Starting phenix.real_space_refine on Fri Dec 8 16:03:41 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iuh_35722/12_2023/8iuh_35722_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iuh_35722/12_2023/8iuh_35722.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iuh_35722/12_2023/8iuh_35722.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iuh_35722/12_2023/8iuh_35722.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iuh_35722/12_2023/8iuh_35722_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iuh_35722/12_2023/8iuh_35722_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Fe 4 7.16 5 Zn 8 6.06 5 P 162 5.49 5 Mg 1 5.21 5 S 358 5.16 5 C 36357 2.51 5 N 10187 2.21 5 O 11162 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "1 PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ASP 132": "OD1" <-> "OD2" Residue "1 ARG 133": "NH1" <-> "NH2" Residue "1 PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 337": "NH1" <-> "NH2" Residue "3 TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 163": "OE1" <-> "OE2" Residue "4 GLU 178": "OE1" <-> "OE2" Residue "4 PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 279": "OE1" <-> "OE2" Residue "4 PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 390": "NH1" <-> "NH2" Residue "4 TYR 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 407": "OE1" <-> "OE2" Residue "4 GLU 408": "OE1" <-> "OE2" Residue "4 PHE 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 482": "OE1" <-> "OE2" Residue "A PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 488": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 848": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 900": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 958": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 987": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 521": "OE1" <-> "OE2" Residue "B PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 584": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 851": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 914": "OE1" <-> "OE2" Residue "B PHE 934": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 958": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 25": "OE1" <-> "OE2" Residue "L PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 299": "NH1" <-> "NH2" Residue "V TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 364": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 58239 Number of models: 1 Model: "" Number of chains: 32 Chain: "1" Number of atoms: 1233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1233 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 6, 'TRANS': 139} Chain: "3" Number of atoms: 3037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 3037 Classifications: {'peptide': 374} Link IDs: {'PTRANS': 16, 'TRANS': 357} Chain breaks: 2 Chain: "4" Number of atoms: 3058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 3058 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 10, 'TRANS': 354} Chain: "A" Number of atoms: 10814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1378, 10814 Classifications: {'peptide': 1378} Link IDs: {'PTRANS': 64, 'TRANS': 1313} Chain: "B" Number of atoms: 8680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1097, 8680 Classifications: {'peptide': 1097} Link IDs: {'PTRANS': 50, 'TRANS': 1046} Chain breaks: 2 Chain: "C" Number of atoms: 2736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2736 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 17, 'TRANS': 325} Chain: "D" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 985 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "E" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1715 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "F" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 610 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 5, 'TRANS': 70} Chain: "G" Number of atoms: 1337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1337 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 10, 'TRANS': 155} Chain breaks: 2 Chain: "H" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1186 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain: "I" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 848 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "J" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 512 Classifications: {'peptide': 65} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 62} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 822 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 4, 'TRANS': 98} Chain: "L" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 388 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "M" Number of atoms: 3382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3382 Classifications: {'peptide': 422} Link IDs: {'PTRANS': 23, 'TRANS': 398} Chain breaks: 1 Chain: "N" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1128 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 6, 'TRANS': 139} Chain breaks: 2 Chain: "O" Number of atoms: 4075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 4075 Classifications: {'peptide': 512} Link IDs: {'PTRANS': 22, 'TRANS': 489} Chain breaks: 1 Chain: "P" Number of atoms: 2403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2403 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 12, 'TRANS': 290} Chain: "Q" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 754 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 12, 'TRANS': 74} Chain: "U" Number of atoms: 1396 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 176, 1391 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 9, 'TRANS': 166} Conformer: "B" Number of residues, atoms: 176, 1391 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 9, 'TRANS': 166} bond proxies already assigned to first conformer: 1410 Chain: "V" Number of atoms: 2853 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 361, 2847 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 19, 'TRANS': 341} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 361, 2847 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 19, 'TRANS': 341} Chain breaks: 1 bond proxies already assigned to first conformer: 2891 Chain: "W" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 943 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 4, 'TRANS': 106} Chain: "X" Number of atoms: 1661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 1661 Classifications: {'DNA': 81} Link IDs: {'rna3p': 80} Chain breaks: 1 Chain: "Y" Number of atoms: 1666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 1666 Classifications: {'DNA': 81} Link IDs: {'rna3p': 80} Chain breaks: 1 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 7871 SG CYS A 69 109.137 132.778 148.280 1.00103.58 S ATOM 7893 SG CYS A 72 109.907 132.308 152.006 1.00106.71 S ATOM 7941 SG CYS A 79 107.629 129.552 150.268 1.00104.11 S ATOM 8182 SG CYS A 109 65.397 153.139 151.996 1.00114.77 S ATOM 8204 SG CYS A 112 67.134 155.703 154.704 1.00118.64 S ATOM 8573 SG CYS A 156 63.635 154.956 155.411 1.00130.18 S ATOM 8599 SG CYS A 159 64.500 157.380 152.746 1.00130.36 S ATOM 26409 SG CYS B1080 101.067 139.826 164.241 1.00102.14 S ATOM 26428 SG CYS B1083 98.056 140.039 161.547 1.00101.99 S ATOM 26494 SG CYS B1092 101.541 140.041 160.419 1.00 97.16 S ATOM 26522 SG CYS B1095 99.532 143.498 162.083 1.00100.21 S ATOM 35432 SG CYS I 5 23.985 115.044 118.636 1.00130.73 S ATOM 35449 SG CYS I 8 27.788 116.653 117.982 1.00130.05 S ATOM 35579 SG CYS I 25 27.269 118.429 121.229 1.00130.27 S ATOM 35600 SG CYS I 28 24.662 118.525 118.455 1.00128.16 S ATOM 35921 SG CYS I 69 61.953 75.683 175.179 1.00228.50 S ATOM 35943 SG CYS I 72 59.675 77.278 177.673 1.00234.26 S ATOM 36155 SG CYS I 97 58.470 76.329 174.505 1.00227.88 S ATOM 36294 SG CYS J 7 104.067 61.500 144.102 1.00 75.41 S ATOM 36318 SG CYS J 10 105.720 58.876 146.188 1.00 75.83 S ATOM 36582 SG CYS J 44 102.122 58.455 145.602 1.00 81.33 S ATOM 36588 SG CYS J 45 104.495 57.244 142.752 1.00 82.39 S ATOM 37631 SG CYS L 19 116.948 86.595 112.394 1.00103.46 S ATOM 37767 SG CYS L 36 118.079 89.113 110.058 1.00117.09 S ATOM 37793 SG CYS L 39 114.962 88.724 108.283 1.00117.30 S ATOM 51116 SG CYS V 7 131.053 115.313 157.078 1.00178.33 S ATOM 51294 SG CYS V 31 132.811 111.317 158.827 1.00175.49 S Residues with excluded nonbonded symmetry interactions: 12 residue: pdb=" N ACYS V 177 " occ=0.47 ... (10 atoms not shown) pdb=" SG BCYS V 177 " occ=0.53 residue: pdb=" N LYS V 364 " occ=0.00 ... (7 atoms not shown) pdb=" NZ LYS V 364 " occ=0.00 residue: pdb=" N SER V 365 " occ=0.00 ... (4 atoms not shown) pdb=" OG SER V 365 " occ=0.00 residue: pdb=" N PRO V 366 " occ=0.00 ... (5 atoms not shown) pdb=" CD PRO V 366 " occ=0.00 residue: pdb=" N LYS V 367 " occ=0.00 ... (7 atoms not shown) pdb=" NZ LYS V 367 " occ=0.00 residue: pdb=" N ARG V 368 " occ=0.00 ... (9 atoms not shown) pdb=" NH2 ARG V 368 " occ=0.00 residue: pdb=" N ILE V 369 " occ=0.00 ... (6 atoms not shown) pdb=" CD1 ILE V 369 " occ=0.00 residue: pdb=" N CYS V 370 " occ=0.00 ... (4 atoms not shown) pdb=" SG CYS V 370 " occ=0.00 residue: pdb=" N PRO V 371 " occ=0.00 ... (5 atoms not shown) pdb=" CD PRO V 371 " occ=0.00 residue: pdb=" N SER V 376 " occ=0.00 ... (4 atoms not shown) pdb=" OG SER V 376 " occ=0.00 residue: pdb=" N THR V 377 " occ=0.00 ... (5 atoms not shown) pdb=" CG2 THR V 377 " occ=0.00 residue: pdb=" N VAL V 378 " occ=0.00 ... (5 atoms not shown) pdb=" CG2 VAL V 378 " occ=0.00 Time building chain proxies: 23.43, per 1000 atoms: 0.40 Number of scatterers: 58239 At special positions: 0 Unit cell: (162.748, 212.106, 228.114, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 8 29.99 Fe 4 26.01 S 358 16.00 P 162 15.00 Mg 1 11.99 O 11162 8.00 N 10187 7.00 C 36357 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 17.94 Conformation dependent library (CDL) restraints added in 7.9 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 P 401 " pdb="FE1 SF4 P 401 " - pdb=" SG CYS P 290 " pdb="FE4 SF4 P 401 " - pdb=" SG CYS P 307 " pdb="FE3 SF4 P 401 " - pdb=" SG CYS P 287 " pdb="FE2 SF4 P 401 " - pdb=" SG CYS P 296 " Number of angles added : 12 Zn2+ tetrahedral coordination pdb=" ZN A1401 " pdb="ZN ZN A1401 " - pdb=" NE2 HIS A 82 " pdb="ZN ZN A1401 " - pdb=" SG CYS A 79 " pdb="ZN ZN A1401 " - pdb=" SG CYS A 69 " pdb="ZN ZN A1401 " - pdb=" SG CYS A 72 " pdb=" ZN A1402 " pdb="ZN ZN A1402 " - pdb=" SG CYS A 112 " pdb="ZN ZN A1402 " - pdb=" SG CYS A 109 " pdb="ZN ZN A1402 " - pdb=" SG CYS A 159 " pdb="ZN ZN A1402 " - pdb=" SG CYS A 156 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1095 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1080 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1092 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1083 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 8 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 28 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 25 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 5 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 72 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 69 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 97 " pdb=" ZN J2000 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 7 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 44 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 45 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 10 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 39 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 19 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb=" ZN V 700 " pdb="ZN ZN V 700 " - pdb=" SG CYS V 7 " pdb="ZN ZN V 700 " - pdb=" SG CYS V 31 " Number of angles added : 27 13598 Ramachandran restraints generated. 6799 Oldfield, 0 Emsley, 6799 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12954 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 261 helices and 61 sheets defined 38.5% alpha, 11.0% beta 27 base pairs and 102 stacking pairs defined. Time for finding SS restraints: 19.18 Creating SS restraints... Processing helix chain '1' and resid 5 through 20 removed outlier: 3.604A pdb=" N THR 1 9 " --> pdb=" O PRO 1 5 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLU 1 12 " --> pdb=" O GLN 1 8 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER 1 16 " --> pdb=" O GLU 1 12 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ARG 1 17 " --> pdb=" O ALA 1 13 " (cutoff:3.500A) Processing helix chain '1' and resid 27 through 34 removed outlier: 3.832A pdb=" N ARG 1 34 " --> pdb=" O THR 1 30 " (cutoff:3.500A) Processing helix chain '1' and resid 49 through 66 removed outlier: 3.832A pdb=" N TYR 1 65 " --> pdb=" O LEU 1 61 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N PHE 1 66 " --> pdb=" O ALA 1 62 " (cutoff:3.500A) Processing helix chain '1' and resid 72 through 87 Processing helix chain '1' and resid 103 through 116 removed outlier: 3.783A pdb=" N GLU 1 106 " --> pdb=" O ASP 1 103 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N VAL 1 107 " --> pdb=" O TRP 1 104 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU 1 108 " --> pdb=" O ASP 1 105 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASN 1 116 " --> pdb=" O ASP 1 113 " (cutoff:3.500A) Processing helix chain '1' and resid 120 through 131 removed outlier: 3.670A pdb=" N PHE 1 126 " --> pdb=" O ALA 1 122 " (cutoff:3.500A) Processing helix chain '3' and resid 44 through 54 removed outlier: 4.856A pdb=" N TRP 3 51 " --> pdb=" O GLY 3 48 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ARG 3 54 " --> pdb=" O TRP 3 51 " (cutoff:3.500A) Processing helix chain '3' and resid 77 through 89 removed outlier: 4.198A pdb=" N ARG 3 88 " --> pdb=" O ALA 3 84 " (cutoff:3.500A) Processing helix chain '3' and resid 98 through 105 Processing helix chain '3' and resid 128 through 142 Processing helix chain '3' and resid 151 through 163 removed outlier: 4.024A pdb=" N VAL 3 156 " --> pdb=" O GLN 3 152 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ALA 3 163 " --> pdb=" O MET 3 159 " (cutoff:3.500A) Processing helix chain '3' and resid 171 through 173 No H-bonds generated for 'chain '3' and resid 171 through 173' Processing helix chain '3' and resid 212 through 218 Processing helix chain '3' and resid 222 through 224 No H-bonds generated for 'chain '3' and resid 222 through 224' Processing helix chain '3' and resid 243 through 246 No H-bonds generated for 'chain '3' and resid 243 through 246' Processing helix chain '3' and resid 270 through 279 removed outlier: 3.795A pdb=" N THR 3 273 " --> pdb=" O LEU 3 270 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ILE 3 274 " --> pdb=" O SER 3 271 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ILE 3 275 " --> pdb=" O ARG 3 272 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TRP 3 277 " --> pdb=" O ILE 3 274 " (cutoff:3.500A) Processing helix chain '3' and resid 298 through 300 No H-bonds generated for 'chain '3' and resid 298 through 300' Processing helix chain '3' and resid 381 through 388 removed outlier: 4.012A pdb=" N HIS 3 388 " --> pdb=" O PHE 3 384 " (cutoff:3.500A) Processing helix chain '3' and resid 407 through 409 No H-bonds generated for 'chain '3' and resid 407 through 409' Processing helix chain '4' and resid 164 through 170 Processing helix chain '4' and resid 186 through 221 Proline residue: 4 207 - end of helix Processing helix chain '4' and resid 225 through 246 Processing helix chain '4' and resid 252 through 254 No H-bonds generated for 'chain '4' and resid 252 through 254' Processing helix chain '4' and resid 263 through 268 Processing helix chain '4' and resid 277 through 285 removed outlier: 3.656A pdb=" N PHE 4 283 " --> pdb=" O GLU 4 279 " (cutoff:3.500A) Processing helix chain '4' and resid 302 through 312 Processing helix chain '4' and resid 317 through 324 Processing helix chain '4' and resid 330 through 340 removed outlier: 3.591A pdb=" N GLN 4 335 " --> pdb=" O PHE 4 331 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N LYS 4 336 " --> pdb=" O GLN 4 332 " (cutoff:3.500A) Processing helix chain '4' and resid 352 through 364 removed outlier: 3.615A pdb=" N MET 4 356 " --> pdb=" O GLU 4 352 " (cutoff:3.500A) Processing helix chain '4' and resid 372 through 378 Processing helix chain '4' and resid 388 through 391 Processing helix chain '4' and resid 408 through 411 No H-bonds generated for 'chain '4' and resid 408 through 411' Processing helix chain '4' and resid 413 through 418 Processing helix chain '4' and resid 424 through 428 removed outlier: 3.723A pdb=" N ARG 4 428 " --> pdb=" O PHE 4 425 " (cutoff:3.500A) Processing helix chain '4' and resid 436 through 447 removed outlier: 3.798A pdb=" N ASP 4 441 " --> pdb=" O ALA 4 437 " (cutoff:3.500A) Processing helix chain '4' and resid 460 through 467 Processing helix chain '4' and resid 478 through 481 Processing helix chain '4' and resid 488 through 501 removed outlier: 5.274A pdb=" N SER 4 493 " --> pdb=" O SER 4 489 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N LYS 4 494 " --> pdb=" O GLN 4 490 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ILE 4 497 " --> pdb=" O SER 4 493 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N MET 4 499 " --> pdb=" O TRP 4 495 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N GLY 4 500 " --> pdb=" O LYS 4 496 " (cutoff:3.500A) Processing helix chain '4' and resid 505 through 512 removed outlier: 4.827A pdb=" N ARG 4 511 " --> pdb=" O ARG 4 507 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N ALA 4 512 " --> pdb=" O ARG 4 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 31 Processing helix chain 'A' and resid 58 through 60 No H-bonds generated for 'chain 'A' and resid 58 through 60' Processing helix chain 'A' and resid 95 through 107 removed outlier: 4.410A pdb=" N ARG A 99 " --> pdb=" O VAL A 95 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N ALA A 100 " --> pdb=" O GLY A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 129 Processing helix chain 'A' and resid 136 through 152 Processing helix chain 'A' and resid 188 through 203 removed outlier: 4.289A pdb=" N PHE A 197 " --> pdb=" O PHE A 193 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N GLU A 198 " --> pdb=" O LEU A 194 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N THR A 199 " --> pdb=" O GLN A 195 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N ALA A 200 " --> pdb=" O SER A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 211 Proline residue: A 209 - end of helix Processing helix chain 'A' and resid 220 through 229 removed outlier: 3.609A pdb=" N ARG A 229 " --> pdb=" O ASN A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 234 No H-bonds generated for 'chain 'A' and resid 232 through 234' Processing helix chain 'A' and resid 236 through 238 No H-bonds generated for 'chain 'A' and resid 236 through 238' Processing helix chain 'A' and resid 247 through 249 No H-bonds generated for 'chain 'A' and resid 247 through 249' Processing helix chain 'A' and resid 278 through 299 Processing helix chain 'A' and resid 303 through 321 Processing helix chain 'A' and resid 341 through 345 Processing helix chain 'A' and resid 351 through 355 Processing helix chain 'A' and resid 384 through 387 No H-bonds generated for 'chain 'A' and resid 384 through 387' Processing helix chain 'A' and resid 401 through 410 Processing helix chain 'A' and resid 437 through 442 Processing helix chain 'A' and resid 470 through 472 No H-bonds generated for 'chain 'A' and resid 470 through 472' Processing helix chain 'A' and resid 490 through 496 removed outlier: 4.389A pdb=" N THR A 494 " --> pdb=" O CYS A 491 " (cutoff:3.500A) Proline residue: A 495 - end of helix Processing helix chain 'A' and resid 513 through 522 Processing helix chain 'A' and resid 546 through 552 Processing helix chain 'A' and resid 561 through 571 removed outlier: 4.392A pdb=" N ILE A 571 " --> pdb=" O ILE A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 578 removed outlier: 3.781A pdb=" N LYS A 578 " --> pdb=" O LYS A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 605 removed outlier: 3.742A pdb=" N ILE A 604 " --> pdb=" O ILE A 600 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU A 605 " --> pdb=" O PHE A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 655 No H-bonds generated for 'chain 'A' and resid 652 through 655' Processing helix chain 'A' and resid 663 through 671 Processing helix chain 'A' and resid 673 through 694 Proline residue: A 688 - end of helix Processing helix chain 'A' and resid 700 through 702 No H-bonds generated for 'chain 'A' and resid 700 through 702' Processing helix chain 'A' and resid 707 through 732 Processing helix chain 'A' and resid 744 through 770 Processing helix chain 'A' and resid 776 through 782 Processing helix chain 'A' and resid 789 through 796 Processing helix chain 'A' and resid 844 through 879 removed outlier: 3.639A pdb=" N ALA A 866 " --> pdb=" O ALA A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 902 through 904 No H-bonds generated for 'chain 'A' and resid 902 through 904' Processing helix chain 'A' and resid 909 through 911 No H-bonds generated for 'chain 'A' and resid 909 through 911' Processing helix chain 'A' and resid 921 through 931 Processing helix chain 'A' and resid 942 through 953 Processing helix chain 'A' and resid 963 through 986 Processing helix chain 'A' and resid 998 through 1002 Processing helix chain 'A' and resid 1008 through 1024 Processing helix chain 'A' and resid 1033 through 1047 Proline residue: A1044 - end of helix Processing helix chain 'A' and resid 1067 through 1075 Processing helix chain 'A' and resid 1095 through 1105 Processing helix chain 'A' and resid 1110 through 1113 No H-bonds generated for 'chain 'A' and resid 1110 through 1113' Processing helix chain 'A' and resid 1134 through 1140 Processing helix chain 'A' and resid 1146 through 1152 Processing helix chain 'A' and resid 1186 through 1195 removed outlier: 5.003A pdb=" N GLN A1190 " --> pdb=" O TYR A1187 " (cutoff:3.500A) Processing helix chain 'A' and resid 1232 through 1237 Processing helix chain 'A' and resid 1243 through 1245 No H-bonds generated for 'chain 'A' and resid 1243 through 1245' Processing helix chain 'A' and resid 1251 through 1258 Processing helix chain 'A' and resid 1260 through 1278 removed outlier: 3.883A pdb=" N HIS A1278 " --> pdb=" O THR A1274 " (cutoff:3.500A) Processing helix chain 'A' and resid 1284 through 1294 Processing helix chain 'A' and resid 1305 through 1311 Processing helix chain 'A' and resid 1315 through 1321 Processing helix chain 'A' and resid 1324 through 1334 Processing helix chain 'A' and resid 1343 through 1349 Processing helix chain 'A' and resid 1356 through 1358 No H-bonds generated for 'chain 'A' and resid 1356 through 1358' Processing helix chain 'B' and resid 24 through 35 removed outlier: 4.318A pdb=" N TRP B 27 " --> pdb=" O GLU B 24 " (cutoff:3.500A) Proline residue: B 31 - end of helix Processing helix chain 'B' and resid 41 through 52 Processing helix chain 'B' and resid 54 through 61 Processing helix chain 'B' and resid 99 through 104 Processing helix chain 'B' and resid 152 through 157 Processing helix chain 'B' and resid 236 through 242 Processing helix chain 'B' and resid 248 through 255 Processing helix chain 'B' and resid 259 through 274 Proline residue: B 267 - end of helix Processing helix chain 'B' and resid 280 through 290 Processing helix chain 'B' and resid 304 through 314 Processing helix chain 'B' and resid 329 through 345 Processing helix chain 'B' and resid 357 through 359 No H-bonds generated for 'chain 'B' and resid 357 through 359' Processing helix chain 'B' and resid 365 through 391 Processing helix chain 'B' and resid 402 through 405 Processing helix chain 'B' and resid 409 through 420 Processing helix chain 'B' and resid 445 through 453 removed outlier: 4.062A pdb=" N THR B 453 " --> pdb=" O LEU B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 475 No H-bonds generated for 'chain 'B' and resid 473 through 475' Processing helix chain 'B' and resid 509 through 517 Processing helix chain 'B' and resid 523 through 525 No H-bonds generated for 'chain 'B' and resid 523 through 525' Processing helix chain 'B' and resid 528 through 532 Processing helix chain 'B' and resid 552 through 565 Processing helix chain 'B' and resid 608 through 616 Processing helix chain 'B' and resid 621 through 626 Processing helix chain 'B' and resid 635 through 640 removed outlier: 3.952A pdb=" N ASP B 640 " --> pdb=" O ASN B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 661 through 664 Processing helix chain 'B' and resid 669 through 671 No H-bonds generated for 'chain 'B' and resid 669 through 671' Processing helix chain 'B' and resid 675 through 677 No H-bonds generated for 'chain 'B' and resid 675 through 677' Processing helix chain 'B' and resid 680 through 690 Processing helix chain 'B' and resid 723 through 728 Processing helix chain 'B' and resid 730 through 732 No H-bonds generated for 'chain 'B' and resid 730 through 732' Processing helix chain 'B' and resid 759 through 763 Processing helix chain 'B' and resid 931 through 937 Proline residue: B 935 - end of helix Processing helix chain 'B' and resid 940 through 955 Processing helix chain 'B' and resid 969 through 978 Processing helix chain 'B' and resid 1016 through 1019 No H-bonds generated for 'chain 'B' and resid 1016 through 1019' Processing helix chain 'B' and resid 1049 through 1058 Processing helix chain 'B' and resid 1061 through 1068 Processing helix chain 'B' and resid 1070 through 1073 No H-bonds generated for 'chain 'B' and resid 1070 through 1073' Processing helix chain 'B' and resid 1108 through 1119 Processing helix chain 'C' and resid 3 through 12 Processing helix chain 'C' and resid 42 through 48 Processing helix chain 'C' and resid 70 through 82 Processing helix chain 'C' and resid 103 through 111 Processing helix chain 'C' and resid 119 through 121 No H-bonds generated for 'chain 'C' and resid 119 through 121' Processing helix chain 'C' and resid 159 through 162 No H-bonds generated for 'chain 'C' and resid 159 through 162' Processing helix chain 'C' and resid 170 through 172 No H-bonds generated for 'chain 'C' and resid 170 through 172' Processing helix chain 'C' and resid 181 through 184 No H-bonds generated for 'chain 'C' and resid 181 through 184' Processing helix chain 'C' and resid 223 through 225 No H-bonds generated for 'chain 'C' and resid 223 through 225' Processing helix chain 'C' and resid 247 through 256 Processing helix chain 'C' and resid 278 through 280 No H-bonds generated for 'chain 'C' and resid 278 through 280' Processing helix chain 'C' and resid 318 through 343 Processing helix chain 'D' and resid 13 through 29 Processing helix chain 'D' and resid 33 through 38 Processing helix chain 'D' and resid 41 through 55 Processing helix chain 'D' and resid 63 through 76 removed outlier: 4.089A pdb=" N SER D 75 " --> pdb=" O THR D 71 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N HIS D 76 " --> pdb=" O ALA D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 89 Processing helix chain 'D' and resid 95 through 98 No H-bonds generated for 'chain 'D' and resid 95 through 98' Processing helix chain 'D' and resid 112 through 120 Processing helix chain 'E' and resid 5 through 24 Processing helix chain 'E' and resid 30 through 33 No H-bonds generated for 'chain 'E' and resid 30 through 33' Processing helix chain 'E' and resid 37 through 43 Processing helix chain 'E' and resid 84 through 97 Processing helix chain 'E' and resid 112 through 119 Processing helix chain 'E' and resid 132 through 135 No H-bonds generated for 'chain 'E' and resid 132 through 135' Processing helix chain 'E' and resid 153 through 163 Processing helix chain 'E' and resid 178 through 183 Processing helix chain 'F' and resid 59 through 75 Processing helix chain 'F' and resid 89 through 99 Processing helix chain 'G' and resid 15 through 17 No H-bonds generated for 'chain 'G' and resid 15 through 17' Processing helix chain 'G' and resid 22 through 33 Processing helix chain 'H' and resid 84 through 87 Processing helix chain 'I' and resid 56 through 59 No H-bonds generated for 'chain 'I' and resid 56 through 59' Processing helix chain 'J' and resid 15 through 26 removed outlier: 3.629A pdb=" N TRP J 18 " --> pdb=" O GLY J 15 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N GLU J 19 " --> pdb=" O ASN J 16 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ALA J 20 " --> pdb=" O LYS J 17 " (cutoff:3.500A) Processing helix chain 'J' and resid 31 through 37 Processing helix chain 'J' and resid 43 through 50 Processing helix chain 'J' and resid 56 through 62 removed outlier: 3.835A pdb=" N TYR J 62 " --> pdb=" O LYS J 58 " (cutoff:3.500A) Processing helix chain 'K' and resid 49 through 60 Processing helix chain 'K' and resid 94 through 125 Processing helix chain 'M' and resid 71 through 81 Processing helix chain 'M' and resid 141 through 160 Processing helix chain 'M' and resid 183 through 190 Processing helix chain 'M' and resid 193 through 202 Processing helix chain 'M' and resid 216 through 225 removed outlier: 4.079A pdb=" N GLN M 223 " --> pdb=" O GLU M 219 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N TYR M 224 " --> pdb=" O HIS M 220 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N LEU M 225 " --> pdb=" O GLU M 221 " (cutoff:3.500A) Processing helix chain 'M' and resid 242 through 249 Processing helix chain 'M' and resid 265 through 267 No H-bonds generated for 'chain 'M' and resid 265 through 267' Processing helix chain 'M' and resid 270 through 274 Processing helix chain 'M' and resid 278 through 288 Processing helix chain 'M' and resid 294 through 301 Processing helix chain 'M' and resid 307 through 317 removed outlier: 3.775A pdb=" N LYS M 316 " --> pdb=" O ARG M 312 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N VAL M 317 " --> pdb=" O GLY M 313 " (cutoff:3.500A) Processing helix chain 'M' and resid 329 through 332 No H-bonds generated for 'chain 'M' and resid 329 through 332' Processing helix chain 'M' and resid 346 through 362 Processing helix chain 'M' and resid 368 through 375 Processing helix chain 'M' and resid 379 through 387 Processing helix chain 'M' and resid 406 through 411 Processing helix chain 'M' and resid 413 through 434 Processing helix chain 'N' and resid 148 through 150 No H-bonds generated for 'chain 'N' and resid 148 through 150' Processing helix chain 'N' and resid 250 through 258 Processing helix chain 'N' and resid 333 through 335 No H-bonds generated for 'chain 'N' and resid 333 through 335' Processing helix chain 'N' and resid 389 through 395 Processing helix chain 'O' and resid 3 through 16 Processing helix chain 'O' and resid 20 through 31 removed outlier: 4.081A pdb=" N ILE O 24 " --> pdb=" O ILE O 20 " (cutoff:3.500A) Processing helix chain 'O' and resid 36 through 43 Processing helix chain 'O' and resid 47 through 59 Processing helix chain 'O' and resid 69 through 71 No H-bonds generated for 'chain 'O' and resid 69 through 71' Processing helix chain 'O' and resid 79 through 98 removed outlier: 4.091A pdb=" N LEU O 86 " --> pdb=" O VAL O 82 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ARG O 87 " --> pdb=" O LEU O 83 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N TYR O 88 " --> pdb=" O ARG O 84 " (cutoff:3.500A) Proline residue: O 89 - end of helix Processing helix chain 'O' and resid 101 through 113 Processing helix chain 'O' and resid 118 through 132 removed outlier: 3.988A pdb=" N GLU O 131 " --> pdb=" O ASP O 127 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N THR O 132 " --> pdb=" O ARG O 128 " (cutoff:3.500A) Processing helix chain 'O' and resid 141 through 153 Processing helix chain 'O' and resid 239 through 258 Processing helix chain 'O' and resid 261 through 277 removed outlier: 4.482A pdb=" N ILE O 276 " --> pdb=" O ARG O 272 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N THR O 277 " --> pdb=" O MET O 273 " (cutoff:3.500A) Processing helix chain 'O' and resid 290 through 296 Processing helix chain 'O' and resid 305 through 316 Processing helix chain 'O' and resid 338 through 358 Processing helix chain 'O' and resid 360 through 371 Processing helix chain 'O' and resid 377 through 384 Processing helix chain 'O' and resid 391 through 400 Processing helix chain 'O' and resid 417 through 419 No H-bonds generated for 'chain 'O' and resid 417 through 419' Processing helix chain 'O' and resid 428 through 472 removed outlier: 5.273A pdb=" N ARG O 459 " --> pdb=" O LYS O 455 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N LEU O 460 " --> pdb=" O GLU O 456 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ILE O 471 " --> pdb=" O VAL O 467 " (cutoff:3.500A) Processing helix chain 'O' and resid 481 through 483 No H-bonds generated for 'chain 'O' and resid 481 through 483' Processing helix chain 'O' and resid 492 through 529 removed outlier: 4.405A pdb=" N GLN O 497 " --> pdb=" O ALA O 493 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N GLN O 498 " --> pdb=" O PRO O 494 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASP O 517 " --> pdb=" O GLU O 513 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLU O 518 " --> pdb=" O ILE O 514 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N THR O 519 " --> pdb=" O GLN O 515 " (cutoff:3.500A) Processing helix chain 'P' and resid 15 through 28 Processing helix chain 'P' and resid 35 through 41 Processing helix chain 'P' and resid 47 through 60 Processing helix chain 'P' and resid 89 through 105 removed outlier: 5.676A pdb=" N ILE P 98 " --> pdb=" O LEU P 94 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N ASN P 104 " --> pdb=" O GLU P 100 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LYS P 105 " --> pdb=" O ASP P 101 " (cutoff:3.500A) Processing helix chain 'P' and resid 109 through 116 Processing helix chain 'P' and resid 120 through 132 Processing helix chain 'P' and resid 174 through 198 Processing helix chain 'P' and resid 202 through 209 Processing helix chain 'P' and resid 213 through 223 Processing helix chain 'P' and resid 232 through 244 Processing helix chain 'P' and resid 282 through 284 No H-bonds generated for 'chain 'P' and resid 282 through 284' Processing helix chain 'P' and resid 293 through 295 No H-bonds generated for 'chain 'P' and resid 293 through 295' Processing helix chain 'P' and resid 308 through 315 Processing helix chain 'Q' and resid 52 through 69 removed outlier: 3.929A pdb=" N LYS Q 69 " --> pdb=" O ARG Q 65 " (cutoff:3.500A) Processing helix chain 'Q' and resid 87 through 92 removed outlier: 3.876A pdb=" N ARG Q 90 " --> pdb=" O TYR Q 87 " (cutoff:3.500A) Processing helix chain 'Q' and resid 108 through 110 No H-bonds generated for 'chain 'Q' and resid 108 through 110' Processing helix chain 'U' and resid 180 through 185 Processing helix chain 'U' and resid 227 through 244 Processing helix chain 'U' and resid 270 through 276 removed outlier: 3.890A pdb=" N VAL U 274 " --> pdb=" O LEU U 270 " (cutoff:3.500A) Processing helix chain 'U' and resid 278 through 280 No H-bonds generated for 'chain 'U' and resid 278 through 280' Processing helix chain 'U' and resid 318 through 333 Proline residue: U 330 - end of helix Processing helix chain 'V' and resid 44 through 47 No H-bonds generated for 'chain 'V' and resid 44 through 47' Processing helix chain 'V' and resid 67 through 82 Processing helix chain 'V' and resid 87 through 102 removed outlier: 3.916A pdb=" N ARG V 102 " --> pdb=" O GLN V 98 " (cutoff:3.500A) Processing helix chain 'V' and resid 104 through 107 No H-bonds generated for 'chain 'V' and resid 104 through 107' Processing helix chain 'V' and resid 111 through 128 Processing helix chain 'V' and resid 135 through 141 removed outlier: 3.854A pdb=" N LEU V 141 " --> pdb=" O ALA V 137 " (cutoff:3.500A) Processing helix chain 'V' and resid 146 through 159 Processing helix chain 'V' and resid 169 through 179 removed outlier: 3.953A pdb=" N SER V 178 " --> pdb=" O LYS V 174 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N SER V 179 " --> pdb=" O THR V 175 " (cutoff:3.500A) Processing helix chain 'V' and resid 191 through 193 No H-bonds generated for 'chain 'V' and resid 191 through 193' Processing helix chain 'V' and resid 197 through 213 Processing helix chain 'V' and resid 222 through 242 removed outlier: 3.791A pdb=" N GLN V 238 " --> pdb=" O TRP V 234 " (cutoff:3.500A) Proline residue: V 239 - end of helix Processing helix chain 'V' and resid 247 through 254 Processing helix chain 'V' and resid 262 through 277 Processing helix chain 'V' and resid 281 through 286 Processing helix chain 'V' and resid 294 through 302 removed outlier: 5.023A pdb=" N GLY V 298 " --> pdb=" O LYS V 295 " (cutoff:3.500A) Processing helix chain 'V' and resid 304 through 312 Processing helix chain 'V' and resid 387 through 392 Processing helix chain 'V' and resid 396 through 405 Processing helix chain 'W' and resid 305 through 318 Processing helix chain 'W' and resid 322 through 327 Processing helix chain 'W' and resid 334 through 347 Processing helix chain 'W' and resid 349 through 357 Processing helix chain 'W' and resid 365 through 383 Processing sheet with id= A, first strand: chain '1' and resid 97 through 100 Processing sheet with id= B, first strand: chain '3' and resid 326 through 328 Processing sheet with id= C, first strand: chain '3' and resid 185 through 187 removed outlier: 3.668A pdb=" N VAL 3 320 " --> pdb=" O LEU 3 187 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N LEU 3 310 " --> pdb=" O TYR 3 253 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N TYR 3 253 " --> pdb=" O LEU 3 310 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain '3' and resid 257 through 260 removed outlier: 6.942A pdb=" N GLN 3 289 " --> pdb=" O PHE 3 258 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N ASN 3 260 " --> pdb=" O GLN 3 289 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ALA 3 291 " --> pdb=" O ASN 3 260 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain '3' and resid 364 through 367 Processing sheet with id= F, first strand: chain 'A' and resid 17 through 19 Processing sheet with id= G, first strand: chain 'A' and resid 84 through 87 Processing sheet with id= H, first strand: chain 'A' and resid 166 through 168 Processing sheet with id= I, first strand: chain 'A' and resid 364 through 368 Processing sheet with id= J, first strand: chain 'A' and resid 369 through 371 removed outlier: 5.934A pdb=" N PHE A 486 " --> pdb=" O SER A 370 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'A' and resid 391 through 395 Processing sheet with id= L, first strand: chain 'A' and resid 420 through 422 Processing sheet with id= M, first strand: chain 'A' and resid 617 through 620 Processing sheet with id= N, first strand: chain 'A' and resid 1085 through 1088 Processing sheet with id= O, first strand: chain 'A' and resid 1165 through 1167 removed outlier: 3.697A pdb=" N TYR A1116 " --> pdb=" O LYS A1131 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 125 through 128 removed outlier: 6.535A pdb=" N GLU B 118 " --> pdb=" O TYR B 77 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N TYR B 77 " --> pdb=" O GLU B 118 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N THR B 120 " --> pdb=" O LEU B 75 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N LEU B 75 " --> pdb=" O THR B 120 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 169 through 171 Processing sheet with id= R, first strand: chain 'B' and resid 181 through 184 Processing sheet with id= S, first strand: chain 'B' and resid 189 through 193 Processing sheet with id= T, first strand: chain 'B' and resid 424 through 426 Processing sheet with id= U, first strand: chain 'B' and resid 454 through 456 Processing sheet with id= V, first strand: chain 'B' and resid 573 through 577 Processing sheet with id= W, first strand: chain 'B' and resid 593 through 597 Processing sheet with id= X, first strand: chain 'B' and resid 708 through 712 removed outlier: 3.849A pdb=" N LYS B 868 " --> pdb=" O LEU B 884 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ARG B 886 " --> pdb=" O ILE B 866 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N ILE B 866 " --> pdb=" O ARG B 886 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'B' and resid 1003 through 1009 removed outlier: 4.005A pdb=" N TYR B1003 " --> pdb=" O VAL B 743 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE B 927 " --> pdb=" O ALA B 742 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N LEU B 757 " --> pdb=" O GLY B 908 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ILE B 910 " --> pdb=" O LEU B 757 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'B' and resid 831 through 833 Processing sheet with id= AA, first strand: chain 'B' and resid 1074 through 1080 Processing sheet with id= AB, first strand: chain 'B' and resid 110 through 115 removed outlier: 6.179A pdb=" N VAL B 115 " --> pdb=" O PRO B 132 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'B' and resid 536 through 541 removed outlier: 6.057A pdb=" N LEU B 541 " --> pdb=" O ILE B 545 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N ILE B 545 " --> pdb=" O LEU B 541 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'B' and resid 825 through 828 removed outlier: 4.437A pdb=" N GLN B 825 " --> pdb=" O TYR B 858 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ILE B 856 " --> pdb=" O LEU B 827 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'C' and resid 13 through 15 Processing sheet with id= AF, first strand: chain 'C' and resid 50 through 57 removed outlier: 6.864A pdb=" N GLU C 62 " --> pdb=" O VAL C 54 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N MET C 56 " --> pdb=" O SER C 60 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N SER C 60 " --> pdb=" O MET C 56 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'C' and resid 174 through 176 removed outlier: 4.272A pdb=" N GLN C 139 " --> pdb=" O ILE C 176 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL C 215 " --> pdb=" O VAL C 89 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N VAL C 89 " --> pdb=" O VAL C 215 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N GLY C 217 " --> pdb=" O MET C 87 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N MET C 87 " --> pdb=" O GLY C 217 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'C' and resid 262 through 266 Processing sheet with id= AI, first strand: chain 'C' and resid 167 through 169 removed outlier: 3.560A pdb=" N ALA C 200 " --> pdb=" O VAL C 168 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'E' and resid 72 through 75 removed outlier: 6.692A pdb=" N ARG E 101 " --> pdb=" O PHE E 73 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N PHE E 75 " --> pdb=" O ARG E 101 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU E 103 " --> pdb=" O PHE E 75 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE E 126 " --> pdb=" O ALA E 102 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N ILE E 104 " --> pdb=" O ILE E 126 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N GLU E 128 " --> pdb=" O ILE E 104 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N VAL E 106 " --> pdb=" O GLU E 128 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N PHE E 130 " --> pdb=" O VAL E 106 " (cutoff:3.500A) No H-bonds generated for sheet with id= AJ Processing sheet with id= AK, first strand: chain 'E' and resid 147 through 151 removed outlier: 3.616A pdb=" N GLU E 147 " --> pdb=" O ILE E 194 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N VAL E 190 " --> pdb=" O MET E 151 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'F' and resid 105 through 109 Processing sheet with id= AM, first strand: chain 'G' and resid 3 through 13 Processing sheet with id= AN, first strand: chain 'G' and resid 37 through 39 removed outlier: 4.254A pdb=" N LYS G 37 " --> pdb=" O CYS G 45 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU G 44 " --> pdb=" O PHE G 77 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N VAL G 75 " --> pdb=" O ILE G 46 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'G' and resid 146 through 149 Processing sheet with id= AP, first strand: chain 'G' and resid 50 through 54 removed outlier: 6.800A pdb=" N HIS G 71 " --> pdb=" O THR G 52 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'H' and resid 25 through 31 removed outlier: 5.607A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N SER H 139 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N HIS H 29 " --> pdb=" O LYS H 13 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'I' and resid 13 through 16 Processing sheet with id= AS, first strand: chain 'I' and resid 78 through 82 Processing sheet with id= AT, first strand: chain 'K' and resid 26 through 30 Processing sheet with id= AU, first strand: chain 'L' and resid 25 through 27 Processing sheet with id= AV, first strand: chain 'M' and resid 14 through 18 Processing sheet with id= AW, first strand: chain 'M' and resid 26 through 30 removed outlier: 7.247A pdb=" N GLY M 131 " --> pdb=" O LEU M 27 " (cutoff:3.500A) removed outlier: 8.556A pdb=" N GLN M 29 " --> pdb=" O GLY M 131 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N LEU M 133 " --> pdb=" O GLN M 29 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N ALA M 61 " --> pdb=" O HIS M 44 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N HIS M 44 " --> pdb=" O ALA M 61 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'M' and resid 318 through 321 Processing sheet with id= AY, first strand: chain 'M' and resid 390 through 393 Processing sheet with id= AZ, first strand: chain 'N' and resid 267 through 270 removed outlier: 6.867A pdb=" N HIS N 381 " --> pdb=" O PHE N 268 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N GLN N 270 " --> pdb=" O HIS N 381 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N LEU N 383 " --> pdb=" O GLN N 270 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N VAL N 337 " --> pdb=" O VAL N 348 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'N' and resid 359 through 364 removed outlier: 6.127A pdb=" N SER N 362 " --> pdb=" O VAL N 375 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N VAL N 375 " --> pdb=" O SER N 362 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N GLY N 364 " --> pdb=" O MET N 373 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N MET N 373 " --> pdb=" O GLY N 364 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'O' and resid 63 through 67 Processing sheet with id= BC, first strand: chain 'O' and resid 157 through 159 Processing sheet with id= BD, first strand: chain 'P' and resid 63 through 68 Processing sheet with id= BE, first strand: chain 'P' and resid 136 through 140 Processing sheet with id= BF, first strand: chain 'P' and resid 248 through 253 Processing sheet with id= BG, first strand: chain 'U' and resid 170 through 173 Processing sheet with id= BH, first strand: chain 'U' and resid 291 through 295 removed outlier: 3.710A pdb=" N GLY U 314 " --> pdb=" O MET U 258 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N MET U 258 " --> pdb=" O GLY U 314 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N SER U 261 " --> pdb=" O LEU U 165 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N LEU U 165 " --> pdb=" O SER U 261 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'V' and resid 15 through 19 removed outlier: 3.583A pdb=" N VAL V 27 " --> pdb=" O VAL V 16 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ASP V 18 " --> pdb=" O GLN V 25 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLN V 25 " --> pdb=" O ASP V 18 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N THR V 36 " --> pdb=" O LEU V 26 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N CYS V 28 " --> pdb=" O VAL V 34 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL V 34 " --> pdb=" O CYS V 28 " (cutoff:3.500A) 1972 hydrogen bonds defined for protein. 5571 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 68 hydrogen bonds 136 hydrogen bond angles 0 basepair planarities 27 basepair parallelities 102 stacking parallelities Total time for adding SS restraints: 21.02 Time building geometry restraints manager: 19.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.43: 24807 1.43 - 1.64: 34332 1.64 - 1.85: 547 1.85 - 2.07: 0 2.07 - 2.28: 12 Bond restraints: 59698 Sorted by residual: bond pdb=" C PRO 1 68 " pdb=" N PRO 1 69 " ideal model delta sigma weight residual 1.335 1.368 -0.034 1.19e-02 7.06e+03 7.96e+00 bond pdb=" C ASP 3 375 " pdb=" N PRO 3 376 " ideal model delta sigma weight residual 1.334 1.376 -0.042 2.34e-02 1.83e+03 3.21e+00 bond pdb=" C TYR 3 340 " pdb=" N PRO 3 341 " ideal model delta sigma weight residual 1.334 1.372 -0.039 2.34e-02 1.83e+03 2.72e+00 bond pdb=" C3' DA X 15 " pdb=" O3' DA X 15 " ideal model delta sigma weight residual 1.422 1.462 -0.040 3.00e-02 1.11e+03 1.81e+00 bond pdb=" C GLN G 116 " pdb=" N PRO G 117 " ideal model delta sigma weight residual 1.334 1.364 -0.030 2.34e-02 1.83e+03 1.62e+00 ... (remaining 59693 not shown) Histogram of bond angle deviations from ideal: 73.71 - 85.77: 12 85.77 - 97.82: 0 97.82 - 109.88: 8083 109.88 - 121.93: 60792 121.93 - 133.99: 12401 Bond angle restraints: 81288 Sorted by residual: angle pdb=" N VAL K 93 " pdb=" CA VAL K 93 " pdb=" C VAL K 93 " ideal model delta sigma weight residual 111.81 107.82 3.99 8.60e-01 1.35e+00 2.15e+01 angle pdb=" N ILE A1303 " pdb=" CA ILE A1303 " pdb=" C ILE A1303 " ideal model delta sigma weight residual 112.80 108.28 4.52 1.15e+00 7.56e-01 1.55e+01 angle pdb=" N VAL B 36 " pdb=" CA VAL B 36 " pdb=" C VAL B 36 " ideal model delta sigma weight residual 113.53 110.29 3.24 9.80e-01 1.04e+00 1.10e+01 angle pdb=" C LEU 3 339 " pdb=" N TYR 3 340 " pdb=" CA TYR 3 340 " ideal model delta sigma weight residual 122.28 118.92 3.36 1.02e+00 9.61e-01 1.08e+01 angle pdb=" N SER P 79 " pdb=" CA SER P 79 " pdb=" C SER P 79 " ideal model delta sigma weight residual 114.56 110.44 4.12 1.27e+00 6.20e-01 1.05e+01 ... (remaining 81283 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.33: 35306 34.33 - 68.65: 829 68.65 - 102.98: 40 102.98 - 137.30: 0 137.30 - 171.63: 4 Dihedral angle restraints: 36179 sinusoidal: 16157 harmonic: 20022 Sorted by residual: dihedral pdb=" CA TYR A1187 " pdb=" C TYR A1187 " pdb=" N VAL A1188 " pdb=" CA VAL A1188 " ideal model delta harmonic sigma weight residual 180.00 157.63 22.37 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA TYR 3 340 " pdb=" C TYR 3 340 " pdb=" N PRO 3 341 " pdb=" CA PRO 3 341 " ideal model delta harmonic sigma weight residual 180.00 158.54 21.46 0 5.00e+00 4.00e-02 1.84e+01 dihedral pdb=" C4' DG X -18 " pdb=" C3' DG X -18 " pdb=" O3' DG X -18 " pdb=" P DT X -17 " ideal model delta sinusoidal sigma weight residual -140.00 31.63 -171.63 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 36176 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 6363 0.032 - 0.064: 1821 0.064 - 0.096: 561 0.096 - 0.128: 291 0.128 - 0.160: 15 Chirality restraints: 9051 Sorted by residual: chirality pdb=" CA ILE G 148 " pdb=" N ILE G 148 " pdb=" C ILE G 148 " pdb=" CB ILE G 148 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.38e-01 chirality pdb=" CA ILE A1117 " pdb=" N ILE A1117 " pdb=" C ILE A1117 " pdb=" CB ILE A1117 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.18e-01 chirality pdb=" CA ILE O 375 " pdb=" N ILE O 375 " pdb=" C ILE O 375 " pdb=" CB ILE O 375 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.90e-01 ... (remaining 9048 not shown) Planarity restraints: 9902 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 56 " 0.028 5.00e-02 4.00e+02 4.29e-02 2.95e+00 pdb=" N PRO D 57 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO D 57 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 57 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DT X -29 " -0.022 2.00e-02 2.50e+03 9.80e-03 2.40e+00 pdb=" N1 DT X -29 " 0.017 2.00e-02 2.50e+03 pdb=" C2 DT X -29 " 0.003 2.00e-02 2.50e+03 pdb=" O2 DT X -29 " 0.005 2.00e-02 2.50e+03 pdb=" N3 DT X -29 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DT X -29 " -0.004 2.00e-02 2.50e+03 pdb=" O4 DT X -29 " -0.008 2.00e-02 2.50e+03 pdb=" C5 DT X -29 " -0.002 2.00e-02 2.50e+03 pdb=" C7 DT X -29 " 0.003 2.00e-02 2.50e+03 pdb=" C6 DT X -29 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU P 94 " -0.007 2.00e-02 2.50e+03 1.38e-02 1.92e+00 pdb=" C LEU P 94 " 0.024 2.00e-02 2.50e+03 pdb=" O LEU P 94 " -0.009 2.00e-02 2.50e+03 pdb=" N VAL P 95 " -0.008 2.00e-02 2.50e+03 ... (remaining 9899 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 276 2.49 - 3.09: 40672 3.09 - 3.69: 88799 3.69 - 4.30: 129738 4.30 - 4.90: 209851 Nonbonded interactions: 469336 Sorted by model distance: nonbonded pdb=" OD2 ASP B 401 " pdb=" NZ LYS B 404 " model vdw 1.886 2.520 nonbonded pdb=" O CYS 3 221 " pdb=" OD1 ASP 3 224 " model vdw 1.959 3.040 nonbonded pdb=" O ARG 3 101 " pdb=" SG CYS 3 104 " model vdw 2.087 3.400 nonbonded pdb=" CD1 LEU V 111 " pdb=" OP2 DT X -17 " model vdw 2.128 3.460 nonbonded pdb=" OD2 ASP A 503 " pdb="MG MG A1403 " model vdw 2.128 2.170 ... (remaining 469331 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 8.960 Check model and map are aligned: 0.660 Set scattering table: 0.400 Process input model: 144.770 Find NCS groups from input model: 1.310 Set up NCS constraints: 0.180 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: 0.000 Load rotamer database and sin/cos tables:2.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 159.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6519 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 59698 Z= 0.117 Angle : 0.469 10.904 81288 Z= 0.285 Chirality : 0.037 0.160 9051 Planarity : 0.003 0.043 9902 Dihedral : 12.781 171.627 23225 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.56 % Favored : 97.42 % Rotamer: Outliers : 0.02 % Allowed : 4.29 % Favored : 95.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.09), residues: 6799 helix: -0.27 (0.09), residues: 2750 sheet: -1.14 (0.17), residues: 834 loop : -1.76 (0.10), residues: 3215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP P 313 HIS 0.002 0.000 HIS M 44 PHE 0.008 0.001 PHE U 266 TYR 0.011 0.001 TYR A1116 ARG 0.003 0.000 ARG 4 442 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13598 Ramachandran restraints generated. 6799 Oldfield, 0 Emsley, 6799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13598 Ramachandran restraints generated. 6799 Oldfield, 0 Emsley, 6799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1507 residues out of total 6063 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1506 time to evaluate : 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: 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 outliers start: 1 outliers final: 1 residues processed: 1507 average time/residue: 0.6414 time to fit residues: 1542.4950 Evaluate side-chains 659 residues out of total 6063 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 658 time to evaluate : 4.924 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.5924 time to fit residues: 7.6265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 691 random chunks: chunk 583 optimal weight: 6.9990 chunk 523 optimal weight: 0.6980 chunk 290 optimal weight: 6.9990 chunk 178 optimal weight: 0.0020 chunk 353 optimal weight: 0.6980 chunk 279 optimal weight: 7.9990 chunk 541 optimal weight: 0.0040 chunk 209 optimal weight: 6.9990 chunk 329 optimal weight: 1.9990 chunk 403 optimal weight: 0.6980 chunk 627 optimal weight: 6.9990 overall best weight: 0.4200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 48 ASN ** 1 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 185 ASN 3 226 GLN 3 281 HIS 3 367 ASN 3 388 HIS 4 171 GLN 4 186 ASN 4 243 GLN 4 295 GLN 4 312 HIS ** 4 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 457 ASN A 275 ASN A 374 ASN A 423 GLN A 528 ASN A 599 GLN ** A1039 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1054 HIS A1168 HIS ** A1364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 253 GLN B 395 GLN B 408 GLN B 616 GLN B 913 GLN ** C 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 160 ASN D 61 GLN E 138 ASN H 29 HIS H 76 ASN I 99 ASN I 104 HIS K 38 HIS K 81 ASN ** M 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 395 HIS O 158 GLN O 377 GLN O 402 ASN O 475 GLN O 497 GLN P 129 ASN P 201 ASN U 242 GLN V 155 GLN V 206 GLN V 397 GLN W 327 GLN Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6620 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.066 59698 Z= 0.148 Angle : 0.503 11.722 81288 Z= 0.257 Chirality : 0.040 0.180 9051 Planarity : 0.004 0.079 9902 Dihedral : 15.441 172.139 9296 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.71 % Allowed : 10.04 % Favored : 88.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.10), residues: 6799 helix: 0.62 (0.10), residues: 2751 sheet: -0.72 (0.18), residues: 796 loop : -1.30 (0.10), residues: 3252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP Q 103 HIS 0.013 0.001 HIS 3 281 PHE 0.033 0.001 PHE G 157 TYR 0.023 0.001 TYR V 55 ARG 0.011 0.000 ARG V 309 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13598 Ramachandran restraints generated. 6799 Oldfield, 0 Emsley, 6799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13598 Ramachandran restraints generated. 6799 Oldfield, 0 Emsley, 6799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 790 residues out of total 6063 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 686 time to evaluate : 5.178 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 outliers start: 104 outliers final: 55 residues processed: 762 average time/residue: 0.5810 time to fit residues: 741.8691 Evaluate side-chains 606 residues out of total 6063 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 551 time to evaluate : 4.939 Switching outliers to nearest non-outliers outliers start: 55 outliers final: 0 residues processed: 55 average time/residue: 0.4231 time to fit residues: 50.8731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 691 random chunks: chunk 348 optimal weight: 6.9990 chunk 194 optimal weight: 2.9990 chunk 522 optimal weight: 6.9990 chunk 427 optimal weight: 5.9990 chunk 173 optimal weight: 8.9990 chunk 628 optimal weight: 0.5980 chunk 679 optimal weight: 10.0000 chunk 559 optimal weight: 4.9990 chunk 623 optimal weight: 0.9990 chunk 214 optimal weight: 7.9990 chunk 504 optimal weight: 0.0000 overall best weight: 1.9190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 73 GLN ** 1 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 193 HIS 4 186 ASN 4 234 GLN 4 286 ASN ** 4 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 465 GLN A 599 GLN ** A 661 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1039 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 253 GLN B 405 HIS B 524 ASN B 959 HIS ** C 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 151 HIS D 61 GLN D 85 GLN D 112 GLN E 138 ASN H 76 ASN I 83 GLN K 38 HIS ** M 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 200 GLN P 266 HIS ** U 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6750 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 59698 Z= 0.224 Angle : 0.526 12.197 81288 Z= 0.271 Chirality : 0.041 0.200 9051 Planarity : 0.004 0.065 9902 Dihedral : 15.468 165.773 9296 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.52 % Allowed : 11.11 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.10), residues: 6799 helix: 0.90 (0.10), residues: 2760 sheet: -0.50 (0.18), residues: 817 loop : -1.05 (0.10), residues: 3222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP I 59 HIS 0.009 0.001 HIS A 415 PHE 0.031 0.002 PHE G 157 TYR 0.027 0.001 TYR U 192 ARG 0.008 0.001 ARG P 159 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13598 Ramachandran restraints generated. 6799 Oldfield, 0 Emsley, 6799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13598 Ramachandran restraints generated. 6799 Oldfield, 0 Emsley, 6799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 701 residues out of total 6063 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 609 time to evaluate : 4.924 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 outliers start: 92 outliers final: 36 residues processed: 671 average time/residue: 0.5643 time to fit residues: 640.2048 Evaluate side-chains 549 residues out of total 6063 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 513 time to evaluate : 4.910 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 0 residues processed: 36 average time/residue: 0.4211 time to fit residues: 35.3831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 691 random chunks: chunk 621 optimal weight: 7.9990 chunk 472 optimal weight: 4.9990 chunk 326 optimal weight: 0.9990 chunk 69 optimal weight: 20.0000 chunk 300 optimal weight: 8.9990 chunk 422 optimal weight: 6.9990 chunk 630 optimal weight: 0.9980 chunk 667 optimal weight: 3.9990 chunk 329 optimal weight: 7.9990 chunk 597 optimal weight: 8.9990 chunk 180 optimal weight: 4.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 73 GLN 3 198 HIS 4 186 ASN ** 4 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 158 HIS A 296 HIS ** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 469 HIS A 528 ASN A 543 GLN A 739 GLN ** A1039 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1239 HIS ** C 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 151 HIS E 98 ASN E 138 ASN H 131 ASN I 61 ASN ** I 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 HIS ** O 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 377 GLN P 129 ASN ** U 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 98 GLN ** V 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 406 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6841 moved from start: 0.4037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.100 59698 Z= 0.327 Angle : 0.607 17.070 81288 Z= 0.311 Chirality : 0.044 0.314 9051 Planarity : 0.004 0.059 9902 Dihedral : 15.565 159.741 9296 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.28 % Favored : 95.70 % Rotamer: Outliers : 2.06 % Allowed : 12.12 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.10), residues: 6799 helix: 0.84 (0.10), residues: 2734 sheet: -0.58 (0.18), residues: 807 loop : -0.97 (0.11), residues: 3258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP W 350 HIS 0.014 0.002 HIS P 297 PHE 0.027 0.002 PHE E 73 TYR 0.042 0.002 TYR 3 404 ARG 0.013 0.001 ARG W 334 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13598 Ramachandran restraints generated. 6799 Oldfield, 0 Emsley, 6799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13598 Ramachandran restraints generated. 6799 Oldfield, 0 Emsley, 6799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 687 residues out of total 6063 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 562 time to evaluate : 4.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 125 outliers final: 47 residues processed: 652 average time/residue: 0.6176 time to fit residues: 682.7676 Evaluate side-chains 508 residues out of total 6063 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 461 time to evaluate : 4.933 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 0 residues processed: 47 average time/residue: 0.4472 time to fit residues: 46.2671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 691 random chunks: chunk 556 optimal weight: 6.9990 chunk 379 optimal weight: 0.8980 chunk 9 optimal weight: 10.0000 chunk 497 optimal weight: 7.9990 chunk 275 optimal weight: 4.9990 chunk 569 optimal weight: 8.9990 chunk 461 optimal weight: 1.9990 chunk 0 optimal weight: 30.0000 chunk 341 optimal weight: 0.8980 chunk 599 optimal weight: 8.9990 chunk 168 optimal weight: 0.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 4 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1039 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 ASN ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 138 ASN ** I 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 HIS M 209 HIS O 475 GLN P 129 ASN P 266 HIS V 296 HIS V 303 HIS V 403 GLN W 327 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6831 moved from start: 0.4215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 59698 Z= 0.221 Angle : 0.526 13.110 81288 Z= 0.271 Chirality : 0.041 0.239 9051 Planarity : 0.004 0.055 9902 Dihedral : 15.472 158.400 9296 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.97 % Allowed : 13.88 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.10), residues: 6799 helix: 1.03 (0.10), residues: 2721 sheet: -0.62 (0.18), residues: 780 loop : -0.88 (0.11), residues: 3298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP W 350 HIS 0.009 0.001 HIS P 297 PHE 0.021 0.001 PHE P 210 TYR 0.027 0.001 TYR 3 201 ARG 0.015 0.000 ARG W 334 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13598 Ramachandran restraints generated. 6799 Oldfield, 0 Emsley, 6799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13598 Ramachandran restraints generated. 6799 Oldfield, 0 Emsley, 6799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 6063 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 511 time to evaluate : 5.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 59 outliers final: 31 residues processed: 554 average time/residue: 0.5793 time to fit residues: 542.3743 Evaluate side-chains 485 residues out of total 6063 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 454 time to evaluate : 4.941 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.4482 time to fit residues: 32.5222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.6906 > 50: distance: 60 - 190: 35.360 distance: 63 - 187: 35.175 distance: 73 - 174: 36.341 distance: 76 - 171: 36.896 distance: 92 - 155: 34.487 distance: 95 - 152: 31.265 distance: 147 - 152: 30.466 distance: 152 - 153: 11.519 distance: 153 - 154: 8.194 distance: 153 - 156: 31.043 distance: 154 - 160: 30.358 distance: 156 - 157: 39.498 distance: 157 - 159: 49.723 distance: 160 - 161: 48.946 distance: 161 - 162: 8.399 distance: 161 - 164: 4.888 distance: 162 - 163: 19.653 distance: 162 - 171: 34.123 distance: 164 - 165: 34.379 distance: 167 - 168: 40.439 distance: 168 - 169: 40.244 distance: 168 - 170: 33.075 distance: 171 - 172: 34.718 distance: 172 - 173: 23.477 distance: 172 - 175: 42.696 distance: 173 - 174: 37.171 distance: 173 - 180: 36.195 distance: 175 - 176: 32.389 distance: 176 - 177: 15.197 distance: 177 - 178: 25.350 distance: 177 - 179: 13.005 distance: 180 - 181: 23.652 distance: 181 - 182: 14.626 distance: 181 - 184: 41.537 distance: 182 - 183: 40.201 distance: 184 - 185: 31.082 distance: 184 - 186: 37.288 distance: 187 - 188: 40.278 distance: 188 - 189: 56.034 distance: 189 - 190: 39.526 distance: 191 - 192: 51.953 distance: 192 - 193: 40.417 distance: 193 - 194: 33.018 distance: 194 - 195: 19.779 distance: 195 - 196: 19.589 distance: 195 - 197: 10.897 distance: 198 - 199: 51.053 distance: 199 - 200: 48.652 distance: 199 - 202: 32.054 distance: 200 - 201: 39.237 distance: 200 - 209: 56.700 distance: 202 - 203: 43.524 distance: 204 - 205: 19.338 distance: 205 - 206: 24.459 distance: 206 - 207: 33.707 distance: 206 - 208: 23.124 distance: 209 - 210: 21.354 distance: 209 - 215: 27.280 distance: 210 - 211: 26.152 distance: 210 - 213: 5.601 distance: 211 - 212: 25.623 distance: 211 - 216: 42.603 distance: 214 - 215: 10.570 distance: 217 - 218: 53.158 distance: 217 - 220: 53.616 distance: 218 - 219: 50.194 distance: 218 - 225: 53.640 distance: 220 - 221: 42.754 distance: 221 - 222: 44.064 distance: 222 - 223: 55.337 distance: 222 - 224: 37.774 distance: 225 - 226: 46.771 distance: 226 - 227: 40.702 distance: 226 - 229: 13.972 distance: 227 - 228: 43.668 distance: 227 - 233: 24.352 distance: 229 - 230: 40.233 distance: 229 - 231: 20.964 distance: 230 - 232: 39.599 distance: 233 - 234: 41.084 distance: 234 - 235: 38.596 distance: 235 - 237: 35.093