chi-restraints excluded: chain y residue 43 THR Chi-restraints excluded: chain y residue 51 VAL Chi-restraints excluded: chain y residue 68 LYS Chi-restraints excluded: chain y residue 72 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 607 random chunks: chunk 566 optimal weight: 6.9990 chunk 66 optimal weight: 10.0000 chunk 334 optimal weight: 9.9990 chunk 428 optimal weight: 20.0000 chunk 332 optimal weight: 20.0000 chunk 494 optimal weight: 6.9990 chunk 327 optimal weight: 10.0000 chunk 585 optimal weight: 40.0000 chunk 366 optimal weight: 0.9980 chunk 356 optimal weight: 1.9990 chunk 270 optimal weight: 50.0000 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 5 GLN 6 29 GLN d 173 GLN g 104 ASN ** j 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 128 ASN ** k 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 3 GLN q 56 GLN r 86 GLN s 31 GLN t 59 ASN ** u 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6601 moved from start: 0.4190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 98998 Z= 0.341 Angle : 0.719 11.581 149023 Z= 0.374 Chirality : 0.044 0.359 19174 Planarity : 0.006 0.091 7331 Dihedral : 24.261 179.837 51740 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.14 % Favored : 94.77 % Rotamer: Outliers : 8.75 % Allowed : 25.30 % Favored : 65.95 % 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: -0.67 (0.15), residues: 3057 helix: 0.53 (0.18), residues: 803 sheet: -0.37 (0.19), residues: 707 loop : -0.96 (0.15), residues: 1547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP c 213 HIS 0.010 0.002 HIS r 89 PHE 0.021 0.002 PHE h 29 TYR 0.018 0.002 TYR q 32 ARG 0.015 0.001 ARG f 150 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 696 residues out of total 2526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 221 poor density : 475 time to evaluate : 3.853 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 62 LYS cc_start: 0.7493 (OUTLIER) cc_final: 0.7080 (mmmt) REVERT: 0 72 ARG cc_start: 0.6917 (mtm-85) cc_final: 0.6693 (mtm-85) REVERT: 0 76 GLU cc_start: 0.5794 (OUTLIER) cc_final: 0.5384 (tt0) REVERT: 1 4 LYS cc_start: 0.4939 (OUTLIER) cc_final: 0.4083 (ttmt) REVERT: 1 24 GLU cc_start: 0.6313 (tp30) cc_final: 0.5596 (tp30) REVERT: 1 44 LYS cc_start: 0.6394 (OUTLIER) cc_final: 0.5793 (ttmt) REVERT: 1 59 GLU cc_start: 0.6775 (OUTLIER) cc_final: 0.6485 (mt-10) REVERT: 2 19 LYS cc_start: 0.7281 (OUTLIER) cc_final: 0.7014 (tttm) REVERT: 2 56 LYS cc_start: 0.7460 (OUTLIER) cc_final: 0.6949 (ttpp) REVERT: 3 9 THR cc_start: 0.7267 (m) cc_final: 0.6792 (p) REVERT: 3 15 MET cc_start: 0.8226 (mtm) cc_final: 0.7992 (mtm) REVERT: 4 30 LYS cc_start: 0.6252 (OUTLIER) cc_final: 0.5806 (ptmt) REVERT: 4 37 LYS cc_start: 0.7502 (OUTLIER) cc_final: 0.7238 (mttp) REVERT: 4 44 ARG cc_start: 0.6407 (OUTLIER) cc_final: 0.5899 (mmm160) REVERT: 4 45 GLN cc_start: 0.7153 (mm110) cc_final: 0.6590 (mm110) REVERT: 6 1 MET cc_start: 0.7209 (OUTLIER) cc_final: 0.6772 (mpp) REVERT: 8 15 LYS cc_start: 0.6877 (ttmm) cc_final: 0.6013 (tttp) REVERT: c 5 LYS cc_start: 0.7105 (tttp) cc_final: 0.6562 (tptp) REVERT: c 7 LYS cc_start: 0.7955 (OUTLIER) cc_final: 0.7605 (mttt) REVERT: c 74 ILE cc_start: 0.6920 (OUTLIER) cc_final: 0.6687 (mm) REVERT: c 79 GLU cc_start: 0.7146 (OUTLIER) cc_final: 0.6670 (mt-10) REVERT: c 87 ARG cc_start: 0.7242 (OUTLIER) cc_final: 0.5807 (mtm-85) REVERT: c 108 LYS cc_start: 0.7343 (OUTLIER) cc_final: 0.6782 (ttmt) REVERT: c 110 LEU cc_start: 0.7295 (OUTLIER) cc_final: 0.7014 (tp) REVERT: c 125 LYS cc_start: 0.7367 (ptmm) cc_final: 0.6988 (pttt) REVERT: c 146 MET cc_start: 0.7816 (mtm) cc_final: 0.7488 (mtp) REVERT: c 163 GLN cc_start: 0.7387 (OUTLIER) cc_final: 0.7178 (mt0) REVERT: c 183 LYS cc_start: 0.7507 (OUTLIER) cc_final: 0.7009 (mttm) REVERT: c 265 LYS cc_start: 0.8011 (OUTLIER) cc_final: 0.7766 (pttm) REVERT: c 269 ARG cc_start: 0.6752 (ttp80) cc_final: 0.6287 (ttt90) REVERT: d 1 MET cc_start: 0.5398 (ttm) cc_final: 0.4920 (ttm) REVERT: d 7 LYS cc_start: 0.7912 (ttpp) cc_final: 0.7436 (ttmm) REVERT: d 13 ARG cc_start: 0.8095 (OUTLIER) cc_final: 0.6434 (ptt180) REVERT: d 40 LEU cc_start: 0.8034 (mp) cc_final: 0.7803 (mp) REVERT: d 48 ILE cc_start: 0.7602 (OUTLIER) cc_final: 0.7291 (pp) REVERT: d 64 GLU cc_start: 0.6421 (mt-10) cc_final: 0.6014 (mt-10) REVERT: d 103 ASP cc_start: 0.6204 (OUTLIER) cc_final: 0.5713 (m-30) REVERT: d 157 LYS cc_start: 0.7884 (OUTLIER) cc_final: 0.7053 (tptp) REVERT: d 183 GLU cc_start: 0.6347 (pm20) cc_final: 0.5826 (pt0) REVERT: d 202 ILE cc_start: 0.8016 (mt) cc_final: 0.7709 (mm) REVERT: d 204 LYS cc_start: 0.7869 (OUTLIER) cc_final: 0.7022 (mtpt) REVERT: e 21 ARG cc_start: 0.6643 (OUTLIER) cc_final: 0.6031 (mtp85) REVERT: e 22 ASP cc_start: 0.7243 (p0) cc_final: 0.6879 (p0) REVERT: e 25 GLU cc_start: 0.7527 (tt0) cc_final: 0.7161 (tt0) REVERT: e 61 ARG cc_start: 0.6600 (mtp180) cc_final: 0.6344 (ptm-80) REVERT: e 139 LYS cc_start: 0.7116 (tttp) cc_final: 0.6461 (ttmp) REVERT: e 153 LEU cc_start: 0.3846 (OUTLIER) cc_final: 0.3507 (tm) REVERT: e 194 LYS cc_start: 0.5694 (mmmt) cc_final: 0.5336 (mmtm) REVERT: e 197 GLU cc_start: 0.6672 (tt0) cc_final: 0.6376 (mt-10) REVERT: f 3 LYS cc_start: 0.5444 (ptmm) cc_final: 0.5228 (ttmt) REVERT: f 21 ASN cc_start: 0.5865 (OUTLIER) cc_final: 0.5449 (t0) REVERT: f 38 MET cc_start: 0.7053 (ptp) cc_final: 0.6758 (ptp) REVERT: f 64 LYS cc_start: 0.3317 (mptp) cc_final: 0.2841 (tttm) REVERT: f 88 LYS cc_start: 0.6420 (OUTLIER) cc_final: 0.5965 (tttt) REVERT: f 141 ILE cc_start: 0.5377 (OUTLIER) cc_final: 0.4880 (pp) REVERT: g 25 THR cc_start: 0.6488 (m) cc_final: 0.5959 (t) REVERT: g 36 THR cc_start: 0.6626 (t) cc_final: 0.6292 (m) REVERT: g 81 GLU cc_start: 0.5876 (OUTLIER) cc_final: 0.4714 (tm-30) REVERT: g 85 LYS cc_start: 0.7083 (OUTLIER) cc_final: 0.6489 (tppt) REVERT: g 153 ARG cc_start: 0.7261 (ptp90) cc_final: 0.6469 (mtt90) REVERT: g 158 LYS cc_start: 0.6635 (mttm) cc_final: 0.6399 (mttp) REVERT: g 169 VAL cc_start: 0.6362 (OUTLIER) cc_final: 0.6005 (p) REVERT: h 15 LEU cc_start: 0.5135 (OUTLIER) cc_final: 0.4844 (pp) REVERT: j 2 LYS cc_start: 0.7496 (mmmt) cc_final: 0.6813 (mtmt) REVERT: j 12 LYS cc_start: 0.7173 (tppt) cc_final: 0.6015 (tttm) REVERT: j 43 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.6960 (pm20) REVERT: j 95 ARG cc_start: 0.6705 (OUTLIER) cc_final: 0.5482 (ttp-110) REVERT: j 98 GLU cc_start: 0.7314 (OUTLIER) cc_final: 0.7007 (mp0) REVERT: j 106 LYS cc_start: 0.7531 (tttp) cc_final: 0.6605 (ttpt) REVERT: k 4 GLU cc_start: 0.7702 (mt-10) cc_final: 0.7234 (mt-10) REVERT: k 53 LYS cc_start: 0.6908 (mmpt) cc_final: 0.5830 (mppt) REVERT: k 98 ARG cc_start: 0.5520 (mtt180) cc_final: 0.4904 (mtm110) REVERT: l 29 LYS cc_start: 0.6379 (OUTLIER) cc_final: 0.5700 (tttp) REVERT: l 55 MET cc_start: 0.8105 (tpp) cc_final: 0.7828 (tpp) REVERT: l 69 ARG cc_start: 0.6957 (OUTLIER) cc_final: 0.6152 (ttt-90) REVERT: l 106 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.7119 (pm20) REVERT: m 22 GLN cc_start: 0.5967 (OUTLIER) cc_final: 0.4824 (mp10) REVERT: m 81 ARG cc_start: 0.7149 (OUTLIER) cc_final: 0.6561 (mmt-90) REVERT: m 126 ILE cc_start: 0.7426 (OUTLIER) cc_final: 0.7039 (mm) REVERT: m 127 LYS cc_start: 0.6976 (OUTLIER) cc_final: 0.6548 (mtpp) REVERT: m 133 LYS cc_start: 0.7471 (tttm) cc_final: 0.7135 (ptmm) REVERT: n 18 GLN cc_start: 0.6794 (OUTLIER) cc_final: 0.6381 (tt0) REVERT: o 3 LYS cc_start: 0.5952 (OUTLIER) cc_final: 0.5579 (tttp) REVERT: o 10 ARG cc_start: 0.7411 (OUTLIER) cc_final: 0.5812 (mtp180) REVERT: o 16 ARG cc_start: 0.5840 (OUTLIER) cc_final: 0.5398 (mmt-90) REVERT: o 20 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7380 (pp20) REVERT: o 55 GLU cc_start: 0.6516 (mt-10) cc_final: 0.6184 (mt-10) REVERT: o 62 LEU cc_start: 0.7284 (OUTLIER) cc_final: 0.7032 (mp) REVERT: p 11 GLU cc_start: 0.7313 (pt0) cc_final: 0.6943 (pt0) REVERT: p 89 ARG cc_start: 0.6837 (mtm-85) cc_final: 0.5783 (mtt-85) REVERT: p 102 GLU cc_start: 0.6714 (mm-30) cc_final: 0.6390 (mp0) REVERT: p 112 GLU cc_start: 0.6984 (tt0) cc_final: 0.6300 (tt0) REVERT: q 58 ARG cc_start: 0.8121 (OUTLIER) cc_final: 0.7149 (ttt-90) REVERT: q 85 LYS cc_start: 0.7427 (mtmt) cc_final: 0.6875 (mttt) REVERT: r 13 ARG cc_start: 0.8434 (ttp80) cc_final: 0.7985 (ttp80) REVERT: r 26 ASP cc_start: 0.6618 (OUTLIER) cc_final: 0.6352 (t0) REVERT: r 34 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7026 (mp0) REVERT: r 37 GLU cc_start: 0.7407 (mt-10) cc_final: 0.7089 (pt0) REVERT: r 45 GLU cc_start: 0.6226 (OUTLIER) cc_final: 0.5976 (pt0) REVERT: r 60 LYS cc_start: 0.7604 (mptp) cc_final: 0.7313 (mttp) REVERT: r 70 GLU cc_start: 0.7015 (tt0) cc_final: 0.6214 (tp30) REVERT: s 28 LYS cc_start: 0.7284 (mttp) cc_final: 0.6870 (mttm) REVERT: s 34 ASP cc_start: 0.6434 (m-30) cc_final: 0.6216 (m-30) REVERT: s 70 LYS cc_start: 0.7471 (mttp) cc_final: 0.7136 (mtmm) REVERT: s 73 LYS cc_start: 0.7743 (OUTLIER) cc_final: 0.7224 (mtpt) REVERT: s 92 ARG cc_start: 0.6611 (mtp-110) cc_final: 0.5411 (mtm110) REVERT: s 95 ARG cc_start: 0.6937 (tpp80) cc_final: 0.5091 (ppt90) REVERT: s 109 ASP cc_start: 0.6544 (p0) cc_final: 0.5557 (p0) REVERT: t 26 LYS cc_start: 0.6706 (tppp) cc_final: 0.6380 (mmtp) REVERT: t 32 LEU cc_start: 0.7678 (OUTLIER) cc_final: 0.7304 (pp) REVERT: t 49 LYS cc_start: 0.7232 (ttmm) cc_final: 0.6690 (tttp) REVERT: t 54 GLU cc_start: 0.5615 (pm20) cc_final: 0.5260 (mm-30) REVERT: t 56 GLU cc_start: 0.7381 (mm-30) cc_final: 0.6984 (tt0) REVERT: t 68 ARG cc_start: 0.6831 (OUTLIER) cc_final: 0.6379 (ptp90) REVERT: u 10 GLU cc_start: 0.7156 (mm-30) cc_final: 0.6411 (tp30) REVERT: u 21 LYS cc_start: 0.8280 (OUTLIER) cc_final: 0.7860 (mmmm) REVERT: u 22 ARG cc_start: 0.7774 (mtm-85) cc_final: 0.7561 (mtp180) REVERT: u 24 LYS cc_start: 0.7269 (ttmm) cc_final: 0.6250 (ttpp) REVERT: u 37 GLU cc_start: 0.6957 (tp30) cc_final: 0.6536 (mm-30) REVERT: u 46 GLN cc_start: 0.7401 (mm-40) cc_final: 0.7010 (mm-40) REVERT: u 62 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.6909 (pm20) REVERT: u 79 LYS cc_start: 0.7358 (OUTLIER) cc_final: 0.6955 (mttm) REVERT: w 25 LYS cc_start: 0.7183 (mtpt) cc_final: 0.6605 (mtpp) REVERT: w 34 LYS cc_start: 0.5787 (tppp) cc_final: 0.5137 (ptmt) REVERT: w 41 GLU cc_start: 0.7293 (mt-10) cc_final: 0.7052 (mt-10) REVERT: w 53 LYS cc_start: 0.6240 (mttm) cc_final: 0.5351 (mmtt) REVERT: w 68 LYS cc_start: 0.5882 (ttmt) cc_final: 0.5125 (tptt) REVERT: y 11 ARG cc_start: 0.6363 (ptm160) cc_final: 0.5950 (ptt-90) REVERT: y 62 LYS cc_start: 0.8125 (mtmt) cc_final: 0.7500 (mttm) REVERT: y 68 LYS cc_start: 0.7998 (OUTLIER) cc_final: 0.7343 (tptp) REVERT: y 70 GLU cc_start: 0.7816 (mt-10) cc_final: 0.6530 (mp0) outliers start: 221 outliers final: 130 residues processed: 625 average time/residue: 2.0172 time to fit residues: 1651.3432 Evaluate side-chains 664 residues out of total 2526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 473 time to evaluate : 3.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 2 SER Chi-restraints excluded: chain 0 residue 25 THR Chi-restraints excluded: chain 0 residue 35 SER Chi-restraints excluded: chain 0 residue 56 MET Chi-restraints excluded: chain 0 residue 62 LYS Chi-restraints excluded: chain 0 residue 66 THR Chi-restraints excluded: chain 0 residue 76 GLU Chi-restraints excluded: chain 1 residue 4 LYS Chi-restraints excluded: chain 1 residue 38 GLN Chi-restraints excluded: chain 1 residue 44 LYS Chi-restraints excluded: chain 1 residue 58 ASN Chi-restraints excluded: chain 1 residue 59 GLU Chi-restraints excluded: chain 2 residue 7 ILE Chi-restraints excluded: chain 2 residue 19 LYS Chi-restraints excluded: chain 2 residue 36 VAL Chi-restraints excluded: chain 2 residue 56 LYS Chi-restraints excluded: chain 4 residue 5 ILE Chi-restraints excluded: chain 4 residue 17 THR Chi-restraints excluded: chain 4 residue 30 LYS Chi-restraints excluded: chain 4 residue 37 LYS Chi-restraints excluded: chain 4 residue 42 VAL Chi-restraints excluded: chain 4 residue 43 VAL Chi-restraints excluded: chain 4 residue 44 ARG Chi-restraints excluded: chain 6 residue 1 MET Chi-restraints excluded: chain 7 residue 52 LYS Chi-restraints excluded: chain 8 residue 10 LEU Chi-restraints excluded: chain 8 residue 17 VAL Chi-restraints excluded: chain 8 residue 32 LYS Chi-restraints excluded: chain c residue 7 LYS Chi-restraints excluded: chain c residue 20 VAL Chi-restraints excluded: chain c residue 26 LYS Chi-restraints excluded: chain c residue 74 ILE Chi-restraints excluded: chain c residue 79 GLU Chi-restraints excluded: chain c residue 87 ARG Chi-restraints excluded: chain c residue 108 LYS Chi-restraints excluded: chain c residue 110 LEU Chi-restraints excluded: chain c residue 116 ILE Chi-restraints excluded: chain c residue 118 SER Chi-restraints excluded: chain c residue 120 VAL Chi-restraints excluded: chain c residue 132 MET Chi-restraints excluded: chain c residue 162 VAL Chi-restraints excluded: chain c residue 163 GLN Chi-restraints excluded: chain c residue 183 LYS Chi-restraints excluded: chain c residue 265 LYS Chi-restraints excluded: chain d residue 13 ARG Chi-restraints excluded: chain d residue 29 VAL Chi-restraints excluded: chain d residue 48 ILE Chi-restraints excluded: chain d residue 99 GLU Chi-restraints excluded: chain d residue 103 ASP Chi-restraints excluded: chain d residue 106 LYS Chi-restraints excluded: chain d residue 151 THR Chi-restraints excluded: chain d residue 157 LYS Chi-restraints excluded: chain d residue 175 LEU Chi-restraints excluded: chain d residue 179 ARG Chi-restraints excluded: chain d residue 204 LYS Chi-restraints excluded: chain e residue 10 SER Chi-restraints excluded: chain e residue 21 ARG Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain e residue 80 SER Chi-restraints excluded: chain e residue 95 LYS Chi-restraints excluded: chain e residue 119 ILE Chi-restraints excluded: chain e residue 122 GLU Chi-restraints excluded: chain e residue 153 LEU Chi-restraints excluded: chain e residue 166 LYS Chi-restraints excluded: chain e residue 173 THR Chi-restraints excluded: chain f residue 16 LEU Chi-restraints excluded: chain f residue 21 ASN Chi-restraints excluded: chain f residue 26 MET Chi-restraints excluded: chain f residue 35 THR Chi-restraints excluded: chain f residue 49 LEU Chi-restraints excluded: chain f residue 72 LYS Chi-restraints excluded: chain f residue 88 LYS Chi-restraints excluded: chain f residue 89 VAL Chi-restraints excluded: chain f residue 103 LEU Chi-restraints excluded: chain f residue 104 ILE Chi-restraints excluded: chain f residue 108 VAL Chi-restraints excluded: chain f residue 117 LEU Chi-restraints excluded: chain f residue 132 VAL Chi-restraints excluded: chain f residue 141 ILE Chi-restraints excluded: chain f residue 155 THR Chi-restraints excluded: chain f residue 170 LEU Chi-restraints excluded: chain g residue 11 VAL Chi-restraints excluded: chain g residue 17 VAL Chi-restraints excluded: chain g residue 49 THR Chi-restraints excluded: chain g residue 51 THR Chi-restraints excluded: chain g residue 81 GLU Chi-restraints excluded: chain g residue 85 LYS Chi-restraints excluded: chain g residue 90 VAL Chi-restraints excluded: chain g residue 99 LYS Chi-restraints excluded: chain g residue 107 LEU Chi-restraints excluded: chain g residue 113 VAL Chi-restraints excluded: chain g residue 169 VAL Chi-restraints excluded: chain h residue 3 VAL Chi-restraints excluded: chain h residue 9 VAL Chi-restraints excluded: chain h residue 15 LEU Chi-restraints excluded: chain h residue 22 LYS Chi-restraints excluded: chain h residue 37 VAL Chi-restraints excluded: chain j residue 1 MET Chi-restraints excluded: chain j residue 5 THR Chi-restraints excluded: chain j residue 10 THR Chi-restraints excluded: chain j residue 11 VAL Chi-restraints excluded: chain j residue 43 GLU Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 62 VAL Chi-restraints excluded: chain j residue 64 VAL Chi-restraints excluded: chain j residue 95 ARG Chi-restraints excluded: chain j residue 98 GLU Chi-restraints excluded: chain j residue 131 ASN Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain l residue 29 LYS Chi-restraints excluded: chain l residue 69 ARG Chi-restraints excluded: chain l residue 104 GLN Chi-restraints excluded: chain l residue 106 GLU Chi-restraints excluded: chain l residue 117 THR Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain m residue 5 LYS Chi-restraints excluded: chain m residue 7 THR Chi-restraints excluded: chain m residue 22 GLN Chi-restraints excluded: chain m residue 30 SER Chi-restraints excluded: chain m residue 53 MET Chi-restraints excluded: chain m residue 78 LEU Chi-restraints excluded: chain m residue 81 ARG Chi-restraints excluded: chain m residue 104 GLU Chi-restraints excluded: chain m residue 126 ILE Chi-restraints excluded: chain m residue 127 LYS Chi-restraints excluded: chain m residue 129 THR Chi-restraints excluded: chain n residue 14 SER Chi-restraints excluded: chain n residue 18 GLN Chi-restraints excluded: chain n residue 48 VAL Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain n residue 70 THR Chi-restraints excluded: chain n residue 74 GLU Chi-restraints excluded: chain o residue 3 LYS Chi-restraints excluded: chain o residue 9 ARG Chi-restraints excluded: chain o residue 10 ARG Chi-restraints excluded: chain o residue 16 ARG Chi-restraints excluded: chain o residue 20 GLU Chi-restraints excluded: chain o residue 21 LEU Chi-restraints excluded: chain o residue 24 THR Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain o residue 48 LEU Chi-restraints excluded: chain o residue 49 VAL Chi-restraints excluded: chain o residue 54 VAL Chi-restraints excluded: chain o residue 62 LEU Chi-restraints excluded: chain p residue 7 GLN Chi-restraints excluded: chain p residue 36 SER Chi-restraints excluded: chain p residue 46 VAL Chi-restraints excluded: chain p residue 63 LYS Chi-restraints excluded: chain p residue 70 VAL Chi-restraints excluded: chain p residue 76 THR Chi-restraints excluded: chain p residue 96 LYS Chi-restraints excluded: chain p residue 110 ILE Chi-restraints excluded: chain q residue 58 ARG Chi-restraints excluded: chain q residue 84 LYS Chi-restraints excluded: chain q residue 91 ASP Chi-restraints excluded: chain r residue 26 ASP Chi-restraints excluded: chain r residue 34 GLU Chi-restraints excluded: chain r residue 45 GLU Chi-restraints excluded: chain r residue 47 VAL Chi-restraints excluded: chain r residue 48 LYS Chi-restraints excluded: chain s residue 33 LEU Chi-restraints excluded: chain s residue 66 ILE Chi-restraints excluded: chain s residue 73 LYS Chi-restraints excluded: chain s residue 101 SER Chi-restraints excluded: chain s residue 106 VAL Chi-restraints excluded: chain t residue 4 GLU Chi-restraints excluded: chain t residue 6 ARG Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain t residue 36 LYS Chi-restraints excluded: chain t residue 50 LEU Chi-restraints excluded: chain t residue 55 VAL Chi-restraints excluded: chain t residue 67 VAL Chi-restraints excluded: chain t residue 68 ARG Chi-restraints excluded: chain t residue 69 GLN Chi-restraints excluded: chain t residue 100 ASN Chi-restraints excluded: chain u residue 17 LYS Chi-restraints excluded: chain u residue 21 LYS Chi-restraints excluded: chain u residue 27 ASN Chi-restraints excluded: chain u residue 30 SER Chi-restraints excluded: chain u residue 62 GLU Chi-restraints excluded: chain u residue 68 SER Chi-restraints excluded: chain u residue 79 LYS Chi-restraints excluded: chain u residue 88 GLU Chi-restraints excluded: chain w residue 72 VAL Chi-restraints excluded: chain y residue 17 GLU Chi-restraints excluded: chain y residue 19 LYS Chi-restraints excluded: chain y residue 43 THR Chi-restraints excluded: chain y residue 51 VAL Chi-restraints excluded: chain y residue 68 LYS Chi-restraints excluded: chain y residue 72 LYS Chi-restraints excluded: chain y residue 78 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 607 random chunks: chunk 361 optimal weight: 10.0000 chunk 233 optimal weight: 10.0000 chunk 349 optimal weight: 9.9990 chunk 176 optimal weight: 8.9990 chunk 114 optimal weight: 10.0000 chunk 113 optimal weight: 10.0000 chunk 371 optimal weight: 2.9990 chunk 398 optimal weight: 6.9990 chunk 289 optimal weight: 10.0000 chunk 54 optimal weight: 8.9990 chunk 459 optimal weight: 6.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 5 GLN 6 29 GLN c 260 ASN d 173 GLN g 104 ASN j 77 HIS j 128 ASN ** k 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 3 GLN q 56 GLN r 86 GLN s 31 GLN t 59 ASN ** u 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6616 moved from start: 0.4266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 98998 Z= 0.432 Angle : 0.810 12.211 149023 Z= 0.416 Chirality : 0.048 0.396 19174 Planarity : 0.007 0.101 7331 Dihedral : 24.337 179.562 51740 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.33 % Favored : 94.57 % Rotamer: Outliers : 9.11 % Allowed : 24.58 % Favored : 66.31 % 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: -0.78 (0.14), residues: 3057 helix: 0.41 (0.18), residues: 801 sheet: -0.41 (0.18), residues: 711 loop : -1.02 (0.15), residues: 1545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP c 213 HIS 0.011 0.002 HIS r 89 PHE 0.025 0.003 PHE h 29 TYR 0.022 0.003 TYR q 32 ARG 0.017 0.001 ARG d 184 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 702 residues out of total 2526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 230 poor density : 472 time to evaluate : 3.773 Fit side-chains revert: symmetry clash REVERT: 0 62 LYS cc_start: 0.7552 (OUTLIER) cc_final: 0.7130 (mmmt) REVERT: 0 72 ARG cc_start: 0.6904 (mtm-85) cc_final: 0.6634 (mtm-85) REVERT: 0 76 GLU cc_start: 0.5801 (OUTLIER) cc_final: 0.5396 (tt0) REVERT: 1 4 LYS cc_start: 0.5137 (OUTLIER) cc_final: 0.4263 (ttmm) REVERT: 1 9 LYS cc_start: 0.7218 (mttt) cc_final: 0.6671 (mttp) REVERT: 1 24 GLU cc_start: 0.6328 (tp30) cc_final: 0.5615 (tp30) REVERT: 1 44 LYS cc_start: 0.6423 (OUTLIER) cc_final: 0.5824 (ttmt) REVERT: 1 59 GLU cc_start: 0.6803 (OUTLIER) cc_final: 0.6504 (mt-10) REVERT: 2 19 LYS cc_start: 0.7297 (OUTLIER) cc_final: 0.7054 (tttm) REVERT: 2 56 LYS cc_start: 0.7491 (OUTLIER) cc_final: 0.6986 (ttpp) REVERT: 3 9 THR cc_start: 0.7285 (m) cc_final: 0.6813 (p) REVERT: 4 30 LYS cc_start: 0.6219 (OUTLIER) cc_final: 0.5638 (ptmt) REVERT: 4 37 LYS cc_start: 0.7482 (OUTLIER) cc_final: 0.7272 (mttp) REVERT: 4 44 ARG cc_start: 0.6452 (OUTLIER) cc_final: 0.6003 (mmm160) REVERT: 4 45 GLN cc_start: 0.7130 (mm110) cc_final: 0.6476 (mm110) REVERT: 8 15 LYS cc_start: 0.6877 (ttmm) cc_final: 0.5961 (tttp) REVERT: c 5 LYS cc_start: 0.7126 (tttp) cc_final: 0.6576 (tptp) REVERT: c 7 LYS cc_start: 0.7966 (OUTLIER) cc_final: 0.7581 (mttt) REVERT: c 74 ILE cc_start: 0.7091 (OUTLIER) cc_final: 0.6869 (mm) REVERT: c 79 GLU cc_start: 0.7135 (OUTLIER) cc_final: 0.6650 (mt-10) REVERT: c 87 ARG cc_start: 0.7116 (OUTLIER) cc_final: 0.5598 (mtm-85) REVERT: c 108 LYS cc_start: 0.7338 (OUTLIER) cc_final: 0.7095 (ttmt) REVERT: c 110 LEU cc_start: 0.7222 (OUTLIER) cc_final: 0.6898 (tp) REVERT: c 125 LYS cc_start: 0.7362 (OUTLIER) cc_final: 0.6976 (pttt) REVERT: c 146 MET cc_start: 0.7820 (mtm) cc_final: 0.7558 (mtp) REVERT: c 183 LYS cc_start: 0.7532 (OUTLIER) cc_final: 0.7189 (mttt) REVERT: c 265 LYS cc_start: 0.8014 (OUTLIER) cc_final: 0.7756 (pttm) REVERT: c 269 ARG cc_start: 0.6776 (ttp80) cc_final: 0.6313 (ttt90) REVERT: c 270 ARG cc_start: 0.7155 (ttt-90) cc_final: 0.5298 (mmm160) REVERT: d 1 MET cc_start: 0.5243 (ttm) cc_final: 0.4726 (ttm) REVERT: d 7 LYS cc_start: 0.7956 (ttpp) cc_final: 0.7440 (ttmm) REVERT: d 13 ARG cc_start: 0.8101 (OUTLIER) cc_final: 0.6693 (ptt180) REVERT: d 40 LEU cc_start: 0.8025 (mp) cc_final: 0.7797 (mp) REVERT: d 48 ILE cc_start: 0.7644 (OUTLIER) cc_final: 0.7354 (pp) REVERT: d 64 GLU cc_start: 0.6435 (mt-10) cc_final: 0.6089 (mt-10) REVERT: d 157 LYS cc_start: 0.7884 (OUTLIER) cc_final: 0.7049 (tptp) REVERT: d 183 GLU cc_start: 0.6411 (pm20) cc_final: 0.5861 (pt0) REVERT: d 202 ILE cc_start: 0.7988 (mt) cc_final: 0.7669 (mm) REVERT: d 204 LYS cc_start: 0.7878 (OUTLIER) cc_final: 0.7013 (mtpt) REVERT: e 21 ARG cc_start: 0.6609 (OUTLIER) cc_final: 0.6031 (mtp85) REVERT: e 22 ASP cc_start: 0.7141 (p0) cc_final: 0.6746 (p0) REVERT: e 25 GLU cc_start: 0.7546 (tt0) cc_final: 0.7269 (tt0) REVERT: e 61 ARG cc_start: 0.6676 (mtp180) cc_final: 0.6393 (ptm-80) REVERT: e 139 LYS cc_start: 0.7164 (tttp) cc_final: 0.6505 (ttmp) REVERT: e 153 LEU cc_start: 0.3714 (OUTLIER) cc_final: 0.3371 (tm) REVERT: e 165 HIS cc_start: 0.5332 (OUTLIER) cc_final: 0.4956 (t70) REVERT: e 194 LYS cc_start: 0.5710 (mmmt) cc_final: 0.5395 (mmtm) REVERT: e 197 GLU cc_start: 0.6660 (tt0) cc_final: 0.6390 (mt-10) REVERT: e 199 MET cc_start: 0.5977 (ttm) cc_final: 0.5266 (mtp) REVERT: f 3 LYS cc_start: 0.5481 (ptmm) cc_final: 0.5144 (ttmt) REVERT: f 21 ASN cc_start: 0.5857 (OUTLIER) cc_final: 0.5436 (t0) REVERT: f 38 MET cc_start: 0.7037 (ptp) cc_final: 0.6817 (ptp) REVERT: f 64 LYS cc_start: 0.3192 (mptp) cc_final: 0.2752 (tttm) REVERT: f 67 ILE cc_start: 0.7955 (OUTLIER) cc_final: 0.7571 (mm) REVERT: f 141 ILE cc_start: 0.5114 (OUTLIER) cc_final: 0.4604 (pt) REVERT: g 25 THR cc_start: 0.6346 (m) cc_final: 0.5817 (t) REVERT: g 81 GLU cc_start: 0.5679 (OUTLIER) cc_final: 0.4503 (tm-30) REVERT: g 85 LYS cc_start: 0.7096 (OUTLIER) cc_final: 0.6496 (tppt) REVERT: g 153 ARG cc_start: 0.7250 (ptp90) cc_final: 0.6473 (mtt90) REVERT: g 158 LYS cc_start: 0.6720 (mttm) cc_final: 0.6508 (mttp) REVERT: g 169 VAL cc_start: 0.6362 (OUTLIER) cc_final: 0.6004 (p) REVERT: h 15 LEU cc_start: 0.5213 (OUTLIER) cc_final: 0.4931 (pp) REVERT: j 2 LYS cc_start: 0.7617 (mmmt) cc_final: 0.6817 (mtmt) REVERT: j 12 LYS cc_start: 0.7184 (tppt) cc_final: 0.6030 (tttm) REVERT: j 43 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.6978 (pm20) REVERT: j 95 ARG cc_start: 0.6793 (OUTLIER) cc_final: 0.5526 (ttp-110) REVERT: j 98 GLU cc_start: 0.7406 (OUTLIER) cc_final: 0.7086 (mp0) REVERT: j 106 LYS cc_start: 0.7537 (tttp) cc_final: 0.6615 (ttpt) REVERT: j 138 GLN cc_start: 0.7846 (OUTLIER) cc_final: 0.7526 (pt0) REVERT: k 4 GLU cc_start: 0.7717 (mt-10) cc_final: 0.7257 (mt-10) REVERT: k 53 LYS cc_start: 0.6849 (mmpt) cc_final: 0.5725 (mppt) REVERT: k 98 ARG cc_start: 0.5601 (mtt180) cc_final: 0.4932 (mtm110) REVERT: l 29 LYS cc_start: 0.6414 (OUTLIER) cc_final: 0.5777 (tttp) REVERT: l 55 MET cc_start: 0.8099 (tpp) cc_final: 0.7853 (tpp) REVERT: l 69 ARG cc_start: 0.6952 (OUTLIER) cc_final: 0.6152 (ttt-90) REVERT: l 106 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7163 (pm20) REVERT: l 123 ARG cc_start: 0.7912 (tpp80) cc_final: 0.7426 (tpp80) REVERT: m 81 ARG cc_start: 0.7174 (OUTLIER) cc_final: 0.6567 (mmt-90) REVERT: m 126 ILE cc_start: 0.7411 (OUTLIER) cc_final: 0.7046 (mm) REVERT: m 127 LYS cc_start: 0.6956 (OUTLIER) cc_final: 0.6506 (mtpp) REVERT: m 133 LYS cc_start: 0.7449 (tttm) cc_final: 0.7143 (ptmm) REVERT: n 18 GLN cc_start: 0.6884 (OUTLIER) cc_final: 0.6478 (tt0) REVERT: n 82 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.6608 (mp0) REVERT: o 3 LYS cc_start: 0.5782 (OUTLIER) cc_final: 0.5452 (tttp) REVERT: o 10 ARG cc_start: 0.7436 (OUTLIER) cc_final: 0.6179 (mtp180) REVERT: o 16 ARG cc_start: 0.5795 (OUTLIER) cc_final: 0.5384 (mmt-90) REVERT: o 20 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7559 (pp20) REVERT: o 55 GLU cc_start: 0.6569 (mt-10) cc_final: 0.6239 (mt-10) REVERT: o 62 LEU cc_start: 0.7203 (OUTLIER) cc_final: 0.6921 (mp) REVERT: p 7 GLN cc_start: 0.6711 (OUTLIER) cc_final: 0.6184 (pp30) REVERT: p 10 GLN cc_start: 0.6923 (mt0) cc_final: 0.6583 (mt0) REVERT: p 11 GLU cc_start: 0.7309 (pt0) cc_final: 0.6942 (pt0) REVERT: p 89 ARG cc_start: 0.6773 (mtm-85) cc_final: 0.5770 (mtt-85) REVERT: p 102 GLU cc_start: 0.6691 (mm-30) cc_final: 0.6388 (mp0) REVERT: p 112 GLU cc_start: 0.6943 (tt0) cc_final: 0.6246 (tt0) REVERT: q 58 ARG cc_start: 0.8137 (OUTLIER) cc_final: 0.7301 (ttt-90) REVERT: q 85 LYS cc_start: 0.7451 (mtmt) cc_final: 0.6884 (mttt) REVERT: r 13 ARG cc_start: 0.8416 (ttp80) cc_final: 0.7962 (ttp80) REVERT: r 26 ASP cc_start: 0.6635 (OUTLIER) cc_final: 0.6360 (t0) REVERT: r 34 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7030 (mp0) REVERT: r 37 GLU cc_start: 0.7478 (mt-10) cc_final: 0.7099 (pt0) REVERT: r 60 LYS cc_start: 0.7635 (mptp) cc_final: 0.7368 (mttp) REVERT: r 73 LYS cc_start: 0.7753 (ttpt) cc_final: 0.7513 (tttt) REVERT: s 22 ASP cc_start: 0.7350 (OUTLIER) cc_final: 0.6811 (m-30) REVERT: s 28 LYS cc_start: 0.7311 (mttp) cc_final: 0.6905 (mttm) REVERT: s 34 ASP cc_start: 0.6418 (m-30) cc_final: 0.6208 (m-30) REVERT: s 70 LYS cc_start: 0.7521 (mttp) cc_final: 0.7183 (mtmm) REVERT: s 73 LYS cc_start: 0.7747 (OUTLIER) cc_final: 0.7262 (mtpt) REVERT: s 92 ARG cc_start: 0.6609 (mtp-110) cc_final: 0.5415 (mtm-85) REVERT: s 95 ARG cc_start: 0.6975 (tpp80) cc_final: 0.5174 (ppt90) REVERT: s 109 ASP cc_start: 0.6385 (p0) cc_final: 0.5398 (p0) REVERT: t 6 ARG cc_start: 0.6758 (OUTLIER) cc_final: 0.6521 (tmt-80) REVERT: t 26 LYS cc_start: 0.6825 (tppp) cc_final: 0.6394 (mmtp) REVERT: t 32 LEU cc_start: 0.7843 (OUTLIER) cc_final: 0.7453 (pp) REVERT: t 49 LYS cc_start: 0.7242 (ttmm) cc_final: 0.6693 (tttp) REVERT: t 56 GLU cc_start: 0.7368 (mm-30) cc_final: 0.6971 (tt0) REVERT: t 68 ARG cc_start: 0.6885 (OUTLIER) cc_final: 0.6358 (ptp90) REVERT: u 10 GLU cc_start: 0.7120 (mm-30) cc_final: 0.6541 (tp30) REVERT: u 21 LYS cc_start: 0.8323 (OUTLIER) cc_final: 0.7919 (mmmm) REVERT: u 22 ARG cc_start: 0.7737 (mtm-85) cc_final: 0.7530 (mtp180) REVERT: u 24 LYS cc_start: 0.7251 (ttmm) cc_final: 0.6394 (ttpp) REVERT: u 37 GLU cc_start: 0.6886 (tp30) cc_final: 0.6467 (mm-30) REVERT: u 46 GLN cc_start: 0.7400 (mm-40) cc_final: 0.6996 (mm-40) REVERT: u 62 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.6948 (pm20) REVERT: u 79 LYS cc_start: 0.7378 (OUTLIER) cc_final: 0.6972 (mttm) REVERT: w 34 LYS cc_start: 0.5846 (tppp) cc_final: 0.5148 (ptmt) REVERT: w 53 LYS cc_start: 0.6373 (OUTLIER) cc_final: 0.5446 (mmtt) REVERT: w 68 LYS cc_start: 0.5825 (ttmt) cc_final: 0.5139 (tptt) REVERT: y 62 LYS cc_start: 0.8230 (mtmt) cc_final: 0.7479 (mttm) REVERT: y 68 LYS cc_start: 0.8051 (OUTLIER) cc_final: 0.7077 (tptp) REVERT: y 70 GLU cc_start: 0.7813 (mt-10) cc_final: 0.6516 (mp0) outliers start: 230 outliers final: 132 residues processed: 626 average time/residue: 2.0142 time to fit residues: 1647.2782 Evaluate side-chains 667 residues out of total 2526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 471 time to evaluate : 3.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 2 SER Chi-restraints excluded: chain 0 residue 25 THR Chi-restraints excluded: chain 0 residue 35 SER Chi-restraints excluded: chain 0 residue 62 LYS Chi-restraints excluded: chain 0 residue 66 THR Chi-restraints excluded: chain 0 residue 76 GLU Chi-restraints excluded: chain 1 residue 4 LYS Chi-restraints excluded: chain 1 residue 38 GLN Chi-restraints excluded: chain 1 residue 44 LYS Chi-restraints excluded: chain 1 residue 58 ASN Chi-restraints excluded: chain 1 residue 59 GLU Chi-restraints excluded: chain 2 residue 7 ILE Chi-restraints excluded: chain 2 residue 19 LYS Chi-restraints excluded: chain 2 residue 36 VAL Chi-restraints excluded: chain 2 residue 56 LYS Chi-restraints excluded: chain 4 residue 5 ILE Chi-restraints excluded: chain 4 residue 17 THR Chi-restraints excluded: chain 4 residue 30 LYS Chi-restraints excluded: chain 4 residue 37 LYS Chi-restraints excluded: chain 4 residue 42 VAL Chi-restraints excluded: chain 4 residue 43 VAL Chi-restraints excluded: chain 4 residue 44 ARG Chi-restraints excluded: chain 6 residue 25 LYS Chi-restraints excluded: chain 7 residue 52 LYS Chi-restraints excluded: chain 8 residue 10 LEU Chi-restraints excluded: chain 8 residue 17 VAL Chi-restraints excluded: chain 8 residue 32 LYS Chi-restraints excluded: chain 8 residue 36 ARG Chi-restraints excluded: chain c residue 7 LYS Chi-restraints excluded: chain c residue 20 VAL Chi-restraints excluded: chain c residue 74 ILE Chi-restraints excluded: chain c residue 79 GLU Chi-restraints excluded: chain c residue 87 ARG Chi-restraints excluded: chain c residue 108 LYS Chi-restraints excluded: chain c residue 110 LEU Chi-restraints excluded: chain c residue 116 ILE Chi-restraints excluded: chain c residue 118 SER Chi-restraints excluded: chain c residue 120 VAL Chi-restraints excluded: chain c residue 125 LYS Chi-restraints excluded: chain c residue 132 MET Chi-restraints excluded: chain c residue 162 VAL Chi-restraints excluded: chain c residue 183 LYS Chi-restraints excluded: chain c residue 265 LYS Chi-restraints excluded: chain d residue 13 ARG Chi-restraints excluded: chain d residue 29 VAL Chi-restraints excluded: chain d residue 48 ILE Chi-restraints excluded: chain d residue 99 GLU Chi-restraints excluded: chain d residue 103 ASP Chi-restraints excluded: chain d residue 106 LYS Chi-restraints excluded: chain d residue 151 THR Chi-restraints excluded: chain d residue 157 LYS Chi-restraints excluded: chain d residue 175 LEU Chi-restraints excluded: chain d residue 179 ARG Chi-restraints excluded: chain d residue 204 LYS Chi-restraints excluded: chain e residue 5 LEU Chi-restraints excluded: chain e residue 10 SER Chi-restraints excluded: chain e residue 21 ARG Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain e residue 80 SER Chi-restraints excluded: chain e residue 95 LYS Chi-restraints excluded: chain e residue 119 ILE Chi-restraints excluded: chain e residue 122 GLU Chi-restraints excluded: chain e residue 153 LEU Chi-restraints excluded: chain e residue 165 HIS Chi-restraints excluded: chain e residue 166 LYS Chi-restraints excluded: chain e residue 173 THR Chi-restraints excluded: chain e residue 200 LEU Chi-restraints excluded: chain f residue 9 LYS Chi-restraints excluded: chain f residue 16 LEU Chi-restraints excluded: chain f residue 21 ASN Chi-restraints excluded: chain f residue 26 MET Chi-restraints excluded: chain f residue 35 THR Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 49 LEU Chi-restraints excluded: chain f residue 67 ILE Chi-restraints excluded: chain f residue 72 LYS Chi-restraints excluded: chain f residue 89 VAL Chi-restraints excluded: chain f residue 104 ILE Chi-restraints excluded: chain f residue 108 VAL Chi-restraints excluded: chain f residue 117 LEU Chi-restraints excluded: chain f residue 132 VAL Chi-restraints excluded: chain f residue 141 ILE Chi-restraints excluded: chain f residue 155 THR Chi-restraints excluded: chain f residue 170 LEU Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 11 VAL Chi-restraints excluded: chain g residue 17 VAL Chi-restraints excluded: chain g residue 51 THR Chi-restraints excluded: chain g residue 81 GLU Chi-restraints excluded: chain g residue 85 LYS Chi-restraints excluded: chain g residue 90 VAL Chi-restraints excluded: chain g residue 99 LYS Chi-restraints excluded: chain g residue 107 LEU Chi-restraints excluded: chain g residue 169 VAL Chi-restraints excluded: chain h residue 3 VAL Chi-restraints excluded: chain h residue 9 VAL Chi-restraints excluded: chain h residue 15 LEU Chi-restraints excluded: chain h residue 22 LYS Chi-restraints excluded: chain h residue 37 VAL Chi-restraints excluded: chain j residue 1 MET Chi-restraints excluded: chain j residue 5 THR Chi-restraints excluded: chain j residue 10 THR Chi-restraints excluded: chain j residue 11 VAL Chi-restraints excluded: chain j residue 43 GLU Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 62 VAL Chi-restraints excluded: chain j residue 64 VAL Chi-restraints excluded: chain j residue 95 ARG Chi-restraints excluded: chain j residue 98 GLU Chi-restraints excluded: chain j residue 131 ASN Chi-restraints excluded: chain j residue 138 GLN Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 88 ASN Chi-restraints excluded: chain l residue 29 LYS Chi-restraints excluded: chain l residue 69 ARG Chi-restraints excluded: chain l residue 104 GLN Chi-restraints excluded: chain l residue 106 GLU Chi-restraints excluded: chain l residue 117 THR Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain m residue 5 LYS Chi-restraints excluded: chain m residue 7 THR Chi-restraints excluded: chain m residue 30 SER Chi-restraints excluded: chain m residue 53 MET Chi-restraints excluded: chain m residue 58 LYS Chi-restraints excluded: chain m residue 78 LEU Chi-restraints excluded: chain m residue 81 ARG Chi-restraints excluded: chain m residue 104 GLU Chi-restraints excluded: chain m residue 126 ILE Chi-restraints excluded: chain m residue 127 LYS Chi-restraints excluded: chain m residue 129 THR Chi-restraints excluded: chain n residue 14 SER Chi-restraints excluded: chain n residue 18 GLN Chi-restraints excluded: chain n residue 48 VAL Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain n residue 70 THR Chi-restraints excluded: chain n residue 74 GLU Chi-restraints excluded: chain n residue 82 GLU Chi-restraints excluded: chain o residue 3 LYS Chi-restraints excluded: chain o residue 9 ARG Chi-restraints excluded: chain o residue 10 ARG Chi-restraints excluded: chain o residue 16 ARG Chi-restraints excluded: chain o residue 20 GLU Chi-restraints excluded: chain o residue 24 THR Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain o residue 49 VAL Chi-restraints excluded: chain o residue 54 VAL Chi-restraints excluded: chain o residue 62 LEU Chi-restraints excluded: chain p residue 7 GLN Chi-restraints excluded: chain p residue 36 SER Chi-restraints excluded: chain p residue 46 VAL Chi-restraints excluded: chain p residue 63 LYS Chi-restraints excluded: chain p residue 70 VAL Chi-restraints excluded: chain p residue 76 THR Chi-restraints excluded: chain p residue 96 LYS Chi-restraints excluded: chain p residue 110 ILE Chi-restraints excluded: chain q residue 41 LYS Chi-restraints excluded: chain q residue 58 ARG Chi-restraints excluded: chain q residue 84 LYS Chi-restraints excluded: chain q residue 91 ASP Chi-restraints excluded: chain r residue 26 ASP Chi-restraints excluded: chain r residue 34 GLU Chi-restraints excluded: chain r residue 45 GLU Chi-restraints excluded: chain r residue 47 VAL Chi-restraints excluded: chain s residue 13 SER Chi-restraints excluded: chain s residue 22 ASP Chi-restraints excluded: chain s residue 33 LEU Chi-restraints excluded: chain s residue 66 ILE Chi-restraints excluded: chain s residue 73 LYS Chi-restraints excluded: chain s residue 101 SER Chi-restraints excluded: chain s residue 106 VAL Chi-restraints excluded: chain t residue 4 GLU Chi-restraints excluded: chain t residue 6 ARG Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain t residue 36 LYS Chi-restraints excluded: chain t residue 50 LEU Chi-restraints excluded: chain t residue 55 VAL Chi-restraints excluded: chain t residue 67 VAL Chi-restraints excluded: chain t residue 68 ARG Chi-restraints excluded: chain t residue 69 GLN Chi-restraints excluded: chain t residue 100 ASN Chi-restraints excluded: chain u residue 21 LYS Chi-restraints excluded: chain u residue 27 ASN Chi-restraints excluded: chain u residue 30 SER Chi-restraints excluded: chain u residue 62 GLU Chi-restraints excluded: chain u residue 68 SER Chi-restraints excluded: chain u residue 79 LYS Chi-restraints excluded: chain u residue 88 GLU Chi-restraints excluded: chain w residue 53 LYS Chi-restraints excluded: chain w residue 72 VAL Chi-restraints excluded: chain y residue 17 GLU Chi-restraints excluded: chain y residue 19 LYS Chi-restraints excluded: chain y residue 43 THR Chi-restraints excluded: chain y residue 51 VAL Chi-restraints excluded: chain y residue 68 LYS Chi-restraints excluded: chain y residue 72 LYS Chi-restraints excluded: chain y residue 78 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 607 random chunks: chunk 532 optimal weight: 4.9990 chunk 560 optimal weight: 20.0000 chunk 511 optimal weight: 1.9990 chunk 545 optimal weight: 8.9990 chunk 328 optimal weight: 10.0000 chunk 237 optimal weight: 10.0000 chunk 428 optimal weight: 20.0000 chunk 167 optimal weight: 10.0000 chunk 492 optimal weight: 4.9990 chunk 515 optimal weight: 10.0000 chunk 543 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 5 GLN 6 29 GLN c 260 ASN g 104 ASN j 128 ASN ** k 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 3 GLN q 56 GLN r 86 GLN s 31 GLN t 59 ASN ** u 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6602 moved from start: 0.4287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 98998 Z= 0.350 Angle : 0.725 11.443 149023 Z= 0.376 Chirality : 0.044 0.357 19174 Planarity : 0.006 0.093 7331 Dihedral : 24.274 179.736 51740 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.97 % Favored : 94.93 % Rotamer: Outliers : 7.92 % Allowed : 25.85 % Favored : 66.23 % 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: -0.71 (0.14), residues: 3057 helix: 0.50 (0.18), residues: 802 sheet: -0.37 (0.19), residues: 707 loop : -0.99 (0.15), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP c 213 HIS 0.009 0.002 HIS r 89 PHE 0.022 0.002 PHE h 29 TYR 0.019 0.002 TYR q 32 ARG 0.014 0.001 ARG d 184 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 2526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 472 time to evaluate : 3.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 62 LYS cc_start: 0.7502 (OUTLIER) cc_final: 0.7073 (mmmt) REVERT: 0 72 ARG cc_start: 0.6903 (mtm-85) cc_final: 0.6632 (mtm-85) REVERT: 0 76 GLU cc_start: 0.5777 (OUTLIER) cc_final: 0.5352 (tt0) REVERT: 1 4 LYS cc_start: 0.5178 (OUTLIER) cc_final: 0.4331 (ttmm) REVERT: 1 9 LYS cc_start: 0.7230 (mttt) cc_final: 0.6628 (mttp) REVERT: 1 24 GLU cc_start: 0.6315 (tp30) cc_final: 0.5601 (tp30) REVERT: 1 44 LYS cc_start: 0.6392 (OUTLIER) cc_final: 0.5788 (ttmt) REVERT: 1 59 GLU cc_start: 0.6865 (OUTLIER) cc_final: 0.6555 (mt-10) REVERT: 2 19 LYS cc_start: 0.7280 (OUTLIER) cc_final: 0.7015 (tttm) REVERT: 2 56 LYS cc_start: 0.7453 (OUTLIER) cc_final: 0.6944 (ttpp) REVERT: 3 9 THR cc_start: 0.7268 (m) cc_final: 0.6784 (p) REVERT: 3 15 MET cc_start: 0.8159 (mtm) cc_final: 0.7900 (mtm) REVERT: 4 24 THR cc_start: 0.7693 (p) cc_final: 0.7444 (p) REVERT: 4 30 LYS cc_start: 0.6271 (OUTLIER) cc_final: 0.5822 (ptmt) REVERT: 4 37 LYS cc_start: 0.7500 (OUTLIER) cc_final: 0.7292 (mttp) REVERT: 4 44 ARG cc_start: 0.6404 (OUTLIER) cc_final: 0.5900 (mmm160) REVERT: 4 45 GLN cc_start: 0.7157 (mm110) cc_final: 0.6504 (mm110) REVERT: 6 1 MET cc_start: 0.7290 (mpp) cc_final: 0.6903 (mpp) REVERT: 8 15 LYS cc_start: 0.7099 (ttmm) cc_final: 0.6068 (tttp) REVERT: c 5 LYS cc_start: 0.7124 (tttp) cc_final: 0.6581 (tptp) REVERT: c 7 LYS cc_start: 0.7951 (OUTLIER) cc_final: 0.7604 (mttt) REVERT: c 74 ILE cc_start: 0.7062 (OUTLIER) cc_final: 0.6855 (mm) REVERT: c 79 GLU cc_start: 0.7127 (OUTLIER) cc_final: 0.6629 (mt-10) REVERT: c 87 ARG cc_start: 0.7215 (OUTLIER) cc_final: 0.5731 (mtm-85) REVERT: c 108 LYS cc_start: 0.7283 (OUTLIER) cc_final: 0.6733 (ttmt) REVERT: c 110 LEU cc_start: 0.7226 (OUTLIER) cc_final: 0.6924 (tp) REVERT: c 125 LYS cc_start: 0.7367 (OUTLIER) cc_final: 0.6977 (pttt) REVERT: c 146 MET cc_start: 0.7813 (mtm) cc_final: 0.7484 (mtp) REVERT: c 183 LYS cc_start: 0.7501 (OUTLIER) cc_final: 0.7187 (mttt) REVERT: c 265 LYS cc_start: 0.8013 (OUTLIER) cc_final: 0.7792 (pttm) REVERT: c 269 ARG cc_start: 0.6764 (ttp80) cc_final: 0.6303 (ttt90) REVERT: d 1 MET cc_start: 0.5346 (ttm) cc_final: 0.4899 (ttm) REVERT: d 7 LYS cc_start: 0.7899 (ttpp) cc_final: 0.7428 (ttmm) REVERT: d 13 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.6507 (ptt180) REVERT: d 40 LEU cc_start: 0.8007 (mp) cc_final: 0.7776 (mp) REVERT: d 48 ILE cc_start: 0.7568 (OUTLIER) cc_final: 0.7260 (pp) REVERT: d 64 GLU cc_start: 0.6427 (mt-10) cc_final: 0.6083 (mt-10) REVERT: d 157 LYS cc_start: 0.7887 (OUTLIER) cc_final: 0.7055 (tptp) REVERT: d 183 GLU cc_start: 0.6233 (pm20) cc_final: 0.5709 (pt0) REVERT: d 202 ILE cc_start: 0.8020 (mt) cc_final: 0.7711 (mm) REVERT: d 204 LYS cc_start: 0.7867 (OUTLIER) cc_final: 0.7016 (mtpt) REVERT: e 21 ARG cc_start: 0.6600 (OUTLIER) cc_final: 0.6015 (mtp85) REVERT: e 22 ASP cc_start: 0.7232 (p0) cc_final: 0.6874 (p0) REVERT: e 25 GLU cc_start: 0.7507 (tt0) cc_final: 0.7127 (tt0) REVERT: e 61 ARG cc_start: 0.6558 (mtp180) cc_final: 0.6284 (ptm-80) REVERT: e 139 LYS cc_start: 0.7152 (tttp) cc_final: 0.6500 (ttmp) REVERT: e 153 LEU cc_start: 0.3695 (OUTLIER) cc_final: 0.3353 (tm) REVERT: e 194 LYS cc_start: 0.5618 (mmmt) cc_final: 0.5314 (mmtm) REVERT: e 197 GLU cc_start: 0.6639 (tt0) cc_final: 0.6381 (mt-10) REVERT: f 3 LYS cc_start: 0.5443 (ptmm) cc_final: 0.5138 (ttmt) REVERT: f 21 ASN cc_start: 0.5867 (OUTLIER) cc_final: 0.5452 (t0) REVERT: f 38 MET cc_start: 0.6997 (ptp) cc_final: 0.6717 (ptp) REVERT: f 64 LYS cc_start: 0.3177 (mptp) cc_final: 0.2748 (tttm) REVERT: f 130 MET cc_start: 0.6333 (mtp) cc_final: 0.6112 (mtp) REVERT: f 141 ILE cc_start: 0.5238 (OUTLIER) cc_final: 0.4738 (pp) REVERT: g 25 THR cc_start: 0.6585 (m) cc_final: 0.6079 (t) REVERT: g 36 THR cc_start: 0.6570 (t) cc_final: 0.6254 (m) REVERT: g 85 LYS cc_start: 0.7103 (OUTLIER) cc_final: 0.6506 (tppt) REVERT: g 153 ARG cc_start: 0.7253 (ptp90) cc_final: 0.6518 (mtt90) REVERT: g 158 LYS cc_start: 0.6785 (mttm) cc_final: 0.6546 (mttp) REVERT: g 169 VAL cc_start: 0.6338 (OUTLIER) cc_final: 0.5994 (p) REVERT: h 15 LEU cc_start: 0.5217 (OUTLIER) cc_final: 0.4927 (pp) REVERT: j 2 LYS cc_start: 0.7600 (mmmt) cc_final: 0.6806 (mtmt) REVERT: j 12 LYS cc_start: 0.7173 (tppt) cc_final: 0.6013 (tttm) REVERT: j 43 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.6970 (pm20) REVERT: j 95 ARG cc_start: 0.6772 (OUTLIER) cc_final: 0.5519 (ttp-110) REVERT: j 98 GLU cc_start: 0.7282 (OUTLIER) cc_final: 0.6984 (mp0) REVERT: j 106 LYS cc_start: 0.7530 (tttp) cc_final: 0.6598 (ttpt) REVERT: k 4 GLU cc_start: 0.7706 (mt-10) cc_final: 0.7205 (mt-10) REVERT: k 53 LYS cc_start: 0.6844 (mmpt) cc_final: 0.5733 (mppt) REVERT: k 98 ARG cc_start: 0.5532 (mtt180) cc_final: 0.4912 (mtm110) REVERT: k 114 LYS cc_start: 0.6706 (mtpp) cc_final: 0.6502 (mmmm) REVERT: l 29 LYS cc_start: 0.6356 (OUTLIER) cc_final: 0.5682 (tttp) REVERT: l 55 MET cc_start: 0.8085 (tpp) cc_final: 0.7826 (tpp) REVERT: l 69 ARG cc_start: 0.6947 (OUTLIER) cc_final: 0.6112 (ttt-90) REVERT: l 106 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7124 (pm20) REVERT: l 123 ARG cc_start: 0.7916 (tpp80) cc_final: 0.7378 (tpp80) REVERT: m 1 MET cc_start: 0.6420 (tpt) cc_final: 0.6180 (tpp) REVERT: m 22 GLN cc_start: 0.6113 (OUTLIER) cc_final: 0.5446 (mp10) REVERT: m 81 ARG cc_start: 0.7177 (OUTLIER) cc_final: 0.6730 (mmt-90) REVERT: m 126 ILE cc_start: 0.7416 (OUTLIER) cc_final: 0.7073 (mm) REVERT: m 127 LYS cc_start: 0.6909 (OUTLIER) cc_final: 0.6604 (mtpp) REVERT: m 133 LYS cc_start: 0.7445 (tttm) cc_final: 0.7146 (ptmm) REVERT: n 18 GLN cc_start: 0.6796 (OUTLIER) cc_final: 0.6383 (tt0) REVERT: o 3 LYS cc_start: 0.5830 (OUTLIER) cc_final: 0.5444 (tttp) REVERT: o 10 ARG cc_start: 0.7428 (OUTLIER) cc_final: 0.6003 (mtp180) REVERT: o 16 ARG cc_start: 0.5838 (OUTLIER) cc_final: 0.5396 (mmt-90) REVERT: o 20 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7539 (pp20) REVERT: o 55 GLU cc_start: 0.6510 (mt-10) cc_final: 0.6153 (mt-10) REVERT: o 62 LEU cc_start: 0.7243 (OUTLIER) cc_final: 0.6988 (mp) REVERT: p 7 GLN cc_start: 0.6534 (OUTLIER) cc_final: 0.6112 (pp30) REVERT: p 10 GLN cc_start: 0.7032 (mt0) cc_final: 0.6707 (mt0) REVERT: p 11 GLU cc_start: 0.7301 (pt0) cc_final: 0.6913 (pt0) REVERT: p 89 ARG cc_start: 0.6811 (mtm-85) cc_final: 0.5765 (mtt-85) REVERT: p 102 GLU cc_start: 0.6673 (mm-30) cc_final: 0.6369 (mp0) REVERT: p 112 GLU cc_start: 0.6950 (tt0) cc_final: 0.6248 (tt0) REVERT: q 58 ARG cc_start: 0.8121 (OUTLIER) cc_final: 0.7206 (ttt-90) REVERT: q 85 LYS cc_start: 0.7426 (mtmt) cc_final: 0.6874 (mttt) REVERT: r 13 ARG cc_start: 0.8429 (ttp80) cc_final: 0.7984 (ttp80) REVERT: r 26 ASP cc_start: 0.6627 (OUTLIER) cc_final: 0.6348 (t0) REVERT: r 34 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7076 (mp0) REVERT: r 37 GLU cc_start: 0.7461 (mt-10) cc_final: 0.7079 (pt0) REVERT: r 45 GLU cc_start: 0.6223 (OUTLIER) cc_final: 0.5997 (pt0) REVERT: r 60 LYS cc_start: 0.7705 (OUTLIER) cc_final: 0.7428 (mttp) REVERT: s 22 ASP cc_start: 0.7352 (OUTLIER) cc_final: 0.6812 (m-30) REVERT: s 28 LYS cc_start: 0.7284 (mttp) cc_final: 0.6868 (mttm) REVERT: s 34 ASP cc_start: 0.6445 (m-30) cc_final: 0.6216 (m-30) REVERT: s 70 LYS cc_start: 0.7533 (mttp) cc_final: 0.7204 (mtmm) REVERT: s 73 LYS cc_start: 0.7748 (OUTLIER) cc_final: 0.7261 (mtpt) REVERT: s 92 ARG cc_start: 0.6605 (mtp-110) cc_final: 0.5410 (mtm-85) REVERT: s 95 ARG cc_start: 0.6890 (tpp80) cc_final: 0.5121 (ppt90) REVERT: s 109 ASP cc_start: 0.6539 (p0) cc_final: 0.5566 (p0) REVERT: t 26 LYS cc_start: 0.6819 (tppp) cc_final: 0.6420 (mmtp) REVERT: t 32 LEU cc_start: 0.7678 (OUTLIER) cc_final: 0.7308 (pp) REVERT: t 49 LYS cc_start: 0.7216 (ttmm) cc_final: 0.6659 (tttp) REVERT: t 54 GLU cc_start: 0.5622 (pm20) cc_final: 0.5255 (mm-30) REVERT: t 56 GLU cc_start: 0.7404 (mm-30) cc_final: 0.6988 (tt0) REVERT: t 68 ARG cc_start: 0.6819 (OUTLIER) cc_final: 0.6307 (ptp90) REVERT: u 10 GLU cc_start: 0.7133 (mm-30) cc_final: 0.6419 (tp30) REVERT: u 21 LYS cc_start: 0.8283 (OUTLIER) cc_final: 0.7861 (mmmm) REVERT: u 22 ARG cc_start: 0.7776 (mtm-85) cc_final: 0.7566 (mtp180) REVERT: u 24 LYS cc_start: 0.7266 (ttmm) cc_final: 0.6353 (ttpp) REVERT: u 37 GLU cc_start: 0.6974 (tp30) cc_final: 0.6576 (mm-30) REVERT: u 46 GLN cc_start: 0.7399 (mm-40) cc_final: 0.7007 (mm-40) REVERT: u 62 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.6941 (pm20) REVERT: u 79 LYS cc_start: 0.7323 (OUTLIER) cc_final: 0.6929 (mttm) REVERT: w 25 LYS cc_start: 0.7118 (mtpt) cc_final: 0.6582 (mtpp) REVERT: w 34 LYS cc_start: 0.5860 (tppp) cc_final: 0.5160 (ptmt) REVERT: w 53 LYS cc_start: 0.6241 (mttm) cc_final: 0.5395 (mmtt) REVERT: w 68 LYS cc_start: 0.5770 (ttmt) cc_final: 0.5072 (tptt) REVERT: y 44 LYS cc_start: 0.6861 (ttmm) cc_final: 0.6542 (tttm) REVERT: y 62 LYS cc_start: 0.8224 (mtmt) cc_final: 0.7493 (mttm) REVERT: y 68 LYS cc_start: 0.7944 (OUTLIER) cc_final: 0.7316 (tptp) REVERT: y 70 GLU cc_start: 0.7813 (mt-10) cc_final: 0.6525 (mp0) outliers start: 200 outliers final: 127 residues processed: 607 average time/residue: 2.0241 time to fit residues: 1611.8727 Evaluate side-chains 656 residues out of total 2526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 469 time to evaluate : 3.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 2 SER Chi-restraints excluded: chain 0 residue 25 THR Chi-restraints excluded: chain 0 residue 62 LYS Chi-restraints excluded: chain 0 residue 66 THR Chi-restraints excluded: chain 0 residue 76 GLU Chi-restraints excluded: chain 1 residue 4 LYS Chi-restraints excluded: chain 1 residue 38 GLN Chi-restraints excluded: chain 1 residue 44 LYS Chi-restraints excluded: chain 1 residue 58 ASN Chi-restraints excluded: chain 1 residue 59 GLU Chi-restraints excluded: chain 2 residue 19 LYS Chi-restraints excluded: chain 2 residue 36 VAL Chi-restraints excluded: chain 2 residue 56 LYS Chi-restraints excluded: chain 4 residue 5 ILE Chi-restraints excluded: chain 4 residue 17 THR Chi-restraints excluded: chain 4 residue 28 ARG Chi-restraints excluded: chain 4 residue 30 LYS Chi-restraints excluded: chain 4 residue 37 LYS Chi-restraints excluded: chain 4 residue 42 VAL Chi-restraints excluded: chain 4 residue 43 VAL Chi-restraints excluded: chain 4 residue 44 ARG Chi-restraints excluded: chain 6 residue 25 LYS Chi-restraints excluded: chain 7 residue 52 LYS Chi-restraints excluded: chain 8 residue 10 LEU Chi-restraints excluded: chain 8 residue 17 VAL Chi-restraints excluded: chain 8 residue 32 LYS Chi-restraints excluded: chain c residue 7 LYS Chi-restraints excluded: chain c residue 20 VAL Chi-restraints excluded: chain c residue 74 ILE Chi-restraints excluded: chain c residue 79 GLU Chi-restraints excluded: chain c residue 87 ARG Chi-restraints excluded: chain c residue 108 LYS Chi-restraints excluded: chain c residue 110 LEU Chi-restraints excluded: chain c residue 116 ILE Chi-restraints excluded: chain c residue 118 SER Chi-restraints excluded: chain c residue 120 VAL Chi-restraints excluded: chain c residue 125 LYS Chi-restraints excluded: chain c residue 132 MET Chi-restraints excluded: chain c residue 162 VAL Chi-restraints excluded: chain c residue 183 LYS Chi-restraints excluded: chain c residue 265 LYS Chi-restraints excluded: chain d residue 13 ARG Chi-restraints excluded: chain d residue 29 VAL Chi-restraints excluded: chain d residue 48 ILE Chi-restraints excluded: chain d residue 99 GLU Chi-restraints excluded: chain d residue 106 LYS Chi-restraints excluded: chain d residue 151 THR Chi-restraints excluded: chain d residue 157 LYS Chi-restraints excluded: chain d residue 175 LEU Chi-restraints excluded: chain d residue 179 ARG Chi-restraints excluded: chain d residue 204 LYS Chi-restraints excluded: chain e residue 5 LEU Chi-restraints excluded: chain e residue 10 SER Chi-restraints excluded: chain e residue 21 ARG Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain e residue 80 SER Chi-restraints excluded: chain e residue 95 LYS Chi-restraints excluded: chain e residue 119 ILE Chi-restraints excluded: chain e residue 122 GLU Chi-restraints excluded: chain e residue 153 LEU Chi-restraints excluded: chain e residue 166 LYS Chi-restraints excluded: chain e residue 173 THR Chi-restraints excluded: chain f residue 16 LEU Chi-restraints excluded: chain f residue 21 ASN Chi-restraints excluded: chain f residue 26 MET Chi-restraints excluded: chain f residue 28 VAL Chi-restraints excluded: chain f residue 35 THR Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 49 LEU Chi-restraints excluded: chain f residue 72 LYS Chi-restraints excluded: chain f residue 103 LEU Chi-restraints excluded: chain f residue 104 ILE Chi-restraints excluded: chain f residue 108 VAL Chi-restraints excluded: chain f residue 117 LEU Chi-restraints excluded: chain f residue 132 VAL Chi-restraints excluded: chain f residue 141 ILE Chi-restraints excluded: chain f residue 155 THR Chi-restraints excluded: chain f residue 170 LEU Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 11 VAL Chi-restraints excluded: chain g residue 17 VAL Chi-restraints excluded: chain g residue 51 THR Chi-restraints excluded: chain g residue 81 GLU Chi-restraints excluded: chain g residue 85 LYS Chi-restraints excluded: chain g residue 90 VAL Chi-restraints excluded: chain g residue 99 LYS Chi-restraints excluded: chain g residue 107 LEU Chi-restraints excluded: chain g residue 169 VAL Chi-restraints excluded: chain h residue 3 VAL Chi-restraints excluded: chain h residue 9 VAL Chi-restraints excluded: chain h residue 15 LEU Chi-restraints excluded: chain h residue 22 LYS Chi-restraints excluded: chain h residue 37 VAL Chi-restraints excluded: chain j residue 1 MET Chi-restraints excluded: chain j residue 5 THR Chi-restraints excluded: chain j residue 10 THR Chi-restraints excluded: chain j residue 11 VAL Chi-restraints excluded: chain j residue 43 GLU Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 62 VAL Chi-restraints excluded: chain j residue 64 VAL Chi-restraints excluded: chain j residue 95 ARG Chi-restraints excluded: chain j residue 98 GLU Chi-restraints excluded: chain j residue 131 ASN Chi-restraints excluded: chain j residue 138 GLN Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 88 ASN Chi-restraints excluded: chain l residue 29 LYS Chi-restraints excluded: chain l residue 69 ARG Chi-restraints excluded: chain l residue 92 LEU Chi-restraints excluded: chain l residue 104 GLN Chi-restraints excluded: chain l residue 106 GLU Chi-restraints excluded: chain l residue 117 THR Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain m residue 5 LYS Chi-restraints excluded: chain m residue 7 THR Chi-restraints excluded: chain m residue 22 GLN Chi-restraints excluded: chain m residue 30 SER Chi-restraints excluded: chain m residue 53 MET Chi-restraints excluded: chain m residue 78 LEU Chi-restraints excluded: chain m residue 81 ARG Chi-restraints excluded: chain m residue 104 GLU Chi-restraints excluded: chain m residue 126 ILE Chi-restraints excluded: chain m residue 127 LYS Chi-restraints excluded: chain m residue 129 THR Chi-restraints excluded: chain n residue 14 SER Chi-restraints excluded: chain n residue 18 GLN Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain n residue 70 THR Chi-restraints excluded: chain n residue 74 GLU Chi-restraints excluded: chain o residue 3 LYS Chi-restraints excluded: chain o residue 9 ARG Chi-restraints excluded: chain o residue 10 ARG Chi-restraints excluded: chain o residue 16 ARG Chi-restraints excluded: chain o residue 20 GLU Chi-restraints excluded: chain o residue 24 THR Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain o residue 48 LEU Chi-restraints excluded: chain o residue 49 VAL Chi-restraints excluded: chain o residue 54 VAL Chi-restraints excluded: chain o residue 62 LEU Chi-restraints excluded: chain p residue 7 GLN Chi-restraints excluded: chain p residue 36 SER Chi-restraints excluded: chain p residue 46 VAL Chi-restraints excluded: chain p residue 63 LYS Chi-restraints excluded: chain p residue 70 VAL Chi-restraints excluded: chain p residue 76 THR Chi-restraints excluded: chain p residue 96 LYS Chi-restraints excluded: chain p residue 110 ILE Chi-restraints excluded: chain q residue 6 ARG Chi-restraints excluded: chain q residue 58 ARG Chi-restraints excluded: chain q residue 84 LYS Chi-restraints excluded: chain q residue 91 ASP Chi-restraints excluded: chain r residue 26 ASP Chi-restraints excluded: chain r residue 34 GLU Chi-restraints excluded: chain r residue 45 GLU Chi-restraints excluded: chain r residue 47 VAL Chi-restraints excluded: chain r residue 60 LYS Chi-restraints excluded: chain s residue 13 SER Chi-restraints excluded: chain s residue 22 ASP Chi-restraints excluded: chain s residue 33 LEU Chi-restraints excluded: chain s residue 66 ILE Chi-restraints excluded: chain s residue 73 LYS Chi-restraints excluded: chain s residue 101 SER Chi-restraints excluded: chain t residue 4 GLU Chi-restraints excluded: chain t residue 6 ARG Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain t residue 36 LYS Chi-restraints excluded: chain t residue 50 LEU Chi-restraints excluded: chain t residue 55 VAL Chi-restraints excluded: chain t residue 67 VAL Chi-restraints excluded: chain t residue 68 ARG Chi-restraints excluded: chain t residue 69 GLN Chi-restraints excluded: chain t residue 100 ASN Chi-restraints excluded: chain u residue 21 LYS Chi-restraints excluded: chain u residue 30 SER Chi-restraints excluded: chain u residue 62 GLU Chi-restraints excluded: chain u residue 68 SER Chi-restraints excluded: chain u residue 79 LYS Chi-restraints excluded: chain u residue 88 GLU Chi-restraints excluded: chain w residue 72 VAL Chi-restraints excluded: chain y residue 17 GLU Chi-restraints excluded: chain y residue 19 LYS Chi-restraints excluded: chain y residue 43 THR Chi-restraints excluded: chain y residue 51 VAL Chi-restraints excluded: chain y residue 68 LYS Chi-restraints excluded: chain y residue 72 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 607 random chunks: chunk 358 optimal weight: 4.9990 chunk 576 optimal weight: 8.9990 chunk 351 optimal weight: 0.9980 chunk 273 optimal weight: 10.0000 chunk 400 optimal weight: 4.9990 chunk 604 optimal weight: 8.9990 chunk 556 optimal weight: 6.9990 chunk 481 optimal weight: 6.9990 chunk 50 optimal weight: 10.0000 chunk 371 optimal weight: 1.9990 chunk 295 optimal weight: 9.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 5 GLN 6 29 GLN d 173 GLN g 104 ASN j 128 ASN ** k 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 56 GLN r 86 GLN s 31 GLN t 59 ASN u 54 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6594 moved from start: 0.4292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 98998 Z= 0.273 Angle : 0.681 11.544 149023 Z= 0.358 Chirality : 0.041 0.336 19174 Planarity : 0.006 0.085 7331 Dihedral : 24.273 179.797 51740 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.00 % Favored : 94.90 % Rotamer: Outliers : 7.76 % Allowed : 26.13 % Favored : 66.11 % 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: -0.67 (0.14), residues: 3057 helix: 0.56 (0.18), residues: 803 sheet: -0.36 (0.19), residues: 707 loop : -0.98 (0.15), residues: 1547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP c 213 HIS 0.007 0.001 HIS r 89 PHE 0.022 0.002 PHE h 29 TYR 0.016 0.002 TYR q 32 ARG 0.013 0.001 ARG f 150 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 666 residues out of total 2526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 470 time to evaluate : 3.907 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 62 LYS cc_start: 0.7490 (OUTLIER) cc_final: 0.7062 (mmmt) REVERT: 0 72 ARG cc_start: 0.6902 (mtm-85) cc_final: 0.6630 (mtm-85) REVERT: 0 76 GLU cc_start: 0.5771 (OUTLIER) cc_final: 0.5344 (tt0) REVERT: 1 4 LYS cc_start: 0.5176 (OUTLIER) cc_final: 0.4330 (ttmm) REVERT: 1 9 LYS cc_start: 0.7173 (mttt) cc_final: 0.6567 (mttp) REVERT: 1 24 GLU cc_start: 0.6310 (tp30) cc_final: 0.5596 (tp30) REVERT: 1 44 LYS cc_start: 0.6365 (OUTLIER) cc_final: 0.5764 (ttmt) REVERT: 1 59 GLU cc_start: 0.6769 (OUTLIER) cc_final: 0.6471 (mt-10) REVERT: 2 19 LYS cc_start: 0.7265 (OUTLIER) cc_final: 0.7006 (tttm) REVERT: 2 56 LYS cc_start: 0.7485 (OUTLIER) cc_final: 0.6959 (ttpp) REVERT: 3 9 THR cc_start: 0.7255 (m) cc_final: 0.6772 (p) REVERT: 3 15 MET cc_start: 0.8140 (mtm) cc_final: 0.7880 (mtm) REVERT: 4 24 THR cc_start: 0.7706 (p) cc_final: 0.7458 (p) REVERT: 4 30 LYS cc_start: 0.6264 (OUTLIER) cc_final: 0.5805 (ptmt) REVERT: 4 37 LYS cc_start: 0.7503 (OUTLIER) cc_final: 0.7300 (mttp) REVERT: 4 44 ARG cc_start: 0.6380 (OUTLIER) cc_final: 0.5873 (mmm160) REVERT: 4 45 GLN cc_start: 0.7153 (mm110) cc_final: 0.6504 (mm110) REVERT: 6 1 MET cc_start: 0.7295 (mpp) cc_final: 0.6932 (mpp) REVERT: 8 15 LYS cc_start: 0.7095 (ttmm) cc_final: 0.6054 (tttp) REVERT: c 5 LYS cc_start: 0.7124 (tttp) cc_final: 0.6581 (tptp) REVERT: c 7 LYS cc_start: 0.7948 (OUTLIER) cc_final: 0.7610 (mttt) REVERT: c 74 ILE cc_start: 0.7054 (OUTLIER) cc_final: 0.6848 (mm) REVERT: c 79 GLU cc_start: 0.7122 (OUTLIER) cc_final: 0.6623 (mt-10) REVERT: c 87 ARG cc_start: 0.7197 (OUTLIER) cc_final: 0.5743 (mtm-85) REVERT: c 97 LYS cc_start: 0.7484 (OUTLIER) cc_final: 0.6903 (ptmm) REVERT: c 108 LYS cc_start: 0.7248 (OUTLIER) cc_final: 0.6698 (ttmt) REVERT: c 110 LEU cc_start: 0.7219 (OUTLIER) cc_final: 0.6920 (tp) REVERT: c 125 LYS cc_start: 0.7363 (OUTLIER) cc_final: 0.6974 (pttt) REVERT: c 146 MET cc_start: 0.7810 (mtm) cc_final: 0.7479 (mtp) REVERT: c 183 LYS cc_start: 0.7496 (OUTLIER) cc_final: 0.7031 (mttt) REVERT: c 265 LYS cc_start: 0.7985 (OUTLIER) cc_final: 0.7754 (pttm) REVERT: c 269 ARG cc_start: 0.6761 (ttp80) cc_final: 0.6301 (ttt90) REVERT: d 1 MET cc_start: 0.5344 (ttm) cc_final: 0.4922 (ttm) REVERT: d 7 LYS cc_start: 0.7902 (ttpp) cc_final: 0.7425 (ttmm) REVERT: d 13 ARG cc_start: 0.8097 (OUTLIER) cc_final: 0.6451 (ptt180) REVERT: d 40 LEU cc_start: 0.8010 (mp) cc_final: 0.7778 (mp) REVERT: d 48 ILE cc_start: 0.7576 (OUTLIER) cc_final: 0.7266 (pp) REVERT: d 64 GLU cc_start: 0.6417 (mt-10) cc_final: 0.6075 (mt-10) REVERT: d 88 GLU cc_start: 0.6736 (OUTLIER) cc_final: 0.6414 (pt0) REVERT: d 157 LYS cc_start: 0.7885 (OUTLIER) cc_final: 0.7166 (tttp) REVERT: d 179 ARG cc_start: 0.7789 (OUTLIER) cc_final: 0.7498 (ptp-170) REVERT: d 183 GLU cc_start: 0.6257 (pm20) cc_final: 0.5693 (pt0) REVERT: d 202 ILE cc_start: 0.8021 (mt) cc_final: 0.7714 (mm) REVERT: d 204 LYS cc_start: 0.7870 (OUTLIER) cc_final: 0.7017 (mtpt) REVERT: e 21 ARG cc_start: 0.6612 (OUTLIER) cc_final: 0.6006 (mtp85) REVERT: e 22 ASP cc_start: 0.7223 (p0) cc_final: 0.6863 (p0) REVERT: e 25 GLU cc_start: 0.7501 (tt0) cc_final: 0.7120 (tt0) REVERT: e 61 ARG cc_start: 0.6583 (mtp180) cc_final: 0.6321 (ptm-80) REVERT: e 139 LYS cc_start: 0.7160 (tttp) cc_final: 0.6837 (tttp) REVERT: e 153 LEU cc_start: 0.3686 (OUTLIER) cc_final: 0.3345 (tm) REVERT: e 194 LYS cc_start: 0.5614 (mmmt) cc_final: 0.5309 (mmtm) REVERT: e 197 GLU cc_start: 0.6633 (tt0) cc_final: 0.6379 (mt-10) REVERT: f 3 LYS cc_start: 0.5442 (ptmm) cc_final: 0.5137 (ttmt) REVERT: f 21 ASN cc_start: 0.5865 (OUTLIER) cc_final: 0.5451 (t0) REVERT: f 38 MET cc_start: 0.7016 (ptp) cc_final: 0.6726 (ptp) REVERT: f 64 LYS cc_start: 0.3165 (mptp) cc_final: 0.2747 (tttm) REVERT: f 141 ILE cc_start: 0.5277 (OUTLIER) cc_final: 0.4808 (pp) REVERT: g 25 THR cc_start: 0.6576 (m) cc_final: 0.6072 (t) REVERT: g 36 THR cc_start: 0.6576 (t) cc_final: 0.6258 (m) REVERT: g 85 LYS cc_start: 0.7105 (OUTLIER) cc_final: 0.6509 (tppt) REVERT: g 153 ARG cc_start: 0.7252 (ptp90) cc_final: 0.6455 (mtt90) REVERT: g 158 LYS cc_start: 0.6779 (mttm) cc_final: 0.6560 (mttp) REVERT: g 169 VAL cc_start: 0.6338 (OUTLIER) cc_final: 0.5992 (p) REVERT: h 15 LEU cc_start: 0.5203 (OUTLIER) cc_final: 0.4930 (pp) REVERT: j 2 LYS cc_start: 0.7602 (mmmt) cc_final: 0.6806 (mtmt) REVERT: j 12 LYS cc_start: 0.7163 (tppt) cc_final: 0.6007 (tttm) REVERT: j 43 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.6970 (pm20) REVERT: j 95 ARG cc_start: 0.6771 (OUTLIER) cc_final: 0.5517 (ttp-110) REVERT: j 98 GLU cc_start: 0.7204 (OUTLIER) cc_final: 0.6926 (mp0) REVERT: j 106 LYS cc_start: 0.7525 (tttp) cc_final: 0.6596 (ttpt) REVERT: j 138 GLN cc_start: 0.7807 (OUTLIER) cc_final: 0.7464 (pt0) REVERT: k 4 GLU cc_start: 0.7700 (mt-10) cc_final: 0.7198 (mt-10) REVERT: k 53 LYS cc_start: 0.6910 (mmpt) cc_final: 0.5844 (mppt) REVERT: k 98 ARG cc_start: 0.5517 (mtt180) cc_final: 0.4903 (mtm110) REVERT: l 55 MET cc_start: 0.8085 (tpp) cc_final: 0.7824 (tpp) REVERT: l 69 ARG cc_start: 0.6941 (OUTLIER) cc_final: 0.6129 (ttt-90) REVERT: l 106 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.7154 (pm20) REVERT: l 123 ARG cc_start: 0.7910 (tpp80) cc_final: 0.7372 (tpp80) REVERT: m 1 MET cc_start: 0.6443 (tpt) cc_final: 0.6209 (tpp) REVERT: m 22 GLN cc_start: 0.6067 (OUTLIER) cc_final: 0.5432 (mp10) REVERT: m 81 ARG cc_start: 0.7180 (OUTLIER) cc_final: 0.6653 (mmt-90) REVERT: m 126 ILE cc_start: 0.7423 (OUTLIER) cc_final: 0.7031 (mm) REVERT: m 127 LYS cc_start: 0.6906 (OUTLIER) cc_final: 0.6599 (mtpp) REVERT: m 133 LYS cc_start: 0.7443 (tttm) cc_final: 0.7135 (ptmm) REVERT: n 18 GLN cc_start: 0.6794 (OUTLIER) cc_final: 0.6384 (tt0) REVERT: o 3 LYS cc_start: 0.5875 (OUTLIER) cc_final: 0.5505 (tttp) REVERT: o 10 ARG cc_start: 0.7425 (OUTLIER) cc_final: 0.5980 (mtp180) REVERT: o 16 ARG cc_start: 0.5838 (OUTLIER) cc_final: 0.5392 (mmt-90) REVERT: o 20 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7584 (pp20) REVERT: o 55 GLU cc_start: 0.6510 (mt-10) cc_final: 0.6157 (mt-10) REVERT: o 62 LEU cc_start: 0.7241 (OUTLIER) cc_final: 0.6983 (mp) REVERT: p 7 GLN cc_start: 0.6545 (OUTLIER) cc_final: 0.6075 (pp30) REVERT: p 10 GLN cc_start: 0.7048 (mt0) cc_final: 0.6713 (mt0) REVERT: p 11 GLU cc_start: 0.7260 (pt0) cc_final: 0.6849 (pt0) REVERT: p 89 ARG cc_start: 0.6808 (mtm-85) cc_final: 0.5763 (mtt-85) REVERT: p 102 GLU cc_start: 0.6671 (mm-30) cc_final: 0.6364 (mp0) REVERT: p 112 GLU cc_start: 0.6950 (tt0) cc_final: 0.6249 (tt0) REVERT: q 58 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.7185 (ttt-90) REVERT: q 85 LYS cc_start: 0.7426 (mtmt) cc_final: 0.6873 (mttt) REVERT: r 13 ARG cc_start: 0.8432 (ttp80) cc_final: 0.7982 (ttp80) REVERT: r 26 ASP cc_start: 0.6601 (OUTLIER) cc_final: 0.6326 (t0) REVERT: r 37 GLU cc_start: 0.7458 (mt-10) cc_final: 0.7083 (pt0) REVERT: r 60 LYS cc_start: 0.7644 (OUTLIER) cc_final: 0.7376 (mttp) REVERT: r 85 LYS cc_start: 0.7731 (OUTLIER) cc_final: 0.7177 (mmmm) REVERT: s 22 ASP cc_start: 0.7347 (OUTLIER) cc_final: 0.6809 (m-30) REVERT: s 28 LYS cc_start: 0.7268 (mttp) cc_final: 0.6862 (mttm) REVERT: s 34 ASP cc_start: 0.6428 (m-30) cc_final: 0.6219 (m-30) REVERT: s 70 LYS cc_start: 0.7528 (mttp) cc_final: 0.7204 (mtmm) REVERT: s 73 LYS cc_start: 0.7733 (OUTLIER) cc_final: 0.7246 (mtpt) REVERT: s 92 ARG cc_start: 0.6595 (mtp-110) cc_final: 0.5401 (mtm-85) REVERT: s 95 ARG cc_start: 0.6884 (tpp80) cc_final: 0.5110 (ppt90) REVERT: s 109 ASP cc_start: 0.6543 (p0) cc_final: 0.5564 (p0) REVERT: t 26 LYS cc_start: 0.6812 (tppp) cc_final: 0.6446 (mmtp) REVERT: t 32 LEU cc_start: 0.7671 (OUTLIER) cc_final: 0.7299 (pp) REVERT: t 49 LYS cc_start: 0.7225 (ttmm) cc_final: 0.6690 (tttp) REVERT: t 54 GLU cc_start: 0.5596 (pm20) cc_final: 0.5247 (mm-30) REVERT: t 56 GLU cc_start: 0.7403 (mm-30) cc_final: 0.7002 (tt0) REVERT: u 10 GLU cc_start: 0.7132 (mm-30) cc_final: 0.6418 (tp30) REVERT: u 21 LYS cc_start: 0.8280 (OUTLIER) cc_final: 0.7856 (mmmm) REVERT: u 22 ARG cc_start: 0.7771 (mtm-85) cc_final: 0.7559 (mtp180) REVERT: u 24 LYS cc_start: 0.7262 (ttmm) cc_final: 0.6347 (ttpp) REVERT: u 37 GLU cc_start: 0.6972 (tp30) cc_final: 0.6569 (mm-30) REVERT: u 46 GLN cc_start: 0.7393 (mm-40) cc_final: 0.7003 (mm-40) REVERT: u 62 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.6942 (pm20) REVERT: u 79 LYS cc_start: 0.7343 (OUTLIER) cc_final: 0.6933 (mttm) REVERT: w 25 LYS cc_start: 0.7118 (mtpt) cc_final: 0.6578 (mtpp) REVERT: w 34 LYS cc_start: 0.5856 (tppp) cc_final: 0.5156 (ptmt) REVERT: w 53 LYS cc_start: 0.6277 (mttm) cc_final: 0.5406 (mmtt) REVERT: w 68 LYS cc_start: 0.5767 (ttmt) cc_final: 0.5078 (tptt) REVERT: y 44 LYS cc_start: 0.6893 (ttmm) cc_final: 0.6492 (tttm) REVERT: y 62 LYS cc_start: 0.8219 (mtmt) cc_final: 0.7453 (mttm) REVERT: y 68 LYS cc_start: 0.7942 (OUTLIER) cc_final: 0.7314 (tptp) REVERT: y 70 GLU cc_start: 0.7809 (mt-10) cc_final: 0.6526 (mp0) outliers start: 196 outliers final: 124 residues processed: 600 average time/residue: 2.0154 time to fit residues: 1584.1868 Evaluate side-chains 654 residues out of total 2526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 469 time to evaluate : 3.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 2 SER Chi-restraints excluded: chain 0 residue 25 THR Chi-restraints excluded: chain 0 residue 35 SER Chi-restraints excluded: chain 0 residue 62 LYS Chi-restraints excluded: chain 0 residue 66 THR Chi-restraints excluded: chain 0 residue 76 GLU Chi-restraints excluded: chain 1 residue 4 LYS Chi-restraints excluded: chain 1 residue 38 GLN Chi-restraints excluded: chain 1 residue 44 LYS Chi-restraints excluded: chain 1 residue 45 GLN Chi-restraints excluded: chain 1 residue 58 ASN Chi-restraints excluded: chain 1 residue 59 GLU Chi-restraints excluded: chain 2 residue 19 LYS Chi-restraints excluded: chain 2 residue 36 VAL Chi-restraints excluded: chain 2 residue 56 LYS Chi-restraints excluded: chain 4 residue 5 ILE Chi-restraints excluded: chain 4 residue 17 THR Chi-restraints excluded: chain 4 residue 30 LYS Chi-restraints excluded: chain 4 residue 37 LYS Chi-restraints excluded: chain 4 residue 42 VAL Chi-restraints excluded: chain 4 residue 43 VAL Chi-restraints excluded: chain 4 residue 44 ARG Chi-restraints excluded: chain 6 residue 25 LYS Chi-restraints excluded: chain 7 residue 52 LYS Chi-restraints excluded: chain 8 residue 10 LEU Chi-restraints excluded: chain 8 residue 17 VAL Chi-restraints excluded: chain 8 residue 32 LYS Chi-restraints excluded: chain c residue 7 LYS Chi-restraints excluded: chain c residue 20 VAL Chi-restraints excluded: chain c residue 74 ILE Chi-restraints excluded: chain c residue 79 GLU Chi-restraints excluded: chain c residue 87 ARG Chi-restraints excluded: chain c residue 97 LYS Chi-restraints excluded: chain c residue 108 LYS Chi-restraints excluded: chain c residue 110 LEU Chi-restraints excluded: chain c residue 116 ILE Chi-restraints excluded: chain c residue 118 SER Chi-restraints excluded: chain c residue 120 VAL Chi-restraints excluded: chain c residue 125 LYS Chi-restraints excluded: chain c residue 132 MET Chi-restraints excluded: chain c residue 162 VAL Chi-restraints excluded: chain c residue 183 LYS Chi-restraints excluded: chain c residue 265 LYS Chi-restraints excluded: chain d residue 13 ARG Chi-restraints excluded: chain d residue 29 VAL Chi-restraints excluded: chain d residue 48 ILE Chi-restraints excluded: chain d residue 88 GLU Chi-restraints excluded: chain d residue 99 GLU Chi-restraints excluded: chain d residue 106 LYS Chi-restraints excluded: chain d residue 151 THR Chi-restraints excluded: chain d residue 157 LYS Chi-restraints excluded: chain d residue 175 LEU Chi-restraints excluded: chain d residue 179 ARG Chi-restraints excluded: chain d residue 204 LYS Chi-restraints excluded: chain e residue 5 LEU Chi-restraints excluded: chain e residue 10 SER Chi-restraints excluded: chain e residue 21 ARG Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain e residue 80 SER Chi-restraints excluded: chain e residue 95 LYS Chi-restraints excluded: chain e residue 119 ILE Chi-restraints excluded: chain e residue 122 GLU Chi-restraints excluded: chain e residue 153 LEU Chi-restraints excluded: chain e residue 166 LYS Chi-restraints excluded: chain e residue 173 THR Chi-restraints excluded: chain f residue 16 LEU Chi-restraints excluded: chain f residue 21 ASN Chi-restraints excluded: chain f residue 26 MET Chi-restraints excluded: chain f residue 35 THR Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 49 LEU Chi-restraints excluded: chain f residue 72 LYS Chi-restraints excluded: chain f residue 104 ILE Chi-restraints excluded: chain f residue 117 LEU Chi-restraints excluded: chain f residue 132 VAL Chi-restraints excluded: chain f residue 141 ILE Chi-restraints excluded: chain f residue 155 THR Chi-restraints excluded: chain f residue 170 LEU Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 11 VAL Chi-restraints excluded: chain g residue 17 VAL Chi-restraints excluded: chain g residue 49 THR Chi-restraints excluded: chain g residue 51 THR Chi-restraints excluded: chain g residue 81 GLU Chi-restraints excluded: chain g residue 85 LYS Chi-restraints excluded: chain g residue 90 VAL Chi-restraints excluded: chain g residue 99 LYS Chi-restraints excluded: chain g residue 107 LEU Chi-restraints excluded: chain g residue 113 VAL Chi-restraints excluded: chain g residue 169 VAL Chi-restraints excluded: chain h residue 3 VAL Chi-restraints excluded: chain h residue 9 VAL Chi-restraints excluded: chain h residue 15 LEU Chi-restraints excluded: chain h residue 22 LYS Chi-restraints excluded: chain h residue 37 VAL Chi-restraints excluded: chain j residue 1 MET Chi-restraints excluded: chain j residue 5 THR Chi-restraints excluded: chain j residue 10 THR Chi-restraints excluded: chain j residue 11 VAL Chi-restraints excluded: chain j residue 43 GLU Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 62 VAL Chi-restraints excluded: chain j residue 64 VAL Chi-restraints excluded: chain j residue 95 ARG Chi-restraints excluded: chain j residue 98 GLU Chi-restraints excluded: chain j residue 131 ASN Chi-restraints excluded: chain j residue 138 GLN Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 88 ASN Chi-restraints excluded: chain l residue 69 ARG Chi-restraints excluded: chain l residue 92 LEU Chi-restraints excluded: chain l residue 104 GLN Chi-restraints excluded: chain l residue 106 GLU Chi-restraints excluded: chain l residue 117 THR Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain m residue 7 THR Chi-restraints excluded: chain m residue 22 GLN Chi-restraints excluded: chain m residue 30 SER Chi-restraints excluded: chain m residue 53 MET Chi-restraints excluded: chain m residue 78 LEU Chi-restraints excluded: chain m residue 81 ARG Chi-restraints excluded: chain m residue 104 GLU Chi-restraints excluded: chain m residue 126 ILE Chi-restraints excluded: chain m residue 127 LYS Chi-restraints excluded: chain m residue 129 THR Chi-restraints excluded: chain n residue 14 SER Chi-restraints excluded: chain n residue 18 GLN Chi-restraints excluded: chain n residue 57 THR Chi-restraints excluded: chain n residue 70 THR Chi-restraints excluded: chain n residue 74 GLU Chi-restraints excluded: chain o residue 3 LYS Chi-restraints excluded: chain o residue 9 ARG Chi-restraints excluded: chain o residue 10 ARG Chi-restraints excluded: chain o residue 16 ARG Chi-restraints excluded: chain o residue 20 GLU Chi-restraints excluded: chain o residue 24 THR Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain o residue 49 VAL Chi-restraints excluded: chain o residue 54 VAL Chi-restraints excluded: chain o residue 62 LEU Chi-restraints excluded: chain p residue 7 GLN Chi-restraints excluded: chain p residue 36 SER Chi-restraints excluded: chain p residue 46 VAL Chi-restraints excluded: chain p residue 63 LYS Chi-restraints excluded: chain p residue 70 VAL Chi-restraints excluded: chain p residue 76 THR Chi-restraints excluded: chain p residue 96 LYS Chi-restraints excluded: chain q residue 6 ARG Chi-restraints excluded: chain q residue 58 ARG Chi-restraints excluded: chain q residue 84 LYS Chi-restraints excluded: chain q residue 91 ASP Chi-restraints excluded: chain r residue 26 ASP Chi-restraints excluded: chain r residue 47 VAL Chi-restraints excluded: chain r residue 60 LYS Chi-restraints excluded: chain r residue 85 LYS Chi-restraints excluded: chain s residue 13 SER Chi-restraints excluded: chain s residue 22 ASP Chi-restraints excluded: chain s residue 33 LEU Chi-restraints excluded: chain s residue 66 ILE Chi-restraints excluded: chain s residue 73 LYS Chi-restraints excluded: chain s residue 101 SER Chi-restraints excluded: chain t residue 4 GLU Chi-restraints excluded: chain t residue 6 ARG Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain t residue 36 LYS Chi-restraints excluded: chain t residue 50 LEU Chi-restraints excluded: chain t residue 55 VAL Chi-restraints excluded: chain t residue 67 VAL Chi-restraints excluded: chain t residue 69 GLN Chi-restraints excluded: chain t residue 100 ASN Chi-restraints excluded: chain u residue 17 LYS Chi-restraints excluded: chain u residue 21 LYS Chi-restraints excluded: chain u residue 30 SER Chi-restraints excluded: chain u residue 62 GLU Chi-restraints excluded: chain u residue 68 SER Chi-restraints excluded: chain u residue 79 LYS Chi-restraints excluded: chain u residue 88 GLU Chi-restraints excluded: chain w residue 72 VAL Chi-restraints excluded: chain y residue 17 GLU Chi-restraints excluded: chain y residue 19 LYS Chi-restraints excluded: chain y residue 43 THR Chi-restraints excluded: chain y residue 51 VAL Chi-restraints excluded: chain y residue 68 LYS Chi-restraints excluded: chain y residue 72 LYS Chi-restraints excluded: chain y residue 78 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 607 random chunks: chunk 382 optimal weight: 9.9990 chunk 512 optimal weight: 6.9990 chunk 147 optimal weight: 10.0000 chunk 444 optimal weight: 4.9990 chunk 71 optimal weight: 10.0000 chunk 133 optimal weight: 10.0000 chunk 482 optimal weight: 3.9990 chunk 201 optimal weight: 10.0000 chunk 495 optimal weight: 5.9990 chunk 61 optimal weight: 10.0000 chunk 88 optimal weight: 30.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 5 GLN 6 29 GLN g 104 ASN j 128 ASN ** k 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 56 GLN r 86 GLN s 31 GLN t 59 ASN ** u 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.147516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.114472 restraints weight = 77529.690| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 0.89 r_work: 0.2798 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.2699 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.4322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 98998 Z= 0.398 Angle : 0.776 11.802 149023 Z= 0.400 Chirality : 0.046 0.383 19174 Planarity : 0.007 0.097 7331 Dihedral : 24.285 179.211 51740 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.33 % Favored : 94.57 % Rotamer: Outliers : 8.00 % Allowed : 25.89 % Favored : 66.11 % 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: -0.74 (0.14), residues: 3057 helix: 0.45 (0.18), residues: 801 sheet: -0.39 (0.19), residues: 712 loop : -0.99 (0.15), residues: 1544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP c 213 HIS 0.010 0.002 HIS r 89 PHE 0.025 0.003 PHE h 29 TYR 0.021 0.003 TYR q 32 ARG 0.014 0.001 ARG f 150 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23980.66 seconds wall clock time: 420 minutes 57.51 seconds (25257.51 seconds total)