Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 28 14:14:34 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f4g_31450/04_2023/7f4g_31450.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f4g_31450/04_2023/7f4g_31450.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f4g_31450/04_2023/7f4g_31450.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f4g_31450/04_2023/7f4g_31450.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f4g_31450/04_2023/7f4g_31450.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f4g_31450/04_2023/7f4g_31450.pdb" } resolution = 2.78 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= -0.003 sd= 0.111 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: 5 Type Number sf(0) Gaussians Zn 5 6.06 5 S 162 5.16 5 C 17703 2.51 5 N 4833 2.21 5 O 5254 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 500": "OE1" <-> "OE2" Residue "A GLU 510": "OE1" <-> "OE2" Residue "A GLU 514": "OE1" <-> "OE2" Residue "A GLU 556": "OE1" <-> "OE2" Residue "A ARG 583": "NH1" <-> "NH2" Residue "A GLU 659": "OE1" <-> "OE2" Residue "A ARG 734": "NH1" <-> "NH2" Residue "A PHE 737": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 818": "OE1" <-> "OE2" Residue "A GLU 856": "OE1" <-> "OE2" Residue "A GLU 951": "OE1" <-> "OE2" Residue "A GLU 953": "OE1" <-> "OE2" Residue "A GLU 1057": "OE1" <-> "OE2" Residue "A GLU 1097": "OE1" <-> "OE2" Residue "A GLU 1126": "OE1" <-> "OE2" Residue "A ARG 1149": "NH1" <-> "NH2" Residue "A GLU 1215": "OE1" <-> "OE2" Residue "A GLU 1253": "OE1" <-> "OE2" Residue "A GLU 1266": "OE1" <-> "OE2" Residue "A GLU 1273": "OE1" <-> "OE2" Residue "A GLU 1381": "OE1" <-> "OE2" Residue "A ARG 1408": "NH1" <-> "NH2" Residue "A GLU 1478": "OE1" <-> "OE2" Residue "B GLU 173": "OE1" <-> "OE2" Residue "B GLU 296": "OE1" <-> "OE2" Residue "B GLU 381": "OE1" <-> "OE2" Residue "B ARG 491": "NH1" <-> "NH2" Residue "B GLU 516": "OE1" <-> "OE2" Residue "B GLU 555": "OE1" <-> "OE2" Residue "B GLU 816": "OE1" <-> "OE2" Residue "B GLU 959": "OE1" <-> "OE2" Residue "C GLU 92": "OE1" <-> "OE2" Residue "C GLU 96": "OE1" <-> "OE2" Residue "C ARG 160": "NH1" <-> "NH2" Residue "C GLU 172": "OE1" <-> "OE2" Residue "C GLU 207": "OE1" <-> "OE2" Residue "C GLU 266": "OE1" <-> "OE2" Residue "E GLU 38": "OE1" <-> "OE2" Residue "E ARG 52": "NH1" <-> "NH2" Residue "E GLU 78": "OE1" <-> "OE2" Residue "E GLU 134": "OE1" <-> "OE2" Residue "E GLU 141": "OE1" <-> "OE2" Residue "E GLU 167": "OE1" <-> "OE2" Residue "E ARG 181": "NH1" <-> "NH2" Residue "F ARG 100": "NH1" <-> "NH2" Residue "F TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 116": "OE1" <-> "OE2" Residue "F GLU 122": "OE1" <-> "OE2" Residue "H GLU 89": "OE1" <-> "OE2" Residue "J GLU 28": "OE1" <-> "OE2" Residue "J TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 57": "OE1" <-> "OE2" Residue "K GLU 14": "OE1" <-> "OE2" Residue "K GLU 16": "OE1" <-> "OE2" Residue "K GLU 102": "OE1" <-> "OE2" Residue "L ARG 31": "NH1" <-> "NH2" Residue "L ARG 35": "NH1" <-> "NH2" Residue "R GLU 67": "OE1" <-> "OE2" Residue "R GLU 93": "OE1" <-> "OE2" Residue "R GLU 201": "OE1" <-> "OE2" Residue "D GLU 30": "OE1" <-> "OE2" Residue "D GLU 36": "OE1" <-> "OE2" Residue "D GLU 42": "OE1" <-> "OE2" Residue "D GLU 59": "OE1" <-> "OE2" Residue "D GLU 96": "OE1" <-> "OE2" Residue "G GLU 8": "OE1" <-> "OE2" Residue "G TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 116": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 27957 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 8179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1026, 8179 Classifications: {'peptide': 1026} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 982} Chain breaks: 6 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 7820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 978, 7820 Classifications: {'peptide': 978} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 45, 'TRANS': 932} Chain breaks: 5 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 2038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 2038 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 15, 'TRANS': 238} Chain breaks: 1 Chain: "E" Number of atoms: 1703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1703 Classifications: {'peptide': 208} Incomplete info: {'backbone_only': 2} Link IDs: {'PTRANS': 11, 'TRANS': 196} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 609 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 5, 'TRANS': 70} 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: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 927 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "J" Number of atoms: 524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 524 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "K" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 920 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "L" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 372 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "R" Number of atoms: 1335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1335 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 7, 'TRANS': 155} Chain: "D" Number of atoms: 1005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1005 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 3, 'TRANS': 124} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "G" Number of atoms: 1334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1334 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 10, 'TRANS': 160} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 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: "R" 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 21582 SG CYS I 17 37.971 100.229 138.807 1.00 88.60 S ATOM 21606 SG CYS I 20 41.791 100.886 137.557 1.00 90.53 S ATOM 21767 SG CYS I 39 41.159 97.743 138.696 1.00 96.96 S ATOM 21792 SG CYS I 42 41.465 100.917 140.979 1.00101.32 S ATOM 22144 SG CYS I 86 10.786 98.574 103.888 1.00 86.89 S ATOM 22168 SG CYS I 89 9.770 101.931 103.105 1.00 88.50 S ATOM 22372 SG CYS I 114 12.931 100.997 101.748 1.00 73.84 S ATOM 22407 SG CYS I 119 12.341 101.481 105.283 1.00 84.48 S ATOM 22517 SG CYS J 7 51.508 98.144 40.982 1.00 32.48 S ATOM 22541 SG CYS J 10 50.924 97.140 37.600 1.00 36.95 S ATOM 22805 SG CYS J 44 48.463 96.157 40.502 1.00 40.01 S ATOM 22811 SG CYS J 45 48.849 99.419 38.764 1.00 40.13 S ATOM 24769 SG CYS R 100 63.096 54.764 141.450 1.00173.07 S ATOM 24806 SG CYS R 105 62.977 53.749 145.282 1.00177.93 S ATOM 25063 SG CYS R 136 59.838 54.641 144.515 1.00172.29 S ATOM 25094 SG CYS R 140 62.843 57.228 144.642 1.00175.77 S Time building chain proxies: 15.71, per 1000 atoms: 0.56 Number of scatterers: 27957 At special positions: 0 Unit cell: (170.172, 146.16, 161.82, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 5 29.99 S 162 16.00 O 5254 8.00 N 4833 7.00 C 17703 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 90 " - pdb=" SG CYS C 94 " distance=2.03 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: 11.21 Conformation dependent library (CDL) restraints added in 4.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 17 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 39 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 20 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 42 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 89 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 114 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 119 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 86 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb=" ZN R 800 " pdb="ZN ZN R 800 " - pdb=" SG CYS R 140 " pdb="ZN ZN R 800 " - pdb=" SG CYS R 105 " pdb="ZN ZN R 800 " - pdb=" SG CYS R 100 " pdb="ZN ZN R 800 " - pdb=" SG CYS R 136 " Number of angles added : 24 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6604 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 40 sheets defined 36.7% alpha, 18.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.69 Creating SS restraints... Processing helix chain 'A' and resid 381 through 386 Processing helix chain 'A' and resid 398 through 409 Processing helix chain 'A' and resid 508 through 519 removed outlier: 3.642A pdb=" N ARG A 512 " --> pdb=" O SER A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 549 removed outlier: 3.947A pdb=" N ALA A 544 " --> pdb=" O ASP A 540 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N VAL A 545 " --> pdb=" O THR A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 565 Processing helix chain 'A' and resid 587 through 596 Processing helix chain 'A' and resid 641 through 646 Processing helix chain 'A' and resid 651 through 660 removed outlier: 3.593A pdb=" N ILE A 655 " --> pdb=" O SER A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 684 removed outlier: 3.652A pdb=" N ARG A 666 " --> pdb=" O HIS A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 722 Processing helix chain 'A' and resid 733 through 758 Processing helix chain 'A' and resid 764 through 772 removed outlier: 3.961A pdb=" N SER A 772 " --> pdb=" O SER A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 777 through 786 Processing helix chain 'A' and resid 816 through 821 removed outlier: 3.529A pdb=" N ARG A 820 " --> pdb=" O GLY A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 868 removed outlier: 3.708A pdb=" N GLU A 845 " --> pdb=" O MET A 841 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLY A 846 " --> pdb=" O GLY A 842 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU A 847 " --> pdb=" O GLY A 843 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA A 851 " --> pdb=" O LEU A 847 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 894 Processing helix chain 'A' and resid 914 through 921 Processing helix chain 'A' and resid 935 through 944 removed outlier: 3.567A pdb=" N LEU A 943 " --> pdb=" O VAL A 939 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 970 Processing helix chain 'A' and resid 982 through 994 removed outlier: 3.712A pdb=" N TRP A 988 " --> pdb=" O LEU A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1017 Processing helix chain 'A' and resid 1027 through 1038 Processing helix chain 'A' and resid 1038 through 1049 removed outlier: 3.561A pdb=" N ASN A1042 " --> pdb=" O THR A1038 " (cutoff:3.500A) Processing helix chain 'A' and resid 1052 through 1057 Processing helix chain 'A' and resid 1061 through 1078 removed outlier: 3.541A pdb=" N ASP A1066 " --> pdb=" O GLY A1062 " (cutoff:3.500A) Processing helix chain 'A' and resid 1086 through 1097 Processing helix chain 'A' and resid 1098 through 1101 Processing helix chain 'A' and resid 1119 through 1129 removed outlier: 3.997A pdb=" N ARG A1123 " --> pdb=" O LEU A1119 " (cutoff:3.500A) Processing helix chain 'A' and resid 1150 through 1162 Processing helix chain 'A' and resid 1189 through 1198 removed outlier: 3.574A pdb=" N ASN A1194 " --> pdb=" O GLN A1190 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL A1195 " --> pdb=" O GLU A1191 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR A1196 " --> pdb=" O TRP A1192 " (cutoff:3.500A) Processing helix chain 'A' and resid 1218 through 1224 removed outlier: 3.508A pdb=" N ARG A1224 " --> pdb=" O HIS A1220 " (cutoff:3.500A) Processing helix chain 'A' and resid 1227 through 1239 Processing helix chain 'A' and resid 1280 through 1292 Processing helix chain 'A' and resid 1342 through 1347 Processing helix chain 'A' and resid 1361 through 1369 Processing helix chain 'A' and resid 1370 through 1388 Processing helix chain 'A' and resid 1394 through 1405 removed outlier: 3.615A pdb=" N LEU A1398 " --> pdb=" O ASN A1394 " (cutoff:3.500A) Processing helix chain 'A' and resid 1476 through 1481 removed outlier: 3.791A pdb=" N LYS A1481 " --> pdb=" O ALA A1477 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 37 removed outlier: 4.129A pdb=" N TRP B 27 " --> pdb=" O GLN B 23 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE B 30 " --> pdb=" O CYS B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 60 removed outlier: 5.295A pdb=" N VAL B 55 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N GLN B 56 " --> pdb=" O GLN B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 117 Processing helix chain 'B' and resid 167 through 173 Processing helix chain 'B' and resid 269 through 276 Processing helix chain 'B' and resid 281 through 286 Processing helix chain 'B' and resid 294 through 302 removed outlier: 3.578A pdb=" N GLU B 299 " --> pdb=" O PRO B 295 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N MET B 300 " --> pdb=" O GLU B 296 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL B 301 " --> pdb=" O MET B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 305 No H-bonds generated for 'chain 'B' and resid 303 through 305' Processing helix chain 'B' and resid 313 through 323 Processing helix chain 'B' and resid 331 through 346 Processing helix chain 'B' and resid 360 through 377 Processing helix chain 'B' and resid 387 through 389 No H-bonds generated for 'chain 'B' and resid 387 through 389' Processing helix chain 'B' and resid 395 through 426 removed outlier: 3.926A pdb=" N GLY B 406 " --> pdb=" O PHE B 402 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N MET B 407 " --> pdb=" O LEU B 403 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LYS B 421 " --> pdb=" O ILE B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 434 Processing helix chain 'B' and resid 437 through 451 Processing helix chain 'B' and resid 474 through 482 Processing helix chain 'B' and resid 490 through 494 Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 538 through 548 Processing helix chain 'B' and resid 579 through 592 Processing helix chain 'B' and resid 636 through 645 removed outlier: 3.720A pdb=" N ILE B 640 " --> pdb=" O LYS B 636 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLU B 645 " --> pdb=" O ASP B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 658 Processing helix chain 'B' and resid 668 through 672 removed outlier: 3.643A pdb=" N GLU B 671 " --> pdb=" O LEU B 668 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 683 removed outlier: 3.593A pdb=" N GLN B 683 " --> pdb=" O PRO B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 704 removed outlier: 3.789A pdb=" N ILE B 703 " --> pdb=" O PRO B 700 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU B 704 " --> pdb=" O SER B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 717 removed outlier: 3.614A pdb=" N ASN B 717 " --> pdb=" O PRO B 714 " (cutoff:3.500A) Processing helix chain 'B' and resid 718 through 729 Processing helix chain 'B' and resid 761 through 765 removed outlier: 3.523A pdb=" N GLU B 765 " --> pdb=" O ARG B 762 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 803 Processing helix chain 'B' and resid 950 through 954 removed outlier: 3.535A pdb=" N MET B 954 " --> pdb=" O GLN B 951 " (cutoff:3.500A) Processing helix chain 'B' and resid 969 through 976 Proline residue: B 973 - end of helix Processing helix chain 'B' and resid 977 through 994 removed outlier: 4.257A pdb=" N LEU B 981 " --> pdb=" O THR B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 1008 through 1016 Processing helix chain 'C' and resid 27 through 41 Processing helix chain 'C' and resid 60 through 70 Processing helix chain 'C' and resid 173 through 177 Processing helix chain 'C' and resid 199 through 203 removed outlier: 3.512A pdb=" N GLU C 202 " --> pdb=" O LYS C 199 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TRP C 203 " --> pdb=" O PRO C 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 199 through 203' Processing helix chain 'C' and resid 240 through 268 removed outlier: 3.540A pdb=" N ILE C 244 " --> pdb=" O ARG C 240 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLN C 268 " --> pdb=" O SER C 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 24 Processing helix chain 'E' and resid 36 through 45 Processing helix chain 'E' and resid 83 through 96 removed outlier: 3.949A pdb=" N GLU E 96 " --> pdb=" O GLN E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 99 No H-bonds generated for 'chain 'E' and resid 97 through 99' Processing helix chain 'E' and resid 111 through 120 Processing helix chain 'E' and resid 138 through 142 Processing helix chain 'E' and resid 152 through 164 Processing helix chain 'E' and resid 166 through 170 Processing helix chain 'E' and resid 177 through 184 removed outlier: 3.513A pdb=" N PHE E 183 " --> pdb=" O VAL E 179 " (cutoff:3.500A) Processing helix chain 'F' and resid 58 through 75 Processing helix chain 'F' and resid 88 through 99 Processing helix chain 'I' and resid 69 through 75 Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 30 through 38 Processing helix chain 'J' and resid 42 through 51 removed outlier: 4.056A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 60 Processing helix chain 'K' and resid 5 through 10 removed outlier: 3.815A pdb=" N SER K 9 " --> pdb=" O ALA K 6 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE K 10 " --> pdb=" O PHE K 7 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 51 removed outlier: 3.930A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE K 46 " --> pdb=" O LEU K 42 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 113 Processing helix chain 'R' and resid 43 through 66 Processing helix chain 'R' and resid 71 through 80 Processing helix chain 'R' and resid 83 through 97 Processing helix chain 'R' and resid 131 through 135 Processing helix chain 'R' and resid 137 through 150 Processing helix chain 'R' and resid 155 through 159 Processing helix chain 'R' and resid 162 through 183 removed outlier: 3.548A pdb=" N ASP R 166 " --> pdb=" O GLU R 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 50 removed outlier: 3.515A pdb=" N VAL D 37 " --> pdb=" O LEU D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 71 Processing helix chain 'D' and resid 76 through 89 Processing helix chain 'D' and resid 93 through 104 removed outlier: 3.744A pdb=" N CYS D 104 " --> pdb=" O LEU D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 115 Processing helix chain 'D' and resid 116 through 119 removed outlier: 3.722A pdb=" N GLU D 119 " --> pdb=" O PRO D 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 116 through 119' Processing helix chain 'D' and resid 123 through 137 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 35 removed outlier: 3.694A pdb=" N GLU G 35 " --> pdb=" O PHE G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 113 No H-bonds generated for 'chain 'G' and resid 111 through 113' Processing sheet with id=AA1, first strand: chain 'A' and resid 367 through 369 Processing sheet with id=AA2, first strand: chain 'A' and resid 389 through 393 removed outlier: 6.638A pdb=" N LYS A 445 " --> pdb=" O ILE A 419 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ILE A 419 " --> pdb=" O LYS A 445 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N GLU A 447 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 579 through 581 removed outlier: 6.207A pdb=" N VAL H 91 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG H 98 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N HIS H 29 " --> pdb=" O LYS H 13 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N ILE H 9 " --> pdb=" O GLU H 33 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N LYS H 55 " --> pdb=" O LEU H 148 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 579 through 581 removed outlier: 6.207A pdb=" N VAL H 91 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N LYS H 55 " --> pdb=" O LEU H 148 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 789 through 790 Processing sheet with id=AA6, first strand: chain 'A' and resid 872 through 873 removed outlier: 6.765A pdb=" N VAL A 879 " --> pdb=" O VAL A 887 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 902 through 904 Processing sheet with id=AA8, first strand: chain 'A' and resid 1140 through 1142 Processing sheet with id=AA9, first strand: chain 'A' and resid 1243 through 1247 removed outlier: 4.895A pdb=" N ILE A1261 " --> pdb=" O TRP A1210 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N TRP A1210 " --> pdb=" O ILE A1261 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N TYR I 54 " --> pdb=" O ILE A1175 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N TYR A1177 " --> pdb=" O CYS I 52 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N CYS I 52 " --> pdb=" O TYR A1177 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1319 through 1322 Processing sheet with id=AB2, first strand: chain 'A' and resid 1471 through 1475 Processing sheet with id=AB3, first strand: chain 'B' and resid 91 through 93 removed outlier: 5.935A pdb=" N ALA B 122 " --> pdb=" O LYS B 151 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N LYS B 151 " --> pdb=" O ALA B 122 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N LEU B 124 " --> pdb=" O ILE B 149 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE B 128 " --> pdb=" O GLN B 145 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N GLN B 145 " --> pdb=" O ILE B 128 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AB5, first strand: chain 'B' and resid 185 through 187 Processing sheet with id=AB6, first strand: chain 'B' and resid 391 through 394 removed outlier: 3.609A pdb=" N LYS B 524 " --> pdb=" O LEU B 485 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 206 through 208 removed outlier: 6.823A pdb=" N MET B 239 " --> pdb=" O ALA B 216 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N THR B 218 " --> pdb=" O VAL B 237 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N VAL B 237 " --> pdb=" O THR B 218 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N GLU B 220 " --> pdb=" O ILE B 235 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ILE B 235 " --> pdb=" O GLU B 220 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N ARG B 222 " --> pdb=" O SER B 233 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N SER B 233 " --> pdb=" O ARG B 222 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=AB9, first strand: chain 'B' and resid 632 through 633 Processing sheet with id=AC1, first strand: chain 'B' and resid 551 through 552 removed outlier: 5.671A pdb=" N TRP B 573 " --> pdb=" O VAL B 569 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N VAL B 569 " --> pdb=" O TRP B 573 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 748 through 751 removed outlier: 4.201A pdb=" N LYS B 917 " --> pdb=" O GLU B 818 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ARG B 924 " --> pdb=" O VAL B 904 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N VAL B 904 " --> pdb=" O ARG B 924 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N VAL B 926 " --> pdb=" O GLY B 902 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N GLY B 902 " --> pdb=" O VAL B 926 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 748 through 751 removed outlier: 4.201A pdb=" N LYS B 917 " --> pdb=" O GLU B 818 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ARG B 924 " --> pdb=" O VAL B 904 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N VAL B 904 " --> pdb=" O ARG B 924 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N VAL B 926 " --> pdb=" O GLY B 902 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N GLY B 902 " --> pdb=" O VAL B 926 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 759 through 760 Processing sheet with id=AC5, first strand: chain 'B' and resid 1025 through 1026 removed outlier: 7.178A pdb=" N VAL B 794 " --> pdb=" O GLY B 946 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N GLN B 948 " --> pdb=" O VAL B 794 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N MET B 796 " --> pdb=" O GLN B 948 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N ILE B 965 " --> pdb=" O ASN B 777 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N ILE B 779 " --> pdb=" O ILE B 965 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N ILE B 967 " --> pdb=" O ILE B 779 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ALA B 781 " --> pdb=" O ILE B 967 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N PHE B1042 " --> pdb=" O ILE B 782 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 827 through 829 Processing sheet with id=AC7, first strand: chain 'B' and resid 865 through 867 removed outlier: 6.469A pdb=" N THR B 894 " --> pdb=" O ILE B 866 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 956 through 957 Processing sheet with id=AC9, first strand: chain 'C' and resid 8 through 15 removed outlier: 6.258A pdb=" N LYS C 20 " --> pdb=" O THR C 12 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LEU C 14 " --> pdb=" O ASN C 18 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ASN C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE C 21 " --> pdb=" O TYR C 231 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 121 through 122 removed outlier: 6.309A pdb=" N GLU C 158 " --> pdb=" O ALA C 54 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ALA C 54 " --> pdb=" O GLU C 158 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ARG C 160 " --> pdb=" O ILE C 52 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ILE C 52 " --> pdb=" O ARG C 160 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ARG C 162 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N VAL C 50 " --> pdb=" O ARG C 162 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N TYR C 164 " --> pdb=" O ASP C 48 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 113 through 116 Processing sheet with id=AD3, first strand: chain 'E' and resid 60 through 63 Processing sheet with id=AD4, first strand: chain 'E' and resid 104 through 106 removed outlier: 6.236A pdb=" N ILE E 104 " --> pdb=" O PHE E 130 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'E' and resid 147 through 151 removed outlier: 4.913A pdb=" N VAL E 190 " --> pdb=" O MET E 151 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 25 through 29 Processing sheet with id=AD7, first strand: chain 'I' and resid 80 through 81 Processing sheet with id=AD8, first strand: chain 'K' and resid 20 through 24 removed outlier: 4.606A pdb=" N ALA K 30 " --> pdb=" O ASP K 24 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ILE K 72 " --> pdb=" O TYR K 61 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N TYR K 61 " --> pdb=" O ILE K 72 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ARG K 74 " --> pdb=" O ALA K 59 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ALA K 59 " --> pdb=" O ARG K 74 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N GLN K 76 " --> pdb=" O LEU K 57 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'R' and resid 117 through 120 removed outlier: 3.606A pdb=" N LYS R 125 " --> pdb=" O SER R 120 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 3 through 13 removed outlier: 3.584A pdb=" N THR G 39 " --> pdb=" O GLY G 43 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 3 through 13 Processing sheet with id=AE3, first strand: chain 'G' and resid 169 through 170 removed outlier: 3.685A pdb=" N GLY G 169 " --> pdb=" O ARG G 144 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N ILE G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N SER G 162 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N SER G 105 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLY G 161 " --> pdb=" O PHE G 107 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N SER G 109 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N GLY G 96 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N VAL G 92 " --> pdb=" O GLY G 96 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N PHE G 98 " --> pdb=" O THR G 90 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 118 through 120 removed outlier: 3.992A pdb=" N TYR G 128 " --> pdb=" O ILE G 137 " (cutoff:3.500A) 1168 hydrogen bonds defined for protein. 3237 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.02 Time building geometry restraints manager: 12.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 4766 1.29 - 1.42: 7014 1.42 - 1.55: 16449 1.55 - 1.68: 1 1.68 - 1.81: 254 Bond restraints: 28484 Sorted by residual: bond pdb=" C LEU J 24 " pdb=" O LEU J 24 " ideal model delta sigma weight residual 1.236 1.164 0.072 1.34e-02 5.57e+03 2.87e+01 bond pdb=" CA SER B 304 " pdb=" CB SER B 304 " ideal model delta sigma weight residual 1.537 1.466 0.071 1.41e-02 5.03e+03 2.55e+01 bond pdb=" N HIS B 842 " pdb=" CA HIS B 842 " ideal model delta sigma weight residual 1.457 1.489 -0.032 6.40e-03 2.44e+04 2.50e+01 bond pdb=" C LEU B 348 " pdb=" O LEU B 348 " ideal model delta sigma weight residual 1.235 1.212 0.023 4.70e-03 4.53e+04 2.34e+01 bond pdb=" C LYS B 302 " pdb=" O LYS B 302 " ideal model delta sigma weight residual 1.241 1.194 0.047 9.80e-03 1.04e+04 2.33e+01 ... (remaining 28479 not shown) Histogram of bond angle deviations from ideal: 95.62 - 103.55: 431 103.55 - 111.49: 12508 111.49 - 119.43: 11645 119.43 - 127.36: 13615 127.36 - 135.30: 278 Bond angle restraints: 38477 Sorted by residual: angle pdb=" C ILE B 556 " pdb=" N SER B 557 " pdb=" CA SER B 557 " ideal model delta sigma weight residual 121.83 135.30 -13.47 1.56e+00 4.11e-01 7.46e+01 angle pdb=" N LEU B 305 " pdb=" CA LEU B 305 " pdb=" C LEU B 305 " ideal model delta sigma weight residual 113.02 104.49 8.53 1.20e+00 6.94e-01 5.05e+01 angle pdb=" C PRO B 303 " pdb=" CA PRO B 303 " pdb=" CB PRO B 303 " ideal model delta sigma weight residual 111.56 100.76 10.80 1.65e+00 3.67e-01 4.29e+01 angle pdb=" N VAL B 742 " pdb=" CA VAL B 742 " pdb=" C VAL B 742 " ideal model delta sigma weight residual 113.71 107.61 6.10 9.50e-01 1.11e+00 4.12e+01 angle pdb=" CA THR B 898 " pdb=" C THR B 898 " pdb=" O THR B 898 " ideal model delta sigma weight residual 122.27 115.25 7.02 1.16e+00 7.43e-01 3.66e+01 ... (remaining 38472 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 15585 17.99 - 35.97: 1534 35.97 - 53.96: 265 53.96 - 71.94: 45 71.94 - 89.93: 23 Dihedral angle restraints: 17452 sinusoidal: 7260 harmonic: 10192 Sorted by residual: dihedral pdb=" CA GLY B 940 " pdb=" C GLY B 940 " pdb=" N GLN B 941 " pdb=" CA GLN B 941 " ideal model delta harmonic sigma weight residual 180.00 150.06 29.94 0 5.00e+00 4.00e-02 3.59e+01 dihedral pdb=" CA ASP A1295 " pdb=" C ASP A1295 " pdb=" N MET A1296 " pdb=" CA MET A1296 " ideal model delta harmonic sigma weight residual 180.00 151.20 28.80 0 5.00e+00 4.00e-02 3.32e+01 dihedral pdb=" CA ARG C 240 " pdb=" C ARG C 240 " pdb=" N PRO C 241 " pdb=" CA PRO C 241 " ideal model delta harmonic sigma weight residual -180.00 -153.11 -26.89 0 5.00e+00 4.00e-02 2.89e+01 ... (remaining 17449 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 3916 0.110 - 0.221: 369 0.221 - 0.331: 12 0.331 - 0.442: 6 0.442 - 0.552: 1 Chirality restraints: 4304 Sorted by residual: chirality pdb=" CB ILE A 811 " pdb=" CA ILE A 811 " pdb=" CG1 ILE A 811 " pdb=" CG2 ILE A 811 " both_signs ideal model delta sigma weight residual False 2.64 2.09 0.55 2.00e-01 2.50e+01 7.63e+00 chirality pdb=" CA TYR J 29 " pdb=" N TYR J 29 " pdb=" C TYR J 29 " pdb=" CB TYR J 29 " both_signs ideal model delta sigma weight residual False 2.51 2.91 -0.40 2.00e-01 2.50e+01 3.94e+00 chirality pdb=" CA ASN B 164 " pdb=" N ASN B 164 " pdb=" C ASN B 164 " pdb=" CB ASN B 164 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.81e+00 ... (remaining 4301 not shown) Planarity restraints: 4983 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 388 " 0.035 2.00e-02 2.50e+03 2.81e-02 1.58e+01 pdb=" CG TYR B 388 " -0.067 2.00e-02 2.50e+03 pdb=" CD1 TYR B 388 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TYR B 388 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR B 388 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR B 388 " 0.012 2.00e-02 2.50e+03 pdb=" CZ TYR B 388 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR B 388 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 752 " 0.014 2.00e-02 2.50e+03 2.26e-02 1.03e+01 pdb=" CG TYR B 752 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 TYR B 752 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR B 752 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR B 752 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 752 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR B 752 " 0.014 2.00e-02 2.50e+03 pdb=" OH TYR B 752 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 668 " -0.018 2.00e-02 2.50e+03 2.29e-02 9.14e+00 pdb=" CG PHE A 668 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 PHE A 668 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 PHE A 668 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE A 668 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE A 668 " -0.010 2.00e-02 2.50e+03 pdb=" CZ PHE A 668 " 0.002 2.00e-02 2.50e+03 ... (remaining 4980 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 193 2.50 - 3.10: 20892 3.10 - 3.70: 42043 3.70 - 4.30: 64924 4.30 - 4.90: 109894 Nonbonded interactions: 237946 Sorted by model distance: nonbonded pdb=" O GLU L 38 " pdb="ZN ZN L 101 " model vdw 1.898 2.230 nonbonded pdb=" NE2 HIS B 387 " pdb=" OE2 GLU B 671 " model vdw 2.047 2.520 nonbonded pdb=" OD1 ASP B 953 " pdb=" NH2 ARG C 36 " model vdw 2.069 2.520 nonbonded pdb=" O ASN C 190 " pdb=" NH1 ARG C 193 " model vdw 2.089 2.520 nonbonded pdb=" OG SER R 95 " pdb=" OG SER R 134 " model vdw 2.090 2.440 ... (remaining 237941 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 10.690 Check model and map are aligned: 0.440 Set scattering table: 0.260 Process input model: 76.740 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 105.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 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 : 0.017 0.127 28484 Z= 1.103 Angle : 1.109 13.471 38477 Z= 0.631 Chirality : 0.067 0.552 4304 Planarity : 0.006 0.071 4983 Dihedral : 14.672 89.931 10845 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.35 % Allowed : 8.69 % Favored : 90.96 % Rotamer Outliers : 1.43 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.63 % 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: -3.97 (0.12), residues: 3441 helix: -2.63 (0.11), residues: 1201 sheet: -2.51 (0.20), residues: 487 loop : -2.66 (0.13), residues: 1753 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 3114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 523 time to evaluate : 3.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 13 residues processed: 560 average time/residue: 1.6448 time to fit residues: 1052.0096 Evaluate side-chains 405 residues out of total 3114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 392 time to evaluate : 3.324 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 13 residues processed: 0 time to fit residues: 4.6536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 288 optimal weight: 0.9990 chunk 259 optimal weight: 0.8980 chunk 143 optimal weight: 0.6980 chunk 88 optimal weight: 0.7980 chunk 174 optimal weight: 0.6980 chunk 138 optimal weight: 5.9990 chunk 268 optimal weight: 2.9990 chunk 103 optimal weight: 0.5980 chunk 162 optimal weight: 0.7980 chunk 199 optimal weight: 3.9990 chunk 310 optimal weight: 40.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 GLN A 432 HIS ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 ASN A 678 ASN A 721 HIS A 735 GLN ** A 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 791 GLN A 839 HIS A 885 GLN A 949 GLN A1005 HIS A1034 GLN A1291 ASN A1332 GLN A1397 HIS A1410 HIS B 56 GLN B 117 ASN B 265 GLN B 452 ASN B 471 ASN B 500 GLN B 552 ASN B 582 GLN B 639 HIS B 649 ASN B 650 ASN B 654 GLN B 699 HIS ** B 749 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1021 HIS ** B1040 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 ASN C 108 ASN C 265 HIS E 19 GLN E 64 HIS ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 95 GLN E 108 GLN E 174 GLN I 41 ASN I 84 HIS J 52 HIS K 22 ASN K 29 ASN K 69 HIS ** K 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 89 ASN R 64 GLN R 86 HIS R 138 ASN R 199 HIS D 89 GLN Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 28484 Z= 0.239 Angle : 0.680 16.643 38477 Z= 0.351 Chirality : 0.047 0.257 4304 Planarity : 0.005 0.060 4983 Dihedral : 5.638 24.134 3803 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.25 % Favored : 93.66 % Rotamer Outliers : 3.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % 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: -2.53 (0.13), residues: 3441 helix: -1.07 (0.14), residues: 1212 sheet: -2.05 (0.21), residues: 486 loop : -1.99 (0.14), residues: 1743 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 3114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 427 time to evaluate : 3.466 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 outliers start: 115 outliers final: 37 residues processed: 490 average time/residue: 1.5227 time to fit residues: 865.3638 Evaluate side-chains 403 residues out of total 3114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 366 time to evaluate : 3.338 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 25 residues processed: 14 average time/residue: 0.7627 time to fit residues: 18.5985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 172 optimal weight: 3.9990 chunk 96 optimal weight: 0.7980 chunk 258 optimal weight: 8.9990 chunk 211 optimal weight: 0.8980 chunk 85 optimal weight: 8.9990 chunk 311 optimal weight: 0.3980 chunk 336 optimal weight: 30.0000 chunk 277 optimal weight: 0.9990 chunk 308 optimal weight: 6.9990 chunk 106 optimal weight: 7.9990 chunk 249 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 539 GLN A 606 HIS A 662 HIS A 671 ASN A 711 GLN ** A 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 420 GLN B 582 GLN B 649 ASN B1025 ASN ** B1040 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 GLN I 41 ASN ** K 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.088 28484 Z= 0.285 Angle : 0.642 11.237 38477 Z= 0.329 Chirality : 0.047 0.190 4304 Planarity : 0.004 0.062 4983 Dihedral : 5.307 24.341 3803 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.87 % Favored : 94.04 % Rotamer Outliers : 4.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % 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: -1.84 (0.14), residues: 3441 helix: -0.41 (0.15), residues: 1221 sheet: -1.57 (0.22), residues: 482 loop : -1.68 (0.14), residues: 1738 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 3114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 403 time to evaluate : 3.271 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 outliers start: 125 outliers final: 54 residues processed: 480 average time/residue: 1.5298 time to fit residues: 851.9559 Evaluate side-chains 431 residues out of total 3114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 377 time to evaluate : 3.377 Switching outliers to nearest non-outliers outliers start: 54 outliers final: 40 residues processed: 16 average time/residue: 0.6444 time to fit residues: 18.7215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 307 optimal weight: 5.9990 chunk 233 optimal weight: 10.0000 chunk 161 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 148 optimal weight: 0.9990 chunk 208 optimal weight: 0.9990 chunk 312 optimal weight: 20.0000 chunk 330 optimal weight: 5.9990 chunk 163 optimal weight: 0.2980 chunk 295 optimal weight: 0.9980 chunk 89 optimal weight: 10.0000 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 502 ASN A 576 GLN ** A 662 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 ASN ** A 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 582 GLN B 941 GLN ** B1040 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 GLN ** K 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.068 28484 Z= 0.216 Angle : 0.604 12.840 38477 Z= 0.307 Chirality : 0.045 0.176 4304 Planarity : 0.004 0.060 4983 Dihedral : 5.016 23.745 3803 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.49 % Favored : 94.42 % Rotamer Outliers : 4.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % 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: -1.37 (0.14), residues: 3441 helix: -0.02 (0.15), residues: 1219 sheet: -1.34 (0.22), residues: 486 loop : -1.40 (0.15), residues: 1736 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 3114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 413 time to evaluate : 3.671 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 outliers start: 135 outliers final: 58 residues processed: 506 average time/residue: 1.4537 time to fit residues: 858.3153 Evaluate side-chains 421 residues out of total 3114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 363 time to evaluate : 3.303 Switching outliers to nearest non-outliers outliers start: 58 outliers final: 42 residues processed: 18 average time/residue: 0.8195 time to fit residues: 23.6140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 275 optimal weight: 0.0770 chunk 187 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 246 optimal weight: 10.0000 chunk 136 optimal weight: 5.9990 chunk 282 optimal weight: 0.9990 chunk 228 optimal weight: 0.1980 chunk 0 optimal weight: 5.9990 chunk 168 optimal weight: 1.9990 chunk 296 optimal weight: 5.9990 chunk 83 optimal weight: 10.0000 overall best weight: 1.4544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 502 ASN ** A 662 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 ASN A 711 GLN A 780 ASN B 582 GLN B 749 HIS ** B1040 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 ASN E 108 GLN H 44 ASN K 84 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.069 28484 Z= 0.305 Angle : 0.628 12.233 38477 Z= 0.317 Chirality : 0.047 0.236 4304 Planarity : 0.004 0.059 4983 Dihedral : 4.978 28.753 3803 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.58 % Favored : 94.36 % Rotamer Outliers : 4.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % 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: -1.15 (0.14), residues: 3441 helix: 0.17 (0.15), residues: 1213 sheet: -1.20 (0.22), residues: 487 loop : -1.26 (0.15), residues: 1741 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 3114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 385 time to evaluate : 3.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 131 outliers final: 67 residues processed: 474 average time/residue: 1.5161 time to fit residues: 839.2607 Evaluate side-chains 438 residues out of total 3114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 371 time to evaluate : 3.467 Switching outliers to nearest non-outliers outliers start: 67 outliers final: 50 residues processed: 19 average time/residue: 0.9378 time to fit residues: 27.6449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 111 optimal weight: 7.9990 chunk 297 optimal weight: 1.9990 chunk 65 optimal weight: 0.0270 chunk 194 optimal weight: 1.9990 chunk 81 optimal weight: 10.0000 chunk 330 optimal weight: 0.4980 chunk 274 optimal weight: 10.0000 chunk 153 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 109 optimal weight: 2.9990 chunk 173 optimal weight: 0.7980 overall best weight: 0.8440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 502 ASN ** A 662 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 ASN B 500 GLN B 582 GLN B 649 ASN ** B1040 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 GLN H 44 ASN I 45 GLN L 26 ASN R 115 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 28484 Z= 0.218 Angle : 0.597 12.400 38477 Z= 0.301 Chirality : 0.045 0.235 4304 Planarity : 0.004 0.057 4983 Dihedral : 4.823 26.672 3803 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.32 % Favored : 94.62 % Rotamer Outliers : 3.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % 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: -0.85 (0.14), residues: 3441 helix: 0.46 (0.15), residues: 1206 sheet: -1.07 (0.23), residues: 493 loop : -1.11 (0.15), residues: 1742 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 3114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 393 time to evaluate : 3.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 114 outliers final: 63 residues processed: 470 average time/residue: 1.5387 time to fit residues: 840.7587 Evaluate side-chains 428 residues out of total 3114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 365 time to evaluate : 3.151 Switching outliers to nearest non-outliers outliers start: 63 outliers final: 51 residues processed: 12 average time/residue: 0.5748 time to fit residues: 14.1187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 319 optimal weight: 30.0000 chunk 37 optimal weight: 1.9990 chunk 188 optimal weight: 1.9990 chunk 241 optimal weight: 3.9990 chunk 187 optimal weight: 3.9990 chunk 278 optimal weight: 1.9990 chunk 184 optimal weight: 0.8980 chunk 329 optimal weight: 7.9990 chunk 206 optimal weight: 2.9990 chunk 200 optimal weight: 0.3980 chunk 152 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 502 ASN ** A 662 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 ASN B 265 GLN B 582 GLN B1007 ASN ** B1040 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 GLN H 44 ASN L 26 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.065 28484 Z= 0.304 Angle : 0.628 15.639 38477 Z= 0.316 Chirality : 0.047 0.219 4304 Planarity : 0.004 0.057 4983 Dihedral : 4.834 23.846 3803 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.87 % Favored : 94.10 % Rotamer Outliers : 3.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % 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: -0.81 (0.14), residues: 3441 helix: 0.48 (0.15), residues: 1215 sheet: -1.02 (0.23), residues: 494 loop : -1.09 (0.15), residues: 1732 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 3114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 373 time to evaluate : 3.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 120 outliers final: 75 residues processed: 456 average time/residue: 1.5607 time to fit residues: 828.7611 Evaluate side-chains 439 residues out of total 3114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 364 time to evaluate : 3.468 Switching outliers to nearest non-outliers outliers start: 75 outliers final: 58 residues processed: 18 average time/residue: 0.7749 time to fit residues: 23.0987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 203 optimal weight: 0.9980 chunk 131 optimal weight: 1.9990 chunk 196 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 209 optimal weight: 0.9980 chunk 224 optimal weight: 6.9990 chunk 162 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 259 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 502 ASN ** A 662 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 ASN B 649 ASN ** B1040 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 GLN H 44 ASN L 26 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.077 28484 Z= 0.323 Angle : 0.636 13.358 38477 Z= 0.320 Chirality : 0.047 0.286 4304 Planarity : 0.004 0.057 4983 Dihedral : 4.843 23.364 3803 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.67 % Favored : 94.30 % Rotamer Outliers : 3.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % 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: -0.76 (0.14), residues: 3441 helix: 0.53 (0.15), residues: 1213 sheet: -1.00 (0.23), residues: 494 loop : -1.06 (0.15), residues: 1734 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 3114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 368 time to evaluate : 3.325 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 109 outliers final: 75 residues processed: 450 average time/residue: 1.4988 time to fit residues: 786.5917 Evaluate side-chains 434 residues out of total 3114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 359 time to evaluate : 3.363 Switching outliers to nearest non-outliers outliers start: 75 outliers final: 59 residues processed: 16 average time/residue: 0.6538 time to fit residues: 18.9499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 299 optimal weight: 1.9990 chunk 315 optimal weight: 7.9990 chunk 288 optimal weight: 0.0770 chunk 307 optimal weight: 3.9990 chunk 184 optimal weight: 0.9990 chunk 133 optimal weight: 3.9990 chunk 241 optimal weight: 0.7980 chunk 94 optimal weight: 3.9990 chunk 277 optimal weight: 0.6980 chunk 290 optimal weight: 0.9980 chunk 306 optimal weight: 6.9990 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 502 ASN ** A 662 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 ASN A 780 ASN A1384 HIS B 582 GLN B 649 ASN ** B1040 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 GLN I 18 GLN I 91 HIS L 26 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 28484 Z= 0.202 Angle : 0.599 14.239 38477 Z= 0.302 Chirality : 0.045 0.290 4304 Planarity : 0.004 0.057 4983 Dihedral : 4.697 24.223 3803 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.46 % Favored : 94.51 % Rotamer Outliers : 3.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.15), residues: 3441 helix: 0.71 (0.15), residues: 1215 sheet: -0.86 (0.23), residues: 487 loop : -1.00 (0.15), residues: 1739 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 3114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 373 time to evaluate : 3.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 96 outliers final: 67 residues processed: 447 average time/residue: 1.5699 time to fit residues: 818.3775 Evaluate side-chains 422 residues out of total 3114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 355 time to evaluate : 3.276 Switching outliers to nearest non-outliers outliers start: 67 outliers final: 60 residues processed: 8 average time/residue: 0.6367 time to fit residues: 11.9109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 201 optimal weight: 3.9990 chunk 324 optimal weight: 4.9990 chunk 198 optimal weight: 0.5980 chunk 154 optimal weight: 0.8980 chunk 225 optimal weight: 4.9990 chunk 340 optimal weight: 50.0000 chunk 313 optimal weight: 0.9990 chunk 271 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 209 optimal weight: 4.9990 chunk 166 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 502 ASN ** A 662 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 ASN A1384 HIS B 582 GLN ** B1040 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 GLN E 108 GLN H 44 ASN I 18 GLN L 26 ASN G 14 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 28484 Z= 0.216 Angle : 0.608 14.786 38477 Z= 0.305 Chirality : 0.045 0.247 4304 Planarity : 0.004 0.056 4983 Dihedral : 4.642 23.724 3803 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.49 % Favored : 94.48 % Rotamer Outliers : 2.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.15), residues: 3441 helix: 0.81 (0.15), residues: 1215 sheet: -0.79 (0.23), residues: 487 loop : -0.96 (0.15), residues: 1739 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 3114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 367 time to evaluate : 3.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 78 outliers final: 61 residues processed: 432 average time/residue: 1.5131 time to fit residues: 762.0692 Evaluate side-chains 416 residues out of total 3114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 355 time to evaluate : 3.315 Switching outliers to nearest non-outliers outliers start: 61 outliers final: 57 residues processed: 5 average time/residue: 1.0275 time to fit residues: 11.0212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 215 optimal weight: 0.2980 chunk 289 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 250 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 75 optimal weight: 8.9990 chunk 271 optimal weight: 0.9980 chunk 113 optimal weight: 1.9990 chunk 279 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 502 ASN ** A 662 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 ASN A1384 HIS ** B1040 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 GLN H 44 ASN I 18 GLN L 26 ASN G 14 HIS G 21 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.184284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.117632 restraints weight = 32479.090| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 2.32 r_work: 0.3445 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 28484 Z= 0.210 Angle : 0.602 13.965 38477 Z= 0.301 Chirality : 0.045 0.234 4304 Planarity : 0.004 0.056 4983 Dihedral : 4.591 23.394 3803 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.41 % Favored : 94.57 % Rotamer Outliers : 2.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % 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: -0.41 (0.15), residues: 3441 helix: 0.88 (0.15), residues: 1215 sheet: -0.76 (0.23), residues: 487 loop : -0.93 (0.15), residues: 1739 =============================================================================== Job complete usr+sys time: 12545.85 seconds wall clock time: 222 minutes 33.32 seconds (13353.32 seconds total)