Starting phenix.real_space_refine on Mon Mar 11 15:25:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iue_35719/03_2024/8iue_35719_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iue_35719/03_2024/8iue_35719.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iue_35719/03_2024/8iue_35719.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iue_35719/03_2024/8iue_35719.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iue_35719/03_2024/8iue_35719_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iue_35719/03_2024/8iue_35719_updated.pdb" } resolution = 4.1 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Fe 4 7.16 5 Zn 8 6.06 5 P 144 5.49 5 Mg 1 5.21 5 S 359 5.16 5 C 36221 2.51 5 N 10129 2.21 5 O 11061 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 488": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 848": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 900": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 958": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 772": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 851": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 918": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 958": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1094": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 89": "OE1" <-> "OE2" Residue "K PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 47": "OE1" <-> "OE2" Residue "K PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 54": "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 ARG 133": "NH1" <-> "NH2" Residue "1 PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ASP 91": "OD1" <-> "OD2" Residue "3 PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 337": "NH1" <-> "NH2" Residue "3 TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 152": "OD1" <-> "OD2" Residue "4 GLU 163": "OE1" <-> "OE2" Residue "4 GLU 177": "OE1" <-> "OE2" Residue "4 GLU 178": "OE1" <-> "OE2" Residue "4 PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 279": "OE1" <-> "OE2" Residue "4 PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 390": "NH1" <-> "NH2" Residue "4 TYR 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 407": "OE1" <-> "OE2" Residue "4 GLU 408": "OE1" <-> "OE2" Residue "4 GLU 482": "OE1" <-> "OE2" Residue "U TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 299": "NH1" <-> "NH2" Residue "V TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 52": "OE1" <-> "OE2" Residue "V GLU 115": "OE1" <-> "OE2" Residue "V TYR 153": "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 "W TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 364": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 57927 Number of models: 1 Model: "" Number of chains: 32 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: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 848 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "J" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 512 Classifications: {'peptide': 65} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 62} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 822 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 4, 'TRANS': 98} Chain: "L" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 388 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "M" Number of atoms: 3382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3382 Classifications: {'peptide': 422} Link IDs: {'PTRANS': 23, 'TRANS': 398} Chain breaks: 1 Chain: "N" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1128 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 6, 'TRANS': 139} Chain breaks: 2 Chain: "O" Number of atoms: 4075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 4075 Classifications: {'peptide': 512} Link IDs: {'PTRANS': 22, 'TRANS': 489} Chain breaks: 1 Chain: "P" Number of atoms: 2403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2403 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 12, 'TRANS': 290} Chain: "Q" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 754 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 12, 'TRANS': 74} Chain: "X" Number of atoms: 1517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1517 Classifications: {'DNA': 74} Link IDs: {'rna3p': 73} Chain breaks: 1 Chain: "Y" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 1437 Classifications: {'DNA': 70} Link IDs: {'rna3p': 69} Chain breaks: 1 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: "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: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 543 SG CYS A 69 108.334 133.848 147.041 1.00126.90 S ATOM 565 SG CYS A 72 108.718 133.394 150.655 1.00125.00 S ATOM 613 SG CYS A 79 106.554 130.986 149.021 1.00128.92 S ATOM 854 SG CYS A 109 65.955 157.197 147.066 1.00135.32 S ATOM 876 SG CYS A 112 67.157 159.385 150.170 1.00134.77 S ATOM 1245 SG CYS A 156 63.458 159.011 149.983 1.00154.63 S ATOM 1271 SG CYS A 159 64.647 161.441 147.795 1.00149.24 S ATOM 19142 SG CYS B1080 99.535 141.365 162.797 1.00117.16 S ATOM 19161 SG CYS B1083 96.842 141.589 159.796 1.00117.13 S ATOM 19227 SG CYS B1092 100.319 141.544 158.837 1.00113.04 S ATOM 19255 SG CYS B1095 98.399 144.966 160.368 1.00118.73 S ATOM 28165 SG CYS I 5 24.146 116.485 110.848 1.00157.68 S ATOM 28182 SG CYS I 8 28.403 118.232 110.093 1.00159.27 S ATOM 28312 SG CYS I 25 27.175 119.695 113.222 1.00160.84 S ATOM 28333 SG CYS I 28 24.983 119.797 110.182 1.00152.92 S ATOM 28654 SG CYS I 69 58.048 78.564 170.915 1.00274.12 S ATOM 28676 SG CYS I 72 55.748 79.130 173.488 1.00275.60 S ATOM 28888 SG CYS I 97 54.759 79.565 170.067 1.00272.04 S ATOM 29027 SG CYS J 7 101.416 62.910 142.662 1.00 97.85 S ATOM 29051 SG CYS J 10 103.407 60.228 144.945 1.00100.35 S ATOM 29315 SG CYS J 44 99.856 59.778 144.446 1.00102.73 S ATOM 29321 SG CYS J 45 102.429 58.416 141.821 1.00104.68 S ATOM 30364 SG CYS L 19 117.105 87.080 111.765 1.00121.79 S ATOM 30500 SG CYS L 36 118.084 89.513 109.264 1.00139.15 S ATOM 30526 SG CYS L 39 114.287 89.136 107.688 1.00138.13 S ATOM 54131 SG CYS V 7 128.632 116.300 156.827 1.00178.33 S ATOM 54309 SG CYS V 31 130.202 112.129 158.941 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: 22.91, per 1000 atoms: 0.40 Number of scatterers: 57927 At special positions: 0 Unit cell: (164.082, 217.442, 224.112, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 8 29.99 Fe 4 26.01 S 359 16.00 P 144 15.00 Mg 1 11.99 O 11061 8.00 N 10129 7.00 C 36221 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 17.01 Conformation dependent library (CDL) restraints added in 7.5 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 P 401 " pdb="FE1 SF4 P 401 " - pdb=" SG CYS P 290 " pdb="FE4 SF4 P 401 " - pdb=" SG CYS P 307 " pdb="FE3 SF4 P 401 " - pdb=" SG CYS P 287 " pdb="FE2 SF4 P 401 " - pdb=" SG CYS P 296 " Number of angles added : 12 Zn2+ tetrahedral coordination pdb=" ZN A1401 " pdb="ZN ZN A1401 " - pdb=" NE2 HIS A 82 " pdb="ZN ZN A1401 " - pdb=" SG CYS A 79 " pdb="ZN ZN A1401 " - pdb=" SG CYS A 72 " pdb="ZN ZN A1401 " - pdb=" SG CYS A 69 " pdb=" ZN A1402 " pdb="ZN ZN A1402 " - pdb=" SG CYS A 109 " pdb="ZN ZN A1402 " - pdb=" SG CYS A 112 " pdb="ZN ZN A1402 " - pdb=" SG CYS A 159 " pdb="ZN ZN A1402 " - pdb=" SG CYS A 156 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1095 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1080 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1083 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1092 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 8 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 28 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 5 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 25 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 69 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 72 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 97 " pdb=" ZN J2000 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 44 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 7 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 45 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 10 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 39 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 19 " pdb=" ZN V 700 " pdb="ZN ZN V 700 " - pdb=" SG CYS V 7 " pdb="ZN ZN V 700 " - pdb=" SG CYS V 31 " Number of angles added : 27 13618 Ramachandran restraints generated. 6809 Oldfield, 0 Emsley, 6809 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12964 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 261 helices and 62 sheets defined 37.9% alpha, 10.8% beta 25 base pairs and 88 stacking pairs defined. Time for finding SS restraints: 18.35 Creating SS restraints... Processing helix chain 'A' and resid 25 through 31 Processing helix chain 'A' and resid 58 through 60 No H-bonds generated for 'chain 'A' and resid 58 through 60' Processing helix chain 'A' and resid 98 through 107 Processing helix chain 'A' and resid 119 through 129 Processing helix chain 'A' and resid 136 through 152 Processing helix chain 'A' and resid 188 through 196 Processing helix chain 'A' and resid 198 through 203 Processing helix chain 'A' and resid 205 through 209 Proline residue: A 209 - end of helix Processing helix chain 'A' and resid 220 through 229 removed outlier: 3.607A pdb=" N ARG A 229 " --> pdb=" O ASN A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 238 No H-bonds generated for 'chain 'A' and resid 236 through 238' Processing helix chain 'A' and resid 247 through 249 No H-bonds generated for 'chain 'A' and resid 247 through 249' Processing helix chain 'A' and resid 278 through 299 Processing helix chain 'A' and resid 303 through 321 Processing helix chain 'A' and resid 341 through 345 Processing helix chain 'A' and resid 351 through 355 Processing helix chain 'A' and resid 384 through 387 No H-bonds generated for 'chain 'A' and resid 384 through 387' Processing helix chain 'A' and resid 401 through 410 Processing helix chain 'A' and resid 437 through 442 Processing helix chain 'A' and resid 470 through 472 No H-bonds generated for 'chain 'A' and resid 470 through 472' Processing helix chain 'A' and resid 490 through 496 removed outlier: 4.407A 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 521 Processing helix chain 'A' and resid 546 through 552 Processing helix chain 'A' and resid 561 through 571 removed outlier: 4.411A pdb=" N ILE A 571 " --> pdb=" O ILE A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 578 removed outlier: 3.944A pdb=" N LYS A 578 " --> pdb=" O LYS A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 605 removed outlier: 3.630A pdb=" N ILE A 604 " --> pdb=" O ILE A 600 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU A 605 " --> pdb=" O PHE A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 671 Processing helix chain 'A' and resid 673 through 694 Proline residue: A 688 - end of helix Processing helix chain 'A' and resid 700 through 702 No H-bonds generated for 'chain 'A' and resid 700 through 702' Processing helix chain 'A' and resid 707 through 732 Processing helix chain 'A' and resid 744 through 770 Processing helix chain 'A' and resid 776 through 783 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 878 removed outlier: 3.723A 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 921 through 931 Processing helix chain 'A' and resid 942 through 953 Processing helix chain 'A' and resid 963 through 987 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 1046 Proline residue: A1044 - end of helix Processing helix chain 'A' and resid 1067 through 1075 Processing helix chain 'A' and resid 1095 through 1105 Processing helix chain 'A' and resid 1110 through 1113 No H-bonds generated for 'chain 'A' and resid 1110 through 1113' Processing helix chain 'A' and resid 1134 through 1139 Processing helix chain 'A' and resid 1146 through 1152 Processing helix chain 'A' and resid 1189 through 1196 Processing helix chain 'A' and resid 1232 through 1237 Processing helix chain 'A' and resid 1243 through 1245 No H-bonds generated for 'chain 'A' and resid 1243 through 1245' Processing helix chain 'A' and resid 1251 through 1278 removed outlier: 7.933A pdb=" N ILE A1260 " --> pdb=" O LYS A1256 " (cutoff:3.500A) removed outlier: 9.610A pdb=" N GLU A1261 " --> pdb=" O THR A1257 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ALA A1262 " --> pdb=" O LEU A1258 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N HIS A1278 " --> pdb=" O THR A1274 " (cutoff:3.500A) Processing helix chain 'A' and resid 1284 through 1294 Processing helix chain 'A' and resid 1305 through 1311 Processing helix chain 'A' and resid 1315 through 1321 Processing helix chain 'A' and resid 1324 through 1334 Processing helix chain 'A' and resid 1343 through 1349 Processing helix chain 'A' and resid 1356 through 1359 removed outlier: 3.642A pdb=" N LEU A1359 " --> pdb=" O GLY A1356 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1356 through 1359' Processing helix chain 'B' and resid 26 through 35 Proline residue: B 31 - end of helix Processing helix chain 'B' and resid 41 through 52 Processing helix chain 'B' and resid 54 through 61 Processing helix chain 'B' and resid 99 through 105 Processing helix chain 'B' and resid 152 through 158 Processing helix chain 'B' and resid 236 through 242 Processing helix chain 'B' and resid 248 through 255 Processing helix chain 'B' and resid 259 through 274 Proline residue: B 267 - end of helix Processing helix chain 'B' and resid 280 through 289 Processing helix chain 'B' and resid 307 through 314 Processing helix chain 'B' and resid 329 through 345 Processing helix chain 'B' and resid 357 through 359 No H-bonds generated for 'chain 'B' and resid 357 through 359' Processing helix chain 'B' and resid 365 through 391 Processing helix chain 'B' and resid 402 through 405 Processing helix chain 'B' and resid 408 through 421 removed outlier: 3.564A pdb=" N THR B 412 " --> pdb=" O GLN B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 453 removed outlier: 3.946A pdb=" N THR B 453 " --> pdb=" O LEU B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 475 No H-bonds generated for 'chain 'B' and resid 473 through 475' Processing helix chain 'B' and resid 509 through 517 Processing helix chain 'B' and resid 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 639 Processing helix chain 'B' and resid 661 through 664 Processing helix chain 'B' and resid 669 through 671 No H-bonds generated for 'chain 'B' and resid 669 through 671' Processing helix chain 'B' and resid 675 through 677 No H-bonds generated for 'chain 'B' and resid 675 through 677' Processing helix chain 'B' and resid 680 through 692 removed outlier: 3.710A pdb=" N GLN B 692 " --> pdb=" O ALA B 688 " (cutoff:3.500A) Processing helix chain 'B' and resid 723 through 728 Processing helix chain 'B' and resid 730 through 732 No H-bonds generated for 'chain 'B' and resid 730 through 732' Processing helix chain 'B' and resid 759 through 763 Processing helix chain 'B' and resid 931 through 937 Proline residue: B 935 - end of helix Processing helix chain 'B' and resid 940 through 955 Processing helix chain 'B' and resid 969 through 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 1049 through 1058 Processing helix chain 'B' and resid 1061 through 1068 Processing helix chain 'B' and resid 1108 through 1119 Processing helix chain 'C' and resid 3 through 12 Processing helix chain 'C' and resid 42 through 48 Processing helix chain 'C' and resid 70 through 82 Processing helix chain 'C' and resid 103 through 111 Processing helix chain 'C' and resid 119 through 121 No H-bonds generated for 'chain 'C' and resid 119 through 121' Processing helix chain 'C' and resid 134 through 136 No H-bonds generated for 'chain 'C' and resid 134 through 136' 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 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 248 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 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: 4.065A pdb=" N SER D 75 " --> pdb=" O THR D 71 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N HIS D 76 " --> pdb=" O ALA D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 89 Processing helix chain 'D' and resid 95 through 98 No H-bonds generated for 'chain 'D' and resid 95 through 98' Processing helix chain 'D' and resid 112 through 121 Processing helix chain 'E' and resid 5 through 23 Processing helix chain 'E' and resid 30 through 33 No H-bonds generated for 'chain 'E' and resid 30 through 33' Processing helix chain 'E' and resid 37 through 43 Processing helix chain 'E' and resid 84 through 97 Processing helix chain 'E' and resid 112 through 119 Processing helix chain 'E' and resid 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 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 removed outlier: 3.918A pdb=" N ALA G 27 " --> pdb=" O ASN G 23 " (cutoff:3.500A) Processing helix chain 'H' and resid 84 through 87 Processing helix chain 'I' and resid 56 through 59 No H-bonds generated for 'chain 'I' and resid 56 through 59' Processing helix chain 'J' and resid 18 through 26 Processing helix chain 'J' and resid 31 through 37 Processing helix chain 'J' and resid 43 through 50 Processing helix chain 'J' and resid 56 through 62 removed outlier: 3.566A pdb=" N TYR J 62 " --> pdb=" O LYS J 58 " (cutoff:3.500A) Processing helix chain 'K' and resid 49 through 60 Processing helix chain 'K' and resid 94 through 125 Processing helix chain 'M' and resid 71 through 81 Processing helix chain 'M' and resid 141 through 160 Processing helix chain 'M' and resid 183 through 190 Processing helix chain 'M' and resid 193 through 202 Processing helix chain 'M' and resid 216 through 225 removed outlier: 3.967A pdb=" N GLN M 223 " --> pdb=" O GLU M 219 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N TYR M 224 " --> pdb=" O HIS M 220 " (cutoff:3.500A) removed outlier: 4.413A 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 274 Processing helix chain 'M' and resid 278 through 288 Processing helix chain 'M' and resid 294 through 301 Processing helix chain 'M' and resid 307 through 317 removed outlier: 4.056A pdb=" N LYS M 316 " --> pdb=" O ARG M 312 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL M 317 " --> pdb=" O GLY M 313 " (cutoff:3.500A) Processing helix chain 'M' and resid 329 through 332 No H-bonds generated for 'chain 'M' and resid 329 through 332' Processing helix chain 'M' and resid 346 through 362 Processing helix chain 'M' and resid 368 through 375 Processing helix chain 'M' and resid 379 through 389 removed outlier: 4.005A pdb=" N HIS M 388 " --> pdb=" O ASP M 384 " (cutoff:3.500A) removed outlier: 4.443A 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 removed outlier: 3.676A pdb=" N GLY M 425 " --> pdb=" O MET M 421 " (cutoff:3.500A) Processing helix chain 'N' and resid 148 through 150 No H-bonds generated for 'chain 'N' and resid 148 through 150' Processing helix chain 'N' and resid 250 through 258 Processing helix chain 'N' and resid 333 through 335 No H-bonds generated for 'chain 'N' and resid 333 through 335' Processing helix chain 'N' and resid 389 through 395 Processing helix chain 'O' and resid 3 through 16 Processing helix chain 'O' and resid 20 through 31 removed outlier: 4.171A pdb=" N ILE O 24 " --> pdb=" O ILE O 20 " (cutoff:3.500A) Processing helix chain 'O' and resid 36 through 43 Processing helix chain 'O' and resid 47 through 59 Processing helix chain 'O' and resid 69 through 71 No H-bonds generated for 'chain 'O' and resid 69 through 71' Processing helix chain 'O' and resid 79 through 97 removed outlier: 4.531A pdb=" N LEU O 86 " --> pdb=" O VAL O 82 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ARG O 87 " --> pdb=" O LEU O 83 " (cutoff:3.500A) removed outlier: 4.129A 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 130 Processing helix chain 'O' and resid 142 through 153 Processing helix chain 'O' and resid 185 through 187 No H-bonds generated for 'chain 'O' and resid 185 through 187' Processing helix chain 'O' and resid 239 through 258 Processing helix chain 'O' and resid 261 through 277 removed outlier: 4.715A pdb=" N ILE O 276 " --> pdb=" O ARG O 272 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N THR O 277 " --> pdb=" O MET O 273 " (cutoff:3.500A) Processing helix chain 'O' and resid 290 through 296 Processing helix chain 'O' and resid 305 through 316 Processing helix chain 'O' and resid 338 through 358 Processing helix chain 'O' and resid 360 through 371 Processing helix chain 'O' and resid 377 through 384 Processing helix chain 'O' and resid 391 through 399 Processing helix chain 'O' and resid 417 through 419 No H-bonds generated for 'chain 'O' and resid 417 through 419' Processing helix chain 'O' and resid 428 through 456 Processing helix chain 'O' and resid 458 through 472 removed outlier: 4.108A pdb=" N ILE O 471 " --> pdb=" O VAL O 467 " (cutoff:3.500A) Processing helix chain 'O' and resid 481 through 483 No H-bonds generated for 'chain 'O' and resid 481 through 483' Processing helix chain 'O' and resid 496 through 529 removed outlier: 3.648A pdb=" N GLU O 518 " --> pdb=" O ILE O 514 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR O 519 " --> pdb=" O GLN O 515 " (cutoff:3.500A) Processing helix chain 'P' and resid 15 through 28 Processing helix chain 'P' and resid 35 through 41 Processing helix chain 'P' and resid 47 through 60 Processing helix chain 'P' and resid 78 through 80 No H-bonds generated for 'chain 'P' and resid 78 through 80' Processing helix chain 'P' and resid 90 through 105 removed outlier: 3.779A pdb=" N ILE P 98 " --> pdb=" O LEU P 94 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N ASN P 104 " --> pdb=" O GLU P 100 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LYS P 105 " --> pdb=" O ASP P 101 " (cutoff:3.500A) Processing helix chain 'P' and resid 109 through 116 Processing helix chain 'P' and resid 120 through 132 removed outlier: 4.383A pdb=" N LYS P 125 " --> pdb=" O THR P 121 " (cutoff:3.500A) 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 244 Processing helix chain 'P' and resid 282 through 284 No H-bonds generated for 'chain 'P' and resid 282 through 284' Processing helix chain 'P' and resid 293 through 295 No H-bonds generated for 'chain 'P' and resid 293 through 295' Processing helix chain 'P' and resid 308 through 315 Processing helix chain 'Q' and resid 52 through 67 Processing helix chain 'Q' and resid 87 through 92 removed outlier: 4.117A pdb=" N ARG Q 90 " --> pdb=" O TYR Q 87 " (cutoff:3.500A) Processing helix chain 'Q' and resid 108 through 110 No H-bonds generated for 'chain 'Q' and resid 108 through 110' Processing helix chain '1' and resid 5 through 20 removed outlier: 3.605A pdb=" N THR 1 9 " --> pdb=" O PRO 1 5 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLU 1 12 " --> pdb=" O GLN 1 8 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER 1 16 " --> pdb=" O GLU 1 12 " (cutoff:3.500A) removed outlier: 3.944A 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: 3.903A pdb=" N TYR 1 65 " --> pdb=" O LEU 1 61 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N PHE 1 66 " --> pdb=" O ALA 1 62 " (cutoff:3.500A) Processing helix chain '1' and resid 72 through 87 Processing helix chain '1' and resid 103 through 116 removed outlier: 3.831A pdb=" N VAL 1 107 " --> pdb=" O ASP 1 103 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N LEU 1 108 " --> pdb=" O TRP 1 104 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LYS 1 109 " --> pdb=" O ASP 1 105 " (cutoff:3.500A) Processing helix chain '1' and resid 120 through 132 removed outlier: 3.614A pdb=" N PHE 1 126 " --> pdb=" O ALA 1 122 " (cutoff:3.500A) Processing helix chain '3' and resid 44 through 53 removed outlier: 4.988A pdb=" N TRP 3 51 " --> pdb=" O GLY 3 48 " (cutoff:3.500A) Processing helix chain '3' and resid 77 through 89 removed outlier: 4.241A 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 155 through 163 removed outlier: 4.122A pdb=" N GLU 3 160 " --> pdb=" O VAL 3 156 " (cutoff:3.500A) removed outlier: 4.221A 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: 3.954A pdb=" N THR 3 273 " --> pdb=" O LEU 3 270 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILE 3 274 " --> pdb=" O SER 3 271 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ILE 3 275 " --> pdb=" O ARG 3 272 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N TRP 3 277 " --> pdb=" O ILE 3 274 " (cutoff:3.500A) Processing helix chain '3' and resid 298 through 300 No H-bonds generated for 'chain '3' and resid 298 through 300' Processing helix chain '3' and resid 381 through 388 removed outlier: 4.024A 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: 3.612A 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: 4.281A pdb=" N LYS 4 336 " --> pdb=" O GLN 4 332 " (cutoff:3.500A) Processing helix chain '4' and resid 352 through 364 removed outlier: 3.622A pdb=" N MET 4 356 " --> pdb=" O GLU 4 352 " (cutoff:3.500A) Processing helix chain '4' and resid 372 through 378 Processing helix chain '4' and resid 388 through 391 Processing helix chain '4' and resid 408 through 411 No H-bonds generated for 'chain '4' and resid 408 through 411' Processing helix chain '4' and resid 413 through 418 Processing helix chain '4' and resid 424 through 428 removed outlier: 3.732A pdb=" N ARG 4 428 " --> pdb=" O PHE 4 425 " (cutoff:3.500A) Processing helix chain '4' and resid 436 through 447 removed outlier: 3.991A pdb=" N ASP 4 441 " --> pdb=" O ALA 4 437 " (cutoff:3.500A) Processing helix chain '4' and resid 460 through 467 Processing helix chain '4' and resid 478 through 481 Processing helix chain '4' and resid 488 through 498 removed outlier: 5.354A pdb=" N SER 4 493 " --> pdb=" O SER 4 489 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N LYS 4 494 " --> pdb=" O GLN 4 490 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ILE 4 497 " --> pdb=" O SER 4 493 " (cutoff:3.500A) Processing helix chain '4' and resid 505 through 512 removed outlier: 4.781A pdb=" N ARG 4 511 " --> pdb=" O ARG 4 507 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N ALA 4 512 " --> pdb=" O ARG 4 508 " (cutoff:3.500A) Processing helix chain 'U' and resid 180 through 185 Processing helix chain 'U' and resid 227 through 244 Processing helix chain 'U' and resid 270 through 276 removed outlier: 3.850A pdb=" N VAL U 274 " --> pdb=" O LEU U 270 " (cutoff:3.500A) Processing helix chain 'U' and resid 278 through 280 No H-bonds generated for 'chain 'U' and resid 278 through 280' Processing helix chain 'U' and resid 318 through 333 Proline residue: U 330 - end of helix Processing helix chain 'V' and resid 44 through 47 No H-bonds generated for 'chain 'V' and resid 44 through 47' Processing helix chain 'V' and resid 67 through 82 Processing helix chain 'V' and resid 87 through 102 removed outlier: 3.883A pdb=" N ARG V 102 " --> pdb=" O GLN V 98 " (cutoff:3.500A) Processing helix chain 'V' and resid 104 through 107 No H-bonds generated for 'chain 'V' and resid 104 through 107' Processing helix chain 'V' and resid 111 through 128 Processing helix chain 'V' and resid 135 through 141 removed outlier: 3.816A pdb=" N LEU V 141 " --> pdb=" O ALA V 137 " (cutoff:3.500A) Processing helix chain 'V' and resid 146 through 159 Processing helix chain 'V' and resid 169 through 179 removed outlier: 3.914A pdb=" N SER V 178 " --> pdb=" O LYS V 174 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N SER V 179 " --> pdb=" O THR V 175 " (cutoff:3.500A) Processing helix chain 'V' and resid 191 through 193 No H-bonds generated for 'chain 'V' and resid 191 through 193' Processing helix chain 'V' and resid 197 through 213 Processing helix chain 'V' and resid 222 through 242 removed outlier: 3.767A pdb=" N GLN V 238 " --> pdb=" O TRP V 234 " (cutoff:3.500A) Proline residue: V 239 - end of helix Processing helix chain 'V' and resid 247 through 254 Processing helix chain 'V' and resid 262 through 277 Processing helix chain 'V' and resid 281 through 286 Processing helix chain 'V' and resid 294 through 302 removed outlier: 5.025A pdb=" N GLY V 298 " --> pdb=" O LYS V 295 " (cutoff:3.500A) Processing helix chain 'V' and resid 304 through 312 Processing helix chain 'V' and resid 387 through 392 Processing helix chain 'V' and resid 396 through 405 Processing helix chain 'W' and resid 305 through 318 Processing helix chain 'W' and resid 322 through 327 Processing helix chain 'W' and resid 334 through 347 Processing helix chain 'W' and resid 349 through 357 Processing helix chain 'W' and resid 365 through 383 Processing sheet with id= A, first strand: chain 'A' and resid 84 through 87 Processing sheet with id= B, first strand: chain 'A' and resid 166 through 168 removed outlier: 4.644A pdb=" N ILE A 174 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 266 through 268 removed outlier: 4.092A pdb=" N GLY A 273 " --> pdb=" O SER A 268 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 364 through 368 Processing sheet with id= E, first strand: chain 'A' and resid 369 through 371 removed outlier: 5.924A pdb=" N PHE A 486 " --> pdb=" O SER A 370 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'A' and resid 379 through 383 removed outlier: 8.073A pdb=" N VAL A 380 " --> pdb=" O ALA A 475 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N LEU A 477 " --> pdb=" O VAL A 380 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N VAL A 382 " --> pdb=" O LEU A 477 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N ARG A 479 " --> pdb=" O VAL A 382 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 391 through 395 Processing sheet with id= H, first strand: chain 'A' and resid 420 through 422 Processing sheet with id= I, first strand: chain 'A' and resid 617 through 620 Processing sheet with id= J, first strand: chain 'A' and resid 1085 through 1088 Processing sheet with id= K, first strand: chain 'A' and resid 1165 through 1167 removed outlier: 3.583A pdb=" N TYR A1116 " --> pdb=" O LYS A1131 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 110 through 113 removed outlier: 4.492A pdb=" N GLY B 134 " --> pdb=" O ILE B 113 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 125 through 127 removed outlier: 6.374A pdb=" N GLU B 118 " --> pdb=" O TYR B 77 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N TYR B 77 " --> pdb=" O GLU B 118 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N THR B 120 " --> pdb=" O LEU B 75 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N LEU B 75 " --> pdb=" O THR B 120 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 169 through 171 Processing sheet with id= O, first strand: chain 'B' and resid 181 through 184 Processing sheet with id= P, first strand: chain 'B' and resid 189 through 193 removed outlier: 3.970A pdb=" N ALA B 201 " --> pdb=" O MET B 216 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 424 through 426 Processing sheet with id= R, first strand: chain 'B' and resid 454 through 456 Processing sheet with id= S, first strand: chain 'B' and resid 573 through 577 Processing sheet with id= T, first strand: chain 'B' and resid 593 through 597 Processing sheet with id= U, first strand: chain 'B' and resid 708 through 712 removed outlier: 4.074A pdb=" N LYS B 868 " --> pdb=" O LEU B 884 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ARG B 886 " --> pdb=" O ILE B 866 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N ILE B 866 " --> pdb=" O ARG B 886 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'B' and resid 1003 through 1009 removed outlier: 4.171A pdb=" N TYR B1003 " --> pdb=" O VAL B 743 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ILE B 927 " --> pdb=" O ALA B 742 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'B' and resid 831 through 833 Processing sheet with id= X, first strand: chain 'B' and resid 1074 through 1080 Processing sheet with id= Y, first strand: chain 'B' and resid 536 through 541 removed outlier: 5.971A pdb=" N LEU B 541 " --> pdb=" O ILE B 545 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N ILE B 545 " --> pdb=" O LEU B 541 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'B' and resid 754 through 758 removed outlier: 5.834A pdb=" N VAL B 906 " --> pdb=" O LEU B 755 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N LEU B 757 " --> pdb=" O VAL B 906 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N GLY B 908 " --> pdb=" O LEU B 757 " (cutoff:3.500A) No H-bonds generated for sheet with id= Z Processing sheet with id= AA, first strand: chain 'B' and resid 825 through 828 removed outlier: 4.564A pdb=" N GLN B 825 " --> pdb=" O TYR B 858 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ILE B 856 " --> pdb=" O LEU B 827 " (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: 6.897A pdb=" N GLU C 62 " --> pdb=" O VAL C 54 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N MET C 56 " --> pdb=" O SER C 60 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N SER C 60 " --> pdb=" O MET C 56 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR C 230 " --> pdb=" O GLU C 311 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'C' and resid 174 through 176 removed outlier: 4.313A pdb=" N GLN C 139 " --> pdb=" O ILE C 176 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS C 91 " --> pdb=" O HIS C 213 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL C 215 " --> pdb=" O VAL C 89 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N VAL C 89 " --> pdb=" O VAL C 215 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N GLY C 217 " --> pdb=" O MET C 87 " (cutoff:3.500A) removed outlier: 5.225A 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 removed outlier: 3.688A pdb=" N ALA C 200 " --> pdb=" O VAL C 168 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'E' and resid 72 through 75 removed outlier: 6.901A pdb=" N ARG E 101 " --> pdb=" O PHE E 73 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N PHE E 75 " --> pdb=" O ARG E 101 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LEU E 103 " --> pdb=" O PHE E 75 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ILE E 126 " --> pdb=" O ALA E 102 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N ILE E 104 " --> pdb=" O ILE E 126 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N GLU E 128 " --> pdb=" O ILE E 104 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N VAL E 106 " --> pdb=" O GLU E 128 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N PHE E 130 " --> pdb=" O VAL E 106 " (cutoff:3.500A) No H-bonds generated for sheet with id= AG Processing sheet with id= AH, first strand: chain 'E' and resid 147 through 150 removed outlier: 3.531A pdb=" N GLU E 147 " --> pdb=" O ILE E 194 " (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: 4.191A pdb=" N LYS G 37 " --> pdb=" O CYS G 45 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU G 44 " --> pdb=" O PHE G 77 " (cutoff:3.500A) removed outlier: 7.047A 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 removed outlier: 3.684A pdb=" N VAL G 97 " --> pdb=" O PRO G 110 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU G 108 " --> pdb=" O VAL G 99 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'G' and resid 50 through 54 removed outlier: 6.823A 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: 3.886A pdb=" N SER H 26 " --> pdb=" O VAL H 43 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N VAL H 43 " --> pdb=" O SER H 26 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N LYS H 55 " --> pdb=" O LEU H 148 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N HIS H 29 " --> pdb=" O LYS H 13 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'I' and resid 12 through 15 Processing sheet with id= AP, first strand: chain 'I' and resid 79 through 82 Processing sheet with id= AQ, first strand: chain 'K' and resid 26 through 30 Processing sheet with id= AR, first strand: chain 'M' and resid 14 through 18 Processing sheet with id= AS, first strand: chain 'M' and resid 26 through 30 removed outlier: 7.263A pdb=" N GLY M 131 " --> pdb=" O LEU M 27 " (cutoff:3.500A) removed outlier: 8.763A pdb=" N GLN M 29 " --> pdb=" O GLY M 131 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N LEU M 133 " --> pdb=" O GLN M 29 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER M 46 " --> pdb=" O GLU M 59 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ALA M 61 " --> pdb=" O HIS M 44 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N HIS M 44 " --> pdb=" O ALA M 61 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ALA M 47 " --> pdb=" O LEU M 208 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL M 206 " --> pdb=" O ILE M 49 " (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 268 through 270 removed outlier: 3.729A pdb=" N VAL N 348 " --> pdb=" O VAL N 337 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N VAL N 337 " --> pdb=" O VAL N 348 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'N' and resid 358 through 364 removed outlier: 4.361A pdb=" N GLN N 358 " --> pdb=" O VAL N 379 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N SER N 362 " --> pdb=" O VAL N 375 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N VAL N 375 " --> pdb=" O SER N 362 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N GLY N 364 " --> pdb=" O MET N 373 " (cutoff:3.500A) removed outlier: 5.101A 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 67 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 63 through 68 Processing sheet with id= BA, first strand: chain 'P' and resid 136 through 140 Processing sheet with id= BB, first strand: chain 'P' and resid 248 through 253 Processing sheet with id= BC, first strand: chain '1' and resid 97 through 100 Processing sheet with id= BD, first strand: chain '3' and resid 326 through 328 Processing sheet with id= BE, first strand: chain '3' and resid 185 through 187 removed outlier: 3.550A pdb=" N VAL 3 320 " --> pdb=" O LEU 3 187 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N CYS 3 312 " --> pdb=" O PHE 3 251 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain '3' and resid 257 through 260 removed outlier: 6.901A pdb=" N GLN 3 289 " --> pdb=" O PHE 3 258 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ASN 3 260 " --> pdb=" O GLN 3 289 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ALA 3 291 " --> pdb=" O ASN 3 260 " (cutoff:3.500A) No H-bonds generated for sheet with id= BF Processing sheet with id= BG, first strand: chain '3' and resid 364 through 367 Processing sheet with id= BH, first strand: chain 'U' and resid 170 through 173 Processing sheet with id= BI, first strand: chain 'U' and resid 291 through 295 removed outlier: 3.675A pdb=" N GLY U 314 " --> pdb=" O MET U 258 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N MET U 258 " --> pdb=" O GLY U 314 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N SER U 261 " --> pdb=" O LEU U 165 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N LEU U 165 " --> pdb=" O SER U 261 " (cutoff:3.500A) Processing sheet with id= BJ, first strand: chain 'V' and resid 15 through 19 removed outlier: 3.534A pdb=" N VAL V 27 " --> pdb=" O VAL V 16 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ASP V 18 " --> pdb=" O GLN V 25 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N GLN V 25 " --> pdb=" O ASP V 18 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N THR V 36 " --> pdb=" O LEU V 26 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N CYS V 28 " --> pdb=" O VAL V 34 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N VAL V 34 " --> pdb=" O CYS V 28 " (cutoff:3.500A) 1927 hydrogen bonds defined for protein. 5514 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 60 hydrogen bonds 120 hydrogen bond angles 0 basepair planarities 25 basepair parallelities 88 stacking parallelities Total time for adding SS restraints: 19.71 Time building geometry restraints manager: 18.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.36: 19062 1.36 - 1.59: 39438 1.59 - 1.82: 832 1.82 - 2.05: 0 2.05 - 2.28: 12 Bond restraints: 59344 Sorted by residual: bond pdb=" O3' DC X -21 " pdb=" P DT X -20 " ideal model delta sigma weight residual 1.607 1.128 0.479 1.50e-02 4.44e+03 1.02e+03 bond pdb=" C PRO 1 68 " pdb=" N PRO 1 69 " ideal model delta sigma weight residual 1.335 1.368 -0.033 1.19e-02 7.06e+03 7.80e+00 bond pdb=" O3' DG X -18 " pdb=" P DT X -17 " ideal model delta sigma weight residual 1.607 1.639 -0.032 1.50e-02 4.44e+03 4.67e+00 bond pdb=" C ASP 3 375 " pdb=" N PRO 3 376 " ideal model delta sigma weight residual 1.334 1.376 -0.042 2.34e-02 1.83e+03 3.29e+00 bond pdb=" C ILE B 392 " pdb=" N PRO B 393 " ideal model delta sigma weight residual 1.334 1.372 -0.038 2.34e-02 1.83e+03 2.69e+00 ... (remaining 59339 not shown) Histogram of bond angle deviations from ideal: 73.70 - 85.76: 12 85.76 - 97.82: 2 97.82 - 109.88: 7934 109.88 - 121.95: 60573 121.95 - 134.01: 12207 Bond angle restraints: 80728 Sorted by residual: angle pdb=" O3' DC X -21 " pdb=" P DT X -20 " pdb=" O5' DT X -20 " ideal model delta sigma weight residual 104.00 87.53 16.47 1.50e+00 4.44e-01 1.21e+02 angle pdb=" C4' DG X -18 " pdb=" C3' DG X -18 " pdb=" O3' DG X -18 " ideal model delta sigma weight residual 110.00 121.91 -11.91 1.50e+00 4.44e-01 6.30e+01 angle pdb=" C3' DC X -21 " pdb=" O3' DC X -21 " pdb=" P DT X -20 " ideal model delta sigma weight residual 120.20 110.22 9.98 1.50e+00 4.44e-01 4.43e+01 angle pdb=" O3' DT X -19 " pdb=" C3' DT X -19 " pdb=" C2' DT X -19 " ideal model delta sigma weight residual 111.50 102.65 8.85 1.50e+00 4.44e-01 3.48e+01 angle pdb=" N VAL K 93 " pdb=" CA VAL K 93 " pdb=" C VAL K 93 " ideal model delta sigma weight residual 111.90 108.09 3.81 8.10e-01 1.52e+00 2.21e+01 ... (remaining 80723 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.57: 35240 35.57 - 71.13: 747 71.13 - 106.70: 36 106.70 - 142.27: 0 142.27 - 177.83: 4 Dihedral angle restraints: 36027 sinusoidal: 15986 harmonic: 20041 Sorted by residual: dihedral pdb=" CA TYR 3 340 " pdb=" C TYR 3 340 " pdb=" N PRO 3 341 " pdb=" CA PRO 3 341 " ideal model delta harmonic sigma weight residual 180.00 156.62 23.38 0 5.00e+00 4.00e-02 2.19e+01 dihedral pdb=" C4' DG X -18 " pdb=" C3' DG X -18 " pdb=" O3' DG X -18 " pdb=" P DT X -17 " ideal model delta sinusoidal sigma weight residual 220.00 42.17 177.83 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DT X 9 " pdb=" C3' DT X 9 " pdb=" O3' DT X 9 " pdb=" P DT X 10 " ideal model delta sinusoidal sigma weight residual -140.00 36.63 -176.63 1 3.50e+01 8.16e-04 1.57e+01 ... (remaining 36024 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 8495 0.087 - 0.175: 486 0.175 - 0.262: 2 0.262 - 0.349: 0 0.349 - 0.437: 1 Chirality restraints: 8984 Sorted by residual: chirality pdb=" C3' DG X -18 " pdb=" C4' DG X -18 " pdb=" O3' DG X -18 " pdb=" C2' DG X -18 " both_signs ideal model delta sigma weight residual False -2.66 -2.22 -0.44 2.00e-01 2.50e+01 4.76e+00 chirality pdb=" C3' DT X -19 " pdb=" C4' DT X -19 " pdb=" O3' DT X -19 " pdb=" C2' DT X -19 " both_signs ideal model delta sigma weight residual False -2.66 -2.88 0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" C1' DT X -19 " pdb=" O4' DT X -19 " pdb=" C2' DT X -19 " pdb=" N1 DT X -19 " both_signs ideal model delta sigma weight residual False 2.47 2.27 0.20 2.00e-01 2.50e+01 9.76e-01 ... (remaining 8981 not shown) Planarity restraints: 9896 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT X -19 " 0.057 2.00e-02 2.50e+03 2.82e-02 1.99e+01 pdb=" N1 DT X -19 " -0.057 2.00e-02 2.50e+03 pdb=" C2 DT X -19 " -0.020 2.00e-02 2.50e+03 pdb=" O2 DT X -19 " 0.000 2.00e-02 2.50e+03 pdb=" N3 DT X -19 " 0.000 2.00e-02 2.50e+03 pdb=" C4 DT X -19 " 0.019 2.00e-02 2.50e+03 pdb=" O4 DT X -19 " 0.019 2.00e-02 2.50e+03 pdb=" C5 DT X -19 " -0.018 2.00e-02 2.50e+03 pdb=" C7 DT X -19 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DT X -19 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG X -18 " -0.046 2.00e-02 2.50e+03 2.28e-02 1.56e+01 pdb=" N9 DG X -18 " 0.048 2.00e-02 2.50e+03 pdb=" C8 DG X -18 " 0.030 2.00e-02 2.50e+03 pdb=" N7 DG X -18 " -0.030 2.00e-02 2.50e+03 pdb=" C5 DG X -18 " -0.000 2.00e-02 2.50e+03 pdb=" C6 DG X -18 " 0.000 2.00e-02 2.50e+03 pdb=" O6 DG X -18 " -0.007 2.00e-02 2.50e+03 pdb=" N1 DG X -18 " -0.000 2.00e-02 2.50e+03 pdb=" C2 DG X -18 " 0.000 2.00e-02 2.50e+03 pdb=" N2 DG X -18 " -0.000 2.00e-02 2.50e+03 pdb=" N3 DG X -18 " 0.007 2.00e-02 2.50e+03 pdb=" C4 DG X -18 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR D 56 " 0.030 5.00e-02 4.00e+02 4.59e-02 3.36e+00 pdb=" N PRO D 57 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO D 57 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 57 " 0.026 5.00e-02 4.00e+02 ... (remaining 9893 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.37: 129 2.37 - 3.00: 29772 3.00 - 3.63: 88121 3.63 - 4.27: 133056 4.27 - 4.90: 216568 Nonbonded interactions: 467646 Sorted by model distance: nonbonded pdb=" CG1 VAL B 741 " pdb=" OH TYR B1009 " model vdw 1.734 3.460 nonbonded pdb=" CG2 VAL B 741 " pdb=" OH TYR B1009 " model vdw 1.740 3.460 nonbonded pdb=" N MET L 15 " pdb=" OE2 GLU L 27 " model vdw 1.841 2.520 nonbonded pdb=" OG SER P 88 " pdb=" OE1 GLN P 91 " model vdw 1.857 2.440 nonbonded pdb=" CG2 VAL B 741 " pdb=" CE2 TYR B1009 " model vdw 1.867 3.760 ... (remaining 467641 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: 0.010 Normalize map: mean=0, sd=1: 1.820 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: 8.970 Check model and map are aligned: 0.640 Set scattering table: 0.400 Process input model: 140.180 Find NCS groups from input model: 1.320 Set up NCS constraints: 0.170 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:2.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 155.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6976 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 0.479 59344 Z= 0.145 Angle : 0.492 16.467 80728 Z= 0.303 Chirality : 0.038 0.437 8984 Planarity : 0.003 0.046 9896 Dihedral : 12.737 177.834 23063 Min Nonbonded Distance : 1.734 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.09), residues: 6809 helix: -0.36 (0.09), residues: 2730 sheet: -1.06 (0.17), residues: 777 loop : -1.82 (0.10), residues: 3302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 297 HIS 0.003 0.000 HIS 3 198 PHE 0.008 0.001 PHE U 266 TYR 0.010 0.001 TYR A1116 ARG 0.004 0.000 ARG B 900 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13618 Ramachandran restraints generated. 6809 Oldfield, 0 Emsley, 6809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13618 Ramachandran restraints generated. 6809 Oldfield, 0 Emsley, 6809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1158 residues out of total 6068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1158 time to evaluate : 4.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 HIS cc_start: 0.6564 (t-90) cc_final: 0.6234 (m-70) REVERT: A 312 PHE cc_start: 0.8376 (t80) cc_final: 0.7991 (t80) REVERT: A 505 MET cc_start: 0.7912 (tpt) cc_final: 0.7162 (tpt) REVERT: A 724 CYS cc_start: 0.9244 (m) cc_final: 0.8890 (m) REVERT: A 852 MET cc_start: 0.7855 (mtt) cc_final: 0.7641 (mtt) REVERT: A 965 PHE cc_start: 0.8367 (t80) cc_final: 0.8165 (t80) REVERT: A 1134 LEU cc_start: 0.8185 (mt) cc_final: 0.7722 (pt) REVERT: A 1236 MET cc_start: 0.7587 (ptp) cc_final: 0.7368 (mtp) REVERT: A 1326 ASP cc_start: 0.8102 (t0) cc_final: 0.7690 (m-30) REVERT: A 1327 HIS cc_start: 0.7050 (m90) cc_final: 0.6506 (t-90) REVERT: A 1349 MET cc_start: 0.8605 (mmm) cc_final: 0.8354 (mmm) REVERT: B 59 MET cc_start: 0.8610 (tmm) cc_final: 0.8289 (tmm) REVERT: B 68 ASP cc_start: 0.6520 (p0) cc_final: 0.6271 (m-30) REVERT: B 89 GLU cc_start: 0.6800 (pp20) cc_final: 0.6287 (pp20) REVERT: B 107 MET cc_start: 0.8946 (ptm) cc_final: 0.8462 (ptm) REVERT: B 126 ILE cc_start: 0.8383 (mm) cc_final: 0.6495 (mm) REVERT: B 274 LYS cc_start: 0.7710 (mtpt) cc_final: 0.7437 (mmtt) REVERT: B 311 GLU cc_start: 0.9017 (mm-30) cc_final: 0.8759 (mt-10) REVERT: B 324 LYS cc_start: 0.8030 (tttm) cc_final: 0.7779 (tppt) REVERT: B 429 PHE cc_start: 0.5008 (m-80) cc_final: 0.4614 (m-80) REVERT: B 431 MET cc_start: 0.4216 (mmt) cc_final: 0.3699 (ttp) REVERT: B 643 ILE cc_start: 0.8892 (mt) cc_final: 0.8550 (mp) REVERT: B 689 MET cc_start: 0.5980 (mmt) cc_final: 0.5203 (mmt) REVERT: B 719 MET cc_start: 0.8240 (mmm) cc_final: 0.7482 (mmp) REVERT: B 750 ASP cc_start: 0.7093 (p0) cc_final: 0.6849 (p0) REVERT: B 763 ASP cc_start: 0.8315 (m-30) cc_final: 0.7782 (m-30) REVERT: B 794 MET cc_start: 0.8196 (tmm) cc_final: 0.7950 (mtt) REVERT: B 996 GLU cc_start: 0.8046 (mt-10) cc_final: 0.7242 (mt-10) REVERT: B 1050 MET cc_start: 0.7521 (pmm) cc_final: 0.6870 (pmm) REVERT: C 56 MET cc_start: 0.8297 (tmm) cc_final: 0.7775 (tmm) REVERT: C 83 GLU cc_start: 0.7665 (mm-30) cc_final: 0.7390 (tp30) REVERT: C 87 MET cc_start: 0.8702 (mmm) cc_final: 0.8389 (mmt) REVERT: C 212 MET cc_start: 0.8979 (mtt) cc_final: 0.8750 (mtp) REVERT: D 26 GLN cc_start: 0.8422 (tp-100) cc_final: 0.8188 (tp-100) REVERT: D 82 GLU cc_start: 0.7624 (mm-30) cc_final: 0.7092 (tp30) REVERT: E 14 ARG cc_start: 0.8554 (ttt90) cc_final: 0.7900 (ttt180) REVERT: E 94 MET cc_start: 0.6676 (mmp) cc_final: 0.6472 (mmp) REVERT: E 110 MET cc_start: 0.5329 (ttm) cc_final: 0.5061 (mtp) REVERT: E 121 MET cc_start: 0.6726 (ppp) cc_final: 0.6249 (ppp) REVERT: F 88 ASP cc_start: 0.7297 (t70) cc_final: 0.6814 (t0) REVERT: F 94 MET cc_start: 0.8773 (mmm) cc_final: 0.8492 (mmm) REVERT: G 106 ASP cc_start: 0.8198 (p0) cc_final: 0.6871 (t70) REVERT: G 190 ILE cc_start: 0.5180 (mp) cc_final: 0.4786 (mp) REVERT: H 24 ARG cc_start: 0.7654 (mtt90) cc_final: 0.7407 (mtt180) REVERT: H 31 GLU cc_start: 0.7891 (tp30) cc_final: 0.7675 (tp30) REVERT: H 42 ASP cc_start: 0.8286 (m-30) cc_final: 0.7541 (m-30) REVERT: H 64 LEU cc_start: 0.8472 (tp) cc_final: 0.8182 (tp) REVERT: H 78 THR cc_start: 0.8026 (p) cc_final: 0.7757 (p) REVERT: H 92 MET cc_start: 0.8953 (mtp) cc_final: 0.7797 (mtp) REVERT: H 107 GLU cc_start: 0.5891 (mp0) cc_final: 0.5347 (pt0) REVERT: H 122 LEU cc_start: 0.8370 (mt) cc_final: 0.8068 (mm) REVERT: H 123 MET cc_start: 0.8259 (tmm) cc_final: 0.7798 (tmm) REVERT: H 146 LYS cc_start: 0.7800 (mtpt) cc_final: 0.7244 (mtpp) REVERT: I 2 LEU cc_start: 0.8284 (mt) cc_final: 0.8024 (mp) REVERT: J 1 MET cc_start: 0.8354 (ppp) cc_final: 0.7620 (ptt) REVERT: J 7 CYS cc_start: 0.7114 (t) cc_final: 0.6752 (t) REVERT: J 33 ASP cc_start: 0.7281 (p0) cc_final: 0.6383 (p0) REVERT: L 18 ILE cc_start: 0.8396 (mm) cc_final: 0.8133 (mm) REVERT: L 28 ILE cc_start: 0.7419 (pt) cc_final: 0.6843 (pt) REVERT: L 44 MET cc_start: 0.8829 (mmm) cc_final: 0.8449 (mmm) REVERT: M 12 GLU cc_start: 0.8012 (tt0) cc_final: 0.7594 (tm-30) REVERT: M 17 LEU cc_start: 0.6485 (tt) cc_final: 0.5462 (mp) REVERT: M 48 LYS cc_start: 0.7689 (mtpt) cc_final: 0.7267 (ttmt) REVERT: M 65 LEU cc_start: 0.8279 (pp) cc_final: 0.8028 (tp) REVERT: M 286 MET cc_start: 0.8863 (mmm) cc_final: 0.8610 (mmm) REVERT: M 383 LYS cc_start: 0.7105 (tttm) cc_final: 0.6796 (mptt) REVERT: N 157 MET cc_start: 0.0555 (ptp) cc_final: 0.0104 (ptp) REVERT: N 341 LEU cc_start: 0.8923 (tp) cc_final: 0.8526 (mp) REVERT: N 373 MET cc_start: 0.7004 (mpp) cc_final: 0.6481 (mpp) REVERT: O 8 LEU cc_start: 0.9402 (tp) cc_final: 0.9192 (tp) REVERT: O 79 CYS cc_start: 0.7548 (p) cc_final: 0.6867 (m) REVERT: O 85 MET cc_start: 0.8113 (ptt) cc_final: 0.7823 (ptp) REVERT: O 133 MET cc_start: 0.6126 (ppp) cc_final: 0.3923 (mtp) REVERT: O 351 GLU cc_start: 0.7499 (pt0) cc_final: 0.6984 (mt-10) REVERT: O 394 MET cc_start: 0.8565 (mmp) cc_final: 0.8088 (mmt) REVERT: O 398 MET cc_start: 0.8099 (ttm) cc_final: 0.7615 (ttp) REVERT: O 404 MET cc_start: 0.8338 (mtm) cc_final: 0.7901 (mtm) REVERT: O 512 SER cc_start: 0.9394 (m) cc_final: 0.9194 (p) REVERT: O 531 MET cc_start: 0.7981 (mmm) cc_final: 0.7757 (mmm) REVERT: P 135 LEU cc_start: 0.6288 (mt) cc_final: 0.6049 (mt) REVERT: P 159 ARG cc_start: 0.6172 (ttt-90) cc_final: 0.5587 (mmp-170) REVERT: P 167 TYR cc_start: 0.7132 (m-80) cc_final: 0.6818 (m-10) REVERT: P 297 HIS cc_start: 0.7145 (t-90) cc_final: 0.6887 (t-90) REVERT: Q 33 LYS cc_start: 0.7841 (tptp) cc_final: 0.7466 (mptt) REVERT: Q 42 ASP cc_start: 0.8055 (p0) cc_final: 0.7696 (p0) REVERT: Q 111 MET cc_start: 0.7854 (mpp) cc_final: 0.7093 (mpp) REVERT: 1 8 GLN cc_start: 0.3622 (mm110) cc_final: 0.2690 (mt0) REVERT: 1 33 TRP cc_start: 0.3289 (t-100) cc_final: 0.2196 (t-100) REVERT: 1 46 MET cc_start: 0.3640 (ptm) cc_final: 0.2932 (tmm) REVERT: 1 52 ASN cc_start: 0.6726 (t0) cc_final: 0.6511 (m110) REVERT: 1 53 MET cc_start: 0.6289 (mmm) cc_final: 0.5597 (ppp) REVERT: 1 96 LYS cc_start: 0.1246 (mtmm) cc_final: 0.0527 (mttt) REVERT: 1 148 MET cc_start: 0.0375 (pmm) cc_final: -0.0303 (tpt) REVERT: 3 136 PHE cc_start: 0.6111 (m-80) cc_final: 0.5379 (t80) REVERT: 3 174 MET cc_start: 0.0564 (tpt) cc_final: -0.0055 (tpp) REVERT: 3 214 GLN cc_start: 0.6897 (mp10) cc_final: 0.6583 (mp10) REVERT: 3 295 ASP cc_start: 0.4662 (p0) cc_final: 0.4370 (t70) REVERT: 3 314 GLN cc_start: 0.4064 (mt0) cc_final: 0.3643 (tt0) REVERT: 3 316 ASP cc_start: 0.5092 (p0) cc_final: 0.4759 (t0) REVERT: 3 318 GLU cc_start: 0.5147 (pt0) cc_final: 0.4549 (pm20) REVERT: 3 349 LEU cc_start: 0.4969 (tt) cc_final: 0.4414 (tt) REVERT: 3 368 ASN cc_start: 0.5299 (m110) cc_final: 0.4939 (t0) REVERT: 4 269 ILE cc_start: 0.6085 (mt) cc_final: 0.5864 (mt) REVERT: 4 278 GLU cc_start: 0.6568 (mp0) cc_final: 0.5888 (pp20) REVERT: 4 348 GLU cc_start: 0.5630 (tp30) cc_final: 0.5082 (mm-30) REVERT: 4 385 MET cc_start: 0.0833 (tmm) cc_final: 0.0109 (mmm) REVERT: U 178 LEU cc_start: 0.7461 (mp) cc_final: 0.6806 (tp) REVERT: U 186 ARG cc_start: 0.7938 (mtt-85) cc_final: 0.7136 (ttt90) REVERT: U 192 TYR cc_start: 0.8258 (t80) cc_final: 0.7803 (t80) REVERT: U 195 LYS cc_start: 0.6688 (mttt) cc_final: 0.6219 (tttt) REVERT: U 212 LEU cc_start: 0.6794 (mm) cc_final: 0.6361 (tp) REVERT: U 285 PRO cc_start: 0.8893 (Cg_endo) cc_final: 0.8669 (Cg_exo) REVERT: V 143 TYR cc_start: 0.6947 (m-80) cc_final: 0.6731 (m-10) REVERT: V 168 CYS cc_start: 0.6563 (t) cc_final: 0.5876 (m) REVERT: V 283 LEU cc_start: 0.7573 (mt) cc_final: 0.7136 (tt) REVERT: V 291 ARG cc_start: 0.7444 (mtp85) cc_final: 0.7091 (ttp-110) REVERT: V 404 ARG cc_start: 0.6300 (tmm-80) cc_final: 0.6040 (ptt180) REVERT: W 300 SER cc_start: 0.3044 (t) cc_final: 0.2416 (p) REVERT: W 307 GLU cc_start: 0.6861 (tt0) cc_final: 0.6628 (tt0) REVERT: W 324 MET cc_start: 0.6933 (mmp) cc_final: 0.6729 (mmm) REVERT: W 357 GLN cc_start: 0.5358 (mt0) cc_final: 0.5082 (mt0) outliers start: 0 outliers final: 0 residues processed: 1158 average time/residue: 0.6082 time to fit residues: 1137.0190 Evaluate side-chains 541 residues out of total 6068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 541 time to evaluate : 4.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 690 random chunks: chunk 582 optimal weight: 30.0000 chunk 522 optimal weight: 20.0000 chunk 290 optimal weight: 1.9990 chunk 178 optimal weight: 10.0000 chunk 352 optimal weight: 8.9990 chunk 279 optimal weight: 8.9990 chunk 540 optimal weight: 10.0000 chunk 209 optimal weight: 10.0000 chunk 328 optimal weight: 30.0000 chunk 402 optimal weight: 20.0000 chunk 626 optimal weight: 8.9990 overall best weight: 7.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 GLN A 423 GLN A 528 ASN ** A 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1039 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1190 GLN A1213 HIS A1217 GLN B 395 GLN ** B 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 517 ASN B 979 HIS ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1093 HIS C 127 GLN C 160 ASN C 194 HIS C 344 GLN ** D 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 26 GLN D 61 GLN E 71 GLN E 108 GLN ** G 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 41 ASN ** G 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 97 GLN M 417 GLN O 60 HIS O 286 GLN O 465 GLN O 534 GLN P 182 GLN 1 48 ASN ** 1 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 139 HIS ** 3 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 171 GLN 4 229 GLN 4 234 GLN 4 243 GLN 4 285 GLN ** 4 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 166 GLN ** U 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 49 ASN V 129 HIS V 206 GLN V 212 ASN V 303 HIS V 397 GLN V 403 GLN W 279 ASN W 327 GLN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.3513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.146 59344 Z= 0.543 Angle : 0.854 13.784 80728 Z= 0.435 Chirality : 0.051 0.413 8984 Planarity : 0.007 0.134 9896 Dihedral : 15.383 177.901 9118 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 0.13 % Allowed : 4.25 % Favored : 95.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.10), residues: 6809 helix: 0.08 (0.09), residues: 2720 sheet: -1.08 (0.17), residues: 787 loop : -1.43 (0.10), residues: 3302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP 3 51 HIS 0.015 0.002 HIS O 27 PHE 0.031 0.003 PHE A 431 TYR 0.036 0.003 TYR U 322 ARG 0.033 0.001 ARG V 6 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13618 Ramachandran restraints generated. 6809 Oldfield, 0 Emsley, 6809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13618 Ramachandran restraints generated. 6809 Oldfield, 0 Emsley, 6809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 6068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 541 time to evaluate : 4.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 LEU cc_start: 0.8620 (mm) cc_final: 0.8394 (mt) REVERT: A 505 MET cc_start: 0.8159 (tpt) cc_final: 0.7203 (tpt) REVERT: A 523 MET cc_start: 0.8962 (mtm) cc_final: 0.8704 (mtm) REVERT: A 630 ASP cc_start: 0.6628 (t0) cc_final: 0.6390 (t0) REVERT: A 724 CYS cc_start: 0.9165 (m) cc_final: 0.8921 (m) REVERT: A 811 ASP cc_start: 0.8752 (OUTLIER) cc_final: 0.8093 (p0) REVERT: A 908 ASP cc_start: 0.8462 (t0) cc_final: 0.8138 (t0) REVERT: A 912 MET cc_start: 0.8123 (tpp) cc_final: 0.7547 (mmm) REVERT: A 1236 MET cc_start: 0.7707 (ptp) cc_final: 0.7079 (mtm) REVERT: A 1327 HIS cc_start: 0.7881 (m90) cc_final: 0.6642 (t70) REVERT: B 107 MET cc_start: 0.8924 (ptm) cc_final: 0.8526 (ptm) REVERT: B 719 MET cc_start: 0.9177 (mmm) cc_final: 0.8811 (mmm) REVERT: B 763 ASP cc_start: 0.8426 (m-30) cc_final: 0.8126 (m-30) REVERT: B 794 MET cc_start: 0.8052 (tmm) cc_final: 0.7678 (mmt) REVERT: B 916 MET cc_start: 0.8986 (tpp) cc_final: 0.8747 (tpp) REVERT: B 1050 MET cc_start: 0.7250 (pmm) cc_final: 0.6601 (pmm) REVERT: C 56 MET cc_start: 0.8558 (tmm) cc_final: 0.8001 (tmm) REVERT: C 83 GLU cc_start: 0.8193 (mm-30) cc_final: 0.7586 (tp30) REVERT: C 87 MET cc_start: 0.8978 (mmm) cc_final: 0.8523 (mmm) REVERT: C 103 ASP cc_start: 0.8537 (m-30) cc_final: 0.8274 (m-30) REVERT: C 212 MET cc_start: 0.9041 (mtt) cc_final: 0.8383 (mtm) REVERT: C 330 MET cc_start: 0.8473 (mmm) cc_final: 0.8217 (mtt) REVERT: D 26 GLN cc_start: 0.8675 (tp40) cc_final: 0.8329 (tp-100) REVERT: D 90 ARG cc_start: 0.3999 (mtm-85) cc_final: 0.2273 (tpt170) REVERT: E 94 MET cc_start: 0.6984 (mmp) cc_final: 0.6599 (mmp) REVERT: G 73 ARG cc_start: 0.8199 (mtm-85) cc_final: 0.7481 (mtm-85) REVERT: H 64 LEU cc_start: 0.8687 (tp) cc_final: 0.8421 (tp) REVERT: H 74 GLU cc_start: 0.7707 (pp20) cc_final: 0.7379 (pp20) REVERT: H 123 MET cc_start: 0.8611 (tmm) cc_final: 0.8239 (tmm) REVERT: I 1 MET cc_start: 0.5348 (tpp) cc_final: 0.5117 (mtt) REVERT: I 12 LEU cc_start: 0.8772 (mt) cc_final: 0.8560 (mp) REVERT: I 15 GLU cc_start: 0.7798 (tp30) cc_final: 0.6960 (tp30) REVERT: J 33 ASP cc_start: 0.7189 (p0) cc_final: 0.6917 (p0) REVERT: L 38 GLU cc_start: 0.8328 (tm-30) cc_final: 0.8106 (tm-30) REVERT: L 44 MET cc_start: 0.8885 (mmm) cc_final: 0.8339 (mmm) REVERT: M 12 GLU cc_start: 0.8314 (tt0) cc_final: 0.7730 (tm-30) REVERT: M 17 LEU cc_start: 0.7166 (tt) cc_final: 0.6588 (tt) REVERT: M 97 MET cc_start: 0.7527 (ttm) cc_final: 0.7243 (ttt) REVERT: M 133 LEU cc_start: 0.9061 (mt) cc_final: 0.8687 (mt) REVERT: M 292 MET cc_start: 0.8495 (tpt) cc_final: 0.8218 (tpt) REVERT: M 298 MET cc_start: 0.7677 (mmm) cc_final: 0.7383 (mmm) REVERT: M 383 LYS cc_start: 0.7477 (tttm) cc_final: 0.7091 (tptm) REVERT: N 157 MET cc_start: 0.0547 (ptp) cc_final: 0.0302 (ptp) REVERT: N 248 ASP cc_start: 0.7756 (p0) cc_final: 0.7501 (p0) REVERT: N 341 LEU cc_start: 0.8973 (tp) cc_final: 0.8592 (tt) REVERT: O 5 GLU cc_start: 0.8492 (mt-10) cc_final: 0.8144 (mt-10) REVERT: O 8 LEU cc_start: 0.9420 (tp) cc_final: 0.9209 (tp) REVERT: O 20 ILE cc_start: 0.8792 (pt) cc_final: 0.8454 (tt) REVERT: O 85 MET cc_start: 0.8362 (ptt) cc_final: 0.8116 (ptp) REVERT: O 133 MET cc_start: 0.6775 (ppp) cc_final: 0.6178 (ppp) REVERT: O 398 MET cc_start: 0.8167 (ttm) cc_final: 0.7653 (ttp) REVERT: O 404 MET cc_start: 0.8558 (mtm) cc_final: 0.8220 (mtm) REVERT: P 85 MET cc_start: 0.3622 (mmp) cc_final: 0.3214 (mpp) REVERT: P 125 LYS cc_start: 0.7166 (tppt) cc_final: 0.6868 (mmtm) REVERT: P 159 ARG cc_start: 0.6707 (ttt-90) cc_final: 0.5881 (mmp-170) REVERT: Q 111 MET cc_start: 0.7752 (mpp) cc_final: 0.7314 (mpp) REVERT: 1 33 TRP cc_start: 0.3630 (t-100) cc_final: 0.2541 (t-100) REVERT: 1 46 MET cc_start: 0.3635 (ptm) cc_final: 0.2508 (mtm) REVERT: 1 52 ASN cc_start: 0.6607 (t0) cc_final: 0.6252 (m110) REVERT: 1 53 MET cc_start: 0.5891 (mmm) cc_final: 0.5648 (ppp) REVERT: 3 136 PHE cc_start: 0.6421 (m-80) cc_final: 0.5670 (t80) REVERT: 3 314 GLN cc_start: 0.5031 (mt0) cc_final: 0.4401 (tt0) REVERT: 3 316 ASP cc_start: 0.5652 (p0) cc_final: 0.4520 (t0) REVERT: 3 368 ASN cc_start: 0.5834 (m110) cc_final: 0.5228 (p0) REVERT: 4 348 GLU cc_start: 0.5230 (tp30) cc_final: 0.4646 (mm-30) REVERT: 4 385 MET cc_start: 0.1171 (tmm) cc_final: 0.0356 (mmm) REVERT: U 186 ARG cc_start: 0.7985 (mtt-85) cc_final: 0.7238 (mtp85) REVERT: U 212 LEU cc_start: 0.7102 (mm) cc_final: 0.6702 (tp) REVERT: V 130 ASN cc_start: 0.8351 (m-40) cc_final: 0.8123 (m-40) REVERT: V 243 LEU cc_start: 0.7477 (tt) cc_final: 0.7233 (tp) REVERT: W 307 GLU cc_start: 0.6979 (tt0) cc_final: 0.6697 (tt0) REVERT: W 353 ASP cc_start: 0.7263 (p0) cc_final: 0.6720 (t0) REVERT: W 375 LEU cc_start: 0.6828 (mt) cc_final: 0.6291 (tt) outliers start: 8 outliers final: 4 residues processed: 549 average time/residue: 0.6026 time to fit residues: 562.3261 Evaluate side-chains 377 residues out of total 6068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 372 time to evaluate : 4.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 690 random chunks: chunk 348 optimal weight: 1.9990 chunk 194 optimal weight: 6.9990 chunk 521 optimal weight: 5.9990 chunk 426 optimal weight: 1.9990 chunk 172 optimal weight: 0.9990 chunk 627 optimal weight: 7.9990 chunk 678 optimal weight: 5.9990 chunk 559 optimal weight: 0.0870 chunk 622 optimal weight: 20.0000 chunk 214 optimal weight: 6.9990 chunk 503 optimal weight: 0.9990 overall best weight: 1.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 ASN ** A 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1039 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 273 GLN C 305 HIS ** D 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 118 HIS E 71 GLN ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 87 GLN ** I 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 282 GLN O 34 GLN O 291 ASN ** P 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 111 GLN 3 185 ASN ** 4 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 moved from start: 0.3412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 59344 Z= 0.158 Angle : 0.524 13.562 80728 Z= 0.270 Chirality : 0.041 0.245 8984 Planarity : 0.004 0.052 9896 Dihedral : 15.161 178.572 9118 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % 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: -0.55 (0.10), residues: 6809 helix: 0.75 (0.10), residues: 2719 sheet: -0.83 (0.18), residues: 760 loop : -1.17 (0.11), residues: 3330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP M 398 HIS 0.006 0.001 HIS D 118 PHE 0.017 0.001 PHE 4 176 TYR 0.024 0.001 TYR U 322 ARG 0.011 0.000 ARG V 291 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13618 Ramachandran restraints generated. 6809 Oldfield, 0 Emsley, 6809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13618 Ramachandran restraints generated. 6809 Oldfield, 0 Emsley, 6809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 6068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 557 time to evaluate : 4.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 312 PHE cc_start: 0.8867 (t80) cc_final: 0.8569 (t80) REVERT: A 471 LEU cc_start: 0.8373 (mp) cc_final: 0.8143 (mt) REVERT: A 474 MET cc_start: 0.7791 (mtp) cc_final: 0.6769 (mtp) REVERT: A 505 MET cc_start: 0.8025 (tpt) cc_final: 0.7047 (tpt) REVERT: A 724 CYS cc_start: 0.9082 (m) cc_final: 0.8817 (m) REVERT: A 908 ASP cc_start: 0.8544 (t0) cc_final: 0.8249 (t0) REVERT: A 912 MET cc_start: 0.8262 (tpp) cc_final: 0.7588 (mmm) REVERT: A 1023 MET cc_start: 0.8330 (tpp) cc_final: 0.8040 (mmt) REVERT: A 1236 MET cc_start: 0.7807 (ptp) cc_final: 0.7231 (mtm) REVERT: A 1280 MET cc_start: 0.7764 (pmm) cc_final: 0.6959 (pmm) REVERT: A 1288 MET cc_start: 0.8245 (mtp) cc_final: 0.7552 (mtt) REVERT: A 1327 HIS cc_start: 0.7878 (m90) cc_final: 0.6383 (t-90) REVERT: B 72 MET cc_start: 0.6589 (tpt) cc_final: 0.6238 (tpt) REVERT: B 107 MET cc_start: 0.8954 (ptm) cc_final: 0.8656 (ptm) REVERT: B 410 GLN cc_start: 0.8466 (tp40) cc_final: 0.8251 (tp40) REVERT: B 588 ASP cc_start: 0.8479 (p0) cc_final: 0.8068 (m-30) REVERT: B 709 MET cc_start: 0.8848 (ttp) cc_final: 0.8605 (ttp) REVERT: B 719 MET cc_start: 0.9062 (mmm) cc_final: 0.8628 (mmm) REVERT: B 763 ASP cc_start: 0.8352 (m-30) cc_final: 0.7948 (m-30) REVERT: B 794 MET cc_start: 0.8127 (tmm) cc_final: 0.7722 (mmt) REVERT: B 1050 MET cc_start: 0.7227 (pmm) cc_final: 0.6694 (pmm) REVERT: C 56 MET cc_start: 0.8599 (tmm) cc_final: 0.7980 (tmm) REVERT: C 83 GLU cc_start: 0.8214 (mm-30) cc_final: 0.7502 (tp30) REVERT: C 87 MET cc_start: 0.8918 (mmm) cc_final: 0.8565 (mmm) REVERT: C 103 ASP cc_start: 0.8541 (m-30) cc_final: 0.8206 (m-30) REVERT: D 26 GLN cc_start: 0.8582 (tp40) cc_final: 0.8195 (tp-100) REVERT: D 60 HIS cc_start: 0.7007 (m90) cc_final: 0.6747 (m-70) REVERT: D 90 ARG cc_start: 0.3969 (mtm-85) cc_final: 0.2075 (tpt170) REVERT: E 14 ARG cc_start: 0.8759 (ttt90) cc_final: 0.8165 (ttt180) REVERT: E 27 LEU cc_start: 0.8929 (mt) cc_final: 0.8592 (mt) REVERT: E 38 GLU cc_start: 0.7889 (mm-30) cc_final: 0.7666 (tm-30) REVERT: E 94 MET cc_start: 0.6847 (mmp) cc_final: 0.6533 (mmp) REVERT: G 73 ARG cc_start: 0.7887 (mtm-85) cc_final: 0.7320 (mtm-85) REVERT: G 106 ASP cc_start: 0.7984 (p0) cc_final: 0.6880 (t70) REVERT: G 190 ILE cc_start: 0.5101 (mp) cc_final: 0.4851 (mp) REVERT: H 64 LEU cc_start: 0.8575 (tp) cc_final: 0.8105 (tt) REVERT: H 74 GLU cc_start: 0.7713 (pp20) cc_final: 0.7396 (pp20) REVERT: H 92 MET cc_start: 0.8966 (mtp) cc_final: 0.7965 (mtp) REVERT: H 107 GLU cc_start: 0.5946 (mp0) cc_final: 0.5163 (pm20) REVERT: H 118 TYR cc_start: 0.8238 (m-80) cc_final: 0.8007 (m-80) REVERT: H 123 MET cc_start: 0.8577 (tmm) cc_final: 0.8300 (tmm) REVERT: I 12 LEU cc_start: 0.8680 (mt) cc_final: 0.7991 (mp) REVERT: I 15 GLU cc_start: 0.7761 (tp30) cc_final: 0.6879 (tp30) REVERT: K 46 GLU cc_start: 0.7854 (tm-30) cc_final: 0.7613 (tm-30) REVERT: K 47 GLU cc_start: 0.8774 (tp30) cc_final: 0.8325 (tp30) REVERT: L 38 GLU cc_start: 0.8212 (tm-30) cc_final: 0.7781 (tm-30) REVERT: L 44 MET cc_start: 0.8776 (mmm) cc_final: 0.8231 (mmm) REVERT: M 12 GLU cc_start: 0.8225 (tt0) cc_final: 0.7997 (tm-30) REVERT: M 292 MET cc_start: 0.8375 (tpt) cc_final: 0.7883 (tpt) REVERT: M 383 LYS cc_start: 0.7321 (tttm) cc_final: 0.6957 (tptp) REVERT: N 157 MET cc_start: 0.0468 (ptp) cc_final: 0.0224 (ptp) REVERT: N 341 LEU cc_start: 0.8985 (tp) cc_final: 0.8696 (tt) REVERT: N 373 MET cc_start: 0.6548 (mpp) cc_final: 0.5964 (mpp) REVERT: O 8 LEU cc_start: 0.9329 (tp) cc_final: 0.9072 (tp) REVERT: O 85 MET cc_start: 0.8242 (ptt) cc_final: 0.7979 (ptp) REVERT: O 133 MET cc_start: 0.6576 (ppp) cc_final: 0.6136 (ppp) REVERT: O 187 MET cc_start: 0.7786 (ttt) cc_final: 0.7387 (tpp) REVERT: O 338 LEU cc_start: 0.8711 (mm) cc_final: 0.8279 (mp) REVERT: O 351 GLU cc_start: 0.7902 (pt0) cc_final: 0.7624 (mt-10) REVERT: O 394 MET cc_start: 0.8660 (mmp) cc_final: 0.8078 (mmt) REVERT: O 398 MET cc_start: 0.8167 (ttm) cc_final: 0.7611 (ttp) REVERT: O 404 MET cc_start: 0.8436 (mtm) cc_final: 0.8057 (mtm) REVERT: O 512 SER cc_start: 0.9411 (m) cc_final: 0.9199 (p) REVERT: P 85 MET cc_start: 0.3495 (mmp) cc_final: 0.3184 (mpp) REVERT: P 125 LYS cc_start: 0.7091 (tppt) cc_final: 0.6772 (mmtm) REVERT: P 159 ARG cc_start: 0.6277 (ttt-90) cc_final: 0.5559 (mmp-170) REVERT: P 297 HIS cc_start: 0.7271 (t-90) cc_final: 0.6930 (t-90) REVERT: Q 69 LYS cc_start: 0.8726 (mtmt) cc_final: 0.8439 (mtmm) REVERT: Q 111 MET cc_start: 0.7400 (mpp) cc_final: 0.7146 (mpp) REVERT: 1 33 TRP cc_start: 0.3725 (t-100) cc_final: 0.2681 (t-100) REVERT: 1 52 ASN cc_start: 0.6598 (t0) cc_final: 0.6091 (m110) REVERT: 1 53 MET cc_start: 0.6230 (mmm) cc_final: 0.5890 (ppp) REVERT: 3 136 PHE cc_start: 0.6421 (m-80) cc_final: 0.5687 (t80) REVERT: 3 174 MET cc_start: 0.0143 (tpt) cc_final: -0.0464 (tpp) REVERT: 3 275 ILE cc_start: 0.8136 (mm) cc_final: 0.7807 (tt) REVERT: 3 314 GLN cc_start: 0.5135 (mt0) cc_final: 0.4736 (tt0) REVERT: 3 368 ASN cc_start: 0.5624 (m110) cc_final: 0.5014 (p0) REVERT: 4 348 GLU cc_start: 0.4959 (tp30) cc_final: 0.4295 (mm-30) REVERT: 4 377 TYR cc_start: 0.4369 (t80) cc_final: 0.3844 (t80) REVERT: 4 385 MET cc_start: 0.1148 (tmm) cc_final: 0.0194 (mmm) REVERT: U 186 ARG cc_start: 0.7979 (mtt-85) cc_final: 0.7105 (ttt90) REVERT: U 212 LEU cc_start: 0.6778 (mm) cc_final: 0.6492 (tp) REVERT: U 214 PHE cc_start: 0.3470 (m-80) cc_final: 0.2939 (m-80) REVERT: U 246 PHE cc_start: 0.4518 (m-80) cc_final: 0.4304 (m-10) REVERT: V 130 ASN cc_start: 0.8152 (m-40) cc_final: 0.7864 (m-40) REVERT: V 182 LEU cc_start: 0.7450 (mp) cc_final: 0.6963 (mp) REVERT: V 404 ARG cc_start: 0.6260 (tmm-80) cc_final: 0.5934 (tmm160) REVERT: W 284 GLU cc_start: 0.6941 (mp0) cc_final: 0.6706 (mp0) REVERT: W 285 ARG cc_start: 0.6179 (tpt90) cc_final: 0.5859 (tpm170) REVERT: W 307 GLU cc_start: 0.7005 (tt0) cc_final: 0.6723 (tt0) REVERT: W 353 ASP cc_start: 0.7315 (p0) cc_final: 0.6703 (t0) REVERT: W 375 LEU cc_start: 0.6701 (mt) cc_final: 0.6251 (tt) outliers start: 0 outliers final: 0 residues processed: 557 average time/residue: 0.5660 time to fit residues: 532.7141 Evaluate side-chains 407 residues out of total 6068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 407 time to evaluate : 4.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 690 random chunks: chunk 620 optimal weight: 30.0000 chunk 471 optimal weight: 10.0000 chunk 325 optimal weight: 10.0000 chunk 69 optimal weight: 0.8980 chunk 299 optimal weight: 0.7980 chunk 421 optimal weight: 9.9990 chunk 629 optimal weight: 6.9990 chunk 666 optimal weight: 10.0000 chunk 329 optimal weight: 7.9990 chunk 597 optimal weight: 30.0000 chunk 179 optimal weight: 10.0000 overall best weight: 5.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1039 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 273 GLN ** B 626 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1014 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 42 GLN C 180 ASN ** C 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 109 HIS M 184 GLN ** N 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 34 GLN P 90 ASN ** P 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 303 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.4228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 59344 Z= 0.379 Angle : 0.680 11.085 80728 Z= 0.349 Chirality : 0.045 0.279 8984 Planarity : 0.005 0.073 9896 Dihedral : 15.329 177.273 9118 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 0.03 % Allowed : 4.17 % Favored : 95.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.10), residues: 6809 helix: 0.55 (0.10), residues: 2732 sheet: -0.99 (0.18), residues: 753 loop : -1.23 (0.11), residues: 3324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP M 398 HIS 0.012 0.002 HIS 3 43 PHE 0.089 0.002 PHE 3 47 TYR 0.034 0.002 TYR C 306 ARG 0.008 0.001 ARG V 291 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13618 Ramachandran restraints generated. 6809 Oldfield, 0 Emsley, 6809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13618 Ramachandran restraints generated. 6809 Oldfield, 0 Emsley, 6809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 6068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 481 time to evaluate : 4.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 MET cc_start: 0.5761 (mmp) cc_final: 0.5556 (mmp) REVERT: A 474 MET cc_start: 0.8009 (mtp) cc_final: 0.7197 (mtp) REVERT: A 505 MET cc_start: 0.8018 (tpt) cc_final: 0.6910 (tpt) REVERT: A 646 MET cc_start: 0.8730 (mmt) cc_final: 0.8493 (mmt) REVERT: A 724 CYS cc_start: 0.9149 (m) cc_final: 0.8894 (m) REVERT: A 908 ASP cc_start: 0.8686 (t0) cc_final: 0.8393 (t0) REVERT: A 912 MET cc_start: 0.8262 (tpp) cc_final: 0.7418 (mmp) REVERT: A 1327 HIS cc_start: 0.7933 (m90) cc_final: 0.6603 (t70) REVERT: B 107 MET cc_start: 0.8923 (ptm) cc_final: 0.8595 (ptm) REVERT: B 243 MET cc_start: 0.8479 (ttm) cc_final: 0.8113 (ttm) REVERT: B 719 MET cc_start: 0.9146 (mmm) cc_final: 0.8883 (mmm) REVERT: B 763 ASP cc_start: 0.8365 (m-30) cc_final: 0.7903 (m-30) REVERT: B 794 MET cc_start: 0.8113 (tmm) cc_final: 0.7736 (mmt) REVERT: B 1015 MET cc_start: 0.8403 (mtp) cc_final: 0.7793 (mmm) REVERT: B 1050 MET cc_start: 0.7233 (pmm) cc_final: 0.6605 (pmm) REVERT: C 56 MET cc_start: 0.8524 (tmm) cc_final: 0.7489 (tmm) REVERT: C 87 MET cc_start: 0.8782 (mmm) cc_final: 0.8484 (mmm) REVERT: C 103 ASP cc_start: 0.8370 (m-30) cc_final: 0.8152 (m-30) REVERT: D 26 GLN cc_start: 0.8645 (tp40) cc_final: 0.8229 (tp-100) REVERT: D 60 HIS cc_start: 0.7321 (m90) cc_final: 0.6692 (p-80) REVERT: D 90 ARG cc_start: 0.4100 (mtm-85) cc_final: 0.2190 (tpt170) REVERT: E 27 LEU cc_start: 0.8650 (mt) cc_final: 0.8361 (mt) REVERT: E 94 MET cc_start: 0.6997 (mmp) cc_final: 0.6682 (mmp) REVERT: G 7 MET cc_start: 0.7056 (tpt) cc_final: 0.6736 (tpt) REVERT: G 106 ASP cc_start: 0.8355 (p0) cc_final: 0.6970 (t70) REVERT: G 150 PHE cc_start: 0.5281 (t80) cc_final: 0.4227 (t80) REVERT: H 64 LEU cc_start: 0.8600 (tp) cc_final: 0.7770 (tt) REVERT: H 87 GLN cc_start: 0.8443 (mm110) cc_final: 0.7893 (mp10) REVERT: H 123 MET cc_start: 0.8709 (tmm) cc_final: 0.8129 (tmm) REVERT: I 15 GLU cc_start: 0.7715 (tp30) cc_final: 0.6967 (tp30) REVERT: K 38 HIS cc_start: 0.7881 (m90) cc_final: 0.7679 (m-70) REVERT: K 60 MET cc_start: 0.9191 (tpp) cc_final: 0.8903 (mmm) REVERT: L 38 GLU cc_start: 0.8244 (tm-30) cc_final: 0.7746 (tm-30) REVERT: L 44 MET cc_start: 0.8751 (mmm) cc_final: 0.8131 (mmm) REVERT: L 52 LEU cc_start: 0.8569 (tt) cc_final: 0.8330 (pp) REVERT: M 12 GLU cc_start: 0.8424 (tt0) cc_final: 0.8129 (tm-30) REVERT: M 292 MET cc_start: 0.8581 (tpt) cc_final: 0.8177 (tpt) REVERT: M 357 MET cc_start: 0.8826 (mtm) cc_final: 0.8591 (mtt) REVERT: M 383 LYS cc_start: 0.7491 (tttm) cc_final: 0.7158 (tptp) REVERT: N 157 MET cc_start: 0.0553 (ptp) cc_final: 0.0283 (ptp) REVERT: N 341 LEU cc_start: 0.8921 (tp) cc_final: 0.8625 (tt) REVERT: O 8 LEU cc_start: 0.9392 (tp) cc_final: 0.9176 (tp) REVERT: O 85 MET cc_start: 0.8335 (ptt) cc_final: 0.8098 (ptp) REVERT: O 133 MET cc_start: 0.6875 (ppp) cc_final: 0.6401 (ppp) REVERT: O 187 MET cc_start: 0.8055 (ttt) cc_final: 0.7136 (tpp) REVERT: O 394 MET cc_start: 0.8661 (mmp) cc_final: 0.8031 (mmt) REVERT: O 398 MET cc_start: 0.8199 (ttm) cc_final: 0.7728 (ttp) REVERT: O 404 MET cc_start: 0.8546 (mtm) cc_final: 0.8216 (mtm) REVERT: P 122 GLU cc_start: 0.6714 (mp0) cc_final: 0.6090 (tp30) REVERT: P 125 LYS cc_start: 0.7188 (tppt) cc_final: 0.6855 (mmtm) REVERT: P 159 ARG cc_start: 0.6476 (ttt-90) cc_final: 0.5549 (mmp-170) REVERT: P 214 HIS cc_start: 0.8378 (t70) cc_final: 0.8165 (t-90) REVERT: P 297 HIS cc_start: 0.7390 (t-90) cc_final: 0.6968 (t-90) REVERT: Q 111 MET cc_start: 0.7442 (mpp) cc_final: 0.7191 (mpp) REVERT: 1 33 TRP cc_start: 0.3362 (t-100) cc_final: 0.2571 (t-100) REVERT: 1 46 MET cc_start: 0.3037 (ppp) cc_final: 0.1373 (mtm) REVERT: 1 52 ASN cc_start: 0.6188 (t0) cc_final: 0.5816 (m110) REVERT: 1 53 MET cc_start: 0.6278 (mmm) cc_final: 0.5990 (ppp) REVERT: 3 136 PHE cc_start: 0.6359 (m-80) cc_final: 0.5653 (t80) REVERT: 3 368 ASN cc_start: 0.5972 (m110) cc_final: 0.5302 (p0) REVERT: 4 348 GLU cc_start: 0.5224 (tp30) cc_final: 0.4567 (mm-30) REVERT: 4 364 MET cc_start: 0.2344 (tmm) cc_final: 0.1590 (mmp) REVERT: 4 377 TYR cc_start: 0.4350 (t80) cc_final: 0.3941 (t80) REVERT: 4 385 MET cc_start: 0.1430 (tmm) cc_final: 0.0813 (mmm) REVERT: U 192 TYR cc_start: 0.7953 (t80) cc_final: 0.7739 (t80) REVERT: U 212 LEU cc_start: 0.6970 (mm) cc_final: 0.6747 (tp) REVERT: U 214 PHE cc_start: 0.3463 (m-80) cc_final: 0.2960 (m-80) REVERT: U 284 GLU cc_start: 0.7940 (mm-30) cc_final: 0.7712 (mm-30) REVERT: V 130 ASN cc_start: 0.8357 (m-40) cc_final: 0.8120 (m-40) REVERT: W 284 GLU cc_start: 0.7368 (mp0) cc_final: 0.7056 (mp0) REVERT: W 307 GLU cc_start: 0.7001 (tt0) cc_final: 0.6754 (tt0) outliers start: 2 outliers final: 1 residues processed: 483 average time/residue: 0.5352 time to fit residues: 445.7281 Evaluate side-chains 381 residues out of total 6068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 380 time to evaluate : 4.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 690 random chunks: chunk 555 optimal weight: 9.9990 chunk 378 optimal weight: 7.9990 chunk 9 optimal weight: 7.9990 chunk 496 optimal weight: 10.0000 chunk 275 optimal weight: 0.7980 chunk 569 optimal weight: 20.0000 chunk 461 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 340 optimal weight: 4.9990 chunk 598 optimal weight: 10.0000 chunk 168 optimal weight: 2.9990 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 801 GLN ** A 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1039 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 626 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 34 GLN ** O 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 278 GLN V 129 HIS ** V 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 303 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.4556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 59344 Z= 0.335 Angle : 0.620 10.971 80728 Z= 0.320 Chirality : 0.044 0.304 8984 Planarity : 0.004 0.053 9896 Dihedral : 15.360 178.022 9118 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % 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: -0.66 (0.10), residues: 6809 helix: 0.60 (0.10), residues: 2730 sheet: -0.98 (0.18), residues: 758 loop : -1.16 (0.11), residues: 3321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP M 398 HIS 0.008 0.001 HIS M 44 PHE 0.023 0.002 PHE 3 47 TYR 0.023 0.002 TYR C 306 ARG 0.006 0.001 ARG V 291 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13618 Ramachandran restraints generated. 6809 Oldfield, 0 Emsley, 6809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13618 Ramachandran restraints generated. 6809 Oldfield, 0 Emsley, 6809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 6068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 469 time to evaluate : 5.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLN cc_start: 0.7540 (tt0) cc_final: 0.7112 (tp-100) REVERT: A 274 THR cc_start: 0.7853 (p) cc_final: 0.7628 (p) REVERT: A 474 MET cc_start: 0.7847 (mtp) cc_final: 0.7148 (mtp) REVERT: A 505 MET cc_start: 0.7774 (tpp) cc_final: 0.7508 (tpt) REVERT: A 560 ASP cc_start: 0.8160 (p0) cc_final: 0.7920 (p0) REVERT: A 724 CYS cc_start: 0.9105 (m) cc_final: 0.8902 (m) REVERT: A 912 MET cc_start: 0.8376 (tpp) cc_final: 0.7382 (tpp) REVERT: A 1236 MET cc_start: 0.7663 (ptp) cc_final: 0.6975 (mtm) REVERT: B 107 MET cc_start: 0.8857 (ptm) cc_final: 0.8576 (ptm) REVERT: B 243 MET cc_start: 0.8470 (ttm) cc_final: 0.8065 (ttm) REVERT: B 689 MET cc_start: 0.5907 (mmp) cc_final: 0.5363 (mmt) REVERT: B 763 ASP cc_start: 0.8300 (m-30) cc_final: 0.7897 (m-30) REVERT: B 794 MET cc_start: 0.8165 (tmm) cc_final: 0.7677 (mmt) REVERT: B 916 MET cc_start: 0.9354 (mmt) cc_final: 0.8939 (mmm) REVERT: B 1015 MET cc_start: 0.8628 (mtp) cc_final: 0.7888 (mmm) REVERT: B 1020 MET cc_start: 0.7970 (ttm) cc_final: 0.7465 (ttm) REVERT: B 1050 MET cc_start: 0.7575 (pmm) cc_final: 0.7096 (pmm) REVERT: C 56 MET cc_start: 0.8520 (tmm) cc_final: 0.7505 (tmm) REVERT: C 87 MET cc_start: 0.8777 (mmm) cc_final: 0.8468 (mmm) REVERT: C 103 ASP cc_start: 0.8363 (m-30) cc_final: 0.8082 (m-30) REVERT: C 326 ILE cc_start: 0.8782 (mm) cc_final: 0.8527 (mt) REVERT: D 26 GLN cc_start: 0.8610 (tp40) cc_final: 0.8212 (tp-100) REVERT: D 60 HIS cc_start: 0.7433 (m90) cc_final: 0.6533 (p-80) REVERT: D 90 ARG cc_start: 0.4432 (mtm-85) cc_final: 0.2293 (tpt170) REVERT: D 107 ARG cc_start: 0.5982 (mtm180) cc_final: 0.5112 (mtm180) REVERT: E 27 LEU cc_start: 0.8636 (mt) cc_final: 0.8350 (mt) REVERT: E 94 MET cc_start: 0.6857 (mmp) cc_final: 0.6464 (mmp) REVERT: E 141 GLU cc_start: 0.8500 (tp30) cc_final: 0.8173 (tm-30) REVERT: G 7 MET cc_start: 0.7008 (tpt) cc_final: 0.6701 (tpt) REVERT: G 106 ASP cc_start: 0.8159 (p0) cc_final: 0.6908 (t70) REVERT: H 64 LEU cc_start: 0.8587 (tp) cc_final: 0.8352 (tp) REVERT: H 74 GLU cc_start: 0.7688 (pp20) cc_final: 0.7422 (pp20) REVERT: H 123 MET cc_start: 0.8781 (tmm) cc_final: 0.8055 (tmm) REVERT: I 12 LEU cc_start: 0.8615 (mt) cc_final: 0.8362 (mt) REVERT: I 15 GLU cc_start: 0.7732 (tp30) cc_final: 0.6990 (tp30) REVERT: K 38 HIS cc_start: 0.7976 (m90) cc_final: 0.7705 (m-70) REVERT: K 46 GLU cc_start: 0.7831 (tm-30) cc_final: 0.7535 (tm-30) REVERT: K 47 GLU cc_start: 0.8801 (tp30) cc_final: 0.8377 (tp30) REVERT: L 44 MET cc_start: 0.8928 (mmm) cc_final: 0.8346 (mmm) REVERT: M 12 GLU cc_start: 0.8363 (tt0) cc_final: 0.8048 (mp0) REVERT: M 17 LEU cc_start: 0.7000 (tp) cc_final: 0.6358 (tt) REVERT: M 250 MET cc_start: 0.9114 (tpp) cc_final: 0.8648 (tpp) REVERT: M 292 MET cc_start: 0.8721 (tpt) cc_final: 0.7851 (tpp) REVERT: M 357 MET cc_start: 0.8756 (mtm) cc_final: 0.8487 (mtt) REVERT: M 383 LYS cc_start: 0.7503 (tttm) cc_final: 0.7198 (tptp) REVERT: N 157 MET cc_start: 0.0522 (ptp) cc_final: 0.0243 (ptp) REVERT: N 341 LEU cc_start: 0.8939 (tp) cc_final: 0.8656 (tt) REVERT: N 350 MET cc_start: 0.8289 (tpp) cc_final: 0.7877 (mpp) REVERT: N 373 MET cc_start: 0.6898 (mpp) cc_final: 0.6272 (mpp) REVERT: O 8 LEU cc_start: 0.9388 (tp) cc_final: 0.9156 (tp) REVERT: O 85 MET cc_start: 0.8333 (ptt) cc_final: 0.8077 (ptp) REVERT: O 187 MET cc_start: 0.8069 (ttt) cc_final: 0.7855 (ttt) REVERT: O 398 MET cc_start: 0.8186 (ttm) cc_final: 0.7756 (ttp) REVERT: O 404 MET cc_start: 0.8513 (mtm) cc_final: 0.8117 (mtm) REVERT: P 85 MET cc_start: -0.0008 (mpp) cc_final: -0.0220 (mpp) REVERT: P 125 LYS cc_start: 0.7208 (tppt) cc_final: 0.6859 (mmtm) REVERT: P 297 HIS cc_start: 0.7488 (t-90) cc_final: 0.7083 (t-90) REVERT: Q 68 MET cc_start: 0.8442 (tpp) cc_final: 0.8078 (tpp) REVERT: Q 111 MET cc_start: 0.7481 (mpp) cc_final: 0.7102 (mpp) REVERT: 1 33 TRP cc_start: 0.3357 (t-100) cc_final: 0.2776 (t-100) REVERT: 1 52 ASN cc_start: 0.6430 (t0) cc_final: 0.6049 (m110) REVERT: 1 53 MET cc_start: 0.6119 (mmm) cc_final: 0.5885 (ppp) REVERT: 1 96 LYS cc_start: 0.1197 (mtmm) cc_final: 0.0689 (mttt) REVERT: 3 136 PHE cc_start: 0.6356 (m-80) cc_final: 0.5626 (t80) REVERT: 3 174 MET cc_start: -0.0011 (tpt) cc_final: -0.0843 (mmt) REVERT: 3 179 GLU cc_start: 0.5523 (tm-30) cc_final: 0.5248 (tm-30) REVERT: 3 272 ARG cc_start: 0.5584 (mmt90) cc_final: 0.4561 (tpm170) REVERT: 4 348 GLU cc_start: 0.5293 (tp30) cc_final: 0.4707 (mm-30) REVERT: 4 377 TYR cc_start: 0.4283 (t80) cc_final: 0.3985 (t80) REVERT: 4 385 MET cc_start: 0.1009 (tmm) cc_final: 0.0602 (mmm) REVERT: U 192 TYR cc_start: 0.7968 (t80) cc_final: 0.7754 (t80) REVERT: U 212 LEU cc_start: 0.6883 (mm) cc_final: 0.6645 (tp) REVERT: U 214 PHE cc_start: 0.3439 (m-80) cc_final: 0.2948 (m-80) REVERT: U 284 GLU cc_start: 0.7970 (mm-30) cc_final: 0.7737 (mm-30) REVERT: V 62 ASN cc_start: 0.8230 (t0) cc_final: 0.7944 (t0) REVERT: V 130 ASN cc_start: 0.8346 (m-40) cc_final: 0.8123 (m-40) REVERT: V 135 MET cc_start: 0.8497 (mtt) cc_final: 0.8047 (mtt) REVERT: W 284 GLU cc_start: 0.7486 (mp0) cc_final: 0.7239 (mp0) REVERT: W 307 GLU cc_start: 0.7212 (tt0) cc_final: 0.6952 (tt0) outliers start: 0 outliers final: 0 residues processed: 469 average time/residue: 0.5395 time to fit residues: 436.6868 Evaluate side-chains 379 residues out of total 6068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 379 time to evaluate : 4.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 690 random chunks: chunk 224 optimal weight: 4.9990 chunk 600 optimal weight: 7.9990 chunk 131 optimal weight: 0.9980 chunk 391 optimal weight: 10.0000 chunk 164 optimal weight: 10.0000 chunk 667 optimal weight: 10.0000 chunk 554 optimal weight: 0.1980 chunk 309 optimal weight: 7.9990 chunk 55 optimal weight: 6.9990 chunk 220 optimal weight: 0.7980 chunk 350 optimal weight: 10.0000 overall best weight: 2.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1039 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 626 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 959 HIS ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 GLN ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 87 GLN ** I 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 34 GLN P 90 ASN ** P 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 388 HIS ** 4 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 303 HIS V 403 GLN ** W 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.4616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 59344 Z= 0.225 Angle : 0.559 13.398 80728 Z= 0.288 Chirality : 0.042 0.286 8984 Planarity : 0.004 0.051 9896 Dihedral : 15.309 178.156 9118 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 0.02 % Allowed : 1.60 % Favored : 98.39 % 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: -0.45 (0.10), residues: 6809 helix: 0.82 (0.10), residues: 2726 sheet: -0.86 (0.18), residues: 753 loop : -1.09 (0.11), residues: 3330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP G 201 HIS 0.012 0.001 HIS C 305 PHE 0.016 0.001 PHE C 336 TYR 0.026 0.001 TYR O 311 ARG 0.007 0.000 ARG L 42 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13618 Ramachandran restraints generated. 6809 Oldfield, 0 Emsley, 6809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13618 Ramachandran restraints generated. 6809 Oldfield, 0 Emsley, 6809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 6068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 456 time to evaluate : 4.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLN cc_start: 0.7672 (tt0) cc_final: 0.7169 (tp-100) REVERT: A 274 THR cc_start: 0.7835 (p) cc_final: 0.7583 (p) REVERT: A 474 MET cc_start: 0.8016 (mtp) cc_final: 0.7481 (mtp) REVERT: A 505 MET cc_start: 0.7801 (tpp) cc_final: 0.7496 (tpt) REVERT: A 560 ASP cc_start: 0.8285 (p0) cc_final: 0.7991 (p0) REVERT: A 724 CYS cc_start: 0.9084 (m) cc_final: 0.8867 (m) REVERT: A 912 MET cc_start: 0.8425 (tpp) cc_final: 0.7424 (tpp) REVERT: A 1236 MET cc_start: 0.7743 (ptp) cc_final: 0.7107 (mtm) REVERT: B 243 MET cc_start: 0.8451 (ttm) cc_final: 0.8024 (ttm) REVERT: B 410 GLN cc_start: 0.8547 (tp40) cc_final: 0.8318 (tp40) REVERT: B 689 MET cc_start: 0.6023 (mmp) cc_final: 0.5301 (mmt) REVERT: B 719 MET cc_start: 0.9093 (mmm) cc_final: 0.8726 (tpp) REVERT: B 763 ASP cc_start: 0.8280 (m-30) cc_final: 0.7800 (m-30) REVERT: B 794 MET cc_start: 0.8240 (tmm) cc_final: 0.7697 (mmt) REVERT: B 916 MET cc_start: 0.9333 (mmt) cc_final: 0.8867 (mmm) REVERT: B 1015 MET cc_start: 0.8612 (mtp) cc_final: 0.8143 (mmm) REVERT: B 1020 MET cc_start: 0.7996 (ttm) cc_final: 0.7219 (tpp) REVERT: B 1050 MET cc_start: 0.7583 (pmm) cc_final: 0.7112 (pmm) REVERT: C 56 MET cc_start: 0.8553 (tmm) cc_final: 0.7506 (tmm) REVERT: C 87 MET cc_start: 0.8726 (mmm) cc_final: 0.8435 (mmm) REVERT: C 103 ASP cc_start: 0.8367 (m-30) cc_final: 0.8038 (m-30) REVERT: C 256 CYS cc_start: 0.7907 (m) cc_final: 0.7590 (m) REVERT: D 26 GLN cc_start: 0.8528 (tp40) cc_final: 0.8190 (tp-100) REVERT: D 60 HIS cc_start: 0.7196 (m90) cc_final: 0.6414 (p-80) REVERT: D 90 ARG cc_start: 0.4580 (mtm-85) cc_final: 0.2351 (tpt170) REVERT: D 107 ARG cc_start: 0.6084 (mtm180) cc_final: 0.5511 (mtm180) REVERT: E 27 LEU cc_start: 0.8644 (mt) cc_final: 0.8353 (mt) REVERT: E 94 MET cc_start: 0.6790 (mmp) cc_final: 0.6363 (mmp) REVERT: E 141 GLU cc_start: 0.8480 (tp30) cc_final: 0.8158 (tm-30) REVERT: G 106 ASP cc_start: 0.7934 (p0) cc_final: 0.7043 (t70) REVERT: H 64 LEU cc_start: 0.8417 (tp) cc_final: 0.8121 (tp) REVERT: H 74 GLU cc_start: 0.7681 (pp20) cc_final: 0.7272 (pp20) REVERT: H 107 GLU cc_start: 0.6046 (mp0) cc_final: 0.5159 (pm20) REVERT: H 118 TYR cc_start: 0.8099 (m-80) cc_final: 0.7675 (m-80) REVERT: H 123 MET cc_start: 0.8747 (tmm) cc_final: 0.7749 (tmm) REVERT: I 12 LEU cc_start: 0.8646 (mt) cc_final: 0.8380 (mt) REVERT: I 15 GLU cc_start: 0.7640 (tp30) cc_final: 0.6927 (tp30) REVERT: K 47 GLU cc_start: 0.8760 (tp30) cc_final: 0.8544 (tp30) REVERT: L 38 GLU cc_start: 0.8191 (tm-30) cc_final: 0.7886 (tm-30) REVERT: L 44 MET cc_start: 0.9043 (mmm) cc_final: 0.8339 (mmm) REVERT: L 52 LEU cc_start: 0.8485 (tt) cc_final: 0.8278 (pp) REVERT: M 12 GLU cc_start: 0.8330 (tt0) cc_final: 0.8052 (tm-30) REVERT: M 250 MET cc_start: 0.9111 (tpp) cc_final: 0.8666 (tpp) REVERT: M 292 MET cc_start: 0.8618 (tpt) cc_final: 0.7932 (tpp) REVERT: M 357 MET cc_start: 0.8723 (mtm) cc_final: 0.8445 (mtt) REVERT: M 383 LYS cc_start: 0.7383 (tttm) cc_final: 0.7086 (tptp) REVERT: N 157 MET cc_start: 0.0399 (ptp) cc_final: 0.0146 (ptp) REVERT: N 341 LEU cc_start: 0.8939 (tp) cc_final: 0.8629 (tt) REVERT: N 350 MET cc_start: 0.8324 (tpp) cc_final: 0.7839 (mpp) REVERT: N 373 MET cc_start: 0.6886 (mpp) cc_final: 0.6254 (mpp) REVERT: O 8 LEU cc_start: 0.9367 (tp) cc_final: 0.9118 (tp) REVERT: O 85 MET cc_start: 0.8298 (ptt) cc_final: 0.8030 (ptp) REVERT: O 398 MET cc_start: 0.8199 (ttm) cc_final: 0.7725 (ttp) REVERT: O 404 MET cc_start: 0.8504 (mtm) cc_final: 0.8100 (mtm) REVERT: P 85 MET cc_start: 0.0063 (mpp) cc_final: -0.0166 (mpp) REVERT: P 122 GLU cc_start: 0.5605 (pm20) cc_final: 0.5314 (mp0) REVERT: P 125 LYS cc_start: 0.7192 (tppt) cc_final: 0.6804 (mmtm) REVERT: P 297 HIS cc_start: 0.7294 (t-90) cc_final: 0.6912 (t-90) REVERT: Q 111 MET cc_start: 0.7449 (mpp) cc_final: 0.6930 (mpp) REVERT: 1 33 TRP cc_start: 0.3700 (t-100) cc_final: 0.3025 (t-100) REVERT: 1 52 ASN cc_start: 0.6478 (t0) cc_final: 0.6090 (m110) REVERT: 1 53 MET cc_start: 0.6340 (mmm) cc_final: 0.6039 (ppp) REVERT: 1 96 LYS cc_start: 0.1120 (mtmm) cc_final: 0.0772 (mttt) REVERT: 3 136 PHE cc_start: 0.6344 (m-80) cc_final: 0.5588 (t80) REVERT: 3 174 MET cc_start: -0.0043 (tpt) cc_final: -0.0824 (mmt) REVERT: 3 179 GLU cc_start: 0.5806 (tm-30) cc_final: 0.5524 (tm-30) REVERT: 4 348 GLU cc_start: 0.5184 (tp30) cc_final: 0.4660 (mm-30) REVERT: 4 377 TYR cc_start: 0.4301 (t80) cc_final: 0.3996 (t80) REVERT: 4 385 MET cc_start: 0.0820 (tmm) cc_final: 0.0616 (mtt) REVERT: U 192 TYR cc_start: 0.8027 (t80) cc_final: 0.7758 (t80) REVERT: U 212 LEU cc_start: 0.6929 (mm) cc_final: 0.6606 (tp) REVERT: U 214 PHE cc_start: 0.3357 (m-80) cc_final: 0.2851 (m-80) REVERT: U 284 GLU cc_start: 0.7928 (mm-30) cc_final: 0.7691 (mm-30) REVERT: W 284 GLU cc_start: 0.7475 (mp0) cc_final: 0.7213 (mp0) REVERT: W 307 GLU cc_start: 0.7342 (tt0) cc_final: 0.6941 (tt0) outliers start: 1 outliers final: 0 residues processed: 457 average time/residue: 0.5482 time to fit residues: 428.2625 Evaluate side-chains 382 residues out of total 6068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 382 time to evaluate : 4.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 690 random chunks: chunk 643 optimal weight: 0.9980 chunk 75 optimal weight: 0.8980 chunk 380 optimal weight: 20.0000 chunk 487 optimal weight: 0.9990 chunk 377 optimal weight: 6.9990 chunk 561 optimal weight: 0.0020 chunk 372 optimal weight: 7.9990 chunk 665 optimal weight: 10.0000 chunk 416 optimal weight: 7.9990 chunk 405 optimal weight: 20.0000 chunk 307 optimal weight: 8.9990 overall best weight: 1.9792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 528 ASN ** A 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1039 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 626 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 43 ASN ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 90 ASN ** P 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 303 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.4647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 59344 Z= 0.185 Angle : 0.538 13.320 80728 Z= 0.277 Chirality : 0.041 0.378 8984 Planarity : 0.004 0.091 9896 Dihedral : 15.254 179.063 9118 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.02 % Allowed : 1.14 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.10), residues: 6809 helix: 0.97 (0.10), residues: 2719 sheet: -0.80 (0.18), residues: 759 loop : -1.02 (0.11), residues: 3331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP M 398 HIS 0.008 0.001 HIS M 44 PHE 0.023 0.001 PHE V 402 TYR 0.026 0.001 TYR B1003 ARG 0.005 0.000 ARG B 428 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13618 Ramachandran restraints generated. 6809 Oldfield, 0 Emsley, 6809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13618 Ramachandran restraints generated. 6809 Oldfield, 0 Emsley, 6809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 6068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 463 time to evaluate : 4.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLN cc_start: 0.7644 (tt0) cc_final: 0.7256 (tm-30) REVERT: A 274 THR cc_start: 0.7883 (p) cc_final: 0.7656 (p) REVERT: A 474 MET cc_start: 0.8070 (mtp) cc_final: 0.7569 (mtp) REVERT: A 505 MET cc_start: 0.7863 (tpp) cc_final: 0.7473 (tpt) REVERT: A 523 MET cc_start: 0.8940 (mtm) cc_final: 0.8626 (mtp) REVERT: A 560 ASP cc_start: 0.8271 (p0) cc_final: 0.7978 (p0) REVERT: A 724 CYS cc_start: 0.9085 (m) cc_final: 0.8871 (m) REVERT: A 912 MET cc_start: 0.8437 (tpp) cc_final: 0.7430 (tpp) REVERT: A 1236 MET cc_start: 0.7717 (ptp) cc_final: 0.7062 (mtm) REVERT: B 243 MET cc_start: 0.8428 (ttm) cc_final: 0.8032 (ttm) REVERT: B 410 GLN cc_start: 0.8591 (tp40) cc_final: 0.8361 (tp40) REVERT: B 689 MET cc_start: 0.5931 (mmp) cc_final: 0.5184 (mmt) REVERT: B 719 MET cc_start: 0.9023 (mmm) cc_final: 0.8655 (tpp) REVERT: B 763 ASP cc_start: 0.8271 (m-30) cc_final: 0.7773 (m-30) REVERT: B 794 MET cc_start: 0.8239 (tmm) cc_final: 0.7694 (mmt) REVERT: B 916 MET cc_start: 0.9321 (mmt) cc_final: 0.8897 (mmm) REVERT: B 1015 MET cc_start: 0.8598 (mtp) cc_final: 0.8113 (mmm) REVERT: B 1020 MET cc_start: 0.7982 (ttm) cc_final: 0.7172 (tpp) REVERT: B 1050 MET cc_start: 0.7240 (pmm) cc_final: 0.6996 (pmm) REVERT: C 56 MET cc_start: 0.8557 (tmm) cc_final: 0.7520 (tmm) REVERT: C 87 MET cc_start: 0.8725 (mmm) cc_final: 0.8428 (mmm) REVERT: C 103 ASP cc_start: 0.8369 (m-30) cc_final: 0.8034 (m-30) REVERT: C 256 CYS cc_start: 0.7590 (m) cc_final: 0.7373 (m) REVERT: D 22 ASP cc_start: 0.7230 (m-30) cc_final: 0.6326 (t0) REVERT: D 26 GLN cc_start: 0.8542 (tp40) cc_final: 0.8174 (tp-100) REVERT: D 60 HIS cc_start: 0.7214 (m90) cc_final: 0.6343 (p-80) REVERT: D 90 ARG cc_start: 0.4507 (mtm-85) cc_final: 0.2147 (tpt170) REVERT: E 27 LEU cc_start: 0.8704 (mt) cc_final: 0.8377 (mt) REVERT: E 94 MET cc_start: 0.6783 (mmp) cc_final: 0.6410 (mmp) REVERT: E 141 GLU cc_start: 0.8507 (tp30) cc_final: 0.8176 (tm-30) REVERT: G 106 ASP cc_start: 0.7797 (p0) cc_final: 0.7066 (t70) REVERT: H 64 LEU cc_start: 0.8343 (tp) cc_final: 0.8089 (tp) REVERT: H 74 GLU cc_start: 0.7667 (pp20) cc_final: 0.7259 (pp20) REVERT: H 107 GLU cc_start: 0.6015 (mp0) cc_final: 0.5200 (pm20) REVERT: H 118 TYR cc_start: 0.8033 (m-80) cc_final: 0.7529 (m-80) REVERT: H 123 MET cc_start: 0.8670 (tmm) cc_final: 0.7677 (tmm) REVERT: I 12 LEU cc_start: 0.8661 (mt) cc_final: 0.8363 (mt) REVERT: I 15 GLU cc_start: 0.7533 (tp30) cc_final: 0.6792 (tp30) REVERT: K 38 HIS cc_start: 0.7825 (m90) cc_final: 0.7528 (m-70) REVERT: L 38 GLU cc_start: 0.8105 (tm-30) cc_final: 0.7721 (tm-30) REVERT: L 44 MET cc_start: 0.9037 (mmm) cc_final: 0.8437 (mmm) REVERT: M 12 GLU cc_start: 0.8369 (tt0) cc_final: 0.8136 (tm-30) REVERT: M 250 MET cc_start: 0.9099 (tpp) cc_final: 0.8672 (tpp) REVERT: M 292 MET cc_start: 0.8621 (tpt) cc_final: 0.7823 (tpp) REVERT: M 319 MET cc_start: 0.8226 (mmm) cc_final: 0.7802 (mmm) REVERT: M 357 MET cc_start: 0.8690 (mtm) cc_final: 0.8406 (mtt) REVERT: M 383 LYS cc_start: 0.7367 (tttm) cc_final: 0.7083 (tptp) REVERT: N 157 MET cc_start: 0.0429 (ptp) cc_final: 0.0180 (ptp) REVERT: N 341 LEU cc_start: 0.8929 (tp) cc_final: 0.8608 (tt) REVERT: N 350 MET cc_start: 0.8449 (tpp) cc_final: 0.7895 (mpp) REVERT: N 373 MET cc_start: 0.7057 (mpp) cc_final: 0.6346 (mpp) REVERT: O 5 GLU cc_start: 0.8497 (mt-10) cc_final: 0.8153 (mt-10) REVERT: O 8 LEU cc_start: 0.9378 (tp) cc_final: 0.9131 (tp) REVERT: O 85 MET cc_start: 0.8259 (ptt) cc_final: 0.7991 (ptp) REVERT: O 398 MET cc_start: 0.8204 (ttm) cc_final: 0.7722 (ttp) REVERT: O 404 MET cc_start: 0.8518 (mtm) cc_final: 0.8107 (mtm) REVERT: P 85 MET cc_start: 0.0039 (mpp) cc_final: -0.0187 (mpp) REVERT: P 122 GLU cc_start: 0.5534 (pm20) cc_final: 0.5223 (mp0) REVERT: P 125 LYS cc_start: 0.7265 (tppt) cc_final: 0.6887 (mmtm) REVERT: P 267 MET cc_start: 0.4720 (mmm) cc_final: 0.3630 (tpp) REVERT: P 297 HIS cc_start: 0.7276 (t-90) cc_final: 0.6874 (t-90) REVERT: Q 111 MET cc_start: 0.7601 (mpp) cc_final: 0.7226 (tpt) REVERT: 1 33 TRP cc_start: 0.3750 (t-100) cc_final: 0.3046 (t-100) REVERT: 1 52 ASN cc_start: 0.6527 (t0) cc_final: 0.6145 (m110) REVERT: 1 53 MET cc_start: 0.6337 (mmm) cc_final: 0.6041 (ppp) REVERT: 1 96 LYS cc_start: 0.0944 (mtmm) cc_final: 0.0640 (mttt) REVERT: 3 136 PHE cc_start: 0.6346 (m-80) cc_final: 0.5585 (t80) REVERT: 3 174 MET cc_start: 0.0302 (tpt) cc_final: -0.0264 (mmt) REVERT: 4 348 GLU cc_start: 0.5142 (tp30) cc_final: 0.4609 (mm-30) REVERT: 4 377 TYR cc_start: 0.4345 (t80) cc_final: 0.3989 (t80) REVERT: 4 385 MET cc_start: 0.0817 (tmm) cc_final: 0.0576 (mtt) REVERT: U 212 LEU cc_start: 0.7102 (mm) cc_final: 0.6754 (tp) REVERT: U 214 PHE cc_start: 0.3641 (m-80) cc_final: 0.2866 (m-80) REVERT: U 284 GLU cc_start: 0.7860 (mm-30) cc_final: 0.7619 (mm-30) REVERT: V 130 ASN cc_start: 0.8087 (m-40) cc_final: 0.7846 (m-40) REVERT: W 284 GLU cc_start: 0.7403 (mp0) cc_final: 0.7195 (mp0) REVERT: W 307 GLU cc_start: 0.7254 (tt0) cc_final: 0.6955 (tt0) outliers start: 1 outliers final: 0 residues processed: 464 average time/residue: 0.5348 time to fit residues: 426.5621 Evaluate side-chains 384 residues out of total 6068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 384 time to evaluate : 4.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 690 random chunks: chunk 411 optimal weight: 0.6980 chunk 265 optimal weight: 0.9990 chunk 397 optimal weight: 20.0000 chunk 200 optimal weight: 9.9990 chunk 130 optimal weight: 4.9990 chunk 128 optimal weight: 8.9990 chunk 422 optimal weight: 3.9990 chunk 453 optimal weight: 4.9990 chunk 328 optimal weight: 20.0000 chunk 61 optimal weight: 1.9990 chunk 522 optimal weight: 0.6980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 872 GLN ** A1039 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 626 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 42 GLN ** D 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 81 GLN ** I 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 90 ASN P 117 ASN ** 4 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 303 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.4666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 59344 Z= 0.169 Angle : 0.525 14.129 80728 Z= 0.269 Chirality : 0.041 0.304 8984 Planarity : 0.004 0.067 9896 Dihedral : 15.223 179.637 9118 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 0.02 % Allowed : 0.84 % Favored : 99.14 % 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: -0.14 (0.10), residues: 6809 helix: 1.10 (0.10), residues: 2710 sheet: -0.73 (0.19), residues: 736 loop : -0.92 (0.11), residues: 3363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP M 398 HIS 0.008 0.001 HIS M 44 PHE 0.021 0.001 PHE V 402 TYR 0.031 0.001 TYR B1003 ARG 0.006 0.000 ARG E 54 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13618 Ramachandran restraints generated. 6809 Oldfield, 0 Emsley, 6809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13618 Ramachandran restraints generated. 6809 Oldfield, 0 Emsley, 6809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 6068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 464 time to evaluate : 4.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 THR cc_start: 0.7945 (p) cc_final: 0.7672 (p) REVERT: A 474 MET cc_start: 0.8184 (mtp) cc_final: 0.7666 (mtp) REVERT: A 505 MET cc_start: 0.7848 (tpp) cc_final: 0.7534 (tpt) REVERT: A 523 MET cc_start: 0.8841 (mtm) cc_final: 0.8473 (mtp) REVERT: A 560 ASP cc_start: 0.8256 (p0) cc_final: 0.7976 (p0) REVERT: A 724 CYS cc_start: 0.9136 (m) cc_final: 0.8867 (m) REVERT: A 912 MET cc_start: 0.8444 (tpp) cc_final: 0.7443 (tpp) REVERT: A 1236 MET cc_start: 0.7697 (ptp) cc_final: 0.7050 (mtm) REVERT: B 243 MET cc_start: 0.8495 (ttm) cc_final: 0.8085 (ttm) REVERT: B 410 GLN cc_start: 0.8623 (tp40) cc_final: 0.8339 (tp40) REVERT: B 506 MET cc_start: 0.8581 (mpp) cc_final: 0.8303 (mpp) REVERT: B 689 MET cc_start: 0.5928 (mmp) cc_final: 0.5175 (mmt) REVERT: B 719 MET cc_start: 0.8964 (mmm) cc_final: 0.8560 (tpp) REVERT: B 744 MET cc_start: 0.8811 (ptm) cc_final: 0.8541 (ptm) REVERT: B 763 ASP cc_start: 0.8258 (m-30) cc_final: 0.7748 (m-30) REVERT: B 794 MET cc_start: 0.8212 (tmm) cc_final: 0.7625 (mmt) REVERT: B 916 MET cc_start: 0.9301 (mmt) cc_final: 0.8900 (mmm) REVERT: B 1015 MET cc_start: 0.8599 (mtp) cc_final: 0.8093 (mmm) REVERT: B 1020 MET cc_start: 0.7986 (ttm) cc_final: 0.7241 (tpp) REVERT: B 1050 MET cc_start: 0.7309 (pmm) cc_final: 0.7087 (pmm) REVERT: C 56 MET cc_start: 0.8564 (tmm) cc_final: 0.7519 (tmm) REVERT: C 87 MET cc_start: 0.8769 (mmm) cc_final: 0.8448 (mmm) REVERT: C 103 ASP cc_start: 0.8381 (m-30) cc_final: 0.8099 (m-30) REVERT: C 256 CYS cc_start: 0.7885 (m) cc_final: 0.7586 (m) REVERT: C 330 MET cc_start: 0.8339 (mmm) cc_final: 0.7883 (mmm) REVERT: D 22 ASP cc_start: 0.7231 (m-30) cc_final: 0.6180 (t0) REVERT: D 60 HIS cc_start: 0.7104 (m90) cc_final: 0.6869 (m90) REVERT: D 90 ARG cc_start: 0.4491 (mtm-85) cc_final: 0.2279 (tpt170) REVERT: E 27 LEU cc_start: 0.8661 (mt) cc_final: 0.8348 (mt) REVERT: E 94 MET cc_start: 0.6903 (mmp) cc_final: 0.6603 (mmp) REVERT: E 141 GLU cc_start: 0.8510 (tp30) cc_final: 0.8160 (tm-30) REVERT: G 106 ASP cc_start: 0.8066 (p0) cc_final: 0.7050 (t70) REVERT: H 64 LEU cc_start: 0.8337 (tp) cc_final: 0.8075 (tp) REVERT: H 74 GLU cc_start: 0.7662 (pp20) cc_final: 0.7265 (pp20) REVERT: H 92 MET cc_start: 0.8931 (mtp) cc_final: 0.7829 (mtp) REVERT: H 107 GLU cc_start: 0.6112 (mp0) cc_final: 0.5131 (pt0) REVERT: H 118 TYR cc_start: 0.8024 (m-80) cc_final: 0.7631 (m-80) REVERT: H 123 MET cc_start: 0.8685 (tmm) cc_final: 0.8335 (tmm) REVERT: I 12 LEU cc_start: 0.8701 (mt) cc_final: 0.8399 (mt) REVERT: I 15 GLU cc_start: 0.7566 (tp30) cc_final: 0.6709 (tp30) REVERT: K 38 HIS cc_start: 0.7793 (m90) cc_final: 0.7511 (m-70) REVERT: K 60 MET cc_start: 0.9234 (tpp) cc_final: 0.8951 (mmm) REVERT: L 38 GLU cc_start: 0.8187 (tm-30) cc_final: 0.7763 (tm-30) REVERT: L 44 MET cc_start: 0.8988 (mmm) cc_final: 0.8374 (mmm) REVERT: M 250 MET cc_start: 0.9094 (tpp) cc_final: 0.8658 (tpp) REVERT: M 292 MET cc_start: 0.8612 (tpt) cc_final: 0.7817 (tpp) REVERT: M 319 MET cc_start: 0.8274 (mmm) cc_final: 0.7879 (mmm) REVERT: M 357 MET cc_start: 0.8715 (mtm) cc_final: 0.8440 (mtt) REVERT: M 383 LYS cc_start: 0.7350 (tttm) cc_final: 0.7085 (tptp) REVERT: N 157 MET cc_start: 0.0534 (ptp) cc_final: 0.0281 (ptm) REVERT: N 341 LEU cc_start: 0.8926 (tp) cc_final: 0.8599 (tt) REVERT: N 350 MET cc_start: 0.8606 (tpp) cc_final: 0.7867 (mpp) REVERT: N 373 MET cc_start: 0.7083 (mpp) cc_final: 0.6402 (mpp) REVERT: O 5 GLU cc_start: 0.8476 (mt-10) cc_final: 0.8169 (mt-10) REVERT: O 8 LEU cc_start: 0.9347 (tp) cc_final: 0.9106 (tp) REVERT: O 85 MET cc_start: 0.8278 (ptt) cc_final: 0.7966 (ptp) REVERT: O 398 MET cc_start: 0.8215 (ttm) cc_final: 0.7726 (ttp) REVERT: O 404 MET cc_start: 0.8519 (mtm) cc_final: 0.8083 (mtm) REVERT: P 85 MET cc_start: 0.0058 (mpp) cc_final: -0.0189 (mpp) REVERT: P 113 ARG cc_start: 0.4757 (tpt-90) cc_final: 0.4491 (ttp-110) REVERT: P 122 GLU cc_start: 0.5472 (pm20) cc_final: 0.5157 (mp0) REVERT: P 125 LYS cc_start: 0.7234 (tppt) cc_final: 0.6861 (mmtm) REVERT: P 204 ILE cc_start: 0.8243 (mm) cc_final: 0.8005 (tt) REVERT: P 267 MET cc_start: 0.5243 (mmm) cc_final: 0.4912 (tpp) REVERT: P 297 HIS cc_start: 0.7251 (t-90) cc_final: 0.6831 (t-90) REVERT: Q 111 MET cc_start: 0.7576 (mpp) cc_final: 0.7247 (tpt) REVERT: 1 33 TRP cc_start: 0.3778 (t-100) cc_final: 0.3058 (t-100) REVERT: 1 53 MET cc_start: 0.6350 (mmm) cc_final: 0.6116 (ppp) REVERT: 1 96 LYS cc_start: 0.0942 (mtmm) cc_final: 0.0601 (mttt) REVERT: 3 136 PHE cc_start: 0.6387 (m-80) cc_final: 0.5607 (t80) REVERT: 4 348 GLU cc_start: 0.5165 (tp30) cc_final: 0.4645 (mm-30) REVERT: 4 377 TYR cc_start: 0.4465 (t80) cc_final: 0.4063 (t80) REVERT: 4 385 MET cc_start: 0.0817 (tmm) cc_final: 0.0530 (mtt) REVERT: U 212 LEU cc_start: 0.7219 (mm) cc_final: 0.6883 (tp) REVERT: U 214 PHE cc_start: 0.3616 (m-80) cc_final: 0.2837 (m-80) REVERT: U 284 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7633 (mm-30) REVERT: V 130 ASN cc_start: 0.8063 (m-40) cc_final: 0.7824 (m-40) REVERT: V 283 LEU cc_start: 0.7818 (mt) cc_final: 0.7317 (tt) REVERT: W 307 GLU cc_start: 0.7252 (tt0) cc_final: 0.6934 (tt0) REVERT: W 324 MET cc_start: 0.6215 (mtt) cc_final: 0.5997 (mmm) outliers start: 1 outliers final: 0 residues processed: 465 average time/residue: 0.5320 time to fit residues: 426.0306 Evaluate side-chains 381 residues out of total 6068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 381 time to evaluate : 4.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 690 random chunks: chunk 604 optimal weight: 30.0000 chunk 637 optimal weight: 10.0000 chunk 581 optimal weight: 6.9990 chunk 619 optimal weight: 30.0000 chunk 636 optimal weight: 4.9990 chunk 373 optimal weight: 5.9990 chunk 269 optimal weight: 5.9990 chunk 486 optimal weight: 10.0000 chunk 190 optimal weight: 9.9990 chunk 560 optimal weight: 9.9990 chunk 586 optimal weight: 8.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1039 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 626 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 GLN D 43 ASN ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 90 ASN ** P 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 303 HIS V 403 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.5378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.087 59344 Z= 0.442 Angle : 0.736 14.944 80728 Z= 0.377 Chirality : 0.047 0.301 8984 Planarity : 0.005 0.085 9896 Dihedral : 15.523 178.663 9118 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 0.02 % Allowed : 0.69 % Favored : 99.29 % 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: -0.79 (0.10), residues: 6809 helix: 0.49 (0.10), residues: 2700 sheet: -1.00 (0.18), residues: 758 loop : -1.23 (0.11), residues: 3351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP M 398 HIS 0.013 0.002 HIS M 44 PHE 0.026 0.002 PHE O 148 TYR 0.038 0.002 TYR B1003 ARG 0.010 0.001 ARG Q 70 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13618 Ramachandran restraints generated. 6809 Oldfield, 0 Emsley, 6809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13618 Ramachandran restraints generated. 6809 Oldfield, 0 Emsley, 6809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 6068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 433 time to evaluate : 4.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 PHE cc_start: 0.7689 (m-80) cc_final: 0.7299 (m-80) REVERT: A 274 THR cc_start: 0.7970 (p) cc_final: 0.7741 (p) REVERT: A 474 MET cc_start: 0.7844 (mtp) cc_final: 0.7381 (mtp) REVERT: A 505 MET cc_start: 0.8050 (tpp) cc_final: 0.7583 (tpt) REVERT: A 724 CYS cc_start: 0.9180 (m) cc_final: 0.8961 (m) REVERT: A 912 MET cc_start: 0.8458 (tpp) cc_final: 0.7526 (tpp) REVERT: B 506 MET cc_start: 0.8686 (mpp) cc_final: 0.8356 (mpp) REVERT: B 588 ASP cc_start: 0.7559 (m-30) cc_final: 0.7341 (m-30) REVERT: B 689 MET cc_start: 0.5844 (mmp) cc_final: 0.5284 (mmt) REVERT: B 709 MET cc_start: 0.8956 (ttp) cc_final: 0.8612 (ttm) REVERT: B 719 MET cc_start: 0.9162 (mmm) cc_final: 0.8947 (tpp) REVERT: B 794 MET cc_start: 0.8249 (tmm) cc_final: 0.7715 (mmt) REVERT: B 916 MET cc_start: 0.9338 (mmt) cc_final: 0.8844 (mmm) REVERT: B 1015 MET cc_start: 0.8724 (mtp) cc_final: 0.8202 (mmm) REVERT: B 1050 MET cc_start: 0.7201 (pmm) cc_final: 0.6707 (pmm) REVERT: C 56 MET cc_start: 0.8518 (tmm) cc_final: 0.7448 (tmm) REVERT: C 87 MET cc_start: 0.8792 (mmm) cc_final: 0.8511 (mmm) REVERT: C 103 ASP cc_start: 0.8342 (m-30) cc_final: 0.8037 (m-30) REVERT: C 252 GLU cc_start: 0.8321 (mt-10) cc_final: 0.7546 (tp30) REVERT: C 256 CYS cc_start: 0.7819 (m) cc_final: 0.6677 (m) REVERT: C 330 MET cc_start: 0.8129 (mmm) cc_final: 0.7763 (mmt) REVERT: D 60 HIS cc_start: 0.7357 (m90) cc_final: 0.7108 (m90) REVERT: D 90 ARG cc_start: 0.4565 (mtm-85) cc_final: 0.2461 (tpt170) REVERT: D 107 ARG cc_start: 0.5796 (mtm180) cc_final: 0.5001 (mtm180) REVERT: E 27 LEU cc_start: 0.8569 (mt) cc_final: 0.8268 (mt) REVERT: E 94 MET cc_start: 0.6956 (mmp) cc_final: 0.6619 (mmp) REVERT: E 141 GLU cc_start: 0.8732 (tp30) cc_final: 0.8382 (tm-30) REVERT: G 106 ASP cc_start: 0.8306 (p0) cc_final: 0.7277 (t70) REVERT: G 150 PHE cc_start: 0.5176 (t80) cc_final: 0.3691 (t80) REVERT: H 74 GLU cc_start: 0.7663 (pp20) cc_final: 0.7211 (pp20) REVERT: H 123 MET cc_start: 0.8788 (tmm) cc_final: 0.7899 (tmm) REVERT: I 15 GLU cc_start: 0.7680 (tp30) cc_final: 0.6947 (tp30) REVERT: K 46 GLU cc_start: 0.7855 (tm-30) cc_final: 0.7481 (tm-30) REVERT: L 44 MET cc_start: 0.8889 (mmm) cc_final: 0.8350 (mmm) REVERT: M 250 MET cc_start: 0.9111 (tpp) cc_final: 0.8648 (tpp) REVERT: M 292 MET cc_start: 0.8770 (tpt) cc_final: 0.7962 (tpp) REVERT: M 319 MET cc_start: 0.8287 (mmm) cc_final: 0.7956 (mmm) REVERT: N 157 MET cc_start: 0.1249 (ptp) cc_final: 0.1046 (ptp) REVERT: N 256 ARG cc_start: 0.8514 (tmm160) cc_final: 0.8154 (ttp80) REVERT: N 341 LEU cc_start: 0.9010 (tp) cc_final: 0.8648 (tt) REVERT: N 373 MET cc_start: 0.6892 (mpp) cc_final: 0.6239 (mpp) REVERT: O 8 LEU cc_start: 0.9366 (tp) cc_final: 0.9131 (tp) REVERT: O 85 MET cc_start: 0.8338 (ptt) cc_final: 0.8067 (ptp) REVERT: O 398 MET cc_start: 0.8188 (ttm) cc_final: 0.7682 (ttp) REVERT: O 404 MET cc_start: 0.8578 (mtm) cc_final: 0.8269 (mtm) REVERT: P 85 MET cc_start: 0.0359 (mpp) cc_final: -0.0005 (mpp) REVERT: P 125 LYS cc_start: 0.7155 (tppt) cc_final: 0.6920 (mmtm) REVERT: P 267 MET cc_start: 0.4299 (mmm) cc_final: 0.3308 (tpp) REVERT: P 297 HIS cc_start: 0.7491 (t-90) cc_final: 0.7078 (t-90) REVERT: Q 71 MET cc_start: 0.8924 (ttp) cc_final: 0.8434 (ttm) REVERT: Q 111 MET cc_start: 0.7505 (mpp) cc_final: 0.7143 (tpt) REVERT: 1 53 MET cc_start: 0.6317 (mmm) cc_final: 0.5999 (ppp) REVERT: 1 96 LYS cc_start: 0.0861 (mtmm) cc_final: 0.0617 (mttt) REVERT: 3 136 PHE cc_start: 0.6305 (m-80) cc_final: 0.5422 (t80) REVERT: 4 348 GLU cc_start: 0.5297 (tp30) cc_final: 0.4929 (mm-30) REVERT: 4 377 TYR cc_start: 0.4393 (t80) cc_final: 0.3926 (t80) REVERT: 4 385 MET cc_start: 0.1318 (tmm) cc_final: 0.1018 (mtt) REVERT: 4 429 GLU cc_start: -0.0321 (mm-30) cc_final: -0.0536 (pt0) REVERT: U 179 ASP cc_start: 0.8020 (t70) cc_final: 0.7334 (m-30) REVERT: U 212 LEU cc_start: 0.7002 (mm) cc_final: 0.6463 (tp) REVERT: U 284 GLU cc_start: 0.7965 (mm-30) cc_final: 0.7739 (mm-30) REVERT: W 324 MET cc_start: 0.6197 (mtt) cc_final: 0.5888 (mmm) outliers start: 1 outliers final: 0 residues processed: 434 average time/residue: 0.5498 time to fit residues: 412.2038 Evaluate side-chains 358 residues out of total 6068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 358 time to evaluate : 4.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 690 random chunks: chunk 617 optimal weight: 30.0000 chunk 406 optimal weight: 8.9990 chunk 655 optimal weight: 0.9990 chunk 399 optimal weight: 7.9990 chunk 310 optimal weight: 6.9990 chunk 455 optimal weight: 3.9990 chunk 687 optimal weight: 6.9990 chunk 632 optimal weight: 3.9990 chunk 547 optimal weight: 20.0000 chunk 56 optimal weight: 0.8980 chunk 422 optimal weight: 3.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 872 GLN ** A1039 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 626 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 43 ASN ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 GLN I 74 HIS I 83 GLN ** M 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 34 GLN ** O 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 314 GLN ** 4 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 303 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.5306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 59344 Z= 0.226 Angle : 0.579 13.021 80728 Z= 0.299 Chirality : 0.042 0.460 8984 Planarity : 0.004 0.083 9896 Dihedral : 15.389 177.939 9118 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.02 % Allowed : 0.33 % Favored : 99.65 % 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: -0.48 (0.10), residues: 6809 helix: 0.78 (0.10), residues: 2690 sheet: -0.90 (0.18), residues: 743 loop : -1.06 (0.11), residues: 3376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP M 398 HIS 0.008 0.001 HIS M 44 PHE 0.020 0.001 PHE V 402 TYR 0.033 0.001 TYR B1003 ARG 0.007 0.000 ARG N 369 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13618 Ramachandran restraints generated. 6809 Oldfield, 0 Emsley, 6809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13618 Ramachandran restraints generated. 6809 Oldfield, 0 Emsley, 6809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 6068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 436 time to evaluate : 4.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 PHE cc_start: 0.7744 (m-80) cc_final: 0.6789 (m-10) REVERT: A 274 THR cc_start: 0.7957 (p) cc_final: 0.7680 (p) REVERT: A 474 MET cc_start: 0.8069 (mtp) cc_final: 0.7628 (mtp) REVERT: A 505 MET cc_start: 0.7980 (tpp) cc_final: 0.7552 (tpt) REVERT: A 560 ASP cc_start: 0.8350 (p0) cc_final: 0.7995 (p0) REVERT: A 724 CYS cc_start: 0.9101 (m) cc_final: 0.8881 (m) REVERT: A 749 GLU cc_start: 0.8277 (mm-30) cc_final: 0.7792 (mm-30) REVERT: A 1027 MET cc_start: 0.8116 (tpt) cc_final: 0.7601 (tpt) REVERT: B 243 MET cc_start: 0.8427 (ttm) cc_final: 0.8080 (ttm) REVERT: B 689 MET cc_start: 0.5942 (mmp) cc_final: 0.5200 (mmt) REVERT: B 709 MET cc_start: 0.8797 (ttp) cc_final: 0.8383 (ttm) REVERT: B 719 MET cc_start: 0.9067 (mmm) cc_final: 0.8748 (tpp) REVERT: B 744 MET cc_start: 0.8877 (ptm) cc_final: 0.8596 (ptm) REVERT: B 794 MET cc_start: 0.8223 (tmm) cc_final: 0.7616 (mmt) REVERT: B 916 MET cc_start: 0.9371 (mmt) cc_final: 0.8943 (mmm) REVERT: B 1015 MET cc_start: 0.8691 (mtp) cc_final: 0.8239 (mmm) REVERT: B 1020 MET cc_start: 0.8081 (ttm) cc_final: 0.7322 (tpp) REVERT: B 1050 MET cc_start: 0.7521 (pmm) cc_final: 0.7232 (pmm) REVERT: C 56 MET cc_start: 0.8647 (tmm) cc_final: 0.7633 (tmm) REVERT: C 87 MET cc_start: 0.8808 (mmm) cc_final: 0.8514 (mmt) REVERT: C 103 ASP cc_start: 0.8500 (m-30) cc_final: 0.8156 (m-30) REVERT: C 252 GLU cc_start: 0.8316 (mt-10) cc_final: 0.7471 (tp30) REVERT: C 256 CYS cc_start: 0.7885 (m) cc_final: 0.6800 (m) REVERT: D 22 ASP cc_start: 0.7144 (m-30) cc_final: 0.6228 (t0) REVERT: D 60 HIS cc_start: 0.7095 (m90) cc_final: 0.6890 (m170) REVERT: D 90 ARG cc_start: 0.4370 (mtm-85) cc_final: 0.2286 (tpt170) REVERT: E 27 LEU cc_start: 0.8634 (mt) cc_final: 0.8303 (mt) REVERT: E 94 MET cc_start: 0.6877 (mmp) cc_final: 0.6606 (mmp) REVERT: E 141 GLU cc_start: 0.8736 (tp30) cc_final: 0.8404 (tm-30) REVERT: G 106 ASP cc_start: 0.8258 (p0) cc_final: 0.7158 (t70) REVERT: H 64 LEU cc_start: 0.8320 (tp) cc_final: 0.7946 (tt) REVERT: H 74 GLU cc_start: 0.7490 (pp20) cc_final: 0.7034 (pp20) REVERT: H 90 TYR cc_start: 0.8337 (t80) cc_final: 0.7936 (t80) REVERT: H 107 GLU cc_start: 0.5860 (mp0) cc_final: 0.4859 (pm20) REVERT: H 118 TYR cc_start: 0.8218 (m-80) cc_final: 0.7612 (m-80) REVERT: H 123 MET cc_start: 0.8786 (tmm) cc_final: 0.8414 (tmm) REVERT: I 15 GLU cc_start: 0.7612 (tp30) cc_final: 0.6909 (tp30) REVERT: K 46 GLU cc_start: 0.7894 (tm-30) cc_final: 0.7685 (tm-30) REVERT: K 70 TYR cc_start: 0.8523 (p90) cc_final: 0.8274 (p90) REVERT: L 44 MET cc_start: 0.8941 (mmm) cc_final: 0.8289 (mmm) REVERT: M 292 MET cc_start: 0.8751 (tpt) cc_final: 0.7917 (tpp) REVERT: M 319 MET cc_start: 0.8292 (mmm) cc_final: 0.7960 (mmm) REVERT: N 157 MET cc_start: 0.1774 (ptp) cc_final: 0.0992 (ppp) REVERT: N 256 ARG cc_start: 0.8452 (tmm160) cc_final: 0.8076 (ttp80) REVERT: N 341 LEU cc_start: 0.9044 (tp) cc_final: 0.8708 (tt) REVERT: N 373 MET cc_start: 0.7092 (mpp) cc_final: 0.6354 (mpp) REVERT: O 8 LEU cc_start: 0.9374 (tp) cc_final: 0.9143 (tp) REVERT: O 85 MET cc_start: 0.8265 (ptt) cc_final: 0.7973 (ptp) REVERT: O 398 MET cc_start: 0.8187 (ttm) cc_final: 0.7635 (ttp) REVERT: O 404 MET cc_start: 0.8527 (mtm) cc_final: 0.8010 (mtm) REVERT: P 85 MET cc_start: 0.0399 (mpp) cc_final: 0.0186 (mpp) REVERT: P 125 LYS cc_start: 0.7149 (tppt) cc_final: 0.6939 (mmtm) REVERT: P 267 MET cc_start: 0.4384 (mmm) cc_final: 0.3939 (tpp) REVERT: P 297 HIS cc_start: 0.7296 (t-90) cc_final: 0.6897 (t-90) REVERT: Q 71 MET cc_start: 0.8999 (ttp) cc_final: 0.8424 (ttm) REVERT: Q 111 MET cc_start: 0.7499 (mpp) cc_final: 0.7198 (tpt) REVERT: 1 46 MET cc_start: 0.2747 (tmm) cc_final: 0.2107 (tmm) REVERT: 1 53 MET cc_start: 0.6453 (mmm) cc_final: 0.6140 (ppp) REVERT: 1 96 LYS cc_start: 0.0911 (mtmm) cc_final: 0.0653 (mttt) REVERT: 3 136 PHE cc_start: 0.6218 (m-80) cc_final: 0.5375 (t80) REVERT: 4 348 GLU cc_start: 0.5103 (tp30) cc_final: 0.4799 (mm-30) REVERT: 4 364 MET cc_start: 0.2321 (tmm) cc_final: 0.1705 (mmp) REVERT: 4 377 TYR cc_start: 0.4288 (t80) cc_final: 0.3758 (t80) REVERT: 4 385 MET cc_start: 0.1388 (tmm) cc_final: 0.1096 (mtt) REVERT: U 179 ASP cc_start: 0.8212 (t70) cc_final: 0.7671 (m-30) REVERT: U 212 LEU cc_start: 0.7044 (mm) cc_final: 0.6708 (tp) REVERT: U 214 PHE cc_start: 0.3329 (m-80) cc_final: 0.3012 (m-80) REVERT: U 284 GLU cc_start: 0.7915 (mm-30) cc_final: 0.7653 (mm-30) REVERT: V 283 LEU cc_start: 0.7964 (mt) cc_final: 0.7748 (tp) REVERT: W 307 GLU cc_start: 0.7502 (tt0) cc_final: 0.7284 (tt0) outliers start: 1 outliers final: 0 residues processed: 437 average time/residue: 0.5431 time to fit residues: 414.3821 Evaluate side-chains 367 residues out of total 6068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 367 time to evaluate : 5.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 690 random chunks: chunk 335 optimal weight: 6.9990 chunk 434 optimal weight: 7.9990 chunk 583 optimal weight: 20.0000 chunk 167 optimal weight: 4.9990 chunk 504 optimal weight: 7.9990 chunk 80 optimal weight: 2.9990 chunk 152 optimal weight: 1.9990 chunk 548 optimal weight: 8.9990 chunk 229 optimal weight: 6.9990 chunk 562 optimal weight: 6.9990 chunk 69 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1039 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 626 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 314 GLN ** 4 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 485 HIS V 62 ASN ** V 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 303 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.090163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.067288 restraints weight = 217909.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.067018 restraints weight = 172175.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.067087 restraints weight = 138984.294| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3189 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3189 r_free = 0.3189 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 83 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3189 r_free = 0.3189 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 83 | |-----------------------------------------------------------------------------| r_final: 0.3189 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.5494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 59344 Z= 0.302 Angle : 0.622 11.358 80728 Z= 0.320 Chirality : 0.043 0.458 8984 Planarity : 0.004 0.086 9896 Dihedral : 15.429 177.381 9118 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 0.02 % Allowed : 0.23 % Favored : 99.75 % 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: -0.58 (0.10), residues: 6809 helix: 0.70 (0.10), residues: 2696 sheet: -0.98 (0.18), residues: 755 loop : -1.13 (0.11), residues: 3358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP M 398 HIS 0.010 0.001 HIS M 44 PHE 0.020 0.002 PHE V 402 TYR 0.032 0.002 TYR B1003 ARG 0.006 0.001 ARG B 900 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9794.18 seconds wall clock time: 175 minutes 53.26 seconds (10553.26 seconds total)