Starting phenix.real_space_refine on Mon Mar 11 11:40:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ity_35712/03_2024/8ity_35712_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ity_35712/03_2024/8ity_35712.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ity_35712/03_2024/8ity_35712.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ity_35712/03_2024/8ity_35712.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ity_35712/03_2024/8ity_35712_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ity_35712/03_2024/8ity_35712_neut_updated.pdb" } resolution = 3.9 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= 0.003 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 7 6.06 5 P 164 5.49 5 Mg 1 5.21 5 S 349 5.16 5 C 35688 2.51 5 N 9981 2.21 5 O 10946 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "1 GLU 12": "OE1" <-> "OE2" Residue "1 PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ASP 103": "OD1" <-> "OD2" 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 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ASP 78": "OD1" <-> "OD2" Residue "3 ASP 80": "OD1" <-> "OD2" Residue "3 ASP 83": "OD1" <-> "OD2" Residue "3 ASP 89": "OD1" <-> "OD2" Residue "3 ASP 91": "OD1" <-> "OD2" Residue "3 PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 141": "OE1" <-> "OE2" Residue "3 GLU 158": "OE1" <-> "OE2" Residue "3 ASP 173": "OD1" <-> "OD2" Residue "3 GLU 177": "OE1" <-> "OE2" Residue "3 GLU 179": "OE1" <-> "OE2" Residue "3 PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ASP 224": "OD1" <-> "OD2" Residue "3 GLU 240": "OE1" <-> "OE2" 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 ASP 269": "OD1" <-> "OD2" Residue "3 GLU 279": "OE1" <-> "OE2" 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 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ASP 381": "OD1" <-> "OD2" Residue "4 PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 152": "OD1" <-> "OD2" Residue "4 GLU 163": "OE1" <-> "OE2" Residue "4 GLU 177": "OE1" <-> "OE2" Residue "4 GLU 178": "OE1" <-> "OE2" Residue "4 GLU 227": "OE1" <-> "OE2" Residue "4 GLU 232": "OE1" <-> "OE2" Residue "4 GLU 241": "OE1" <-> "OE2" Residue "4 PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 272": "OE1" <-> "OE2" Residue "4 GLU 279": "OE1" <-> "OE2" Residue "4 PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 303": "OE1" <-> "OE2" Residue "4 GLU 348": "OE1" <-> "OE2" Residue "4 GLU 351": "OE1" <-> "OE2" Residue "4 GLU 363": "OE1" <-> "OE2" 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 GLU 429": "OE1" <-> "OE2" Residue "4 ASP 441": "OD1" <-> "OD2" Residue "4 TYR 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 461": "OE1" <-> "OE2" Residue "4 GLU 466": "OE1" <-> "OE2" Residue "4 GLU 482": "OE1" <-> "OE2" Residue "B ARG 128": "NH1" <-> "NH2" Residue "B GLU 363": "OE1" <-> "OE2" Residue "B GLU 507": "OE1" <-> "OE2" Residue "B GLU 622": "OE1" <-> "OE2" Residue "F GLU 84": "OE1" <-> "OE2" Residue "I GLU 48": "OE1" <-> "OE2" Residue "K GLU 102": "OE1" <-> "OE2" Residue "O GLU 76": "OE1" <-> "OE2" Residue "Q GLU 55": "OE1" <-> "OE2" Residue "U TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 299": "NH1" <-> "NH2" Residue "V GLU 14": "OE1" <-> "OE2" Residue "V ASP 18": "OD1" <-> "OD2" Residue "V TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 37": "OE1" <-> "OE2" Residue "V PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 46": "OD1" <-> "OD2" Residue "V GLU 47": "OE1" <-> "OE2" Residue "V GLU 52": "OE1" <-> "OE2" Residue "V GLU 115": "OE1" <-> "OE2" Residue "V PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 213": "OE1" <-> "OE2" Residue "V PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 241": "OD1" <-> "OD2" Residue "V GLU 268": "OE1" <-> "OE2" Residue "V GLU 278": "OE1" <-> "OE2" Residue "V ASP 381": "OD1" <-> "OD2" Residue "V GLU 388": "OE1" <-> "OE2" Residue "W GLU 277": "OE1" <-> "OE2" Residue "W GLU 278": "OE1" <-> "OE2" Residue "W ASP 280": "OD1" <-> "OD2" Residue "W GLU 284": "OE1" <-> "OE2" Residue "W TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 309": "OD1" <-> "OD2" Residue "W PHE 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 57140 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: 8741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1105, 8741 Classifications: {'peptide': 1105} Link IDs: {'PTRANS': 51, 'TRANS': 1053} Chain breaks: 1 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: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 435 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 3, 'TRANS': 52} 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: 3167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3167 Classifications: {'peptide': 394} Link IDs: {'PTRANS': 22, 'TRANS': 371} Chain breaks: 2 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: 1837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1837 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 9, 'TRANS': 222} 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: 1677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 1677 Classifications: {'DNA': 82} Link IDs: {'rna3p': 81} Chain: "Y" Number of atoms: 1685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 1685 Classifications: {'DNA': 82} Link IDs: {'rna3p': 81} 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 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 7893 SG CYS A 72 110.500 136.552 153.918 1.00229.13 S ATOM 26470 SG CYS B1080 100.923 143.060 166.856 1.00185.38 S ATOM 26489 SG CYS B1083 98.315 142.034 164.227 1.00179.66 S ATOM 26555 SG CYS B1092 101.426 143.664 163.131 1.00180.90 S ATOM 26583 SG CYS B1095 98.930 145.755 164.963 1.00179.34 S ATOM 35493 SG CYS I 5 23.742 108.025 122.146 1.00124.68 S ATOM 35510 SG CYS I 8 26.674 109.850 120.450 1.00127.71 S ATOM 35640 SG CYS I 25 25.501 111.327 123.534 1.00129.56 S ATOM 35661 SG CYS I 28 22.962 111.143 120.659 1.00126.98 S ATOM 35942 SG CYS J 7 110.293 64.311 144.492 1.00 75.73 S ATOM 36230 SG CYS J 44 109.150 62.099 145.738 1.00 83.12 S ATOM 36236 SG CYS J 45 111.362 60.368 143.229 1.00 85.64 S ATOM 37298 SG CYS L 22 116.080 87.100 107.923 1.00119.56 S ATOM 37415 SG CYS L 36 117.788 90.877 108.213 1.00120.93 S ATOM 47606 SG CYS P 290 94.379 165.064 147.994 1.00268.17 S ATOM 47588 SG CYS P 287 92.231 167.503 153.862 1.00262.37 S ATOM 47730 SG CYS P 307 98.180 164.772 151.742 1.00255.50 S ATOM 47653 SG CYS P 296 94.244 161.803 154.048 1.00255.77 S ATOM 49983 SG CYS V 7 132.064 121.673 153.024 1.00178.33 S ATOM 50161 SG CYS V 31 134.765 118.628 155.274 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: 23.37, per 1000 atoms: 0.41 Number of scatterers: 57140 At special positions: 0 Unit cell: (162.748, 216.108, 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 7 29.99 Fe 4 26.01 S 349 16.00 P 164 15.00 Mg 1 11.99 O 10946 8.00 N 9981 7.00 C 35688 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 112 " - pdb=" SG CYS A 156 " distance=2.04 Simple disulfide: pdb=" SG CYS A 112 " - pdb=" SG CYS A 159 " distance=2.03 Simple disulfide: pdb=" SG CYS A 156 " - pdb=" SG CYS A 159 " distance=2.13 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: 16.96 Conformation dependent library (CDL) restraints added in 7.4 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 P 401 " pdb="FE3 SF4 P 401 " - pdb=" SG CYS P 307 " pdb="FE2 SF4 P 401 " - pdb=" SG CYS P 287 " pdb="FE1 SF4 P 401 " - pdb=" SG CYS P 290 " pdb="FE4 SF4 P 401 " - pdb=" SG CYS P 296 " Number of angles added : 12 Zn2+ tetrahedral coordination pdb=" ZN A1401 " pdb="ZN ZN A1401 " - pdb=" SG CYS A 72 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1092 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1083 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1095 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1080 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 28 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 8 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 5 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 25 " pdb=" ZN J2000 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 45 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 44 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 22 " pdb=" ZN V 700 " pdb="ZN ZN V 700 " - pdb=" SG CYS V 31 " pdb="ZN ZN V 700 " - pdb=" SG CYS V 7 " Number of angles added : 12 13314 Ramachandran restraints generated. 6657 Oldfield, 0 Emsley, 6657 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12676 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 258 helices and 56 sheets defined 39.0% alpha, 10.9% beta 53 base pairs and 125 stacking pairs defined. Time for finding SS restraints: 18.29 Creating SS restraints... Processing helix chain '1' and resid 5 through 20 removed outlier: 3.769A pdb=" N THR 1 9 " --> pdb=" O PRO 1 5 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU 1 12 " --> pdb=" O GLN 1 8 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER 1 16 " --> pdb=" O GLU 1 12 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ARG 1 17 " --> pdb=" O ALA 1 13 " (cutoff:3.500A) Processing helix chain '1' and resid 27 through 33 Processing helix chain '1' and resid 49 through 66 removed outlier: 3.728A pdb=" N TYR 1 65 " --> pdb=" O LEU 1 61 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N PHE 1 66 " --> pdb=" O ALA 1 62 " (cutoff:3.500A) Processing helix chain '1' and resid 72 through 88 Processing helix chain '1' and resid 102 through 104 No H-bonds generated for 'chain '1' and resid 102 through 104' Processing helix chain '1' and resid 106 through 116 Processing helix chain '1' and resid 120 through 132 removed outlier: 3.718A pdb=" N PHE 1 126 " --> pdb=" O ALA 1 122 " (cutoff:3.500A) Processing helix chain '3' and resid 44 through 54 removed outlier: 3.989A pdb=" N GLY 3 48 " --> pdb=" O VAL 3 44 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLU 3 49 " --> pdb=" O GLY 3 45 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ARG 3 52 " --> pdb=" O GLY 3 48 " (cutoff:3.500A) Processing helix chain '3' and resid 77 through 89 removed outlier: 4.737A 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: 4.042A pdb=" N VAL 3 156 " --> pdb=" O GLN 3 152 " (cutoff:3.500A) removed outlier: 4.173A 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 225 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: 3.605A pdb=" N THR 3 273 " --> pdb=" O LEU 3 270 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE 3 274 " --> pdb=" O SER 3 271 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ILE 3 275 " --> pdb=" O ARG 3 272 " (cutoff:3.500A) removed outlier: 3.964A 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: 3.537A pdb=" N MET 3 386 " --> pdb=" O VAL 3 382 " (cutoff:3.500A) removed outlier: 3.842A 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: 3.782A 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: 3.726A pdb=" N GLN 4 335 " --> pdb=" O PHE 4 331 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LYS 4 336 " --> pdb=" O GLN 4 332 " (cutoff:3.500A) Processing helix chain '4' and resid 352 through 364 removed outlier: 3.742A 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 386 through 392 removed outlier: 3.520A pdb=" N TYR 4 389 " --> pdb=" O GLN 4 386 " (cutoff:3.500A) 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 removed outlier: 3.500A pdb=" N LYS 4 418 " --> pdb=" O ALA 4 415 " (cutoff:3.500A) Processing helix chain '4' and resid 424 through 429 removed outlier: 3.927A pdb=" N ARG 4 428 " --> pdb=" O PHE 4 425 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU 4 429 " --> pdb=" O LYS 4 426 " (cutoff:3.500A) Processing helix chain '4' and resid 436 through 447 removed outlier: 3.921A pdb=" N ASP 4 441 " --> pdb=" O ALA 4 437 " (cutoff:3.500A) Processing helix chain '4' and resid 460 through 468 Processing helix chain '4' and resid 478 through 481 Processing helix chain '4' and resid 488 through 498 removed outlier: 5.368A pdb=" N SER 4 493 " --> pdb=" O SER 4 489 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N LYS 4 494 " --> pdb=" O GLN 4 490 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ILE 4 497 " --> pdb=" O SER 4 493 " (cutoff:3.500A) Processing helix chain '4' and resid 506 through 512 removed outlier: 4.694A pdb=" N ARG 4 511 " --> pdb=" O ARG 4 507 " (cutoff:3.500A) removed outlier: 4.894A 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 95 through 107 removed outlier: 4.524A pdb=" N ARG A 99 " --> pdb=" O VAL A 95 " (cutoff:3.500A) removed outlier: 4.899A 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 150 Processing helix chain 'A' and resid 188 through 195 Processing helix chain 'A' and resid 198 through 203 Processing helix chain 'A' and resid 205 through 211 Proline residue: A 209 - end of helix Processing helix chain 'A' and resid 220 through 228 Processing helix chain 'A' and resid 233 through 237 removed outlier: 4.382A pdb=" N LEU A 237 " --> pdb=" O GLU A 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 233 through 237' 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 389 removed outlier: 3.600A pdb=" N ILE A 389 " --> pdb=" O HIS A 385 " (cutoff:3.500A) 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: 4.729A 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 525 through 527 No H-bonds generated for 'chain 'A' and resid 525 through 527' Processing helix chain 'A' and resid 546 through 553 Processing helix chain 'A' and resid 561 through 571 removed outlier: 4.482A pdb=" N ILE A 571 " --> pdb=" O ILE A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 578 removed outlier: 3.728A pdb=" N LYS A 578 " --> pdb=" O LYS A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 605 removed outlier: 3.819A pdb=" N ILE A 604 " --> pdb=" O ILE A 600 " (cutoff:3.500A) removed outlier: 4.069A 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 694 removed outlier: 8.033A pdb=" N GLN A 673 " --> pdb=" O ARG A 669 " (cutoff:3.500A) removed outlier: 9.437A pdb=" N ASN A 674 " --> pdb=" O ASP A 670 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N GLU A 675 " --> pdb=" O TRP A 671 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA A 676 " --> pdb=" O GLY A 672 " (cutoff:3.500A) 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 828 through 831 No H-bonds generated for 'chain 'A' and resid 828 through 831' Processing helix chain 'A' and resid 844 through 879 removed outlier: 4.087A 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 954 Processing helix chain 'A' and resid 956 through 960 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 1066 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 1139 Processing helix chain 'A' and resid 1146 through 1152 Processing helix chain 'A' and resid 1186 through 1195 Processing helix chain 'A' and resid 1232 through 1237 Processing helix chain 'A' and resid 1251 through 1258 Processing helix chain 'A' and resid 1260 through 1278 removed outlier: 3.590A pdb=" N HIS A1278 " --> pdb=" O THR A1274 " (cutoff:3.500A) Processing helix chain 'A' and resid 1284 through 1295 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 1333 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 36 removed outlier: 4.426A 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 61 removed outlier: 5.488A pdb=" N ILE B 55 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N LYS B 56 " --> pdb=" O ASN B 52 " (cutoff:3.500A) 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 243 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 308 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 392 Processing helix chain 'B' and resid 402 through 405 Processing helix chain 'B' and resid 408 through 421 removed outlier: 3.732A pdb=" N ILE B 411 " --> pdb=" O GLN B 408 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR B 412 " --> pdb=" O ASP B 409 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N THR B 421 " --> pdb=" O ALA B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 452 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 518 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: 3.853A 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 667 through 671 removed outlier: 3.883A pdb=" N LEU B 671 " --> pdb=" O VAL B 667 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 667 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 692 removed outlier: 3.534A pdb=" N GLN B 692 " --> pdb=" O ALA B 688 " (cutoff:3.500A) Processing helix chain 'B' and resid 723 through 727 Processing helix chain 'B' and resid 730 through 733 Processing helix chain 'B' and resid 759 through 763 Processing helix chain 'B' and resid 804 through 806 No H-bonds generated for 'chain 'B' and resid 804 through 806' Processing helix chain 'B' and resid 913 through 915 No H-bonds generated for 'chain 'B' and resid 913 through 915' 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 979 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 1039 through 1041 No H-bonds generated for 'chain 'B' and resid 1039 through 1041' Processing helix chain 'B' and resid 1049 through 1058 Processing helix chain 'B' and resid 1061 through 1069 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 112 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 286 through 288 No H-bonds generated for 'chain 'C' and resid 286 through 288' Processing helix chain 'C' and resid 292 through 294 No H-bonds generated for 'chain 'C' and resid 292 through 294' 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: 3.714A pdb=" N SER D 75 " --> pdb=" O THR D 71 " (cutoff:3.500A) removed outlier: 3.964A 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 94 through 98 Processing helix chain 'D' and resid 112 through 121 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 96 Processing helix chain 'E' and resid 112 through 119 Processing helix chain 'E' and resid 134 through 136 No H-bonds generated for 'chain 'E' and resid 134 through 136' Processing helix chain 'E' and resid 153 through 163 Processing helix chain 'E' and resid 167 through 169 No H-bonds generated for 'chain 'E' and resid 167 through 169' 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 'G' and resid 198 through 200 No H-bonds generated for 'chain 'G' and resid 198 through 200' Processing helix chain 'H' and resid 84 through 87 removed outlier: 3.511A pdb=" N GLN H 87 " --> pdb=" O ARG H 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 84 through 87' Processing helix chain 'J' and resid 15 through 26 removed outlier: 4.611A pdb=" N GLU J 19 " --> pdb=" O GLY J 15 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ALA J 20 " --> pdb=" O ASN J 16 " (cutoff:3.500A) Processing helix chain 'J' and resid 31 through 38 Processing helix chain 'J' and resid 43 through 51 Processing helix chain 'J' and resid 55 through 62 removed outlier: 3.596A 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 140 through 153 Processing helix chain 'M' and resid 193 through 201 Processing helix chain 'M' and resid 216 through 225 removed outlier: 4.289A pdb=" N TYR M 224 " --> pdb=" O HIS M 220 " (cutoff:3.500A) removed outlier: 4.211A 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 270 through 275 removed outlier: 3.840A pdb=" N THR M 275 " --> pdb=" O ALA M 271 " (cutoff:3.500A) Processing helix chain 'M' and resid 278 through 289 Processing helix chain 'M' and resid 294 through 301 removed outlier: 3.506A pdb=" N SER M 299 " --> pdb=" O ALA M 295 " (cutoff:3.500A) Processing helix chain 'M' and resid 307 through 317 removed outlier: 3.733A pdb=" N GLN M 315 " --> pdb=" O LEU M 311 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LYS M 316 " --> pdb=" O ARG M 312 " (cutoff:3.500A) removed outlier: 3.752A 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 removed outlier: 3.685A pdb=" N THR M 361 " --> pdb=" O MET M 357 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN M 362 " --> pdb=" O TRP M 358 " (cutoff:3.500A) Processing helix chain 'M' and resid 368 through 375 Processing helix chain 'M' and resid 379 through 389 removed outlier: 3.664A pdb=" N MET M 389 " --> pdb=" O PHE M 385 " (cutoff:3.500A) Processing helix chain 'M' and resid 406 through 411 Processing helix chain 'M' and resid 413 through 434 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 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: 3.799A pdb=" N MET O 85 " --> pdb=" O ARG O 81 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N LEU O 86 " --> pdb=" O VAL O 82 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ARG O 87 " --> pdb=" O LEU O 83 " (cutoff:3.500A) removed outlier: 3.776A 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: 3.846A pdb=" N GLU O 131 " --> pdb=" O ASP O 127 " (cutoff:3.500A) removed outlier: 4.033A 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 184 through 186 No H-bonds generated for 'chain 'O' and resid 184 through 186' Processing helix chain 'O' and resid 239 through 258 Processing helix chain 'O' and resid 261 through 273 Processing helix chain 'O' and resid 290 through 296 Processing helix chain 'O' and resid 305 through 317 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 428 through 456 Processing helix chain 'O' and resid 458 through 472 removed outlier: 3.903A pdb=" N ILE O 471 " --> pdb=" O VAL O 467 " (cutoff:3.500A) Processing helix chain 'O' and resid 481 through 486 removed outlier: 4.981A pdb=" N GLN O 485 " --> pdb=" O ALA O 482 " (cutoff:3.500A) Processing helix chain 'O' and resid 491 through 529 Proline residue: O 494 - end of helix removed outlier: 4.149A pdb=" N GLU O 524 " --> pdb=" O PHE O 521 " (cutoff:3.500A) Processing helix chain 'P' and resid 87 through 105 removed outlier: 6.235A pdb=" N ASN P 104 " --> pdb=" O GLU P 100 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N LYS P 105 " --> pdb=" O ASP P 101 " (cutoff:3.500A) Processing helix chain 'P' and resid 120 through 133 Processing helix chain 'P' and resid 168 through 170 No H-bonds generated for 'chain 'P' and resid 168 through 170' 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 245 Processing helix chain 'P' and resid 308 through 315 Processing helix chain 'Q' and resid 52 through 70 removed outlier: 3.505A pdb=" N GLU Q 66 " --> pdb=" O GLN Q 62 " (cutoff:3.500A) Processing helix chain 'Q' and resid 87 through 90 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 243 Processing helix chain 'U' and resid 270 through 276 removed outlier: 3.959A 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 55 through 59 Processing helix chain 'V' and resid 67 through 82 Processing helix chain 'V' and resid 87 through 102 removed outlier: 4.084A 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: 4.161A pdb=" N LEU V 141 " --> pdb=" O ALA V 137 " (cutoff:3.500A) Processing helix chain 'V' and resid 146 through 160 Processing helix chain 'V' and resid 169 through 179 removed outlier: 3.870A pdb=" N SER V 178 " --> pdb=" O LYS V 174 " (cutoff:3.500A) removed outlier: 4.042A 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: 4.023A 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 260 through 279 removed outlier: 3.773A pdb=" N SER V 263 " --> pdb=" O TYR V 260 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU V 278 " --> pdb=" O ARG V 275 " (cutoff:3.500A) Processing helix chain 'V' and resid 281 through 286 Processing helix chain 'V' and resid 294 through 302 removed outlier: 4.345A pdb=" N GLY V 298 " --> pdb=" O LYS V 295 " (cutoff:3.500A) Processing helix chain 'V' and resid 304 through 313 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 357 removed outlier: 3.608A pdb=" N GLY W 349 " --> pdb=" O GLU W 345 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N TRP W 350 " --> pdb=" O LYS W 346 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ARG W 351 " --> pdb=" O THR W 347 " (cutoff:3.500A) 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: 4.097A pdb=" N VAL 3 320 " --> pdb=" O LEU 3 187 " (cutoff:3.500A) removed outlier: 4.549A 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) removed outlier: 3.569A pdb=" N CYS 3 312 " --> pdb=" O PHE 3 251 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain '3' and resid 257 through 260 removed outlier: 6.830A pdb=" N GLN 3 289 " --> pdb=" O PHE 3 258 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N ASN 3 260 " --> pdb=" O GLN 3 289 " (cutoff:3.500A) removed outlier: 6.713A 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 265 through 268 removed outlier: 4.356A pdb=" N GLY A 273 " --> pdb=" O SER A 268 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 364 through 368 Processing sheet with id= K, first strand: chain 'A' and resid 369 through 371 removed outlier: 5.644A pdb=" N PHE A 486 " --> pdb=" O SER A 370 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'A' and resid 391 through 395 removed outlier: 3.947A pdb=" N PHE A 420 " --> pdb=" O GLU A 451 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N HIS A 453 " --> pdb=" O ALA A 418 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ALA A 418 " --> pdb=" O HIS A 453 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 617 through 619 removed outlier: 6.359A pdb=" N GLN A 641 " --> pdb=" O LEU A 645 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N LEU A 645 " --> pdb=" O GLN A 641 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'A' and resid 1085 through 1088 removed outlier: 3.719A pdb=" N LYS A1222 " --> pdb=" O ASP A1215 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'A' and resid 1172 through 1175 removed outlier: 3.503A 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: 3.756A pdb=" N ASN B 79 " --> pdb=" O ASP B 116 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N GLU B 118 " --> pdb=" O TYR B 77 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N TYR B 77 " --> pdb=" O GLU B 118 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N THR B 120 " --> pdb=" O LEU B 75 " (cutoff:3.500A) removed outlier: 7.483A 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 455 through 457 removed outlier: 6.434A pdb=" N ILE B 180 " --> pdb=" O SER B 456 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'B' and resid 190 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 573 through 577 removed outlier: 6.337A pdb=" N LEU B 538 " --> pdb=" O VAL B 583 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N ILE B 585 " --> pdb=" O LEU B 538 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N PHE B 540 " --> pdb=" O ILE B 585 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY B 547 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N LEU B 541 " --> pdb=" O ILE B 545 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ILE B 545 " --> pdb=" O LEU B 541 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'B' and resid 593 through 597 Processing sheet with id= W, first strand: chain 'B' and resid 708 through 712 removed outlier: 4.145A pdb=" N LYS B 868 " --> pdb=" O LEU B 884 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ARG B 886 " --> pdb=" O ILE B 866 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N ILE B 866 " --> pdb=" O ARG B 886 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'B' and resid 1003 through 1009 removed outlier: 4.014A pdb=" N TYR B1003 " --> pdb=" O VAL B 743 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ILE B 927 " --> pdb=" O ALA B 742 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL B 756 " --> pdb=" O ILE B 928 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N VAL B 906 " --> pdb=" O LEU B 755 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N LEU B 757 " --> pdb=" O VAL B 906 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N GLY B 908 " --> pdb=" O LEU B 757 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'B' and resid 831 through 833 Processing sheet with id= Z, first strand: chain 'B' and resid 1074 through 1078 Processing sheet with id= AA, first strand: chain 'B' and resid 110 through 115 removed outlier: 4.018A pdb=" N GLY B 134 " --> pdb=" O ILE B 113 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N VAL B 115 " --> pdb=" O PRO B 132 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'C' and resid 13 through 15 Processing sheet with id= AC, first strand: chain 'C' and resid 50 through 57 removed outlier: 6.804A pdb=" N GLU C 62 " --> pdb=" O VAL C 54 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N MET C 56 " --> pdb=" O SER C 60 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N SER C 60 " --> pdb=" O MET C 56 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'C' and resid 174 through 176 removed outlier: 4.130A pdb=" N GLN C 139 " --> pdb=" O ILE C 176 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASP C 209 " --> pdb=" O TYR C 95 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N VAL C 215 " --> pdb=" O VAL C 89 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N VAL C 89 " --> pdb=" O VAL C 215 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N GLY C 217 " --> pdb=" O MET C 87 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N MET C 87 " --> pdb=" O GLY C 217 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'C' and resid 262 through 266 Processing sheet with id= AF, first strand: chain 'C' and resid 167 through 169 Processing sheet with id= AG, first strand: chain 'E' and resid 126 through 131 removed outlier: 4.244A pdb=" N ARG E 101 " --> pdb=" O GLN E 71 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N THR E 69 " --> pdb=" O LEU E 61 " (cutoff:3.500A) removed outlier: 9.612A pdb=" N LEU E 61 " --> pdb=" O THR E 69 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'E' and resid 147 through 151 removed outlier: 3.833A pdb=" N GLU E 147 " --> pdb=" O ILE E 194 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N VAL E 190 " --> pdb=" O MET E 151 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'F' and resid 105 through 109 Processing sheet with id= AJ, first strand: chain 'G' and resid 3 through 13 Processing sheet with id= AK, first strand: chain 'G' and resid 37 through 39 removed outlier: 4.245A pdb=" N LYS G 37 " --> pdb=" O CYS G 45 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N CYS G 45 " --> pdb=" O LYS G 37 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N VAL G 75 " --> pdb=" O ILE G 46 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'G' and resid 146 through 149 Processing sheet with id= AM, first strand: chain 'G' and resid 50 through 54 removed outlier: 6.568A pdb=" N HIS G 71 " --> pdb=" O THR G 52 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'H' and resid 25 through 31 removed outlier: 5.362A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER H 139 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N LYS H 55 " --> pdb=" O LEU H 148 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N HIS H 29 " --> pdb=" O LYS H 13 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'I' and resid 13 through 16 Processing sheet with id= AP, first strand: chain 'K' and resid 26 through 30 Processing sheet with id= AQ, first strand: chain 'L' and resid 25 through 27 Processing sheet with id= AR, first strand: chain 'M' and resid 15 through 18 removed outlier: 6.683A pdb=" N LEU M 124 " --> pdb=" O TYR M 16 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N ALA M 18 " --> pdb=" O LEU M 124 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU M 126 " --> pdb=" O ALA M 18 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'M' and resid 26 through 29 removed outlier: 7.099A pdb=" N GLY M 131 " --> pdb=" O LEU M 27 " (cutoff:3.500A) removed outlier: 8.432A pdb=" N GLN M 29 " --> pdb=" O GLY M 131 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N LEU M 133 " --> pdb=" O GLN M 29 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N ALA M 61 " --> pdb=" O HIS M 44 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N HIS M 44 " --> pdb=" O ALA M 61 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ALA M 47 " --> pdb=" O LEU M 208 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'M' and resid 318 through 321 Processing sheet with id= AU, first strand: chain 'M' and resid 390 through 393 Processing sheet with id= AV, first strand: chain 'N' and resid 267 through 270 removed outlier: 6.476A pdb=" N HIS N 381 " --> pdb=" O PHE N 268 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N GLN N 270 " --> pdb=" O HIS N 381 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N LEU N 383 " --> pdb=" O GLN N 270 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL N 348 " --> pdb=" O VAL N 337 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N VAL N 337 " --> pdb=" O VAL N 348 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'N' and resid 359 through 364 removed outlier: 3.552A pdb=" N GLY N 377 " --> pdb=" O LEU N 360 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N SER N 362 " --> pdb=" O VAL N 375 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N VAL N 375 " --> pdb=" O SER N 362 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N GLY N 364 " --> pdb=" O MET N 373 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N MET N 373 " --> pdb=" O GLY N 364 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'O' and resid 63 through 68 removed outlier: 3.640A pdb=" N VAL O 72 " --> pdb=" O HIS O 68 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'O' and resid 157 through 159 Processing sheet with id= AZ, first strand: chain 'P' and resid 136 through 139 Processing sheet with id= BA, first strand: chain 'P' and resid 248 through 253 removed outlier: 3.544A pdb=" N LEU P 269 " --> pdb=" O THR P 251 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'U' and resid 170 through 173 removed outlier: 3.871A pdb=" N SER U 170 " --> pdb=" O CYS U 221 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'U' and resid 291 through 295 removed outlier: 6.181A pdb=" N SER U 261 " --> pdb=" O LEU U 165 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N LEU U 165 " --> pdb=" O SER U 261 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'V' and resid 15 through 19 removed outlier: 3.608A pdb=" N VAL V 27 " --> pdb=" O VAL V 16 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASP V 18 " --> pdb=" O GLN V 25 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLN V 25 " --> pdb=" O ASP V 18 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR V 36 " --> pdb=" O LEU V 26 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N CYS V 28 " --> pdb=" O VAL V 34 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N VAL V 34 " --> pdb=" O CYS V 28 " (cutoff:3.500A) 1945 hydrogen bonds defined for protein. 5382 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 123 hydrogen bonds 246 hydrogen bond angles 0 basepair planarities 53 basepair parallelities 125 stacking parallelities Total time for adding SS restraints: 20.72 Time building geometry restraints manager: 18.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.43: 24384 1.43 - 1.65: 33654 1.65 - 1.86: 535 1.86 - 2.08: 0 2.08 - 2.30: 12 Bond restraints: 58585 Sorted by residual: bond pdb=" CA THR V 175 " pdb=" C THR V 175 " ideal model delta sigma weight residual 1.524 1.477 0.047 1.32e-02 5.74e+03 1.28e+01 bond pdb=" CA GLN B 294 " pdb=" C GLN B 294 " ideal model delta sigma weight residual 1.523 1.470 0.053 1.62e-02 3.81e+03 1.09e+01 bond pdb=" N GLU L 21 " pdb=" CA GLU L 21 " ideal model delta sigma weight residual 1.454 1.497 -0.042 1.31e-02 5.83e+03 1.04e+01 bond pdb=" CA ALA V 108 " pdb=" C ALA V 108 " ideal model delta sigma weight residual 1.526 1.491 0.036 1.11e-02 8.12e+03 1.04e+01 bond pdb=" N CYS L 22 " pdb=" CA CYS L 22 " ideal model delta sigma weight residual 1.456 1.497 -0.042 1.32e-02 5.74e+03 1.01e+01 ... (remaining 58580 not shown) Histogram of bond angle deviations from ideal: 22.30 - 47.91: 10 47.91 - 73.53: 7 73.53 - 99.14: 19 99.14 - 124.75: 78385 124.75 - 150.37: 1370 Bond angle restraints: 79791 Sorted by residual: angle pdb=" O3' DT Y 49 " pdb=" P DT Y 50 " pdb=" OP1 DT Y 50 " ideal model delta sigma weight residual 108.00 22.30 85.70 3.00e+00 1.11e-01 8.16e+02 angle pdb=" O3' DA Y 67 " pdb=" P DT Y 68 " pdb=" OP1 DT Y 68 " ideal model delta sigma weight residual 108.00 22.48 85.52 3.00e+00 1.11e-01 8.13e+02 angle pdb=" O3' DA Y 69 " pdb=" P DT Y 70 " pdb=" OP1 DT Y 70 " ideal model delta sigma weight residual 108.00 22.50 85.50 3.00e+00 1.11e-01 8.12e+02 angle pdb=" O3' DA X -70 " pdb=" P DT X -69 " pdb=" OP1 DT X -69 " ideal model delta sigma weight residual 108.00 22.62 85.38 3.00e+00 1.11e-01 8.10e+02 angle pdb=" O3' DT Y 50 " pdb=" P DT Y 51 " pdb=" OP1 DT Y 51 " ideal model delta sigma weight residual 108.00 22.98 85.02 3.00e+00 1.11e-01 8.03e+02 ... (remaining 79786 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.38: 34257 35.38 - 70.76: 1194 70.76 - 106.14: 54 106.14 - 141.52: 0 141.52 - 176.90: 3 Dihedral angle restraints: 35508 sinusoidal: 15909 harmonic: 19599 Sorted by residual: dihedral pdb=" C ARG B 295 " pdb=" N ARG B 295 " pdb=" CA ARG B 295 " pdb=" CB ARG B 295 " ideal model delta harmonic sigma weight residual -122.60 -148.89 26.29 0 2.50e+00 1.60e-01 1.11e+02 dihedral pdb=" N ARG B 295 " pdb=" C ARG B 295 " pdb=" CA ARG B 295 " pdb=" CB ARG B 295 " ideal model delta harmonic sigma weight residual 122.80 147.32 -24.52 0 2.50e+00 1.60e-01 9.62e+01 dihedral pdb=" CB CYS A 112 " pdb=" SG CYS A 112 " pdb=" SG CYS A 159 " pdb=" CB CYS A 159 " ideal model delta sinusoidal sigma weight residual -86.00 -4.67 -81.33 1 1.00e+01 1.00e-02 8.15e+01 ... (remaining 35505 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.227: 8791 0.227 - 0.455: 90 0.455 - 0.682: 6 0.682 - 0.910: 1 0.910 - 1.137: 1 Chirality restraints: 8889 Sorted by residual: chirality pdb=" CA ARG B 295 " pdb=" N ARG B 295 " pdb=" C ARG B 295 " pdb=" CB ARG B 295 " both_signs ideal model delta sigma weight residual False 2.51 1.37 1.14 2.00e-01 2.50e+01 3.23e+01 chirality pdb=" CA ALA O 416 " pdb=" N ALA O 416 " pdb=" C ALA O 416 " pdb=" CB ALA O 416 " both_signs ideal model delta sigma weight residual False 2.48 1.73 0.75 2.00e-01 2.50e+01 1.41e+01 chirality pdb=" P DT X -22 " pdb=" OP1 DT X -22 " pdb=" OP2 DT X -22 " pdb=" O5' DT X -22 " both_signs ideal model delta sigma weight residual True 2.35 -2.92 -0.57 2.00e-01 2.50e+01 8.21e+00 ... (remaining 8886 not shown) Planarity restraints: 9690 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG B 293 " 0.027 2.00e-02 2.50e+03 5.35e-02 2.87e+01 pdb=" C ARG B 293 " -0.093 2.00e-02 2.50e+03 pdb=" O ARG B 293 " 0.035 2.00e-02 2.50e+03 pdb=" N GLN B 294 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR O 412 " -0.071 5.00e-02 4.00e+02 1.08e-01 1.88e+01 pdb=" N PRO O 413 " 0.187 5.00e-02 4.00e+02 pdb=" CA PRO O 413 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO O 413 " -0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB HIS L 23 " -0.027 2.00e-02 2.50e+03 2.19e-02 7.16e+00 pdb=" CG HIS L 23 " 0.044 2.00e-02 2.50e+03 pdb=" ND1 HIS L 23 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 HIS L 23 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 HIS L 23 " -0.007 2.00e-02 2.50e+03 pdb=" NE2 HIS L 23 " -0.014 2.00e-02 2.50e+03 ... (remaining 9687 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.27: 58 2.27 - 2.93: 24521 2.93 - 3.59: 87763 3.59 - 4.24: 135319 4.24 - 4.90: 221053 Nonbonded interactions: 468714 Sorted by model distance: nonbonded pdb=" O ASN A 154 " pdb="ZN ZN A1402 " model vdw 1.615 2.230 nonbonded pdb=" NZ LYS E 85 " pdb=" OP2 DG Y -8 " model vdw 1.709 2.520 nonbonded pdb=" NZ LYS B 404 " pdb=" O THR V 140 " model vdw 1.930 2.520 nonbonded pdb=" OE1 GLU 4 167 " pdb=" NZ LYS M 316 " model vdw 1.969 2.520 nonbonded pdb=" C3' DA X -46 " pdb=" OP1 DT X -45 " model vdw 1.988 2.776 ... (remaining 468709 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 9.220 Check model and map are aligned: 0.620 Set scattering table: 0.370 Process input model: 139.250 Find NCS groups from input model: 1.520 Set up NCS constraints: 0.190 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:2.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 154.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 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 : 0.003 0.055 58585 Z= 0.202 Angle : 1.236 85.699 79791 Z= 0.513 Chirality : 0.060 1.137 8889 Planarity : 0.004 0.108 9690 Dihedral : 16.228 176.903 22823 Min Nonbonded Distance : 1.615 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.88 % Favored : 95.94 % Rotamer: Outliers : 0.66 % Allowed : 2.54 % Favored : 96.80 % Cbeta Deviations : 0.05 % 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: -0.59 (0.10), residues: 6657 helix: 0.65 (0.10), residues: 2657 sheet: -0.74 (0.19), residues: 714 loop : -1.16 (0.11), residues: 3286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP O 235 HIS 0.013 0.001 HIS L 23 PHE 0.026 0.001 PHE Q 38 TYR 0.020 0.001 TYR G 40 ARG 0.007 0.000 ARG A1138 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13314 Ramachandran restraints generated. 6657 Oldfield, 0 Emsley, 6657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13314 Ramachandran restraints generated. 6657 Oldfield, 0 Emsley, 6657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 5937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 294 time to evaluate : 5.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 108 LEU cc_start: 0.5302 (mt) cc_final: 0.5011 (tp) REVERT: 1 140 MET cc_start: 0.6965 (ptp) cc_final: 0.6748 (ttt) REVERT: 3 386 MET cc_start: 0.1855 (pp-130) cc_final: 0.1488 (ptt) REVERT: 4 264 GLU cc_start: 0.8931 (mp0) cc_final: 0.8695 (mm-30) REVERT: 4 385 MET cc_start: -0.0517 (tmm) cc_final: -0.2563 (tpt) REVERT: 4 499 MET cc_start: 0.1891 (ptp) cc_final: 0.0749 (tpp) REVERT: A 79 CYS cc_start: 0.7565 (OUTLIER) cc_final: 0.7290 (t) REVERT: A 116 MET cc_start: 0.6449 (tmm) cc_final: 0.5644 (mtp) REVERT: A 523 MET cc_start: 0.8992 (mtm) cc_final: 0.8735 (mtm) REVERT: A 680 MET cc_start: 0.8847 (mmt) cc_final: 0.8640 (mmm) REVERT: A 912 MET cc_start: 0.8364 (tpp) cc_final: 0.8057 (tpp) REVERT: A 1317 MET cc_start: 0.8167 (tmm) cc_final: 0.7950 (tmm) REVERT: A 1349 MET cc_start: 0.8379 (tpt) cc_final: 0.8173 (mmm) REVERT: B 243 MET cc_start: 0.8468 (tpt) cc_final: 0.8191 (tpp) REVERT: B 262 MET cc_start: 0.9328 (mpp) cc_final: 0.8918 (mpp) REVERT: B 478 MET cc_start: 0.8682 (mpp) cc_final: 0.8026 (mpp) REVERT: B 929 MET cc_start: 0.8396 (ttt) cc_final: 0.8161 (ttp) REVERT: B 1069 MET cc_start: 0.8804 (tmm) cc_final: 0.8497 (tmm) REVERT: E 94 MET cc_start: 0.8376 (tpt) cc_final: 0.7926 (tpt) REVERT: E 121 MET cc_start: 0.8253 (mpp) cc_final: 0.7957 (mpp) REVERT: H 37 MET cc_start: 0.9178 (mmm) cc_final: 0.8822 (mmm) REVERT: K 28 GLU cc_start: 0.8378 (mp0) cc_final: 0.8151 (mp0) REVERT: K 60 MET cc_start: 0.9055 (tpp) cc_final: 0.8774 (tpt) REVERT: K 97 GLN cc_start: 0.8800 (pp30) cc_final: 0.8347 (pp30) REVERT: K 102 GLU cc_start: 0.8596 (mt-10) cc_final: 0.8366 (mt-10) REVERT: L 25 GLU cc_start: 0.8519 (mm-30) cc_final: 0.8138 (mm-30) REVERT: M 60 MET cc_start: 0.7591 (pmm) cc_final: 0.7337 (pmm) REVERT: M 298 MET cc_start: 0.8812 (mmt) cc_final: 0.8451 (mpp) REVERT: O 133 MET cc_start: 0.4112 (ptt) cc_final: 0.3866 (ptt) REVERT: O 333 MET cc_start: 0.7946 (tmm) cc_final: 0.7130 (tmm) REVERT: O 420 THR cc_start: 0.6320 (OUTLIER) cc_final: 0.5677 (t) REVERT: P 310 MET cc_start: 0.8509 (mmt) cc_final: 0.7668 (mpp) REVERT: U 252 ASP cc_start: 0.8869 (t70) cc_final: 0.8489 (p0) REVERT: U 258 MET cc_start: 0.6742 (ptp) cc_final: 0.6493 (ptm) REVERT: W 282 ILE cc_start: 0.7741 (mm) cc_final: 0.7339 (mm) outliers start: 39 outliers final: 10 residues processed: 329 average time/residue: 0.5647 time to fit residues: 313.9010 Evaluate side-chains 241 residues out of total 5937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 229 time to evaluate : 4.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain B residue 305 LYS Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain O residue 412 THR Chi-restraints excluded: chain O residue 418 SER Chi-restraints excluded: chain O residue 420 THR Chi-restraints excluded: chain V residue 19 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 677 random chunks: chunk 571 optimal weight: 0.0370 chunk 513 optimal weight: 4.9990 chunk 284 optimal weight: 0.1980 chunk 175 optimal weight: 9.9990 chunk 346 optimal weight: 4.9990 chunk 274 optimal weight: 10.0000 chunk 530 optimal weight: 6.9990 chunk 205 optimal weight: 0.4980 chunk 322 optimal weight: 8.9990 chunk 394 optimal weight: 2.9990 chunk 614 optimal weight: 3.9990 overall best weight: 1.5462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 8 GLN 1 48 ASN ** 1 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 185 ASN 3 202 GLN 3 210 GLN ** 3 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 314 GLN 3 367 ASN 4 247 GLN 4 286 ASN 4 438 GLN A 158 HIS A 427 GLN ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1100 HIS ** G 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 106 GLN O 183 ASN ** O 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 129 HIS V 212 ASN V 267 GLN W 279 ASN W 339 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.0902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 58585 Z= 0.171 Angle : 0.691 30.759 79791 Z= 0.319 Chirality : 0.076 2.045 8889 Planarity : 0.004 0.071 9690 Dihedral : 15.447 179.934 9201 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.19 % Favored : 95.73 % Rotamer: Outliers : 0.42 % Allowed : 6.30 % Favored : 93.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.32 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.10), residues: 6657 helix: 0.88 (0.10), residues: 2672 sheet: -0.67 (0.18), residues: 745 loop : -0.94 (0.11), residues: 3240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP V 234 HIS 0.014 0.001 HIS O 415 PHE 0.022 0.001 PHE 1 120 TYR 0.018 0.001 TYR O 422 ARG 0.005 0.000 ARG B 293 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13314 Ramachandran restraints generated. 6657 Oldfield, 0 Emsley, 6657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13314 Ramachandran restraints generated. 6657 Oldfield, 0 Emsley, 6657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 5937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 240 time to evaluate : 4.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 108 LEU cc_start: 0.5715 (mt) cc_final: 0.5419 (tp) REVERT: 1 140 MET cc_start: 0.7035 (ptp) cc_final: 0.6809 (ttt) REVERT: 3 386 MET cc_start: 0.2250 (pp-130) cc_final: 0.1853 (ptt) REVERT: 4 385 MET cc_start: -0.0202 (tmm) cc_final: -0.2039 (tpt) REVERT: 4 499 MET cc_start: 0.1913 (ptp) cc_final: 0.0810 (tpp) REVERT: A 60 MET cc_start: 0.7711 (ttt) cc_final: 0.6342 (tmm) REVERT: A 116 MET cc_start: 0.6798 (tmm) cc_final: 0.5929 (mtp) REVERT: A 680 MET cc_start: 0.8892 (mmt) cc_final: 0.8608 (mmm) REVERT: A 1275 MET cc_start: 0.8858 (mmm) cc_final: 0.8156 (mmm) REVERT: A 1311 MET cc_start: 0.8199 (pmm) cc_final: 0.7927 (pmm) REVERT: A 1317 MET cc_start: 0.8236 (tmm) cc_final: 0.8015 (tmm) REVERT: B 262 MET cc_start: 0.9393 (mpp) cc_final: 0.9059 (mpp) REVERT: B 478 MET cc_start: 0.8777 (mpp) cc_final: 0.8136 (mpp) REVERT: B 1062 MET cc_start: 0.8468 (mpp) cc_final: 0.7916 (mpp) REVERT: B 1069 MET cc_start: 0.8877 (tmm) cc_final: 0.8579 (tmm) REVERT: C 212 MET cc_start: 0.9192 (mtp) cc_final: 0.8792 (mtp) REVERT: E 94 MET cc_start: 0.8549 (tpt) cc_final: 0.8052 (tpp) REVERT: G 157 PHE cc_start: 0.7741 (OUTLIER) cc_final: 0.7133 (m-10) REVERT: H 37 MET cc_start: 0.9215 (mmm) cc_final: 0.8797 (mmm) REVERT: K 28 GLU cc_start: 0.8394 (mp0) cc_final: 0.8154 (mp0) REVERT: K 29 MET cc_start: 0.8229 (tmm) cc_final: 0.7773 (tmm) REVERT: K 97 GLN cc_start: 0.8795 (pp30) cc_final: 0.8324 (pp30) REVERT: L 25 GLU cc_start: 0.8320 (mm-30) cc_final: 0.7951 (mm-30) REVERT: L 56 ASP cc_start: 0.8550 (t0) cc_final: 0.8344 (m-30) REVERT: M 60 MET cc_start: 0.7553 (pmm) cc_final: 0.7296 (pmm) REVERT: O 270 MET cc_start: 0.9109 (ppp) cc_final: 0.8901 (ppp) REVERT: O 404 MET cc_start: 0.6843 (tpt) cc_final: 0.6146 (tpt) REVERT: O 531 MET cc_start: 0.7641 (tpp) cc_final: 0.7017 (tpp) REVERT: P 310 MET cc_start: 0.8664 (mmt) cc_final: 0.7938 (mpp) REVERT: U 202 MET cc_start: 0.9293 (mmm) cc_final: 0.8509 (tpt) outliers start: 25 outliers final: 8 residues processed: 260 average time/residue: 0.5298 time to fit residues: 242.6844 Evaluate side-chains 236 residues out of total 5937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 227 time to evaluate : 4.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 8 GLN Chi-restraints excluded: chain 4 residue 226 LEU Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain B residue 305 LYS Chi-restraints excluded: chain D residue 118 HIS Chi-restraints excluded: chain G residue 157 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 677 random chunks: chunk 341 optimal weight: 1.9990 chunk 190 optimal weight: 3.9990 chunk 511 optimal weight: 10.0000 chunk 418 optimal weight: 0.0070 chunk 169 optimal weight: 8.9990 chunk 615 optimal weight: 20.0000 chunk 665 optimal weight: 10.0000 chunk 548 optimal weight: 6.9990 chunk 610 optimal weight: 7.9990 chunk 209 optimal weight: 10.0000 chunk 494 optimal weight: 10.0000 overall best weight: 4.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 438 GLN A 296 HIS A 427 GLN ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 31 GLN ** M 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 324 ASN ** O 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 445 ASN P 200 GLN U 327 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 58585 Z= 0.284 Angle : 0.725 28.482 79791 Z= 0.338 Chirality : 0.079 2.065 8889 Planarity : 0.004 0.068 9690 Dihedral : 15.457 168.933 9192 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.58 % Favored : 95.39 % Rotamer: Outliers : 0.69 % Allowed : 9.12 % Favored : 90.19 % 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: -0.15 (0.10), residues: 6657 helix: 0.98 (0.10), residues: 2663 sheet: -0.68 (0.18), residues: 749 loop : -0.84 (0.11), residues: 3245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP 4 284 HIS 0.010 0.001 HIS O 415 PHE 0.033 0.002 PHE G 150 TYR 0.015 0.001 TYR B1003 ARG 0.028 0.000 ARG G 151 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13314 Ramachandran restraints generated. 6657 Oldfield, 0 Emsley, 6657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13314 Ramachandran restraints generated. 6657 Oldfield, 0 Emsley, 6657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 5937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 230 time to evaluate : 5.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 108 LEU cc_start: 0.5699 (mt) cc_final: 0.5377 (tp) REVERT: 3 47 PHE cc_start: -0.2441 (OUTLIER) cc_final: -0.3346 (m-80) REVERT: 3 51 TRP cc_start: -0.0506 (OUTLIER) cc_final: -0.1120 (t60) REVERT: 4 385 MET cc_start: -0.0065 (tmm) cc_final: -0.1943 (tpt) REVERT: 4 499 MET cc_start: 0.1966 (ptp) cc_final: 0.0871 (tpp) REVERT: A 60 MET cc_start: 0.7990 (ttt) cc_final: 0.6627 (tmm) REVERT: A 116 MET cc_start: 0.6695 (tmm) cc_final: 0.6309 (mtp) REVERT: A 1027 MET cc_start: 0.8691 (tpt) cc_final: 0.8458 (tpt) REVERT: A 1317 MET cc_start: 0.8333 (tmm) cc_final: 0.8129 (tmm) REVERT: B 478 MET cc_start: 0.8849 (mpp) cc_final: 0.8204 (mpp) REVERT: B 870 MET cc_start: 0.8789 (ppp) cc_final: 0.8574 (ppp) REVERT: B 1062 MET cc_start: 0.8583 (mpp) cc_final: 0.7963 (mpp) REVERT: B 1069 MET cc_start: 0.8929 (tmm) cc_final: 0.8604 (tmm) REVERT: E 94 MET cc_start: 0.8543 (tpt) cc_final: 0.7810 (tpp) REVERT: E 110 MET cc_start: 0.8168 (tpp) cc_final: 0.7536 (tpp) REVERT: E 121 MET cc_start: 0.8576 (mpp) cc_final: 0.8371 (mpp) REVERT: H 37 MET cc_start: 0.9266 (mmm) cc_final: 0.8812 (mmm) REVERT: K 29 MET cc_start: 0.8235 (tmm) cc_final: 0.7763 (tmm) REVERT: K 31 GLN cc_start: 0.7496 (OUTLIER) cc_final: 0.7269 (pp30) REVERT: L 25 GLU cc_start: 0.8516 (mm-30) cc_final: 0.8061 (mm-30) REVERT: M 60 MET cc_start: 0.7850 (pmm) cc_final: 0.7586 (pmm) REVERT: O 118 MET cc_start: 0.7637 (mmm) cc_final: 0.7374 (mmm) REVERT: O 404 MET cc_start: 0.6623 (tpt) cc_final: 0.5878 (tpt) REVERT: O 531 MET cc_start: 0.7735 (tpp) cc_final: 0.6983 (tpp) REVERT: P 310 MET cc_start: 0.8839 (mmt) cc_final: 0.8620 (mmm) REVERT: Q 68 MET cc_start: 0.7688 (ptp) cc_final: 0.7479 (ptp) REVERT: U 202 MET cc_start: 0.9407 (mmm) cc_final: 0.8708 (tmm) outliers start: 41 outliers final: 20 residues processed: 262 average time/residue: 0.5092 time to fit residues: 235.0105 Evaluate side-chains 243 residues out of total 5937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 220 time to evaluate : 4.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 47 PHE Chi-restraints excluded: chain 3 residue 51 TRP Chi-restraints excluded: chain 4 residue 226 LEU Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 1280 MET Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain B residue 305 LYS Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 653 ASP Chi-restraints excluded: chain B residue 1009 TYR Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain D residue 60 HIS Chi-restraints excluded: chain D residue 118 HIS Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain J residue 48 MET Chi-restraints excluded: chain K residue 31 GLN Chi-restraints excluded: chain P residue 214 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 677 random chunks: chunk 608 optimal weight: 4.9990 chunk 463 optimal weight: 6.9990 chunk 319 optimal weight: 3.9990 chunk 68 optimal weight: 20.0000 chunk 293 optimal weight: 1.9990 chunk 413 optimal weight: 20.0000 chunk 618 optimal weight: 20.0000 chunk 654 optimal weight: 10.0000 chunk 322 optimal weight: 0.0870 chunk 585 optimal weight: 8.9990 chunk 176 optimal weight: 5.9990 overall best weight: 3.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 8 GLN ** 1 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 427 GLN ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 160 ASN ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 31 GLN K 108 GLN L 26 ASN ** M 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 339 HIS W 331 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 58585 Z= 0.233 Angle : 0.685 27.457 79791 Z= 0.318 Chirality : 0.079 2.087 8889 Planarity : 0.004 0.070 9690 Dihedral : 15.470 157.897 9192 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.61 % Favored : 95.36 % Rotamer: Outliers : 1.04 % Allowed : 10.20 % Favored : 88.75 % 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: -0.06 (0.10), residues: 6657 helix: 1.05 (0.10), residues: 2673 sheet: -0.61 (0.18), residues: 746 loop : -0.80 (0.11), residues: 3238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP M 423 HIS 0.007 0.001 HIS O 415 PHE 0.016 0.001 PHE Q 38 TYR 0.020 0.001 TYR 3 247 ARG 0.007 0.000 ARG O 268 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13314 Ramachandran restraints generated. 6657 Oldfield, 0 Emsley, 6657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13314 Ramachandran restraints generated. 6657 Oldfield, 0 Emsley, 6657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 5937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 224 time to evaluate : 4.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 108 LEU cc_start: 0.5275 (mt) cc_final: 0.4991 (tp) REVERT: 3 47 PHE cc_start: -0.2415 (OUTLIER) cc_final: -0.3061 (m-80) REVERT: 3 51 TRP cc_start: -0.0391 (OUTLIER) cc_final: -0.0656 (t60) REVERT: 3 326 ILE cc_start: 0.1567 (OUTLIER) cc_final: 0.1355 (tt) REVERT: 4 385 MET cc_start: -0.0035 (tmm) cc_final: -0.1928 (tpt) REVERT: 4 499 MET cc_start: 0.2000 (ptp) cc_final: 0.1023 (tpp) REVERT: A 60 MET cc_start: 0.8026 (ttt) cc_final: 0.6565 (tmm) REVERT: A 116 MET cc_start: 0.6740 (tmm) cc_final: 0.6378 (mtp) REVERT: A 1317 MET cc_start: 0.8345 (tmm) cc_final: 0.8117 (tmm) REVERT: B 59 MET cc_start: 0.8868 (ppp) cc_final: 0.8662 (ppp) REVERT: B 262 MET cc_start: 0.9364 (mpp) cc_final: 0.8902 (mpp) REVERT: B 431 MET cc_start: 0.8225 (tmm) cc_final: 0.7793 (tmm) REVERT: B 870 MET cc_start: 0.8830 (ppp) cc_final: 0.8509 (ppp) REVERT: B 916 MET cc_start: 0.9193 (mmm) cc_final: 0.8847 (mmm) REVERT: B 1062 MET cc_start: 0.8517 (mpp) cc_final: 0.7860 (mpp) REVERT: B 1069 MET cc_start: 0.8942 (tmm) cc_final: 0.8600 (tmm) REVERT: E 110 MET cc_start: 0.8365 (tpp) cc_final: 0.8083 (tpp) REVERT: F 57 MET cc_start: 0.8874 (tmm) cc_final: 0.8651 (tmm) REVERT: G 157 PHE cc_start: 0.7581 (OUTLIER) cc_final: 0.7068 (m-10) REVERT: H 37 MET cc_start: 0.9269 (mmm) cc_final: 0.8804 (mmm) REVERT: K 29 MET cc_start: 0.8260 (tmm) cc_final: 0.7911 (tmm) REVERT: L 16 ILE cc_start: 0.9302 (OUTLIER) cc_final: 0.8970 (mp) REVERT: L 25 GLU cc_start: 0.8494 (mm-30) cc_final: 0.8037 (mm-30) REVERT: M 60 MET cc_start: 0.7797 (pmm) cc_final: 0.7513 (pmm) REVERT: M 270 MET cc_start: 0.8498 (mmm) cc_final: 0.7652 (tpp) REVERT: M 292 MET cc_start: 0.8461 (tmm) cc_final: 0.7921 (tmm) REVERT: O 118 MET cc_start: 0.8037 (mmm) cc_final: 0.7775 (mmm) REVERT: O 404 MET cc_start: 0.6717 (tpt) cc_final: 0.5969 (tpt) REVERT: O 531 MET cc_start: 0.8085 (tpp) cc_final: 0.7300 (tpp) REVERT: P 310 MET cc_start: 0.8884 (mmt) cc_final: 0.8641 (mmm) REVERT: U 202 MET cc_start: 0.9404 (mmm) cc_final: 0.8710 (tmm) REVERT: W 331 HIS cc_start: 0.7859 (OUTLIER) cc_final: 0.7559 (t70) outliers start: 62 outliers final: 26 residues processed: 276 average time/residue: 0.5172 time to fit residues: 251.4503 Evaluate side-chains 250 residues out of total 5937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 218 time to evaluate : 4.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 47 PHE Chi-restraints excluded: chain 3 residue 51 TRP Chi-restraints excluded: chain 3 residue 326 ILE Chi-restraints excluded: chain 3 residue 405 VAL Chi-restraints excluded: chain 4 residue 226 LEU Chi-restraints excluded: chain 4 residue 364 MET Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 1164 ASP Chi-restraints excluded: chain A residue 1280 MET Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain B residue 305 LYS Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 877 ASP Chi-restraints excluded: chain B residue 1009 TYR Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain D residue 60 HIS Chi-restraints excluded: chain D residue 118 HIS Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain G residue 157 PHE Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain J residue 48 MET Chi-restraints excluded: chain L residue 16 ILE Chi-restraints excluded: chain O residue 130 THR Chi-restraints excluded: chain O residue 133 MET Chi-restraints excluded: chain W residue 282 ILE Chi-restraints excluded: chain W residue 331 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 677 random chunks: chunk 545 optimal weight: 40.0000 chunk 371 optimal weight: 30.0000 chunk 9 optimal weight: 20.0000 chunk 487 optimal weight: 8.9990 chunk 270 optimal weight: 5.9990 chunk 558 optimal weight: 20.0000 chunk 452 optimal weight: 6.9990 chunk 0 optimal weight: 40.0000 chunk 334 optimal weight: 1.9990 chunk 587 optimal weight: 1.9990 chunk 165 optimal weight: 0.8980 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 73 GLN ** 1 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 247 GLN A 427 GLN ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 10 ASN J 26 GLN ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 78 GLN ** O 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 58585 Z= 0.244 Angle : 0.687 27.462 79791 Z= 0.318 Chirality : 0.078 2.082 8889 Planarity : 0.004 0.061 9690 Dihedral : 15.464 157.524 9190 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.01 % Favored : 94.96 % Rotamer: Outliers : 1.23 % Allowed : 11.14 % Favored : 87.63 % 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: -0.03 (0.10), residues: 6657 helix: 1.07 (0.10), residues: 2683 sheet: -0.60 (0.18), residues: 743 loop : -0.77 (0.11), residues: 3231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP M 423 HIS 0.034 0.001 HIS W 331 PHE 0.015 0.001 PHE Q 38 TYR 0.016 0.001 TYR A1116 ARG 0.005 0.000 ARG O 268 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13314 Ramachandran restraints generated. 6657 Oldfield, 0 Emsley, 6657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13314 Ramachandran restraints generated. 6657 Oldfield, 0 Emsley, 6657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 5937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 221 time to evaluate : 4.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 108 LEU cc_start: 0.5252 (mt) cc_final: 0.4968 (tp) REVERT: 3 47 PHE cc_start: -0.2184 (OUTLIER) cc_final: -0.3079 (m-80) REVERT: 3 51 TRP cc_start: 0.0031 (OUTLIER) cc_final: -0.0824 (t60) REVERT: 4 385 MET cc_start: -0.0034 (tmm) cc_final: -0.1870 (tpt) REVERT: 4 499 MET cc_start: 0.1668 (ptp) cc_final: 0.0689 (tpp) REVERT: A 116 MET cc_start: 0.6826 (tmm) cc_final: 0.6455 (mtp) REVERT: A 680 MET cc_start: 0.8921 (mmt) cc_final: 0.8379 (mmm) REVERT: A 912 MET cc_start: 0.8165 (tpp) cc_final: 0.7697 (mmt) REVERT: A 1275 MET cc_start: 0.8701 (mmm) cc_final: 0.8329 (mmm) REVERT: A 1280 MET cc_start: 0.7725 (OUTLIER) cc_final: 0.7522 (ptp) REVERT: A 1317 MET cc_start: 0.8371 (tmm) cc_final: 0.8151 (tmm) REVERT: B 59 MET cc_start: 0.8844 (ppp) cc_final: 0.8624 (ppp) REVERT: B 262 MET cc_start: 0.9350 (mpp) cc_final: 0.8868 (mpp) REVERT: B 431 MET cc_start: 0.8202 (tmm) cc_final: 0.7806 (tmm) REVERT: B 870 MET cc_start: 0.8855 (ppp) cc_final: 0.8491 (ppp) REVERT: B 916 MET cc_start: 0.9154 (mmm) cc_final: 0.8865 (mmm) REVERT: B 1062 MET cc_start: 0.8591 (mpp) cc_final: 0.8038 (mpp) REVERT: B 1069 MET cc_start: 0.8987 (tmm) cc_final: 0.8600 (tmm) REVERT: C 315 VAL cc_start: 0.9529 (OUTLIER) cc_final: 0.9249 (t) REVERT: E 110 MET cc_start: 0.8307 (tpp) cc_final: 0.8107 (tpp) REVERT: E 121 MET cc_start: 0.8833 (mpp) cc_final: 0.8576 (mpp) REVERT: F 57 MET cc_start: 0.8969 (tmm) cc_final: 0.8645 (tmm) REVERT: H 37 MET cc_start: 0.9283 (mmm) cc_final: 0.8871 (mmt) REVERT: K 29 MET cc_start: 0.8100 (tmm) cc_final: 0.7696 (tmm) REVERT: L 25 GLU cc_start: 0.8476 (mm-30) cc_final: 0.8038 (mm-30) REVERT: M 60 MET cc_start: 0.7815 (pmm) cc_final: 0.7528 (pmm) REVERT: M 270 MET cc_start: 0.8528 (mmm) cc_final: 0.7650 (tpp) REVERT: M 292 MET cc_start: 0.8526 (tmm) cc_final: 0.7406 (tmm) REVERT: M 319 MET cc_start: 0.8612 (OUTLIER) cc_final: 0.7908 (tmm) REVERT: O 118 MET cc_start: 0.8317 (mmm) cc_final: 0.8067 (mmm) REVERT: O 270 MET cc_start: 0.9162 (ppp) cc_final: 0.8826 (ppp) REVERT: O 333 MET cc_start: 0.7139 (tmm) cc_final: 0.6344 (tmm) REVERT: O 404 MET cc_start: 0.6644 (tpt) cc_final: 0.5836 (tpt) REVERT: O 531 MET cc_start: 0.8213 (tpp) cc_final: 0.7371 (tpp) outliers start: 73 outliers final: 34 residues processed: 280 average time/residue: 0.5078 time to fit residues: 252.5184 Evaluate side-chains 257 residues out of total 5937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 218 time to evaluate : 4.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 40 THR Chi-restraints excluded: chain 1 residue 140 MET Chi-restraints excluded: chain 3 residue 47 PHE Chi-restraints excluded: chain 3 residue 51 TRP Chi-restraints excluded: chain 3 residue 405 VAL Chi-restraints excluded: chain 4 residue 176 PHE Chi-restraints excluded: chain 4 residue 226 LEU Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 1164 ASP Chi-restraints excluded: chain A residue 1175 VAL Chi-restraints excluded: chain A residue 1280 MET Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain B residue 305 LYS Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 653 ASP Chi-restraints excluded: chain B residue 689 MET Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 877 ASP Chi-restraints excluded: chain B residue 1009 TYR Chi-restraints excluded: chain B residue 1015 MET Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain D residue 60 HIS Chi-restraints excluded: chain D residue 118 HIS Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain G residue 41 ASN Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 48 MET Chi-restraints excluded: chain L residue 56 ASP Chi-restraints excluded: chain M residue 319 MET Chi-restraints excluded: chain O residue 130 THR Chi-restraints excluded: chain Q residue 110 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 677 random chunks: chunk 220 optimal weight: 8.9990 chunk 589 optimal weight: 50.0000 chunk 129 optimal weight: 10.0000 chunk 384 optimal weight: 2.9990 chunk 161 optimal weight: 2.9990 chunk 655 optimal weight: 2.9990 chunk 543 optimal weight: 20.0000 chunk 303 optimal weight: 4.9990 chunk 54 optimal weight: 0.0050 chunk 216 optimal weight: 4.9990 chunk 343 optimal weight: 0.8980 overall best weight: 1.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 427 GLN A 872 GLN B 289 ASN ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 129 GLN ** G 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 31 GLN ** M 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 58585 Z= 0.170 Angle : 0.662 27.306 79791 Z= 0.304 Chirality : 0.078 2.086 8889 Planarity : 0.003 0.060 9690 Dihedral : 15.460 157.550 9190 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.40 % Favored : 95.57 % Rotamer: Outliers : 1.21 % Allowed : 11.67 % Favored : 87.12 % 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: 0.07 (0.11), residues: 6657 helix: 1.15 (0.10), residues: 2682 sheet: -0.50 (0.19), residues: 743 loop : -0.73 (0.11), residues: 3232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP 4 476 HIS 0.010 0.001 HIS P 214 PHE 0.030 0.001 PHE Q 38 TYR 0.015 0.001 TYR M 119 ARG 0.006 0.000 ARG W 332 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13314 Ramachandran restraints generated. 6657 Oldfield, 0 Emsley, 6657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13314 Ramachandran restraints generated. 6657 Oldfield, 0 Emsley, 6657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 5937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 223 time to evaluate : 5.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 108 LEU cc_start: 0.5227 (mt) cc_final: 0.4953 (tp) REVERT: 3 47 PHE cc_start: -0.2195 (OUTLIER) cc_final: -0.3010 (m-80) REVERT: 3 51 TRP cc_start: -0.0340 (OUTLIER) cc_final: -0.1109 (t60) REVERT: 4 385 MET cc_start: 0.0443 (tmm) cc_final: -0.1396 (tpt) REVERT: 4 499 MET cc_start: 0.1852 (ptp) cc_final: 0.0999 (tpp) REVERT: A 116 MET cc_start: 0.7012 (tmm) cc_final: 0.6411 (mtp) REVERT: A 680 MET cc_start: 0.8931 (mmt) cc_final: 0.8390 (mmm) REVERT: A 912 MET cc_start: 0.8103 (tpp) cc_final: 0.7674 (tpp) REVERT: A 1317 MET cc_start: 0.8375 (tmm) cc_final: 0.8147 (tmm) REVERT: B 59 MET cc_start: 0.8966 (ppp) cc_final: 0.8737 (ppp) REVERT: B 262 MET cc_start: 0.9302 (mpp) cc_final: 0.8851 (mpp) REVERT: B 431 MET cc_start: 0.8073 (tmm) cc_final: 0.7702 (tmm) REVERT: B 870 MET cc_start: 0.8855 (ppp) cc_final: 0.8474 (ppp) REVERT: B 916 MET cc_start: 0.9110 (mmm) cc_final: 0.8855 (mmm) REVERT: B 1062 MET cc_start: 0.8556 (mpp) cc_final: 0.7880 (mpp) REVERT: B 1069 MET cc_start: 0.8986 (tmm) cc_final: 0.8586 (tmm) REVERT: C 315 VAL cc_start: 0.9504 (OUTLIER) cc_final: 0.9214 (t) REVERT: E 110 MET cc_start: 0.8366 (tpp) cc_final: 0.8121 (tpp) REVERT: E 121 MET cc_start: 0.8786 (mpp) cc_final: 0.8549 (mpp) REVERT: G 157 PHE cc_start: 0.7582 (OUTLIER) cc_final: 0.7058 (m-10) REVERT: H 37 MET cc_start: 0.9310 (mmm) cc_final: 0.8890 (mmt) REVERT: K 29 MET cc_start: 0.8119 (tmm) cc_final: 0.7517 (tmm) REVERT: K 31 GLN cc_start: 0.7418 (OUTLIER) cc_final: 0.6961 (pm20) REVERT: K 104 MET cc_start: 0.8888 (mmm) cc_final: 0.8579 (mmm) REVERT: L 16 ILE cc_start: 0.9291 (OUTLIER) cc_final: 0.9052 (mp) REVERT: L 25 GLU cc_start: 0.8502 (mm-30) cc_final: 0.7962 (mm-30) REVERT: M 60 MET cc_start: 0.7874 (pmm) cc_final: 0.7580 (pmm) REVERT: M 270 MET cc_start: 0.8528 (mmm) cc_final: 0.7628 (tpp) REVERT: M 292 MET cc_start: 0.8411 (tmm) cc_final: 0.7368 (tmm) REVERT: O 139 MET cc_start: 0.5931 (mmm) cc_final: 0.5599 (ttt) REVERT: O 333 MET cc_start: 0.7144 (tmm) cc_final: 0.6316 (tmm) REVERT: O 404 MET cc_start: 0.6599 (tpt) cc_final: 0.5978 (tpp) REVERT: O 531 MET cc_start: 0.8293 (tpp) cc_final: 0.7523 (tpp) REVERT: P 310 MET cc_start: 0.9073 (mmm) cc_final: 0.8634 (mpp) outliers start: 72 outliers final: 45 residues processed: 280 average time/residue: 0.5026 time to fit residues: 249.2045 Evaluate side-chains 271 residues out of total 5937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 220 time to evaluate : 4.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 40 THR Chi-restraints excluded: chain 3 residue 47 PHE Chi-restraints excluded: chain 3 residue 51 TRP Chi-restraints excluded: chain 3 residue 405 VAL Chi-restraints excluded: chain 4 residue 176 PHE Chi-restraints excluded: chain 4 residue 226 LEU Chi-restraints excluded: chain 4 residue 447 LEU Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 994 THR Chi-restraints excluded: chain A residue 1175 VAL Chi-restraints excluded: chain A residue 1280 MET Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain B residue 305 LYS Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 653 ASP Chi-restraints excluded: chain B residue 689 MET Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 1004 PHE Chi-restraints excluded: chain B residue 1009 TYR Chi-restraints excluded: chain B residue 1015 MET Chi-restraints excluded: chain B residue 1047 LEU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain D residue 60 HIS Chi-restraints excluded: chain D residue 118 HIS Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain G residue 157 PHE Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 48 MET Chi-restraints excluded: chain K residue 31 GLN Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain L residue 16 ILE Chi-restraints excluded: chain L residue 18 ILE Chi-restraints excluded: chain L residue 56 ASP Chi-restraints excluded: chain M residue 41 ASP Chi-restraints excluded: chain M residue 319 MET Chi-restraints excluded: chain O residue 130 THR Chi-restraints excluded: chain O residue 133 MET Chi-restraints excluded: chain P residue 302 ILE Chi-restraints excluded: chain Q residue 110 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 677 random chunks: chunk 631 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 373 optimal weight: 4.9990 chunk 478 optimal weight: 0.5980 chunk 370 optimal weight: 5.9990 chunk 551 optimal weight: 0.0570 chunk 365 optimal weight: 0.9990 chunk 652 optimal weight: 4.9990 chunk 408 optimal weight: 0.9990 chunk 397 optimal weight: 6.9990 chunk 301 optimal weight: 7.9990 overall best weight: 0.9304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 268 ASN A 17 HIS A 508 HIS ** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 197 GLN M 266 ASN ** N 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.074 58585 Z= 0.141 Angle : 0.661 27.237 79791 Z= 0.301 Chirality : 0.078 2.083 8889 Planarity : 0.003 0.056 9690 Dihedral : 15.432 157.566 9190 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.28 % Favored : 95.69 % Rotamer: Outliers : 1.01 % Allowed : 12.22 % Favored : 86.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.11), residues: 6657 helix: 1.19 (0.10), residues: 2683 sheet: -0.39 (0.19), residues: 728 loop : -0.71 (0.11), residues: 3246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 297 HIS 0.016 0.001 HIS P 214 PHE 0.017 0.001 PHE Q 38 TYR 0.014 0.001 TYR L 17 ARG 0.004 0.000 ARG W 285 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13314 Ramachandran restraints generated. 6657 Oldfield, 0 Emsley, 6657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13314 Ramachandran restraints generated. 6657 Oldfield, 0 Emsley, 6657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 5937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 226 time to evaluate : 5.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 36 MET cc_start: 0.2224 (ttm) cc_final: 0.1864 (mtp) REVERT: 1 108 LEU cc_start: 0.5205 (mt) cc_final: 0.4936 (tp) REVERT: 3 47 PHE cc_start: -0.2186 (OUTLIER) cc_final: -0.3024 (m-80) REVERT: 3 51 TRP cc_start: -0.0379 (OUTLIER) cc_final: -0.1178 (t60) REVERT: 4 385 MET cc_start: 0.0353 (tmm) cc_final: -0.1475 (tpt) REVERT: 4 499 MET cc_start: 0.1856 (ptp) cc_final: 0.1021 (tpp) REVERT: A 116 MET cc_start: 0.7006 (tmm) cc_final: 0.6396 (mtp) REVERT: A 680 MET cc_start: 0.8913 (mmt) cc_final: 0.8366 (mmm) REVERT: A 912 MET cc_start: 0.8086 (tpp) cc_final: 0.7641 (tpp) REVERT: A 1275 MET cc_start: 0.8475 (mmm) cc_final: 0.8260 (mmm) REVERT: A 1317 MET cc_start: 0.8382 (tmm) cc_final: 0.8143 (tmm) REVERT: B 59 MET cc_start: 0.8957 (ppp) cc_final: 0.8712 (ppp) REVERT: B 262 MET cc_start: 0.9296 (mpp) cc_final: 0.8870 (mpp) REVERT: B 431 MET cc_start: 0.7921 (tmm) cc_final: 0.7608 (tmm) REVERT: B 870 MET cc_start: 0.8839 (ppp) cc_final: 0.8441 (ppp) REVERT: B 916 MET cc_start: 0.9074 (mmm) cc_final: 0.8789 (mmm) REVERT: B 1062 MET cc_start: 0.8500 (mpp) cc_final: 0.7814 (mpp) REVERT: B 1069 MET cc_start: 0.8975 (tmm) cc_final: 0.8564 (tmm) REVERT: E 56 THR cc_start: 0.8224 (OUTLIER) cc_final: 0.7957 (p) REVERT: E 110 MET cc_start: 0.8439 (tpp) cc_final: 0.8231 (tpp) REVERT: F 57 MET cc_start: 0.8911 (tmm) cc_final: 0.8682 (tmm) REVERT: G 157 PHE cc_start: 0.7538 (OUTLIER) cc_final: 0.7024 (m-10) REVERT: H 37 MET cc_start: 0.9306 (mmm) cc_final: 0.8879 (mmt) REVERT: J 54 ASP cc_start: 0.8077 (t70) cc_final: 0.7725 (t0) REVERT: K 29 MET cc_start: 0.8221 (tmm) cc_final: 0.7795 (tmm) REVERT: K 104 MET cc_start: 0.8846 (mmm) cc_final: 0.8409 (mmm) REVERT: L 16 ILE cc_start: 0.9351 (OUTLIER) cc_final: 0.9014 (mp) REVERT: L 25 GLU cc_start: 0.8483 (mm-30) cc_final: 0.7924 (mm-30) REVERT: M 60 MET cc_start: 0.7810 (pmm) cc_final: 0.7596 (pmm) REVERT: M 270 MET cc_start: 0.8525 (mmm) cc_final: 0.7630 (tpp) REVERT: M 292 MET cc_start: 0.8315 (tmm) cc_final: 0.8044 (tmm) REVERT: O 118 MET cc_start: 0.8094 (mmm) cc_final: 0.7560 (mmm) REVERT: O 333 MET cc_start: 0.7368 (tmm) cc_final: 0.6465 (tmm) REVERT: O 404 MET cc_start: 0.6880 (tpt) cc_final: 0.5392 (tmm) REVERT: P 310 MET cc_start: 0.8961 (mmm) cc_final: 0.8595 (mpp) outliers start: 60 outliers final: 37 residues processed: 273 average time/residue: 0.5039 time to fit residues: 244.5001 Evaluate side-chains 264 residues out of total 5937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 222 time to evaluate : 4.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 40 THR Chi-restraints excluded: chain 3 residue 47 PHE Chi-restraints excluded: chain 3 residue 51 TRP Chi-restraints excluded: chain 3 residue 405 VAL Chi-restraints excluded: chain 4 residue 176 PHE Chi-restraints excluded: chain 4 residue 226 LEU Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 994 THR Chi-restraints excluded: chain A residue 1175 VAL Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain B residue 305 LYS Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 653 ASP Chi-restraints excluded: chain B residue 689 MET Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 1004 PHE Chi-restraints excluded: chain B residue 1009 TYR Chi-restraints excluded: chain B residue 1015 MET Chi-restraints excluded: chain B residue 1047 LEU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain D residue 60 HIS Chi-restraints excluded: chain D residue 118 HIS Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 157 PHE Chi-restraints excluded: chain J residue 48 MET Chi-restraints excluded: chain L residue 16 ILE Chi-restraints excluded: chain O residue 130 THR Chi-restraints excluded: chain P residue 302 ILE Chi-restraints excluded: chain Q residue 110 MET Chi-restraints excluded: chain W residue 290 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 677 random chunks: chunk 403 optimal weight: 8.9990 chunk 260 optimal weight: 6.9990 chunk 389 optimal weight: 5.9990 chunk 196 optimal weight: 0.9990 chunk 128 optimal weight: 8.9990 chunk 126 optimal weight: 5.9990 chunk 414 optimal weight: 2.9990 chunk 444 optimal weight: 0.4980 chunk 322 optimal weight: 0.9980 chunk 60 optimal weight: 7.9990 chunk 512 optimal weight: 4.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 247 GLN ** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 58585 Z= 0.177 Angle : 0.672 27.224 79791 Z= 0.306 Chirality : 0.078 2.079 8889 Planarity : 0.003 0.056 9690 Dihedral : 15.458 157.237 9190 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.36 % Favored : 95.61 % Rotamer: Outliers : 1.06 % Allowed : 12.53 % Favored : 86.41 % 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: 0.19 (0.11), residues: 6657 helix: 1.24 (0.10), residues: 2688 sheet: -0.39 (0.19), residues: 744 loop : -0.66 (0.11), residues: 3225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP 4 476 HIS 0.011 0.001 HIS P 214 PHE 0.014 0.001 PHE A 601 TYR 0.012 0.001 TYR L 17 ARG 0.018 0.000 ARG Q 65 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13314 Ramachandran restraints generated. 6657 Oldfield, 0 Emsley, 6657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13314 Ramachandran restraints generated. 6657 Oldfield, 0 Emsley, 6657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 5937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 221 time to evaluate : 5.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 36 MET cc_start: 0.2196 (ttm) cc_final: 0.1790 (mtp) REVERT: 3 47 PHE cc_start: -0.2131 (OUTLIER) cc_final: -0.2907 (m-80) REVERT: 3 51 TRP cc_start: -0.0285 (OUTLIER) cc_final: -0.1008 (t60) REVERT: 4 385 MET cc_start: 0.0376 (tmm) cc_final: -0.1454 (tpt) REVERT: A 116 MET cc_start: 0.7253 (tmm) cc_final: 0.6624 (mtp) REVERT: A 505 MET cc_start: 0.8524 (tpt) cc_final: 0.8151 (mmm) REVERT: A 680 MET cc_start: 0.8931 (mmt) cc_final: 0.8434 (mmm) REVERT: A 780 MET cc_start: 0.9100 (mtm) cc_final: 0.8622 (mtp) REVERT: A 912 MET cc_start: 0.8146 (tpp) cc_final: 0.7752 (tpp) REVERT: A 1275 MET cc_start: 0.8551 (mmm) cc_final: 0.8260 (mmm) REVERT: A 1311 MET cc_start: 0.8458 (ptp) cc_final: 0.8177 (pmm) REVERT: A 1317 MET cc_start: 0.8415 (tmm) cc_final: 0.8135 (tmm) REVERT: B 59 MET cc_start: 0.8952 (ppp) cc_final: 0.8720 (ppp) REVERT: B 262 MET cc_start: 0.9300 (mpp) cc_final: 0.8833 (mpp) REVERT: B 870 MET cc_start: 0.8841 (ppp) cc_final: 0.8429 (ppp) REVERT: B 916 MET cc_start: 0.9095 (mmm) cc_final: 0.8836 (mmm) REVERT: B 1062 MET cc_start: 0.8500 (mpp) cc_final: 0.7841 (mpp) REVERT: B 1069 MET cc_start: 0.9019 (tmm) cc_final: 0.8730 (tmm) REVERT: E 56 THR cc_start: 0.8009 (OUTLIER) cc_final: 0.7718 (p) REVERT: F 57 MET cc_start: 0.8956 (tmm) cc_final: 0.8684 (tmm) REVERT: G 157 PHE cc_start: 0.7595 (OUTLIER) cc_final: 0.7071 (m-10) REVERT: H 37 MET cc_start: 0.9310 (mmm) cc_final: 0.8878 (mmt) REVERT: K 29 MET cc_start: 0.8056 (tmm) cc_final: 0.7704 (tmm) REVERT: K 104 MET cc_start: 0.8885 (mmm) cc_final: 0.8595 (mmm) REVERT: L 25 GLU cc_start: 0.8527 (mm-30) cc_final: 0.7982 (mm-30) REVERT: M 60 MET cc_start: 0.7911 (pmm) cc_final: 0.7623 (pmm) REVERT: M 247 MET cc_start: 0.8690 (tpp) cc_final: 0.8450 (tpt) REVERT: M 270 MET cc_start: 0.8576 (mmm) cc_final: 0.7692 (tpp) REVERT: M 292 MET cc_start: 0.8336 (tmm) cc_final: 0.7517 (tmm) REVERT: M 319 MET cc_start: 0.8552 (OUTLIER) cc_final: 0.8214 (ppp) REVERT: O 118 MET cc_start: 0.8453 (mmm) cc_final: 0.8025 (mmm) REVERT: O 333 MET cc_start: 0.7068 (tmm) cc_final: 0.6093 (tmm) REVERT: O 404 MET cc_start: 0.6898 (tpt) cc_final: 0.6337 (tpp) REVERT: O 531 MET cc_start: 0.8172 (tpp) cc_final: 0.7484 (tpp) outliers start: 63 outliers final: 44 residues processed: 271 average time/residue: 0.5069 time to fit residues: 244.2116 Evaluate side-chains 268 residues out of total 5937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 219 time to evaluate : 4.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 40 THR Chi-restraints excluded: chain 3 residue 47 PHE Chi-restraints excluded: chain 3 residue 51 TRP Chi-restraints excluded: chain 3 residue 405 VAL Chi-restraints excluded: chain 4 residue 176 PHE Chi-restraints excluded: chain 4 residue 226 LEU Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 994 THR Chi-restraints excluded: chain A residue 1164 ASP Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain B residue 305 LYS Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 653 ASP Chi-restraints excluded: chain B residue 689 MET Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 1004 PHE Chi-restraints excluded: chain B residue 1009 TYR Chi-restraints excluded: chain B residue 1015 MET Chi-restraints excluded: chain B residue 1047 LEU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain D residue 60 HIS Chi-restraints excluded: chain D residue 118 HIS Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 157 PHE Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 48 MET Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain L residue 56 ASP Chi-restraints excluded: chain M residue 41 ASP Chi-restraints excluded: chain M residue 319 MET Chi-restraints excluded: chain O residue 130 THR Chi-restraints excluded: chain O residue 133 MET Chi-restraints excluded: chain P residue 302 ILE Chi-restraints excluded: chain Q residue 110 MET Chi-restraints excluded: chain W residue 290 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 677 random chunks: chunk 593 optimal weight: 9.9990 chunk 625 optimal weight: 5.9990 chunk 570 optimal weight: 8.9990 chunk 608 optimal weight: 0.5980 chunk 624 optimal weight: 0.0010 chunk 365 optimal weight: 8.9990 chunk 264 optimal weight: 1.9990 chunk 477 optimal weight: 4.9990 chunk 186 optimal weight: 0.9990 chunk 549 optimal weight: 6.9990 chunk 575 optimal weight: 3.9990 overall best weight: 1.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1277 ASN ** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 58585 Z= 0.155 Angle : 0.669 27.219 79791 Z= 0.303 Chirality : 0.078 2.081 8889 Planarity : 0.003 0.053 9690 Dihedral : 15.462 156.813 9190 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.25 % Favored : 95.72 % Rotamer: Outliers : 0.88 % Allowed : 12.83 % Favored : 86.30 % 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: 0.22 (0.11), residues: 6657 helix: 1.27 (0.10), residues: 2687 sheet: -0.32 (0.19), residues: 731 loop : -0.66 (0.11), residues: 3239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP 4 476 HIS 0.014 0.001 HIS P 214 PHE 0.019 0.001 PHE D 69 TYR 0.015 0.001 TYR L 17 ARG 0.005 0.000 ARG W 285 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13314 Ramachandran restraints generated. 6657 Oldfield, 0 Emsley, 6657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13314 Ramachandran restraints generated. 6657 Oldfield, 0 Emsley, 6657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 5937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 225 time to evaluate : 4.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 36 MET cc_start: 0.1941 (ttm) cc_final: 0.1445 (mtp) REVERT: 3 47 PHE cc_start: -0.2123 (OUTLIER) cc_final: -0.2908 (m-80) REVERT: 3 51 TRP cc_start: -0.0294 (OUTLIER) cc_final: -0.1011 (t60) REVERT: 3 204 MET cc_start: 0.4578 (tmm) cc_final: 0.4296 (tmm) REVERT: 4 385 MET cc_start: 0.0298 (tmm) cc_final: -0.1276 (tpt) REVERT: 4 499 MET cc_start: 0.1454 (OUTLIER) cc_final: -0.0969 (ttp) REVERT: A 116 MET cc_start: 0.7234 (tmm) cc_final: 0.6594 (mtp) REVERT: A 505 MET cc_start: 0.8513 (tpt) cc_final: 0.8150 (mmm) REVERT: A 680 MET cc_start: 0.8914 (mmt) cc_final: 0.8383 (mmm) REVERT: A 780 MET cc_start: 0.9086 (mtm) cc_final: 0.8604 (mtp) REVERT: A 871 MET cc_start: 0.8514 (tpp) cc_final: 0.8307 (tpp) REVERT: A 912 MET cc_start: 0.8108 (tpp) cc_final: 0.7693 (tpp) REVERT: A 1048 MET cc_start: 0.7589 (tpp) cc_final: 0.7272 (mmm) REVERT: A 1280 MET cc_start: 0.7840 (pmm) cc_final: 0.7602 (pmm) REVERT: A 1288 MET cc_start: 0.9029 (OUTLIER) cc_final: 0.8605 (ptm) REVERT: A 1317 MET cc_start: 0.8428 (tmm) cc_final: 0.8149 (tmm) REVERT: B 59 MET cc_start: 0.8942 (ppp) cc_final: 0.8704 (ppp) REVERT: B 243 MET cc_start: 0.8716 (tpp) cc_final: 0.8443 (tpp) REVERT: B 262 MET cc_start: 0.9291 (mpp) cc_final: 0.8872 (mpp) REVERT: B 338 MET cc_start: 0.9344 (ttt) cc_final: 0.9112 (mtp) REVERT: B 431 MET cc_start: 0.8025 (tmm) cc_final: 0.7456 (tmm) REVERT: B 870 MET cc_start: 0.8813 (ppp) cc_final: 0.8409 (ppp) REVERT: B 916 MET cc_start: 0.9078 (mmm) cc_final: 0.8843 (mmm) REVERT: B 1062 MET cc_start: 0.8496 (mpp) cc_final: 0.7853 (mpp) REVERT: B 1069 MET cc_start: 0.9002 (tmm) cc_final: 0.8708 (tmm) REVERT: E 56 THR cc_start: 0.8223 (OUTLIER) cc_final: 0.7967 (p) REVERT: E 72 MET cc_start: 0.8048 (tpt) cc_final: 0.7651 (tpt) REVERT: F 57 MET cc_start: 0.8961 (tmm) cc_final: 0.8683 (tmm) REVERT: G 157 PHE cc_start: 0.7567 (OUTLIER) cc_final: 0.7058 (m-10) REVERT: H 37 MET cc_start: 0.9306 (mmm) cc_final: 0.8909 (mmt) REVERT: J 54 ASP cc_start: 0.8022 (t70) cc_final: 0.7643 (t0) REVERT: K 29 MET cc_start: 0.8064 (tmm) cc_final: 0.7445 (tmm) REVERT: K 104 MET cc_start: 0.8860 (mmm) cc_final: 0.8428 (mmm) REVERT: L 25 GLU cc_start: 0.8519 (mm-30) cc_final: 0.8028 (mm-30) REVERT: M 60 MET cc_start: 0.7996 (pmm) cc_final: 0.7731 (pmm) REVERT: M 247 MET cc_start: 0.8677 (tpp) cc_final: 0.8439 (tpt) REVERT: M 270 MET cc_start: 0.8605 (mmm) cc_final: 0.7748 (tpp) REVERT: M 292 MET cc_start: 0.8296 (tmm) cc_final: 0.7459 (tmm) REVERT: M 319 MET cc_start: 0.8383 (OUTLIER) cc_final: 0.8128 (ppp) REVERT: O 118 MET cc_start: 0.8493 (mmm) cc_final: 0.8084 (mmm) REVERT: O 133 MET cc_start: 0.3281 (OUTLIER) cc_final: 0.2932 (ppp) REVERT: O 333 MET cc_start: 0.7309 (tmm) cc_final: 0.6750 (tmm) REVERT: O 404 MET cc_start: 0.6880 (tpt) cc_final: 0.6183 (tpp) REVERT: O 531 MET cc_start: 0.8010 (tpp) cc_final: 0.7321 (tpp) REVERT: P 267 MET cc_start: 0.3169 (tmm) cc_final: 0.2789 (tpt) outliers start: 52 outliers final: 39 residues processed: 266 average time/residue: 0.5269 time to fit residues: 248.3003 Evaluate side-chains 269 residues out of total 5937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 222 time to evaluate : 4.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 40 THR Chi-restraints excluded: chain 3 residue 47 PHE Chi-restraints excluded: chain 3 residue 51 TRP Chi-restraints excluded: chain 3 residue 405 VAL Chi-restraints excluded: chain 4 residue 176 PHE Chi-restraints excluded: chain 4 residue 226 LEU Chi-restraints excluded: chain 4 residue 499 MET Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 994 THR Chi-restraints excluded: chain A residue 1288 MET Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain B residue 305 LYS Chi-restraints excluded: chain B residue 653 ASP Chi-restraints excluded: chain B residue 689 MET Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 1004 PHE Chi-restraints excluded: chain B residue 1009 TYR Chi-restraints excluded: chain B residue 1015 MET Chi-restraints excluded: chain B residue 1047 LEU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain D residue 60 HIS Chi-restraints excluded: chain D residue 118 HIS Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 157 PHE Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 48 MET Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain M residue 319 MET Chi-restraints excluded: chain O residue 133 MET Chi-restraints excluded: chain P residue 302 ILE Chi-restraints excluded: chain Q residue 110 MET Chi-restraints excluded: chain W residue 290 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 677 random chunks: chunk 605 optimal weight: 5.9990 chunk 399 optimal weight: 0.9990 chunk 642 optimal weight: 3.9990 chunk 392 optimal weight: 7.9990 chunk 305 optimal weight: 0.9990 chunk 446 optimal weight: 0.5980 chunk 674 optimal weight: 9.9990 chunk 620 optimal weight: 3.9990 chunk 537 optimal weight: 20.0000 chunk 55 optimal weight: 6.9990 chunk 414 optimal weight: 6.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1277 ASN ** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 58585 Z= 0.176 Angle : 0.676 27.215 79791 Z= 0.306 Chirality : 0.078 2.079 8889 Planarity : 0.003 0.049 9690 Dihedral : 15.490 156.693 9190 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.27 % Favored : 95.70 % Rotamer: Outliers : 0.89 % Allowed : 12.86 % Favored : 86.25 % 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: 0.24 (0.11), residues: 6657 helix: 1.30 (0.10), residues: 2689 sheet: -0.36 (0.19), residues: 756 loop : -0.66 (0.11), residues: 3212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP 4 476 HIS 0.013 0.001 HIS P 214 PHE 0.013 0.001 PHE A 462 TYR 0.014 0.001 TYR L 45 ARG 0.005 0.000 ARG W 285 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13314 Ramachandran restraints generated. 6657 Oldfield, 0 Emsley, 6657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13314 Ramachandran restraints generated. 6657 Oldfield, 0 Emsley, 6657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 5937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 220 time to evaluate : 4.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 36 MET cc_start: 0.1751 (ttm) cc_final: 0.1330 (mtp) REVERT: 3 47 PHE cc_start: -0.1927 (OUTLIER) cc_final: -0.2730 (m-80) REVERT: 3 51 TRP cc_start: -0.0240 (OUTLIER) cc_final: -0.0980 (t60) REVERT: 3 204 MET cc_start: 0.4570 (tmm) cc_final: 0.4307 (tmm) REVERT: 4 385 MET cc_start: 0.0290 (tmm) cc_final: -0.1277 (tpt) REVERT: 4 499 MET cc_start: 0.1518 (mmm) cc_final: -0.1105 (ttp) REVERT: A 116 MET cc_start: 0.7222 (tmm) cc_final: 0.6766 (mtp) REVERT: A 680 MET cc_start: 0.8937 (mmt) cc_final: 0.8402 (mmm) REVERT: A 780 MET cc_start: 0.9102 (mtm) cc_final: 0.8664 (mtp) REVERT: A 871 MET cc_start: 0.8526 (tpp) cc_final: 0.8314 (tpp) REVERT: A 912 MET cc_start: 0.8080 (tpp) cc_final: 0.7669 (tpp) REVERT: A 1280 MET cc_start: 0.8169 (pmm) cc_final: 0.7714 (pmm) REVERT: A 1288 MET cc_start: 0.9057 (OUTLIER) cc_final: 0.8615 (ptm) REVERT: A 1311 MET cc_start: 0.8522 (ptp) cc_final: 0.8252 (pmm) REVERT: A 1317 MET cc_start: 0.8421 (tmm) cc_final: 0.8140 (tmm) REVERT: B 59 MET cc_start: 0.8951 (ppp) cc_final: 0.8708 (ppp) REVERT: B 243 MET cc_start: 0.8720 (tpp) cc_final: 0.8453 (tpp) REVERT: B 262 MET cc_start: 0.9297 (mpp) cc_final: 0.8850 (mpp) REVERT: B 431 MET cc_start: 0.7932 (tmm) cc_final: 0.7492 (tmm) REVERT: B 870 MET cc_start: 0.8890 (ppp) cc_final: 0.8484 (ppp) REVERT: B 916 MET cc_start: 0.9094 (mmm) cc_final: 0.8839 (mmm) REVERT: B 1062 MET cc_start: 0.8512 (mpp) cc_final: 0.7825 (mpp) REVERT: B 1069 MET cc_start: 0.9006 (tmm) cc_final: 0.8551 (tmm) REVERT: E 56 THR cc_start: 0.8233 (OUTLIER) cc_final: 0.7977 (p) REVERT: E 72 MET cc_start: 0.8119 (tpt) cc_final: 0.7886 (tpt) REVERT: F 57 MET cc_start: 0.8960 (tmm) cc_final: 0.8668 (tmm) REVERT: G 37 LYS cc_start: 0.9241 (mttt) cc_final: 0.8999 (mmmm) REVERT: G 157 PHE cc_start: 0.7609 (OUTLIER) cc_final: 0.7081 (m-10) REVERT: H 37 MET cc_start: 0.9309 (mmm) cc_final: 0.8815 (mmm) REVERT: K 29 MET cc_start: 0.8061 (tmm) cc_final: 0.7439 (tmm) REVERT: K 104 MET cc_start: 0.8876 (mmm) cc_final: 0.8459 (mmm) REVERT: L 25 GLU cc_start: 0.8544 (mm-30) cc_final: 0.7911 (mm-30) REVERT: M 60 MET cc_start: 0.8014 (pmm) cc_final: 0.7739 (pmm) REVERT: M 270 MET cc_start: 0.8577 (mmm) cc_final: 0.7691 (tpp) REVERT: M 292 MET cc_start: 0.8329 (tmm) cc_final: 0.7470 (tmm) REVERT: M 319 MET cc_start: 0.8363 (OUTLIER) cc_final: 0.8157 (ppp) REVERT: O 133 MET cc_start: 0.3593 (OUTLIER) cc_final: 0.3188 (ppp) REVERT: O 139 MET cc_start: 0.2279 (ptp) cc_final: 0.2065 (ptp) REVERT: O 333 MET cc_start: 0.7038 (tmm) cc_final: 0.6487 (tmm) REVERT: O 404 MET cc_start: 0.6631 (tpt) cc_final: 0.5159 (tmm) REVERT: O 531 MET cc_start: 0.8017 (tpp) cc_final: 0.7261 (tpp) outliers start: 53 outliers final: 44 residues processed: 261 average time/residue: 0.5248 time to fit residues: 242.0859 Evaluate side-chains 270 residues out of total 5937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 219 time to evaluate : 4.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 40 THR Chi-restraints excluded: chain 3 residue 47 PHE Chi-restraints excluded: chain 3 residue 51 TRP Chi-restraints excluded: chain 3 residue 405 VAL Chi-restraints excluded: chain 4 residue 176 PHE Chi-restraints excluded: chain 4 residue 226 LEU Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 994 THR Chi-restraints excluded: chain A residue 1288 MET Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain B residue 305 LYS Chi-restraints excluded: chain B residue 653 ASP Chi-restraints excluded: chain B residue 689 MET Chi-restraints excluded: chain B residue 744 MET Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 1004 PHE Chi-restraints excluded: chain B residue 1009 TYR Chi-restraints excluded: chain B residue 1015 MET Chi-restraints excluded: chain B residue 1047 LEU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain D residue 60 HIS Chi-restraints excluded: chain D residue 118 HIS Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain G residue 41 ASN Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 157 PHE Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 48 MET Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain M residue 41 ASP Chi-restraints excluded: chain M residue 319 MET Chi-restraints excluded: chain M residue 357 MET Chi-restraints excluded: chain O residue 130 THR Chi-restraints excluded: chain O residue 133 MET Chi-restraints excluded: chain P residue 302 ILE Chi-restraints excluded: chain Q residue 110 MET Chi-restraints excluded: chain W residue 290 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 677 random chunks: chunk 329 optimal weight: 3.9990 chunk 426 optimal weight: 8.9990 chunk 572 optimal weight: 50.0000 chunk 164 optimal weight: 0.9980 chunk 495 optimal weight: 8.9990 chunk 79 optimal weight: 10.0000 chunk 149 optimal weight: 0.4980 chunk 537 optimal weight: 20.0000 chunk 225 optimal weight: 0.8980 chunk 552 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 overall best weight: 2.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 26 ASN ** M 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.059279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.041613 restraints weight = 627281.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.042206 restraints weight = 338682.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.042106 restraints weight = 212092.165| |-----------------------------------------------------------------------------| r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3080 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 83 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 83 | |-----------------------------------------------------------------------------| r_final: 0.3080 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 58585 Z= 0.192 Angle : 0.687 27.216 79791 Z= 0.311 Chirality : 0.078 2.081 8889 Planarity : 0.003 0.047 9690 Dihedral : 15.525 155.654 9190 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.37 % Favored : 95.60 % Rotamer: Outliers : 0.93 % Allowed : 12.83 % Favored : 86.25 % 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: 0.26 (0.11), residues: 6657 helix: 1.32 (0.10), residues: 2677 sheet: -0.38 (0.19), residues: 750 loop : -0.63 (0.11), residues: 3230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 297 HIS 0.015 0.001 HIS P 214 PHE 0.024 0.001 PHE H 56 TYR 0.014 0.001 TYR A1333 ARG 0.005 0.000 ARG W 285 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7375.88 seconds wall clock time: 135 minutes 3.42 seconds (8103.42 seconds total)