Starting phenix.real_space_refine on Wed Feb 21 03:23:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tnn_10535/02_2024/6tnn_10535.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tnn_10535/02_2024/6tnn_10535.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tnn_10535/02_2024/6tnn_10535.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tnn_10535/02_2024/6tnn_10535.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tnn_10535/02_2024/6tnn_10535.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tnn_10535/02_2024/6tnn_10535.pdb" } resolution = 3.07 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= 0.014 sd= 0.220 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 3 6.06 5 P 3045 5.49 5 Mg 221 5.21 5 S 84 5.16 5 C 45624 2.51 5 N 17021 2.21 5 O 25842 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "b GLU 6": "OE1" <-> "OE2" Residue "b TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 51": "OE1" <-> "OE2" Residue "b GLU 65": "OE1" <-> "OE2" Residue "b GLU 68": "OE1" <-> "OE2" Residue "b PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 87": "OE1" <-> "OE2" Residue "b ASP 88": "OD1" <-> "OD2" Residue "b ASP 98": "OD1" <-> "OD2" Residue "b GLU 104": "OE1" <-> "OE2" Residue "H PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 27": "OE1" <-> "OE2" Residue "H ARG 51": "NH1" <-> "NH2" Residue "H GLU 74": "OE1" <-> "OE2" Residue "H GLU 119": "OE1" <-> "OE2" Residue "I ASP 44": "OD1" <-> "OD2" Residue "I ARG 51": "NH1" <-> "NH2" Residue "I GLU 60": "OE1" <-> "OE2" Residue "I PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 75": "OE1" <-> "OE2" Residue "I GLU 106": "OE1" <-> "OE2" Residue "I GLU 118": "OE1" <-> "OE2" Residue "W GLU 23": "OE1" <-> "OE2" Residue "W GLU 30": "OE1" <-> "OE2" Residue "W ARG 43": "NH1" <-> "NH2" Residue "W ARG 63": "NH1" <-> "NH2" Residue "W ASP 66": "OD1" <-> "OD2" Residue "W ARG 77": "NH1" <-> "NH2" Residue "W GLU 82": "OE1" <-> "OE2" Residue "W GLU 145": "OE1" <-> "OE2" Residue "W ARG 221": "NH1" <-> "NH2" Residue "X GLU 47": "OE1" <-> "OE2" Residue "X GLU 65": "OE1" <-> "OE2" Residue "X GLU 73": "OE1" <-> "OE2" Residue "X GLU 82": "OE1" <-> "OE2" Residue "X TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 150": "OD1" <-> "OD2" Residue "X GLU 182": "OE1" <-> "OE2" Residue "Y ASP 16": "OD1" <-> "OD2" Residue "Y GLU 27": "OE1" <-> "OE2" Residue "Y ASP 128": "OD1" <-> "OD2" Residue "Y GLU 177": "OE1" <-> "OE2" Residue "Y GLU 204": "OE1" <-> "OE2" Residue "Z ASP 23": "OD1" <-> "OD2" Residue "Z GLU 56": "OE1" <-> "OE2" Residue "Z PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 81": "OE1" <-> "OE2" Residue "Z ARG 92": "NH1" <-> "NH2" Residue "Z ASP 98": "OD1" <-> "OD2" Residue "Z ASP 101": "OD1" <-> "OD2" Residue "Z GLU 134": "OE1" <-> "OE2" Residue "Z ASP 163": "OD1" <-> "OD2" Residue "Z GLU 165": "OE1" <-> "OE2" Residue "Z GLU 168": "OE1" <-> "OE2" Residue "a GLU 33": "OE1" <-> "OE2" Residue "a ASP 41": "OD1" <-> "OD2" Residue "a ASP 48": "OD1" <-> "OD2" Residue "a GLU 115": "OE1" <-> "OE2" Residue "a GLU 120": "OE1" <-> "OE2" Residue "a GLU 140": "OE1" <-> "OE2" Residue "a GLU 168": "OE1" <-> "OE2" Residue "a ARG 172": "NH1" <-> "NH2" Residue "c ASP 20": "OD1" <-> "OD2" Residue "c GLU 64": "OE1" <-> "OE2" Residue "c GLU 103": "OE1" <-> "OE2" Residue "c GLU 139": "OE1" <-> "OE2" Residue "d ASP 37": "OD1" <-> "OD2" Residue "e GLU 73": "OE1" <-> "OE2" Residue "e ASP 80": "OD1" <-> "OD2" Residue "e GLU 87": "OE1" <-> "OE2" Residue "e GLU 118": "OE1" <-> "OE2" Residue "e GLU 134": "OE1" <-> "OE2" Residue "e GLU 137": "OE1" <-> "OE2" Residue "f GLU 80": "OE1" <-> "OE2" Residue "f PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 135": "OE1" <-> "OE2" Residue "f GLU 136": "OE1" <-> "OE2" Residue "g TYR 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 92": "OE1" <-> "OE2" Residue "g GLU 93": "OE1" <-> "OE2" Residue "h ARG 11": "NH1" <-> "NH2" Residue "h GLU 27": "OE1" <-> "OE2" Residue "h ASP 46": "OD1" <-> "OD2" Residue "h ASP 62": "OD1" <-> "OD2" Residue "h GLU 87": "OE1" <-> "OE2" Residue "h PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 114": "NH1" <-> "NH2" Residue "i GLU 9": "OE1" <-> "OE2" Residue "i GLU 14": "OE1" <-> "OE2" Residue "i ASP 19": "OD1" <-> "OD2" Residue "i GLU 41": "OE1" <-> "OE2" Residue "i ARG 42": "NH1" <-> "NH2" Residue "i GLU 60": "OE1" <-> "OE2" Residue "i ARG 65": "NH1" <-> "NH2" Residue "i GLU 74": "OE1" <-> "OE2" Residue "i ARG 96": "NH1" <-> "NH2" Residue "i TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 105": "OE1" <-> "OE2" Residue "i GLU 115": "OE1" <-> "OE2" Residue "k TYR 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k GLU 15": "OE1" <-> "OE2" Residue "k GLU 23": "OE1" <-> "OE2" Residue "k GLU 28": "OE1" <-> "OE2" Residue "k GLU 36": "OE1" <-> "OE2" Residue "k ASP 37": "OD1" <-> "OD2" Residue "k ARG 89": "NH1" <-> "NH2" Residue "l ARG 86": "NH1" <-> "NH2" Residue "m ASP 6": "OD1" <-> "OD2" Residue "m GLU 15": "OE1" <-> "OE2" Residue "m TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 29": "OE1" <-> "OE2" Residue "m ASP 31": "OD1" <-> "OD2" Residue "m ASP 52": "OD1" <-> "OD2" Residue "m ASP 86": "OD1" <-> "OD2" Residue "n ASP 31": "OD1" <-> "OD2" Residue "n GLU 77": "OE1" <-> "OE2" Residue "n ASP 87": "OD1" <-> "OD2" Residue "n ARG 92": "NH1" <-> "NH2" Residue "o ARG 28": "NH1" <-> "NH2" Residue "o PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ASP 72": "OD1" <-> "OD2" Residue "o ARG 84": "NH1" <-> "NH2" Residue "q GLU 47": "OE1" <-> "OE2" Residue "r ARG 12": "NH1" <-> "NH2" Residue "s ARG 8": "NH1" <-> "NH2" Residue "s ASP 54": "OD1" <-> "OD2" Residue "t GLU 28": "OE1" <-> "OE2" Residue "v GLU 5": "OE1" <-> "OE2" Residue "v GLU 59": "OE1" <-> "OE2" Residue "w GLU 5": "OE1" <-> "OE2" Residue "w ASP 18": "OD1" <-> "OD2" Residue "w GLU 58": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 91840 Number of models: 1 Model: "" Number of chains: 40 Chain: "b" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 955 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "H" Number of atoms: 1063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1063 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 2, 'TRANS': 129} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "I" Number of atoms: 1079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1079 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 2, 'TRANS': 131} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "U" Number of atoms: 62920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2930, 62920 Classifications: {'RNA': 2930} Modifications used: {'rna2p_pur': 284, 'rna2p_pyr': 146, 'rna3p_pur': 1416, 'rna3p_pyr': 1084} Link IDs: {'rna2p': 430, 'rna3p': 2499} Chain: "V" Number of atoms: 2475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 2475 Classifications: {'RNA': 116} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 7, 'rna3p_pur': 55, 'rna3p_pyr': 48} Link IDs: {'rna2p': 13, 'rna3p': 102} Chain: "W" Number of atoms: 2110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2110 Classifications: {'peptide': 275} Link IDs: {'PTRANS': 17, 'TRANS': 257} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "X" Number of atoms: 1574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1574 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 10, 'TRANS': 196} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "Y" Number of atoms: 1560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1560 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 7, 'TRANS': 197} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "Z" Number of atoms: 1403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1403 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 7, 'TRANS': 170} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "a" Number of atoms: 1341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1341 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 9, 'TRANS': 165} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "c" Number of atoms: 1122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1122 Classifications: {'peptide': 142} Incomplete info: {'n_c_alpha_c_only': 1} Link IDs: {'PTRANS': 8, 'TRANS': 133} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "d" Number of atoms: 919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 919 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "e" Number of atoms: 1080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1080 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 5, 'TRANS': 140} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "f" Number of atoms: 1096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1096 Classifications: {'peptide': 138} Incomplete info: {'n_c_alpha_c_only': 1} Link IDs: {'PTRANS': 7, 'TRANS': 130} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "g" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 952 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "h" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 911 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "i" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 935 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "j" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 939 Classifications: {'peptide': 117} Link IDs: {'TRANS': 116} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "k" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 785 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "l" Number of atoms: 841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 841 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "m" Number of atoms: 751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 751 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "n" Number of atoms: 761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 761 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 6, 'TRANS': 94} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "o" Number of atoms: 629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 629 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 2, 'TRANS': 79} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "p" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 425 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 3, 'TRANS': 50} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "q" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 400 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "r" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 366 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "s" Number of atoms: 511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 511 Classifications: {'peptide': 64} Link IDs: {'TRANS': 63} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "t" Number of atoms: 287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 287 Classifications: {'peptide': 36} Incomplete info: {'n_c_alpha_c_only': 1} Link IDs: {'PTRANS': 3, 'TRANS': 32} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "u" Number of atoms: 443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 443 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 1, 'TRANS': 56} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "v" Number of atoms: 529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 529 Classifications: {'peptide': 65} Link IDs: {'TRANS': 64} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "w" Number of atoms: 454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 454 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 1, 'TRANS': 56} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 214 Unusual residues: {' MG': 214} Classifications: {'undetermined': 214} Link IDs: {None: 213} Chain: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "e" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "p" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "t" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "u" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 88443 SG CYS p 30 51.994 184.952 99.402 1.00 51.41 S ATOM 88462 SG CYS p 33 49.790 183.093 97.259 1.00 56.10 S ATOM 88540 SG CYS p 43 53.590 181.947 98.180 1.00 45.93 S ATOM 88694 SG CYS q 9 105.627 42.622 131.003 1.00 49.88 S ATOM 88716 SG CYS q 12 103.050 42.502 128.136 1.00 56.99 S ATOM 88925 SG CYS q 36 101.692 43.155 131.401 1.00 42.60 S ATOM 89980 SG CYS t 11 110.242 144.139 191.773 1.00 59.33 S ATOM 90004 SG CYS t 14 107.406 144.219 189.834 1.00 56.06 S ATOM 90108 SG CYS t 27 108.244 147.533 190.965 1.00 55.42 S Time building chain proxies: 35.24, per 1000 atoms: 0.38 Number of scatterers: 91840 At special positions: 0 Unit cell: (183.06, 222.61, 257.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 3 29.99 S 84 16.00 P 3045 15.00 Mg 221 11.99 O 25842 8.00 N 17021 7.00 C 45624 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 35.48 Conformation dependent library (CDL) restraints added in 4.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN p 101 " pdb="ZN ZN p 101 " - pdb=" SG CYS p 33 " pdb="ZN ZN p 101 " - pdb=" SG CYS p 30 " pdb="ZN ZN p 101 " - pdb=" SG CYS p 43 " pdb=" ZN q 101 " pdb="ZN ZN q 101 " - pdb=" SG CYS q 12 " pdb="ZN ZN q 101 " - pdb=" SG CYS q 36 " pdb="ZN ZN q 101 " - pdb=" SG CYS q 9 " pdb=" ZN t 101 " pdb="ZN ZN t 101 " - pdb=" ND1 HIS t 32 " pdb="ZN ZN t 101 " - pdb=" SG CYS t 11 " pdb="ZN ZN t 101 " - pdb=" SG CYS t 27 " pdb="ZN ZN t 101 " - pdb=" SG CYS t 14 " Number of angles added : 3 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6134 Finding SS restraints... Secondary structure from input PDB file: 86 helices and 44 sheets defined 29.4% alpha, 15.7% beta 944 base pairs and 1593 stacking pairs defined. Time for finding SS restraints: 31.01 Creating SS restraints... Processing helix chain 'b' and resid 5 through 19 removed outlier: 3.533A pdb=" N LYS b 9 " --> pdb=" O ILE b 5 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ILE b 15 " --> pdb=" O VAL b 11 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N ALA b 16 " --> pdb=" O VAL b 12 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N SER b 17 " --> pdb=" O GLU b 13 " (cutoff:3.500A) Processing helix chain 'b' and resid 33 through 48 Processing helix chain 'b' and resid 59 through 67 removed outlier: 4.238A pdb=" N ALA b 63 " --> pdb=" O MET b 59 " (cutoff:3.500A) Processing helix chain 'b' and resid 93 through 104 Processing helix chain 'H' and resid 16 through 38 removed outlier: 4.001A pdb=" N ALA H 24 " --> pdb=" O TYR H 20 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY H 38 " --> pdb=" O LEU H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 41 through 54 Processing helix chain 'H' and resid 54 through 68 removed outlier: 3.589A pdb=" N ASN H 67 " --> pdb=" O PHE H 63 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLN H 68 " --> pdb=" O PHE H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 72 through 84 Processing helix chain 'H' and resid 97 through 114 removed outlier: 3.653A pdb=" N TYR H 101 " --> pdb=" O GLN H 97 " (cutoff:3.500A) Processing helix chain 'H' and resid 117 through 133 removed outlier: 3.749A pdb=" N GLN H 123 " --> pdb=" O GLU H 119 " (cutoff:3.500A) Processing helix chain 'I' and resid 14 through 39 removed outlier: 3.856A pdb=" N LEU I 18 " --> pdb=" O ASN I 14 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA I 19 " --> pdb=" O GLY I 15 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ALA I 24 " --> pdb=" O TYR I 20 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLY I 38 " --> pdb=" O LEU I 34 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N PHE I 39 " --> pdb=" O LEU I 35 " (cutoff:3.500A) Processing helix chain 'I' and resid 41 through 53 removed outlier: 4.299A pdb=" N ARG I 51 " --> pdb=" O LYS I 47 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE I 52 " --> pdb=" O LYS I 48 " (cutoff:3.500A) Processing helix chain 'I' and resid 54 through 67 Processing helix chain 'I' and resid 72 through 85 Processing helix chain 'I' and resid 97 through 114 removed outlier: 3.605A pdb=" N PHE I 105 " --> pdb=" O TYR I 101 " (cutoff:3.500A) Processing helix chain 'I' and resid 117 through 133 Processing helix chain 'W' and resid 197 through 202 removed outlier: 3.816A pdb=" N HIS W 200 " --> pdb=" O ASN W 197 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLU W 201 " --> pdb=" O GLU W 198 " (cutoff:3.500A) Processing helix chain 'W' and resid 208 through 213 Processing helix chain 'W' and resid 221 through 225 removed outlier: 3.818A pdb=" N MET W 225 " --> pdb=" O GLY W 222 " (cutoff:3.500A) Processing helix chain 'W' and resid 266 through 268 No H-bonds generated for 'chain 'W' and resid 266 through 268' Processing helix chain 'X' and resid 57 through 61 removed outlier: 3.665A pdb=" N SER X 61 " --> pdb=" O GLU X 58 " (cutoff:3.500A) Processing helix chain 'X' and resid 62 through 70 Processing helix chain 'X' and resid 98 through 102 removed outlier: 3.888A pdb=" N ILE X 101 " --> pdb=" O LYS X 98 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE X 102 " --> pdb=" O VAL X 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 98 through 102' Processing helix chain 'X' and resid 121 through 126 Processing helix chain 'Y' and resid 32 through 45 removed outlier: 3.609A pdb=" N SER Y 43 " --> pdb=" O MET Y 39 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU Y 44 " --> pdb=" O GLN Y 40 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ARG Y 45 " --> pdb=" O ARG Y 41 " (cutoff:3.500A) Processing helix chain 'Y' and resid 102 through 120 removed outlier: 3.614A pdb=" N VAL Y 113 " --> pdb=" O ALA Y 109 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU Y 114 " --> pdb=" O ILE Y 110 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N SER Y 116 " --> pdb=" O SER Y 112 " (cutoff:3.500A) Processing helix chain 'Y' and resid 135 through 146 Processing helix chain 'Y' and resid 160 through 166 removed outlier: 3.958A pdb=" N SER Y 166 " --> pdb=" O ALA Y 162 " (cutoff:3.500A) Processing helix chain 'Y' and resid 182 through 187 Processing helix chain 'Y' and resid 196 through 206 removed outlier: 4.136A pdb=" N GLU Y 200 " --> pdb=" O LYS Y 196 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N LYS Y 201 " --> pdb=" O ALA Y 197 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL Y 205 " --> pdb=" O LYS Y 201 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU Y 206 " --> pdb=" O VAL Y 202 " (cutoff:3.500A) Processing helix chain 'Z' and resid 3 through 20 Proline residue: Z 14 - end of helix Processing helix chain 'Z' and resid 24 through 28 Processing helix chain 'Z' and resid 51 through 61 removed outlier: 4.455A pdb=" N GLU Z 55 " --> pdb=" O ASP Z 51 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N PHE Z 59 " --> pdb=" O GLU Z 55 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE Z 60 " --> pdb=" O GLU Z 56 " (cutoff:3.500A) Processing helix chain 'Z' and resid 93 through 105 removed outlier: 4.009A pdb=" N TYR Z 97 " --> pdb=" O GLY Z 93 " (cutoff:3.500A) Processing helix chain 'Z' and resid 107 through 111 Processing helix chain 'Z' and resid 162 through 172 removed outlier: 4.011A pdb=" N ALA Z 166 " --> pdb=" O THR Z 162 " (cutoff:3.500A) Processing helix chain 'a' and resid 61 through 82 removed outlier: 4.213A pdb=" N GLY a 67 " --> pdb=" O ARG a 63 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ARG a 70 " --> pdb=" O HIS a 66 " (cutoff:3.500A) Processing helix chain 'a' and resid 138 through 151 removed outlier: 4.192A pdb=" N VAL a 142 " --> pdb=" O ASP a 138 " (cutoff:3.500A) Processing helix chain 'c' and resid 32 through 37 Processing helix chain 'c' and resid 59 through 63 removed outlier: 3.993A pdb=" N ILE c 63 " --> pdb=" O ALA c 60 " (cutoff:3.500A) Processing helix chain 'c' and resid 68 through 73 Processing helix chain 'c' and resid 90 through 97 Processing helix chain 'c' and resid 97 through 108 removed outlier: 3.716A pdb=" N GLY c 108 " --> pdb=" O LEU c 104 " (cutoff:3.500A) Processing helix chain 'c' and resid 118 through 121 Processing helix chain 'd' and resid 111 through 116 Processing helix chain 'e' and resid 22 through 26 removed outlier: 4.165A pdb=" N SER e 25 " --> pdb=" O GLY e 22 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY e 26 " --> pdb=" O ILE e 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 22 through 26' Processing helix chain 'e' and resid 56 through 61 removed outlier: 4.006A pdb=" N LEU e 61 " --> pdb=" O PHE e 58 " (cutoff:3.500A) Processing helix chain 'e' and resid 78 through 84 removed outlier: 4.016A pdb=" N LEU e 82 " --> pdb=" O ASN e 78 " (cutoff:3.500A) Processing helix chain 'e' and resid 94 through 100 Processing helix chain 'e' and resid 131 through 139 removed outlier: 3.640A pdb=" N ALA e 139 " --> pdb=" O ALA e 135 " (cutoff:3.500A) Processing helix chain 'f' and resid 43 through 58 removed outlier: 4.207A pdb=" N ILE f 47 " --> pdb=" O THR f 43 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N GLU f 48 " --> pdb=" O ASN f 44 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA f 53 " --> pdb=" O ALA f 49 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N MET f 58 " --> pdb=" O MET f 54 " (cutoff:3.500A) Processing helix chain 'f' and resid 110 through 123 removed outlier: 3.578A pdb=" N ALA f 114 " --> pdb=" O SER f 110 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N HIS f 123 " --> pdb=" O ARG f 119 " (cutoff:3.500A) Processing helix chain 'g' and resid 11 through 28 removed outlier: 3.719A pdb=" N THR g 22 " --> pdb=" O ARG g 18 " (cutoff:3.500A) Processing helix chain 'g' and resid 34 through 39 Processing helix chain 'g' and resid 43 through 52 removed outlier: 3.594A pdb=" N MET g 47 " --> pdb=" O VAL g 43 " (cutoff:3.500A) Processing helix chain 'g' and resid 55 through 64 removed outlier: 3.575A pdb=" N ARG g 59 " --> pdb=" O ASP g 55 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA g 64 " --> pdb=" O ARG g 60 " (cutoff:3.500A) Processing helix chain 'g' and resid 78 through 90 Processing helix chain 'h' and resid 6 through 20 removed outlier: 3.581A pdb=" N ALA h 10 " --> pdb=" O SER h 6 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N LYS h 13 " --> pdb=" O ALA h 9 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ALA h 16 " --> pdb=" O LEU h 12 " (cutoff:3.500A) Processing helix chain 'h' and resid 70 through 89 removed outlier: 3.912A pdb=" N ALA h 74 " --> pdb=" O ASP h 70 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS h 88 " --> pdb=" O ARG h 84 " (cutoff:3.500A) Processing helix chain 'h' and resid 103 through 116 removed outlier: 3.684A pdb=" N LEU h 109 " --> pdb=" O ARG h 105 " (cutoff:3.500A) Processing helix chain 'i' and resid 6 through 14 Processing helix chain 'i' and resid 101 through 105 removed outlier: 3.627A pdb=" N ARG i 104 " --> pdb=" O TYR i 101 " (cutoff:3.500A) Processing helix chain 'j' and resid 8 through 19 removed outlier: 3.783A pdb=" N LYS j 12 " --> pdb=" O THR j 8 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ARG j 14 " --> pdb=" O THR j 10 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL j 17 " --> pdb=" O ARG j 13 " (cutoff:3.500A) Processing helix chain 'j' and resid 31 through 69 removed outlier: 4.418A pdb=" N GLN j 37 " --> pdb=" O LYS j 33 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLY j 43 " --> pdb=" O VAL j 39 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASN j 44 " --> pdb=" O MET j 40 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ALA j 46 " --> pdb=" O SER j 42 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ARG j 51 " --> pdb=" O PHE j 47 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N LYS j 54 " --> pdb=" O ARG j 50 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ARG j 55 " --> pdb=" O ARG j 51 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ARG j 58 " --> pdb=" O LYS j 54 " (cutoff:3.500A) Processing helix chain 'j' and resid 75 through 86 removed outlier: 4.476A pdb=" N HIS j 81 " --> pdb=" O SER j 77 " (cutoff:3.500A) Processing helix chain 'j' and resid 92 through 99 Processing helix chain 'j' and resid 104 through 117 removed outlier: 3.644A pdb=" N GLN j 108 " --> pdb=" O THR j 104 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLN j 116 " --> pdb=" O ALA j 112 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU j 117 " --> pdb=" O ALA j 113 " (cutoff:3.500A) Processing helix chain 'l' and resid 13 through 25 removed outlier: 3.990A pdb=" N LEU l 19 " --> pdb=" O ARG l 15 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N VAL l 20 " --> pdb=" O LYS l 16 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N LEU l 23 " --> pdb=" O LEU l 19 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE l 24 " --> pdb=" O VAL l 20 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ARG l 25 " --> pdb=" O MET l 21 " (cutoff:3.500A) Processing helix chain 'l' and resid 28 through 38 removed outlier: 3.963A pdb=" N VAL l 33 " --> pdb=" O VAL l 29 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N SER l 34 " --> pdb=" O GLY l 30 " (cutoff:3.500A) Processing helix chain 'l' and resid 43 through 61 Processing helix chain 'l' and resid 89 through 91 No H-bonds generated for 'chain 'l' and resid 89 through 91' Processing helix chain 'm' and resid 3 through 7 removed outlier: 3.567A pdb=" N VAL m 7 " --> pdb=" O ASP m 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 3 through 7' Processing helix chain 'm' and resid 14 through 21 Processing helix chain 'm' and resid 35 through 47 removed outlier: 3.871A pdb=" N VAL m 39 " --> pdb=" O ASN m 35 " (cutoff:3.500A) Processing helix chain 'p' and resid 9 through 16 Processing helix chain 'p' and resid 17 through 19 No H-bonds generated for 'chain 'p' and resid 17 through 19' Processing helix chain 'r' and resid 8 through 16 Processing helix chain 'r' and resid 17 through 22 Processing helix chain 'r' and resid 24 through 38 removed outlier: 3.517A pdb=" N ARG r 28 " --> pdb=" O SER r 24 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU r 29 " --> pdb=" O LYS r 25 " (cutoff:3.500A) Processing helix chain 's' and resid 37 through 44 removed outlier: 3.571A pdb=" N ARG s 42 " --> pdb=" O GLN s 38 " (cutoff:3.500A) Processing helix chain 's' and resid 51 through 59 removed outlier: 3.858A pdb=" N ARG s 57 " --> pdb=" O GLY s 53 " (cutoff:3.500A) Processing helix chain 'v' and resid 2 through 8 removed outlier: 4.077A pdb=" N ASP v 8 " --> pdb=" O ASN v 4 " (cutoff:3.500A) Processing helix chain 'v' and resid 9 through 33 removed outlier: 4.102A pdb=" N GLU v 13 " --> pdb=" O LEU v 9 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU v 15 " --> pdb=" O THR v 11 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N GLN v 16 " --> pdb=" O ALA v 12 " (cutoff:3.500A) Processing helix chain 'v' and resid 40 through 63 removed outlier: 4.544A pdb=" N ARG v 44 " --> pdb=" O THR v 40 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA v 51 " --> pdb=" O ARG v 47 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG v 52 " --> pdb=" O LYS v 48 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL v 56 " --> pdb=" O ARG v 52 " (cutoff:3.500A) Processing helix chain 'w' and resid 16 through 25 removed outlier: 3.921A pdb=" N THR w 22 " --> pdb=" O ASP w 18 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL w 23 " --> pdb=" O GLN w 19 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ARG w 24 " --> pdb=" O ARG w 20 " (cutoff:3.500A) Processing helix chain 'w' and resid 42 through 50 Processing sheet with id=AA1, first strand: chain 'W' and resid 3 through 5 Processing sheet with id=AA2, first strand: chain 'W' and resid 34 through 35 Processing sheet with id=AA3, first strand: chain 'W' and resid 100 through 105 removed outlier: 3.851A pdb=" N GLU W 100 " --> pdb=" O TYR W 96 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ARG W 102 " --> pdb=" O ILE W 94 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ILE W 91 " --> pdb=" O VAL W 81 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N VAL W 81 " --> pdb=" O ILE W 91 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU W 93 " --> pdb=" O ALA W 79 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'W' and resid 129 through 131 removed outlier: 3.541A pdb=" N LEU W 130 " --> pdb=" O ALA W 190 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N LEU W 173 " --> pdb=" O LEU W 165 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL W 174 " --> pdb=" O ARG W 182 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG W 272 " --> pdb=" O VAL W 181 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'X' and resid 168 through 171 removed outlier: 4.765A pdb=" N VAL X 113 " --> pdb=" O LEU X 199 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N LEU X 199 " --> pdb=" O VAL X 113 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N LYS X 9 " --> pdb=" O GLU X 29 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N GLU X 29 " --> pdb=" O LYS X 9 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLY X 11 " --> pdb=" O VAL X 27 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N LEU X 187 " --> pdb=" O VAL X 177 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'X' and resid 77 through 83 removed outlier: 6.491A pdb=" N LYS X 77 " --> pdb=" O ASP X 55 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ASP X 55 " --> pdb=" O LYS X 77 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N GLN X 37 " --> pdb=" O GLN X 50 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N GLY X 52 " --> pdb=" O VAL X 35 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N VAL X 35 " --> pdb=" O GLY X 52 " (cutoff:3.500A) removed outlier: 8.549A pdb=" N ASP X 54 " --> pdb=" O ASN X 33 " (cutoff:3.500A) removed outlier: 10.197A pdb=" N ASN X 33 " --> pdb=" O ASP X 54 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'X' and resid 118 through 120 removed outlier: 3.735A pdb=" N GLY X 118 " --> pdb=" O MET X 164 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'Y' and resid 3 through 5 removed outlier: 3.621A pdb=" N ILE Y 17 " --> pdb=" O VAL Y 4 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'Y' and resid 123 through 126 removed outlier: 6.876A pdb=" N LEU Y 153 " --> pdb=" O LEU Y 193 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N THR Y 195 " --> pdb=" O LEU Y 153 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N VAL Y 155 " --> pdb=" O THR Y 195 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'Z' and resid 66 through 69 removed outlier: 6.661A pdb=" N VAL Z 66 " --> pdb=" O ALA Z 87 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ALA Z 87 " --> pdb=" O VAL Z 66 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N THR Z 68 " --> pdb=" O ILE Z 85 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE Z 34 " --> pdb=" O LEU Z 91 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LYS Z 33 " --> pdb=" O VAL Z 157 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'a' and resid 16 through 18 removed outlier: 3.599A pdb=" N GLY a 32 " --> pdb=" O GLY a 29 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'a' and resid 43 through 47 removed outlier: 3.638A pdb=" N GLU a 43 " --> pdb=" O ALA a 54 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'a' and resid 84 through 89 removed outlier: 7.373A pdb=" N LYS a 131 " --> pdb=" O PRO a 127 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'a' and resid 96 through 100 removed outlier: 3.629A pdb=" N ARG a 96 " --> pdb=" O ASN a 107 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL a 105 " --> pdb=" O SER a 98 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER a 100 " --> pdb=" O LYS a 103 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'c' and resid 123 through 125 Processing sheet with id=AB7, first strand: chain 'c' and resid 74 through 78 Processing sheet with id=AB8, first strand: chain 'd' and resid 7 through 10 removed outlier: 5.923A pdb=" N ARG d 17 " --> pdb=" O VAL d 10 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ALA d 16 " --> pdb=" O ALA d 46 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ALA d 46 " --> pdb=" O ALA d 16 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N GLU d 18 " --> pdb=" O LYS d 44 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS d 44 " --> pdb=" O GLU d 18 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VAL d 40 " --> pdb=" O ILE d 22 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N VAL d 24 " --> pdb=" O VAL d 38 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N VAL d 38 " --> pdb=" O VAL d 24 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LYS d 59 " --> pdb=" O ILE d 87 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ALA d 83 " --> pdb=" O VAL d 63 " (cutoff:3.500A) removed outlier: 8.687A pdb=" N CYS d 84 " --> pdb=" O ARG d 7 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LYS d 9 " --> pdb=" O CYS d 84 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N ILE d 86 " --> pdb=" O LYS d 9 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'd' and resid 69 through 70 removed outlier: 3.691A pdb=" N ILE d 77 " --> pdb=" O ALA d 69 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL i 71 " --> pdb=" O SER i 68 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS i 52 " --> pdb=" O THR i 63 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ARG i 65 " --> pdb=" O VAL i 50 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N VAL i 50 " --> pdb=" O ARG i 65 " (cutoff:3.500A) removed outlier: 8.853A pdb=" N ILE i 67 " --> pdb=" O GLY i 48 " (cutoff:3.500A) removed outlier: 9.141A pdb=" N GLY i 48 " --> pdb=" O ILE i 67 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ARG i 30 " --> pdb=" O ILE i 87 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ILE i 87 " --> pdb=" O ARG i 30 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N HIS i 32 " --> pdb=" O ALA i 85 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'e' and resid 110 through 111 Processing sheet with id=AC2, first strand: chain 'e' and resid 124 through 125 removed outlier: 3.568A pdb=" N ALA e 125 " --> pdb=" O GLU e 144 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'f' and resid 32 through 36 Processing sheet with id=AC4, first strand: chain 'f' and resid 40 through 42 removed outlier: 5.898A pdb=" N ALA f 76 " --> pdb=" O PRO f 90 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'f' and resid 63 through 64 removed outlier: 3.588A pdb=" N SER f 107 " --> pdb=" O LYS f 63 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'g' and resid 29 through 33 removed outlier: 4.634A pdb=" N MET g 114 " --> pdb=" O LEU g 104 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'h' and resid 52 through 57 removed outlier: 3.825A pdb=" N ALA h 54 " --> pdb=" O ILE h 44 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'k' and resid 3 through 6 Processing sheet with id=AC9, first strand: chain 'k' and resid 19 through 23 removed outlier: 6.883A pdb=" N LYS k 94 " --> pdb=" O GLU k 63 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU k 98 " --> pdb=" O THR k 59 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N THR k 59 " --> pdb=" O GLU k 98 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'k' and resid 75 through 77 removed outlier: 4.644A pdb=" N VAL k 82 " --> pdb=" O LYS k 77 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'l' and resid 5 through 10 removed outlier: 6.120A pdb=" N SER l 101 " --> pdb=" O THR l 9 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N SER l 94 " --> pdb=" O PHE l 85 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N PHE l 85 " --> pdb=" O SER l 94 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ILE l 96 " --> pdb=" O LYS l 83 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N LYS l 83 " --> pdb=" O ILE l 96 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LYS l 98 " --> pdb=" O THR l 81 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N THR l 81 " --> pdb=" O LYS l 98 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N THR l 100 " --> pdb=" O GLY l 79 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLY l 79 " --> pdb=" O THR l 100 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N SER l 108 " --> pdb=" O ILE l 71 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N ILE l 71 " --> pdb=" O SER l 108 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'm' and resid 8 through 11 removed outlier: 6.843A pdb=" N GLU m 29 " --> pdb=" O LYS m 9 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N THR m 27 " --> pdb=" O PRO m 11 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA m 79 " --> pdb=" O PHE m 28 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN m 55 " --> pdb=" O ILE m 80 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS m 53 " --> pdb=" O LYS m 82 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'm' and resid 65 through 66 removed outlier: 3.509A pdb=" N VAL m 66 " --> pdb=" O TYR m 69 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TYR m 69 " --> pdb=" O VAL m 66 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'n' and resid 9 through 11 removed outlier: 3.523A pdb=" N MET n 69 " --> pdb=" O MET n 10 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'n' and resid 23 through 26 removed outlier: 6.852A pdb=" N LEU n 34 " --> pdb=" O LEU n 24 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N ALA n 26 " --> pdb=" O ARG n 32 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N ARG n 32 " --> pdb=" O ALA n 26 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'n' and resid 40 through 45 removed outlier: 3.525A pdb=" N LYS n 43 " --> pdb=" O SER n 57 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER n 45 " --> pdb=" O GLY n 55 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'n' and resid 81 through 82 Processing sheet with id=AD9, first strand: chain 'o' and resid 30 through 31 removed outlier: 6.699A pdb=" N LEU o 67 " --> pdb=" O LEU o 45 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'o' and resid 38 through 39 Processing sheet with id=AE2, first strand: chain 'p' and resid 27 through 29 Processing sheet with id=AE3, first strand: chain 'q' and resid 15 through 22 removed outlier: 6.348A pdb=" N ARG q 15 " --> pdb=" O CYS q 9 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N CYS q 9 " --> pdb=" O ARG q 15 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TYR q 17 " --> pdb=" O LEU q 7 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 's' and resid 24 through 25 Processing sheet with id=AE5, first strand: chain 't' and resid 3 through 4 removed outlier: 4.647A pdb=" N VAL t 23 " --> pdb=" O GLN t 36 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'u' and resid 13 through 18 Processing sheet with id=AE7, first strand: chain 'u' and resid 34 through 40 removed outlier: 3.513A pdb=" N VAL u 36 " --> pdb=" O VAL u 47 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'w' and resid 34 through 38 removed outlier: 3.568A pdb=" N LEU w 4 " --> pdb=" O HIS w 37 " (cutoff:3.500A) 830 hydrogen bonds defined for protein. 2340 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2422 hydrogen bonds 3958 hydrogen bond angles 0 basepair planarities 944 basepair parallelities 1593 stacking parallelities Total time for adding SS restraints: 174.75 Time building geometry restraints manager: 38.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 12728 1.33 - 1.45: 42638 1.45 - 1.57: 38202 1.57 - 1.69: 6089 1.69 - 1.81: 154 Bond restraints: 99811 Sorted by residual: bond pdb=" C GLY Y 85 " pdb=" O GLY Y 85 " ideal model delta sigma weight residual 1.239 1.285 -0.046 7.10e-03 1.98e+04 4.26e+01 bond pdb=" N LEU X 160 " pdb=" CA LEU X 160 " ideal model delta sigma weight residual 1.455 1.437 0.018 7.00e-03 2.04e+04 6.67e+00 bond pdb=" CA VAL a 117 " pdb=" C VAL a 117 " ideal model delta sigma weight residual 1.522 1.539 -0.016 7.10e-03 1.98e+04 5.30e+00 bond pdb=" CA GLY Y 85 " pdb=" C GLY Y 85 " ideal model delta sigma weight residual 1.511 1.489 0.022 1.03e-02 9.43e+03 4.36e+00 bond pdb=" N9 G U1357 " pdb=" C4 G U1357 " ideal model delta sigma weight residual 1.375 1.343 0.032 2.00e-02 2.50e+03 2.57e+00 ... (remaining 99806 not shown) Histogram of bond angle deviations from ideal: 99.35 - 106.28: 17848 106.28 - 113.20: 58192 113.20 - 120.13: 36099 120.13 - 127.06: 30314 127.06 - 133.99: 7389 Bond angle restraints: 149842 Sorted by residual: angle pdb=" N GLU e 94 " pdb=" CA GLU e 94 " pdb=" C GLU e 94 " ideal model delta sigma weight residual 114.62 107.61 7.01 1.14e+00 7.69e-01 3.78e+01 angle pdb=" N VAL g 43 " pdb=" CA VAL g 43 " pdb=" C VAL g 43 " ideal model delta sigma weight residual 112.96 107.59 5.37 1.00e+00 1.00e+00 2.89e+01 angle pdb=" N VAL Z 146 " pdb=" CA VAL Z 146 " pdb=" C VAL Z 146 " ideal model delta sigma weight residual 111.77 106.79 4.98 1.04e+00 9.25e-01 2.30e+01 angle pdb=" C3' G U 646 " pdb=" C2' G U 646 " pdb=" C1' G U 646 " ideal model delta sigma weight residual 101.30 105.72 -4.42 1.00e+00 1.00e+00 1.95e+01 angle pdb=" C2' A U1024 " pdb=" C1' A U1024 " pdb=" N9 A U1024 " ideal model delta sigma weight residual 112.00 117.88 -5.88 1.50e+00 4.44e-01 1.54e+01 ... (remaining 149837 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.75: 56160 35.75 - 71.51: 6956 71.51 - 107.26: 821 107.26 - 143.01: 16 143.01 - 178.77: 38 Dihedral angle restraints: 63991 sinusoidal: 54450 harmonic: 9541 Sorted by residual: dihedral pdb=" O4' C U1513 " pdb=" C1' C U1513 " pdb=" N1 C U1513 " pdb=" C2 C U1513 " ideal model delta sinusoidal sigma weight residual -160.00 18.77 -178.77 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U U2417 " pdb=" C1' U U2417 " pdb=" N1 U U2417 " pdb=" C2 U U2417 " ideal model delta sinusoidal sigma weight residual -160.00 11.54 -171.54 1 1.50e+01 4.44e-03 8.49e+01 dihedral pdb=" O4' U U 890 " pdb=" C1' U U 890 " pdb=" N1 U U 890 " pdb=" C2 U U 890 " ideal model delta sinusoidal sigma weight residual -160.00 10.80 -170.80 1 1.50e+01 4.44e-03 8.48e+01 ... (remaining 63988 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 17475 0.062 - 0.125: 1519 0.125 - 0.187: 187 0.187 - 0.249: 37 0.249 - 0.311: 5 Chirality restraints: 19223 Sorted by residual: chirality pdb=" C1' A U1027 " pdb=" O4' A U1027 " pdb=" C2' A U1027 " pdb=" N9 A U1027 " both_signs ideal model delta sigma weight residual False 2.46 2.15 0.31 2.00e-01 2.50e+01 2.42e+00 chirality pdb=" C2' G U 646 " pdb=" C3' G U 646 " pdb=" O2' G U 646 " pdb=" C1' G U 646 " both_signs ideal model delta sigma weight residual False -2.75 -2.46 -0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" C1' A U1024 " pdb=" O4' A U1024 " pdb=" C2' A U1024 " pdb=" N9 A U1024 " both_signs ideal model delta sigma weight residual False 2.46 2.18 0.28 2.00e-01 2.50e+01 2.00e+00 ... (remaining 19220 not shown) Planarity restraints: 7620 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G U 294 " -0.042 2.00e-02 2.50e+03 1.93e-02 1.12e+01 pdb=" N9 G U 294 " 0.050 2.00e-02 2.50e+03 pdb=" C8 G U 294 " 0.003 2.00e-02 2.50e+03 pdb=" N7 G U 294 " -0.002 2.00e-02 2.50e+03 pdb=" C5 G U 294 " -0.002 2.00e-02 2.50e+03 pdb=" C6 G U 294 " -0.002 2.00e-02 2.50e+03 pdb=" O6 G U 294 " -0.012 2.00e-02 2.50e+03 pdb=" N1 G U 294 " -0.003 2.00e-02 2.50e+03 pdb=" C2 G U 294 " 0.001 2.00e-02 2.50e+03 pdb=" N2 G U 294 " 0.003 2.00e-02 2.50e+03 pdb=" N3 G U 294 " 0.005 2.00e-02 2.50e+03 pdb=" C4 G U 294 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A U1024 " 0.042 2.00e-02 2.50e+03 1.94e-02 1.04e+01 pdb=" N9 A U1024 " -0.046 2.00e-02 2.50e+03 pdb=" C8 A U1024 " -0.002 2.00e-02 2.50e+03 pdb=" N7 A U1024 " 0.001 2.00e-02 2.50e+03 pdb=" C5 A U1024 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A U1024 " 0.005 2.00e-02 2.50e+03 pdb=" N6 A U1024 " 0.010 2.00e-02 2.50e+03 pdb=" N1 A U1024 " 0.005 2.00e-02 2.50e+03 pdb=" C2 A U1024 " -0.003 2.00e-02 2.50e+03 pdb=" N3 A U1024 " -0.008 2.00e-02 2.50e+03 pdb=" C4 A U1024 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C U2374 " 0.036 2.00e-02 2.50e+03 1.95e-02 8.54e+00 pdb=" N1 C U2374 " -0.044 2.00e-02 2.50e+03 pdb=" C2 C U2374 " -0.005 2.00e-02 2.50e+03 pdb=" O2 C U2374 " -0.000 2.00e-02 2.50e+03 pdb=" N3 C U2374 " 0.002 2.00e-02 2.50e+03 pdb=" C4 C U2374 " 0.004 2.00e-02 2.50e+03 pdb=" N4 C U2374 " 0.010 2.00e-02 2.50e+03 pdb=" C5 C U2374 " 0.002 2.00e-02 2.50e+03 pdb=" C6 C U2374 " -0.004 2.00e-02 2.50e+03 ... (remaining 7617 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.50: 550 2.50 - 3.10: 59385 3.10 - 3.70: 159615 3.70 - 4.30: 246177 4.30 - 4.90: 338646 Nonbonded interactions: 804373 Sorted by model distance: nonbonded pdb=" OP2 U U1690 " pdb="MG MG U3108 " model vdw 1.905 2.170 nonbonded pdb=" OP1 A U2925 " pdb="MG MG U3214 " model vdw 1.943 2.170 nonbonded pdb=" OP2 A U 467 " pdb="MG MG U3020 " model vdw 1.947 2.170 nonbonded pdb=" OP2 G U 837 " pdb="MG MG U3069 " model vdw 1.959 2.170 nonbonded pdb=" OP2 A U 651 " pdb="MG MG U3053 " model vdw 1.960 2.170 ... (remaining 804368 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'H' selection = (chain 'I' and resid 3 through 134) } 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: 2.380 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: 0.080 Extract box with map and model: 12.620 Check model and map are aligned: 1.020 Set scattering table: 0.660 Process input model: 350.980 Find NCS groups from input model: 1.610 Set up NCS constraints: 0.220 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:2.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 371.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 99811 Z= 0.213 Angle : 0.612 10.402 149842 Z= 0.330 Chirality : 0.037 0.311 19223 Planarity : 0.005 0.059 7620 Dihedral : 23.532 178.767 57857 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 0.11 % Allowed : 3.63 % Favored : 96.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.70 (0.11), residues: 3302 helix: -2.44 (0.13), residues: 927 sheet: -2.97 (0.19), residues: 572 loop : -3.67 (0.11), residues: 1803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP W 213 HIS 0.007 0.001 HIS W 142 PHE 0.014 0.001 PHE g 84 TYR 0.013 0.001 TYR o 54 ARG 0.016 0.000 ARG b 62 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 694 residues out of total 2807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 691 time to evaluate : 3.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE d 122 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS l 110 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU n 101 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THR q 48 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE s 65 " (corrupted residue). Skipping it. REVERT: X 29 GLU cc_start: 0.7106 (pp20) cc_final: 0.6885 (pp20) REVERT: X 95 GLN cc_start: 0.8813 (tt0) cc_final: 0.8553 (tt0) REVERT: Y 174 THR cc_start: 0.8530 (p) cc_final: 0.8323 (p) REVERT: Y 201 LYS cc_start: 0.8481 (tptp) cc_final: 0.8245 (tptm) REVERT: a 118 PRO cc_start: 0.8893 (Cg_endo) cc_final: 0.8548 (Cg_exo) REVERT: a 158 TYR cc_start: 0.8201 (m-80) cc_final: 0.7966 (m-80) REVERT: c 74 ILE cc_start: 0.9134 (mm) cc_final: 0.8878 (mm) REVERT: g 87 ILE cc_start: 0.8493 (mp) cc_final: 0.8273 (mt) REVERT: g 110 ASP cc_start: 0.8875 (p0) cc_final: 0.8596 (p0) REVERT: k 101 ASN cc_start: 0.7952 (m-40) cc_final: 0.7719 (m-40) REVERT: l 35 ILE cc_start: 0.9051 (mm) cc_final: 0.8775 (mt) REVERT: o 76 LYS cc_start: 0.8313 (mmtt) cc_final: 0.8089 (mmtp) REVERT: o 85 LYS cc_start: 0.8516 (mttp) cc_final: 0.8279 (mttp) REVERT: p 11 MET cc_start: 0.8503 (ttt) cc_final: 0.8280 (ttp) REVERT: w 10 ARG cc_start: 0.8067 (mmt180) cc_final: 0.7829 (mmt90) REVERT: w 44 ARG cc_start: 0.7735 (tpp-160) cc_final: 0.7509 (mtp85) outliers start: 3 outliers final: 2 residues processed: 694 average time/residue: 0.9809 time to fit residues: 1110.4544 Evaluate side-chains 580 residues out of total 2807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 578 time to evaluate : 3.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 122 ILE Chi-restraints excluded: chain q residue 48 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 626 random chunks: chunk 528 optimal weight: 5.9990 chunk 474 optimal weight: 4.9990 chunk 263 optimal weight: 10.0000 chunk 162 optimal weight: 7.9990 chunk 320 optimal weight: 10.0000 chunk 253 optimal weight: 100.0000 chunk 490 optimal weight: 9.9990 chunk 189 optimal weight: 10.0000 chunk 298 optimal weight: 6.9990 chunk 365 optimal weight: 0.2980 chunk 568 optimal weight: 4.9990 overall best weight: 4.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 97 ASN b 102 ASN H 33 HIS H 58 GLN H 68 GLN I 32 HIS I 43 ASN I 46 HIS I 58 GLN I 67 ASN I 93 ASN I 97 GLN W 58 HIS W 163 GLN ** W 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 126 HIS X 173 ASN Y 9 GLN Z 9 ASN ** Z 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 63 GLN Z 161 ASN a 75 ASN c 8 ASN c 59 ASN e 38 GLN e 39 ASN e 78 ASN h 43 GLN ** i 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 44 GLN j 37 GLN j 52 GLN k 86 GLN l 28 GLN n 64 HIS n 99 GLN p 40 HIS q 16 ASN q 22 ASN q 45 HIS s 35 ASN s 64 ASN t 36 GLN u 20 HIS ** u 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 65 ASN w 33 GLN w 37 HIS w 59 GLN Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.0991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.082 99811 Z= 0.405 Angle : 0.721 10.410 149842 Z= 0.366 Chirality : 0.044 0.375 19223 Planarity : 0.006 0.063 7620 Dihedral : 23.859 179.348 51106 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.69 % Favored : 91.31 % Rotamer: Outliers : 2.57 % Allowed : 12.22 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -3.68 (0.12), residues: 3302 helix: -1.24 (0.16), residues: 944 sheet: -2.27 (0.21), residues: 548 loop : -3.30 (0.11), residues: 1810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP W 213 HIS 0.009 0.002 HIS Y 49 PHE 0.022 0.002 PHE j 57 TYR 0.017 0.002 TYR o 54 ARG 0.010 0.001 ARG i 97 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 651 residues out of total 2807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 579 time to evaluate : 3.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE d 122 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS l 110 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU n 101 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE s 65 " (corrupted residue). Skipping it. REVERT: X 95 GLN cc_start: 0.8824 (tt0) cc_final: 0.8581 (tt0) REVERT: Y 144 LYS cc_start: 0.8224 (tppt) cc_final: 0.7967 (tppt) REVERT: a 118 PRO cc_start: 0.8870 (Cg_endo) cc_final: 0.8565 (Cg_exo) REVERT: c 74 ILE cc_start: 0.9066 (mm) cc_final: 0.8837 (mm) REVERT: g 110 ASP cc_start: 0.8879 (p0) cc_final: 0.8612 (p0) REVERT: h 39 HIS cc_start: 0.8274 (m-70) cc_final: 0.7970 (m90) REVERT: i 63 THR cc_start: 0.9026 (m) cc_final: 0.8813 (m) REVERT: k 101 ASN cc_start: 0.8031 (m-40) cc_final: 0.7807 (m110) REVERT: l 35 ILE cc_start: 0.9026 (mm) cc_final: 0.8809 (mt) REVERT: o 85 LYS cc_start: 0.8522 (mttp) cc_final: 0.8226 (mttp) REVERT: r 22 MET cc_start: 0.8486 (ttm) cc_final: 0.8277 (ttm) REVERT: w 10 ARG cc_start: 0.8076 (mmt180) cc_final: 0.7858 (mmt90) REVERT: w 44 ARG cc_start: 0.7738 (tpp-160) cc_final: 0.7418 (mmt180) outliers start: 72 outliers final: 56 residues processed: 612 average time/residue: 0.9299 time to fit residues: 942.7843 Evaluate side-chains 606 residues out of total 2807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 550 time to evaluate : 3.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 62 ARG Chi-restraints excluded: chain I residue 50 SER Chi-restraints excluded: chain I residue 52 ILE Chi-restraints excluded: chain W residue 219 THR Chi-restraints excluded: chain W residue 224 VAL Chi-restraints excluded: chain W residue 262 LYS Chi-restraints excluded: chain Y residue 118 VAL Chi-restraints excluded: chain Y residue 195 THR Chi-restraints excluded: chain Z residue 156 ILE Chi-restraints excluded: chain a residue 72 LEU Chi-restraints excluded: chain a residue 91 VAL Chi-restraints excluded: chain c residue 18 VAL Chi-restraints excluded: chain c residue 87 SER Chi-restraints excluded: chain c residue 102 LEU Chi-restraints excluded: chain c residue 114 SER Chi-restraints excluded: chain d residue 35 ILE Chi-restraints excluded: chain d residue 77 ILE Chi-restraints excluded: chain d residue 78 SER Chi-restraints excluded: chain d residue 114 ILE Chi-restraints excluded: chain d residue 122 ILE Chi-restraints excluded: chain e residue 19 VAL Chi-restraints excluded: chain e residue 30 THR Chi-restraints excluded: chain e residue 105 LEU Chi-restraints excluded: chain e residue 109 VAL Chi-restraints excluded: chain f residue 25 THR Chi-restraints excluded: chain f residue 27 VAL Chi-restraints excluded: chain f residue 28 HIS Chi-restraints excluded: chain g residue 70 VAL Chi-restraints excluded: chain g residue 81 GLN Chi-restraints excluded: chain h residue 77 VAL Chi-restraints excluded: chain h residue 94 VAL Chi-restraints excluded: chain i residue 61 THR Chi-restraints excluded: chain i residue 76 THR Chi-restraints excluded: chain i residue 95 VAL Chi-restraints excluded: chain j residue 4 VAL Chi-restraints excluded: chain j residue 10 THR Chi-restraints excluded: chain j residue 86 SER Chi-restraints excluded: chain l residue 29 VAL Chi-restraints excluded: chain m residue 22 THR Chi-restraints excluded: chain m residue 63 SER Chi-restraints excluded: chain m residue 87 SER Chi-restraints excluded: chain n residue 22 THR Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain p residue 39 SER Chi-restraints excluded: chain p residue 48 SER Chi-restraints excluded: chain q residue 30 VAL Chi-restraints excluded: chain q residue 43 THR Chi-restraints excluded: chain q residue 44 LEU Chi-restraints excluded: chain s residue 49 VAL Chi-restraints excluded: chain u residue 28 THR Chi-restraints excluded: chain v residue 62 ILE Chi-restraints excluded: chain w residue 7 THR Chi-restraints excluded: chain w residue 33 GLN Chi-restraints excluded: chain w residue 37 HIS Chi-restraints excluded: chain w residue 54 VAL Chi-restraints excluded: chain w residue 56 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 626 random chunks: chunk 315 optimal weight: 7.9990 chunk 176 optimal weight: 4.9990 chunk 473 optimal weight: 0.7980 chunk 387 optimal weight: 0.9980 chunk 156 optimal weight: 4.9990 chunk 569 optimal weight: 2.9990 chunk 615 optimal weight: 2.9990 chunk 507 optimal weight: 5.9990 chunk 564 optimal weight: 0.8980 chunk 194 optimal weight: 10.0000 chunk 456 optimal weight: 3.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 67 ASN ** W 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 173 ASN Y 46 GLN ** Z 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 62 HIS ** i 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 29 HIS ** k 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 64 ASN ** u 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 65 ASN w 33 GLN w 59 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 99811 Z= 0.182 Angle : 0.569 10.399 149842 Z= 0.295 Chirality : 0.035 0.292 19223 Planarity : 0.004 0.050 7620 Dihedral : 23.678 179.438 51105 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 2.49 % Allowed : 14.96 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -3.01 (0.13), residues: 3302 helix: -0.60 (0.17), residues: 948 sheet: -1.91 (0.21), residues: 551 loop : -2.93 (0.12), residues: 1803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP W 213 HIS 0.010 0.001 HIS w 37 PHE 0.017 0.001 PHE Z 20 TYR 0.014 0.001 TYR Z 97 ARG 0.010 0.000 ARG i 42 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 2807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 590 time to evaluate : 3.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS l 110 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU n 101 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE s 65 " (corrupted residue). Skipping it. REVERT: X 95 GLN cc_start: 0.8735 (tt0) cc_final: 0.8515 (tt0) REVERT: X 140 HIS cc_start: 0.7983 (OUTLIER) cc_final: 0.7083 (p-80) REVERT: Z 141 ILE cc_start: -0.0438 (OUTLIER) cc_final: -0.0818 (mm) REVERT: c 74 ILE cc_start: 0.8951 (mm) cc_final: 0.8738 (mm) REVERT: d 66 LYS cc_start: 0.8449 (mtpp) cc_final: 0.8172 (tttt) REVERT: f 82 ARG cc_start: 0.7980 (mmt180) cc_final: 0.7736 (mmt180) REVERT: g 110 ASP cc_start: 0.8758 (p0) cc_final: 0.8504 (p0) REVERT: h 1 MET cc_start: 0.3758 (mtt) cc_final: 0.3507 (mtt) REVERT: l 35 ILE cc_start: 0.8919 (mm) cc_final: 0.8653 (mt) REVERT: n 40 MET cc_start: 0.7979 (mmp) cc_final: 0.7535 (mmt) REVERT: o 79 ARG cc_start: 0.7369 (ptt180) cc_final: 0.7151 (ptt180) REVERT: o 85 LYS cc_start: 0.8428 (mttp) cc_final: 0.8115 (mttp) REVERT: w 10 ARG cc_start: 0.8010 (mmt180) cc_final: 0.7806 (mmt90) outliers start: 70 outliers final: 53 residues processed: 625 average time/residue: 0.9206 time to fit residues: 954.3678 Evaluate side-chains 621 residues out of total 2807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 566 time to evaluate : 3.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 62 ARG Chi-restraints excluded: chain I residue 50 SER Chi-restraints excluded: chain W residue 141 VAL Chi-restraints excluded: chain W residue 262 LYS Chi-restraints excluded: chain X residue 83 LEU Chi-restraints excluded: chain X residue 140 HIS Chi-restraints excluded: chain X residue 206 VAL Chi-restraints excluded: chain Y residue 118 VAL Chi-restraints excluded: chain Y residue 174 THR Chi-restraints excluded: chain Z residue 35 VAL Chi-restraints excluded: chain Z residue 36 ILE Chi-restraints excluded: chain Z residue 67 VAL Chi-restraints excluded: chain Z residue 141 ILE Chi-restraints excluded: chain Z residue 156 ILE Chi-restraints excluded: chain a residue 91 VAL Chi-restraints excluded: chain a residue 117 VAL Chi-restraints excluded: chain a residue 124 ILE Chi-restraints excluded: chain c residue 6 MET Chi-restraints excluded: chain c residue 102 LEU Chi-restraints excluded: chain c residue 104 LEU Chi-restraints excluded: chain c residue 114 SER Chi-restraints excluded: chain d residue 9 LYS Chi-restraints excluded: chain d residue 77 ILE Chi-restraints excluded: chain d residue 78 SER Chi-restraints excluded: chain e residue 19 VAL Chi-restraints excluded: chain e residue 30 THR Chi-restraints excluded: chain f residue 25 THR Chi-restraints excluded: chain f residue 27 VAL Chi-restraints excluded: chain f residue 120 LEU Chi-restraints excluded: chain g residue 70 VAL Chi-restraints excluded: chain g residue 81 GLN Chi-restraints excluded: chain h residue 57 SER Chi-restraints excluded: chain h residue 77 VAL Chi-restraints excluded: chain h residue 94 VAL Chi-restraints excluded: chain h residue 111 ASP Chi-restraints excluded: chain i residue 61 THR Chi-restraints excluded: chain i residue 76 THR Chi-restraints excluded: chain i residue 95 VAL Chi-restraints excluded: chain j residue 4 VAL Chi-restraints excluded: chain j residue 10 THR Chi-restraints excluded: chain j residue 86 SER Chi-restraints excluded: chain j residue 90 VAL Chi-restraints excluded: chain n residue 16 ASP Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain p residue 39 SER Chi-restraints excluded: chain q residue 30 VAL Chi-restraints excluded: chain q residue 43 THR Chi-restraints excluded: chain q residue 44 LEU Chi-restraints excluded: chain r residue 41 VAL Chi-restraints excluded: chain s residue 49 VAL Chi-restraints excluded: chain u residue 28 THR Chi-restraints excluded: chain v residue 57 ILE Chi-restraints excluded: chain v residue 62 ILE Chi-restraints excluded: chain w residue 54 VAL Chi-restraints excluded: chain w residue 56 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 626 random chunks: chunk 562 optimal weight: 1.9990 chunk 428 optimal weight: 7.9990 chunk 295 optimal weight: 6.9990 chunk 63 optimal weight: 5.9990 chunk 271 optimal weight: 30.0000 chunk 382 optimal weight: 6.9990 chunk 571 optimal weight: 10.0000 chunk 605 optimal weight: 4.9990 chunk 298 optimal weight: 6.9990 chunk 541 optimal weight: 4.9990 chunk 163 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 163 GLN ** W 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 173 ASN ** Z 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 96 ASN ** q 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 64 ASN ** u 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 27 ASN v 65 ASN w 19 GLN w 52 HIS w 59 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.086 99811 Z= 0.430 Angle : 0.729 10.722 149842 Z= 0.368 Chirality : 0.044 0.389 19223 Planarity : 0.006 0.065 7620 Dihedral : 23.746 179.100 51103 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 3.67 % Allowed : 15.89 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.90 (0.13), residues: 3302 helix: -0.52 (0.17), residues: 951 sheet: -1.88 (0.21), residues: 559 loop : -2.84 (0.12), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP W 213 HIS 0.012 0.002 HIS Y 49 PHE 0.024 0.002 PHE j 57 TYR 0.014 0.002 TYR Z 97 ARG 0.009 0.001 ARG i 97 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 664 residues out of total 2807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 561 time to evaluate : 3.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS l 110 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU n 101 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THR q 48 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE s 65 " (corrupted residue). Skipping it. REVERT: I 101 TYR cc_start: 0.8571 (m-80) cc_final: 0.8185 (m-80) REVERT: Z 26 MET cc_start: 0.7595 (mtt) cc_final: 0.7250 (mtt) REVERT: Z 141 ILE cc_start: -0.0346 (OUTLIER) cc_final: -0.0745 (mm) REVERT: Z 153 ASP cc_start: 0.7669 (OUTLIER) cc_final: 0.7252 (m-30) REVERT: c 74 ILE cc_start: 0.9035 (mm) cc_final: 0.8813 (mm) REVERT: d 66 LYS cc_start: 0.8548 (mtpp) cc_final: 0.8313 (tttm) REVERT: e 105 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8520 (mp) REVERT: e 134 GLU cc_start: 0.7378 (tp30) cc_final: 0.7169 (tp30) REVERT: g 34 GLU cc_start: 0.7717 (tp30) cc_final: 0.7330 (tp30) REVERT: h 1 MET cc_start: 0.3662 (mtt) cc_final: 0.3415 (mtt) REVERT: m 52 ASP cc_start: 0.7798 (t0) cc_final: 0.7572 (t0) REVERT: o 79 ARG cc_start: 0.7494 (ptt180) cc_final: 0.7220 (ptt180) REVERT: o 85 LYS cc_start: 0.8458 (mttp) cc_final: 0.8177 (mttp) REVERT: w 24 ARG cc_start: 0.8155 (tpp80) cc_final: 0.7933 (tpt90) REVERT: w 29 LYS cc_start: 0.8006 (mttm) cc_final: 0.7727 (mttm) outliers start: 103 outliers final: 83 residues processed: 616 average time/residue: 0.9173 time to fit residues: 942.0025 Evaluate side-chains 627 residues out of total 2807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 541 time to evaluate : 3.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 62 ARG Chi-restraints excluded: chain I residue 50 SER Chi-restraints excluded: chain I residue 52 ILE Chi-restraints excluded: chain W residue 141 VAL Chi-restraints excluded: chain W residue 219 THR Chi-restraints excluded: chain W residue 262 LYS Chi-restraints excluded: chain X residue 83 LEU Chi-restraints excluded: chain X residue 99 VAL Chi-restraints excluded: chain X residue 140 HIS Chi-restraints excluded: chain X residue 184 ASN Chi-restraints excluded: chain X residue 206 VAL Chi-restraints excluded: chain Y residue 118 VAL Chi-restraints excluded: chain Y residue 163 VAL Chi-restraints excluded: chain Y residue 195 THR Chi-restraints excluded: chain Z residue 34 ILE Chi-restraints excluded: chain Z residue 35 VAL Chi-restraints excluded: chain Z residue 36 ILE Chi-restraints excluded: chain Z residue 54 VAL Chi-restraints excluded: chain Z residue 67 VAL Chi-restraints excluded: chain Z residue 141 ILE Chi-restraints excluded: chain Z residue 153 ASP Chi-restraints excluded: chain Z residue 156 ILE Chi-restraints excluded: chain a residue 71 SER Chi-restraints excluded: chain a residue 72 LEU Chi-restraints excluded: chain a residue 91 VAL Chi-restraints excluded: chain a residue 117 VAL Chi-restraints excluded: chain c residue 6 MET Chi-restraints excluded: chain c residue 46 THR Chi-restraints excluded: chain c residue 87 SER Chi-restraints excluded: chain c residue 102 LEU Chi-restraints excluded: chain c residue 104 LEU Chi-restraints excluded: chain c residue 114 SER Chi-restraints excluded: chain d residue 9 LYS Chi-restraints excluded: chain d residue 18 GLU Chi-restraints excluded: chain d residue 77 ILE Chi-restraints excluded: chain d residue 78 SER Chi-restraints excluded: chain d residue 110 ASN Chi-restraints excluded: chain e residue 19 VAL Chi-restraints excluded: chain e residue 30 THR Chi-restraints excluded: chain e residue 105 LEU Chi-restraints excluded: chain e residue 109 VAL Chi-restraints excluded: chain f residue 25 THR Chi-restraints excluded: chain f residue 27 VAL Chi-restraints excluded: chain f residue 28 HIS Chi-restraints excluded: chain f residue 128 LYS Chi-restraints excluded: chain g residue 10 SER Chi-restraints excluded: chain g residue 70 VAL Chi-restraints excluded: chain g residue 81 GLN Chi-restraints excluded: chain h residue 57 SER Chi-restraints excluded: chain h residue 65 VAL Chi-restraints excluded: chain h residue 77 VAL Chi-restraints excluded: chain h residue 94 VAL Chi-restraints excluded: chain i residue 61 THR Chi-restraints excluded: chain i residue 76 THR Chi-restraints excluded: chain i residue 95 VAL Chi-restraints excluded: chain j residue 4 VAL Chi-restraints excluded: chain j residue 10 THR Chi-restraints excluded: chain j residue 86 SER Chi-restraints excluded: chain j residue 90 VAL Chi-restraints excluded: chain k residue 19 THR Chi-restraints excluded: chain k residue 39 LEU Chi-restraints excluded: chain l residue 29 VAL Chi-restraints excluded: chain l residue 48 GLU Chi-restraints excluded: chain l residue 104 THR Chi-restraints excluded: chain m residue 22 THR Chi-restraints excluded: chain m residue 63 SER Chi-restraints excluded: chain n residue 16 ASP Chi-restraints excluded: chain n residue 22 THR Chi-restraints excluded: chain n residue 41 VAL Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain p residue 18 THR Chi-restraints excluded: chain p residue 39 SER Chi-restraints excluded: chain p residue 48 SER Chi-restraints excluded: chain p residue 53 ASP Chi-restraints excluded: chain q residue 30 VAL Chi-restraints excluded: chain q residue 43 THR Chi-restraints excluded: chain q residue 44 LEU Chi-restraints excluded: chain q residue 48 THR Chi-restraints excluded: chain r residue 41 VAL Chi-restraints excluded: chain s residue 49 VAL Chi-restraints excluded: chain u residue 28 THR Chi-restraints excluded: chain v residue 1 MET Chi-restraints excluded: chain v residue 62 ILE Chi-restraints excluded: chain w residue 7 THR Chi-restraints excluded: chain w residue 54 VAL Chi-restraints excluded: chain w residue 56 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 626 random chunks: chunk 503 optimal weight: 8.9990 chunk 343 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 450 optimal weight: 0.6980 chunk 249 optimal weight: 6.9990 chunk 516 optimal weight: 10.0000 chunk 418 optimal weight: 5.9990 chunk 0 optimal weight: 60.0000 chunk 308 optimal weight: 7.9990 chunk 543 optimal weight: 5.9990 chunk 152 optimal weight: 50.0000 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 173 ASN ** Z 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 96 ASN ** k 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 27 ASN v 65 ASN w 19 GLN w 59 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 99811 Z= 0.309 Angle : 0.659 10.475 149842 Z= 0.338 Chirality : 0.040 0.353 19223 Planarity : 0.005 0.047 7620 Dihedral : 23.729 178.874 51103 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 3.74 % Allowed : 17.46 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.71 (0.13), residues: 3302 helix: -0.39 (0.17), residues: 952 sheet: -1.69 (0.21), residues: 573 loop : -2.72 (0.12), residues: 1777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP W 213 HIS 0.007 0.001 HIS W 142 PHE 0.019 0.002 PHE Z 20 TYR 0.017 0.002 TYR Z 97 ARG 0.011 0.001 ARG H 83 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 657 residues out of total 2807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 552 time to evaluate : 3.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS l 110 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU n 101 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THR q 48 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE s 65 " (corrupted residue). Skipping it. REVERT: Z 26 MET cc_start: 0.7607 (mtt) cc_final: 0.7227 (mtt) REVERT: Z 141 ILE cc_start: -0.0375 (OUTLIER) cc_final: -0.0758 (mm) REVERT: Z 152 MET cc_start: 0.6478 (mmp) cc_final: 0.6150 (mmp) REVERT: c 74 ILE cc_start: 0.9019 (mm) cc_final: 0.8803 (mm) REVERT: d 66 LYS cc_start: 0.8519 (mtpp) cc_final: 0.8260 (tttt) REVERT: e 105 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8521 (mp) REVERT: g 34 GLU cc_start: 0.7729 (tp30) cc_final: 0.7365 (tp30) REVERT: n 40 MET cc_start: 0.7988 (mmt) cc_final: 0.7762 (mmp) REVERT: o 19 LYS cc_start: 0.7759 (mtmm) cc_final: 0.7482 (mtmm) REVERT: o 85 LYS cc_start: 0.8436 (mttp) cc_final: 0.8156 (mttp) outliers start: 105 outliers final: 92 residues processed: 608 average time/residue: 0.9404 time to fit residues: 950.4064 Evaluate side-chains 641 residues out of total 2807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 547 time to evaluate : 3.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 62 ARG Chi-restraints excluded: chain I residue 50 SER Chi-restraints excluded: chain I residue 52 ILE Chi-restraints excluded: chain W residue 141 VAL Chi-restraints excluded: chain W residue 195 VAL Chi-restraints excluded: chain W residue 219 THR Chi-restraints excluded: chain W residue 262 LYS Chi-restraints excluded: chain X residue 25 VAL Chi-restraints excluded: chain X residue 83 LEU Chi-restraints excluded: chain X residue 99 VAL Chi-restraints excluded: chain X residue 140 HIS Chi-restraints excluded: chain X residue 206 VAL Chi-restraints excluded: chain Y residue 38 LEU Chi-restraints excluded: chain Y residue 118 VAL Chi-restraints excluded: chain Y residue 125 VAL Chi-restraints excluded: chain Y residue 163 VAL Chi-restraints excluded: chain Z residue 35 VAL Chi-restraints excluded: chain Z residue 36 ILE Chi-restraints excluded: chain Z residue 54 VAL Chi-restraints excluded: chain Z residue 67 VAL Chi-restraints excluded: chain Z residue 141 ILE Chi-restraints excluded: chain Z residue 156 ILE Chi-restraints excluded: chain a residue 4 VAL Chi-restraints excluded: chain a residue 71 SER Chi-restraints excluded: chain a residue 72 LEU Chi-restraints excluded: chain a residue 91 VAL Chi-restraints excluded: chain a residue 117 VAL Chi-restraints excluded: chain a residue 132 VAL Chi-restraints excluded: chain c residue 6 MET Chi-restraints excluded: chain c residue 46 THR Chi-restraints excluded: chain c residue 102 LEU Chi-restraints excluded: chain c residue 104 LEU Chi-restraints excluded: chain c residue 114 SER Chi-restraints excluded: chain d residue 9 LYS Chi-restraints excluded: chain d residue 18 GLU Chi-restraints excluded: chain d residue 77 ILE Chi-restraints excluded: chain d residue 78 SER Chi-restraints excluded: chain d residue 110 ASN Chi-restraints excluded: chain d residue 116 SER Chi-restraints excluded: chain e residue 19 VAL Chi-restraints excluded: chain e residue 30 THR Chi-restraints excluded: chain e residue 105 LEU Chi-restraints excluded: chain e residue 109 VAL Chi-restraints excluded: chain f residue 25 THR Chi-restraints excluded: chain f residue 27 VAL Chi-restraints excluded: chain f residue 120 LEU Chi-restraints excluded: chain f residue 128 LYS Chi-restraints excluded: chain g residue 10 SER Chi-restraints excluded: chain g residue 31 GLU Chi-restraints excluded: chain g residue 70 VAL Chi-restraints excluded: chain g residue 81 GLN Chi-restraints excluded: chain h residue 65 VAL Chi-restraints excluded: chain h residue 77 VAL Chi-restraints excluded: chain h residue 94 VAL Chi-restraints excluded: chain h residue 111 ASP Chi-restraints excluded: chain i residue 61 THR Chi-restraints excluded: chain i residue 76 THR Chi-restraints excluded: chain i residue 95 VAL Chi-restraints excluded: chain j residue 4 VAL Chi-restraints excluded: chain j residue 10 THR Chi-restraints excluded: chain j residue 86 SER Chi-restraints excluded: chain j residue 90 VAL Chi-restraints excluded: chain k residue 7 THR Chi-restraints excluded: chain k residue 19 THR Chi-restraints excluded: chain k residue 39 LEU Chi-restraints excluded: chain l residue 29 VAL Chi-restraints excluded: chain l residue 48 GLU Chi-restraints excluded: chain m residue 22 THR Chi-restraints excluded: chain m residue 63 SER Chi-restraints excluded: chain m residue 87 SER Chi-restraints excluded: chain n residue 16 ASP Chi-restraints excluded: chain n residue 22 THR Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain n residue 41 VAL Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain p residue 24 VAL Chi-restraints excluded: chain p residue 39 SER Chi-restraints excluded: chain p residue 48 SER Chi-restraints excluded: chain p residue 53 ASP Chi-restraints excluded: chain q residue 30 VAL Chi-restraints excluded: chain q residue 43 THR Chi-restraints excluded: chain q residue 44 LEU Chi-restraints excluded: chain q residue 48 THR Chi-restraints excluded: chain r residue 20 SER Chi-restraints excluded: chain r residue 41 VAL Chi-restraints excluded: chain s residue 29 THR Chi-restraints excluded: chain s residue 49 VAL Chi-restraints excluded: chain u residue 22 MET Chi-restraints excluded: chain u residue 28 THR Chi-restraints excluded: chain v residue 1 MET Chi-restraints excluded: chain v residue 62 ILE Chi-restraints excluded: chain w residue 49 LYS Chi-restraints excluded: chain w residue 54 VAL Chi-restraints excluded: chain w residue 56 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 626 random chunks: chunk 203 optimal weight: 5.9990 chunk 544 optimal weight: 6.9990 chunk 119 optimal weight: 5.9990 chunk 355 optimal weight: 3.9990 chunk 149 optimal weight: 70.0000 chunk 605 optimal weight: 0.9990 chunk 502 optimal weight: 8.9990 chunk 280 optimal weight: 6.9990 chunk 50 optimal weight: 6.9990 chunk 200 optimal weight: 7.9990 chunk 317 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 173 ASN ** Z 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 96 ASN ** k 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 61 ASN ** q 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 65 ASN w 59 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.086 99811 Z= 0.414 Angle : 0.715 10.355 149842 Z= 0.362 Chirality : 0.043 0.377 19223 Planarity : 0.005 0.062 7620 Dihedral : 23.725 179.043 51103 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 4.28 % Allowed : 17.99 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.63 (0.13), residues: 3302 helix: -0.34 (0.17), residues: 943 sheet: -1.63 (0.21), residues: 575 loop : -2.67 (0.12), residues: 1784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP W 213 HIS 0.008 0.002 HIS Y 49 PHE 0.026 0.002 PHE H 64 TYR 0.015 0.002 TYR Y 99 ARG 0.007 0.001 ARG i 97 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 675 residues out of total 2807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 555 time to evaluate : 5.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS l 110 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU n 101 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL o 92 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THR q 48 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE s 65 " (corrupted residue). Skipping it. REVERT: I 1 MET cc_start: 0.5124 (mmm) cc_final: 0.4859 (mmp) REVERT: I 101 TYR cc_start: 0.8590 (m-80) cc_final: 0.8216 (m-80) REVERT: Z 26 MET cc_start: 0.7557 (mtt) cc_final: 0.7312 (mtt) REVERT: Z 141 ILE cc_start: -0.0310 (OUTLIER) cc_final: -0.0734 (mm) REVERT: Z 152 MET cc_start: 0.6448 (mmp) cc_final: 0.6129 (mmp) REVERT: c 74 ILE cc_start: 0.9030 (mm) cc_final: 0.8811 (mm) REVERT: e 105 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8588 (mp) REVERT: g 34 GLU cc_start: 0.7818 (tp30) cc_final: 0.7422 (tp30) REVERT: g 118 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.6928 (pm20) REVERT: i 42 ARG cc_start: 0.7156 (mtt-85) cc_final: 0.6762 (mtt-85) REVERT: o 19 LYS cc_start: 0.7763 (OUTLIER) cc_final: 0.7539 (mtmm) REVERT: o 85 LYS cc_start: 0.8442 (mttp) cc_final: 0.8172 (mttp) REVERT: q 38 ARG cc_start: 0.7653 (ttm-80) cc_final: 0.7356 (ttm-80) outliers start: 120 outliers final: 101 residues processed: 625 average time/residue: 0.9265 time to fit residues: 965.3309 Evaluate side-chains 651 residues out of total 2807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 546 time to evaluate : 3.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 62 ARG Chi-restraints excluded: chain I residue 50 SER Chi-restraints excluded: chain I residue 52 ILE Chi-restraints excluded: chain W residue 141 VAL Chi-restraints excluded: chain W residue 195 VAL Chi-restraints excluded: chain W residue 219 THR Chi-restraints excluded: chain W residue 224 VAL Chi-restraints excluded: chain W residue 262 LYS Chi-restraints excluded: chain X residue 25 VAL Chi-restraints excluded: chain X residue 83 LEU Chi-restraints excluded: chain X residue 99 VAL Chi-restraints excluded: chain X residue 140 HIS Chi-restraints excluded: chain X residue 206 VAL Chi-restraints excluded: chain Y residue 38 LEU Chi-restraints excluded: chain Y residue 118 VAL Chi-restraints excluded: chain Y residue 125 VAL Chi-restraints excluded: chain Y residue 163 VAL Chi-restraints excluded: chain Y residue 195 THR Chi-restraints excluded: chain Z residue 35 VAL Chi-restraints excluded: chain Z residue 36 ILE Chi-restraints excluded: chain Z residue 54 VAL Chi-restraints excluded: chain Z residue 67 VAL Chi-restraints excluded: chain Z residue 141 ILE Chi-restraints excluded: chain Z residue 156 ILE Chi-restraints excluded: chain a residue 4 VAL Chi-restraints excluded: chain a residue 71 SER Chi-restraints excluded: chain a residue 72 LEU Chi-restraints excluded: chain a residue 91 VAL Chi-restraints excluded: chain a residue 132 VAL Chi-restraints excluded: chain c residue 6 MET Chi-restraints excluded: chain c residue 18 VAL Chi-restraints excluded: chain c residue 46 THR Chi-restraints excluded: chain c residue 87 SER Chi-restraints excluded: chain c residue 102 LEU Chi-restraints excluded: chain c residue 104 LEU Chi-restraints excluded: chain c residue 114 SER Chi-restraints excluded: chain d residue 9 LYS Chi-restraints excluded: chain d residue 18 GLU Chi-restraints excluded: chain d residue 35 ILE Chi-restraints excluded: chain d residue 77 ILE Chi-restraints excluded: chain d residue 78 SER Chi-restraints excluded: chain d residue 110 ASN Chi-restraints excluded: chain e residue 19 VAL Chi-restraints excluded: chain e residue 30 THR Chi-restraints excluded: chain e residue 105 LEU Chi-restraints excluded: chain e residue 109 VAL Chi-restraints excluded: chain e residue 136 VAL Chi-restraints excluded: chain f residue 25 THR Chi-restraints excluded: chain f residue 27 VAL Chi-restraints excluded: chain f residue 28 HIS Chi-restraints excluded: chain f residue 45 ARG Chi-restraints excluded: chain f residue 128 LYS Chi-restraints excluded: chain g residue 10 SER Chi-restraints excluded: chain g residue 70 VAL Chi-restraints excluded: chain g residue 81 GLN Chi-restraints excluded: chain g residue 118 GLU Chi-restraints excluded: chain h residue 57 SER Chi-restraints excluded: chain h residue 65 VAL Chi-restraints excluded: chain h residue 77 VAL Chi-restraints excluded: chain h residue 94 VAL Chi-restraints excluded: chain h residue 111 ASP Chi-restraints excluded: chain i residue 59 SER Chi-restraints excluded: chain i residue 61 THR Chi-restraints excluded: chain i residue 76 THR Chi-restraints excluded: chain i residue 95 VAL Chi-restraints excluded: chain j residue 4 VAL Chi-restraints excluded: chain j residue 10 THR Chi-restraints excluded: chain j residue 86 SER Chi-restraints excluded: chain j residue 90 VAL Chi-restraints excluded: chain k residue 7 THR Chi-restraints excluded: chain k residue 19 THR Chi-restraints excluded: chain k residue 39 LEU Chi-restraints excluded: chain l residue 29 VAL Chi-restraints excluded: chain l residue 48 GLU Chi-restraints excluded: chain m residue 22 THR Chi-restraints excluded: chain m residue 56 ILE Chi-restraints excluded: chain m residue 63 SER Chi-restraints excluded: chain m residue 87 SER Chi-restraints excluded: chain n residue 16 ASP Chi-restraints excluded: chain n residue 22 THR Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain n residue 41 VAL Chi-restraints excluded: chain o residue 19 LYS Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain p residue 18 THR Chi-restraints excluded: chain p residue 24 VAL Chi-restraints excluded: chain p residue 39 SER Chi-restraints excluded: chain p residue 48 SER Chi-restraints excluded: chain p residue 53 ASP Chi-restraints excluded: chain q residue 30 VAL Chi-restraints excluded: chain q residue 43 THR Chi-restraints excluded: chain q residue 44 LEU Chi-restraints excluded: chain q residue 48 THR Chi-restraints excluded: chain r residue 41 VAL Chi-restraints excluded: chain s residue 29 THR Chi-restraints excluded: chain s residue 49 VAL Chi-restraints excluded: chain u residue 22 MET Chi-restraints excluded: chain u residue 28 THR Chi-restraints excluded: chain v residue 1 MET Chi-restraints excluded: chain v residue 62 ILE Chi-restraints excluded: chain w residue 7 THR Chi-restraints excluded: chain w residue 22 THR Chi-restraints excluded: chain w residue 49 LYS Chi-restraints excluded: chain w residue 54 VAL Chi-restraints excluded: chain w residue 56 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 626 random chunks: chunk 583 optimal weight: 2.9990 chunk 68 optimal weight: 10.0000 chunk 345 optimal weight: 2.9990 chunk 442 optimal weight: 9.9990 chunk 342 optimal weight: 8.9990 chunk 509 optimal weight: 4.9990 chunk 338 optimal weight: 8.9990 chunk 603 optimal weight: 2.9990 chunk 377 optimal weight: 2.9990 chunk 367 optimal weight: 3.9990 chunk 278 optimal weight: 7.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 173 ASN ** Z 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 96 ASN ** k 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 65 ASN w 59 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 99811 Z= 0.285 Angle : 0.633 10.330 149842 Z= 0.325 Chirality : 0.039 0.323 19223 Planarity : 0.005 0.047 7620 Dihedral : 23.670 179.134 51103 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 4.10 % Allowed : 19.17 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.44 (0.14), residues: 3302 helix: -0.17 (0.17), residues: 940 sheet: -1.43 (0.22), residues: 571 loop : -2.58 (0.12), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP W 213 HIS 0.007 0.001 HIS W 142 PHE 0.032 0.002 PHE H 64 TYR 0.015 0.001 TYR Z 97 ARG 0.006 0.000 ARG j 78 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 677 residues out of total 2807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 562 time to evaluate : 3.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS l 110 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU n 101 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL o 92 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THR q 48 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE s 65 " (corrupted residue). Skipping it. REVERT: Z 26 MET cc_start: 0.7532 (mtt) cc_final: 0.7278 (mtt) REVERT: Z 141 ILE cc_start: -0.0334 (OUTLIER) cc_final: -0.0737 (mm) REVERT: Z 152 MET cc_start: 0.6415 (mmp) cc_final: 0.6118 (mmp) REVERT: c 74 ILE cc_start: 0.8994 (mm) cc_final: 0.8791 (mm) REVERT: g 34 GLU cc_start: 0.7768 (tp30) cc_final: 0.7395 (tp30) REVERT: g 118 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.6960 (pm20) REVERT: i 42 ARG cc_start: 0.7095 (mtt-85) cc_final: 0.6668 (mtt-85) REVERT: o 85 LYS cc_start: 0.8428 (mttp) cc_final: 0.8151 (mttp) outliers start: 115 outliers final: 102 residues processed: 627 average time/residue: 0.9231 time to fit residues: 966.5590 Evaluate side-chains 647 residues out of total 2807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 543 time to evaluate : 3.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 62 ARG Chi-restraints excluded: chain H residue 37 GLN Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain I residue 50 SER Chi-restraints excluded: chain I residue 52 ILE Chi-restraints excluded: chain W residue 141 VAL Chi-restraints excluded: chain W residue 195 VAL Chi-restraints excluded: chain W residue 219 THR Chi-restraints excluded: chain W residue 224 VAL Chi-restraints excluded: chain W residue 262 LYS Chi-restraints excluded: chain X residue 25 VAL Chi-restraints excluded: chain X residue 83 LEU Chi-restraints excluded: chain X residue 99 VAL Chi-restraints excluded: chain X residue 140 HIS Chi-restraints excluded: chain X residue 206 VAL Chi-restraints excluded: chain Y residue 38 LEU Chi-restraints excluded: chain Y residue 118 VAL Chi-restraints excluded: chain Y residue 125 VAL Chi-restraints excluded: chain Y residue 136 THR Chi-restraints excluded: chain Y residue 156 THR Chi-restraints excluded: chain Y residue 163 VAL Chi-restraints excluded: chain Z residue 35 VAL Chi-restraints excluded: chain Z residue 36 ILE Chi-restraints excluded: chain Z residue 54 VAL Chi-restraints excluded: chain Z residue 67 VAL Chi-restraints excluded: chain Z residue 141 ILE Chi-restraints excluded: chain Z residue 156 ILE Chi-restraints excluded: chain a residue 4 VAL Chi-restraints excluded: chain a residue 91 VAL Chi-restraints excluded: chain a residue 132 VAL Chi-restraints excluded: chain c residue 6 MET Chi-restraints excluded: chain c residue 46 THR Chi-restraints excluded: chain c residue 87 SER Chi-restraints excluded: chain c residue 102 LEU Chi-restraints excluded: chain c residue 104 LEU Chi-restraints excluded: chain c residue 114 SER Chi-restraints excluded: chain d residue 9 LYS Chi-restraints excluded: chain d residue 18 GLU Chi-restraints excluded: chain d residue 35 ILE Chi-restraints excluded: chain d residue 77 ILE Chi-restraints excluded: chain d residue 78 SER Chi-restraints excluded: chain d residue 110 ASN Chi-restraints excluded: chain d residue 116 SER Chi-restraints excluded: chain e residue 19 VAL Chi-restraints excluded: chain e residue 30 THR Chi-restraints excluded: chain e residue 109 VAL Chi-restraints excluded: chain f residue 25 THR Chi-restraints excluded: chain f residue 27 VAL Chi-restraints excluded: chain f residue 120 LEU Chi-restraints excluded: chain f residue 128 LYS Chi-restraints excluded: chain g residue 10 SER Chi-restraints excluded: chain g residue 31 GLU Chi-restraints excluded: chain g residue 70 VAL Chi-restraints excluded: chain g residue 81 GLN Chi-restraints excluded: chain g residue 118 GLU Chi-restraints excluded: chain h residue 45 ILE Chi-restraints excluded: chain h residue 57 SER Chi-restraints excluded: chain h residue 65 VAL Chi-restraints excluded: chain h residue 77 VAL Chi-restraints excluded: chain h residue 94 VAL Chi-restraints excluded: chain h residue 111 ASP Chi-restraints excluded: chain i residue 59 SER Chi-restraints excluded: chain i residue 61 THR Chi-restraints excluded: chain i residue 76 THR Chi-restraints excluded: chain i residue 95 VAL Chi-restraints excluded: chain j residue 4 VAL Chi-restraints excluded: chain j residue 10 THR Chi-restraints excluded: chain j residue 86 SER Chi-restraints excluded: chain j residue 90 VAL Chi-restraints excluded: chain k residue 19 THR Chi-restraints excluded: chain k residue 39 LEU Chi-restraints excluded: chain l residue 29 VAL Chi-restraints excluded: chain l residue 48 GLU Chi-restraints excluded: chain m residue 22 THR Chi-restraints excluded: chain m residue 56 ILE Chi-restraints excluded: chain m residue 63 SER Chi-restraints excluded: chain m residue 87 SER Chi-restraints excluded: chain n residue 16 ASP Chi-restraints excluded: chain n residue 22 THR Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain n residue 41 VAL Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain p residue 18 THR Chi-restraints excluded: chain p residue 24 VAL Chi-restraints excluded: chain p residue 39 SER Chi-restraints excluded: chain p residue 48 SER Chi-restraints excluded: chain p residue 53 ASP Chi-restraints excluded: chain q residue 30 VAL Chi-restraints excluded: chain q residue 43 THR Chi-restraints excluded: chain q residue 44 LEU Chi-restraints excluded: chain q residue 48 THR Chi-restraints excluded: chain r residue 20 SER Chi-restraints excluded: chain r residue 41 VAL Chi-restraints excluded: chain s residue 49 VAL Chi-restraints excluded: chain u residue 12 THR Chi-restraints excluded: chain u residue 22 MET Chi-restraints excluded: chain u residue 28 THR Chi-restraints excluded: chain v residue 1 MET Chi-restraints excluded: chain v residue 57 ILE Chi-restraints excluded: chain v residue 62 ILE Chi-restraints excluded: chain w residue 22 THR Chi-restraints excluded: chain w residue 49 LYS Chi-restraints excluded: chain w residue 54 VAL Chi-restraints excluded: chain w residue 56 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 626 random chunks: chunk 373 optimal weight: 8.9990 chunk 240 optimal weight: 5.9990 chunk 360 optimal weight: 6.9990 chunk 181 optimal weight: 7.9990 chunk 118 optimal weight: 5.9990 chunk 116 optimal weight: 4.9990 chunk 383 optimal weight: 0.9980 chunk 411 optimal weight: 20.0000 chunk 298 optimal weight: 5.9990 chunk 56 optimal weight: 7.9990 chunk 474 optimal weight: 3.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 173 ASN ** Z 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 96 ASN ** k 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 65 ASN w 59 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 99811 Z= 0.381 Angle : 0.694 10.348 149842 Z= 0.352 Chirality : 0.042 0.362 19223 Planarity : 0.005 0.059 7620 Dihedral : 23.688 179.244 51103 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 4.24 % Allowed : 19.45 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.46 (0.13), residues: 3302 helix: -0.21 (0.17), residues: 941 sheet: -1.51 (0.22), residues: 560 loop : -2.55 (0.12), residues: 1801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP W 213 HIS 0.007 0.002 HIS W 142 PHE 0.028 0.002 PHE H 64 TYR 0.015 0.002 TYR Y 99 ARG 0.015 0.001 ARG o 79 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 663 residues out of total 2807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 544 time to evaluate : 3.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS l 110 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU n 101 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "VAL o 92 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THR q 48 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE s 65 " (corrupted residue). Skipping it. REVERT: Y 49 HIS cc_start: 0.9049 (OUTLIER) cc_final: 0.8689 (p90) REVERT: Z 26 MET cc_start: 0.7564 (mtt) cc_final: 0.7306 (mtt) REVERT: Z 141 ILE cc_start: -0.0275 (OUTLIER) cc_final: -0.0686 (mm) REVERT: Z 152 MET cc_start: 0.6448 (mmp) cc_final: 0.6151 (mmp) REVERT: a 158 TYR cc_start: 0.8124 (m-80) cc_final: 0.7700 (m-80) REVERT: c 74 ILE cc_start: 0.9020 (mm) cc_final: 0.8808 (mm) REVERT: f 1 MET cc_start: 0.8219 (tpt) cc_final: 0.7983 (tpp) REVERT: g 34 GLU cc_start: 0.7803 (tp30) cc_final: 0.7412 (tp30) REVERT: g 118 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.6973 (pm20) REVERT: i 42 ARG cc_start: 0.7073 (mtt-85) cc_final: 0.6641 (mtt-85) REVERT: o 19 LYS cc_start: 0.7774 (OUTLIER) cc_final: 0.7525 (mtmm) REVERT: o 85 LYS cc_start: 0.8438 (mttp) cc_final: 0.8167 (mttp) REVERT: q 38 ARG cc_start: 0.7672 (ttm-80) cc_final: 0.7342 (ttm-80) outliers start: 119 outliers final: 106 residues processed: 612 average time/residue: 0.9652 time to fit residues: 972.6286 Evaluate side-chains 646 residues out of total 2807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 536 time to evaluate : 3.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 62 ARG Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 13 LEU Chi-restraints excluded: chain I residue 50 SER Chi-restraints excluded: chain I residue 52 ILE Chi-restraints excluded: chain W residue 141 VAL Chi-restraints excluded: chain W residue 195 VAL Chi-restraints excluded: chain W residue 219 THR Chi-restraints excluded: chain W residue 224 VAL Chi-restraints excluded: chain W residue 262 LYS Chi-restraints excluded: chain X residue 25 VAL Chi-restraints excluded: chain X residue 83 LEU Chi-restraints excluded: chain X residue 99 VAL Chi-restraints excluded: chain X residue 140 HIS Chi-restraints excluded: chain X residue 206 VAL Chi-restraints excluded: chain Y residue 38 LEU Chi-restraints excluded: chain Y residue 49 HIS Chi-restraints excluded: chain Y residue 118 VAL Chi-restraints excluded: chain Y residue 125 VAL Chi-restraints excluded: chain Y residue 136 THR Chi-restraints excluded: chain Y residue 156 THR Chi-restraints excluded: chain Y residue 163 VAL Chi-restraints excluded: chain Y residue 195 THR Chi-restraints excluded: chain Z residue 35 VAL Chi-restraints excluded: chain Z residue 36 ILE Chi-restraints excluded: chain Z residue 54 VAL Chi-restraints excluded: chain Z residue 67 VAL Chi-restraints excluded: chain Z residue 141 ILE Chi-restraints excluded: chain Z residue 156 ILE Chi-restraints excluded: chain Z residue 159 THR Chi-restraints excluded: chain a residue 4 VAL Chi-restraints excluded: chain a residue 72 LEU Chi-restraints excluded: chain a residue 91 VAL Chi-restraints excluded: chain a residue 132 VAL Chi-restraints excluded: chain c residue 6 MET Chi-restraints excluded: chain c residue 18 VAL Chi-restraints excluded: chain c residue 46 THR Chi-restraints excluded: chain c residue 87 SER Chi-restraints excluded: chain c residue 102 LEU Chi-restraints excluded: chain c residue 104 LEU Chi-restraints excluded: chain c residue 114 SER Chi-restraints excluded: chain d residue 9 LYS Chi-restraints excluded: chain d residue 18 GLU Chi-restraints excluded: chain d residue 19 VAL Chi-restraints excluded: chain d residue 35 ILE Chi-restraints excluded: chain d residue 77 ILE Chi-restraints excluded: chain d residue 78 SER Chi-restraints excluded: chain d residue 110 ASN Chi-restraints excluded: chain d residue 116 SER Chi-restraints excluded: chain e residue 19 VAL Chi-restraints excluded: chain e residue 30 THR Chi-restraints excluded: chain e residue 109 VAL Chi-restraints excluded: chain f residue 25 THR Chi-restraints excluded: chain f residue 27 VAL Chi-restraints excluded: chain f residue 128 LYS Chi-restraints excluded: chain g residue 10 SER Chi-restraints excluded: chain g residue 70 VAL Chi-restraints excluded: chain g residue 81 GLN Chi-restraints excluded: chain g residue 118 GLU Chi-restraints excluded: chain h residue 45 ILE Chi-restraints excluded: chain h residue 65 VAL Chi-restraints excluded: chain h residue 77 VAL Chi-restraints excluded: chain h residue 94 VAL Chi-restraints excluded: chain h residue 111 ASP Chi-restraints excluded: chain i residue 59 SER Chi-restraints excluded: chain i residue 61 THR Chi-restraints excluded: chain i residue 76 THR Chi-restraints excluded: chain i residue 95 VAL Chi-restraints excluded: chain j residue 4 VAL Chi-restraints excluded: chain j residue 10 THR Chi-restraints excluded: chain j residue 86 SER Chi-restraints excluded: chain j residue 90 VAL Chi-restraints excluded: chain k residue 19 THR Chi-restraints excluded: chain k residue 39 LEU Chi-restraints excluded: chain l residue 29 VAL Chi-restraints excluded: chain l residue 48 GLU Chi-restraints excluded: chain l residue 70 VAL Chi-restraints excluded: chain m residue 56 ILE Chi-restraints excluded: chain m residue 63 SER Chi-restraints excluded: chain m residue 87 SER Chi-restraints excluded: chain n residue 16 ASP Chi-restraints excluded: chain n residue 22 THR Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain n residue 41 VAL Chi-restraints excluded: chain n residue 68 VAL Chi-restraints excluded: chain o residue 19 LYS Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain p residue 18 THR Chi-restraints excluded: chain p residue 24 VAL Chi-restraints excluded: chain p residue 39 SER Chi-restraints excluded: chain p residue 48 SER Chi-restraints excluded: chain p residue 53 ASP Chi-restraints excluded: chain q residue 30 VAL Chi-restraints excluded: chain q residue 43 THR Chi-restraints excluded: chain q residue 44 LEU Chi-restraints excluded: chain q residue 48 THR Chi-restraints excluded: chain r residue 20 SER Chi-restraints excluded: chain r residue 41 VAL Chi-restraints excluded: chain s residue 49 VAL Chi-restraints excluded: chain t residue 17 ILE Chi-restraints excluded: chain u residue 12 THR Chi-restraints excluded: chain u residue 28 THR Chi-restraints excluded: chain v residue 1 MET Chi-restraints excluded: chain v residue 57 ILE Chi-restraints excluded: chain v residue 62 ILE Chi-restraints excluded: chain w residue 22 THR Chi-restraints excluded: chain w residue 49 LYS Chi-restraints excluded: chain w residue 54 VAL Chi-restraints excluded: chain w residue 56 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 626 random chunks: chunk 548 optimal weight: 2.9990 chunk 578 optimal weight: 6.9990 chunk 527 optimal weight: 3.9990 chunk 562 optimal weight: 2.9990 chunk 577 optimal weight: 10.0000 chunk 338 optimal weight: 8.9990 chunk 244 optimal weight: 5.9990 chunk 441 optimal weight: 0.1980 chunk 172 optimal weight: 5.9990 chunk 508 optimal weight: 8.9990 chunk 531 optimal weight: 2.9990 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 173 ASN Z 27 GLN ** Z 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 96 ASN e 78 ASN ** k 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 65 ASN w 59 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 99811 Z= 0.247 Angle : 0.630 10.217 149842 Z= 0.325 Chirality : 0.038 0.334 19223 Planarity : 0.005 0.061 7620 Dihedral : 23.692 179.269 51103 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 3.99 % Allowed : 19.99 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.37 (0.14), residues: 3302 helix: -0.13 (0.17), residues: 941 sheet: -1.45 (0.22), residues: 558 loop : -2.50 (0.12), residues: 1803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP W 213 HIS 0.007 0.001 HIS W 142 PHE 0.030 0.002 PHE H 64 TYR 0.014 0.001 TYR Z 97 ARG 0.012 0.000 ARG u 18 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 652 residues out of total 2807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 540 time to evaluate : 3.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS l 110 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU n 101 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "VAL o 92 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THR q 48 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE s 65 " (corrupted residue). Skipping it. REVERT: Z 141 ILE cc_start: -0.0188 (OUTLIER) cc_final: -0.0618 (mm) REVERT: Z 152 MET cc_start: 0.6419 (mmp) cc_final: 0.6120 (mmp) REVERT: a 158 TYR cc_start: 0.8068 (m-80) cc_final: 0.7644 (m-80) REVERT: c 74 ILE cc_start: 0.8999 (mm) cc_final: 0.8792 (mm) REVERT: f 1 MET cc_start: 0.8206 (tpt) cc_final: 0.7962 (tpp) REVERT: g 34 GLU cc_start: 0.7769 (tp30) cc_final: 0.7396 (tp30) REVERT: g 118 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.6951 (pm20) REVERT: i 42 ARG cc_start: 0.7037 (mtt-85) cc_final: 0.6596 (mtt-85) REVERT: o 19 LYS cc_start: 0.7742 (OUTLIER) cc_final: 0.7493 (mtmm) REVERT: o 85 LYS cc_start: 0.8442 (mttp) cc_final: 0.8158 (mttp) REVERT: q 38 ARG cc_start: 0.7675 (ttm-80) cc_final: 0.7329 (ttm-80) outliers start: 112 outliers final: 101 residues processed: 606 average time/residue: 0.9363 time to fit residues: 947.7068 Evaluate side-chains 641 residues out of total 2807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 537 time to evaluate : 4.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 62 ARG Chi-restraints excluded: chain H residue 37 GLN Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain I residue 13 LEU Chi-restraints excluded: chain I residue 52 ILE Chi-restraints excluded: chain W residue 141 VAL Chi-restraints excluded: chain W residue 195 VAL Chi-restraints excluded: chain W residue 219 THR Chi-restraints excluded: chain W residue 262 LYS Chi-restraints excluded: chain X residue 25 VAL Chi-restraints excluded: chain X residue 40 THR Chi-restraints excluded: chain X residue 83 LEU Chi-restraints excluded: chain X residue 99 VAL Chi-restraints excluded: chain X residue 140 HIS Chi-restraints excluded: chain X residue 204 SER Chi-restraints excluded: chain X residue 206 VAL Chi-restraints excluded: chain Y residue 38 LEU Chi-restraints excluded: chain Y residue 93 THR Chi-restraints excluded: chain Y residue 118 VAL Chi-restraints excluded: chain Y residue 125 VAL Chi-restraints excluded: chain Y residue 136 THR Chi-restraints excluded: chain Y residue 156 THR Chi-restraints excluded: chain Y residue 163 VAL Chi-restraints excluded: chain Z residue 35 VAL Chi-restraints excluded: chain Z residue 36 ILE Chi-restraints excluded: chain Z residue 54 VAL Chi-restraints excluded: chain Z residue 67 VAL Chi-restraints excluded: chain Z residue 141 ILE Chi-restraints excluded: chain Z residue 156 ILE Chi-restraints excluded: chain a residue 71 SER Chi-restraints excluded: chain a residue 72 LEU Chi-restraints excluded: chain a residue 91 VAL Chi-restraints excluded: chain a residue 132 VAL Chi-restraints excluded: chain c residue 6 MET Chi-restraints excluded: chain c residue 102 LEU Chi-restraints excluded: chain c residue 104 LEU Chi-restraints excluded: chain c residue 114 SER Chi-restraints excluded: chain d residue 9 LYS Chi-restraints excluded: chain d residue 18 GLU Chi-restraints excluded: chain d residue 19 VAL Chi-restraints excluded: chain d residue 77 ILE Chi-restraints excluded: chain d residue 78 SER Chi-restraints excluded: chain d residue 110 ASN Chi-restraints excluded: chain d residue 116 SER Chi-restraints excluded: chain e residue 19 VAL Chi-restraints excluded: chain e residue 30 THR Chi-restraints excluded: chain e residue 109 VAL Chi-restraints excluded: chain f residue 25 THR Chi-restraints excluded: chain f residue 27 VAL Chi-restraints excluded: chain f residue 120 LEU Chi-restraints excluded: chain f residue 128 LYS Chi-restraints excluded: chain g residue 10 SER Chi-restraints excluded: chain g residue 70 VAL Chi-restraints excluded: chain g residue 81 GLN Chi-restraints excluded: chain g residue 118 GLU Chi-restraints excluded: chain h residue 45 ILE Chi-restraints excluded: chain h residue 65 VAL Chi-restraints excluded: chain h residue 77 VAL Chi-restraints excluded: chain h residue 94 VAL Chi-restraints excluded: chain h residue 111 ASP Chi-restraints excluded: chain i residue 59 SER Chi-restraints excluded: chain i residue 61 THR Chi-restraints excluded: chain i residue 76 THR Chi-restraints excluded: chain i residue 95 VAL Chi-restraints excluded: chain j residue 4 VAL Chi-restraints excluded: chain j residue 10 THR Chi-restraints excluded: chain j residue 86 SER Chi-restraints excluded: chain j residue 90 VAL Chi-restraints excluded: chain k residue 7 THR Chi-restraints excluded: chain k residue 19 THR Chi-restraints excluded: chain k residue 39 LEU Chi-restraints excluded: chain l residue 29 VAL Chi-restraints excluded: chain m residue 56 ILE Chi-restraints excluded: chain m residue 63 SER Chi-restraints excluded: chain m residue 87 SER Chi-restraints excluded: chain n residue 16 ASP Chi-restraints excluded: chain n residue 22 THR Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain n residue 41 VAL Chi-restraints excluded: chain n residue 68 VAL Chi-restraints excluded: chain o residue 19 LYS Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain o residue 78 GLU Chi-restraints excluded: chain p residue 18 THR Chi-restraints excluded: chain p residue 24 VAL Chi-restraints excluded: chain p residue 48 SER Chi-restraints excluded: chain p residue 53 ASP Chi-restraints excluded: chain q residue 30 VAL Chi-restraints excluded: chain q residue 43 THR Chi-restraints excluded: chain q residue 44 LEU Chi-restraints excluded: chain q residue 48 THR Chi-restraints excluded: chain r residue 20 SER Chi-restraints excluded: chain r residue 41 VAL Chi-restraints excluded: chain s residue 49 VAL Chi-restraints excluded: chain t residue 17 ILE Chi-restraints excluded: chain u residue 12 THR Chi-restraints excluded: chain u residue 22 MET Chi-restraints excluded: chain u residue 28 THR Chi-restraints excluded: chain v residue 1 MET Chi-restraints excluded: chain v residue 62 ILE Chi-restraints excluded: chain w residue 22 THR Chi-restraints excluded: chain w residue 49 LYS Chi-restraints excluded: chain w residue 54 VAL Chi-restraints excluded: chain w residue 56 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 626 random chunks: chunk 560 optimal weight: 4.9990 chunk 369 optimal weight: 6.9990 chunk 594 optimal weight: 7.9990 chunk 362 optimal weight: 6.9990 chunk 282 optimal weight: 7.9990 chunk 413 optimal weight: 4.9990 chunk 623 optimal weight: 0.6980 chunk 574 optimal weight: 5.9990 chunk 496 optimal weight: 4.9990 chunk 51 optimal weight: 10.0000 chunk 383 optimal weight: 0.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 173 ASN ** Z 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 96 ASN i 44 GLN ** k 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 9 ASN ** u 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 65 ASN w 59 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 99811 Z= 0.297 Angle : 0.644 10.343 149842 Z= 0.330 Chirality : 0.039 0.333 19223 Planarity : 0.005 0.055 7620 Dihedral : 23.660 179.315 51103 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 3.85 % Allowed : 20.02 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.33 (0.14), residues: 3302 helix: -0.12 (0.17), residues: 943 sheet: -1.44 (0.22), residues: 568 loop : -2.46 (0.12), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP W 213 HIS 0.007 0.001 HIS W 142 PHE 0.038 0.002 PHE H 64 TYR 0.014 0.001 TYR Z 97 ARG 0.011 0.000 ARG u 18 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 655 residues out of total 2807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 547 time to evaluate : 3.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS l 110 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU n 101 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "VAL o 92 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THR q 48 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE s 65 " (corrupted residue). Skipping it. REVERT: W 269 PHE cc_start: 0.8380 (m-10) cc_final: 0.7988 (m-10) REVERT: Z 26 MET cc_start: 0.7587 (mtt) cc_final: 0.7331 (mtt) REVERT: Z 141 ILE cc_start: -0.0158 (OUTLIER) cc_final: -0.0586 (mm) REVERT: Z 152 MET cc_start: 0.6492 (mmp) cc_final: 0.6115 (mmp) REVERT: a 158 TYR cc_start: 0.8118 (m-80) cc_final: 0.7686 (m-80) REVERT: f 1 MET cc_start: 0.8239 (tpt) cc_final: 0.7988 (tpp) REVERT: g 34 GLU cc_start: 0.7777 (tp30) cc_final: 0.7397 (tp30) REVERT: g 118 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.6985 (pm20) REVERT: i 42 ARG cc_start: 0.7059 (mtt-85) cc_final: 0.6615 (mtt-85) REVERT: o 85 LYS cc_start: 0.8452 (mttp) cc_final: 0.8169 (mttp) REVERT: q 38 ARG cc_start: 0.7676 (ttm-80) cc_final: 0.7320 (ttm-80) outliers start: 108 outliers final: 102 residues processed: 613 average time/residue: 0.9331 time to fit residues: 950.1527 Evaluate side-chains 652 residues out of total 2807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 548 time to evaluate : 3.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 62 ARG Chi-restraints excluded: chain H residue 37 GLN Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain I residue 13 LEU Chi-restraints excluded: chain I residue 52 ILE Chi-restraints excluded: chain W residue 141 VAL Chi-restraints excluded: chain W residue 195 VAL Chi-restraints excluded: chain W residue 219 THR Chi-restraints excluded: chain W residue 262 LYS Chi-restraints excluded: chain X residue 25 VAL Chi-restraints excluded: chain X residue 83 LEU Chi-restraints excluded: chain X residue 99 VAL Chi-restraints excluded: chain X residue 140 HIS Chi-restraints excluded: chain X residue 204 SER Chi-restraints excluded: chain X residue 206 VAL Chi-restraints excluded: chain Y residue 38 LEU Chi-restraints excluded: chain Y residue 93 THR Chi-restraints excluded: chain Y residue 118 VAL Chi-restraints excluded: chain Y residue 125 VAL Chi-restraints excluded: chain Y residue 136 THR Chi-restraints excluded: chain Y residue 156 THR Chi-restraints excluded: chain Y residue 163 VAL Chi-restraints excluded: chain Z residue 35 VAL Chi-restraints excluded: chain Z residue 36 ILE Chi-restraints excluded: chain Z residue 54 VAL Chi-restraints excluded: chain Z residue 67 VAL Chi-restraints excluded: chain Z residue 141 ILE Chi-restraints excluded: chain Z residue 156 ILE Chi-restraints excluded: chain Z residue 159 THR Chi-restraints excluded: chain a residue 4 VAL Chi-restraints excluded: chain a residue 72 LEU Chi-restraints excluded: chain a residue 91 VAL Chi-restraints excluded: chain a residue 132 VAL Chi-restraints excluded: chain c residue 6 MET Chi-restraints excluded: chain c residue 102 LEU Chi-restraints excluded: chain c residue 104 LEU Chi-restraints excluded: chain c residue 114 SER Chi-restraints excluded: chain d residue 9 LYS Chi-restraints excluded: chain d residue 18 GLU Chi-restraints excluded: chain d residue 77 ILE Chi-restraints excluded: chain d residue 78 SER Chi-restraints excluded: chain d residue 110 ASN Chi-restraints excluded: chain d residue 116 SER Chi-restraints excluded: chain e residue 19 VAL Chi-restraints excluded: chain e residue 30 THR Chi-restraints excluded: chain e residue 109 VAL Chi-restraints excluded: chain f residue 25 THR Chi-restraints excluded: chain f residue 27 VAL Chi-restraints excluded: chain f residue 120 LEU Chi-restraints excluded: chain f residue 128 LYS Chi-restraints excluded: chain g residue 10 SER Chi-restraints excluded: chain g residue 70 VAL Chi-restraints excluded: chain g residue 81 GLN Chi-restraints excluded: chain g residue 118 GLU Chi-restraints excluded: chain h residue 45 ILE Chi-restraints excluded: chain h residue 57 SER Chi-restraints excluded: chain h residue 65 VAL Chi-restraints excluded: chain h residue 77 VAL Chi-restraints excluded: chain h residue 94 VAL Chi-restraints excluded: chain h residue 111 ASP Chi-restraints excluded: chain i residue 59 SER Chi-restraints excluded: chain i residue 61 THR Chi-restraints excluded: chain i residue 76 THR Chi-restraints excluded: chain i residue 95 VAL Chi-restraints excluded: chain j residue 4 VAL Chi-restraints excluded: chain j residue 10 THR Chi-restraints excluded: chain j residue 86 SER Chi-restraints excluded: chain j residue 90 VAL Chi-restraints excluded: chain k residue 7 THR Chi-restraints excluded: chain k residue 19 THR Chi-restraints excluded: chain k residue 39 LEU Chi-restraints excluded: chain l residue 29 VAL Chi-restraints excluded: chain l residue 70 VAL Chi-restraints excluded: chain m residue 56 ILE Chi-restraints excluded: chain m residue 63 SER Chi-restraints excluded: chain m residue 87 SER Chi-restraints excluded: chain n residue 16 ASP Chi-restraints excluded: chain n residue 22 THR Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain n residue 41 VAL Chi-restraints excluded: chain n residue 68 VAL Chi-restraints excluded: chain o residue 15 VAL Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain o residue 78 GLU Chi-restraints excluded: chain p residue 18 THR Chi-restraints excluded: chain p residue 24 VAL Chi-restraints excluded: chain p residue 48 SER Chi-restraints excluded: chain p residue 53 ASP Chi-restraints excluded: chain q residue 30 VAL Chi-restraints excluded: chain q residue 43 THR Chi-restraints excluded: chain q residue 44 LEU Chi-restraints excluded: chain q residue 48 THR Chi-restraints excluded: chain r residue 20 SER Chi-restraints excluded: chain r residue 41 VAL Chi-restraints excluded: chain s residue 49 VAL Chi-restraints excluded: chain t residue 17 ILE Chi-restraints excluded: chain u residue 12 THR Chi-restraints excluded: chain u residue 28 THR Chi-restraints excluded: chain v residue 1 MET Chi-restraints excluded: chain v residue 62 ILE Chi-restraints excluded: chain w residue 22 THR Chi-restraints excluded: chain w residue 49 LYS Chi-restraints excluded: chain w residue 54 VAL Chi-restraints excluded: chain w residue 56 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 626 random chunks: chunk 304 optimal weight: 8.9990 chunk 394 optimal weight: 0.9980 chunk 529 optimal weight: 8.9990 chunk 152 optimal weight: 50.0000 chunk 457 optimal weight: 0.6980 chunk 73 optimal weight: 7.9990 chunk 138 optimal weight: 6.9990 chunk 497 optimal weight: 0.9980 chunk 208 optimal weight: 6.9990 chunk 510 optimal weight: 9.9990 chunk 62 optimal weight: 6.9990 overall best weight: 3.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 57 ASN ** H 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 173 ASN ** Z 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 96 ASN ** k 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 9 ASN ** u 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 65 ASN w 59 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.158917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.115408 restraints weight = 119043.513| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 1.08 r_work: 0.3022 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 99811 Z= 0.296 Angle : 0.642 13.433 149842 Z= 0.329 Chirality : 0.039 0.332 19223 Planarity : 0.005 0.069 7620 Dihedral : 23.655 179.356 51103 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 4.03 % Allowed : 19.99 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.31 (0.14), residues: 3302 helix: -0.12 (0.17), residues: 943 sheet: -1.43 (0.21), residues: 577 loop : -2.43 (0.12), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP W 213 HIS 0.010 0.001 HIS H 33 PHE 0.033 0.002 PHE H 64 TYR 0.016 0.001 TYR Z 97 ARG 0.011 0.001 ARG u 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17597.13 seconds wall clock time: 312 minutes 19.39 seconds (18739.39 seconds total)