Starting phenix.real_space_refine on Mon Mar 11 16:21:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iuh_35722/03_2024/8iuh_35722_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iuh_35722/03_2024/8iuh_35722.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iuh_35722/03_2024/8iuh_35722.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iuh_35722/03_2024/8iuh_35722.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iuh_35722/03_2024/8iuh_35722_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iuh_35722/03_2024/8iuh_35722_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.008 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: 8 Type Number sf(0) Gaussians Fe 4 7.16 5 Zn 8 6.06 5 P 162 5.49 5 Mg 1 5.21 5 S 358 5.16 5 C 36357 2.51 5 N 10187 2.21 5 O 11162 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "1 PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ASP 132": "OD1" <-> "OD2" Residue "1 ARG 133": "NH1" <-> "NH2" Residue "1 PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 337": "NH1" <-> "NH2" Residue "3 TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 163": "OE1" <-> "OE2" Residue "4 GLU 178": "OE1" <-> "OE2" Residue "4 PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 279": "OE1" <-> "OE2" Residue "4 PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 390": "NH1" <-> "NH2" Residue "4 TYR 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 407": "OE1" <-> "OE2" Residue "4 GLU 408": "OE1" <-> "OE2" Residue "4 PHE 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 482": "OE1" <-> "OE2" Residue "A PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 488": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 848": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 900": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 958": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 987": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 521": "OE1" <-> "OE2" Residue "B PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 584": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 851": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 914": "OE1" <-> "OE2" Residue "B PHE 934": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 958": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 25": "OE1" <-> "OE2" Residue "L PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 299": "NH1" <-> "NH2" Residue "V TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 364": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 58239 Number of models: 1 Model: "" Number of chains: 32 Chain: "1" Number of atoms: 1233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1233 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 6, 'TRANS': 139} Chain: "3" Number of atoms: 3037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 3037 Classifications: {'peptide': 374} Link IDs: {'PTRANS': 16, 'TRANS': 357} Chain breaks: 2 Chain: "4" Number of atoms: 3058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 3058 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 10, 'TRANS': 354} Chain: "A" Number of atoms: 10814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1378, 10814 Classifications: {'peptide': 1378} Link IDs: {'PTRANS': 64, 'TRANS': 1313} Chain: "B" Number of atoms: 8680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1097, 8680 Classifications: {'peptide': 1097} Link IDs: {'PTRANS': 50, 'TRANS': 1046} Chain breaks: 2 Chain: "C" Number of atoms: 2736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2736 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 17, 'TRANS': 325} Chain: "D" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 985 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "E" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1715 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "F" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 610 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 5, 'TRANS': 70} Chain: "G" Number of atoms: 1337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1337 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 10, 'TRANS': 155} Chain breaks: 2 Chain: "H" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1186 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain: "I" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 848 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "J" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 512 Classifications: {'peptide': 65} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 62} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 822 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 4, 'TRANS': 98} Chain: "L" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 388 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "M" Number of atoms: 3382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3382 Classifications: {'peptide': 422} Link IDs: {'PTRANS': 23, 'TRANS': 398} Chain breaks: 1 Chain: "N" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1128 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 6, 'TRANS': 139} Chain breaks: 2 Chain: "O" Number of atoms: 4075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 4075 Classifications: {'peptide': 512} Link IDs: {'PTRANS': 22, 'TRANS': 489} Chain breaks: 1 Chain: "P" Number of atoms: 2403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2403 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 12, 'TRANS': 290} Chain: "Q" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 754 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 12, 'TRANS': 74} Chain: "U" Number of atoms: 1396 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 176, 1391 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 9, 'TRANS': 166} Conformer: "B" Number of residues, atoms: 176, 1391 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 9, 'TRANS': 166} bond proxies already assigned to first conformer: 1410 Chain: "V" Number of atoms: 2853 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 361, 2847 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 19, 'TRANS': 341} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 361, 2847 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 19, 'TRANS': 341} Chain breaks: 1 bond proxies already assigned to first conformer: 2891 Chain: "W" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 943 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 4, 'TRANS': 106} Chain: "X" Number of atoms: 1661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 1661 Classifications: {'DNA': 81} Link IDs: {'rna3p': 80} Chain breaks: 1 Chain: "Y" Number of atoms: 1666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 1666 Classifications: {'DNA': 81} Link IDs: {'rna3p': 80} Chain breaks: 1 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 7871 SG CYS A 69 109.137 132.778 148.280 1.00103.58 S ATOM 7893 SG CYS A 72 109.907 132.308 152.006 1.00106.71 S ATOM 7941 SG CYS A 79 107.629 129.552 150.268 1.00104.11 S ATOM 8182 SG CYS A 109 65.397 153.139 151.996 1.00114.77 S ATOM 8204 SG CYS A 112 67.134 155.703 154.704 1.00118.64 S ATOM 8573 SG CYS A 156 63.635 154.956 155.411 1.00130.18 S ATOM 8599 SG CYS A 159 64.500 157.380 152.746 1.00130.36 S ATOM 26409 SG CYS B1080 101.067 139.826 164.241 1.00102.14 S ATOM 26428 SG CYS B1083 98.056 140.039 161.547 1.00101.99 S ATOM 26494 SG CYS B1092 101.541 140.041 160.419 1.00 97.16 S ATOM 26522 SG CYS B1095 99.532 143.498 162.083 1.00100.21 S ATOM 35432 SG CYS I 5 23.985 115.044 118.636 1.00130.73 S ATOM 35449 SG CYS I 8 27.788 116.653 117.982 1.00130.05 S ATOM 35579 SG CYS I 25 27.269 118.429 121.229 1.00130.27 S ATOM 35600 SG CYS I 28 24.662 118.525 118.455 1.00128.16 S ATOM 35921 SG CYS I 69 61.953 75.683 175.179 1.00228.50 S ATOM 35943 SG CYS I 72 59.675 77.278 177.673 1.00234.26 S ATOM 36155 SG CYS I 97 58.470 76.329 174.505 1.00227.88 S ATOM 36294 SG CYS J 7 104.067 61.500 144.102 1.00 75.41 S ATOM 36318 SG CYS J 10 105.720 58.876 146.188 1.00 75.83 S ATOM 36582 SG CYS J 44 102.122 58.455 145.602 1.00 81.33 S ATOM 36588 SG CYS J 45 104.495 57.244 142.752 1.00 82.39 S ATOM 37631 SG CYS L 19 116.948 86.595 112.394 1.00103.46 S ATOM 37767 SG CYS L 36 118.079 89.113 110.058 1.00117.09 S ATOM 37793 SG CYS L 39 114.962 88.724 108.283 1.00117.30 S ATOM 51116 SG CYS V 7 131.053 115.313 157.078 1.00178.33 S ATOM 51294 SG CYS V 31 132.811 111.317 158.827 1.00175.49 S Residues with excluded nonbonded symmetry interactions: 12 residue: pdb=" N ACYS V 177 " occ=0.47 ... (10 atoms not shown) pdb=" SG BCYS V 177 " occ=0.53 residue: pdb=" N LYS V 364 " occ=0.00 ... (7 atoms not shown) pdb=" NZ LYS V 364 " occ=0.00 residue: pdb=" N SER V 365 " occ=0.00 ... (4 atoms not shown) pdb=" OG SER V 365 " occ=0.00 residue: pdb=" N PRO V 366 " occ=0.00 ... (5 atoms not shown) pdb=" CD PRO V 366 " occ=0.00 residue: pdb=" N LYS V 367 " occ=0.00 ... (7 atoms not shown) pdb=" NZ LYS V 367 " occ=0.00 residue: pdb=" N ARG V 368 " occ=0.00 ... (9 atoms not shown) pdb=" NH2 ARG V 368 " occ=0.00 residue: pdb=" N ILE V 369 " occ=0.00 ... (6 atoms not shown) pdb=" CD1 ILE V 369 " occ=0.00 residue: pdb=" N CYS V 370 " occ=0.00 ... (4 atoms not shown) pdb=" SG CYS V 370 " occ=0.00 residue: pdb=" N PRO V 371 " occ=0.00 ... (5 atoms not shown) pdb=" CD PRO V 371 " occ=0.00 residue: pdb=" N SER V 376 " occ=0.00 ... (4 atoms not shown) pdb=" OG SER V 376 " occ=0.00 residue: pdb=" N THR V 377 " occ=0.00 ... (5 atoms not shown) pdb=" CG2 THR V 377 " occ=0.00 residue: pdb=" N VAL V 378 " occ=0.00 ... (5 atoms not shown) pdb=" CG2 VAL V 378 " occ=0.00 Time building chain proxies: 23.66, per 1000 atoms: 0.41 Number of scatterers: 58239 At special positions: 0 Unit cell: (162.748, 212.106, 228.114, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 8 29.99 Fe 4 26.01 S 358 16.00 P 162 15.00 Mg 1 11.99 O 11162 8.00 N 10187 7.00 C 36357 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: 18.21 Conformation dependent library (CDL) restraints added in 7.9 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 P 401 " pdb="FE1 SF4 P 401 " - pdb=" SG CYS P 290 " pdb="FE4 SF4 P 401 " - pdb=" SG CYS P 307 " pdb="FE3 SF4 P 401 " - pdb=" SG CYS P 287 " pdb="FE2 SF4 P 401 " - pdb=" SG CYS P 296 " Number of angles added : 12 Zn2+ tetrahedral coordination pdb=" ZN A1401 " pdb="ZN ZN A1401 " - pdb=" NE2 HIS A 82 " pdb="ZN ZN A1401 " - pdb=" SG CYS A 79 " pdb="ZN ZN A1401 " - pdb=" SG CYS A 69 " pdb="ZN ZN A1401 " - pdb=" SG CYS A 72 " pdb=" ZN A1402 " pdb="ZN ZN A1402 " - pdb=" SG CYS A 112 " pdb="ZN ZN A1402 " - pdb=" SG CYS A 109 " pdb="ZN ZN A1402 " - pdb=" SG CYS A 159 " pdb="ZN ZN A1402 " - pdb=" SG CYS A 156 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1095 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1080 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1092 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1083 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 8 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 28 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 25 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 5 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 72 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 69 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 97 " pdb=" ZN J2000 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 7 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 44 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 45 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 10 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 39 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 19 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb=" ZN V 700 " pdb="ZN ZN V 700 " - pdb=" SG CYS V 7 " pdb="ZN ZN V 700 " - pdb=" SG CYS V 31 " Number of angles added : 27 13598 Ramachandran restraints generated. 6799 Oldfield, 0 Emsley, 6799 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12954 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 261 helices and 61 sheets defined 38.5% alpha, 11.0% beta 27 base pairs and 102 stacking pairs defined. Time for finding SS restraints: 18.76 Creating SS restraints... Processing helix chain '1' and resid 5 through 20 removed outlier: 3.604A pdb=" N THR 1 9 " --> pdb=" O PRO 1 5 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLU 1 12 " --> pdb=" O GLN 1 8 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER 1 16 " --> pdb=" O GLU 1 12 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ARG 1 17 " --> pdb=" O ALA 1 13 " (cutoff:3.500A) Processing helix chain '1' and resid 27 through 34 removed outlier: 3.832A pdb=" N ARG 1 34 " --> pdb=" O THR 1 30 " (cutoff:3.500A) Processing helix chain '1' and resid 49 through 66 removed outlier: 3.832A pdb=" N TYR 1 65 " --> pdb=" O LEU 1 61 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N PHE 1 66 " --> pdb=" O ALA 1 62 " (cutoff:3.500A) Processing helix chain '1' and resid 72 through 87 Processing helix chain '1' and resid 103 through 116 removed outlier: 3.783A pdb=" N GLU 1 106 " --> pdb=" O ASP 1 103 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N VAL 1 107 " --> pdb=" O TRP 1 104 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU 1 108 " --> pdb=" O ASP 1 105 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASN 1 116 " --> pdb=" O ASP 1 113 " (cutoff:3.500A) Processing helix chain '1' and resid 120 through 131 removed outlier: 3.670A pdb=" N PHE 1 126 " --> pdb=" O ALA 1 122 " (cutoff:3.500A) Processing helix chain '3' and resid 44 through 54 removed outlier: 4.856A pdb=" N TRP 3 51 " --> pdb=" O GLY 3 48 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ARG 3 54 " --> pdb=" O TRP 3 51 " (cutoff:3.500A) Processing helix chain '3' and resid 77 through 89 removed outlier: 4.198A pdb=" N ARG 3 88 " --> pdb=" O ALA 3 84 " (cutoff:3.500A) Processing helix chain '3' and resid 98 through 105 Processing helix chain '3' and resid 128 through 142 Processing helix chain '3' and resid 151 through 163 removed outlier: 4.024A pdb=" N VAL 3 156 " --> pdb=" O GLN 3 152 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ALA 3 163 " --> pdb=" O MET 3 159 " (cutoff:3.500A) Processing helix chain '3' and resid 171 through 173 No H-bonds generated for 'chain '3' and resid 171 through 173' Processing helix chain '3' and resid 212 through 218 Processing helix chain '3' and resid 222 through 224 No H-bonds generated for 'chain '3' and resid 222 through 224' Processing helix chain '3' and resid 243 through 246 No H-bonds generated for 'chain '3' and resid 243 through 246' Processing helix chain '3' and resid 270 through 279 removed outlier: 3.795A pdb=" N THR 3 273 " --> pdb=" O LEU 3 270 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ILE 3 274 " --> pdb=" O SER 3 271 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ILE 3 275 " --> pdb=" O ARG 3 272 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TRP 3 277 " --> pdb=" O ILE 3 274 " (cutoff:3.500A) Processing helix chain '3' and resid 298 through 300 No H-bonds generated for 'chain '3' and resid 298 through 300' Processing helix chain '3' and resid 381 through 388 removed outlier: 4.012A pdb=" N HIS 3 388 " --> pdb=" O PHE 3 384 " (cutoff:3.500A) Processing helix chain '3' and resid 407 through 409 No H-bonds generated for 'chain '3' and resid 407 through 409' Processing helix chain '4' and resid 164 through 170 Processing helix chain '4' and resid 186 through 221 Proline residue: 4 207 - end of helix Processing helix chain '4' and resid 225 through 246 Processing helix chain '4' and resid 252 through 254 No H-bonds generated for 'chain '4' and resid 252 through 254' Processing helix chain '4' and resid 263 through 268 Processing helix chain '4' and resid 277 through 285 removed outlier: 3.656A pdb=" N PHE 4 283 " --> pdb=" O GLU 4 279 " (cutoff:3.500A) Processing helix chain '4' and resid 302 through 312 Processing helix chain '4' and resid 317 through 324 Processing helix chain '4' and resid 330 through 340 removed outlier: 3.591A pdb=" N GLN 4 335 " --> pdb=" O PHE 4 331 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N LYS 4 336 " --> pdb=" O GLN 4 332 " (cutoff:3.500A) Processing helix chain '4' and resid 352 through 364 removed outlier: 3.615A pdb=" N MET 4 356 " --> pdb=" O GLU 4 352 " (cutoff:3.500A) Processing helix chain '4' and resid 372 through 378 Processing helix chain '4' and resid 388 through 391 Processing helix chain '4' and resid 408 through 411 No H-bonds generated for 'chain '4' and resid 408 through 411' Processing helix chain '4' and resid 413 through 418 Processing helix chain '4' and resid 424 through 428 removed outlier: 3.723A pdb=" N ARG 4 428 " --> pdb=" O PHE 4 425 " (cutoff:3.500A) Processing helix chain '4' and resid 436 through 447 removed outlier: 3.798A pdb=" N ASP 4 441 " --> pdb=" O ALA 4 437 " (cutoff:3.500A) Processing helix chain '4' and resid 460 through 467 Processing helix chain '4' and resid 478 through 481 Processing helix chain '4' and resid 488 through 501 removed outlier: 5.274A pdb=" N SER 4 493 " --> pdb=" O SER 4 489 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N LYS 4 494 " --> pdb=" O GLN 4 490 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ILE 4 497 " --> pdb=" O SER 4 493 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N MET 4 499 " --> pdb=" O TRP 4 495 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N GLY 4 500 " --> pdb=" O LYS 4 496 " (cutoff:3.500A) Processing helix chain '4' and resid 505 through 512 removed outlier: 4.827A pdb=" N ARG 4 511 " --> pdb=" O ARG 4 507 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N ALA 4 512 " --> pdb=" O ARG 4 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 31 Processing helix chain 'A' and resid 58 through 60 No H-bonds generated for 'chain 'A' and resid 58 through 60' Processing helix chain 'A' and resid 95 through 107 removed outlier: 4.410A pdb=" N ARG A 99 " --> pdb=" O VAL A 95 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N ALA A 100 " --> pdb=" O GLY A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 129 Processing helix chain 'A' and resid 136 through 152 Processing helix chain 'A' and resid 188 through 203 removed outlier: 4.289A pdb=" N PHE A 197 " --> pdb=" O PHE A 193 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N GLU A 198 " --> pdb=" O LEU A 194 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N THR A 199 " --> pdb=" O GLN A 195 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N ALA A 200 " --> pdb=" O SER A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 211 Proline residue: A 209 - end of helix Processing helix chain 'A' and resid 220 through 229 removed outlier: 3.609A pdb=" N ARG A 229 " --> pdb=" O ASN A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 234 No H-bonds generated for 'chain 'A' and resid 232 through 234' Processing helix chain 'A' and resid 236 through 238 No H-bonds generated for 'chain 'A' and resid 236 through 238' Processing helix chain 'A' and resid 247 through 249 No H-bonds generated for 'chain 'A' and resid 247 through 249' Processing helix chain 'A' and resid 278 through 299 Processing helix chain 'A' and resid 303 through 321 Processing helix chain 'A' and resid 341 through 345 Processing helix chain 'A' and resid 351 through 355 Processing helix chain 'A' and resid 384 through 387 No H-bonds generated for 'chain 'A' and resid 384 through 387' Processing helix chain 'A' and resid 401 through 410 Processing helix chain 'A' and resid 437 through 442 Processing helix chain 'A' and resid 470 through 472 No H-bonds generated for 'chain 'A' and resid 470 through 472' Processing helix chain 'A' and resid 490 through 496 removed outlier: 4.389A pdb=" N THR A 494 " --> pdb=" O CYS A 491 " (cutoff:3.500A) Proline residue: A 495 - end of helix Processing helix chain 'A' and resid 513 through 522 Processing helix chain 'A' and resid 546 through 552 Processing helix chain 'A' and resid 561 through 571 removed outlier: 4.392A pdb=" N ILE A 571 " --> pdb=" O ILE A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 578 removed outlier: 3.781A pdb=" N LYS A 578 " --> pdb=" O LYS A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 605 removed outlier: 3.742A pdb=" N ILE A 604 " --> pdb=" O ILE A 600 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU A 605 " --> pdb=" O PHE A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 655 No H-bonds generated for 'chain 'A' and resid 652 through 655' Processing helix chain 'A' and resid 663 through 671 Processing helix chain 'A' and resid 673 through 694 Proline residue: A 688 - end of helix Processing helix chain 'A' and resid 700 through 702 No H-bonds generated for 'chain 'A' and resid 700 through 702' Processing helix chain 'A' and resid 707 through 732 Processing helix chain 'A' and resid 744 through 770 Processing helix chain 'A' and resid 776 through 782 Processing helix chain 'A' and resid 789 through 796 Processing helix chain 'A' and resid 844 through 879 removed outlier: 3.639A pdb=" N ALA A 866 " --> pdb=" O ALA A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 902 through 904 No H-bonds generated for 'chain 'A' and resid 902 through 904' Processing helix chain 'A' and resid 909 through 911 No H-bonds generated for 'chain 'A' and resid 909 through 911' Processing helix chain 'A' and resid 921 through 931 Processing helix chain 'A' and resid 942 through 953 Processing helix chain 'A' and resid 963 through 986 Processing helix chain 'A' and resid 998 through 1002 Processing helix chain 'A' and resid 1008 through 1024 Processing helix chain 'A' and resid 1033 through 1047 Proline residue: A1044 - end of helix Processing helix chain 'A' and resid 1067 through 1075 Processing helix chain 'A' and resid 1095 through 1105 Processing helix chain 'A' and resid 1110 through 1113 No H-bonds generated for 'chain 'A' and resid 1110 through 1113' Processing helix chain 'A' and resid 1134 through 1140 Processing helix chain 'A' and resid 1146 through 1152 Processing helix chain 'A' and resid 1186 through 1195 removed outlier: 5.003A pdb=" N GLN A1190 " --> pdb=" O TYR A1187 " (cutoff:3.500A) Processing helix chain 'A' and resid 1232 through 1237 Processing helix chain 'A' and resid 1243 through 1245 No H-bonds generated for 'chain 'A' and resid 1243 through 1245' Processing helix chain 'A' and resid 1251 through 1258 Processing helix chain 'A' and resid 1260 through 1278 removed outlier: 3.883A pdb=" N HIS A1278 " --> pdb=" O THR A1274 " (cutoff:3.500A) Processing helix chain 'A' and resid 1284 through 1294 Processing helix chain 'A' and resid 1305 through 1311 Processing helix chain 'A' and resid 1315 through 1321 Processing helix chain 'A' and resid 1324 through 1334 Processing helix chain 'A' and resid 1343 through 1349 Processing helix chain 'A' and resid 1356 through 1358 No H-bonds generated for 'chain 'A' and resid 1356 through 1358' Processing helix chain 'B' and resid 24 through 35 removed outlier: 4.318A pdb=" N TRP B 27 " --> pdb=" O GLU B 24 " (cutoff:3.500A) Proline residue: B 31 - end of helix Processing helix chain 'B' and resid 41 through 52 Processing helix chain 'B' and resid 54 through 61 Processing helix chain 'B' and resid 99 through 104 Processing helix chain 'B' and resid 152 through 157 Processing helix chain 'B' and resid 236 through 242 Processing helix chain 'B' and resid 248 through 255 Processing helix chain 'B' and resid 259 through 274 Proline residue: B 267 - end of helix Processing helix chain 'B' and resid 280 through 290 Processing helix chain 'B' and resid 304 through 314 Processing helix chain 'B' and resid 329 through 345 Processing helix chain 'B' and resid 357 through 359 No H-bonds generated for 'chain 'B' and resid 357 through 359' Processing helix chain 'B' and resid 365 through 391 Processing helix chain 'B' and resid 402 through 405 Processing helix chain 'B' and resid 409 through 420 Processing helix chain 'B' and resid 445 through 453 removed outlier: 4.062A pdb=" N THR B 453 " --> pdb=" O LEU B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 475 No H-bonds generated for 'chain 'B' and resid 473 through 475' Processing helix chain 'B' and resid 509 through 517 Processing helix chain 'B' and resid 523 through 525 No H-bonds generated for 'chain 'B' and resid 523 through 525' Processing helix chain 'B' and resid 528 through 532 Processing helix chain 'B' and resid 552 through 565 Processing helix chain 'B' and resid 608 through 616 Processing helix chain 'B' and resid 621 through 626 Processing helix chain 'B' and resid 635 through 640 removed outlier: 3.952A pdb=" N ASP B 640 " --> pdb=" O ASN B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 661 through 664 Processing helix chain 'B' and resid 669 through 671 No H-bonds generated for 'chain 'B' and resid 669 through 671' Processing helix chain 'B' and resid 675 through 677 No H-bonds generated for 'chain 'B' and resid 675 through 677' Processing helix chain 'B' and resid 680 through 690 Processing helix chain 'B' and resid 723 through 728 Processing helix chain 'B' and resid 730 through 732 No H-bonds generated for 'chain 'B' and resid 730 through 732' Processing helix chain 'B' and resid 759 through 763 Processing helix chain 'B' and resid 931 through 937 Proline residue: B 935 - end of helix Processing helix chain 'B' and resid 940 through 955 Processing helix chain 'B' and resid 969 through 978 Processing helix chain 'B' and resid 1016 through 1019 No H-bonds generated for 'chain 'B' and resid 1016 through 1019' Processing helix chain 'B' and resid 1049 through 1058 Processing helix chain 'B' and resid 1061 through 1068 Processing helix chain 'B' and resid 1070 through 1073 No H-bonds generated for 'chain 'B' and resid 1070 through 1073' Processing helix chain 'B' and resid 1108 through 1119 Processing helix chain 'C' and resid 3 through 12 Processing helix chain 'C' and resid 42 through 48 Processing helix chain 'C' and resid 70 through 82 Processing helix chain 'C' and resid 103 through 111 Processing helix chain 'C' and resid 119 through 121 No H-bonds generated for 'chain 'C' and resid 119 through 121' Processing helix chain 'C' and resid 159 through 162 No H-bonds generated for 'chain 'C' and resid 159 through 162' Processing helix chain 'C' and resid 170 through 172 No H-bonds generated for 'chain 'C' and resid 170 through 172' Processing helix chain 'C' and resid 181 through 184 No H-bonds generated for 'chain 'C' and resid 181 through 184' Processing helix chain 'C' and resid 223 through 225 No H-bonds generated for 'chain 'C' and resid 223 through 225' Processing helix chain 'C' and resid 247 through 256 Processing helix chain 'C' and resid 278 through 280 No H-bonds generated for 'chain 'C' and resid 278 through 280' Processing helix chain 'C' and resid 318 through 343 Processing helix chain 'D' and resid 13 through 29 Processing helix chain 'D' and resid 33 through 38 Processing helix chain 'D' and resid 41 through 55 Processing helix chain 'D' and resid 63 through 76 removed outlier: 4.089A pdb=" N SER D 75 " --> pdb=" O THR D 71 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N HIS D 76 " --> pdb=" O ALA D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 89 Processing helix chain 'D' and resid 95 through 98 No H-bonds generated for 'chain 'D' and resid 95 through 98' Processing helix chain 'D' and resid 112 through 120 Processing helix chain 'E' and resid 5 through 24 Processing helix chain 'E' and resid 30 through 33 No H-bonds generated for 'chain 'E' and resid 30 through 33' Processing helix chain 'E' and resid 37 through 43 Processing helix chain 'E' and resid 84 through 97 Processing helix chain 'E' and resid 112 through 119 Processing helix chain 'E' and resid 132 through 135 No H-bonds generated for 'chain 'E' and resid 132 through 135' Processing helix chain 'E' and resid 153 through 163 Processing helix chain 'E' and resid 178 through 183 Processing helix chain 'F' and resid 59 through 75 Processing helix chain 'F' and resid 89 through 99 Processing helix chain 'G' and resid 15 through 17 No H-bonds generated for 'chain 'G' and resid 15 through 17' Processing helix chain 'G' and resid 22 through 33 Processing helix chain 'H' and resid 84 through 87 Processing helix chain 'I' and resid 56 through 59 No H-bonds generated for 'chain 'I' and resid 56 through 59' Processing helix chain 'J' and resid 15 through 26 removed outlier: 3.629A pdb=" N TRP J 18 " --> pdb=" O GLY J 15 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N GLU J 19 " --> pdb=" O ASN J 16 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ALA J 20 " --> pdb=" O LYS J 17 " (cutoff:3.500A) Processing helix chain 'J' and resid 31 through 37 Processing helix chain 'J' and resid 43 through 50 Processing helix chain 'J' and resid 56 through 62 removed outlier: 3.835A pdb=" N TYR J 62 " --> pdb=" O LYS J 58 " (cutoff:3.500A) Processing helix chain 'K' and resid 49 through 60 Processing helix chain 'K' and resid 94 through 125 Processing helix chain 'M' and resid 71 through 81 Processing helix chain 'M' and resid 141 through 160 Processing helix chain 'M' and resid 183 through 190 Processing helix chain 'M' and resid 193 through 202 Processing helix chain 'M' and resid 216 through 225 removed outlier: 4.079A pdb=" N GLN M 223 " --> pdb=" O GLU M 219 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N TYR M 224 " --> pdb=" O HIS M 220 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N LEU M 225 " --> pdb=" O GLU M 221 " (cutoff:3.500A) Processing helix chain 'M' and resid 242 through 249 Processing helix chain 'M' and resid 265 through 267 No H-bonds generated for 'chain 'M' and resid 265 through 267' Processing helix chain 'M' and resid 270 through 274 Processing helix chain 'M' and resid 278 through 288 Processing helix chain 'M' and resid 294 through 301 Processing helix chain 'M' and resid 307 through 317 removed outlier: 3.775A pdb=" N LYS M 316 " --> pdb=" O ARG M 312 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N VAL M 317 " --> pdb=" O GLY M 313 " (cutoff:3.500A) Processing helix chain 'M' and resid 329 through 332 No H-bonds generated for 'chain 'M' and resid 329 through 332' Processing helix chain 'M' and resid 346 through 362 Processing helix chain 'M' and resid 368 through 375 Processing helix chain 'M' and resid 379 through 387 Processing helix chain 'M' and resid 406 through 411 Processing helix chain 'M' and resid 413 through 434 Processing helix chain 'N' and resid 148 through 150 No H-bonds generated for 'chain 'N' and resid 148 through 150' Processing helix chain 'N' and resid 250 through 258 Processing helix chain 'N' and resid 333 through 335 No H-bonds generated for 'chain 'N' and resid 333 through 335' Processing helix chain 'N' and resid 389 through 395 Processing helix chain 'O' and resid 3 through 16 Processing helix chain 'O' and resid 20 through 31 removed outlier: 4.081A pdb=" N ILE O 24 " --> pdb=" O ILE O 20 " (cutoff:3.500A) Processing helix chain 'O' and resid 36 through 43 Processing helix chain 'O' and resid 47 through 59 Processing helix chain 'O' and resid 69 through 71 No H-bonds generated for 'chain 'O' and resid 69 through 71' Processing helix chain 'O' and resid 79 through 98 removed outlier: 4.091A pdb=" N LEU O 86 " --> pdb=" O VAL O 82 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ARG O 87 " --> pdb=" O LEU O 83 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N TYR O 88 " --> pdb=" O ARG O 84 " (cutoff:3.500A) Proline residue: O 89 - end of helix Processing helix chain 'O' and resid 101 through 113 Processing helix chain 'O' and resid 118 through 132 removed outlier: 3.988A pdb=" N GLU O 131 " --> pdb=" O ASP O 127 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N THR O 132 " --> pdb=" O ARG O 128 " (cutoff:3.500A) Processing helix chain 'O' and resid 141 through 153 Processing helix chain 'O' and resid 239 through 258 Processing helix chain 'O' and resid 261 through 277 removed outlier: 4.482A pdb=" N ILE O 276 " --> pdb=" O ARG O 272 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N THR O 277 " --> pdb=" O MET O 273 " (cutoff:3.500A) Processing helix chain 'O' and resid 290 through 296 Processing helix chain 'O' and resid 305 through 316 Processing helix chain 'O' and resid 338 through 358 Processing helix chain 'O' and resid 360 through 371 Processing helix chain 'O' and resid 377 through 384 Processing helix chain 'O' and resid 391 through 400 Processing helix chain 'O' and resid 417 through 419 No H-bonds generated for 'chain 'O' and resid 417 through 419' Processing helix chain 'O' and resid 428 through 472 removed outlier: 5.273A pdb=" N ARG O 459 " --> pdb=" O LYS O 455 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N LEU O 460 " --> pdb=" O GLU O 456 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ILE O 471 " --> pdb=" O VAL O 467 " (cutoff:3.500A) Processing helix chain 'O' and resid 481 through 483 No H-bonds generated for 'chain 'O' and resid 481 through 483' Processing helix chain 'O' and resid 492 through 529 removed outlier: 4.405A pdb=" N GLN O 497 " --> pdb=" O ALA O 493 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N GLN O 498 " --> pdb=" O PRO O 494 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASP O 517 " --> pdb=" O GLU O 513 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLU O 518 " --> pdb=" O ILE O 514 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N THR O 519 " --> pdb=" O GLN O 515 " (cutoff:3.500A) Processing helix chain 'P' and resid 15 through 28 Processing helix chain 'P' and resid 35 through 41 Processing helix chain 'P' and resid 47 through 60 Processing helix chain 'P' and resid 89 through 105 removed outlier: 5.676A pdb=" N ILE P 98 " --> pdb=" O LEU P 94 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N ASN P 104 " --> pdb=" O GLU P 100 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LYS P 105 " --> pdb=" O ASP P 101 " (cutoff:3.500A) Processing helix chain 'P' and resid 109 through 116 Processing helix chain 'P' and resid 120 through 132 Processing helix chain 'P' and resid 174 through 198 Processing helix chain 'P' and resid 202 through 209 Processing helix chain 'P' and resid 213 through 223 Processing helix chain 'P' and resid 232 through 244 Processing helix chain 'P' and resid 282 through 284 No H-bonds generated for 'chain 'P' and resid 282 through 284' Processing helix chain 'P' and resid 293 through 295 No H-bonds generated for 'chain 'P' and resid 293 through 295' Processing helix chain 'P' and resid 308 through 315 Processing helix chain 'Q' and resid 52 through 69 removed outlier: 3.929A pdb=" N LYS Q 69 " --> pdb=" O ARG Q 65 " (cutoff:3.500A) Processing helix chain 'Q' and resid 87 through 92 removed outlier: 3.876A pdb=" N ARG Q 90 " --> pdb=" O TYR Q 87 " (cutoff:3.500A) Processing helix chain 'Q' and resid 108 through 110 No H-bonds generated for 'chain 'Q' and resid 108 through 110' Processing helix chain 'U' and resid 180 through 185 Processing helix chain 'U' and resid 227 through 244 Processing helix chain 'U' and resid 270 through 276 removed outlier: 3.890A pdb=" N VAL U 274 " --> pdb=" O LEU U 270 " (cutoff:3.500A) Processing helix chain 'U' and resid 278 through 280 No H-bonds generated for 'chain 'U' and resid 278 through 280' Processing helix chain 'U' and resid 318 through 333 Proline residue: U 330 - end of helix Processing helix chain 'V' and resid 44 through 47 No H-bonds generated for 'chain 'V' and resid 44 through 47' Processing helix chain 'V' and resid 67 through 82 Processing helix chain 'V' and resid 87 through 102 removed outlier: 3.916A pdb=" N ARG V 102 " --> pdb=" O GLN V 98 " (cutoff:3.500A) Processing helix chain 'V' and resid 104 through 107 No H-bonds generated for 'chain 'V' and resid 104 through 107' Processing helix chain 'V' and resid 111 through 128 Processing helix chain 'V' and resid 135 through 141 removed outlier: 3.854A pdb=" N LEU V 141 " --> pdb=" O ALA V 137 " (cutoff:3.500A) Processing helix chain 'V' and resid 146 through 159 Processing helix chain 'V' and resid 169 through 179 removed outlier: 3.953A pdb=" N SER V 178 " --> pdb=" O LYS V 174 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N SER V 179 " --> pdb=" O THR V 175 " (cutoff:3.500A) Processing helix chain 'V' and resid 191 through 193 No H-bonds generated for 'chain 'V' and resid 191 through 193' Processing helix chain 'V' and resid 197 through 213 Processing helix chain 'V' and resid 222 through 242 removed outlier: 3.791A pdb=" N GLN V 238 " --> pdb=" O TRP V 234 " (cutoff:3.500A) Proline residue: V 239 - end of helix Processing helix chain 'V' and resid 247 through 254 Processing helix chain 'V' and resid 262 through 277 Processing helix chain 'V' and resid 281 through 286 Processing helix chain 'V' and resid 294 through 302 removed outlier: 5.023A pdb=" N GLY V 298 " --> pdb=" O LYS V 295 " (cutoff:3.500A) Processing helix chain 'V' and resid 304 through 312 Processing helix chain 'V' and resid 387 through 392 Processing helix chain 'V' and resid 396 through 405 Processing helix chain 'W' and resid 305 through 318 Processing helix chain 'W' and resid 322 through 327 Processing helix chain 'W' and resid 334 through 347 Processing helix chain 'W' and resid 349 through 357 Processing helix chain 'W' and resid 365 through 383 Processing sheet with id= A, first strand: chain '1' and resid 97 through 100 Processing sheet with id= B, first strand: chain '3' and resid 326 through 328 Processing sheet with id= C, first strand: chain '3' and resid 185 through 187 removed outlier: 3.668A pdb=" N VAL 3 320 " --> pdb=" O LEU 3 187 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N LEU 3 310 " --> pdb=" O TYR 3 253 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N TYR 3 253 " --> pdb=" O LEU 3 310 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain '3' and resid 257 through 260 removed outlier: 6.942A pdb=" N GLN 3 289 " --> pdb=" O PHE 3 258 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N ASN 3 260 " --> pdb=" O GLN 3 289 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ALA 3 291 " --> pdb=" O ASN 3 260 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain '3' and resid 364 through 367 Processing sheet with id= F, first strand: chain 'A' and resid 17 through 19 Processing sheet with id= G, first strand: chain 'A' and resid 84 through 87 Processing sheet with id= H, first strand: chain 'A' and resid 166 through 168 Processing sheet with id= I, first strand: chain 'A' and resid 364 through 368 Processing sheet with id= J, first strand: chain 'A' and resid 369 through 371 removed outlier: 5.934A pdb=" N PHE A 486 " --> pdb=" O SER A 370 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'A' and resid 391 through 395 Processing sheet with id= L, first strand: chain 'A' and resid 420 through 422 Processing sheet with id= M, first strand: chain 'A' and resid 617 through 620 Processing sheet with id= N, first strand: chain 'A' and resid 1085 through 1088 Processing sheet with id= O, first strand: chain 'A' and resid 1165 through 1167 removed outlier: 3.697A pdb=" N TYR A1116 " --> pdb=" O LYS A1131 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 125 through 128 removed outlier: 6.535A pdb=" N GLU B 118 " --> pdb=" O TYR B 77 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N TYR B 77 " --> pdb=" O GLU B 118 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N THR B 120 " --> pdb=" O LEU B 75 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N LEU B 75 " --> pdb=" O THR B 120 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 169 through 171 Processing sheet with id= R, first strand: chain 'B' and resid 181 through 184 Processing sheet with id= S, first strand: chain 'B' and resid 189 through 193 Processing sheet with id= T, first strand: chain 'B' and resid 424 through 426 Processing sheet with id= U, first strand: chain 'B' and resid 454 through 456 Processing sheet with id= V, first strand: chain 'B' and resid 573 through 577 Processing sheet with id= W, first strand: chain 'B' and resid 593 through 597 Processing sheet with id= X, first strand: chain 'B' and resid 708 through 712 removed outlier: 3.849A pdb=" N LYS B 868 " --> pdb=" O LEU B 884 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ARG B 886 " --> pdb=" O ILE B 866 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N ILE B 866 " --> pdb=" O ARG B 886 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'B' and resid 1003 through 1009 removed outlier: 4.005A pdb=" N TYR B1003 " --> pdb=" O VAL B 743 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE B 927 " --> pdb=" O ALA B 742 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N LEU B 757 " --> pdb=" O GLY B 908 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ILE B 910 " --> pdb=" O LEU B 757 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'B' and resid 831 through 833 Processing sheet with id= AA, first strand: chain 'B' and resid 1074 through 1080 Processing sheet with id= AB, first strand: chain 'B' and resid 110 through 115 removed outlier: 6.179A pdb=" N VAL B 115 " --> pdb=" O PRO B 132 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'B' and resid 536 through 541 removed outlier: 6.057A pdb=" N LEU B 541 " --> pdb=" O ILE B 545 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N ILE B 545 " --> pdb=" O LEU B 541 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'B' and resid 825 through 828 removed outlier: 4.437A pdb=" N GLN B 825 " --> pdb=" O TYR B 858 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ILE B 856 " --> pdb=" O LEU B 827 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'C' and resid 13 through 15 Processing sheet with id= AF, first strand: chain 'C' and resid 50 through 57 removed outlier: 6.864A pdb=" N GLU C 62 " --> pdb=" O VAL C 54 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N MET C 56 " --> pdb=" O SER C 60 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N SER C 60 " --> pdb=" O MET C 56 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'C' and resid 174 through 176 removed outlier: 4.272A pdb=" N GLN C 139 " --> pdb=" O ILE C 176 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL C 215 " --> pdb=" O VAL C 89 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N VAL C 89 " --> pdb=" O VAL C 215 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N GLY C 217 " --> pdb=" O MET C 87 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N MET C 87 " --> pdb=" O GLY C 217 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'C' and resid 262 through 266 Processing sheet with id= AI, first strand: chain 'C' and resid 167 through 169 removed outlier: 3.560A pdb=" N ALA C 200 " --> pdb=" O VAL C 168 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'E' and resid 72 through 75 removed outlier: 6.692A pdb=" N ARG E 101 " --> pdb=" O PHE E 73 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N PHE E 75 " --> pdb=" O ARG E 101 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU E 103 " --> pdb=" O PHE E 75 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE E 126 " --> pdb=" O ALA E 102 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N ILE E 104 " --> pdb=" O ILE E 126 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N GLU E 128 " --> pdb=" O ILE E 104 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N VAL E 106 " --> pdb=" O GLU E 128 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N PHE E 130 " --> pdb=" O VAL E 106 " (cutoff:3.500A) No H-bonds generated for sheet with id= AJ Processing sheet with id= AK, first strand: chain 'E' and resid 147 through 151 removed outlier: 3.616A pdb=" N GLU E 147 " --> pdb=" O ILE E 194 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N VAL E 190 " --> pdb=" O MET E 151 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'F' and resid 105 through 109 Processing sheet with id= AM, first strand: chain 'G' and resid 3 through 13 Processing sheet with id= AN, first strand: chain 'G' and resid 37 through 39 removed outlier: 4.254A pdb=" N LYS G 37 " --> pdb=" O CYS G 45 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU G 44 " --> pdb=" O PHE G 77 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N VAL G 75 " --> pdb=" O ILE G 46 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'G' and resid 146 through 149 Processing sheet with id= AP, first strand: chain 'G' and resid 50 through 54 removed outlier: 6.800A pdb=" N HIS G 71 " --> pdb=" O THR G 52 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'H' and resid 25 through 31 removed outlier: 5.607A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N SER H 139 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N HIS H 29 " --> pdb=" O LYS H 13 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'I' and resid 13 through 16 Processing sheet with id= AS, first strand: chain 'I' and resid 78 through 82 Processing sheet with id= AT, first strand: chain 'K' and resid 26 through 30 Processing sheet with id= AU, first strand: chain 'L' and resid 25 through 27 Processing sheet with id= AV, first strand: chain 'M' and resid 14 through 18 Processing sheet with id= AW, first strand: chain 'M' and resid 26 through 30 removed outlier: 7.247A pdb=" N GLY M 131 " --> pdb=" O LEU M 27 " (cutoff:3.500A) removed outlier: 8.556A pdb=" N GLN M 29 " --> pdb=" O GLY M 131 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N LEU M 133 " --> pdb=" O GLN M 29 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N ALA M 61 " --> pdb=" O HIS M 44 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N HIS M 44 " --> pdb=" O ALA M 61 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'M' and resid 318 through 321 Processing sheet with id= AY, first strand: chain 'M' and resid 390 through 393 Processing sheet with id= AZ, first strand: chain 'N' and resid 267 through 270 removed outlier: 6.867A pdb=" N HIS N 381 " --> pdb=" O PHE N 268 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N GLN N 270 " --> pdb=" O HIS N 381 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N LEU N 383 " --> pdb=" O GLN N 270 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N VAL N 337 " --> pdb=" O VAL N 348 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'N' and resid 359 through 364 removed outlier: 6.127A pdb=" N SER N 362 " --> pdb=" O VAL N 375 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N VAL N 375 " --> pdb=" O SER N 362 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N GLY N 364 " --> pdb=" O MET N 373 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N MET N 373 " --> pdb=" O GLY N 364 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'O' and resid 63 through 67 Processing sheet with id= BC, first strand: chain 'O' and resid 157 through 159 Processing sheet with id= BD, first strand: chain 'P' and resid 63 through 68 Processing sheet with id= BE, first strand: chain 'P' and resid 136 through 140 Processing sheet with id= BF, first strand: chain 'P' and resid 248 through 253 Processing sheet with id= BG, first strand: chain 'U' and resid 170 through 173 Processing sheet with id= BH, first strand: chain 'U' and resid 291 through 295 removed outlier: 3.710A pdb=" N GLY U 314 " --> pdb=" O MET U 258 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N MET U 258 " --> pdb=" O GLY U 314 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N SER U 261 " --> pdb=" O LEU U 165 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N LEU U 165 " --> pdb=" O SER U 261 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'V' and resid 15 through 19 removed outlier: 3.583A pdb=" N VAL V 27 " --> pdb=" O VAL V 16 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ASP V 18 " --> pdb=" O GLN V 25 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLN V 25 " --> pdb=" O ASP V 18 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N THR V 36 " --> pdb=" O LEU V 26 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N CYS V 28 " --> pdb=" O VAL V 34 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL V 34 " --> pdb=" O CYS V 28 " (cutoff:3.500A) 1972 hydrogen bonds defined for protein. 5571 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 68 hydrogen bonds 136 hydrogen bond angles 0 basepair planarities 27 basepair parallelities 102 stacking parallelities Total time for adding SS restraints: 22.16 Time building geometry restraints manager: 19.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.43: 24807 1.43 - 1.64: 34332 1.64 - 1.85: 547 1.85 - 2.07: 0 2.07 - 2.28: 12 Bond restraints: 59698 Sorted by residual: bond pdb=" C PRO 1 68 " pdb=" N PRO 1 69 " ideal model delta sigma weight residual 1.335 1.368 -0.034 1.19e-02 7.06e+03 7.96e+00 bond pdb=" C ASP 3 375 " pdb=" N PRO 3 376 " ideal model delta sigma weight residual 1.334 1.376 -0.042 2.34e-02 1.83e+03 3.21e+00 bond pdb=" C TYR 3 340 " pdb=" N PRO 3 341 " ideal model delta sigma weight residual 1.334 1.372 -0.039 2.34e-02 1.83e+03 2.72e+00 bond pdb=" C3' DA X 15 " pdb=" O3' DA X 15 " ideal model delta sigma weight residual 1.422 1.462 -0.040 3.00e-02 1.11e+03 1.81e+00 bond pdb=" C GLN G 116 " pdb=" N PRO G 117 " ideal model delta sigma weight residual 1.334 1.364 -0.030 2.34e-02 1.83e+03 1.62e+00 ... (remaining 59693 not shown) Histogram of bond angle deviations from ideal: 73.71 - 85.77: 12 85.77 - 97.82: 0 97.82 - 109.88: 8083 109.88 - 121.93: 60792 121.93 - 133.99: 12401 Bond angle restraints: 81288 Sorted by residual: angle pdb=" N VAL K 93 " pdb=" CA VAL K 93 " pdb=" C VAL K 93 " ideal model delta sigma weight residual 111.81 107.82 3.99 8.60e-01 1.35e+00 2.15e+01 angle pdb=" N ILE A1303 " pdb=" CA ILE A1303 " pdb=" C ILE A1303 " ideal model delta sigma weight residual 112.80 108.28 4.52 1.15e+00 7.56e-01 1.55e+01 angle pdb=" N VAL B 36 " pdb=" CA VAL B 36 " pdb=" C VAL B 36 " ideal model delta sigma weight residual 113.53 110.29 3.24 9.80e-01 1.04e+00 1.10e+01 angle pdb=" C LEU 3 339 " pdb=" N TYR 3 340 " pdb=" CA TYR 3 340 " ideal model delta sigma weight residual 122.28 118.92 3.36 1.02e+00 9.61e-01 1.08e+01 angle pdb=" N SER P 79 " pdb=" CA SER P 79 " pdb=" C SER P 79 " ideal model delta sigma weight residual 114.56 110.44 4.12 1.27e+00 6.20e-01 1.05e+01 ... (remaining 81283 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.33: 35306 34.33 - 68.65: 829 68.65 - 102.98: 40 102.98 - 137.30: 0 137.30 - 171.63: 4 Dihedral angle restraints: 36179 sinusoidal: 16157 harmonic: 20022 Sorted by residual: dihedral pdb=" CA TYR A1187 " pdb=" C TYR A1187 " pdb=" N VAL A1188 " pdb=" CA VAL A1188 " ideal model delta harmonic sigma weight residual 180.00 157.63 22.37 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA TYR 3 340 " pdb=" C TYR 3 340 " pdb=" N PRO 3 341 " pdb=" CA PRO 3 341 " ideal model delta harmonic sigma weight residual 180.00 158.54 21.46 0 5.00e+00 4.00e-02 1.84e+01 dihedral pdb=" C4' DG X -18 " pdb=" C3' DG X -18 " pdb=" O3' DG X -18 " pdb=" P DT X -17 " ideal model delta sinusoidal sigma weight residual -140.00 31.63 -171.63 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 36176 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 6363 0.032 - 0.064: 1821 0.064 - 0.096: 561 0.096 - 0.128: 291 0.128 - 0.160: 15 Chirality restraints: 9051 Sorted by residual: chirality pdb=" CA ILE G 148 " pdb=" N ILE G 148 " pdb=" C ILE G 148 " pdb=" CB ILE G 148 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.38e-01 chirality pdb=" CA ILE A1117 " pdb=" N ILE A1117 " pdb=" C ILE A1117 " pdb=" CB ILE A1117 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.18e-01 chirality pdb=" CA ILE O 375 " pdb=" N ILE O 375 " pdb=" C ILE O 375 " pdb=" CB ILE O 375 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.90e-01 ... (remaining 9048 not shown) Planarity restraints: 9902 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 56 " 0.028 5.00e-02 4.00e+02 4.29e-02 2.95e+00 pdb=" N PRO D 57 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO D 57 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 57 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DT X -29 " -0.022 2.00e-02 2.50e+03 9.80e-03 2.40e+00 pdb=" N1 DT X -29 " 0.017 2.00e-02 2.50e+03 pdb=" C2 DT X -29 " 0.003 2.00e-02 2.50e+03 pdb=" O2 DT X -29 " 0.005 2.00e-02 2.50e+03 pdb=" N3 DT X -29 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DT X -29 " -0.004 2.00e-02 2.50e+03 pdb=" O4 DT X -29 " -0.008 2.00e-02 2.50e+03 pdb=" C5 DT X -29 " -0.002 2.00e-02 2.50e+03 pdb=" C7 DT X -29 " 0.003 2.00e-02 2.50e+03 pdb=" C6 DT X -29 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU P 94 " -0.007 2.00e-02 2.50e+03 1.38e-02 1.92e+00 pdb=" C LEU P 94 " 0.024 2.00e-02 2.50e+03 pdb=" O LEU P 94 " -0.009 2.00e-02 2.50e+03 pdb=" N VAL P 95 " -0.008 2.00e-02 2.50e+03 ... (remaining 9899 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 276 2.49 - 3.09: 40672 3.09 - 3.69: 88799 3.69 - 4.30: 129738 4.30 - 4.90: 209851 Nonbonded interactions: 469336 Sorted by model distance: nonbonded pdb=" OD2 ASP B 401 " pdb=" NZ LYS B 404 " model vdw 1.886 2.520 nonbonded pdb=" O CYS 3 221 " pdb=" OD1 ASP 3 224 " model vdw 1.959 3.040 nonbonded pdb=" O ARG 3 101 " pdb=" SG CYS 3 104 " model vdw 2.087 3.400 nonbonded pdb=" CD1 LEU V 111 " pdb=" OP2 DT X -17 " model vdw 2.128 3.460 nonbonded pdb=" OD2 ASP A 503 " pdb="MG MG A1403 " model vdw 2.128 2.170 ... (remaining 469331 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 0.010 Normalize map: mean=0, sd=1: 1.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 9.250 Check model and map are aligned: 0.690 Set scattering table: 0.410 Process input model: 148.540 Find NCS groups from input model: 1.450 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: 0.010 Load rotamer database and sin/cos tables:2.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 164.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6519 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 : 0.002 0.042 59698 Z= 0.117 Angle : 0.469 10.904 81288 Z= 0.285 Chirality : 0.037 0.160 9051 Planarity : 0.003 0.043 9902 Dihedral : 12.781 171.627 23225 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.56 % Favored : 97.42 % Rotamer: Outliers : 0.02 % Allowed : 4.29 % Favored : 95.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.09), residues: 6799 helix: -0.27 (0.09), residues: 2750 sheet: -1.14 (0.17), residues: 834 loop : -1.76 (0.10), residues: 3215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP P 313 HIS 0.002 0.000 HIS M 44 PHE 0.008 0.001 PHE U 266 TYR 0.011 0.001 TYR A1116 ARG 0.003 0.000 ARG 4 442 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13598 Ramachandran restraints generated. 6799 Oldfield, 0 Emsley, 6799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13598 Ramachandran restraints generated. 6799 Oldfield, 0 Emsley, 6799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1507 residues out of total 6063 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1506 time to evaluate : 5.060 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 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 REVERT: 1 45 ARG cc_start: 0.4532 (mmp80) cc_final: 0.3980 (ttp80) REVERT: 1 46 MET cc_start: 0.0369 (ptm) cc_final: -0.1388 (tmm) REVERT: 1 135 PHE cc_start: 0.2897 (m-80) cc_final: 0.2426 (m-80) REVERT: 3 28 ASN cc_start: 0.2894 (t0) cc_final: 0.2520 (m-40) REVERT: 3 33 GLU cc_start: 0.3331 (tt0) cc_final: 0.2864 (tm-30) REVERT: 3 158 GLU cc_start: 0.4135 (tp30) cc_final: 0.3877 (tt0) REVERT: 3 162 HIS cc_start: 0.2311 (m90) cc_final: 0.2033 (m-70) REVERT: 3 281 HIS cc_start: 0.3911 (m90) cc_final: 0.3248 (t-170) REVERT: 3 343 LEU cc_start: 0.2313 (mp) cc_final: 0.2059 (mp) REVERT: 3 358 LYS cc_start: 0.3449 (mmtt) cc_final: 0.3189 (mtmm) REVERT: 3 359 MET cc_start: 0.3252 (mtt) cc_final: 0.2845 (mmm) REVERT: 3 364 TRP cc_start: 0.6234 (m100) cc_final: 0.5667 (m100) REVERT: 3 411 ASN cc_start: 0.4000 (t0) cc_final: 0.3351 (m110) REVERT: 4 210 LEU cc_start: 0.6547 (tp) cc_final: 0.6301 (pp) REVERT: 4 229 GLN cc_start: 0.4246 (mm110) cc_final: 0.3714 (tt0) REVERT: 4 237 GLU cc_start: 0.7182 (mt-10) cc_final: 0.6754 (tp30) REVERT: 4 271 PHE cc_start: 0.7578 (m-80) cc_final: 0.7234 (m-80) REVERT: 4 280 ILE cc_start: 0.6972 (pt) cc_final: 0.6750 (tp) REVERT: 4 288 GLU cc_start: 0.4175 (mm-30) cc_final: 0.3841 (tp30) REVERT: 4 385 MET cc_start: 0.2145 (tmm) cc_final: 0.1290 (tpt) REVERT: A 123 LYS cc_start: 0.7587 (ttpp) cc_final: 0.7327 (tptp) REVERT: A 130 LYS cc_start: 0.7613 (mmtm) cc_final: 0.7386 (mtpp) REVERT: A 240 MET cc_start: 0.7665 (ttp) cc_final: 0.7411 (ttp) REVERT: A 307 MET cc_start: 0.7095 (mmm) cc_final: 0.6882 (mmt) REVERT: A 336 LYS cc_start: 0.7334 (ptmt) cc_final: 0.6789 (tttt) REVERT: A 337 TRP cc_start: 0.7980 (t60) cc_final: 0.7063 (t60) REVERT: A 379 GLU cc_start: 0.7462 (mt-10) cc_final: 0.7073 (mt-10) REVERT: A 424 ARG cc_start: 0.5420 (ttt180) cc_final: 0.4157 (ttp80) REVERT: A 627 LYS cc_start: 0.7684 (tmtt) cc_final: 0.7024 (ttmt) REVERT: A 647 SER cc_start: 0.8841 (t) cc_final: 0.8393 (p) REVERT: A 675 GLU cc_start: 0.5693 (mm-30) cc_final: 0.5468 (mm-30) REVERT: A 729 GLU cc_start: 0.7512 (tp30) cc_final: 0.6733 (tp30) REVERT: A 811 ASP cc_start: 0.7616 (p0) cc_final: 0.7380 (p0) REVERT: A 871 MET cc_start: 0.7107 (ttp) cc_final: 0.6768 (ttt) REVERT: A 872 GLN cc_start: 0.7604 (tp40) cc_final: 0.7204 (tm-30) REVERT: A 917 GLU cc_start: 0.7286 (mm-30) cc_final: 0.6417 (mt-10) REVERT: A 926 ASP cc_start: 0.7711 (m-30) cc_final: 0.7484 (m-30) REVERT: A 1186 TYR cc_start: 0.6228 (m-10) cc_final: 0.5990 (m-10) REVERT: A 1206 GLU cc_start: 0.7558 (mp0) cc_final: 0.7140 (mp0) REVERT: A 1236 MET cc_start: 0.8057 (mtm) cc_final: 0.7685 (mtm) REVERT: B 154 GLU cc_start: 0.8217 (mt-10) cc_final: 0.7835 (mt-10) REVERT: B 253 GLN cc_start: 0.7500 (mt0) cc_final: 0.7277 (mt0) REVERT: B 254 MET cc_start: 0.8143 (mtp) cc_final: 0.7916 (mtp) REVERT: B 259 GLU cc_start: 0.7573 (tp30) cc_final: 0.7268 (pt0) REVERT: B 311 GLU cc_start: 0.8049 (mm-30) cc_final: 0.7115 (mt-10) REVERT: B 315 SER cc_start: 0.8724 (t) cc_final: 0.8463 (p) REVERT: B 355 ASP cc_start: 0.6901 (p0) cc_final: 0.6401 (m-30) REVERT: B 406 MET cc_start: 0.8747 (mmm) cc_final: 0.8272 (mmm) REVERT: B 432 ASP cc_start: 0.6926 (t0) cc_final: 0.6398 (t70) REVERT: B 488 GLU cc_start: 0.6762 (pt0) cc_final: 0.6151 (tp30) REVERT: B 499 MET cc_start: 0.8747 (ttp) cc_final: 0.8115 (ttm) REVERT: B 525 LEU cc_start: 0.7949 (tp) cc_final: 0.7601 (mm) REVERT: B 709 MET cc_start: 0.8826 (ttp) cc_final: 0.8521 (ttp) REVERT: B 719 MET cc_start: 0.7359 (mmm) cc_final: 0.7132 (mmm) REVERT: B 781 ARG cc_start: 0.7224 (ttm-80) cc_final: 0.6786 (ttm170) REVERT: B 791 MET cc_start: 0.7439 (mmt) cc_final: 0.7158 (mmp) REVERT: B 1069 MET cc_start: 0.8243 (tmm) cc_final: 0.8037 (tmm) REVERT: C 50 ARG cc_start: 0.7645 (ptt90) cc_final: 0.7305 (ptt-90) REVERT: C 52 ASP cc_start: 0.7410 (m-30) cc_final: 0.7145 (p0) REVERT: C 289 ARG cc_start: 0.8015 (mtp180) cc_final: 0.7535 (mtm180) REVERT: C 292 LYS cc_start: 0.7420 (tmtt) cc_final: 0.7025 (tptt) REVERT: C 309 SER cc_start: 0.8774 (m) cc_final: 0.8098 (p) REVERT: D 1 MET cc_start: 0.5277 (mmp) cc_final: 0.5045 (mmp) REVERT: D 13 ASN cc_start: 0.6853 (m-40) cc_final: 0.6330 (m-40) REVERT: D 14 TYR cc_start: 0.6302 (t80) cc_final: 0.5986 (t80) REVERT: D 22 ASP cc_start: 0.7481 (m-30) cc_final: 0.7024 (t0) REVERT: D 65 ILE cc_start: 0.7821 (mt) cc_final: 0.7611 (tt) REVERT: D 118 HIS cc_start: 0.7033 (m170) cc_final: 0.6718 (t-90) REVERT: E 56 THR cc_start: 0.5515 (m) cc_final: 0.5278 (p) REVERT: E 61 LEU cc_start: 0.6649 (mm) cc_final: 0.5922 (mm) REVERT: E 75 PHE cc_start: 0.6566 (m-80) cc_final: 0.5533 (m-10) REVERT: E 91 CYS cc_start: 0.6777 (t) cc_final: 0.6315 (m) REVERT: E 100 THR cc_start: 0.7211 (p) cc_final: 0.6977 (p) REVERT: E 121 MET cc_start: 0.6152 (mmp) cc_final: 0.5901 (mmm) REVERT: E 125 TYR cc_start: 0.4199 (m-80) cc_final: 0.3994 (m-80) REVERT: E 137 ILE cc_start: 0.7243 (tp) cc_final: 0.6987 (tt) REVERT: E 168 ASN cc_start: 0.7792 (p0) cc_final: 0.7532 (p0) REVERT: E 177 ASP cc_start: 0.8301 (t70) cc_final: 0.7830 (t0) REVERT: F 51 ARG cc_start: 0.6017 (mtm-85) cc_final: 0.4866 (mmm160) REVERT: F 56 TYR cc_start: 0.8878 (m-80) cc_final: 0.8396 (m-80) REVERT: F 114 SER cc_start: 0.8456 (t) cc_final: 0.8253 (m) REVERT: G 7 MET cc_start: 0.7560 (mtp) cc_final: 0.7205 (mtp) REVERT: G 157 PHE cc_start: 0.6514 (t80) cc_final: 0.6094 (t80) REVERT: H 11 ASP cc_start: 0.6624 (t0) cc_final: 0.6172 (t70) REVERT: H 13 LYS cc_start: 0.8487 (mmtp) cc_final: 0.7774 (mmtt) REVERT: H 15 ILE cc_start: 0.8287 (mm) cc_final: 0.7969 (mp) REVERT: H 51 ASP cc_start: 0.7265 (m-30) cc_final: 0.7020 (m-30) REVERT: H 62 SER cc_start: 0.8535 (t) cc_final: 0.8017 (p) REVERT: H 128 ASP cc_start: 0.7833 (m-30) cc_final: 0.7471 (m-30) REVERT: H 138 ASP cc_start: 0.7420 (t0) cc_final: 0.6875 (t0) REVERT: I 105 ARG cc_start: 0.5234 (ttt90) cc_final: 0.4759 (ttt-90) REVERT: J 36 ASP cc_start: 0.7591 (m-30) cc_final: 0.7314 (m-30) REVERT: J 46 ARG cc_start: 0.8319 (mtp85) cc_final: 0.7739 (mtp180) REVERT: K 46 GLU cc_start: 0.7781 (pm20) cc_final: 0.7264 (pm20) REVERT: K 47 GLU cc_start: 0.6973 (mm-30) cc_final: 0.6550 (mm-30) REVERT: K 78 SER cc_start: 0.8354 (m) cc_final: 0.7976 (p) REVERT: K 98 ARG cc_start: 0.6610 (mmm-85) cc_final: 0.6405 (ttt-90) REVERT: K 108 GLN cc_start: 0.8011 (tp40) cc_final: 0.7259 (tp-100) REVERT: K 112 ASP cc_start: 0.7295 (m-30) cc_final: 0.6849 (m-30) REVERT: L 25 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7271 (mt-10) REVERT: L 47 LYS cc_start: 0.8233 (mtpp) cc_final: 0.8001 (mtpp) REVERT: M 16 TYR cc_start: 0.7067 (m-10) cc_final: 0.6843 (m-80) REVERT: M 60 MET cc_start: 0.6052 (mtm) cc_final: 0.5311 (mtm) REVERT: M 66 ASN cc_start: 0.6710 (p0) cc_final: 0.5864 (p0) REVERT: M 121 GLN cc_start: 0.6518 (pm20) cc_final: 0.6237 (mp10) REVERT: M 143 ASP cc_start: 0.5627 (m-30) cc_final: 0.5333 (t0) REVERT: M 146 ASP cc_start: 0.6106 (m-30) cc_final: 0.5540 (t70) REVERT: M 272 GLN cc_start: 0.7252 (mt0) cc_final: 0.6558 (tp-100) REVERT: M 294 PHE cc_start: 0.7277 (t80) cc_final: 0.7040 (t80) REVERT: M 399 GLU cc_start: 0.6398 (tt0) cc_final: 0.5942 (tt0) REVERT: N 263 GLU cc_start: 0.7633 (tp30) cc_final: 0.6780 (pt0) REVERT: N 314 ASN cc_start: 0.4523 (m-40) cc_final: 0.4181 (m110) REVERT: N 330 LEU cc_start: 0.7498 (mp) cc_final: 0.7268 (mm) REVERT: N 345 THR cc_start: 0.7925 (p) cc_final: 0.7565 (p) REVERT: O 34 GLN cc_start: 0.6862 (mt0) cc_final: 0.5780 (mm110) REVERT: O 85 MET cc_start: 0.8252 (ttm) cc_final: 0.8049 (ttm) REVERT: O 155 HIS cc_start: 0.7468 (m-70) cc_final: 0.7160 (m170) REVERT: O 187 MET cc_start: 0.5857 (tpt) cc_final: 0.5374 (tpp) REVERT: O 340 LYS cc_start: 0.7465 (mmmt) cc_final: 0.7257 (mttt) REVERT: O 474 MET cc_start: 0.1363 (ppp) cc_final: -0.0426 (tmm) REVERT: P 60 MET cc_start: 0.2171 (ptt) cc_final: 0.1338 (tmm) REVERT: P 105 LYS cc_start: 0.7269 (mttt) cc_final: 0.7040 (tppt) REVERT: P 151 MET cc_start: 0.4998 (mtp) cc_final: 0.4744 (mtp) REVERT: P 167 TYR cc_start: 0.6859 (m-80) cc_final: 0.6272 (m-10) REVERT: P 182 GLN cc_start: 0.7629 (mm110) cc_final: 0.7326 (mm-40) REVERT: P 197 GLU cc_start: 0.5640 (mm-30) cc_final: 0.5254 (tp30) REVERT: P 210 PHE cc_start: 0.6931 (m-10) cc_final: 0.6666 (m-80) REVERT: P 236 GLU cc_start: 0.6996 (tt0) cc_final: 0.6612 (tm-30) REVERT: P 250 MET cc_start: 0.6958 (tmm) cc_final: 0.6015 (ttp) REVERT: P 251 THR cc_start: 0.7792 (p) cc_final: 0.7224 (p) REVERT: P 301 GLU cc_start: 0.7684 (mt-10) cc_final: 0.7218 (mp0) REVERT: Q 42 ASP cc_start: 0.6048 (p0) cc_final: 0.5710 (p0) REVERT: Q 44 LYS cc_start: 0.8330 (mmmt) cc_final: 0.8064 (mmmt) REVERT: Q 54 GLU cc_start: 0.7926 (mp0) cc_final: 0.7380 (mp0) REVERT: Q 60 LEU cc_start: 0.6638 (tp) cc_final: 0.6183 (tp) REVERT: Q 63 GLU cc_start: 0.7099 (mt-10) cc_final: 0.6873 (pt0) REVERT: Q 89 LYS cc_start: 0.4222 (tttp) cc_final: 0.3817 (tmtt) REVERT: Q 103 TRP cc_start: 0.7638 (m100) cc_final: 0.7048 (m100) REVERT: U 171 THR cc_start: 0.4981 (t) cc_final: 0.4489 (t) REVERT: U 210 THR cc_start: 0.6799 (m) cc_final: 0.6338 (m) REVERT: U 239 ARG cc_start: 0.6363 (mmm160) cc_final: 0.6139 (mtm180) REVERT: U 279 GLN cc_start: 0.6842 (pm20) cc_final: 0.6099 (mm-40) REVERT: U 280 PHE cc_start: 0.6619 (m-80) cc_final: 0.6040 (m-80) REVERT: U 285 PRO cc_start: 0.8625 (Cg_endo) cc_final: 0.8218 (Cg_exo) REVERT: V 52 GLU cc_start: 0.3006 (pp20) cc_final: 0.2580 (mp0) REVERT: V 61 GLU cc_start: 0.6451 (mp0) cc_final: 0.5372 (mp0) REVERT: V 62 ASN cc_start: 0.7663 (m-40) cc_final: 0.7361 (t0) REVERT: V 88 THR cc_start: 0.8142 (p) cc_final: 0.7917 (t) REVERT: V 91 ASP cc_start: 0.7428 (m-30) cc_final: 0.6779 (m-30) REVERT: V 135 MET cc_start: 0.7669 (mtt) cc_final: 0.7459 (mtp) REVERT: V 139 CYS cc_start: 0.7741 (t) cc_final: 0.7440 (p) REVERT: V 155 GLN cc_start: 0.7659 (tt0) cc_final: 0.6809 (mm110) REVERT: V 209 GLU cc_start: 0.7413 (tp30) cc_final: 0.6953 (tp30) REVERT: V 235 GLN cc_start: 0.6623 (mt0) cc_final: 0.6399 (mm-40) REVERT: W 293 SER cc_start: 0.4266 (p) cc_final: 0.3416 (t) REVERT: W 301 LYS cc_start: 0.6131 (tmtt) cc_final: 0.5639 (mmtm) REVERT: W 307 GLU cc_start: 0.4509 (tt0) cc_final: 0.4269 (tt0) REVERT: W 336 GLU cc_start: 0.8033 (mt-10) cc_final: 0.7556 (mt-10) REVERT: W 370 LEU cc_start: 0.5686 (tt) cc_final: 0.5480 (pp) outliers start: 1 outliers final: 1 residues processed: 1507 average time/residue: 0.6810 time to fit residues: 1653.6082 Evaluate side-chains 734 residues out of total 6063 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 733 time to evaluate : 5.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 55 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 691 random chunks: chunk 583 optimal weight: 6.9990 chunk 523 optimal weight: 1.9990 chunk 290 optimal weight: 6.9990 chunk 178 optimal weight: 3.9990 chunk 353 optimal weight: 0.6980 chunk 279 optimal weight: 7.9990 chunk 541 optimal weight: 0.0040 chunk 209 optimal weight: 5.9990 chunk 329 optimal weight: 1.9990 chunk 403 optimal weight: 0.6980 chunk 627 optimal weight: 6.9990 overall best weight: 1.0796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 48 ASN ** 1 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 185 ASN 3 367 ASN 3 388 HIS 3 411 ASN 4 171 GLN 4 186 ASN 4 229 GLN 4 243 GLN 4 295 GLN 4 312 HIS ** 4 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 457 ASN A 275 ASN A 374 ASN A 423 GLN ** A 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 528 ASN A 599 GLN ** A1039 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1054 HIS A1168 HIS B 395 GLN B 405 HIS B 408 GLN B 616 GLN B 913 GLN ** C 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 138 ASN H 29 HIS H 76 ASN I 83 GLN I 99 ASN I 104 HIS K 38 HIS K 81 ASN ** M 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 395 HIS O 158 GLN O 377 GLN O 402 ASN O 475 GLN O 497 GLN P 129 ASN P 182 GLN P 201 ASN U 242 GLN V 206 GLN V 397 GLN W 327 GLN Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6669 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 59698 Z= 0.170 Angle : 0.507 12.383 81288 Z= 0.259 Chirality : 0.040 0.209 9051 Planarity : 0.004 0.080 9902 Dihedral : 15.462 171.565 9298 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.68 % Allowed : 9.48 % Favored : 88.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.10), residues: 6799 helix: 0.65 (0.10), residues: 2745 sheet: -0.79 (0.17), residues: 842 loop : -1.28 (0.10), residues: 3212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP W 350 HIS 0.007 0.001 HIS E 64 PHE 0.028 0.001 PHE U 214 TYR 0.022 0.001 TYR U 192 ARG 0.011 0.000 ARG V 309 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13598 Ramachandran restraints generated. 6799 Oldfield, 0 Emsley, 6799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13598 Ramachandran restraints generated. 6799 Oldfield, 0 Emsley, 6799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 839 residues out of total 6063 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 737 time to evaluate : 5.166 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 45 ARG cc_start: 0.4290 (mmp80) cc_final: 0.3735 (ttp80) REVERT: 1 135 PHE cc_start: 0.2755 (m-80) cc_final: 0.2392 (m-80) REVERT: 3 33 GLU cc_start: 0.3248 (tt0) cc_final: 0.2879 (tm-30) REVERT: 3 158 GLU cc_start: 0.4003 (tp30) cc_final: 0.3744 (tt0) REVERT: 3 159 MET cc_start: 0.1062 (mtp) cc_final: 0.0811 (mtp) REVERT: 3 162 HIS cc_start: 0.2308 (m90) cc_final: 0.2028 (m-70) REVERT: 3 281 HIS cc_start: 0.4027 (m90) cc_final: 0.3366 (t-170) REVERT: 3 343 LEU cc_start: 0.2363 (mp) cc_final: 0.1998 (mp) REVERT: 3 359 MET cc_start: 0.3430 (mtt) cc_final: 0.3100 (ppp) REVERT: 3 364 TRP cc_start: 0.6158 (m100) cc_final: 0.5572 (m100) REVERT: 4 229 GLN cc_start: 0.4396 (mm-40) cc_final: 0.3822 (tt0) REVERT: 4 237 GLU cc_start: 0.7631 (mt-10) cc_final: 0.7316 (tp30) REVERT: 4 271 PHE cc_start: 0.8050 (m-80) cc_final: 0.7578 (m-80) REVERT: 4 385 MET cc_start: 0.2404 (tmm) cc_final: 0.1599 (tpt) REVERT: A 123 LYS cc_start: 0.7593 (ttpp) cc_final: 0.7359 (tptp) REVERT: A 240 MET cc_start: 0.8013 (ttp) cc_final: 0.7770 (ttp) REVERT: A 336 LYS cc_start: 0.7265 (ptmt) cc_final: 0.6469 (mttp) REVERT: A 379 GLU cc_start: 0.7527 (mt-10) cc_final: 0.7099 (mt-10) REVERT: A 424 ARG cc_start: 0.5482 (ttt180) cc_final: 0.4166 (ttp80) REVERT: A 499 ASP cc_start: 0.6611 (OUTLIER) cc_final: 0.6151 (p0) REVERT: A 627 LYS cc_start: 0.7679 (tmtt) cc_final: 0.7061 (ttmt) REVERT: A 675 GLU cc_start: 0.5718 (mm-30) cc_final: 0.5514 (mm-30) REVERT: A 729 GLU cc_start: 0.7510 (tp30) cc_final: 0.6720 (tp30) REVERT: A 811 ASP cc_start: 0.7630 (p0) cc_final: 0.7366 (p0) REVERT: A 905 ASP cc_start: 0.7152 (m-30) cc_final: 0.6653 (m-30) REVERT: A 917 GLU cc_start: 0.7560 (mm-30) cc_final: 0.6724 (mt-10) REVERT: A 1158 LEU cc_start: 0.7208 (OUTLIER) cc_final: 0.6764 (mt) REVERT: A 1236 MET cc_start: 0.8250 (mtm) cc_final: 0.7904 (mtm) REVERT: B 63 GLU cc_start: 0.7641 (pt0) cc_final: 0.7092 (tt0) REVERT: B 154 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7813 (mt-10) REVERT: B 254 MET cc_start: 0.8212 (mtp) cc_final: 0.7946 (mtp) REVERT: B 259 GLU cc_start: 0.7667 (tp30) cc_final: 0.7280 (pt0) REVERT: B 311 GLU cc_start: 0.7869 (mm-30) cc_final: 0.7179 (mt-10) REVERT: B 406 MET cc_start: 0.8796 (mmm) cc_final: 0.8221 (mmm) REVERT: B 430 LYS cc_start: 0.6433 (mmtm) cc_final: 0.6225 (mmtt) REVERT: B 432 ASP cc_start: 0.6833 (t0) cc_final: 0.6483 (t70) REVERT: B 488 GLU cc_start: 0.6862 (pt0) cc_final: 0.6230 (tp30) REVERT: B 499 MET cc_start: 0.8600 (ttp) cc_final: 0.8389 (ttm) REVERT: B 525 LEU cc_start: 0.8035 (tp) cc_final: 0.7740 (mm) REVERT: B 791 MET cc_start: 0.7535 (mmt) cc_final: 0.7227 (mmp) REVERT: B 853 ASP cc_start: 0.7979 (m-30) cc_final: 0.7584 (m-30) REVERT: B 916 MET cc_start: 0.8803 (mmt) cc_final: 0.8436 (mmt) REVERT: C 50 ARG cc_start: 0.7621 (ptt90) cc_final: 0.7368 (ptt-90) REVERT: C 52 ASP cc_start: 0.7455 (m-30) cc_final: 0.7183 (p0) REVERT: C 248 GLU cc_start: 0.7010 (pp20) cc_final: 0.6728 (tp30) REVERT: C 286 GLU cc_start: 0.8185 (tp30) cc_final: 0.7780 (tp30) REVERT: C 292 LYS cc_start: 0.7478 (tmtt) cc_final: 0.7003 (tptt) REVERT: C 309 SER cc_start: 0.8786 (m) cc_final: 0.8123 (p) REVERT: D 22 ASP cc_start: 0.7505 (m-30) cc_final: 0.6848 (m-30) REVERT: D 47 TYR cc_start: 0.6591 (t80) cc_final: 0.5953 (t80) REVERT: D 64 GLU cc_start: 0.7888 (mp0) cc_final: 0.7577 (pm20) REVERT: D 67 ARG cc_start: 0.5424 (tpt170) cc_final: 0.5062 (tpm170) REVERT: D 105 GLU cc_start: 0.6836 (mt-10) cc_final: 0.5925 (tm-30) REVERT: E 61 LEU cc_start: 0.6314 (mm) cc_final: 0.5779 (mm) REVERT: E 94 MET cc_start: 0.7171 (mmp) cc_final: 0.6281 (mtp) REVERT: E 121 MET cc_start: 0.6459 (mmp) cc_final: 0.6226 (mmm) REVERT: E 134 GLU cc_start: 0.7525 (mt-10) cc_final: 0.7105 (mm-30) REVERT: E 168 ASN cc_start: 0.7947 (p0) cc_final: 0.7590 (p0) REVERT: F 56 TYR cc_start: 0.8784 (m-80) cc_final: 0.8330 (m-80) REVERT: F 114 SER cc_start: 0.8526 (t) cc_final: 0.8293 (m) REVERT: G 7 MET cc_start: 0.7694 (mtp) cc_final: 0.7289 (mtp) REVERT: G 157 PHE cc_start: 0.6478 (t80) cc_final: 0.6124 (t80) REVERT: H 11 ASP cc_start: 0.6498 (t0) cc_final: 0.5983 (t70) REVERT: H 18 GLU cc_start: 0.7598 (mp0) cc_final: 0.7195 (mp0) REVERT: H 31 GLU cc_start: 0.6873 (mt-10) cc_final: 0.6337 (mp0) REVERT: H 51 ASP cc_start: 0.7416 (m-30) cc_final: 0.7100 (m-30) REVERT: H 62 SER cc_start: 0.8617 (t) cc_final: 0.8255 (p) REVERT: H 128 ASP cc_start: 0.7735 (m-30) cc_final: 0.7417 (m-30) REVERT: H 138 ASP cc_start: 0.7456 (t0) cc_final: 0.6876 (t0) REVERT: I 105 ARG cc_start: 0.4903 (ttt90) cc_final: 0.4665 (ttt-90) REVERT: J 33 ASP cc_start: 0.6878 (t0) cc_final: 0.6665 (t0) REVERT: J 36 ASP cc_start: 0.7529 (m-30) cc_final: 0.7227 (m-30) REVERT: K 60 MET cc_start: 0.8530 (mmt) cc_final: 0.8247 (mmm) REVERT: K 66 GLU cc_start: 0.7604 (tp30) cc_final: 0.6096 (tp30) REVERT: K 78 SER cc_start: 0.8392 (m) cc_final: 0.8043 (p) REVERT: K 97 GLN cc_start: 0.7340 (tt0) cc_final: 0.7045 (tt0) REVERT: K 98 ARG cc_start: 0.6689 (mmm-85) cc_final: 0.6457 (ttt-90) REVERT: K 108 GLN cc_start: 0.8010 (tp40) cc_final: 0.7284 (tp-100) REVERT: K 112 ASP cc_start: 0.7271 (m-30) cc_final: 0.6853 (m-30) REVERT: K 115 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7607 (mt-10) REVERT: L 15 MET cc_start: 0.6926 (tpt) cc_final: 0.6053 (tpt) REVERT: L 25 GLU cc_start: 0.7753 (mt-10) cc_final: 0.7539 (mt-10) REVERT: L 27 GLU cc_start: 0.5922 (mp0) cc_final: 0.5630 (mm-30) REVERT: L 35 ARG cc_start: 0.7570 (ttm-80) cc_final: 0.7076 (mtm-85) REVERT: L 47 LYS cc_start: 0.8327 (mtpp) cc_final: 0.7970 (mtpp) REVERT: M 60 MET cc_start: 0.6437 (mtm) cc_final: 0.5909 (mtm) REVERT: M 143 ASP cc_start: 0.5781 (m-30) cc_final: 0.5459 (t0) REVERT: M 146 ASP cc_start: 0.6045 (m-30) cc_final: 0.5691 (t70) REVERT: M 272 GLN cc_start: 0.7238 (mt0) cc_final: 0.6596 (tp-100) REVERT: M 286 MET cc_start: 0.8535 (mmm) cc_final: 0.8332 (mmm) REVERT: M 319 MET cc_start: 0.7566 (mmm) cc_final: 0.6895 (mmm) REVERT: M 399 GLU cc_start: 0.6623 (tt0) cc_final: 0.6294 (tt0) REVERT: N 314 ASN cc_start: 0.4517 (m-40) cc_final: 0.4187 (m110) REVERT: N 330 LEU cc_start: 0.7563 (mp) cc_final: 0.7289 (mm) REVERT: O 66 GLN cc_start: 0.7459 (mt0) cc_final: 0.7195 (tm-30) REVERT: O 85 MET cc_start: 0.8326 (ttm) cc_final: 0.8090 (ttm) REVERT: O 187 MET cc_start: 0.5858 (tpt) cc_final: 0.5542 (tpp) REVERT: O 340 LYS cc_start: 0.7460 (mmmt) cc_final: 0.7255 (mttt) REVERT: O 356 GLU cc_start: 0.8046 (mm-30) cc_final: 0.7799 (mp0) REVERT: O 474 MET cc_start: 0.1230 (ppp) cc_final: -0.0553 (tmm) REVERT: O 531 MET cc_start: 0.7780 (mtm) cc_final: 0.7501 (mtm) REVERT: P 105 LYS cc_start: 0.7284 (mttt) cc_final: 0.7052 (tppt) REVERT: P 159 ARG cc_start: 0.5458 (ttt180) cc_final: 0.4581 (tpt170) REVERT: P 167 TYR cc_start: 0.6858 (m-80) cc_final: 0.5447 (m-10) REVERT: P 197 GLU cc_start: 0.5572 (mm-30) cc_final: 0.5308 (tp30) REVERT: P 250 MET cc_start: 0.7134 (tmm) cc_final: 0.6501 (ttp) REVERT: P 251 THR cc_start: 0.7986 (p) cc_final: 0.7401 (p) REVERT: P 274 ASN cc_start: 0.8002 (m-40) cc_final: 0.7387 (t0) REVERT: P 292 VAL cc_start: 0.8162 (m) cc_final: 0.7924 (p) REVERT: P 301 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7369 (mp0) REVERT: Q 42 ASP cc_start: 0.6290 (p0) cc_final: 0.5936 (p0) REVERT: Q 44 LYS cc_start: 0.8397 (mmmt) cc_final: 0.8084 (mmmt) REVERT: Q 54 GLU cc_start: 0.8023 (mp0) cc_final: 0.7482 (mp0) REVERT: Q 57 MET cc_start: 0.7569 (ttm) cc_final: 0.7360 (mtm) REVERT: Q 103 TRP cc_start: 0.7622 (m100) cc_final: 0.7024 (m100) REVERT: U 202 MET cc_start: 0.6223 (mtp) cc_final: 0.5868 (mmm) REVERT: U 280 PHE cc_start: 0.7029 (m-80) cc_final: 0.6560 (m-80) REVERT: U 285 PRO cc_start: 0.8671 (Cg_endo) cc_final: 0.8267 (Cg_exo) REVERT: V 88 THR cc_start: 0.8153 (p) cc_final: 0.7914 (t) REVERT: V 91 ASP cc_start: 0.7363 (m-30) cc_final: 0.6708 (m-30) REVERT: V 130 ASN cc_start: 0.7648 (t0) cc_final: 0.7110 (t0) REVERT: V 135 MET cc_start: 0.7584 (mtt) cc_final: 0.7266 (mtp) REVERT: V 139 CYS cc_start: 0.7797 (t) cc_final: 0.7365 (p) REVERT: V 155 GLN cc_start: 0.7519 (tt0) cc_final: 0.6942 (mm110) REVERT: V 213 GLU cc_start: 0.6814 (mt-10) cc_final: 0.6490 (mt-10) REVERT: V 362 MET cc_start: 0.2930 (ppp) cc_final: 0.2083 (pmm) REVERT: W 307 GLU cc_start: 0.4614 (tt0) cc_final: 0.4337 (tt0) REVERT: W 337 ILE cc_start: 0.7874 (mm) cc_final: 0.7516 (pt) outliers start: 102 outliers final: 55 residues processed: 813 average time/residue: 0.5755 time to fit residues: 778.9982 Evaluate side-chains 651 residues out of total 6063 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 594 time to evaluate : 5.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 36 MET Chi-restraints excluded: chain 1 residue 52 ASN Chi-restraints excluded: chain 3 residue 157 TYR Chi-restraints excluded: chain 3 residue 193 HIS Chi-restraints excluded: chain 3 residue 233 ASN Chi-restraints excluded: chain 3 residue 320 VAL Chi-restraints excluded: chain 3 residue 336 ASP Chi-restraints excluded: chain 3 residue 367 ASN Chi-restraints excluded: chain 3 residue 382 VAL Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 1158 LEU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 215 ASN Chi-restraints excluded: chain B residue 216 MET Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 663 THR Chi-restraints excluded: chain B residue 755 LEU Chi-restraints excluded: chain B residue 971 ASP Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 55 GLU Chi-restraints excluded: chain H residue 42 ASP Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain K residue 48 ASP Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain K residue 104 MET Chi-restraints excluded: chain M residue 209 HIS Chi-restraints excluded: chain M residue 330 ASP Chi-restraints excluded: chain N residue 254 LEU Chi-restraints excluded: chain N residue 257 GLU Chi-restraints excluded: chain N residue 374 THR Chi-restraints excluded: chain N residue 395 HIS Chi-restraints excluded: chain O residue 180 LEU Chi-restraints excluded: chain O residue 190 VAL Chi-restraints excluded: chain O residue 266 ILE Chi-restraints excluded: chain P residue 237 THR Chi-restraints excluded: chain Q residue 40 ASP Chi-restraints excluded: chain Q residue 68 MET Chi-restraints excluded: chain Q residue 75 ILE Chi-restraints excluded: chain U residue 222 THR Chi-restraints excluded: chain V residue 27 VAL Chi-restraints excluded: chain V residue 55 TYR Chi-restraints excluded: chain V residue 78 ASP Chi-restraints excluded: chain V residue 383 ASN Chi-restraints excluded: chain W residue 308 THR Chi-restraints excluded: chain W residue 311 PHE Chi-restraints excluded: chain W residue 315 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 691 random chunks: chunk 348 optimal weight: 7.9990 chunk 194 optimal weight: 0.9980 chunk 522 optimal weight: 6.9990 chunk 427 optimal weight: 2.9990 chunk 173 optimal weight: 7.9990 chunk 628 optimal weight: 0.9990 chunk 679 optimal weight: 10.0000 chunk 559 optimal weight: 5.9990 chunk 623 optimal weight: 0.9980 chunk 214 optimal weight: 0.7980 chunk 504 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 73 GLN 3 226 GLN 4 186 ASN 4 234 GLN 4 286 ASN ** 4 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 465 GLN A 599 GLN ** A 661 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1039 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 959 HIS ** C 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 151 HIS D 85 GLN D 112 GLN K 38 HIS ** M 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 377 GLN P 124 ASN P 200 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6727 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 59698 Z= 0.178 Angle : 0.491 12.034 81288 Z= 0.252 Chirality : 0.040 0.190 9051 Planarity : 0.004 0.066 9902 Dihedral : 15.436 166.996 9298 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.04 % Allowed : 10.75 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.10), residues: 6799 helix: 0.99 (0.10), residues: 2750 sheet: -0.58 (0.18), residues: 818 loop : -1.03 (0.11), residues: 3231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP I 59 HIS 0.018 0.001 HIS N 395 PHE 0.028 0.001 PHE W 294 TYR 0.027 0.001 TYR U 192 ARG 0.010 0.000 ARG C 255 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13598 Ramachandran restraints generated. 6799 Oldfield, 0 Emsley, 6799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13598 Ramachandran restraints generated. 6799 Oldfield, 0 Emsley, 6799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 765 residues out of total 6063 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 641 time to evaluate : 5.210 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 REVERT: 1 45 ARG cc_start: 0.4197 (mmp80) cc_final: 0.3674 (ttp80) REVERT: 1 135 PHE cc_start: 0.2775 (m-80) cc_final: 0.2449 (m-80) REVERT: 3 33 GLU cc_start: 0.3251 (tt0) cc_final: 0.2871 (tm-30) REVERT: 3 158 GLU cc_start: 0.4382 (tp30) cc_final: 0.4072 (tt0) REVERT: 3 162 HIS cc_start: 0.2437 (m90) cc_final: 0.2173 (m-70) REVERT: 3 281 HIS cc_start: 0.4119 (m90) cc_final: 0.3456 (t-170) REVERT: 3 359 MET cc_start: 0.3529 (mtt) cc_final: 0.3109 (ppp) REVERT: 3 364 TRP cc_start: 0.6255 (m100) cc_final: 0.5800 (m100) REVERT: 3 367 ASN cc_start: 0.3882 (m110) cc_final: 0.3580 (m-40) REVERT: 4 237 GLU cc_start: 0.7598 (mt-10) cc_final: 0.7269 (tp30) REVERT: 4 271 PHE cc_start: 0.8018 (m-80) cc_final: 0.7661 (m-80) REVERT: 4 385 MET cc_start: 0.2414 (tmm) cc_final: 0.1599 (tpt) REVERT: A 123 LYS cc_start: 0.7518 (ttpp) cc_final: 0.7274 (tptp) REVERT: A 240 MET cc_start: 0.8151 (ttp) cc_final: 0.7948 (ttp) REVERT: A 336 LYS cc_start: 0.7324 (ptmt) cc_final: 0.6409 (mttp) REVERT: A 379 GLU cc_start: 0.7589 (mt-10) cc_final: 0.7145 (mt-10) REVERT: A 424 ARG cc_start: 0.5522 (ttt180) cc_final: 0.4151 (ttp80) REVERT: A 627 LYS cc_start: 0.7611 (tmtt) cc_final: 0.7079 (ttmt) REVERT: A 729 GLU cc_start: 0.7567 (tp30) cc_final: 0.6807 (tp30) REVERT: A 811 ASP cc_start: 0.7737 (p0) cc_final: 0.7457 (p0) REVERT: A 917 GLU cc_start: 0.7686 (mm-30) cc_final: 0.6723 (mt-10) REVERT: A 962 GLN cc_start: 0.6519 (mp10) cc_final: 0.6090 (mp10) REVERT: A 1206 GLU cc_start: 0.7683 (tp30) cc_final: 0.7410 (tp30) REVERT: A 1225 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7642 (mp) REVERT: A 1236 MET cc_start: 0.8241 (mtm) cc_final: 0.7935 (mtm) REVERT: A 1311 MET cc_start: 0.7591 (ptm) cc_final: 0.7324 (ptm) REVERT: B 72 MET cc_start: 0.6363 (tmm) cc_final: 0.5801 (mmm) REVERT: B 154 GLU cc_start: 0.8253 (mt-10) cc_final: 0.7876 (mt-10) REVERT: B 259 GLU cc_start: 0.7711 (tp30) cc_final: 0.7313 (pt0) REVERT: B 308 GLU cc_start: 0.6560 (tp30) cc_final: 0.6358 (tp30) REVERT: B 311 GLU cc_start: 0.7883 (mm-30) cc_final: 0.7413 (mt-10) REVERT: B 383 GLU cc_start: 0.7254 (tm-30) cc_final: 0.6895 (tm-30) REVERT: B 406 MET cc_start: 0.8739 (mmm) cc_final: 0.8057 (mmm) REVERT: B 488 GLU cc_start: 0.6882 (pt0) cc_final: 0.6214 (tp30) REVERT: B 525 LEU cc_start: 0.8110 (tp) cc_final: 0.7830 (mm) REVERT: B 719 MET cc_start: 0.8331 (mmm) cc_final: 0.7832 (mmm) REVERT: B 780 LYS cc_start: 0.7128 (ptmt) cc_final: 0.6826 (ptmt) REVERT: B 791 MET cc_start: 0.7481 (mmt) cc_final: 0.7238 (mmp) REVERT: B 853 ASP cc_start: 0.8024 (m-30) cc_final: 0.7641 (m-30) REVERT: C 50 ARG cc_start: 0.7617 (ptt90) cc_final: 0.7330 (ptt-90) REVERT: C 52 ASP cc_start: 0.7539 (m-30) cc_final: 0.6938 (p0) REVERT: C 87 MET cc_start: 0.8900 (mmm) cc_final: 0.8662 (mmt) REVERT: C 248 GLU cc_start: 0.6968 (pp20) cc_final: 0.6436 (tp30) REVERT: C 286 GLU cc_start: 0.8125 (tp30) cc_final: 0.7745 (tp30) REVERT: C 292 LYS cc_start: 0.7544 (tmtt) cc_final: 0.7030 (tptt) REVERT: D 1 MET cc_start: 0.5672 (mmp) cc_final: 0.5470 (mmp) REVERT: D 22 ASP cc_start: 0.7319 (m-30) cc_final: 0.6802 (m-30) REVERT: D 47 TYR cc_start: 0.6783 (t80) cc_final: 0.6477 (t80) REVERT: D 77 LYS cc_start: 0.3410 (tptt) cc_final: 0.3175 (tptp) REVERT: D 90 ARG cc_start: 0.5122 (mtm-85) cc_final: 0.3604 (tpt90) REVERT: E 61 LEU cc_start: 0.6202 (mm) cc_final: 0.5581 (mm) REVERT: E 73 PHE cc_start: 0.6416 (OUTLIER) cc_final: 0.5995 (m-80) REVERT: E 94 MET cc_start: 0.7104 (mmp) cc_final: 0.6238 (ttt) REVERT: E 134 GLU cc_start: 0.7600 (mt-10) cc_final: 0.7171 (mm-30) REVERT: E 168 ASN cc_start: 0.8197 (p0) cc_final: 0.7838 (p0) REVERT: F 56 TYR cc_start: 0.8730 (m-80) cc_final: 0.8284 (m-80) REVERT: G 7 MET cc_start: 0.7661 (mtp) cc_final: 0.7257 (mtp) REVERT: G 81 LEU cc_start: 0.7090 (mp) cc_final: 0.6648 (tt) REVERT: G 83 GLU cc_start: 0.6556 (tt0) cc_final: 0.5847 (tt0) REVERT: G 150 PHE cc_start: 0.5133 (m-80) cc_final: 0.4432 (m-80) REVERT: G 157 PHE cc_start: 0.6627 (t80) cc_final: 0.6259 (t80) REVERT: H 11 ASP cc_start: 0.6570 (t0) cc_final: 0.6234 (t70) REVERT: H 18 GLU cc_start: 0.7713 (mp0) cc_final: 0.7237 (mp0) REVERT: H 31 GLU cc_start: 0.6831 (mt-10) cc_final: 0.6480 (mp0) REVERT: H 37 MET cc_start: 0.7831 (mmm) cc_final: 0.7276 (mmp) REVERT: H 51 ASP cc_start: 0.7467 (m-30) cc_final: 0.7181 (m-30) REVERT: H 62 SER cc_start: 0.8761 (t) cc_final: 0.8327 (p) REVERT: H 128 ASP cc_start: 0.7749 (m-30) cc_final: 0.7450 (m-30) REVERT: H 138 ASP cc_start: 0.7642 (t0) cc_final: 0.6993 (t0) REVERT: H 145 MET cc_start: 0.7786 (mtm) cc_final: 0.7530 (mtp) REVERT: I 105 ARG cc_start: 0.4906 (ttt90) cc_final: 0.4642 (ttt-90) REVERT: J 36 ASP cc_start: 0.7589 (m-30) cc_final: 0.7295 (m-30) REVERT: K 60 MET cc_start: 0.8771 (mmt) cc_final: 0.8398 (mmm) REVERT: K 78 SER cc_start: 0.8309 (m) cc_final: 0.8005 (p) REVERT: K 97 GLN cc_start: 0.7443 (tt0) cc_final: 0.7152 (tt0) REVERT: K 98 ARG cc_start: 0.6793 (mmm-85) cc_final: 0.6591 (ttm-80) REVERT: K 112 ASP cc_start: 0.7281 (m-30) cc_final: 0.6985 (m-30) REVERT: L 15 MET cc_start: 0.7096 (tpt) cc_final: 0.6347 (tpt) REVERT: L 27 GLU cc_start: 0.6084 (mp0) cc_final: 0.5621 (mm-30) REVERT: L 35 ARG cc_start: 0.7940 (ttm-80) cc_final: 0.7562 (mtm-85) REVERT: L 47 LYS cc_start: 0.8332 (mtpp) cc_final: 0.7784 (mtmm) REVERT: M 60 MET cc_start: 0.6696 (mtm) cc_final: 0.6283 (mtm) REVERT: M 143 ASP cc_start: 0.5667 (m-30) cc_final: 0.5376 (t0) REVERT: M 146 ASP cc_start: 0.5980 (m-30) cc_final: 0.5677 (t0) REVERT: M 272 GLN cc_start: 0.7174 (mt0) cc_final: 0.6704 (tp-100) REVERT: M 286 MET cc_start: 0.8505 (mmm) cc_final: 0.8294 (mmp) REVERT: M 319 MET cc_start: 0.7675 (mmm) cc_final: 0.7010 (mmm) REVERT: M 399 GLU cc_start: 0.6742 (tt0) cc_final: 0.6475 (tt0) REVERT: N 330 LEU cc_start: 0.7778 (mp) cc_final: 0.7542 (mm) REVERT: O 85 MET cc_start: 0.8382 (ttm) cc_final: 0.8169 (ttm) REVERT: O 187 MET cc_start: 0.6131 (tpt) cc_final: 0.5698 (tpp) REVERT: O 333 MET cc_start: 0.3635 (tpp) cc_final: 0.3235 (tpt) REVERT: O 340 LYS cc_start: 0.7426 (mmmt) cc_final: 0.7222 (mttt) REVERT: O 356 GLU cc_start: 0.8094 (mm-30) cc_final: 0.7802 (mp0) REVERT: O 474 MET cc_start: 0.0981 (ppp) cc_final: -0.0647 (tmm) REVERT: P 60 MET cc_start: 0.1494 (ptt) cc_final: 0.0984 (tmm) REVERT: P 105 LYS cc_start: 0.7301 (mttt) cc_final: 0.6977 (tppt) REVERT: P 108 TRP cc_start: 0.5732 (m-90) cc_final: 0.4480 (m100) REVERT: P 159 ARG cc_start: 0.5409 (ttt180) cc_final: 0.4590 (tpt170) REVERT: P 167 TYR cc_start: 0.6894 (m-80) cc_final: 0.5519 (m-10) REVERT: P 250 MET cc_start: 0.6695 (tmm) cc_final: 0.5769 (ttp) REVERT: P 292 VAL cc_start: 0.8463 (m) cc_final: 0.8233 (p) REVERT: P 301 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7437 (mp0) REVERT: Q 42 ASP cc_start: 0.6462 (p0) cc_final: 0.6120 (p0) REVERT: Q 44 LYS cc_start: 0.8477 (mmmt) cc_final: 0.8172 (mmmt) REVERT: Q 54 GLU cc_start: 0.7959 (mp0) cc_final: 0.7421 (mp0) REVERT: Q 57 MET cc_start: 0.7558 (ttm) cc_final: 0.7340 (mtm) REVERT: Q 81 ARG cc_start: 0.3695 (tpm170) cc_final: 0.3205 (ttt90) REVERT: Q 103 TRP cc_start: 0.7754 (m100) cc_final: 0.7153 (m100) REVERT: U 279 GLN cc_start: 0.8061 (mm-40) cc_final: 0.7805 (pm20) REVERT: U 285 PRO cc_start: 0.8691 (Cg_endo) cc_final: 0.8272 (Cg_exo) REVERT: U 286 GLU cc_start: 0.7274 (tp30) cc_final: 0.6521 (mm-30) REVERT: V 88 THR cc_start: 0.8172 (p) cc_final: 0.7954 (t) REVERT: V 91 ASP cc_start: 0.7440 (m-30) cc_final: 0.6778 (m-30) REVERT: V 139 CYS cc_start: 0.7963 (t) cc_final: 0.7424 (p) REVERT: V 155 GLN cc_start: 0.7455 (tt0) cc_final: 0.6965 (mm110) REVERT: V 235 GLN cc_start: 0.7017 (mt0) cc_final: 0.6723 (mm-40) REVERT: W 283 PHE cc_start: 0.6011 (t80) cc_final: 0.5776 (m-80) REVERT: W 307 GLU cc_start: 0.4582 (tt0) cc_final: 0.4280 (tt0) outliers start: 124 outliers final: 69 residues processed: 734 average time/residue: 0.5559 time to fit residues: 689.5621 Evaluate side-chains 634 residues out of total 6063 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 563 time to evaluate : 5.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 52 ASN Chi-restraints excluded: chain 3 residue 103 VAL Chi-restraints excluded: chain 3 residue 128 VAL Chi-restraints excluded: chain 3 residue 193 HIS Chi-restraints excluded: chain 3 residue 233 ASN Chi-restraints excluded: chain 3 residue 320 VAL Chi-restraints excluded: chain 3 residue 382 VAL Chi-restraints excluded: chain 4 residue 366 VAL Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 767 CYS Chi-restraints excluded: chain A residue 978 GLU Chi-restraints excluded: chain A residue 1023 MET Chi-restraints excluded: chain A residue 1027 MET Chi-restraints excluded: chain A residue 1225 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 215 ASN Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 755 LEU Chi-restraints excluded: chain B residue 971 ASP Chi-restraints excluded: chain B residue 1040 SER Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain D residue 118 HIS Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 91 CYS Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain H residue 8 ASP Chi-restraints excluded: chain H residue 35 PHE Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain K residue 29 MET Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain K residue 104 MET Chi-restraints excluded: chain M residue 54 GLN Chi-restraints excluded: chain M residue 89 THR Chi-restraints excluded: chain M residue 225 LEU Chi-restraints excluded: chain M residue 330 ASP Chi-restraints excluded: chain N residue 354 CYS Chi-restraints excluded: chain N residue 396 LYS Chi-restraints excluded: chain O residue 21 VAL Chi-restraints excluded: chain O residue 180 LEU Chi-restraints excluded: chain O residue 190 VAL Chi-restraints excluded: chain O residue 380 VAL Chi-restraints excluded: chain P residue 237 THR Chi-restraints excluded: chain Q residue 40 ASP Chi-restraints excluded: chain Q residue 68 MET Chi-restraints excluded: chain U residue 171 THR Chi-restraints excluded: chain V residue 16 VAL Chi-restraints excluded: chain V residue 55 TYR Chi-restraints excluded: chain V residue 78 ASP Chi-restraints excluded: chain W residue 311 PHE Chi-restraints excluded: chain W residue 315 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 691 random chunks: chunk 621 optimal weight: 3.9990 chunk 472 optimal weight: 5.9990 chunk 326 optimal weight: 2.9990 chunk 69 optimal weight: 20.0000 chunk 300 optimal weight: 6.9990 chunk 422 optimal weight: 6.9990 chunk 630 optimal weight: 4.9990 chunk 667 optimal weight: 3.9990 chunk 329 optimal weight: 7.9990 chunk 597 optimal weight: 4.9990 chunk 180 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 73 GLN 3 28 ASN ** 3 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 186 ASN ** 4 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 158 HIS A 296 HIS ** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 469 HIS A 528 ASN A 543 GLN A 739 GLN ** A1039 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1239 HIS ** C 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 151 HIS ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 ASN E 138 ASN G 23 ASN I 32 HIS I 61 ASN ** I 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 HIS M 209 HIS ** N 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 129 ASN P 266 HIS ** U 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 98 GLN ** V 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 406 GLN W 327 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6860 moved from start: 0.4010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.099 59698 Z= 0.417 Angle : 0.651 14.582 81288 Z= 0.336 Chirality : 0.046 0.222 9051 Planarity : 0.005 0.061 9902 Dihedral : 15.633 160.133 9298 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.31 % Favored : 95.67 % Rotamer: Outliers : 2.75 % Allowed : 11.95 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.10), residues: 6799 helix: 0.73 (0.10), residues: 2731 sheet: -0.62 (0.18), residues: 795 loop : -1.06 (0.10), residues: 3273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP W 350 HIS 0.027 0.002 HIS P 297 PHE 0.025 0.002 PHE C 336 TYR 0.031 0.002 TYR B 357 ARG 0.017 0.001 ARG C 255 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13598 Ramachandran restraints generated. 6799 Oldfield, 0 Emsley, 6799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13598 Ramachandran restraints generated. 6799 Oldfield, 0 Emsley, 6799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 757 residues out of total 6063 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 590 time to evaluate : 5.166 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: 1 135 PHE cc_start: 0.2997 (m-80) cc_final: 0.2513 (m-80) REVERT: 3 33 GLU cc_start: 0.3147 (tt0) cc_final: 0.2745 (tm-30) REVERT: 3 158 GLU cc_start: 0.4293 (tp30) cc_final: 0.4072 (tt0) REVERT: 3 162 HIS cc_start: 0.2195 (m90) cc_final: 0.1927 (m90) REVERT: 3 281 HIS cc_start: 0.4271 (m90) cc_final: 0.3498 (t-170) REVERT: 3 359 MET cc_start: 0.3982 (mtt) cc_final: 0.3516 (ppp) REVERT: 4 237 GLU cc_start: 0.7634 (mt-10) cc_final: 0.7307 (tp30) REVERT: 4 271 PHE cc_start: 0.7757 (m-80) cc_final: 0.7416 (m-80) REVERT: 4 385 MET cc_start: 0.2277 (tmm) cc_final: 0.1212 (tpt) REVERT: A 123 LYS cc_start: 0.7501 (ttpp) cc_final: 0.7275 (tptp) REVERT: A 336 LYS cc_start: 0.7383 (ptmt) cc_final: 0.6473 (mttp) REVERT: A 379 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7503 (mt-10) REVERT: A 424 ARG cc_start: 0.5512 (ttt180) cc_final: 0.4184 (ttp80) REVERT: A 505 MET cc_start: 0.8882 (mtp) cc_final: 0.8162 (mtp) REVERT: A 627 LYS cc_start: 0.7616 (tmtt) cc_final: 0.6898 (ttmt) REVERT: A 811 ASP cc_start: 0.7727 (OUTLIER) cc_final: 0.7461 (p0) REVERT: A 917 GLU cc_start: 0.7701 (mm-30) cc_final: 0.7192 (mm-30) REVERT: A 1185 MET cc_start: 0.8122 (ptm) cc_final: 0.7782 (tmm) REVERT: A 1313 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7312 (tm-30) REVERT: B 70 ASP cc_start: 0.8244 (t0) cc_final: 0.8021 (t0) REVERT: B 72 MET cc_start: 0.6599 (tmm) cc_final: 0.6287 (mmm) REVERT: B 247 SER cc_start: 0.8578 (OUTLIER) cc_final: 0.7752 (t) REVERT: B 254 MET cc_start: 0.8420 (mtp) cc_final: 0.8171 (mtp) REVERT: B 311 GLU cc_start: 0.7734 (mm-30) cc_final: 0.7066 (mt-10) REVERT: B 396 ARG cc_start: 0.5527 (ttt-90) cc_final: 0.5311 (mtp-110) REVERT: B 438 GLN cc_start: 0.8009 (mt0) cc_final: 0.7487 (tt0) REVERT: B 488 GLU cc_start: 0.7102 (pt0) cc_final: 0.6081 (tp30) REVERT: B 791 MET cc_start: 0.7505 (mmt) cc_final: 0.7298 (mmp) REVERT: B 853 ASP cc_start: 0.8192 (m-30) cc_final: 0.7771 (m-30) REVERT: B 1069 MET cc_start: 0.7946 (tmm) cc_final: 0.7321 (tmm) REVERT: C 157 SER cc_start: 0.7999 (OUTLIER) cc_final: 0.7606 (p) REVERT: C 248 GLU cc_start: 0.6944 (pp20) cc_final: 0.6467 (tp30) REVERT: C 261 VAL cc_start: 0.7631 (OUTLIER) cc_final: 0.7370 (p) REVERT: C 286 GLU cc_start: 0.8369 (tp30) cc_final: 0.8149 (tp30) REVERT: C 292 LYS cc_start: 0.7666 (tmtt) cc_final: 0.7060 (tptt) REVERT: C 334 ARG cc_start: 0.6933 (tpp-160) cc_final: 0.6704 (tpp-160) REVERT: D 1 MET cc_start: 0.7081 (mmp) cc_final: 0.6425 (mmt) REVERT: D 22 ASP cc_start: 0.7590 (m-30) cc_final: 0.7021 (m-30) REVERT: D 47 TYR cc_start: 0.6858 (t80) cc_final: 0.6573 (t80) REVERT: D 82 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7338 (mm-30) REVERT: D 90 ARG cc_start: 0.5847 (mtm-85) cc_final: 0.3990 (tpt90) REVERT: E 73 PHE cc_start: 0.6539 (OUTLIER) cc_final: 0.6321 (m-80) REVERT: E 94 MET cc_start: 0.7232 (mmp) cc_final: 0.6509 (mtp) REVERT: E 137 ILE cc_start: 0.7503 (tp) cc_final: 0.7250 (tt) REVERT: E 168 ASN cc_start: 0.8521 (p0) cc_final: 0.7991 (p0) REVERT: F 56 TYR cc_start: 0.8737 (m-80) cc_final: 0.8268 (m-80) REVERT: F 117 ASP cc_start: 0.8492 (m-30) cc_final: 0.8224 (m-30) REVERT: G 7 MET cc_start: 0.7644 (mtp) cc_final: 0.7265 (mtp) REVERT: G 32 LYS cc_start: 0.7959 (mtpt) cc_final: 0.7492 (ttpp) REVERT: G 81 LEU cc_start: 0.7449 (mp) cc_final: 0.6649 (tt) REVERT: G 150 PHE cc_start: 0.5024 (m-80) cc_final: 0.4306 (m-80) REVERT: G 157 PHE cc_start: 0.6863 (t80) cc_final: 0.6473 (t80) REVERT: H 37 MET cc_start: 0.8059 (mmm) cc_final: 0.7462 (mmp) REVERT: H 51 ASP cc_start: 0.7611 (m-30) cc_final: 0.7378 (m-30) REVERT: H 62 SER cc_start: 0.9132 (t) cc_final: 0.8705 (p) REVERT: H 90 TYR cc_start: 0.8731 (t80) cc_final: 0.8279 (t80) REVERT: H 128 ASP cc_start: 0.8069 (m-30) cc_final: 0.7657 (t0) REVERT: H 138 ASP cc_start: 0.7795 (t0) cc_final: 0.7196 (t0) REVERT: H 145 MET cc_start: 0.7777 (mtp) cc_final: 0.7497 (mtp) REVERT: I 105 ARG cc_start: 0.4827 (ttt90) cc_final: 0.4611 (ttt-90) REVERT: J 55 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.7897 (tt) REVERT: K 78 SER cc_start: 0.8325 (m) cc_final: 0.8068 (p) REVERT: K 102 GLU cc_start: 0.7714 (mt-10) cc_final: 0.7227 (mt-10) REVERT: K 112 ASP cc_start: 0.7239 (m-30) cc_final: 0.6945 (m-30) REVERT: K 119 LYS cc_start: 0.7586 (ttpp) cc_final: 0.7331 (tttp) REVERT: K 122 LYS cc_start: 0.7479 (mttp) cc_final: 0.7262 (mtmt) REVERT: L 35 ARG cc_start: 0.7777 (ttm-80) cc_final: 0.7348 (mtm-85) REVERT: M 60 MET cc_start: 0.7000 (mtm) cc_final: 0.6759 (mtm) REVERT: M 143 ASP cc_start: 0.5900 (m-30) cc_final: 0.5684 (t0) REVERT: M 146 ASP cc_start: 0.6390 (m-30) cc_final: 0.5908 (t0) REVERT: M 272 GLN cc_start: 0.7425 (mt0) cc_final: 0.6784 (tp-100) REVERT: M 286 MET cc_start: 0.8664 (mmm) cc_final: 0.8191 (mmm) REVERT: N 330 LEU cc_start: 0.7633 (mp) cc_final: 0.7369 (mm) REVERT: N 370 THR cc_start: 0.7479 (m) cc_final: 0.7252 (t) REVERT: O 187 MET cc_start: 0.5880 (tpt) cc_final: 0.5519 (tpp) REVERT: O 340 LYS cc_start: 0.7402 (mmmt) cc_final: 0.7180 (mttt) REVERT: O 356 GLU cc_start: 0.8026 (mm-30) cc_final: 0.7624 (mp0) REVERT: O 474 MET cc_start: 0.0973 (ppp) cc_final: -0.0947 (tpp) REVERT: P 167 TYR cc_start: 0.6807 (m-80) cc_final: 0.6248 (m-10) REVERT: P 250 MET cc_start: 0.6486 (tmm) cc_final: 0.5809 (ttp) REVERT: P 252 ILE cc_start: 0.7231 (mt) cc_final: 0.6905 (tt) REVERT: Q 42 ASP cc_start: 0.6750 (p0) cc_final: 0.6446 (p0) REVERT: Q 44 LYS cc_start: 0.8770 (mmmt) cc_final: 0.8328 (mmmt) REVERT: Q 54 GLU cc_start: 0.7784 (mp0) cc_final: 0.7153 (mp0) REVERT: Q 103 TRP cc_start: 0.7814 (m100) cc_final: 0.7197 (m100) REVERT: U 166 GLN cc_start: 0.6921 (mt0) cc_final: 0.6596 (tt0) REVERT: V 91 ASP cc_start: 0.7960 (m-30) cc_final: 0.7409 (m-30) REVERT: V 139 CYS cc_start: 0.7717 (t) cc_final: 0.7433 (p) REVERT: V 155 GLN cc_start: 0.7622 (tt0) cc_final: 0.7311 (mm110) REVERT: V 181 LYS cc_start: 0.7951 (mttp) cc_final: 0.7590 (mttp) REVERT: V 235 GLN cc_start: 0.7136 (mt0) cc_final: 0.6687 (mm-40) REVERT: V 278 GLU cc_start: 0.6469 (OUTLIER) cc_final: 0.5772 (mm-30) REVERT: W 283 PHE cc_start: 0.6742 (t80) cc_final: 0.5994 (m-80) REVERT: W 284 GLU cc_start: 0.5618 (tm-30) cc_final: 0.5219 (mm-30) REVERT: W 307 GLU cc_start: 0.5134 (tt0) cc_final: 0.4755 (tt0) REVERT: W 328 LEU cc_start: 0.5537 (OUTLIER) cc_final: 0.5325 (mp) outliers start: 167 outliers final: 89 residues processed: 722 average time/residue: 0.5553 time to fit residues: 680.4900 Evaluate side-chains 602 residues out of total 6063 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 504 time to evaluate : 5.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 128 VAL Chi-restraints excluded: chain 3 residue 206 VAL Chi-restraints excluded: chain 3 residue 233 ASN Chi-restraints excluded: chain 3 residue 320 VAL Chi-restraints excluded: chain 3 residue 336 ASP Chi-restraints excluded: chain 3 residue 382 VAL Chi-restraints excluded: chain 4 residue 181 VAL Chi-restraints excluded: chain 4 residue 331 PHE Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 469 HIS Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 767 CYS Chi-restraints excluded: chain A residue 811 ASP Chi-restraints excluded: chain A residue 978 GLU Chi-restraints excluded: chain A residue 1023 MET Chi-restraints excluded: chain A residue 1027 MET Chi-restraints excluded: chain A residue 1167 VAL Chi-restraints excluded: chain A residue 1200 VAL Chi-restraints excluded: chain A residue 1313 GLU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 116 ASP Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 215 ASN Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 472 GLN Chi-restraints excluded: chain B residue 499 MET Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 755 LEU Chi-restraints excluded: chain B residue 795 LEU Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 971 ASP Chi-restraints excluded: chain C residue 8 GLU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 151 HIS Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 212 MET Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain D residue 118 HIS Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain J residue 60 LEU Chi-restraints excluded: chain K residue 48 ASP Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain M residue 89 THR Chi-restraints excluded: chain M residue 91 THR Chi-restraints excluded: chain M residue 225 LEU Chi-restraints excluded: chain M residue 330 ASP Chi-restraints excluded: chain M residue 401 ILE Chi-restraints excluded: chain N residue 251 VAL Chi-restraints excluded: chain N residue 284 ILE Chi-restraints excluded: chain N residue 354 CYS Chi-restraints excluded: chain N residue 374 THR Chi-restraints excluded: chain N residue 395 HIS Chi-restraints excluded: chain O residue 21 VAL Chi-restraints excluded: chain O residue 180 LEU Chi-restraints excluded: chain O residue 182 ILE Chi-restraints excluded: chain O residue 190 VAL Chi-restraints excluded: chain O residue 380 VAL Chi-restraints excluded: chain P residue 237 THR Chi-restraints excluded: chain Q residue 40 ASP Chi-restraints excluded: chain Q residue 50 THR Chi-restraints excluded: chain Q residue 68 MET Chi-restraints excluded: chain U residue 171 THR Chi-restraints excluded: chain V residue 78 ASP Chi-restraints excluded: chain V residue 243 LEU Chi-restraints excluded: chain V residue 278 GLU Chi-restraints excluded: chain V residue 381 ASP Chi-restraints excluded: chain W residue 293 SER Chi-restraints excluded: chain W residue 311 PHE Chi-restraints excluded: chain W residue 315 ILE Chi-restraints excluded: chain W residue 328 LEU Chi-restraints excluded: chain W residue 353 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 691 random chunks: chunk 556 optimal weight: 4.9990 chunk 379 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 497 optimal weight: 8.9990 chunk 275 optimal weight: 1.9990 chunk 569 optimal weight: 8.9990 chunk 461 optimal weight: 0.9980 chunk 0 optimal weight: 30.0000 chunk 341 optimal weight: 0.9980 chunk 599 optimal weight: 9.9990 chunk 168 optimal weight: 0.7980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 44 GLN ** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 469 HIS A 739 GLN ** A1039 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 151 HIS ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 138 ASN I 61 ASN ** I 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 60 HIS ** O 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 236 GLN P 129 ASN P 266 HIS ** U 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 128 GLN ** V 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 406 GLN W 327 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6826 moved from start: 0.4048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 59698 Z= 0.181 Angle : 0.512 13.291 81288 Z= 0.264 Chirality : 0.040 0.238 9051 Planarity : 0.004 0.055 9902 Dihedral : 15.467 157.838 9296 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.01 % Allowed : 13.20 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.10), residues: 6799 helix: 1.01 (0.10), residues: 2728 sheet: -0.63 (0.18), residues: 795 loop : -0.93 (0.11), residues: 3276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP W 350 HIS 0.024 0.001 HIS C 151 PHE 0.024 0.001 PHE W 311 TYR 0.031 0.001 TYR U 192 ARG 0.012 0.000 ARG C 255 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13598 Ramachandran restraints generated. 6799 Oldfield, 0 Emsley, 6799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13598 Ramachandran restraints generated. 6799 Oldfield, 0 Emsley, 6799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 674 residues out of total 6063 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 552 time to evaluate : 5.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 53 MET cc_start: 0.3796 (mmt) cc_final: 0.2395 (ptm) REVERT: 1 135 PHE cc_start: 0.2983 (m-80) cc_final: 0.2499 (m-80) REVERT: 3 359 MET cc_start: 0.3966 (mtt) cc_final: 0.3474 (ppp) REVERT: 3 364 TRP cc_start: 0.6022 (OUTLIER) cc_final: 0.5194 (m100) REVERT: 3 404 TYR cc_start: 0.5864 (t80) cc_final: 0.5589 (t80) REVERT: 4 237 GLU cc_start: 0.7451 (mt-10) cc_final: 0.7095 (tp30) REVERT: 4 271 PHE cc_start: 0.7907 (m-80) cc_final: 0.7508 (m-80) REVERT: 4 385 MET cc_start: 0.1634 (tmm) cc_final: 0.0692 (tpt) REVERT: A 107 MET cc_start: 0.7587 (OUTLIER) cc_final: 0.7236 (mtt) REVERT: A 123 LYS cc_start: 0.7506 (ttpp) cc_final: 0.7269 (tptp) REVERT: A 379 GLU cc_start: 0.7769 (mt-10) cc_final: 0.7415 (mt-10) REVERT: A 424 ARG cc_start: 0.5292 (ttt180) cc_final: 0.4066 (ttp80) REVERT: A 627 LYS cc_start: 0.7652 (tmtt) cc_final: 0.6925 (ttmt) REVERT: A 662 ASN cc_start: 0.7477 (t0) cc_final: 0.7271 (t0) REVERT: A 729 GLU cc_start: 0.7669 (tp30) cc_final: 0.6947 (tp30) REVERT: A 912 MET cc_start: 0.8830 (mmp) cc_final: 0.8545 (mmp) REVERT: A 917 GLU cc_start: 0.7587 (mm-30) cc_final: 0.7088 (mm-30) REVERT: A 944 GLU cc_start: 0.7813 (mt-10) cc_final: 0.7524 (mt-10) REVERT: B 72 MET cc_start: 0.6581 (tmm) cc_final: 0.6325 (mmm) REVERT: B 311 GLU cc_start: 0.7838 (mm-30) cc_final: 0.7333 (mt-10) REVERT: B 354 ARG cc_start: 0.7956 (mmt-90) cc_final: 0.7492 (ttm-80) REVERT: B 406 MET cc_start: 0.8370 (mmm) cc_final: 0.8072 (mmm) REVERT: B 438 GLN cc_start: 0.7974 (mt0) cc_final: 0.7454 (tt0) REVERT: B 488 GLU cc_start: 0.7233 (pt0) cc_final: 0.6227 (tp30) REVERT: B 780 LYS cc_start: 0.7656 (ptmt) cc_final: 0.7442 (ptmt) REVERT: B 853 ASP cc_start: 0.8144 (m-30) cc_final: 0.7691 (m-30) REVERT: B 1050 MET cc_start: 0.7346 (mtm) cc_final: 0.7005 (mtt) REVERT: C 50 ARG cc_start: 0.7479 (ptt90) cc_final: 0.7100 (ptt-90) REVERT: C 248 GLU cc_start: 0.6916 (pp20) cc_final: 0.6491 (tp30) REVERT: C 261 VAL cc_start: 0.7588 (OUTLIER) cc_final: 0.7310 (p) REVERT: C 286 GLU cc_start: 0.8041 (tp30) cc_final: 0.7475 (tp30) REVERT: C 292 LYS cc_start: 0.7572 (tmtt) cc_final: 0.6962 (tptt) REVERT: C 334 ARG cc_start: 0.6765 (tpp-160) cc_final: 0.6533 (tpp-160) REVERT: D 1 MET cc_start: 0.7036 (OUTLIER) cc_final: 0.6755 (mmp) REVERT: D 47 TYR cc_start: 0.6895 (t80) cc_final: 0.6543 (t80) REVERT: D 82 GLU cc_start: 0.8077 (mt-10) cc_final: 0.7403 (mm-30) REVERT: D 90 ARG cc_start: 0.5473 (mtm-85) cc_final: 0.3957 (tpt90) REVERT: E 94 MET cc_start: 0.7135 (mmp) cc_final: 0.6120 (ttt) REVERT: E 168 ASN cc_start: 0.8527 (p0) cc_final: 0.7943 (p0) REVERT: F 56 TYR cc_start: 0.8552 (m-80) cc_final: 0.8117 (m-80) REVERT: G 7 MET cc_start: 0.7474 (mtp) cc_final: 0.7205 (mtp) REVERT: G 32 LYS cc_start: 0.7903 (mtpt) cc_final: 0.7494 (ttpp) REVERT: G 81 LEU cc_start: 0.7464 (mp) cc_final: 0.6762 (tt) REVERT: G 150 PHE cc_start: 0.5088 (m-80) cc_final: 0.4465 (m-80) REVERT: G 157 PHE cc_start: 0.6838 (t80) cc_final: 0.6458 (t80) REVERT: H 31 GLU cc_start: 0.7010 (mt-10) cc_final: 0.6647 (mt-10) REVERT: H 37 MET cc_start: 0.7999 (mmm) cc_final: 0.7420 (mmp) REVERT: H 51 ASP cc_start: 0.7520 (m-30) cc_final: 0.7269 (m-30) REVERT: H 62 SER cc_start: 0.9099 (t) cc_final: 0.8725 (p) REVERT: H 128 ASP cc_start: 0.7819 (m-30) cc_final: 0.7511 (m-30) REVERT: H 138 ASP cc_start: 0.7671 (t0) cc_final: 0.7275 (t0) REVERT: H 145 MET cc_start: 0.7837 (mtp) cc_final: 0.7554 (mtp) REVERT: J 55 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.7960 (tt) REVERT: K 38 HIS cc_start: 0.7265 (m170) cc_final: 0.7018 (m-70) REVERT: K 78 SER cc_start: 0.8226 (m) cc_final: 0.7990 (p) REVERT: K 112 ASP cc_start: 0.7261 (m-30) cc_final: 0.7039 (m-30) REVERT: K 115 GLU cc_start: 0.8015 (mm-30) cc_final: 0.7558 (mt-10) REVERT: K 119 LYS cc_start: 0.7469 (ttpp) cc_final: 0.7253 (tttm) REVERT: L 35 ARG cc_start: 0.7769 (ttm-80) cc_final: 0.7336 (mtm-85) REVERT: M 143 ASP cc_start: 0.5839 (m-30) cc_final: 0.5582 (t0) REVERT: M 146 ASP cc_start: 0.6490 (m-30) cc_final: 0.6064 (t0) REVERT: M 272 GLN cc_start: 0.7380 (mt0) cc_final: 0.6788 (tp-100) REVERT: M 286 MET cc_start: 0.8631 (mmm) cc_final: 0.8280 (mmm) REVERT: N 330 LEU cc_start: 0.7739 (mp) cc_final: 0.7505 (mm) REVERT: O 187 MET cc_start: 0.5836 (tpt) cc_final: 0.5462 (tpp) REVERT: O 340 LYS cc_start: 0.7384 (mmmt) cc_final: 0.7160 (mttt) REVERT: O 356 GLU cc_start: 0.8023 (mm-30) cc_final: 0.7619 (mp0) REVERT: O 404 MET cc_start: 0.8008 (OUTLIER) cc_final: 0.7755 (ptm) REVERT: O 474 MET cc_start: 0.1012 (OUTLIER) cc_final: -0.0842 (tpp) REVERT: P 60 MET cc_start: 0.2412 (ptt) cc_final: 0.1555 (tpp) REVERT: P 167 TYR cc_start: 0.6753 (m-80) cc_final: 0.6236 (m-10) REVERT: P 250 MET cc_start: 0.6500 (tmm) cc_final: 0.5813 (ttp) REVERT: Q 42 ASP cc_start: 0.6685 (p0) cc_final: 0.6371 (p0) REVERT: Q 44 LYS cc_start: 0.8723 (mmmt) cc_final: 0.8448 (mmmt) REVERT: Q 54 GLU cc_start: 0.7879 (mp0) cc_final: 0.7334 (mp0) REVERT: Q 103 TRP cc_start: 0.7959 (m100) cc_final: 0.7321 (m100) REVERT: U 166 GLN cc_start: 0.6706 (mt0) cc_final: 0.6324 (tt0) REVERT: V 91 ASP cc_start: 0.7890 (m-30) cc_final: 0.7354 (m-30) REVERT: V 135 MET cc_start: 0.7598 (mtp) cc_final: 0.7254 (mtp) REVERT: V 139 CYS cc_start: 0.7949 (t) cc_final: 0.7599 (p) REVERT: V 155 GLN cc_start: 0.7704 (tt0) cc_final: 0.7330 (mm110) REVERT: V 235 GLN cc_start: 0.7042 (mt0) cc_final: 0.6570 (mm-40) REVERT: W 283 PHE cc_start: 0.6762 (t80) cc_final: 0.6284 (m-80) REVERT: W 284 GLU cc_start: 0.5534 (tm-30) cc_final: 0.5227 (mm-30) REVERT: W 328 LEU cc_start: 0.5579 (OUTLIER) cc_final: 0.5283 (mp) outliers start: 122 outliers final: 83 residues processed: 640 average time/residue: 0.5538 time to fit residues: 602.0948 Evaluate side-chains 596 residues out of total 6063 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 505 time to evaluate : 5.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 52 ASN Chi-restraints excluded: chain 3 residue 128 VAL Chi-restraints excluded: chain 3 residue 206 VAL Chi-restraints excluded: chain 3 residue 233 ASN Chi-restraints excluded: chain 3 residue 320 VAL Chi-restraints excluded: chain 3 residue 339 LEU Chi-restraints excluded: chain 3 residue 364 TRP Chi-restraints excluded: chain 3 residue 382 VAL Chi-restraints excluded: chain 3 residue 386 MET Chi-restraints excluded: chain 4 residue 299 ARG Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 469 HIS Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 871 MET Chi-restraints excluded: chain A residue 978 GLU Chi-restraints excluded: chain A residue 1023 MET Chi-restraints excluded: chain A residue 1027 MET Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1167 VAL Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 215 ASN Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 451 MET Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 755 LEU Chi-restraints excluded: chain B residue 795 LEU Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 971 ASP Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 85 GLN Chi-restraints excluded: chain D residue 118 HIS Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 18 MET Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 55 GLU Chi-restraints excluded: chain H residue 8 ASP Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain J residue 60 LEU Chi-restraints excluded: chain K residue 48 ASP Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain M residue 89 THR Chi-restraints excluded: chain M residue 225 LEU Chi-restraints excluded: chain M residue 330 ASP Chi-restraints excluded: chain N residue 251 VAL Chi-restraints excluded: chain N residue 354 CYS Chi-restraints excluded: chain N residue 374 THR Chi-restraints excluded: chain N residue 395 HIS Chi-restraints excluded: chain O residue 21 VAL Chi-restraints excluded: chain O residue 180 LEU Chi-restraints excluded: chain O residue 190 VAL Chi-restraints excluded: chain O residue 259 MET Chi-restraints excluded: chain O residue 404 MET Chi-restraints excluded: chain O residue 474 MET Chi-restraints excluded: chain P residue 237 THR Chi-restraints excluded: chain P residue 280 THR Chi-restraints excluded: chain Q residue 40 ASP Chi-restraints excluded: chain Q residue 68 MET Chi-restraints excluded: chain U residue 171 THR Chi-restraints excluded: chain V residue 78 ASP Chi-restraints excluded: chain V residue 243 LEU Chi-restraints excluded: chain W residue 311 PHE Chi-restraints excluded: chain W residue 315 ILE Chi-restraints excluded: chain W residue 328 LEU Chi-restraints excluded: chain W residue 353 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 691 random chunks: chunk 224 optimal weight: 6.9990 chunk 601 optimal weight: 0.0770 chunk 132 optimal weight: 3.9990 chunk 392 optimal weight: 1.9990 chunk 164 optimal weight: 4.9990 chunk 668 optimal weight: 9.9990 chunk 554 optimal weight: 5.9990 chunk 309 optimal weight: 3.9990 chunk 55 optimal weight: 10.0000 chunk 221 optimal weight: 5.9990 chunk 350 optimal weight: 0.1980 overall best weight: 2.0544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 469 HIS ** A1039 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 ASN ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 138 ASN ** I 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 125 HIS O 475 GLN P 129 ASN P 266 HIS ** U 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 296 HIS ** V 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6841 moved from start: 0.4252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 59698 Z= 0.229 Angle : 0.520 13.076 81288 Z= 0.268 Chirality : 0.041 0.258 9051 Planarity : 0.004 0.053 9902 Dihedral : 15.428 158.193 9296 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.31 % Allowed : 13.44 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.10), residues: 6799 helix: 1.08 (0.10), residues: 2728 sheet: -0.65 (0.18), residues: 786 loop : -0.91 (0.11), residues: 3285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP W 350 HIS 0.020 0.001 HIS A 469 PHE 0.022 0.001 PHE W 311 TYR 0.028 0.001 TYR U 192 ARG 0.015 0.000 ARG C 255 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13598 Ramachandran restraints generated. 6799 Oldfield, 0 Emsley, 6799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13598 Ramachandran restraints generated. 6799 Oldfield, 0 Emsley, 6799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 671 residues out of total 6063 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 531 time to evaluate : 5.177 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: 1 53 MET cc_start: 0.3802 (mmt) cc_final: 0.2408 (ptm) REVERT: 1 135 PHE cc_start: 0.2999 (m-80) cc_final: 0.2524 (m-80) REVERT: 3 51 TRP cc_start: 0.0427 (OUTLIER) cc_final: 0.0147 (t-100) REVERT: 3 281 HIS cc_start: 0.4322 (m90) cc_final: 0.3586 (t-170) REVERT: 3 359 MET cc_start: 0.3870 (mtt) cc_final: 0.3625 (ppp) REVERT: 3 364 TRP cc_start: 0.6215 (OUTLIER) cc_final: 0.5942 (m-10) REVERT: 3 404 TYR cc_start: 0.5926 (t80) cc_final: 0.5723 (t80) REVERT: 4 237 GLU cc_start: 0.7534 (mt-10) cc_final: 0.7156 (tp30) REVERT: 4 271 PHE cc_start: 0.7885 (m-80) cc_final: 0.7464 (m-80) REVERT: 4 379 MET cc_start: -0.1228 (ttt) cc_final: -0.1508 (tmm) REVERT: 4 385 MET cc_start: 0.1724 (tmm) cc_final: 0.0807 (tpt) REVERT: A 90 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8297 (mm) REVERT: A 107 MET cc_start: 0.7631 (OUTLIER) cc_final: 0.7334 (mtt) REVERT: A 123 LYS cc_start: 0.7432 (ttpp) cc_final: 0.7187 (tptp) REVERT: A 240 MET cc_start: 0.8461 (ttp) cc_final: 0.8228 (ttp) REVERT: A 379 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7477 (mt-10) REVERT: A 424 ARG cc_start: 0.5277 (ttt180) cc_final: 0.4057 (ttp80) REVERT: A 505 MET cc_start: 0.8626 (mtp) cc_final: 0.8355 (mtm) REVERT: A 627 LYS cc_start: 0.7646 (tmtt) cc_final: 0.6928 (ttmt) REVERT: A 944 GLU cc_start: 0.7828 (mt-10) cc_final: 0.7541 (mt-10) REVERT: A 1131 LYS cc_start: 0.7670 (tppp) cc_final: 0.7427 (tptt) REVERT: A 1185 MET cc_start: 0.8107 (ptm) cc_final: 0.7379 (tmm) REVERT: B 72 MET cc_start: 0.6670 (tmm) cc_final: 0.6400 (mmm) REVERT: B 311 GLU cc_start: 0.7717 (mm-30) cc_final: 0.7154 (mt-10) REVERT: B 354 ARG cc_start: 0.7821 (mmt-90) cc_final: 0.7380 (ttm-80) REVERT: B 406 MET cc_start: 0.8247 (mmm) cc_final: 0.7991 (mmm) REVERT: B 438 GLN cc_start: 0.8013 (mt0) cc_final: 0.7467 (tt0) REVERT: B 780 LYS cc_start: 0.7625 (ptmt) cc_final: 0.7381 (ptmt) REVERT: B 853 ASP cc_start: 0.8178 (m-30) cc_final: 0.7765 (m-30) REVERT: B 1050 MET cc_start: 0.7354 (mtm) cc_final: 0.7029 (mtt) REVERT: C 50 ARG cc_start: 0.7489 (ptt90) cc_final: 0.7112 (ptt-90) REVERT: C 248 GLU cc_start: 0.6951 (pp20) cc_final: 0.6493 (tp30) REVERT: C 261 VAL cc_start: 0.7618 (OUTLIER) cc_final: 0.7344 (p) REVERT: C 292 LYS cc_start: 0.7546 (tmtt) cc_final: 0.6909 (tptt) REVERT: D 1 MET cc_start: 0.6752 (OUTLIER) cc_final: 0.6352 (mmp) REVERT: D 47 TYR cc_start: 0.6944 (t80) cc_final: 0.6635 (t80) REVERT: D 82 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7539 (mm-30) REVERT: D 90 ARG cc_start: 0.5545 (mtm-85) cc_final: 0.3984 (tpt90) REVERT: D 118 HIS cc_start: 0.7730 (OUTLIER) cc_final: 0.7048 (m-70) REVERT: E 94 MET cc_start: 0.7206 (mmp) cc_final: 0.6154 (ttt) REVERT: E 168 ASN cc_start: 0.8595 (p0) cc_final: 0.8137 (p0) REVERT: F 56 TYR cc_start: 0.8528 (m-80) cc_final: 0.8157 (m-80) REVERT: G 7 MET cc_start: 0.7479 (mtp) cc_final: 0.7212 (mtp) REVERT: G 32 LYS cc_start: 0.7986 (mtpt) cc_final: 0.7489 (ttpp) REVERT: G 81 LEU cc_start: 0.7649 (mp) cc_final: 0.6794 (tt) REVERT: G 83 GLU cc_start: 0.6574 (tt0) cc_final: 0.5791 (tp30) REVERT: G 150 PHE cc_start: 0.5122 (m-80) cc_final: 0.4402 (m-80) REVERT: G 157 PHE cc_start: 0.6852 (t80) cc_final: 0.6472 (t80) REVERT: H 36 LYS cc_start: 0.7259 (mmtt) cc_final: 0.6784 (mmmt) REVERT: H 37 MET cc_start: 0.8052 (mmm) cc_final: 0.7396 (mmp) REVERT: H 51 ASP cc_start: 0.7535 (m-30) cc_final: 0.7277 (m-30) REVERT: H 62 SER cc_start: 0.9097 (t) cc_final: 0.8732 (p) REVERT: H 128 ASP cc_start: 0.7768 (m-30) cc_final: 0.7488 (m-30) REVERT: H 138 ASP cc_start: 0.7689 (t0) cc_final: 0.7285 (t0) REVERT: H 145 MET cc_start: 0.7879 (mtp) cc_final: 0.7606 (mtp) REVERT: J 55 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.7956 (tt) REVERT: K 38 HIS cc_start: 0.7322 (m170) cc_final: 0.6883 (m-70) REVERT: K 78 SER cc_start: 0.8276 (m) cc_final: 0.8066 (p) REVERT: K 119 LYS cc_start: 0.7446 (ttpp) cc_final: 0.7226 (tttp) REVERT: L 35 ARG cc_start: 0.7701 (ttm-80) cc_final: 0.7336 (mtm-85) REVERT: L 56 ASP cc_start: 0.8036 (t0) cc_final: 0.7529 (t70) REVERT: M 60 MET cc_start: 0.6771 (mtm) cc_final: 0.6402 (mtm) REVERT: M 143 ASP cc_start: 0.5906 (m-30) cc_final: 0.5628 (t0) REVERT: M 146 ASP cc_start: 0.6373 (m-30) cc_final: 0.6080 (t0) REVERT: M 272 GLN cc_start: 0.7373 (mt0) cc_final: 0.6806 (tp-100) REVERT: M 286 MET cc_start: 0.8636 (mmm) cc_final: 0.8250 (mmm) REVERT: N 350 MET cc_start: 0.8558 (mmm) cc_final: 0.8147 (tpp) REVERT: N 374 THR cc_start: 0.7684 (OUTLIER) cc_final: 0.7020 (p) REVERT: O 187 MET cc_start: 0.5632 (tpt) cc_final: 0.5289 (tpp) REVERT: O 340 LYS cc_start: 0.7385 (mmmt) cc_final: 0.7159 (mttt) REVERT: O 356 GLU cc_start: 0.8025 (mm-30) cc_final: 0.7615 (mp0) REVERT: O 474 MET cc_start: 0.1047 (OUTLIER) cc_final: -0.0798 (tpp) REVERT: P 60 MET cc_start: 0.2147 (ptt) cc_final: 0.1283 (tpp) REVERT: P 167 TYR cc_start: 0.6698 (m-80) cc_final: 0.6278 (m-10) REVERT: P 250 MET cc_start: 0.6589 (tmm) cc_final: 0.5923 (ttp) REVERT: Q 42 ASP cc_start: 0.6640 (p0) cc_final: 0.6334 (p0) REVERT: Q 44 LYS cc_start: 0.8754 (mmmt) cc_final: 0.8472 (mmmt) REVERT: Q 54 GLU cc_start: 0.7879 (mp0) cc_final: 0.7322 (mp0) REVERT: Q 81 ARG cc_start: 0.3381 (tpp-160) cc_final: 0.3156 (ptm-80) REVERT: Q 103 TRP cc_start: 0.7954 (m100) cc_final: 0.7315 (m100) REVERT: Q 110 MET cc_start: 0.7276 (OUTLIER) cc_final: 0.7064 (ptp) REVERT: V 91 ASP cc_start: 0.7921 (m-30) cc_final: 0.7388 (m-30) REVERT: V 139 CYS cc_start: 0.8016 (t) cc_final: 0.7645 (p) REVERT: V 155 GLN cc_start: 0.7722 (tt0) cc_final: 0.7363 (mm110) REVERT: V 181 LYS cc_start: 0.7887 (mttp) cc_final: 0.7342 (ptpt) REVERT: V 235 GLN cc_start: 0.7067 (mt0) cc_final: 0.6496 (mm-40) REVERT: V 238 GLN cc_start: 0.5163 (tp-100) cc_final: 0.4704 (tp40) REVERT: W 283 PHE cc_start: 0.6695 (t80) cc_final: 0.6175 (m-80) REVERT: W 293 SER cc_start: 0.4136 (p) cc_final: 0.3819 (t) REVERT: W 328 LEU cc_start: 0.5602 (OUTLIER) cc_final: 0.5331 (mp) REVERT: W 337 ILE cc_start: 0.7834 (mm) cc_final: 0.7508 (pt) outliers start: 140 outliers final: 101 residues processed: 634 average time/residue: 0.5512 time to fit residues: 597.0514 Evaluate side-chains 609 residues out of total 6063 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 496 time to evaluate : 5.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 52 ASN Chi-restraints excluded: chain 3 residue 51 TRP Chi-restraints excluded: chain 3 residue 128 VAL Chi-restraints excluded: chain 3 residue 206 VAL Chi-restraints excluded: chain 3 residue 233 ASN Chi-restraints excluded: chain 3 residue 320 VAL Chi-restraints excluded: chain 3 residue 339 LEU Chi-restraints excluded: chain 3 residue 364 TRP Chi-restraints excluded: chain 3 residue 365 VAL Chi-restraints excluded: chain 3 residue 382 VAL Chi-restraints excluded: chain 3 residue 386 MET Chi-restraints excluded: chain 4 residue 222 VAL Chi-restraints excluded: chain 4 residue 299 ARG Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 469 HIS Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 722 LYS Chi-restraints excluded: chain A residue 871 MET Chi-restraints excluded: chain A residue 897 ILE Chi-restraints excluded: chain A residue 978 GLU Chi-restraints excluded: chain A residue 1023 MET Chi-restraints excluded: chain A residue 1027 MET Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1167 VAL Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 116 ASP Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 215 ASN Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 357 TYR Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 499 MET Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 755 LEU Chi-restraints excluded: chain B residue 795 LEU Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 971 ASP Chi-restraints excluded: chain B residue 1032 THR Chi-restraints excluded: chain B residue 1131 TYR Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 212 MET Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 118 HIS Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 18 MET Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 55 GLU Chi-restraints excluded: chain H residue 8 ASP Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain J residue 60 LEU Chi-restraints excluded: chain K residue 48 ASP Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain K residue 60 MET Chi-restraints excluded: chain M residue 89 THR Chi-restraints excluded: chain M residue 225 LEU Chi-restraints excluded: chain M residue 330 ASP Chi-restraints excluded: chain N residue 251 VAL Chi-restraints excluded: chain N residue 284 ILE Chi-restraints excluded: chain N residue 354 CYS Chi-restraints excluded: chain N residue 374 THR Chi-restraints excluded: chain N residue 386 SER Chi-restraints excluded: chain N residue 395 HIS Chi-restraints excluded: chain O residue 21 VAL Chi-restraints excluded: chain O residue 85 MET Chi-restraints excluded: chain O residue 163 VAL Chi-restraints excluded: chain O residue 180 LEU Chi-restraints excluded: chain O residue 182 ILE Chi-restraints excluded: chain O residue 190 VAL Chi-restraints excluded: chain O residue 380 VAL Chi-restraints excluded: chain O residue 399 LEU Chi-restraints excluded: chain O residue 474 MET Chi-restraints excluded: chain P residue 237 THR Chi-restraints excluded: chain P residue 280 THR Chi-restraints excluded: chain Q residue 40 ASP Chi-restraints excluded: chain Q residue 68 MET Chi-restraints excluded: chain Q residue 110 MET Chi-restraints excluded: chain Q residue 111 MET Chi-restraints excluded: chain U residue 171 THR Chi-restraints excluded: chain V residue 78 ASP Chi-restraints excluded: chain V residue 243 LEU Chi-restraints excluded: chain W residue 311 PHE Chi-restraints excluded: chain W residue 315 ILE Chi-restraints excluded: chain W residue 328 LEU Chi-restraints excluded: chain W residue 353 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 691 random chunks: chunk 644 optimal weight: 0.1980 chunk 75 optimal weight: 9.9990 chunk 380 optimal weight: 7.9990 chunk 488 optimal weight: 0.6980 chunk 378 optimal weight: 0.6980 chunk 562 optimal weight: 6.9990 chunk 373 optimal weight: 8.9990 chunk 666 optimal weight: 8.9990 chunk 416 optimal weight: 0.9990 chunk 406 optimal weight: 5.9990 chunk 307 optimal weight: 0.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 52 ASN 1 89 GLN 3 210 GLN ** 4 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 528 ASN A 794 GLN ** A1039 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 151 HIS E 138 ASN ** I 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 129 ASN P 266 HIS ** U 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 128 GLN V 296 HIS V 303 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6811 moved from start: 0.4233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 59698 Z= 0.142 Angle : 0.482 12.877 81288 Z= 0.249 Chirality : 0.040 0.266 9051 Planarity : 0.003 0.060 9902 Dihedral : 15.331 156.950 9296 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.81 % Allowed : 14.03 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.10), residues: 6799 helix: 1.26 (0.10), residues: 2734 sheet: -0.55 (0.18), residues: 775 loop : -0.85 (0.11), residues: 3290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP W 350 HIS 0.035 0.001 HIS A 469 PHE 0.024 0.001 PHE W 311 TYR 0.026 0.001 TYR U 192 ARG 0.016 0.000 ARG C 255 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13598 Ramachandran restraints generated. 6799 Oldfield, 0 Emsley, 6799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13598 Ramachandran restraints generated. 6799 Oldfield, 0 Emsley, 6799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 649 residues out of total 6063 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 539 time to evaluate : 5.251 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: 1 53 MET cc_start: 0.3790 (mmt) cc_final: 0.2398 (ptm) REVERT: 1 120 PHE cc_start: 0.5224 (m-10) cc_final: 0.4859 (p90) REVERT: 1 135 PHE cc_start: 0.3034 (m-80) cc_final: 0.2706 (m-80) REVERT: 3 359 MET cc_start: 0.3922 (mtt) cc_final: 0.3655 (ppp) REVERT: 3 404 TYR cc_start: 0.5995 (t80) cc_final: 0.5771 (t80) REVERT: 4 237 GLU cc_start: 0.7538 (mt-10) cc_final: 0.7157 (tp30) REVERT: 4 271 PHE cc_start: 0.7888 (m-80) cc_final: 0.7457 (m-80) REVERT: 4 379 MET cc_start: -0.1234 (ttt) cc_final: -0.1472 (tmm) REVERT: 4 385 MET cc_start: 0.1626 (tmm) cc_final: 0.0672 (tpt) REVERT: A 90 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8281 (mm) REVERT: A 123 LYS cc_start: 0.7429 (ttpp) cc_final: 0.7176 (tptp) REVERT: A 240 MET cc_start: 0.8474 (ttp) cc_final: 0.8226 (ttp) REVERT: A 379 GLU cc_start: 0.7765 (mt-10) cc_final: 0.7407 (mt-10) REVERT: A 424 ARG cc_start: 0.5255 (ttt180) cc_final: 0.3986 (ttp80) REVERT: A 627 LYS cc_start: 0.7657 (tmtt) cc_final: 0.6934 (ttmt) REVERT: A 662 ASN cc_start: 0.7147 (t0) cc_final: 0.6915 (t0) REVERT: A 780 MET cc_start: 0.8561 (mtm) cc_final: 0.8359 (mtm) REVERT: A 944 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7580 (mt-10) REVERT: A 1138 ARG cc_start: 0.8421 (mtm110) cc_final: 0.7999 (ptp-110) REVERT: A 1185 MET cc_start: 0.8066 (ptm) cc_final: 0.7577 (tmm) REVERT: B 72 MET cc_start: 0.6641 (tmm) cc_final: 0.6119 (mmm) REVERT: B 311 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7465 (mt-10) REVERT: B 354 ARG cc_start: 0.7864 (mmt-90) cc_final: 0.7466 (ttm-80) REVERT: B 438 GLN cc_start: 0.7954 (mt0) cc_final: 0.7464 (tt0) REVERT: B 780 LYS cc_start: 0.7624 (ptmt) cc_final: 0.7404 (ptmt) REVERT: B 832 MET cc_start: 0.6972 (ptp) cc_final: 0.6677 (ptp) REVERT: B 853 ASP cc_start: 0.8154 (m-30) cc_final: 0.7755 (m-30) REVERT: B 1050 MET cc_start: 0.7348 (mtm) cc_final: 0.6998 (mtt) REVERT: C 50 ARG cc_start: 0.7407 (ptt90) cc_final: 0.7025 (ptt-90) REVERT: C 248 GLU cc_start: 0.6879 (pp20) cc_final: 0.6494 (tp30) REVERT: C 261 VAL cc_start: 0.7546 (OUTLIER) cc_final: 0.7269 (p) REVERT: C 270 LYS cc_start: 0.6693 (pttp) cc_final: 0.6453 (ptpt) REVERT: C 292 LYS cc_start: 0.7468 (tmtt) cc_final: 0.6900 (tptt) REVERT: D 39 GLN cc_start: 0.6292 (tp40) cc_final: 0.5396 (tp-100) REVERT: D 40 GLN cc_start: 0.7539 (mt0) cc_final: 0.6335 (pm20) REVERT: D 47 TYR cc_start: 0.6910 (t80) cc_final: 0.6594 (t80) REVERT: D 82 GLU cc_start: 0.8278 (mt-10) cc_final: 0.7385 (mm-30) REVERT: D 90 ARG cc_start: 0.5141 (mtm-85) cc_final: 0.4016 (tpt90) REVERT: D 100 MET cc_start: 0.4401 (mtm) cc_final: 0.4068 (ptt) REVERT: D 118 HIS cc_start: 0.7621 (OUTLIER) cc_final: 0.6930 (m-70) REVERT: E 94 MET cc_start: 0.6987 (mmp) cc_final: 0.6253 (mtp) REVERT: E 168 ASN cc_start: 0.8611 (p0) cc_final: 0.8140 (p0) REVERT: F 56 TYR cc_start: 0.8500 (m-80) cc_final: 0.8131 (m-80) REVERT: G 7 MET cc_start: 0.7409 (mtp) cc_final: 0.7185 (mtp) REVERT: G 32 LYS cc_start: 0.7966 (mtpt) cc_final: 0.7473 (ttpp) REVERT: G 83 GLU cc_start: 0.6367 (tt0) cc_final: 0.5679 (tp30) REVERT: G 150 PHE cc_start: 0.4982 (m-80) cc_final: 0.4319 (m-80) REVERT: G 157 PHE cc_start: 0.6811 (t80) cc_final: 0.6472 (t80) REVERT: H 31 GLU cc_start: 0.7007 (mt-10) cc_final: 0.6666 (mt-10) REVERT: H 36 LYS cc_start: 0.7218 (mmtt) cc_final: 0.6756 (mmmt) REVERT: H 37 MET cc_start: 0.7955 (mmm) cc_final: 0.7319 (mmp) REVERT: H 51 ASP cc_start: 0.7620 (m-30) cc_final: 0.7323 (m-30) REVERT: H 62 SER cc_start: 0.9047 (t) cc_final: 0.8713 (p) REVERT: H 128 ASP cc_start: 0.7511 (m-30) cc_final: 0.7247 (m-30) REVERT: H 138 ASP cc_start: 0.7642 (t0) cc_final: 0.7250 (t0) REVERT: H 145 MET cc_start: 0.7810 (mtp) cc_final: 0.7546 (mtp) REVERT: J 55 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8117 (tt) REVERT: K 38 HIS cc_start: 0.7252 (m170) cc_final: 0.6727 (m-70) REVERT: K 115 GLU cc_start: 0.7908 (mm-30) cc_final: 0.7519 (mt-10) REVERT: K 119 LYS cc_start: 0.7503 (ttpp) cc_final: 0.7296 (tttp) REVERT: L 35 ARG cc_start: 0.7668 (ttm-80) cc_final: 0.7292 (mtm-85) REVERT: L 56 ASP cc_start: 0.8079 (t0) cc_final: 0.7621 (t70) REVERT: M 60 MET cc_start: 0.6404 (mtm) cc_final: 0.6032 (mtm) REVERT: M 143 ASP cc_start: 0.5929 (m-30) cc_final: 0.5637 (t0) REVERT: M 146 ASP cc_start: 0.6364 (m-30) cc_final: 0.6051 (t0) REVERT: M 272 GLN cc_start: 0.7343 (mt0) cc_final: 0.6801 (tp-100) REVERT: M 286 MET cc_start: 0.8686 (mmm) cc_final: 0.8312 (mmm) REVERT: N 374 THR cc_start: 0.7770 (OUTLIER) cc_final: 0.7116 (p) REVERT: O 187 MET cc_start: 0.5639 (tpt) cc_final: 0.5277 (tpp) REVERT: O 340 LYS cc_start: 0.7464 (mmmt) cc_final: 0.7210 (mttt) REVERT: O 356 GLU cc_start: 0.7955 (mm-30) cc_final: 0.7581 (mp0) REVERT: O 474 MET cc_start: 0.0941 (OUTLIER) cc_final: -0.0644 (tpp) REVERT: P 60 MET cc_start: 0.2141 (ptt) cc_final: 0.1190 (tpp) REVERT: P 167 TYR cc_start: 0.6679 (m-80) cc_final: 0.5963 (m-10) REVERT: P 250 MET cc_start: 0.6657 (tmm) cc_final: 0.5968 (ttp) REVERT: Q 42 ASP cc_start: 0.6776 (p0) cc_final: 0.6484 (p0) REVERT: Q 44 LYS cc_start: 0.8750 (mmmt) cc_final: 0.8507 (mmmt) REVERT: Q 54 GLU cc_start: 0.7867 (mp0) cc_final: 0.7246 (mt-10) REVERT: Q 81 ARG cc_start: 0.3218 (tpp-160) cc_final: 0.2867 (ttt90) REVERT: Q 103 TRP cc_start: 0.7966 (m100) cc_final: 0.7349 (m100) REVERT: Q 110 MET cc_start: 0.7213 (OUTLIER) cc_final: 0.6983 (ptp) REVERT: V 52 GLU cc_start: 0.3714 (tm-30) cc_final: 0.3009 (mp0) REVERT: V 91 ASP cc_start: 0.7890 (m-30) cc_final: 0.7374 (m-30) REVERT: V 139 CYS cc_start: 0.7959 (t) cc_final: 0.7423 (p) REVERT: V 155 GLN cc_start: 0.7707 (tt0) cc_final: 0.7355 (mm110) REVERT: V 181 LYS cc_start: 0.7927 (mttp) cc_final: 0.7376 (ptpt) REVERT: V 235 GLN cc_start: 0.7114 (mt0) cc_final: 0.6366 (mm-40) REVERT: V 238 GLN cc_start: 0.5165 (tp-100) cc_final: 0.4658 (tp40) REVERT: W 283 PHE cc_start: 0.6624 (t80) cc_final: 0.6168 (m-80) REVERT: W 284 GLU cc_start: 0.6486 (tp30) cc_final: 0.5932 (mm-30) REVERT: W 293 SER cc_start: 0.4042 (p) cc_final: 0.3682 (t) REVERT: W 295 ARG cc_start: 0.2959 (mmp80) cc_final: 0.2425 (mmt-90) REVERT: W 337 ILE cc_start: 0.7871 (mm) cc_final: 0.7523 (pt) outliers start: 110 outliers final: 78 residues processed: 618 average time/residue: 0.5607 time to fit residues: 589.4890 Evaluate side-chains 590 residues out of total 6063 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 505 time to evaluate : 5.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 52 ASN Chi-restraints excluded: chain 3 residue 128 VAL Chi-restraints excluded: chain 3 residue 193 HIS Chi-restraints excluded: chain 3 residue 206 VAL Chi-restraints excluded: chain 3 residue 233 ASN Chi-restraints excluded: chain 3 residue 320 VAL Chi-restraints excluded: chain 3 residue 339 LEU Chi-restraints excluded: chain 3 residue 365 VAL Chi-restraints excluded: chain 3 residue 382 VAL Chi-restraints excluded: chain 3 residue 386 MET Chi-restraints excluded: chain 4 residue 222 VAL Chi-restraints excluded: chain 4 residue 299 ARG Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 469 HIS Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 871 MET Chi-restraints excluded: chain A residue 1023 MET Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1339 SER Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 116 ASP Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 215 ASN Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 499 MET Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 755 LEU Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 971 ASP Chi-restraints excluded: chain B residue 1032 THR Chi-restraints excluded: chain B residue 1131 TYR Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 151 HIS Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain D residue 118 HIS Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 18 MET Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 55 GLU Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 8 ASP Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain K residue 104 MET Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain M residue 89 THR Chi-restraints excluded: chain M residue 225 LEU Chi-restraints excluded: chain M residue 330 ASP Chi-restraints excluded: chain M residue 401 ILE Chi-restraints excluded: chain N residue 251 VAL Chi-restraints excluded: chain N residue 374 THR Chi-restraints excluded: chain N residue 386 SER Chi-restraints excluded: chain O residue 21 VAL Chi-restraints excluded: chain O residue 163 VAL Chi-restraints excluded: chain O residue 180 LEU Chi-restraints excluded: chain O residue 190 VAL Chi-restraints excluded: chain O residue 259 MET Chi-restraints excluded: chain O residue 399 LEU Chi-restraints excluded: chain O residue 474 MET Chi-restraints excluded: chain P residue 237 THR Chi-restraints excluded: chain Q residue 40 ASP Chi-restraints excluded: chain Q residue 50 THR Chi-restraints excluded: chain Q residue 110 MET Chi-restraints excluded: chain Q residue 111 MET Chi-restraints excluded: chain U residue 171 THR Chi-restraints excluded: chain V residue 78 ASP Chi-restraints excluded: chain V residue 243 LEU Chi-restraints excluded: chain W residue 311 PHE Chi-restraints excluded: chain W residue 315 ILE Chi-restraints excluded: chain W residue 352 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 691 random chunks: chunk 412 optimal weight: 3.9990 chunk 265 optimal weight: 4.9990 chunk 397 optimal weight: 9.9990 chunk 200 optimal weight: 9.9990 chunk 130 optimal weight: 4.9990 chunk 129 optimal weight: 1.9990 chunk 423 optimal weight: 9.9990 chunk 453 optimal weight: 7.9990 chunk 329 optimal weight: 8.9990 chunk 62 optimal weight: 4.9990 chunk 523 optimal weight: 0.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 52 ASN 1 111 GLN 3 193 HIS 3 210 GLN 4 270 ASN ** 4 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 528 ASN ** A 739 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1039 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 979 HIS B1132 ASN ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 61 GLN D 89 HIS E 138 ASN G 98 HIS ** I 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 129 ASN P 266 HIS ** U 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 242 GLN V 70 GLN V 128 GLN ** V 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 296 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6870 moved from start: 0.4657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 59698 Z= 0.335 Angle : 0.576 12.250 81288 Z= 0.298 Chirality : 0.043 0.197 9051 Planarity : 0.004 0.050 9902 Dihedral : 15.430 157.298 9296 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.19 % Allowed : 14.09 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.10), residues: 6799 helix: 1.08 (0.10), residues: 2725 sheet: -0.67 (0.18), residues: 781 loop : -0.88 (0.11), residues: 3293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP W 350 HIS 0.021 0.001 HIS C 151 PHE 0.021 0.002 PHE C 336 TYR 0.023 0.002 TYR U 192 ARG 0.011 0.001 ARG C 255 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13598 Ramachandran restraints generated. 6799 Oldfield, 0 Emsley, 6799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13598 Ramachandran restraints generated. 6799 Oldfield, 0 Emsley, 6799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 639 residues out of total 6063 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 506 time to evaluate : 5.253 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: 1 120 PHE cc_start: 0.5449 (m-10) cc_final: 0.4889 (p90) REVERT: 1 135 PHE cc_start: 0.3074 (m-80) cc_final: 0.2742 (m-10) REVERT: 3 51 TRP cc_start: 0.0497 (OUTLIER) cc_final: 0.0196 (t-100) REVERT: 3 281 HIS cc_start: 0.4549 (m90) cc_final: 0.3886 (t-170) REVERT: 3 359 MET cc_start: 0.3840 (mtt) cc_final: 0.3572 (ppp) REVERT: 4 237 GLU cc_start: 0.7499 (mt-10) cc_final: 0.7198 (tp30) REVERT: 4 271 PHE cc_start: 0.7660 (m-80) cc_final: 0.7273 (m-80) REVERT: 4 379 MET cc_start: -0.1633 (ttt) cc_final: -0.2087 (tmm) REVERT: 4 385 MET cc_start: 0.1676 (tmm) cc_final: 0.0756 (tpt) REVERT: A 123 LYS cc_start: 0.7433 (ttpp) cc_final: 0.7186 (tptp) REVERT: A 240 MET cc_start: 0.8537 (ttp) cc_final: 0.8305 (ttp) REVERT: A 379 GLU cc_start: 0.7847 (mt-10) cc_final: 0.7486 (mt-10) REVERT: A 424 ARG cc_start: 0.5307 (ttt180) cc_final: 0.4075 (ttp80) REVERT: A 627 LYS cc_start: 0.7678 (tmtt) cc_final: 0.6960 (ttmt) REVERT: A 729 GLU cc_start: 0.7481 (tp30) cc_final: 0.6658 (tp30) REVERT: A 944 GLU cc_start: 0.7892 (mt-10) cc_final: 0.7603 (mt-10) REVERT: A 1138 ARG cc_start: 0.8432 (mtm110) cc_final: 0.8021 (ptp-110) REVERT: A 1185 MET cc_start: 0.8187 (ptm) cc_final: 0.7635 (tmm) REVERT: B 72 MET cc_start: 0.6660 (tmm) cc_final: 0.6352 (mmm) REVERT: B 208 HIS cc_start: 0.5639 (t70) cc_final: 0.5238 (t70) REVERT: B 247 SER cc_start: 0.8702 (OUTLIER) cc_final: 0.7800 (t) REVERT: B 254 MET cc_start: 0.8360 (mtp) cc_final: 0.8098 (mtp) REVERT: B 311 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7254 (mt-10) REVERT: B 354 ARG cc_start: 0.7866 (mmt-90) cc_final: 0.7425 (ttm-80) REVERT: B 438 GLN cc_start: 0.8111 (mt0) cc_final: 0.7503 (tt0) REVERT: B 780 LYS cc_start: 0.7754 (ptmt) cc_final: 0.7471 (ptmt) REVERT: B 832 MET cc_start: 0.7095 (ptp) cc_final: 0.6788 (ptp) REVERT: B 853 ASP cc_start: 0.8248 (m-30) cc_final: 0.7892 (m-30) REVERT: C 50 ARG cc_start: 0.7483 (ptt90) cc_final: 0.7127 (ptt-90) REVERT: C 248 GLU cc_start: 0.6928 (pp20) cc_final: 0.6466 (tp30) REVERT: C 261 VAL cc_start: 0.7701 (OUTLIER) cc_final: 0.7427 (p) REVERT: C 292 LYS cc_start: 0.7591 (tmtt) cc_final: 0.6969 (tptt) REVERT: C 344 GLN cc_start: 0.6574 (pt0) cc_final: 0.5487 (tp40) REVERT: D 47 TYR cc_start: 0.6879 (t80) cc_final: 0.6527 (t80) REVERT: D 57 PRO cc_start: 0.7045 (Cg_exo) cc_final: 0.6349 (Cg_endo) REVERT: D 82 GLU cc_start: 0.8385 (mt-10) cc_final: 0.7650 (mm-30) REVERT: D 90 ARG cc_start: 0.5774 (mtm-85) cc_final: 0.4282 (tpt170) REVERT: D 100 MET cc_start: 0.4573 (mtm) cc_final: 0.4234 (mtm) REVERT: D 112 GLN cc_start: 0.6535 (tp40) cc_final: 0.6175 (mt0) REVERT: D 118 HIS cc_start: 0.7730 (OUTLIER) cc_final: 0.7010 (m-70) REVERT: E 128 GLU cc_start: 0.6857 (mt-10) cc_final: 0.6572 (mt-10) REVERT: E 168 ASN cc_start: 0.8724 (p0) cc_final: 0.8242 (p0) REVERT: F 56 TYR cc_start: 0.8495 (m-80) cc_final: 0.8151 (m-80) REVERT: G 7 MET cc_start: 0.7519 (mtp) cc_final: 0.7213 (mtp) REVERT: G 32 LYS cc_start: 0.7889 (mtpt) cc_final: 0.7461 (ttpp) REVERT: G 150 PHE cc_start: 0.5099 (m-80) cc_final: 0.4448 (m-80) REVERT: G 157 PHE cc_start: 0.6787 (t80) cc_final: 0.6417 (t80) REVERT: H 36 LYS cc_start: 0.7394 (mmtt) cc_final: 0.6816 (mmmt) REVERT: H 37 MET cc_start: 0.8102 (mmm) cc_final: 0.7431 (mmp) REVERT: H 62 SER cc_start: 0.9118 (t) cc_final: 0.8755 (p) REVERT: H 128 ASP cc_start: 0.7827 (m-30) cc_final: 0.7577 (m-30) REVERT: H 138 ASP cc_start: 0.7728 (t0) cc_final: 0.7312 (t0) REVERT: H 145 MET cc_start: 0.7776 (mtp) cc_final: 0.7551 (mtp) REVERT: J 55 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.7920 (tt) REVERT: K 119 LYS cc_start: 0.7513 (ttpp) cc_final: 0.7250 (tttm) REVERT: L 35 ARG cc_start: 0.7848 (ttm-80) cc_final: 0.7442 (mtm-85) REVERT: L 56 ASP cc_start: 0.8137 (t0) cc_final: 0.7794 (t70) REVERT: M 143 ASP cc_start: 0.5992 (m-30) cc_final: 0.5767 (t0) REVERT: M 146 ASP cc_start: 0.6565 (m-30) cc_final: 0.6130 (t0) REVERT: M 272 GLN cc_start: 0.7281 (mt0) cc_final: 0.6761 (tp-100) REVERT: M 286 MET cc_start: 0.8625 (mmm) cc_final: 0.8236 (mmm) REVERT: N 374 THR cc_start: 0.7964 (OUTLIER) cc_final: 0.7267 (p) REVERT: O 187 MET cc_start: 0.5621 (tpt) cc_final: 0.5277 (tpp) REVERT: O 340 LYS cc_start: 0.7365 (mmmt) cc_final: 0.7151 (mttt) REVERT: O 356 GLU cc_start: 0.8012 (mm-30) cc_final: 0.7505 (mp0) REVERT: O 394 MET cc_start: 0.6579 (mtt) cc_final: 0.6369 (mtt) REVERT: O 474 MET cc_start: 0.0523 (OUTLIER) cc_final: -0.1407 (tpp) REVERT: P 60 MET cc_start: 0.2163 (ptt) cc_final: 0.1365 (tpp) REVERT: P 167 TYR cc_start: 0.6624 (m-80) cc_final: 0.6177 (m-10) REVERT: P 178 GLU cc_start: 0.7668 (mt-10) cc_final: 0.7013 (tm-30) REVERT: P 250 MET cc_start: 0.6739 (tmm) cc_final: 0.6233 (ttp) REVERT: Q 42 ASP cc_start: 0.6793 (p0) cc_final: 0.6545 (p0) REVERT: Q 44 LYS cc_start: 0.8729 (mmmt) cc_final: 0.8493 (mmmt) REVERT: Q 54 GLU cc_start: 0.7921 (mp0) cc_final: 0.7292 (mp0) REVERT: Q 82 GLN cc_start: 0.4609 (OUTLIER) cc_final: 0.4119 (pp30) REVERT: Q 85 GLU cc_start: 0.4458 (pm20) cc_final: 0.3995 (mt-10) REVERT: U 166 GLN cc_start: 0.7004 (mt0) cc_final: 0.6755 (tt0) REVERT: V 91 ASP cc_start: 0.8000 (m-30) cc_final: 0.7447 (m-30) REVERT: V 139 CYS cc_start: 0.8053 (t) cc_final: 0.7496 (p) REVERT: V 155 GLN cc_start: 0.7699 (tt0) cc_final: 0.7373 (mm110) REVERT: V 181 LYS cc_start: 0.7761 (mttp) cc_final: 0.7203 (ptpt) REVERT: V 238 GLN cc_start: 0.5357 (tp-100) cc_final: 0.4904 (tp40) REVERT: W 293 SER cc_start: 0.4039 (p) cc_final: 0.3786 (t) REVERT: W 328 LEU cc_start: 0.5615 (OUTLIER) cc_final: 0.5236 (mp) outliers start: 133 outliers final: 103 residues processed: 608 average time/residue: 0.5578 time to fit residues: 576.4995 Evaluate side-chains 593 residues out of total 6063 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 481 time to evaluate : 5.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 51 TRP Chi-restraints excluded: chain 3 residue 128 VAL Chi-restraints excluded: chain 3 residue 206 VAL Chi-restraints excluded: chain 3 residue 233 ASN Chi-restraints excluded: chain 3 residue 320 VAL Chi-restraints excluded: chain 3 residue 336 ASP Chi-restraints excluded: chain 3 residue 339 LEU Chi-restraints excluded: chain 3 residue 365 VAL Chi-restraints excluded: chain 3 residue 382 VAL Chi-restraints excluded: chain 3 residue 386 MET Chi-restraints excluded: chain 4 residue 222 VAL Chi-restraints excluded: chain 4 residue 299 ARG Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 871 MET Chi-restraints excluded: chain A residue 897 ILE Chi-restraints excluded: chain A residue 978 GLU Chi-restraints excluded: chain A residue 1023 MET Chi-restraints excluded: chain A residue 1027 MET Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1167 VAL Chi-restraints excluded: chain A residue 1200 VAL Chi-restraints excluded: chain A residue 1339 SER Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 116 ASP Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 215 ASN Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 499 MET Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 755 LEU Chi-restraints excluded: chain B residue 784 ASN Chi-restraints excluded: chain B residue 795 LEU Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 971 ASP Chi-restraints excluded: chain B residue 1032 THR Chi-restraints excluded: chain B residue 1131 TYR Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain D residue 61 GLN Chi-restraints excluded: chain D residue 118 HIS Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 18 MET Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 55 GLU Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain J residue 60 LEU Chi-restraints excluded: chain K residue 48 ASP Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain K residue 60 MET Chi-restraints excluded: chain M residue 21 LEU Chi-restraints excluded: chain M residue 89 THR Chi-restraints excluded: chain M residue 225 LEU Chi-restraints excluded: chain M residue 330 ASP Chi-restraints excluded: chain M residue 349 LEU Chi-restraints excluded: chain M residue 401 ILE Chi-restraints excluded: chain N residue 251 VAL Chi-restraints excluded: chain N residue 284 ILE Chi-restraints excluded: chain N residue 354 CYS Chi-restraints excluded: chain N residue 374 THR Chi-restraints excluded: chain N residue 386 SER Chi-restraints excluded: chain N residue 395 HIS Chi-restraints excluded: chain O residue 21 VAL Chi-restraints excluded: chain O residue 63 VAL Chi-restraints excluded: chain O residue 163 VAL Chi-restraints excluded: chain O residue 180 LEU Chi-restraints excluded: chain O residue 190 VAL Chi-restraints excluded: chain O residue 380 VAL Chi-restraints excluded: chain O residue 399 LEU Chi-restraints excluded: chain O residue 474 MET Chi-restraints excluded: chain P residue 237 THR Chi-restraints excluded: chain P residue 280 THR Chi-restraints excluded: chain Q residue 40 ASP Chi-restraints excluded: chain Q residue 50 THR Chi-restraints excluded: chain Q residue 82 GLN Chi-restraints excluded: chain Q residue 110 MET Chi-restraints excluded: chain U residue 171 THR Chi-restraints excluded: chain V residue 78 ASP Chi-restraints excluded: chain V residue 243 LEU Chi-restraints excluded: chain W residue 311 PHE Chi-restraints excluded: chain W residue 315 ILE Chi-restraints excluded: chain W residue 324 MET Chi-restraints excluded: chain W residue 328 LEU Chi-restraints excluded: chain W residue 352 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 691 random chunks: chunk 605 optimal weight: 9.9990 chunk 638 optimal weight: 6.9990 chunk 582 optimal weight: 6.9990 chunk 620 optimal weight: 7.9990 chunk 637 optimal weight: 0.9980 chunk 373 optimal weight: 1.9990 chunk 270 optimal weight: 0.9980 chunk 487 optimal weight: 1.9990 chunk 190 optimal weight: 0.9980 chunk 560 optimal weight: 9.9990 chunk 586 optimal weight: 10.0000 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 4 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 528 ASN ** A1039 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 61 GLN E 138 ASN ** I 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 129 ASN P 266 HIS ** U 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 70 GLN V 255 ASN V 296 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6838 moved from start: 0.4650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 59698 Z= 0.183 Angle : 0.509 12.722 81288 Z= 0.262 Chirality : 0.040 0.218 9051 Planarity : 0.004 0.064 9902 Dihedral : 15.368 155.825 9296 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.81 % Allowed : 14.64 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.10), residues: 6799 helix: 1.20 (0.10), residues: 2739 sheet: -0.63 (0.18), residues: 777 loop : -0.86 (0.11), residues: 3283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP W 350 HIS 0.006 0.001 HIS A 415 PHE 0.024 0.001 PHE W 311 TYR 0.025 0.001 TYR U 192 ARG 0.015 0.000 ARG C 255 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13598 Ramachandran restraints generated. 6799 Oldfield, 0 Emsley, 6799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13598 Ramachandran restraints generated. 6799 Oldfield, 0 Emsley, 6799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 617 residues out of total 6063 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 507 time to evaluate : 5.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 53 MET cc_start: 0.3447 (mmt) cc_final: 0.2265 (ptm) REVERT: 1 120 PHE cc_start: 0.5536 (m-10) cc_final: 0.4972 (p90) REVERT: 1 135 PHE cc_start: 0.3079 (m-80) cc_final: 0.2832 (m-80) REVERT: 3 281 HIS cc_start: 0.4774 (m90) cc_final: 0.4056 (t-170) REVERT: 3 359 MET cc_start: 0.3841 (mtt) cc_final: 0.3606 (ppp) REVERT: 4 150 PHE cc_start: 0.3715 (t80) cc_final: 0.3453 (t80) REVERT: 4 237 GLU cc_start: 0.7578 (mt-10) cc_final: 0.7273 (tp30) REVERT: 4 271 PHE cc_start: 0.7639 (m-80) cc_final: 0.7258 (m-80) REVERT: 4 379 MET cc_start: -0.1868 (ttt) cc_final: -0.2259 (tmm) REVERT: 4 385 MET cc_start: 0.1819 (tmm) cc_final: 0.0904 (tpt) REVERT: A 123 LYS cc_start: 0.7425 (ttpp) cc_final: 0.7172 (tptp) REVERT: A 240 MET cc_start: 0.8544 (ttp) cc_final: 0.8294 (ttp) REVERT: A 379 GLU cc_start: 0.7795 (mt-10) cc_final: 0.7426 (mt-10) REVERT: A 424 ARG cc_start: 0.5280 (ttt180) cc_final: 0.4024 (ttp80) REVERT: A 627 LYS cc_start: 0.7727 (tmtt) cc_final: 0.7008 (ttmt) REVERT: A 662 ASN cc_start: 0.7472 (t0) cc_final: 0.7204 (t0) REVERT: A 729 GLU cc_start: 0.7446 (tp30) cc_final: 0.6615 (tp30) REVERT: A 780 MET cc_start: 0.8433 (mtm) cc_final: 0.8219 (mtm) REVERT: A 944 GLU cc_start: 0.7890 (mt-10) cc_final: 0.7598 (mt-10) REVERT: A 962 GLN cc_start: 0.6628 (mp10) cc_final: 0.6211 (mp10) REVERT: A 1138 ARG cc_start: 0.8413 (mtm110) cc_final: 0.7991 (ptp-110) REVERT: B 72 MET cc_start: 0.6639 (OUTLIER) cc_final: 0.6354 (mmm) REVERT: B 208 HIS cc_start: 0.5611 (t70) cc_final: 0.5150 (t70) REVERT: B 254 MET cc_start: 0.8329 (mtp) cc_final: 0.8014 (mtp) REVERT: B 311 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7218 (mt-10) REVERT: B 354 ARG cc_start: 0.7841 (mmt-90) cc_final: 0.7429 (ttm-80) REVERT: B 438 GLN cc_start: 0.8022 (mt0) cc_final: 0.7448 (tt0) REVERT: B 780 LYS cc_start: 0.7733 (ptmt) cc_final: 0.7483 (ptmt) REVERT: B 832 MET cc_start: 0.7076 (ptp) cc_final: 0.6806 (ptp) REVERT: B 853 ASP cc_start: 0.8251 (m-30) cc_final: 0.7964 (m-30) REVERT: C 50 ARG cc_start: 0.7445 (ptt90) cc_final: 0.7056 (ptt-90) REVERT: C 248 GLU cc_start: 0.6908 (pp20) cc_final: 0.6454 (tp30) REVERT: C 261 VAL cc_start: 0.7645 (OUTLIER) cc_final: 0.7371 (p) REVERT: C 292 LYS cc_start: 0.7540 (tmtt) cc_final: 0.6933 (tptt) REVERT: C 344 GLN cc_start: 0.6790 (pt0) cc_final: 0.5677 (tp40) REVERT: D 39 GLN cc_start: 0.6467 (tp40) cc_final: 0.5555 (tp-100) REVERT: D 47 TYR cc_start: 0.6866 (t80) cc_final: 0.6511 (t80) REVERT: D 82 GLU cc_start: 0.8365 (mt-10) cc_final: 0.7613 (mm-30) REVERT: D 100 MET cc_start: 0.4589 (mtm) cc_final: 0.4273 (mtm) REVERT: D 118 HIS cc_start: 0.7738 (OUTLIER) cc_final: 0.7035 (m-70) REVERT: E 128 GLU cc_start: 0.6813 (mt-10) cc_final: 0.6525 (mt-10) REVERT: E 168 ASN cc_start: 0.8772 (p0) cc_final: 0.8306 (p0) REVERT: F 56 TYR cc_start: 0.8473 (m-80) cc_final: 0.8146 (m-80) REVERT: G 7 MET cc_start: 0.7430 (mtp) cc_final: 0.7184 (mtp) REVERT: G 32 LYS cc_start: 0.7875 (mtpt) cc_final: 0.7449 (ttpp) REVERT: G 83 GLU cc_start: 0.6315 (tt0) cc_final: 0.5775 (tp30) REVERT: G 114 LEU cc_start: 0.2458 (OUTLIER) cc_final: 0.1923 (mp) REVERT: G 150 PHE cc_start: 0.5013 (m-80) cc_final: 0.4358 (m-80) REVERT: G 157 PHE cc_start: 0.6741 (t80) cc_final: 0.6419 (t80) REVERT: H 20 LYS cc_start: 0.7908 (tptp) cc_final: 0.7697 (tptt) REVERT: H 31 GLU cc_start: 0.6922 (mt-10) cc_final: 0.6608 (mt-10) REVERT: H 36 LYS cc_start: 0.7390 (mmtt) cc_final: 0.6815 (mmmt) REVERT: H 37 MET cc_start: 0.8068 (mmm) cc_final: 0.7402 (mmp) REVERT: H 62 SER cc_start: 0.9073 (t) cc_final: 0.8731 (p) REVERT: H 128 ASP cc_start: 0.7789 (m-30) cc_final: 0.7519 (m-30) REVERT: H 138 ASP cc_start: 0.7683 (t0) cc_final: 0.7281 (t0) REVERT: H 145 MET cc_start: 0.7854 (mtp) cc_final: 0.7597 (mtp) REVERT: J 55 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.7988 (tt) REVERT: K 115 GLU cc_start: 0.7965 (mm-30) cc_final: 0.7562 (mt-10) REVERT: K 119 LYS cc_start: 0.7510 (ttpp) cc_final: 0.7271 (tttm) REVERT: L 35 ARG cc_start: 0.7840 (ttm-80) cc_final: 0.7410 (mtm-85) REVERT: L 56 ASP cc_start: 0.8069 (t0) cc_final: 0.7616 (t70) REVERT: M 60 MET cc_start: 0.6723 (mtm) cc_final: 0.6402 (mtm) REVERT: M 143 ASP cc_start: 0.5986 (m-30) cc_final: 0.5776 (t0) REVERT: M 146 ASP cc_start: 0.6529 (m-30) cc_final: 0.6133 (t0) REVERT: M 272 GLN cc_start: 0.7258 (mt0) cc_final: 0.6754 (tp-100) REVERT: M 286 MET cc_start: 0.8683 (mmm) cc_final: 0.8308 (mmm) REVERT: N 374 THR cc_start: 0.7853 (OUTLIER) cc_final: 0.7153 (p) REVERT: O 187 MET cc_start: 0.5608 (tpt) cc_final: 0.5245 (tpp) REVERT: O 356 GLU cc_start: 0.7973 (mm-30) cc_final: 0.7483 (mp0) REVERT: O 394 MET cc_start: 0.6567 (mtt) cc_final: 0.6333 (mtt) REVERT: O 474 MET cc_start: 0.0381 (OUTLIER) cc_final: -0.1208 (tpp) REVERT: P 60 MET cc_start: 0.2125 (ptt) cc_final: 0.1340 (tpp) REVERT: P 85 MET cc_start: -0.0692 (mmm) cc_final: -0.0958 (mmm) REVERT: P 167 TYR cc_start: 0.6690 (m-80) cc_final: 0.5979 (m-10) REVERT: P 178 GLU cc_start: 0.7731 (mt-10) cc_final: 0.7008 (tm-30) REVERT: P 210 PHE cc_start: 0.6947 (OUTLIER) cc_final: 0.6547 (t80) REVERT: P 250 MET cc_start: 0.6731 (tmm) cc_final: 0.6279 (ttp) REVERT: Q 42 ASP cc_start: 0.6796 (p0) cc_final: 0.6508 (p0) REVERT: Q 44 LYS cc_start: 0.8732 (mmmt) cc_final: 0.8501 (mmmt) REVERT: Q 54 GLU cc_start: 0.7846 (mp0) cc_final: 0.7107 (mt-10) REVERT: Q 85 GLU cc_start: 0.4338 (pm20) cc_final: 0.3845 (mt-10) REVERT: Q 103 TRP cc_start: 0.7924 (m100) cc_final: 0.7269 (m100) REVERT: U 166 GLN cc_start: 0.7092 (mt0) cc_final: 0.6873 (tt0) REVERT: V 91 ASP cc_start: 0.7956 (m-30) cc_final: 0.7417 (m-30) REVERT: V 139 CYS cc_start: 0.8046 (t) cc_final: 0.7442 (p) REVERT: V 155 GLN cc_start: 0.7581 (tt0) cc_final: 0.7283 (mm110) REVERT: V 181 LYS cc_start: 0.7748 (mttp) cc_final: 0.7231 (ptpt) REVERT: V 235 GLN cc_start: 0.7135 (mt0) cc_final: 0.6473 (mm-40) REVERT: V 238 GLN cc_start: 0.5235 (tp-100) cc_final: 0.4710 (tp40) REVERT: W 293 SER cc_start: 0.3712 (p) cc_final: 0.3401 (t) REVERT: W 295 ARG cc_start: 0.3223 (mmp80) cc_final: 0.2776 (mmt-90) REVERT: W 328 LEU cc_start: 0.5464 (OUTLIER) cc_final: 0.5138 (mp) REVERT: W 337 ILE cc_start: 0.7872 (mm) cc_final: 0.7514 (pt) outliers start: 110 outliers final: 93 residues processed: 591 average time/residue: 0.5813 time to fit residues: 589.3926 Evaluate side-chains 589 residues out of total 6063 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 487 time to evaluate : 5.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 128 VAL Chi-restraints excluded: chain 3 residue 206 VAL Chi-restraints excluded: chain 3 residue 233 ASN Chi-restraints excluded: chain 3 residue 320 VAL Chi-restraints excluded: chain 3 residue 339 LEU Chi-restraints excluded: chain 3 residue 365 VAL Chi-restraints excluded: chain 3 residue 382 VAL Chi-restraints excluded: chain 3 residue 386 MET Chi-restraints excluded: chain 4 residue 181 VAL Chi-restraints excluded: chain 4 residue 222 VAL Chi-restraints excluded: chain 4 residue 299 ARG Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 871 MET Chi-restraints excluded: chain A residue 897 ILE Chi-restraints excluded: chain A residue 1023 MET Chi-restraints excluded: chain A residue 1027 MET Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1167 VAL Chi-restraints excluded: chain A residue 1339 SER Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 116 ASP Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 215 ASN Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 499 MET Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 755 LEU Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 971 ASP Chi-restraints excluded: chain B residue 1032 THR Chi-restraints excluded: chain B residue 1131 TYR Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain D residue 118 HIS Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 18 MET Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 55 GLU Chi-restraints excluded: chain G residue 107 ILE Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain K residue 27 LEU Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain K residue 60 MET Chi-restraints excluded: chain M residue 21 LEU Chi-restraints excluded: chain M residue 89 THR Chi-restraints excluded: chain M residue 225 LEU Chi-restraints excluded: chain M residue 330 ASP Chi-restraints excluded: chain M residue 401 ILE Chi-restraints excluded: chain N residue 251 VAL Chi-restraints excluded: chain N residue 284 ILE Chi-restraints excluded: chain N residue 374 THR Chi-restraints excluded: chain N residue 386 SER Chi-restraints excluded: chain O residue 21 VAL Chi-restraints excluded: chain O residue 63 VAL Chi-restraints excluded: chain O residue 163 VAL Chi-restraints excluded: chain O residue 180 LEU Chi-restraints excluded: chain O residue 190 VAL Chi-restraints excluded: chain O residue 259 MET Chi-restraints excluded: chain O residue 380 VAL Chi-restraints excluded: chain O residue 399 LEU Chi-restraints excluded: chain O residue 474 MET Chi-restraints excluded: chain O residue 520 ILE Chi-restraints excluded: chain P residue 210 PHE Chi-restraints excluded: chain P residue 237 THR Chi-restraints excluded: chain P residue 280 THR Chi-restraints excluded: chain Q residue 40 ASP Chi-restraints excluded: chain Q residue 50 THR Chi-restraints excluded: chain Q residue 110 MET Chi-restraints excluded: chain Q residue 111 MET Chi-restraints excluded: chain U residue 171 THR Chi-restraints excluded: chain V residue 78 ASP Chi-restraints excluded: chain V residue 243 LEU Chi-restraints excluded: chain W residue 311 PHE Chi-restraints excluded: chain W residue 315 ILE Chi-restraints excluded: chain W residue 328 LEU Chi-restraints excluded: chain W residue 352 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 691 random chunks: chunk 618 optimal weight: 9.9990 chunk 407 optimal weight: 0.1980 chunk 656 optimal weight: 7.9990 chunk 400 optimal weight: 0.9980 chunk 311 optimal weight: 1.9990 chunk 456 optimal weight: 4.9990 chunk 688 optimal weight: 20.0000 chunk 633 optimal weight: 0.4980 chunk 548 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 423 optimal weight: 6.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 4 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1039 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 151 HIS E 138 ASN ** I 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 266 HIS ** U 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 128 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6818 moved from start: 0.4619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 59698 Z= 0.145 Angle : 0.491 12.596 81288 Z= 0.253 Chirality : 0.040 0.208 9051 Planarity : 0.003 0.064 9902 Dihedral : 15.289 155.248 9296 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.67 % Allowed : 15.00 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.10), residues: 6799 helix: 1.37 (0.10), residues: 2730 sheet: -0.55 (0.18), residues: 755 loop : -0.79 (0.11), residues: 3314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP W 350 HIS 0.007 0.001 HIS L 23 PHE 0.023 0.001 PHE W 311 TYR 0.028 0.001 TYR E 90 ARG 0.016 0.000 ARG C 255 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13598 Ramachandran restraints generated. 6799 Oldfield, 0 Emsley, 6799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13598 Ramachandran restraints generated. 6799 Oldfield, 0 Emsley, 6799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 617 residues out of total 6063 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 516 time to evaluate : 6.452 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: 1 53 MET cc_start: 0.3444 (mmt) cc_final: 0.2273 (ptm) REVERT: 1 120 PHE cc_start: 0.5471 (m-10) cc_final: 0.4935 (p90) REVERT: 1 135 PHE cc_start: 0.3124 (m-80) cc_final: 0.2720 (m-80) REVERT: 3 281 HIS cc_start: 0.4789 (m90) cc_final: 0.4022 (t-170) REVERT: 3 359 MET cc_start: 0.3863 (mtt) cc_final: 0.3619 (ppp) REVERT: 4 150 PHE cc_start: 0.3832 (t80) cc_final: 0.3590 (t80) REVERT: 4 226 LEU cc_start: 0.3279 (OUTLIER) cc_final: 0.3071 (pt) REVERT: 4 237 GLU cc_start: 0.7574 (mt-10) cc_final: 0.7268 (tp30) REVERT: 4 271 PHE cc_start: 0.7642 (m-80) cc_final: 0.7257 (m-80) REVERT: 4 379 MET cc_start: -0.1667 (ttt) cc_final: -0.2122 (tmm) REVERT: 4 385 MET cc_start: 0.1798 (tmm) cc_final: 0.0884 (tpt) REVERT: A 123 LYS cc_start: 0.7428 (ttpp) cc_final: 0.7168 (tptp) REVERT: A 240 MET cc_start: 0.8537 (ttp) cc_final: 0.8288 (ttp) REVERT: A 379 GLU cc_start: 0.7778 (mt-10) cc_final: 0.7407 (mt-10) REVERT: A 424 ARG cc_start: 0.5175 (ttt180) cc_final: 0.4218 (ttp-170) REVERT: A 627 LYS cc_start: 0.7664 (tmtt) cc_final: 0.6970 (ttmt) REVERT: A 729 GLU cc_start: 0.7545 (tp30) cc_final: 0.6703 (tp30) REVERT: A 780 MET cc_start: 0.8533 (mtm) cc_final: 0.8317 (mtm) REVERT: A 944 GLU cc_start: 0.7893 (mt-10) cc_final: 0.7649 (mt-10) REVERT: A 962 GLN cc_start: 0.6408 (mp10) cc_final: 0.5993 (mp10) REVERT: A 1138 ARG cc_start: 0.8411 (mtm110) cc_final: 0.7975 (ptp-110) REVERT: B 72 MET cc_start: 0.6631 (tmm) cc_final: 0.6266 (mmm) REVERT: B 208 HIS cc_start: 0.5617 (t70) cc_final: 0.5332 (t70) REVERT: B 254 MET cc_start: 0.8278 (mtp) cc_final: 0.8009 (mtp) REVERT: B 311 GLU cc_start: 0.7909 (mm-30) cc_final: 0.7481 (mt-10) REVERT: B 354 ARG cc_start: 0.7802 (mmt-90) cc_final: 0.7379 (ttm-80) REVERT: B 438 GLN cc_start: 0.7970 (mt0) cc_final: 0.7452 (tt0) REVERT: B 780 LYS cc_start: 0.7729 (ptmt) cc_final: 0.7483 (ptmt) REVERT: B 832 MET cc_start: 0.6989 (ptp) cc_final: 0.6747 (ptp) REVERT: B 853 ASP cc_start: 0.8245 (m-30) cc_final: 0.7964 (m-30) REVERT: B 938 MET cc_start: 0.8886 (mtm) cc_final: 0.8616 (ptp) REVERT: C 50 ARG cc_start: 0.7452 (ptt90) cc_final: 0.7074 (ptt-90) REVERT: C 248 GLU cc_start: 0.6887 (pp20) cc_final: 0.6441 (tp30) REVERT: C 261 VAL cc_start: 0.7577 (OUTLIER) cc_final: 0.7310 (p) REVERT: C 286 GLU cc_start: 0.7882 (tp30) cc_final: 0.7563 (tp30) REVERT: C 292 LYS cc_start: 0.7488 (tmtt) cc_final: 0.6919 (tptt) REVERT: C 344 GLN cc_start: 0.6793 (pt0) cc_final: 0.5687 (tp40) REVERT: D 39 GLN cc_start: 0.6410 (tp40) cc_final: 0.5526 (tp-100) REVERT: D 47 TYR cc_start: 0.6859 (t80) cc_final: 0.6509 (t80) REVERT: D 82 GLU cc_start: 0.8308 (mt-10) cc_final: 0.7398 (mm-30) REVERT: D 100 MET cc_start: 0.4455 (mtm) cc_final: 0.4147 (mtm) REVERT: D 118 HIS cc_start: 0.7736 (OUTLIER) cc_final: 0.7042 (m-70) REVERT: E 128 GLU cc_start: 0.6767 (mt-10) cc_final: 0.6486 (mt-10) REVERT: E 168 ASN cc_start: 0.8785 (p0) cc_final: 0.8318 (p0) REVERT: F 56 TYR cc_start: 0.8479 (m-80) cc_final: 0.8152 (m-80) REVERT: G 7 MET cc_start: 0.7400 (mtp) cc_final: 0.6871 (mtt) REVERT: G 32 LYS cc_start: 0.7881 (mtpt) cc_final: 0.7439 (ttpp) REVERT: G 83 GLU cc_start: 0.6279 (tt0) cc_final: 0.5731 (tp30) REVERT: G 150 PHE cc_start: 0.4632 (m-80) cc_final: 0.4108 (m-80) REVERT: G 157 PHE cc_start: 0.6718 (t80) cc_final: 0.6403 (t80) REVERT: H 20 LYS cc_start: 0.7863 (tptp) cc_final: 0.7593 (tptt) REVERT: H 31 GLU cc_start: 0.6939 (mt-10) cc_final: 0.6592 (mt-10) REVERT: H 36 LYS cc_start: 0.7368 (mmtt) cc_final: 0.6799 (mmmt) REVERT: H 37 MET cc_start: 0.7945 (mmm) cc_final: 0.7266 (mmp) REVERT: H 62 SER cc_start: 0.9042 (t) cc_final: 0.8711 (p) REVERT: H 128 ASP cc_start: 0.7750 (m-30) cc_final: 0.7503 (m-30) REVERT: H 138 ASP cc_start: 0.7653 (t0) cc_final: 0.7267 (t0) REVERT: H 145 MET cc_start: 0.7767 (mtp) cc_final: 0.7527 (mtp) REVERT: J 55 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8115 (tt) REVERT: K 115 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7546 (mt-10) REVERT: K 119 LYS cc_start: 0.7516 (ttpp) cc_final: 0.7276 (tttm) REVERT: L 35 ARG cc_start: 0.7671 (ttm-80) cc_final: 0.7239 (mtm-85) REVERT: L 56 ASP cc_start: 0.8122 (t0) cc_final: 0.7750 (t70) REVERT: M 146 ASP cc_start: 0.6474 (m-30) cc_final: 0.6156 (t0) REVERT: M 272 GLN cc_start: 0.7245 (mt0) cc_final: 0.6749 (tp-100) REVERT: M 286 MET cc_start: 0.8677 (mmm) cc_final: 0.8245 (mmm) REVERT: N 374 THR cc_start: 0.7944 (OUTLIER) cc_final: 0.7341 (p) REVERT: O 101 ASP cc_start: 0.7463 (p0) cc_final: 0.7141 (m-30) REVERT: O 187 MET cc_start: 0.5607 (tpt) cc_final: 0.5310 (tpp) REVERT: O 356 GLU cc_start: 0.7898 (mm-30) cc_final: 0.7412 (mp0) REVERT: O 394 MET cc_start: 0.6555 (mtt) cc_final: 0.6329 (mtt) REVERT: O 474 MET cc_start: 0.0638 (OUTLIER) cc_final: -0.0959 (tpp) REVERT: P 60 MET cc_start: 0.2111 (ptt) cc_final: 0.1331 (tpp) REVERT: P 85 MET cc_start: -0.0688 (mmm) cc_final: -0.0971 (mmm) REVERT: P 167 TYR cc_start: 0.6703 (m-80) cc_final: 0.6035 (m-10) REVERT: P 178 GLU cc_start: 0.7732 (mt-10) cc_final: 0.7006 (tm-30) REVERT: P 210 PHE cc_start: 0.7288 (OUTLIER) cc_final: 0.6905 (t80) REVERT: P 250 MET cc_start: 0.6851 (tmm) cc_final: 0.6386 (ttp) REVERT: Q 42 ASP cc_start: 0.6776 (p0) cc_final: 0.6491 (p0) REVERT: Q 44 LYS cc_start: 0.8725 (mmmt) cc_final: 0.8499 (mmmt) REVERT: Q 54 GLU cc_start: 0.7822 (mp0) cc_final: 0.7074 (mt-10) REVERT: Q 82 GLN cc_start: 0.4469 (OUTLIER) cc_final: 0.4056 (pp30) REVERT: Q 85 GLU cc_start: 0.4380 (pm20) cc_final: 0.3957 (mt-10) REVERT: Q 103 TRP cc_start: 0.7977 (m100) cc_final: 0.7376 (m100) REVERT: V 91 ASP cc_start: 0.7882 (m-30) cc_final: 0.7384 (m-30) REVERT: V 139 CYS cc_start: 0.7982 (t) cc_final: 0.7406 (p) REVERT: V 155 GLN cc_start: 0.7612 (tt0) cc_final: 0.7292 (mm110) REVERT: V 181 LYS cc_start: 0.7831 (mttp) cc_final: 0.7426 (ptpt) REVERT: V 198 GLU cc_start: 0.7997 (mp0) cc_final: 0.7786 (mp0) REVERT: V 235 GLN cc_start: 0.7086 (mt0) cc_final: 0.6840 (mt0) REVERT: V 238 GLN cc_start: 0.5315 (tp-100) cc_final: 0.4840 (tp40) REVERT: W 295 ARG cc_start: 0.3163 (mmp80) cc_final: 0.2849 (mmt-90) REVERT: W 337 ILE cc_start: 0.7906 (mm) cc_final: 0.7478 (pt) outliers start: 101 outliers final: 84 residues processed: 593 average time/residue: 0.5545 time to fit residues: 561.5401 Evaluate side-chains 586 residues out of total 6063 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 494 time to evaluate : 5.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 128 VAL Chi-restraints excluded: chain 3 residue 206 VAL Chi-restraints excluded: chain 3 residue 233 ASN Chi-restraints excluded: chain 3 residue 320 VAL Chi-restraints excluded: chain 3 residue 339 LEU Chi-restraints excluded: chain 3 residue 365 VAL Chi-restraints excluded: chain 3 residue 382 VAL Chi-restraints excluded: chain 3 residue 386 MET Chi-restraints excluded: chain 4 residue 181 VAL Chi-restraints excluded: chain 4 residue 222 VAL Chi-restraints excluded: chain 4 residue 226 LEU Chi-restraints excluded: chain 4 residue 299 ARG Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 871 MET Chi-restraints excluded: chain A residue 897 ILE Chi-restraints excluded: chain A residue 978 GLU Chi-restraints excluded: chain A residue 1023 MET Chi-restraints excluded: chain A residue 1027 MET Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 116 ASP Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 215 ASN Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 499 MET Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 755 LEU Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 971 ASP Chi-restraints excluded: chain B residue 1032 THR Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 118 HIS Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 55 GLU Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain K residue 27 LEU Chi-restraints excluded: chain K residue 48 ASP Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain K residue 60 MET Chi-restraints excluded: chain M residue 7 ASP Chi-restraints excluded: chain M residue 21 LEU Chi-restraints excluded: chain M residue 89 THR Chi-restraints excluded: chain M residue 225 LEU Chi-restraints excluded: chain M residue 330 ASP Chi-restraints excluded: chain M residue 401 ILE Chi-restraints excluded: chain N residue 251 VAL Chi-restraints excluded: chain N residue 284 ILE Chi-restraints excluded: chain N residue 374 THR Chi-restraints excluded: chain N residue 386 SER Chi-restraints excluded: chain O residue 21 VAL Chi-restraints excluded: chain O residue 63 VAL Chi-restraints excluded: chain O residue 163 VAL Chi-restraints excluded: chain O residue 180 LEU Chi-restraints excluded: chain O residue 190 VAL Chi-restraints excluded: chain O residue 259 MET Chi-restraints excluded: chain O residue 380 VAL Chi-restraints excluded: chain O residue 399 LEU Chi-restraints excluded: chain O residue 474 MET Chi-restraints excluded: chain O residue 520 ILE Chi-restraints excluded: chain P residue 210 PHE Chi-restraints excluded: chain P residue 237 THR Chi-restraints excluded: chain P residue 280 THR Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 40 ASP Chi-restraints excluded: chain Q residue 50 THR Chi-restraints excluded: chain Q residue 82 GLN Chi-restraints excluded: chain Q residue 111 MET Chi-restraints excluded: chain V residue 78 ASP Chi-restraints excluded: chain V residue 243 LEU Chi-restraints excluded: chain W residue 311 PHE Chi-restraints excluded: chain W residue 315 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 691 random chunks: chunk 336 optimal weight: 7.9990 chunk 435 optimal weight: 7.9990 chunk 583 optimal weight: 6.9990 chunk 167 optimal weight: 3.9990 chunk 505 optimal weight: 4.9990 chunk 80 optimal weight: 7.9990 chunk 152 optimal weight: 0.0870 chunk 549 optimal weight: 3.9990 chunk 229 optimal weight: 8.9990 chunk 563 optimal weight: 5.9990 chunk 69 optimal weight: 0.1980 overall best weight: 2.6564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 185 ASN 3 367 ASN ** 4 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 528 ASN ** A1039 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 151 HIS ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 138 ASN ** I 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 129 ASN P 266 HIS ** U 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 70 GLN V 128 GLN ** V 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.150226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.115171 restraints weight = 102085.363| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 3.17 r_work: 0.3179 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3178 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3178 r_free = 0.3178 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 83 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3178 r_free = 0.3178 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 83 | |-----------------------------------------------------------------------------| r_final: 0.3178 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.4930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 59698 Z= 0.278 Angle : 0.556 12.142 81288 Z= 0.285 Chirality : 0.042 0.228 9051 Planarity : 0.004 0.058 9902 Dihedral : 15.364 155.192 9296 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.83 % Allowed : 14.85 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.10), residues: 6799 helix: 1.20 (0.10), residues: 2730 sheet: -0.62 (0.18), residues: 776 loop : -0.84 (0.11), residues: 3293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP W 350 HIS 0.009 0.001 HIS A 415 PHE 0.022 0.002 PHE W 311 TYR 0.022 0.001 TYR U 192 ARG 0.016 0.001 ARG C 255 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12932.05 seconds wall clock time: 228 minutes 42.91 seconds (13722.91 seconds total)