Starting phenix.real_space_refine on Sun Dec 29 17:37:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iue_35719/12_2024/8iue_35719.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iue_35719/12_2024/8iue_35719.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8iue_35719/12_2024/8iue_35719.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iue_35719/12_2024/8iue_35719.map" model { file = "/net/cci-nas-00/data/ceres_data/8iue_35719/12_2024/8iue_35719.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iue_35719/12_2024/8iue_35719.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Fe 4 7.16 5 Zn 8 6.06 5 P 144 5.49 5 Mg 1 5.21 5 S 359 5.16 5 C 36221 2.51 5 N 10129 2.21 5 O 11061 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 116 residue(s): 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 57927 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 10814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1378, 10814 Classifications: {'peptide': 1378} Link IDs: {'PTRANS': 64, 'TRANS': 1313} Chain: "B" Number of atoms: 8741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1105, 8741 Classifications: {'peptide': 1105} Link IDs: {'PTRANS': 51, 'TRANS': 1053} Chain breaks: 1 Chain: "C" Number of atoms: 2736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2736 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 17, 'TRANS': 325} Chain: "D" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 985 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "E" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1715 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "F" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 610 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 5, 'TRANS': 70} Chain: "G" Number of atoms: 1337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1337 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 10, 'TRANS': 155} Chain breaks: 2 Chain: "H" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1186 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain: "I" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 848 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "J" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 512 Classifications: {'peptide': 65} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 62} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 822 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 4, 'TRANS': 98} Chain: "L" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 388 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "M" Number of atoms: 3382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3382 Classifications: {'peptide': 422} Link IDs: {'PTRANS': 23, 'TRANS': 398} Chain breaks: 1 Chain: "N" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1128 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 6, 'TRANS': 139} Chain breaks: 2 Chain: "O" Number of atoms: 4075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 4075 Classifications: {'peptide': 512} Link IDs: {'PTRANS': 22, 'TRANS': 489} Chain breaks: 1 Chain: "P" Number of atoms: 2403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2403 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 12, 'TRANS': 290} Chain: "Q" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 754 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 12, 'TRANS': 74} Chain: "X" Number of atoms: 1517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1517 Classifications: {'DNA': 74} Link IDs: {'rna3p': 73} Chain breaks: 1 Chain: "Y" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 1437 Classifications: {'DNA': 70} Link IDs: {'rna3p': 69} Chain breaks: 1 Chain: "1" Number of atoms: 1233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1233 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 6, 'TRANS': 139} Chain: "3" Number of atoms: 3037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 3037 Classifications: {'peptide': 374} Link IDs: {'PTRANS': 16, 'TRANS': 357} Chain breaks: 2 Chain: "4" Number of atoms: 3058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 3058 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 10, 'TRANS': 354} Chain: "U" Number of atoms: 1396 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 176, 1391 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 9, 'TRANS': 166} Conformer: "B" Number of residues, atoms: 176, 1391 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 9, 'TRANS': 166} bond proxies already assigned to first conformer: 1410 Chain: "V" Number of atoms: 2853 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 361, 2847 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 19, 'TRANS': 341} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 361, 2847 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 19, 'TRANS': 341} Chain breaks: 1 bond proxies already assigned to first conformer: 2891 Chain: "W" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 943 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 4, 'TRANS': 106} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 543 SG CYS A 69 108.334 133.848 147.041 1.00126.90 S ATOM 565 SG CYS A 72 108.718 133.394 150.655 1.00125.00 S ATOM 613 SG CYS A 79 106.554 130.986 149.021 1.00128.92 S ATOM 854 SG CYS A 109 65.955 157.197 147.066 1.00135.32 S ATOM 876 SG CYS A 112 67.157 159.385 150.170 1.00134.77 S ATOM 1245 SG CYS A 156 63.458 159.011 149.983 1.00154.63 S ATOM 1271 SG CYS A 159 64.647 161.441 147.795 1.00149.24 S ATOM 19142 SG CYS B1080 99.535 141.365 162.797 1.00117.16 S ATOM 19161 SG CYS B1083 96.842 141.589 159.796 1.00117.13 S ATOM 19227 SG CYS B1092 100.319 141.544 158.837 1.00113.04 S ATOM 19255 SG CYS B1095 98.399 144.966 160.368 1.00118.73 S ATOM 28165 SG CYS I 5 24.146 116.485 110.848 1.00157.68 S ATOM 28182 SG CYS I 8 28.403 118.232 110.093 1.00159.27 S ATOM 28312 SG CYS I 25 27.175 119.695 113.222 1.00160.84 S ATOM 28333 SG CYS I 28 24.983 119.797 110.182 1.00152.92 S ATOM 28654 SG CYS I 69 58.048 78.564 170.915 1.00274.12 S ATOM 28676 SG CYS I 72 55.748 79.130 173.488 1.00275.60 S ATOM 28888 SG CYS I 97 54.759 79.565 170.067 1.00272.04 S ATOM 29027 SG CYS J 7 101.416 62.910 142.662 1.00 97.85 S ATOM 29051 SG CYS J 10 103.407 60.228 144.945 1.00100.35 S ATOM 29315 SG CYS J 44 99.856 59.778 144.446 1.00102.73 S ATOM 29321 SG CYS J 45 102.429 58.416 141.821 1.00104.68 S ATOM 30364 SG CYS L 19 117.105 87.080 111.765 1.00121.79 S ATOM 30500 SG CYS L 36 118.084 89.513 109.264 1.00139.15 S ATOM 30526 SG CYS L 39 114.287 89.136 107.688 1.00138.13 S ATOM 54131 SG CYS V 7 128.632 116.300 156.827 1.00178.33 S ATOM 54309 SG CYS V 31 130.202 112.129 158.941 1.00175.49 S Residues with excluded nonbonded symmetry interactions: 12 residue: pdb=" N ACYS V 177 " occ=0.47 ... (10 atoms not shown) pdb=" SG BCYS V 177 " occ=0.53 residue: pdb=" N LYS V 364 " occ=0.00 ... (7 atoms not shown) pdb=" NZ LYS V 364 " occ=0.00 residue: pdb=" N SER V 365 " occ=0.00 ... (4 atoms not shown) pdb=" OG SER V 365 " occ=0.00 residue: pdb=" N PRO V 366 " occ=0.00 ... (5 atoms not shown) pdb=" CD PRO V 366 " occ=0.00 residue: pdb=" N LYS V 367 " occ=0.00 ... (7 atoms not shown) pdb=" NZ LYS V 367 " occ=0.00 residue: pdb=" N ARG V 368 " occ=0.00 ... (9 atoms not shown) pdb=" NH2 ARG V 368 " occ=0.00 residue: pdb=" N ILE V 369 " occ=0.00 ... (6 atoms not shown) pdb=" CD1 ILE V 369 " occ=0.00 residue: pdb=" N CYS V 370 " occ=0.00 ... (4 atoms not shown) pdb=" SG CYS V 370 " occ=0.00 residue: pdb=" N PRO V 371 " occ=0.00 ... (5 atoms not shown) pdb=" CD PRO V 371 " occ=0.00 residue: pdb=" N SER V 376 " occ=0.00 ... (4 atoms not shown) pdb=" OG SER V 376 " occ=0.00 residue: pdb=" N THR V 377 " occ=0.00 ... (5 atoms not shown) pdb=" CG2 THR V 377 " occ=0.00 residue: pdb=" N VAL V 378 " occ=0.00 ... (5 atoms not shown) pdb=" CG2 VAL V 378 " occ=0.00 Time building chain proxies: 24.25, per 1000 atoms: 0.42 Number of scatterers: 57927 At special positions: 0 Unit cell: (164.082, 217.442, 224.112, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 8 29.99 Fe 4 26.01 S 359 16.00 P 144 15.00 Mg 1 11.99 O 11061 8.00 N 10129 7.00 C 36221 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 10.67 Conformation dependent library (CDL) restraints added in 5.8 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 P 401 " pdb="FE1 SF4 P 401 " - pdb=" SG CYS P 290 " pdb="FE4 SF4 P 401 " - pdb=" SG CYS P 307 " pdb="FE3 SF4 P 401 " - pdb=" SG CYS P 287 " pdb="FE2 SF4 P 401 " - pdb=" SG CYS P 296 " Number of angles added : 12 Zn2+ tetrahedral coordination pdb=" ZN A1401 " pdb="ZN ZN A1401 " - pdb=" NE2 HIS A 82 " pdb="ZN ZN A1401 " - pdb=" SG CYS A 79 " pdb="ZN ZN A1401 " - pdb=" SG CYS A 72 " pdb="ZN ZN A1401 " - pdb=" SG CYS A 69 " pdb=" ZN A1402 " pdb="ZN ZN A1402 " - pdb=" SG CYS A 109 " pdb="ZN ZN A1402 " - pdb=" SG CYS A 112 " pdb="ZN ZN A1402 " - pdb=" SG CYS A 159 " pdb="ZN ZN A1402 " - pdb=" SG CYS A 156 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1095 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1080 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1083 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1092 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 8 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 28 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 5 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 25 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 69 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 72 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 97 " pdb=" ZN J2000 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 44 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 7 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 45 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 10 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 39 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 19 " pdb=" ZN V 700 " pdb="ZN ZN V 700 " - pdb=" SG CYS V 7 " pdb="ZN ZN V 700 " - pdb=" SG CYS V 31 " Number of angles added : 27 13618 Ramachandran restraints generated. 6809 Oldfield, 0 Emsley, 6809 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12964 Finding SS restraints... Secondary structure from input PDB file: 267 helices and 66 sheets defined 44.2% alpha, 15.0% beta 25 base pairs and 88 stacking pairs defined. Time for finding SS restraints: 15.16 Creating SS restraints... Processing helix chain 'A' and resid 24 through 32 Processing helix chain 'A' and resid 57 through 61 removed outlier: 3.543A pdb=" N GLY A 61 " --> pdb=" O HIS A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 108 Processing helix chain 'A' and resid 118 through 130 Processing helix chain 'A' and resid 135 through 153 removed outlier: 3.905A pdb=" N LYS A 153 " --> pdb=" O LYS A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 195 removed outlier: 3.533A pdb=" N SER A 191 " --> pdb=" O ASP A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 204 Processing helix chain 'A' and resid 205 through 208 Processing helix chain 'A' and resid 219 through 229 removed outlier: 3.607A pdb=" N ARG A 229 " --> pdb=" O ASN A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 239 removed outlier: 6.014A pdb=" N GLU A 233 " --> pdb=" O ILE A 230 " (cutoff:3.500A) Proline residue: A 236 - end of helix Processing helix chain 'A' and resid 246 through 250 Processing helix chain 'A' and resid 277 through 300 removed outlier: 3.668A pdb=" N MET A 281 " --> pdb=" O ASP A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 322 Processing helix chain 'A' and resid 340 through 346 Processing helix chain 'A' and resid 350 through 356 Processing helix chain 'A' and resid 384 through 388 Processing helix chain 'A' and resid 400 through 411 Processing helix chain 'A' and resid 436 through 443 removed outlier: 3.658A pdb=" N MET A 440 " --> pdb=" O ASN A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 492 through 497 removed outlier: 3.633A pdb=" N TYR A 496 " --> pdb=" O VAL A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 522 Processing helix chain 'A' and resid 545 through 553 Processing helix chain 'A' and resid 560 through 570 Processing helix chain 'A' and resid 571 through 572 No H-bonds generated for 'chain 'A' and resid 571 through 572' Processing helix chain 'A' and resid 573 through 579 removed outlier: 3.944A pdb=" N LYS A 578 " --> pdb=" O LYS A 575 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE A 579 " --> pdb=" O ASP A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 606 removed outlier: 3.630A pdb=" N ILE A 604 " --> pdb=" O ILE A 600 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU A 605 " --> pdb=" O PHE A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 672 removed outlier: 3.512A pdb=" N GLY A 672 " --> pdb=" O LEU A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 695 removed outlier: 3.914A pdb=" N ALA A 676 " --> pdb=" O GLY A 672 " (cutoff:3.500A) Proline residue: A 688 - end of helix Processing helix chain 'A' and resid 699 through 703 Processing helix chain 'A' and resid 706 through 733 Processing helix chain 'A' and resid 743 through 771 Processing helix chain 'A' and resid 775 through 784 Processing helix chain 'A' and resid 788 through 797 Processing helix chain 'A' and resid 843 through 879 removed outlier: 3.723A pdb=" N ALA A 866 " --> pdb=" O ALA A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 905 Processing helix chain 'A' and resid 908 through 912 Processing helix chain 'A' and resid 920 through 932 Processing helix chain 'A' and resid 941 through 954 Processing helix chain 'A' and resid 962 through 988 Processing helix chain 'A' and resid 997 through 1003 Processing helix chain 'A' and resid 1007 through 1025 Processing helix chain 'A' and resid 1032 through 1047 Proline residue: A1044 - end of helix removed outlier: 3.604A pdb=" N GLN A1047 " --> pdb=" O GLU A1043 " (cutoff:3.500A) Processing helix chain 'A' and resid 1066 through 1076 Processing helix chain 'A' and resid 1094 through 1106 removed outlier: 3.566A pdb=" N ALA A1098 " --> pdb=" O ASP A1094 " (cutoff:3.500A) 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 1133 through 1140 Processing helix chain 'A' and resid 1145 through 1153 Processing helix chain 'A' and resid 1188 through 1196 Processing helix chain 'A' and resid 1231 through 1238 Processing helix chain 'A' and resid 1250 through 1277 removed outlier: 7.933A pdb=" N ILE A1260 " --> pdb=" O LYS A1256 " (cutoff:3.500A) removed outlier: 9.610A pdb=" N GLU A1261 " --> pdb=" O THR A1257 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ALA A1262 " --> pdb=" O LEU A1258 " (cutoff:3.500A) Processing helix chain 'A' and resid 1283 through 1295 removed outlier: 3.922A pdb=" N VAL A1287 " --> pdb=" O ASP A1283 " (cutoff:3.500A) Processing helix chain 'A' and resid 1304 through 1312 Processing helix chain 'A' and resid 1314 through 1322 removed outlier: 3.643A pdb=" N GLU A1322 " --> pdb=" O LEU A1318 " (cutoff:3.500A) Processing helix chain 'A' and resid 1323 through 1335 Processing helix chain 'A' and resid 1342 through 1350 Processing helix chain 'A' and resid 1355 through 1360 removed outlier: 3.708A pdb=" N GLY A1358 " --> pdb=" O ILE A1355 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU A1359 " --> pdb=" O GLY A1356 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N PHE A1360 " --> pdb=" O THR A1357 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1355 through 1360' Processing helix chain 'B' and resid 25 through 27 No H-bonds generated for 'chain 'B' and resid 25 through 27' Processing helix chain 'B' and resid 28 through 35 removed outlier: 3.914A pdb=" N ALA B 32 " --> pdb=" O ARG B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 53 removed outlier: 3.535A pdb=" N ILE B 44 " --> pdb=" O VAL B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 62 Processing helix chain 'B' and resid 98 through 106 Processing helix chain 'B' and resid 151 through 158 Processing helix chain 'B' and resid 236 through 243 Processing helix chain 'B' and resid 247 through 256 Processing helix chain 'B' and resid 258 through 275 Proline residue: B 267 - end of helix removed outlier: 3.898A pdb=" N ALA B 275 " --> pdb=" O GLU B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 290 Processing helix chain 'B' and resid 306 through 315 Processing helix chain 'B' and resid 328 through 346 Processing helix chain 'B' and resid 356 through 358 No H-bonds generated for 'chain 'B' and resid 356 through 358' Processing helix chain 'B' and resid 364 through 392 removed outlier: 3.672A pdb=" N LEU B 368 " --> pdb=" O LEU B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 406 removed outlier: 3.631A pdb=" N LYS B 404 " --> pdb=" O ASP B 401 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N MET B 406 " --> pdb=" O VAL B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 422 removed outlier: 3.564A pdb=" N THR B 412 " --> pdb=" O GLN B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 452 Processing helix chain 'B' and resid 472 through 476 Processing helix chain 'B' and resid 508 through 518 Processing helix chain 'B' and resid 527 through 533 removed outlier: 3.875A pdb=" N GLU B 530 " --> pdb=" O CYS B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 565 Processing helix chain 'B' and resid 607 through 617 Processing helix chain 'B' and resid 620 through 627 Processing helix chain 'B' and resid 635 through 641 removed outlier: 3.938A pdb=" N ASP B 640 " --> pdb=" O ASN B 636 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N CYS B 641 " --> pdb=" O GLU B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 665 removed outlier: 3.508A pdb=" N LEU B 665 " --> pdb=" O PHE B 662 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 672 Processing helix chain 'B' and resid 674 through 678 Processing helix chain 'B' and resid 679 through 691 Processing helix chain 'B' and resid 722 through 729 Processing helix chain 'B' and resid 730 through 733 Processing helix chain 'B' and resid 759 through 764 Processing helix chain 'B' and resid 932 through 938 removed outlier: 4.384A pdb=" N SER B 936 " --> pdb=" O HIS B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 939 through 956 removed outlier: 3.844A pdb=" N LEU B 943 " --> pdb=" O THR B 939 " (cutoff:3.500A) Processing helix chain 'B' and resid 968 through 980 removed outlier: 3.695A pdb=" N VAL B 972 " --> pdb=" O LYS B 968 " (cutoff:3.500A) Processing helix chain 'B' and resid 1015 through 1020 Processing helix chain 'B' and resid 1048 through 1059 Processing helix chain 'B' and resid 1060 through 1069 Processing helix chain 'B' and resid 1108 through 1120 Processing helix chain 'C' and resid 3 through 12 Processing helix chain 'C' and resid 41 through 49 Processing helix chain 'C' and resid 69 through 83 Processing helix chain 'C' and resid 102 through 112 Processing helix chain 'C' and resid 118 through 122 Processing helix chain 'C' and resid 158 through 162 removed outlier: 3.523A pdb=" N LEU C 162 " --> pdb=" O ASP C 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 158 through 162' Processing helix chain 'C' and resid 180 through 185 Processing helix chain 'C' and resid 222 through 226 Processing helix chain 'C' and resid 247 through 257 removed outlier: 3.996A pdb=" N GLU C 251 " --> pdb=" O GLY C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 281 removed outlier: 3.529A pdb=" N LEU C 280 " --> pdb=" O ASN C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 295 removed outlier: 3.581A pdb=" N LYS C 294 " --> pdb=" O GLU C 291 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LYS C 295 " --> pdb=" O LYS C 292 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 291 through 295' Processing helix chain 'C' and resid 317 through 344 Processing helix chain 'D' and resid 12 through 30 removed outlier: 3.864A pdb=" N VAL D 16 " --> pdb=" O SER D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 39 removed outlier: 3.695A pdb=" N GLN D 39 " --> pdb=" O HIS D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 56 removed outlier: 3.500A pdb=" N THR D 44 " --> pdb=" O GLN D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 74 Processing helix chain 'D' and resid 75 through 77 No H-bonds generated for 'chain 'D' and resid 75 through 77' Processing helix chain 'D' and resid 79 through 90 Processing helix chain 'D' and resid 94 through 99 Processing helix chain 'D' and resid 111 through 122 removed outlier: 4.241A pdb=" N ALA D 115 " --> pdb=" O GLU D 111 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER D 122 " --> pdb=" O HIS D 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 24 removed outlier: 3.527A pdb=" N TYR E 8 " --> pdb=" O GLU E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 34 Processing helix chain 'E' and resid 36 through 44 removed outlier: 3.512A pdb=" N PHE E 40 " --> pdb=" O THR E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 98 Processing helix chain 'E' and resid 111 through 120 Processing helix chain 'E' and resid 133 through 137 Processing helix chain 'E' and resid 152 through 164 Processing helix chain 'E' and resid 177 through 184 Processing helix chain 'F' and resid 58 through 75 Processing helix chain 'F' and resid 88 through 100 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 34 removed outlier: 3.918A pdb=" N ALA G 27 " --> pdb=" O ASN G 23 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 88 Processing helix chain 'I' and resid 55 through 60 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: 3.832A pdb=" N ARG J 46 " --> pdb=" O ARG J 42 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 62 removed outlier: 3.566A pdb=" N TYR J 62 " --> pdb=" O LYS J 58 " (cutoff:3.500A) Processing helix chain 'K' and resid 48 through 61 removed outlier: 3.560A pdb=" N GLY K 52 " --> pdb=" O ASP K 48 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LYS K 61 " --> pdb=" O TYR K 57 " (cutoff:3.500A) Processing helix chain 'K' and resid 93 through 126 removed outlier: 3.819A pdb=" N ALA K 126 " --> pdb=" O LYS K 122 " (cutoff:3.500A) Processing helix chain 'M' and resid 70 through 82 Processing helix chain 'M' and resid 140 through 159 Processing helix chain 'M' and resid 182 through 191 Processing helix chain 'M' and resid 192 through 202 Processing helix chain 'M' and resid 215 through 223 removed outlier: 3.765A pdb=" N GLU M 219 " --> pdb=" O ASP M 215 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLN M 223 " --> pdb=" O GLU M 219 " (cutoff:3.500A) Processing helix chain 'M' and resid 224 through 226 No H-bonds generated for 'chain 'M' and resid 224 through 226' Processing helix chain 'M' and resid 241 through 250 Processing helix chain 'M' and resid 269 through 275 removed outlier: 3.738A pdb=" N THR M 275 " --> pdb=" O ALA M 271 " (cutoff:3.500A) Processing helix chain 'M' and resid 277 through 290 Processing helix chain 'M' and resid 293 through 302 Processing helix chain 'M' and resid 306 through 317 removed outlier: 3.556A pdb=" N VAL M 310 " --> pdb=" O ASP M 306 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LYS M 316 " --> pdb=" O ARG M 312 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL M 317 " --> pdb=" O GLY M 313 " (cutoff:3.500A) Processing helix chain 'M' and resid 328 through 333 removed outlier: 3.688A pdb=" N LEU M 332 " --> pdb=" O LYS M 328 " (cutoff:3.500A) Processing helix chain 'M' and resid 345 through 363 removed outlier: 3.679A pdb=" N LEU M 349 " --> pdb=" O PRO M 345 " (cutoff:3.500A) Processing helix chain 'M' and resid 367 through 376 removed outlier: 3.545A pdb=" N VAL M 371 " --> pdb=" O VAL M 367 " (cutoff:3.500A) Processing helix chain 'M' and resid 378 through 389 removed outlier: 4.005A pdb=" N HIS M 388 " --> pdb=" O ASP M 384 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N MET M 389 " --> pdb=" O PHE M 385 " (cutoff:3.500A) Processing helix chain 'M' and resid 405 through 412 removed outlier: 3.822A pdb=" N ILE M 409 " --> pdb=" O ASP M 405 " (cutoff:3.500A) Processing helix chain 'M' and resid 412 through 435 removed outlier: 3.523A pdb=" N VAL M 416 " --> pdb=" O HIS M 412 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY M 425 " --> pdb=" O MET M 421 " (cutoff:3.500A) Processing helix chain 'N' and resid 147 through 151 removed outlier: 3.720A pdb=" N THR N 151 " --> pdb=" O ASP N 148 " (cutoff:3.500A) Processing helix chain 'N' and resid 249 through 259 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 388 through 396 Processing helix chain 'O' and resid 3 through 17 Processing helix chain 'O' and resid 19 through 32 removed outlier: 4.171A pdb=" N ILE O 24 " --> pdb=" O ILE O 20 " (cutoff:3.500A) Processing helix chain 'O' and resid 35 through 44 Processing helix chain 'O' and resid 46 through 60 removed outlier: 3.795A pdb=" N HIS O 60 " --> pdb=" O VAL O 56 " (cutoff:3.500A) 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 78 through 85 Processing helix chain 'O' and resid 87 through 99 Processing helix chain 'O' and resid 100 through 114 Processing helix chain 'O' and resid 117 through 131 removed outlier: 4.331A pdb=" N GLU O 131 " --> pdb=" O ASP O 127 " (cutoff:3.500A) Processing helix chain 'O' and resid 141 through 154 Processing helix chain 'O' and resid 184 through 188 removed outlier: 3.526A pdb=" N MET O 187 " --> pdb=" O GLU O 184 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N TYR O 188 " --> pdb=" O LYS O 185 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 184 through 188' Processing helix chain 'O' and resid 238 through 259 Processing helix chain 'O' and resid 260 through 278 removed outlier: 4.715A pdb=" N ILE O 276 " --> pdb=" O ARG O 272 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N THR O 277 " --> pdb=" O MET O 273 " (cutoff:3.500A) Processing helix chain 'O' and resid 290 through 297 Processing helix chain 'O' and resid 304 through 317 Processing helix chain 'O' and resid 337 through 359 Processing helix chain 'O' and resid 359 through 372 Processing helix chain 'O' and resid 376 through 385 Processing helix chain 'O' and resid 390 through 400 Processing helix chain 'O' and resid 416 through 420 removed outlier: 3.706A pdb=" N THR O 420 " --> pdb=" O PRO O 417 " (cutoff:3.500A) Processing helix chain 'O' and resid 427 through 457 removed outlier: 3.560A pdb=" N ASN O 457 " --> pdb=" O GLU O 453 " (cutoff:3.500A) Processing helix chain 'O' and resid 457 through 473 removed outlier: 4.108A pdb=" N ILE O 471 " --> pdb=" O VAL O 467 " (cutoff:3.500A) Processing helix chain 'O' and resid 480 through 484 removed outlier: 3.670A pdb=" N GLN O 483 " --> pdb=" O GLU O 480 " (cutoff:3.500A) Processing helix chain 'O' and resid 495 through 530 removed outlier: 3.648A pdb=" N GLU O 518 " --> pdb=" O ILE O 514 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR O 519 " --> pdb=" O GLN O 515 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N THR O 530 " --> pdb=" O TYR O 526 " (cutoff:3.500A) Processing helix chain 'P' and resid 15 through 29 Processing helix chain 'P' and resid 34 through 42 Processing helix chain 'P' and resid 46 through 60 Processing helix chain 'P' and resid 78 through 81 Processing helix chain 'P' and resid 89 through 103 removed outlier: 3.779A pdb=" N ILE P 98 " --> pdb=" O LEU P 94 " (cutoff:3.500A) Processing helix chain 'P' and resid 104 through 106 No H-bonds generated for 'chain 'P' and resid 104 through 106' Processing helix chain 'P' and resid 108 through 117 Processing helix chain 'P' and resid 119 through 133 removed outlier: 4.383A pdb=" N LYS P 125 " --> pdb=" O THR P 121 " (cutoff:3.500A) Processing helix chain 'P' and resid 173 through 199 removed outlier: 3.598A pdb=" N VAL P 177 " --> pdb=" O GLU P 173 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LYS P 199 " --> pdb=" O ALA P 195 " (cutoff:3.500A) Processing helix chain 'P' and resid 201 through 210 Processing helix chain 'P' and resid 213 through 224 Processing helix chain 'P' and resid 231 through 245 Processing helix chain 'P' and resid 281 through 285 Processing helix chain 'P' and resid 292 through 296 Processing helix chain 'P' and resid 307 through 316 removed outlier: 3.520A pdb=" N THR P 311 " --> pdb=" O CYS P 307 " (cutoff:3.500A) Processing helix chain 'Q' and resid 51 through 68 Processing helix chain 'Q' and resid 88 through 93 Processing helix chain 'Q' and resid 107 through 111 removed outlier: 3.640A pdb=" N MET Q 110 " --> pdb=" O PRO Q 107 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N MET Q 111 " --> pdb=" O ARG Q 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 107 through 111' Processing helix chain '1' and resid 4 through 21 removed outlier: 3.605A pdb=" N THR 1 9 " --> pdb=" O PRO 1 5 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLU 1 12 " --> pdb=" O GLN 1 8 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER 1 16 " --> pdb=" O GLU 1 12 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ARG 1 17 " --> pdb=" O ALA 1 13 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR 1 21 " --> pdb=" O ARG 1 17 " (cutoff:3.500A) Processing helix chain '1' and resid 26 through 34 removed outlier: 3.840A pdb=" N ARG 1 34 " --> pdb=" O THR 1 30 " (cutoff:3.500A) Processing helix chain '1' and resid 48 through 64 Processing helix chain '1' and resid 65 through 67 No H-bonds generated for 'chain '1' and resid 65 through 67' Processing helix chain '1' and resid 71 through 88 Processing helix chain '1' and resid 105 through 117 removed outlier: 4.000A pdb=" N LYS 1 109 " --> pdb=" O ASP 1 105 " (cutoff:3.500A) Processing helix chain '1' and resid 119 through 133 removed outlier: 3.614A pdb=" N PHE 1 126 " --> pdb=" O ALA 1 122 " (cutoff:3.500A) Processing helix chain '3' and resid 46 through 54 removed outlier: 3.993A pdb=" N ARG 3 52 " --> pdb=" O GLY 3 48 " (cutoff:3.500A) Processing helix chain '3' and resid 77 through 90 removed outlier: 4.241A pdb=" N ARG 3 88 " --> pdb=" O ALA 3 84 " (cutoff:3.500A) Processing helix chain '3' and resid 98 through 106 removed outlier: 4.121A pdb=" N ALA 3 102 " --> pdb=" O ALA 3 98 " (cutoff:3.500A) Processing helix chain '3' and resid 127 through 143 removed outlier: 3.595A pdb=" N THR 3 143 " --> pdb=" O HIS 3 139 " (cutoff:3.500A) Processing helix chain '3' and resid 154 through 162 removed outlier: 4.122A pdb=" N GLU 3 160 " --> pdb=" O VAL 3 156 " (cutoff:3.500A) Processing helix chain '3' and resid 170 through 174 Processing helix chain '3' and resid 211 through 219 removed outlier: 3.787A pdb=" N LEU 3 215 " --> pdb=" O LYS 3 211 " (cutoff:3.500A) Processing helix chain '3' and resid 221 through 226 Processing helix chain '3' and resid 242 through 247 Processing helix chain '3' and resid 270 through 280 removed outlier: 4.389A pdb=" N ILE 3 274 " --> pdb=" O LEU 3 270 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE 3 275 " --> pdb=" O SER 3 271 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLU 3 276 " --> pdb=" O ARG 3 272 " (cutoff:3.500A) Processing helix chain '3' and resid 297 through 300 removed outlier: 3.500A pdb=" N ASP 3 300 " --> pdb=" O THR 3 297 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 297 through 300' Processing helix chain '3' and resid 380 through 389 removed outlier: 4.024A pdb=" N HIS 3 388 " --> pdb=" O PHE 3 384 " (cutoff:3.500A) Processing helix chain '3' and resid 406 through 410 Processing helix chain '4' and resid 163 through 171 removed outlier: 3.897A pdb=" N GLU 4 167 " --> pdb=" O GLU 4 163 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN 4 171 " --> pdb=" O GLU 4 167 " (cutoff:3.500A) Processing helix chain '4' and resid 185 through 222 Proline residue: 4 207 - end of helix Processing helix chain '4' and resid 224 through 247 Processing helix chain '4' and resid 251 through 255 removed outlier: 3.831A pdb=" N LEU 4 254 " --> pdb=" O GLU 4 251 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLY 4 255 " --> pdb=" O ALA 4 252 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 251 through 255' Processing helix chain '4' and resid 262 through 269 removed outlier: 3.509A pdb=" N ILE 4 266 " --> pdb=" O ASP 4 262 " (cutoff:3.500A) Processing helix chain '4' and resid 276 through 286 removed outlier: 3.612A pdb=" N PHE 4 283 " --> pdb=" O GLU 4 279 " (cutoff:3.500A) Processing helix chain '4' and resid 301 through 313 Processing helix chain '4' and resid 316 through 325 removed outlier: 3.691A pdb=" N ILE 4 320 " --> pdb=" O GLU 4 316 " (cutoff:3.500A) Processing helix chain '4' and resid 329 through 341 removed outlier: 4.281A pdb=" N LYS 4 336 " --> pdb=" O GLN 4 332 " (cutoff:3.500A) Processing helix chain '4' and resid 351 through 365 removed outlier: 3.674A pdb=" N ARG 4 355 " --> pdb=" O GLU 4 351 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET 4 356 " --> pdb=" O GLU 4 352 " (cutoff:3.500A) Processing helix chain '4' and resid 371 through 379 removed outlier: 3.571A pdb=" N ILE 4 375 " --> pdb=" O PRO 4 371 " (cutoff:3.500A) Processing helix chain '4' and resid 386 through 392 removed outlier: 3.563A pdb=" N TYR 4 389 " --> pdb=" O GLN 4 386 " (cutoff:3.500A) Processing helix chain '4' and resid 407 through 412 Processing helix chain '4' and resid 413 through 419 removed outlier: 4.034A pdb=" N ALA 4 417 " --> pdb=" O LEU 4 413 " (cutoff:3.500A) Processing helix chain '4' and resid 424 through 429 removed outlier: 3.635A pdb=" N ARG 4 428 " --> pdb=" O TRP 4 424 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLU 4 429 " --> pdb=" O PHE 4 425 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 424 through 429' Processing helix chain '4' and resid 435 through 448 removed outlier: 3.991A pdb=" N ASP 4 441 " --> pdb=" O ALA 4 437 " (cutoff:3.500A) Processing helix chain '4' and resid 459 through 468 removed outlier: 3.749A pdb=" N GLN 4 463 " --> pdb=" O LYS 4 459 " (cutoff:3.500A) Processing helix chain '4' and resid 477 through 482 Processing helix chain '4' and resid 487 through 499 removed outlier: 5.354A pdb=" N SER 4 493 " --> pdb=" O SER 4 489 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N LYS 4 494 " --> pdb=" O GLN 4 490 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ILE 4 497 " --> pdb=" O SER 4 493 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N MET 4 499 " --> pdb=" O TRP 4 495 " (cutoff:3.500A) Processing helix chain '4' and resid 504 through 510 removed outlier: 3.908A pdb=" N ARG 4 508 " --> pdb=" O GLY 4 504 " (cutoff:3.500A) Processing helix chain '4' and resid 511 through 513 No H-bonds generated for 'chain '4' and resid 511 through 513' Processing helix chain 'U' and resid 179 through 186 Processing helix chain 'U' and resid 226 through 244 Processing helix chain 'U' and resid 269 through 277 removed outlier: 3.687A pdb=" N LEU U 273 " --> pdb=" O ARG U 269 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL U 274 " --> pdb=" O LEU U 270 " (cutoff:3.500A) Processing helix chain 'U' and resid 317 through 334 Proline residue: U 330 - end of helix Processing helix chain 'V' and resid 43 through 48 Processing helix chain 'V' and resid 66 through 83 removed outlier: 3.501A pdb=" N LEU V 83 " --> pdb=" O LEU V 79 " (cutoff:3.500A) Processing helix chain 'V' and resid 86 through 101 Processing helix chain 'V' and resid 103 through 108 Processing helix chain 'V' and resid 110 through 129 removed outlier: 3.728A pdb=" N HIS V 129 " --> pdb=" O THR V 125 " (cutoff:3.500A) Processing helix chain 'V' and resid 134 through 141 removed outlier: 3.602A pdb=" N ILE V 138 " --> pdb=" O THR V 134 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU V 141 " --> pdb=" O ALA V 137 " (cutoff:3.500A) Processing helix chain 'V' and resid 145 through 160 Processing helix chain 'V' and resid 168 through 178 removed outlier: 3.914A pdb=" N SER V 178 " --> pdb=" O LYS V 174 " (cutoff:3.500A) Processing helix chain 'V' and resid 190 through 194 Processing helix chain 'V' and resid 196 through 214 Processing helix chain 'V' and resid 221 through 238 removed outlier: 4.093A pdb=" N VAL V 225 " --> pdb=" O HIS V 221 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLN V 238 " --> pdb=" O TRP V 234 " (cutoff:3.500A) Processing helix chain 'V' and resid 238 through 243 Processing helix chain 'V' and resid 246 through 255 Processing helix chain 'V' and resid 261 through 278 Processing helix chain 'V' and resid 280 through 287 Processing helix chain 'V' and resid 293 through 295 No H-bonds generated for 'chain 'V' and resid 293 through 295' Processing helix chain 'V' and resid 296 through 303 removed outlier: 3.576A pdb=" N HIS V 303 " --> pdb=" O ASP V 299 " (cutoff:3.500A) Processing helix chain 'V' and resid 303 through 313 Processing helix chain 'V' and resid 386 through 393 removed outlier: 3.742A pdb=" N GLU V 390 " --> pdb=" O ASP V 386 " (cutoff:3.500A) Processing helix chain 'V' and resid 395 through 406 removed outlier: 3.570A pdb=" N GLN V 406 " --> pdb=" O PHE V 402 " (cutoff:3.500A) Processing helix chain 'W' and resid 304 through 319 Processing helix chain 'W' and resid 321 through 328 Processing helix chain 'W' and resid 333 through 348 Processing helix chain 'W' and resid 348 through 358 Processing helix chain 'W' and resid 364 through 384 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 5 removed outlier: 6.844A pdb=" N GLU A 4 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LYS G 37 " --> pdb=" O CYS G 45 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU G 44 " --> pdb=" O PHE G 77 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N VAL G 75 " --> pdb=" O ILE G 46 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N LEU G 48 " --> pdb=" O ARG G 73 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N ARG G 73 " --> pdb=" O LEU G 48 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N ASP G 50 " --> pdb=" O HIS G 71 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N HIS G 71 " --> pdb=" O ASP G 50 " (cutoff:3.500A) removed outlier: 8.934A pdb=" N THR G 52 " --> pdb=" O LYS G 69 " (cutoff:3.500A) removed outlier: 11.699A pdb=" N LYS G 69 " --> pdb=" O THR G 52 " (cutoff:3.500A) removed outlier: 10.758A pdb=" N LEU G 54 " --> pdb=" O HIS G 67 " (cutoff:3.500A) removed outlier: 11.846A pdb=" N HIS G 67 " --> pdb=" O LEU G 54 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ALA D 9 " --> pdb=" O LEU G 4 " (cutoff:3.500A) removed outlier: 8.514A pdb=" N GLU G 6 " --> pdb=" O ASN D 7 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N ASN D 7 " --> pdb=" O GLU G 6 " (cutoff:3.500A) removed outlier: 9.214A pdb=" N VAL G 8 " --> pdb=" O ASP D 5 " (cutoff:3.500A) removed outlier: 10.410A pdb=" N ASP D 5 " --> pdb=" O VAL G 8 " (cutoff:3.500A) removed outlier: 13.056A pdb=" N THR G 10 " --> pdb=" O VAL D 3 " (cutoff:3.500A) removed outlier: 13.046A pdb=" N VAL D 3 " --> pdb=" O THR G 10 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1338 through 1339 removed outlier: 4.968A pdb=" N ILE A 15 " --> pdb=" O SER B1129 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N SER B1129 " --> pdb=" O ILE A 15 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N HIS A 17 " --> pdb=" O LYS B1127 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 92 removed outlier: 6.940A pdb=" N THR A 253 " --> pdb=" O LEU A 88 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 166 through 168 removed outlier: 4.644A pdb=" N ILE A 174 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 266 through 268 removed outlier: 4.092A pdb=" N GLY A 273 " --> pdb=" O SER A 268 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 359 through 360 removed outlier: 3.545A pdb=" N LYS A 359 " --> pdb=" O LEU B1047 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 1021 through 1023 removed outlier: 3.543A pdb=" N SER A 364 " --> pdb=" O ARG B1023 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N HIS A 508 " --> pdb=" O LEU A 461 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N PHE A 486 " --> pdb=" O ARG A 366 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N VAL A 368 " --> pdb=" O PHE A 486 " (cutoff:3.500A) removed outlier: 8.574A pdb=" N PHE A 488 " --> pdb=" O VAL A 368 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N SER A 370 " --> pdb=" O PHE A 488 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 391 through 395 removed outlier: 4.256A pdb=" N PHE A 420 " --> pdb=" O GLU A 451 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N HIS A 453 " --> pdb=" O ALA A 418 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ALA A 418 " --> pdb=" O HIS A 453 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 558 through 559 Processing sheet with id=AB1, first strand: chain 'A' and resid 617 through 620 removed outlier: 6.815A pdb=" N THR A 639 " --> pdb=" O MET A 646 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 883 through 884 removed outlier: 3.999A pdb=" N CYS A 883 " --> pdb=" O ARG A 891 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG A 891 " --> pdb=" O CYS A 883 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL A 890 " --> pdb=" O ILE A 898 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1210 through 1214 removed outlier: 6.959A pdb=" N TYR A1223 " --> pdb=" O LEU A1089 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LEU A1089 " --> pdb=" O TYR A1223 " (cutoff:3.500A) removed outlier: 11.211A pdb=" N THR A1086 " --> pdb=" O THR A1244 " (cutoff:3.500A) removed outlier: 8.654A pdb=" N THR A1244 " --> pdb=" O THR A1086 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N GLN A1088 " --> pdb=" O LYS A1242 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1108 through 1109 removed outlier: 6.805A pdb=" N THR A1108 " --> pdb=" O VAL A1201 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1114 through 1121 removed outlier: 3.583A pdb=" N TYR A1116 " --> pdb=" O LYS A1131 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1361 through 1364 Processing sheet with id=AB7, first strand: chain 'B' and resid 64 through 65 removed outlier: 6.799A pdb=" N ASP B 116 " --> pdb=" O LEU B 78 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N ILE B 80 " --> pdb=" O THR B 114 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N THR B 114 " --> pdb=" O ILE B 80 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N GLY B 134 " --> pdb=" O ILE B 113 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 64 through 65 removed outlier: 6.799A pdb=" N ASP B 116 " --> pdb=" O LEU B 78 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N ILE B 80 " --> pdb=" O THR B 114 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N THR B 114 " --> pdb=" O ILE B 80 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N ARG B 125 " --> pdb=" O ILE W 282 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 169 through 171 Processing sheet with id=AC1, first strand: chain 'B' and resid 360 through 363 Processing sheet with id=AC2, first strand: chain 'B' and resid 189 through 193 removed outlier: 3.970A pdb=" N ALA B 201 " --> pdb=" O MET B 216 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 424 through 426 Processing sheet with id=AC4, first strand: chain 'B' and resid 501 through 502 removed outlier: 3.517A pdb=" N HIS B 501 " --> pdb=" O CYS B 593 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 603 through 604 Processing sheet with id=AC6, first strand: chain 'B' and resid 544 through 550 removed outlier: 5.423A pdb=" N ILE B 545 " --> pdb=" O LEU B 541 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N LEU B 541 " --> pdb=" O ILE B 545 " (cutoff:3.500A) removed outlier: 8.219A pdb=" N VAL B 583 " --> pdb=" O VAL B 536 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N LEU B 538 " --> pdb=" O VAL B 583 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ILE B 585 " --> pdb=" O LEU B 538 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N PHE B 540 " --> pdb=" O ILE B 585 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 708 through 712 removed outlier: 6.606A pdb=" N LEU B 880 " --> pdb=" O ILE B 871 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ILE B 871 " --> pdb=" O LEU B 880 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N LYS B 882 " --> pdb=" O VAL B 869 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N VAL B 869 " --> pdb=" O LYS B 882 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N LEU B 884 " --> pdb=" O GLU B 867 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 708 through 712 removed outlier: 6.606A pdb=" N LEU B 880 " --> pdb=" O ILE B 871 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ILE B 871 " --> pdb=" O LEU B 880 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N LYS B 882 " --> pdb=" O VAL B 869 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N VAL B 869 " --> pdb=" O LYS B 882 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N LEU B 884 " --> pdb=" O GLU B 867 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N VAL B 869 " --> pdb=" O LYS L 46 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 986 through 987 removed outlier: 6.864A pdb=" N LEU B 755 " --> pdb=" O LEU B 909 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N VAL B 911 " --> pdb=" O LEU B 755 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N LEU B 757 " --> pdb=" O VAL B 911 " (cutoff:3.500A) removed outlier: 9.061A pdb=" N ILE B 927 " --> pdb=" O ASN B 738 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N THR B 740 " --> pdb=" O ILE B 927 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N MET B 929 " --> pdb=" O THR B 740 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ALA B 742 " --> pdb=" O MET B 929 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N TYR B1003 " --> pdb=" O VAL B 743 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 789 through 790 Processing sheet with id=AD2, first strand: chain 'B' and resid 795 through 796 removed outlier: 3.642A pdb=" N LYS B 801 " --> pdb=" O ASP B 796 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1086 through 1087 removed outlier: 3.711A pdb=" N ASP B1078 " --> pdb=" O GLY B1087 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 13 through 15 removed outlier: 7.232A pdb=" N SER C 60 " --> pdb=" O MET C 56 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N MET C 56 " --> pdb=" O SER C 60 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N GLU C 62 " --> pdb=" O VAL C 54 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 13 through 15 removed outlier: 9.420A pdb=" N ARG C 303 " --> pdb=" O PRO C 237 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N HIS C 305 " --> pdb=" O LEU C 235 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N LEU C 235 " --> pdb=" O HIS C 305 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ILE C 307 " --> pdb=" O TYR C 233 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N TYR C 233 " --> pdb=" O ILE C 307 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N SER C 309 " --> pdb=" O ALA C 231 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ALA C 231 " --> pdb=" O SER C 309 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N GLU C 311 " --> pdb=" O ALA C 229 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 174 through 176 removed outlier: 4.313A pdb=" N GLN C 139 " --> pdb=" O ILE C 176 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N ASP C 209 " --> pdb=" O VAL C 94 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N VAL C 94 " --> pdb=" O ASP C 209 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LEU C 211 " --> pdb=" O VAL C 92 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N VAL C 92 " --> pdb=" O LEU C 211 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N HIS C 213 " --> pdb=" O GLU C 90 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL L 53 " --> pdb=" O VAL C 94 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 147 through 148 removed outlier: 3.829A pdb=" N THR C 147 " --> pdb=" O VAL C 164 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 167 through 169 removed outlier: 3.688A pdb=" N ALA C 200 " --> pdb=" O VAL C 168 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 240 through 241 removed outlier: 3.785A pdb=" N THR C 240 " --> pdb=" O ARG C 298 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 262 through 266 Processing sheet with id=AE2, first strand: chain 'E' and resid 58 through 62 removed outlier: 6.091A pdb=" N THR E 59 " --> pdb=" O VAL E 74 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N VAL E 74 " --> pdb=" O THR E 59 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LEU E 61 " --> pdb=" O MET E 72 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ARG E 101 " --> pdb=" O GLN E 71 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 81 through 82 Processing sheet with id=AE4, first strand: chain 'E' and resid 147 through 150 removed outlier: 3.531A pdb=" N GLU E 147 " --> pdb=" O ILE E 194 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 105 through 108 removed outlier: 3.907A pdb=" N ASP G 105 " --> pdb=" O LEU G 101 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N ILE G 107 " --> pdb=" O VAL G 99 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N VAL G 99 " --> pdb=" O ILE G 107 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N GLY G 96 " --> pdb=" O CYS G 92 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N CYS G 92 " --> pdb=" O GLY G 96 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N HIS G 98 " --> pdb=" O LYS G 90 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 4 through 14 removed outlier: 7.028A pdb=" N HIS H 29 " --> pdb=" O LYS H 13 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N SER H 26 " --> pdb=" O VAL H 43 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N VAL H 43 " --> pdb=" O SER H 26 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N LYS H 55 " --> pdb=" O LEU H 148 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 12 through 15 Processing sheet with id=AE8, first strand: chain 'I' and resid 79 through 82 Processing sheet with id=AE9, first strand: chain 'K' and resid 26 through 30 Processing sheet with id=AF1, first strand: chain 'M' and resid 10 through 17 removed outlier: 8.036A pdb=" N LEU M 124 " --> pdb=" O GLU M 12 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ASP M 14 " --> pdb=" O LEU M 124 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N LEU M 126 " --> pdb=" O ASP M 14 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N TYR M 16 " --> pdb=" O LEU M 126 " (cutoff:3.500A) removed outlier: 8.951A pdb=" N LEU N 383 " --> pdb=" O LEU N 266 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N PHE N 268 " --> pdb=" O LEU N 383 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N CYS N 385 " --> pdb=" O PHE N 268 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLN N 270 " --> pdb=" O CYS N 385 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL N 348 " --> pdb=" O VAL N 337 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N VAL N 337 " --> pdb=" O VAL N 348 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLY N 324 " --> pdb=" O LEU M 17 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL M 15 " --> pdb=" O VAL N 326 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N LYS N 328 " --> pdb=" O ILE M 13 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ILE M 13 " --> pdb=" O LYS N 328 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N LEU N 330 " --> pdb=" O GLN M 11 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N GLN M 11 " --> pdb=" O LEU N 330 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'M' and resid 25 through 34 removed outlier: 6.759A pdb=" N LEU M 25 " --> pdb=" O GLY M 131 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N LEU M 133 " --> pdb=" O LEU M 25 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N LEU M 27 " --> pdb=" O LEU M 133 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LEU M 135 " --> pdb=" O LEU M 27 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N GLN M 29 " --> pdb=" O LEU M 135 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N GLU M 57 " --> pdb=" O ALA M 47 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ALA M 47 " --> pdb=" O GLU M 57 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N GLU M 59 " --> pdb=" O LEU M 45 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N LEU M 45 " --> pdb=" O TYR M 210 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N TYR M 210 " --> pdb=" O LEU M 45 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ALA M 47 " --> pdb=" O LEU M 208 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL M 206 " --> pdb=" O ILE M 49 " (cutoff:3.500A) removed outlier: 9.510A pdb=" N MET N 373 " --> pdb=" O HIS M 207 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N HIS M 209 " --> pdb=" O MET N 373 " (cutoff:3.500A) removed outlier: 9.262A pdb=" N VAL N 375 " --> pdb=" O HIS M 209 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N MET N 373 " --> pdb=" O GLY N 364 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N GLY N 364 " --> pdb=" O MET N 373 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N VAL N 375 " --> pdb=" O SER N 362 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N SER N 362 " --> pdb=" O VAL N 375 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N GLN N 358 " --> pdb=" O VAL N 379 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ARG M 33 " --> pdb=" O LEU N 357 " (cutoff:3.500A) removed outlier: 11.555A pdb=" N GLU N 359 " --> pdb=" O PRO M 31 " (cutoff:3.500A) removed outlier: 10.971A pdb=" N VAL N 361 " --> pdb=" O GLN M 29 " (cutoff:3.500A) removed outlier: 9.516A pdb=" N GLN M 29 " --> pdb=" O VAL N 361 " (cutoff:3.500A) removed outlier: 9.962A pdb=" N VAL N 363 " --> pdb=" O LEU M 27 " (cutoff:3.500A) removed outlier: 9.570A pdb=" N LEU M 27 " --> pdb=" O VAL N 363 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'M' and resid 291 through 292 Processing sheet with id=AF4, first strand: chain 'M' and resid 390 through 393 Processing sheet with id=AF5, first strand: chain 'O' and resid 63 through 67 Processing sheet with id=AF6, first strand: chain 'O' and resid 157 through 159 Processing sheet with id=AF7, first strand: chain 'O' and resid 288 through 289 Processing sheet with id=AF8, first strand: chain 'O' and resid 405 through 406 Processing sheet with id=AF9, first strand: chain 'P' and resid 63 through 68 Processing sheet with id=AG1, first strand: chain 'P' and resid 136 through 140 Processing sheet with id=AG2, first strand: chain 'P' and resid 167 through 168 Processing sheet with id=AG3, first strand: chain 'P' and resid 211 through 212 Processing sheet with id=AG4, first strand: chain '1' and resid 97 through 100 removed outlier: 6.864A pdb=" N ILE 1 97 " --> pdb=" O HIS 1 136 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N THR 1 138 " --> pdb=" O ILE 1 97 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N VAL 1 99 " --> pdb=" O THR 1 138 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG4 Processing sheet with id=AG5, first strand: chain '3' and resid 32 through 34 removed outlier: 3.668A pdb=" N LEU 3 34 " --> pdb=" O ASN 3 38 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain '3' and resid 42 through 43 Processing sheet with id=AG7, first strand: chain '3' and resid 203 through 207 removed outlier: 3.550A pdb=" N VAL 3 320 " --> pdb=" O LEU 3 187 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N CYS 3 312 " --> pdb=" O PHE 3 251 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain '3' and resid 203 through 207 Processing sheet with id=AG9, first strand: chain '3' and resid 257 through 260 Processing sheet with id=AH1, first strand: chain '3' and resid 378 through 379 Processing sheet with id=AH2, first strand: chain 'U' and resid 190 through 193 removed outlier: 4.830A pdb=" N ASN U 193 " --> pdb=" O ALA U 199 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N ALA U 199 " --> pdb=" O ASN U 193 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N LEU U 165 " --> pdb=" O SER U 261 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N SER U 261 " --> pdb=" O LEU U 165 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N THR U 171 " --> pdb=" O ILE U 255 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ILE U 255 " --> pdb=" O THR U 171 " (cutoff:3.500A) removed outlier: 8.590A pdb=" N ASN U 173 " --> pdb=" O PHE U 253 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N PHE U 253 " --> pdb=" O ASN U 173 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N MET U 258 " --> pdb=" O GLY U 314 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLY U 314 " --> pdb=" O MET U 258 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ILE U 292 " --> pdb=" O SER U 282 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'V' and resid 15 through 19 removed outlier: 3.534A pdb=" N VAL V 27 " --> pdb=" O VAL V 16 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ASP V 18 " --> pdb=" O GLN V 25 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N GLN V 25 " --> pdb=" O ASP V 18 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N THR V 36 " --> pdb=" O LEU V 26 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N CYS V 28 " --> pdb=" O VAL V 34 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N VAL V 34 " --> pdb=" O CYS V 28 " (cutoff:3.500A) 2406 hydrogen bonds defined for protein. 6822 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 60 hydrogen bonds 120 hydrogen bond angles 0 basepair planarities 25 basepair parallelities 88 stacking parallelities Total time for adding SS restraints: 27.43 Time building geometry restraints manager: 12.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.36: 19062 1.36 - 1.59: 39438 1.59 - 1.82: 832 1.82 - 2.05: 0 2.05 - 2.28: 12 Bond restraints: 59344 Sorted by residual: bond pdb=" O3' DC X -21 " pdb=" P DT X -20 " ideal model delta sigma weight residual 1.607 1.128 0.479 1.50e-02 4.44e+03 1.02e+03 bond pdb=" C PRO 1 68 " pdb=" N PRO 1 69 " ideal model delta sigma weight residual 1.335 1.368 -0.033 1.19e-02 7.06e+03 7.80e+00 bond pdb=" O3' DG X -18 " pdb=" P DT X -17 " ideal model delta sigma weight residual 1.607 1.639 -0.032 1.50e-02 4.44e+03 4.67e+00 bond pdb=" C ASP 3 375 " pdb=" N PRO 3 376 " ideal model delta sigma weight residual 1.334 1.376 -0.042 2.34e-02 1.83e+03 3.29e+00 bond pdb=" C ILE B 392 " pdb=" N PRO B 393 " ideal model delta sigma weight residual 1.334 1.372 -0.038 2.34e-02 1.83e+03 2.69e+00 ... (remaining 59339 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.29: 80600 3.29 - 6.59: 121 6.59 - 9.88: 3 9.88 - 13.17: 3 13.17 - 16.47: 1 Bond angle restraints: 80728 Sorted by residual: angle pdb=" O3' DC X -21 " pdb=" P DT X -20 " pdb=" O5' DT X -20 " ideal model delta sigma weight residual 104.00 87.53 16.47 1.50e+00 4.44e-01 1.21e+02 angle pdb=" C4' DG X -18 " pdb=" C3' DG X -18 " pdb=" O3' DG X -18 " ideal model delta sigma weight residual 110.00 121.91 -11.91 1.50e+00 4.44e-01 6.30e+01 angle pdb=" C3' DC X -21 " pdb=" O3' DC X -21 " pdb=" P DT X -20 " ideal model delta sigma weight residual 120.20 110.22 9.98 1.50e+00 4.44e-01 4.43e+01 angle pdb=" O3' DT X -19 " pdb=" C3' DT X -19 " pdb=" C2' DT X -19 " ideal model delta sigma weight residual 111.50 102.65 8.85 1.50e+00 4.44e-01 3.48e+01 angle pdb=" N VAL K 93 " pdb=" CA VAL K 93 " pdb=" C VAL K 93 " ideal model delta sigma weight residual 111.90 108.09 3.81 8.10e-01 1.52e+00 2.21e+01 ... (remaining 80723 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.57: 35240 35.57 - 71.13: 747 71.13 - 106.70: 36 106.70 - 142.27: 0 142.27 - 177.83: 4 Dihedral angle restraints: 36027 sinusoidal: 15986 harmonic: 20041 Sorted by residual: dihedral pdb=" CA TYR 3 340 " pdb=" C TYR 3 340 " pdb=" N PRO 3 341 " pdb=" CA PRO 3 341 " ideal model delta harmonic sigma weight residual 180.00 156.62 23.38 0 5.00e+00 4.00e-02 2.19e+01 dihedral pdb=" C4' DG X -18 " pdb=" C3' DG X -18 " pdb=" O3' DG X -18 " pdb=" P DT X -17 " ideal model delta sinusoidal sigma weight residual 220.00 42.17 177.83 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DT X 9 " pdb=" C3' DT X 9 " pdb=" O3' DT X 9 " pdb=" P DT X 10 " ideal model delta sinusoidal sigma weight residual -140.00 36.63 -176.63 1 3.50e+01 8.16e-04 1.57e+01 ... (remaining 36024 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 8495 0.087 - 0.175: 486 0.175 - 0.262: 2 0.262 - 0.349: 0 0.349 - 0.437: 1 Chirality restraints: 8984 Sorted by residual: chirality pdb=" C3' DG X -18 " pdb=" C4' DG X -18 " pdb=" O3' DG X -18 " pdb=" C2' DG X -18 " both_signs ideal model delta sigma weight residual False -2.66 -2.22 -0.44 2.00e-01 2.50e+01 4.76e+00 chirality pdb=" C3' DT X -19 " pdb=" C4' DT X -19 " pdb=" O3' DT X -19 " pdb=" C2' DT X -19 " both_signs ideal model delta sigma weight residual False -2.66 -2.88 0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" C1' DT X -19 " pdb=" O4' DT X -19 " pdb=" C2' DT X -19 " pdb=" N1 DT X -19 " both_signs ideal model delta sigma weight residual False 2.47 2.27 0.20 2.00e-01 2.50e+01 9.76e-01 ... (remaining 8981 not shown) Planarity restraints: 9896 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT X -19 " 0.057 2.00e-02 2.50e+03 2.82e-02 1.99e+01 pdb=" N1 DT X -19 " -0.057 2.00e-02 2.50e+03 pdb=" C2 DT X -19 " -0.020 2.00e-02 2.50e+03 pdb=" O2 DT X -19 " 0.000 2.00e-02 2.50e+03 pdb=" N3 DT X -19 " 0.000 2.00e-02 2.50e+03 pdb=" C4 DT X -19 " 0.019 2.00e-02 2.50e+03 pdb=" O4 DT X -19 " 0.019 2.00e-02 2.50e+03 pdb=" C5 DT X -19 " -0.018 2.00e-02 2.50e+03 pdb=" C7 DT X -19 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DT X -19 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG X -18 " -0.046 2.00e-02 2.50e+03 2.28e-02 1.56e+01 pdb=" N9 DG X -18 " 0.048 2.00e-02 2.50e+03 pdb=" C8 DG X -18 " 0.030 2.00e-02 2.50e+03 pdb=" N7 DG X -18 " -0.030 2.00e-02 2.50e+03 pdb=" C5 DG X -18 " -0.000 2.00e-02 2.50e+03 pdb=" C6 DG X -18 " 0.000 2.00e-02 2.50e+03 pdb=" O6 DG X -18 " -0.007 2.00e-02 2.50e+03 pdb=" N1 DG X -18 " -0.000 2.00e-02 2.50e+03 pdb=" C2 DG X -18 " 0.000 2.00e-02 2.50e+03 pdb=" N2 DG X -18 " -0.000 2.00e-02 2.50e+03 pdb=" N3 DG X -18 " 0.007 2.00e-02 2.50e+03 pdb=" C4 DG X -18 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR D 56 " 0.030 5.00e-02 4.00e+02 4.59e-02 3.36e+00 pdb=" N PRO D 57 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO D 57 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 57 " 0.026 5.00e-02 4.00e+02 ... (remaining 9893 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.37: 129 2.37 - 3.00: 29595 3.00 - 3.63: 87672 3.63 - 4.27: 132109 4.27 - 4.90: 216345 Nonbonded interactions: 465850 Sorted by model distance: nonbonded pdb=" CG1 VAL B 741 " pdb=" OH TYR B1009 " model vdw 1.734 3.460 nonbonded pdb=" CG2 VAL B 741 " pdb=" OH TYR B1009 " model vdw 1.740 3.460 nonbonded pdb=" N MET L 15 " pdb=" OE2 GLU L 27 " model vdw 1.841 3.120 nonbonded pdb=" OG SER P 88 " pdb=" OE1 GLN P 91 " model vdw 1.857 3.040 nonbonded pdb=" CG2 VAL B 741 " pdb=" CE2 TYR B1009 " model vdw 1.867 3.760 ... (remaining 465845 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.760 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: 0.080 Extract box with map and model: 1.650 Check model and map are aligned: 0.320 Set scattering table: 0.400 Process input model: 136.160 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 144.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6976 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.479 59344 Z= 0.219 Angle : 0.492 16.467 80728 Z= 0.303 Chirality : 0.038 0.437 8984 Planarity : 0.003 0.046 9896 Dihedral : 12.737 177.834 23063 Min Nonbonded Distance : 1.734 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.09), residues: 6809 helix: -0.36 (0.09), residues: 2730 sheet: -1.06 (0.17), residues: 777 loop : -1.82 (0.10), residues: 3302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 297 HIS 0.003 0.000 HIS 3 198 PHE 0.008 0.001 PHE U 266 TYR 0.010 0.001 TYR A1116 ARG 0.004 0.000 ARG B 900 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13618 Ramachandran restraints generated. 6809 Oldfield, 0 Emsley, 6809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13618 Ramachandran restraints generated. 6809 Oldfield, 0 Emsley, 6809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1158 residues out of total 6068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1158 time to evaluate : 5.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 HIS cc_start: 0.6564 (t-90) cc_final: 0.6234 (m-70) REVERT: A 312 PHE cc_start: 0.8376 (t80) cc_final: 0.7991 (t80) REVERT: A 505 MET cc_start: 0.7912 (tpt) cc_final: 0.7162 (tpt) REVERT: A 724 CYS cc_start: 0.9244 (m) cc_final: 0.8890 (m) REVERT: A 852 MET cc_start: 0.7855 (mtt) cc_final: 0.7641 (mtt) REVERT: A 965 PHE cc_start: 0.8367 (t80) cc_final: 0.8165 (t80) REVERT: A 1134 LEU cc_start: 0.8185 (mt) cc_final: 0.7722 (pt) REVERT: A 1236 MET cc_start: 0.7587 (ptp) cc_final: 0.7368 (mtp) REVERT: A 1326 ASP cc_start: 0.8102 (t0) cc_final: 0.7690 (m-30) REVERT: A 1327 HIS cc_start: 0.7050 (m90) cc_final: 0.6506 (t-90) REVERT: A 1349 MET cc_start: 0.8605 (mmm) cc_final: 0.8354 (mmm) REVERT: B 59 MET cc_start: 0.8610 (tmm) cc_final: 0.8289 (tmm) REVERT: B 68 ASP cc_start: 0.6520 (p0) cc_final: 0.6271 (m-30) REVERT: B 89 GLU cc_start: 0.6800 (pp20) cc_final: 0.6287 (pp20) REVERT: B 107 MET cc_start: 0.8946 (ptm) cc_final: 0.8462 (ptm) REVERT: B 126 ILE cc_start: 0.8383 (mm) cc_final: 0.6495 (mm) REVERT: B 274 LYS cc_start: 0.7710 (mtpt) cc_final: 0.7437 (mmtt) REVERT: B 311 GLU cc_start: 0.9017 (mm-30) cc_final: 0.8759 (mt-10) REVERT: B 324 LYS cc_start: 0.8030 (tttm) cc_final: 0.7779 (tppt) REVERT: B 429 PHE cc_start: 0.5008 (m-80) cc_final: 0.4614 (m-80) REVERT: B 431 MET cc_start: 0.4216 (mmt) cc_final: 0.3699 (ttp) REVERT: B 643 ILE cc_start: 0.8892 (mt) cc_final: 0.8550 (mp) REVERT: B 689 MET cc_start: 0.5980 (mmt) cc_final: 0.5203 (mmt) REVERT: B 719 MET cc_start: 0.8240 (mmm) cc_final: 0.7482 (mmp) REVERT: B 750 ASP cc_start: 0.7093 (p0) cc_final: 0.6849 (p0) REVERT: B 763 ASP cc_start: 0.8315 (m-30) cc_final: 0.7782 (m-30) REVERT: B 794 MET cc_start: 0.8196 (tmm) cc_final: 0.7950 (mtt) REVERT: B 996 GLU cc_start: 0.8046 (mt-10) cc_final: 0.7242 (mt-10) REVERT: B 1050 MET cc_start: 0.7521 (pmm) cc_final: 0.6870 (pmm) REVERT: C 56 MET cc_start: 0.8297 (tmm) cc_final: 0.7775 (tmm) REVERT: C 83 GLU cc_start: 0.7665 (mm-30) cc_final: 0.7390 (tp30) REVERT: C 87 MET cc_start: 0.8702 (mmm) cc_final: 0.8389 (mmt) REVERT: C 212 MET cc_start: 0.8979 (mtt) cc_final: 0.8750 (mtp) REVERT: D 26 GLN cc_start: 0.8422 (tp-100) cc_final: 0.8188 (tp-100) REVERT: D 82 GLU cc_start: 0.7624 (mm-30) cc_final: 0.7092 (tp30) REVERT: E 14 ARG cc_start: 0.8554 (ttt90) cc_final: 0.7900 (ttt180) REVERT: E 94 MET cc_start: 0.6676 (mmp) cc_final: 0.6472 (mmp) REVERT: E 110 MET cc_start: 0.5329 (ttm) cc_final: 0.5061 (mtp) REVERT: E 121 MET cc_start: 0.6726 (ppp) cc_final: 0.6249 (ppp) REVERT: F 88 ASP cc_start: 0.7297 (t70) cc_final: 0.6814 (t0) REVERT: F 94 MET cc_start: 0.8773 (mmm) cc_final: 0.8492 (mmm) REVERT: G 106 ASP cc_start: 0.8198 (p0) cc_final: 0.6871 (t70) REVERT: G 190 ILE cc_start: 0.5180 (mp) cc_final: 0.4786 (mp) REVERT: H 24 ARG cc_start: 0.7654 (mtt90) cc_final: 0.7407 (mtt180) REVERT: H 31 GLU cc_start: 0.7891 (tp30) cc_final: 0.7675 (tp30) REVERT: H 42 ASP cc_start: 0.8286 (m-30) cc_final: 0.7541 (m-30) REVERT: H 64 LEU cc_start: 0.8472 (tp) cc_final: 0.8182 (tp) REVERT: H 78 THR cc_start: 0.8026 (p) cc_final: 0.7757 (p) REVERT: H 92 MET cc_start: 0.8953 (mtp) cc_final: 0.7797 (mtp) REVERT: H 107 GLU cc_start: 0.5891 (mp0) cc_final: 0.5347 (pt0) REVERT: H 122 LEU cc_start: 0.8370 (mt) cc_final: 0.8068 (mm) REVERT: H 123 MET cc_start: 0.8259 (tmm) cc_final: 0.7798 (tmm) REVERT: H 146 LYS cc_start: 0.7800 (mtpt) cc_final: 0.7244 (mtpp) REVERT: I 2 LEU cc_start: 0.8284 (mt) cc_final: 0.8024 (mp) REVERT: J 1 MET cc_start: 0.8354 (ppp) cc_final: 0.7620 (ptt) REVERT: J 7 CYS cc_start: 0.7114 (t) cc_final: 0.6752 (t) REVERT: J 33 ASP cc_start: 0.7281 (p0) cc_final: 0.6383 (p0) REVERT: L 18 ILE cc_start: 0.8396 (mm) cc_final: 0.8133 (mm) REVERT: L 28 ILE cc_start: 0.7419 (pt) cc_final: 0.6843 (pt) REVERT: L 44 MET cc_start: 0.8829 (mmm) cc_final: 0.8449 (mmm) REVERT: M 12 GLU cc_start: 0.8012 (tt0) cc_final: 0.7594 (tm-30) REVERT: M 17 LEU cc_start: 0.6485 (tt) cc_final: 0.5462 (mp) REVERT: M 48 LYS cc_start: 0.7689 (mtpt) cc_final: 0.7267 (ttmt) REVERT: M 65 LEU cc_start: 0.8279 (pp) cc_final: 0.8028 (tp) REVERT: M 286 MET cc_start: 0.8863 (mmm) cc_final: 0.8610 (mmm) REVERT: M 383 LYS cc_start: 0.7105 (tttm) cc_final: 0.6796 (mptt) REVERT: N 157 MET cc_start: 0.0555 (ptp) cc_final: 0.0104 (ptp) REVERT: N 341 LEU cc_start: 0.8923 (tp) cc_final: 0.8526 (mp) REVERT: N 373 MET cc_start: 0.7004 (mpp) cc_final: 0.6481 (mpp) REVERT: O 8 LEU cc_start: 0.9402 (tp) cc_final: 0.9192 (tp) REVERT: O 79 CYS cc_start: 0.7548 (p) cc_final: 0.6867 (m) REVERT: O 85 MET cc_start: 0.8113 (ptt) cc_final: 0.7823 (ptp) REVERT: O 133 MET cc_start: 0.6126 (ppp) cc_final: 0.3923 (mtp) REVERT: O 351 GLU cc_start: 0.7499 (pt0) cc_final: 0.6984 (mt-10) REVERT: O 394 MET cc_start: 0.8565 (mmp) cc_final: 0.8088 (mmt) REVERT: O 398 MET cc_start: 0.8099 (ttm) cc_final: 0.7615 (ttp) REVERT: O 404 MET cc_start: 0.8338 (mtm) cc_final: 0.7901 (mtm) REVERT: O 512 SER cc_start: 0.9394 (m) cc_final: 0.9194 (p) REVERT: O 531 MET cc_start: 0.7981 (mmm) cc_final: 0.7757 (mmm) REVERT: P 135 LEU cc_start: 0.6288 (mt) cc_final: 0.6049 (mt) REVERT: P 159 ARG cc_start: 0.6172 (ttt-90) cc_final: 0.5587 (mmp-170) REVERT: P 167 TYR cc_start: 0.7132 (m-80) cc_final: 0.6818 (m-10) REVERT: P 297 HIS cc_start: 0.7145 (t-90) cc_final: 0.6887 (t-90) REVERT: Q 33 LYS cc_start: 0.7841 (tptp) cc_final: 0.7466 (mptt) REVERT: Q 42 ASP cc_start: 0.8055 (p0) cc_final: 0.7696 (p0) REVERT: Q 111 MET cc_start: 0.7854 (mpp) cc_final: 0.7093 (mpp) REVERT: 1 8 GLN cc_start: 0.3622 (mm110) cc_final: 0.2690 (mt0) REVERT: 1 33 TRP cc_start: 0.3289 (t-100) cc_final: 0.2196 (t-100) REVERT: 1 46 MET cc_start: 0.3640 (ptm) cc_final: 0.2932 (tmm) REVERT: 1 52 ASN cc_start: 0.6726 (t0) cc_final: 0.6511 (m110) REVERT: 1 53 MET cc_start: 0.6289 (mmm) cc_final: 0.5597 (ppp) REVERT: 1 96 LYS cc_start: 0.1246 (mtmm) cc_final: 0.0527 (mttt) REVERT: 1 148 MET cc_start: 0.0375 (pmm) cc_final: -0.0303 (tpt) REVERT: 3 136 PHE cc_start: 0.6111 (m-80) cc_final: 0.5379 (t80) REVERT: 3 174 MET cc_start: 0.0564 (tpt) cc_final: -0.0055 (tpp) REVERT: 3 214 GLN cc_start: 0.6897 (mp10) cc_final: 0.6583 (mp10) REVERT: 3 295 ASP cc_start: 0.4662 (p0) cc_final: 0.4370 (t70) REVERT: 3 314 GLN cc_start: 0.4064 (mt0) cc_final: 0.3643 (tt0) REVERT: 3 316 ASP cc_start: 0.5092 (p0) cc_final: 0.4759 (t0) REVERT: 3 318 GLU cc_start: 0.5147 (pt0) cc_final: 0.4549 (pm20) REVERT: 3 349 LEU cc_start: 0.4969 (tt) cc_final: 0.4414 (tt) REVERT: 3 368 ASN cc_start: 0.5299 (m110) cc_final: 0.4939 (t0) REVERT: 4 269 ILE cc_start: 0.6085 (mt) cc_final: 0.5864 (mt) REVERT: 4 278 GLU cc_start: 0.6568 (mp0) cc_final: 0.5888 (pp20) REVERT: 4 348 GLU cc_start: 0.5630 (tp30) cc_final: 0.5082 (mm-30) REVERT: 4 385 MET cc_start: 0.0833 (tmm) cc_final: 0.0109 (mmm) REVERT: U 178 LEU cc_start: 0.7461 (mp) cc_final: 0.6806 (tp) REVERT: U 186 ARG cc_start: 0.7938 (mtt-85) cc_final: 0.7136 (ttt90) REVERT: U 192 TYR cc_start: 0.8258 (t80) cc_final: 0.7803 (t80) REVERT: U 195 LYS cc_start: 0.6688 (mttt) cc_final: 0.6219 (tttt) REVERT: U 212 LEU cc_start: 0.6794 (mm) cc_final: 0.6361 (tp) REVERT: U 285 PRO cc_start: 0.8893 (Cg_endo) cc_final: 0.8669 (Cg_exo) REVERT: V 143 TYR cc_start: 0.6947 (m-80) cc_final: 0.6731 (m-10) REVERT: V 168 CYS cc_start: 0.6563 (t) cc_final: 0.5876 (m) REVERT: V 283 LEU cc_start: 0.7573 (mt) cc_final: 0.7136 (tt) REVERT: V 291 ARG cc_start: 0.7444 (mtp85) cc_final: 0.7091 (ttp-110) REVERT: V 404 ARG cc_start: 0.6300 (tmm-80) cc_final: 0.6040 (ptt180) REVERT: W 300 SER cc_start: 0.3044 (t) cc_final: 0.2416 (p) REVERT: W 307 GLU cc_start: 0.6861 (tt0) cc_final: 0.6628 (tt0) REVERT: W 324 MET cc_start: 0.6933 (mmp) cc_final: 0.6729 (mmm) REVERT: W 357 GLN cc_start: 0.5358 (mt0) cc_final: 0.5082 (mt0) outliers start: 0 outliers final: 0 residues processed: 1158 average time/residue: 0.6154 time to fit residues: 1153.0092 Evaluate side-chains 541 residues out of total 6068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 541 time to evaluate : 4.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 690 random chunks: chunk 582 optimal weight: 40.0000 chunk 522 optimal weight: 0.6980 chunk 290 optimal weight: 0.0770 chunk 178 optimal weight: 10.0000 chunk 352 optimal weight: 6.9990 chunk 279 optimal weight: 7.9990 chunk 540 optimal weight: 10.0000 chunk 209 optimal weight: 8.9990 chunk 328 optimal weight: 30.0000 chunk 402 optimal weight: 20.0000 chunk 626 optimal weight: 20.0000 overall best weight: 4.9544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 GLN A 423 GLN ** A 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1039 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1190 GLN A1213 HIS A1217 GLN B 100 HIS B 124 GLN B 273 GLN B 395 GLN B 405 HIS B 517 ASN B 626 HIS B 979 HIS ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 GLN C 160 ASN C 305 HIS C 344 GLN D 26 GLN D 61 GLN ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 GLN ** G 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 115 GLN ** G 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 87 GLN ** I 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 97 GLN L 23 HIS N 282 GLN O 286 GLN O 291 ASN O 465 GLN O 534 GLN P 129 ASN P 182 GLN Q 62 GLN 1 48 ASN ** 1 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 139 HIS 3 170 ASN ** 3 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 171 GLN 4 229 GLN 4 234 GLN 4 243 GLN 4 285 GLN ** 4 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 166 GLN V 49 ASN V 206 GLN V 212 ASN V 397 GLN W 279 ASN W 327 GLN Total number of N/Q/H flips: 47 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.115 59344 Z= 0.366 Angle : 0.688 12.024 80728 Z= 0.357 Chirality : 0.046 0.339 8984 Planarity : 0.005 0.105 9896 Dihedral : 15.184 176.981 9118 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.02 % Allowed : 3.05 % Favored : 96.94 % 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: -0.75 (0.10), residues: 6809 helix: 0.49 (0.10), residues: 2761 sheet: -0.97 (0.17), residues: 784 loop : -1.21 (0.11), residues: 3264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP 3 51 HIS 0.012 0.002 HIS D 118 PHE 0.047 0.002 PHE 3 47 TYR 0.052 0.002 TYR U 322 ARG 0.018 0.001 ARG V 6 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13618 Ramachandran restraints generated. 6809 Oldfield, 0 Emsley, 6809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13618 Ramachandran restraints generated. 6809 Oldfield, 0 Emsley, 6809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 597 residues out of total 6068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 596 time to evaluate : 4.927 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: A 312 PHE cc_start: 0.8772 (t80) cc_final: 0.8534 (t80) REVERT: A 505 MET cc_start: 0.7853 (tpt) cc_final: 0.6876 (tpt) REVERT: A 630 ASP cc_start: 0.6562 (t0) cc_final: 0.6306 (t0) REVERT: A 724 CYS cc_start: 0.9139 (m) cc_final: 0.8888 (m) REVERT: A 1138 ARG cc_start: 0.8149 (ttp-110) cc_final: 0.7875 (ttp80) REVERT: A 1139 LEU cc_start: 0.8599 (tp) cc_final: 0.8215 (tp) REVERT: A 1195 ASP cc_start: 0.8288 (t0) cc_final: 0.8059 (m-30) REVERT: A 1236 MET cc_start: 0.7658 (ptp) cc_final: 0.7343 (mtm) REVERT: A 1280 MET cc_start: 0.7528 (pmm) cc_final: 0.7210 (pmm) REVERT: A 1327 HIS cc_start: 0.7120 (m90) cc_final: 0.6386 (t70) REVERT: B 59 MET cc_start: 0.8466 (tmm) cc_final: 0.8212 (tmm) REVERT: B 68 ASP cc_start: 0.7044 (p0) cc_final: 0.6437 (t0) REVERT: B 107 MET cc_start: 0.9003 (ptm) cc_final: 0.8540 (ptm) REVERT: B 410 GLN cc_start: 0.8410 (tp40) cc_final: 0.8169 (tp40) REVERT: B 588 ASP cc_start: 0.8634 (p0) cc_final: 0.8409 (p0) REVERT: B 689 MET cc_start: 0.6513 (mmt) cc_final: 0.5897 (mmt) REVERT: B 719 MET cc_start: 0.8937 (mmm) cc_final: 0.8347 (mmm) REVERT: B 763 ASP cc_start: 0.8422 (m-30) cc_final: 0.8070 (m-30) REVERT: B 794 MET cc_start: 0.8187 (tmm) cc_final: 0.7719 (mmt) REVERT: B 883 MET cc_start: 0.8280 (mpp) cc_final: 0.7988 (mpp) REVERT: B 929 MET cc_start: 0.7748 (tpt) cc_final: 0.7367 (tpt) REVERT: B 1050 MET cc_start: 0.7049 (pmm) cc_final: 0.6423 (pmm) REVERT: C 56 MET cc_start: 0.8673 (tmm) cc_final: 0.8143 (tmm) REVERT: C 65 MET cc_start: 0.8340 (mtp) cc_final: 0.7905 (ttm) REVERT: C 68 ILE cc_start: 0.9222 (tp) cc_final: 0.8927 (tp) REVERT: C 83 GLU cc_start: 0.8094 (mm-30) cc_final: 0.7315 (tp30) REVERT: C 87 MET cc_start: 0.8619 (mmm) cc_final: 0.8248 (mmm) REVERT: C 103 ASP cc_start: 0.8529 (m-30) cc_final: 0.8119 (m-30) REVERT: C 212 MET cc_start: 0.8908 (mtt) cc_final: 0.8687 (mtp) REVERT: C 330 MET cc_start: 0.8365 (mmm) cc_final: 0.8144 (mtt) REVERT: D 26 GLN cc_start: 0.8660 (tp40) cc_final: 0.8305 (tp-100) REVERT: D 60 HIS cc_start: 0.7126 (m90) cc_final: 0.6185 (p-80) REVERT: D 90 ARG cc_start: 0.3986 (mtm-85) cc_final: 0.2012 (tpt170) REVERT: E 14 ARG cc_start: 0.8776 (ttt90) cc_final: 0.8095 (ttt180) REVERT: E 94 MET cc_start: 0.6627 (mmp) cc_final: 0.6215 (mmp) REVERT: E 108 GLN cc_start: 0.7499 (mm-40) cc_final: 0.7223 (mm-40) REVERT: G 73 ARG cc_start: 0.8191 (mtm-85) cc_final: 0.7643 (mtm-85) REVERT: G 106 ASP cc_start: 0.8248 (p0) cc_final: 0.7159 (t70) REVERT: H 64 LEU cc_start: 0.8633 (tp) cc_final: 0.8290 (tp) REVERT: H 74 GLU cc_start: 0.7627 (pp20) cc_final: 0.7311 (pp20) REVERT: H 107 GLU cc_start: 0.5828 (mp0) cc_final: 0.5349 (pt0) REVERT: H 123 MET cc_start: 0.8452 (tmm) cc_final: 0.7882 (tmm) REVERT: I 12 LEU cc_start: 0.8694 (mt) cc_final: 0.8463 (mp) REVERT: I 15 GLU cc_start: 0.7871 (tp30) cc_final: 0.7098 (tp30) REVERT: I 97 CYS cc_start: 0.0150 (t) cc_final: -0.0238 (t) REVERT: L 28 ILE cc_start: 0.8015 (pt) cc_final: 0.7602 (mp) REVERT: L 38 GLU cc_start: 0.8228 (tm-30) cc_final: 0.7953 (tm-30) REVERT: L 44 MET cc_start: 0.8835 (mmm) cc_final: 0.8135 (mmm) REVERT: M 12 GLU cc_start: 0.8198 (tt0) cc_final: 0.7716 (tm-30) REVERT: M 286 MET cc_start: 0.8906 (mmm) cc_final: 0.8642 (mmm) REVERT: M 292 MET cc_start: 0.8514 (tpt) cc_final: 0.8175 (tpt) REVERT: M 298 MET cc_start: 0.7723 (mmm) cc_final: 0.7245 (mmm) REVERT: M 383 LYS cc_start: 0.7473 (tttm) cc_final: 0.7186 (mmtt) REVERT: N 157 MET cc_start: -0.0032 (ptp) cc_final: -0.0541 (ptp) REVERT: N 341 LEU cc_start: 0.8971 (tp) cc_final: 0.8691 (tt) REVERT: O 8 LEU cc_start: 0.9419 (tp) cc_final: 0.9167 (tp) REVERT: O 85 MET cc_start: 0.8295 (ptt) cc_final: 0.8038 (ptp) REVERT: O 133 MET cc_start: 0.6602 (ppp) cc_final: 0.6066 (ppp) REVERT: O 338 LEU cc_start: 0.8661 (mm) cc_final: 0.8352 (mp) REVERT: O 398 MET cc_start: 0.8160 (ttm) cc_final: 0.7749 (ttp) REVERT: O 404 MET cc_start: 0.8415 (mtm) cc_final: 0.7936 (mtm) REVERT: O 512 SER cc_start: 0.9405 (m) cc_final: 0.9191 (p) REVERT: P 85 MET cc_start: 0.3620 (mmp) cc_final: 0.3225 (mpp) REVERT: P 125 LYS cc_start: 0.7195 (tppt) cc_final: 0.6905 (mmtm) REVERT: P 154 ASN cc_start: 0.5326 (m-40) cc_final: 0.5011 (t0) REVERT: P 159 ARG cc_start: 0.6443 (ttt-90) cc_final: 0.5770 (mmp-170) REVERT: P 167 TYR cc_start: 0.7410 (m-80) cc_final: 0.7112 (m-10) REVERT: P 297 HIS cc_start: 0.7379 (t-90) cc_final: 0.7084 (t-90) REVERT: P 310 MET cc_start: 0.8955 (mmm) cc_final: 0.8441 (mpp) REVERT: Q 92 MET cc_start: 0.0049 (ppp) cc_final: -0.0154 (ptt) REVERT: Q 111 MET cc_start: 0.7575 (mpp) cc_final: 0.7115 (mpp) REVERT: 1 8 GLN cc_start: 0.3974 (mm110) cc_final: 0.3630 (mt0) REVERT: 1 33 TRP cc_start: 0.3067 (t-100) cc_final: 0.2072 (t-100) REVERT: 1 46 MET cc_start: 0.3610 (ptm) cc_final: 0.3019 (tmm) REVERT: 1 53 MET cc_start: 0.6162 (mmm) cc_final: 0.5622 (ppp) REVERT: 1 69 PRO cc_start: 0.4151 (Cg_exo) cc_final: 0.3543 (Cg_endo) REVERT: 3 136 PHE cc_start: 0.6123 (m-80) cc_final: 0.5376 (t80) REVERT: 3 174 MET cc_start: 0.0225 (tpt) cc_final: -0.0541 (tpp) REVERT: 3 314 GLN cc_start: 0.4858 (mt0) cc_final: 0.4327 (tt0) REVERT: 3 316 ASP cc_start: 0.5158 (p0) cc_final: 0.4639 (t0) REVERT: 3 368 ASN cc_start: 0.5350 (m110) cc_final: 0.4749 (p0) REVERT: 4 348 GLU cc_start: 0.5380 (tp30) cc_final: 0.4841 (mm-30) REVERT: 4 375 ILE cc_start: 0.1985 (mp) cc_final: 0.1716 (mm) REVERT: 4 385 MET cc_start: 0.1039 (tmm) cc_final: 0.0231 (mmm) REVERT: 4 499 MET cc_start: -0.2578 (tmm) cc_final: -0.2779 (ttm) REVERT: U 178 LEU cc_start: 0.7422 (mp) cc_final: 0.6628 (tp) REVERT: U 186 ARG cc_start: 0.8017 (mtt-85) cc_final: 0.7478 (ttt90) REVERT: U 192 TYR cc_start: 0.8089 (t80) cc_final: 0.7844 (t80) REVERT: U 212 LEU cc_start: 0.6975 (mm) cc_final: 0.6430 (tp) REVERT: U 286 GLU cc_start: 0.8226 (tt0) cc_final: 0.7923 (tt0) REVERT: V 135 MET cc_start: 0.9263 (mtt) cc_final: 0.8137 (mtt) REVERT: V 182 LEU cc_start: 0.7268 (mp) cc_final: 0.6922 (mp) REVERT: V 273 LEU cc_start: 0.8462 (mt) cc_final: 0.8172 (mt) REVERT: W 307 GLU cc_start: 0.6737 (tt0) cc_final: 0.6451 (tt0) outliers start: 1 outliers final: 0 residues processed: 597 average time/residue: 0.5604 time to fit residues: 561.4883 Evaluate side-chains 414 residues out of total 6068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 414 time to evaluate : 4.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 690 random chunks: chunk 348 optimal weight: 7.9990 chunk 194 optimal weight: 0.9980 chunk 521 optimal weight: 0.2980 chunk 426 optimal weight: 10.0000 chunk 172 optimal weight: 7.9990 chunk 627 optimal weight: 9.9990 chunk 678 optimal weight: 5.9990 chunk 559 optimal weight: 8.9990 chunk 622 optimal weight: 0.0970 chunk 214 optimal weight: 10.0000 chunk 503 optimal weight: 9.9990 overall best weight: 3.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1039 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 GLN ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 118 HIS ** G 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 341 HIS O 534 GLN P 117 ASN ** 4 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 59344 Z= 0.240 Angle : 0.560 12.348 80728 Z= 0.293 Chirality : 0.042 0.249 8984 Planarity : 0.004 0.081 9896 Dihedral : 15.143 178.647 9118 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.02 % Allowed : 2.62 % Favored : 97.36 % 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: -0.41 (0.10), residues: 6809 helix: 0.84 (0.10), residues: 2750 sheet: -0.84 (0.18), residues: 769 loop : -1.07 (0.11), residues: 3290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP M 398 HIS 0.006 0.001 HIS D 118 PHE 0.017 0.001 PHE 4 176 TYR 0.035 0.002 TYR U 322 ARG 0.009 0.000 ARG D 107 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13618 Ramachandran restraints generated. 6809 Oldfield, 0 Emsley, 6809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13618 Ramachandran restraints generated. 6809 Oldfield, 0 Emsley, 6809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 6068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 530 time to evaluate : 4.925 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: A 35 GLN cc_start: 0.7710 (tt0) cc_final: 0.7480 (tp-100) REVERT: A 312 PHE cc_start: 0.8812 (t80) cc_final: 0.8514 (t80) REVERT: A 474 MET cc_start: 0.7398 (mtp) cc_final: 0.6853 (mtp) REVERT: A 505 MET cc_start: 0.7812 (tpt) cc_final: 0.6841 (tpt) REVERT: A 724 CYS cc_start: 0.9149 (m) cc_final: 0.8845 (m) REVERT: A 908 ASP cc_start: 0.8596 (t0) cc_final: 0.8346 (t0) REVERT: A 1236 MET cc_start: 0.7570 (ptp) cc_final: 0.7231 (mtm) REVERT: A 1280 MET cc_start: 0.7463 (pmm) cc_final: 0.7084 (pmm) REVERT: A 1326 ASP cc_start: 0.8423 (t0) cc_final: 0.8213 (m-30) REVERT: A 1327 HIS cc_start: 0.7163 (m90) cc_final: 0.6344 (t70) REVERT: B 59 MET cc_start: 0.8460 (tmm) cc_final: 0.8243 (tmm) REVERT: B 107 MET cc_start: 0.9003 (ptm) cc_final: 0.8590 (ptm) REVERT: B 588 ASP cc_start: 0.8587 (p0) cc_final: 0.8370 (p0) REVERT: B 689 MET cc_start: 0.5792 (mmt) cc_final: 0.5559 (mmt) REVERT: B 719 MET cc_start: 0.8969 (mmm) cc_final: 0.8411 (mmm) REVERT: B 763 ASP cc_start: 0.8387 (m-30) cc_final: 0.7987 (m-30) REVERT: B 794 MET cc_start: 0.8063 (tmm) cc_final: 0.7760 (mmt) REVERT: B 883 MET cc_start: 0.8225 (mpp) cc_final: 0.7483 (mpp) REVERT: B 916 MET cc_start: 0.9056 (mmt) cc_final: 0.8465 (mmm) REVERT: B 929 MET cc_start: 0.7626 (tpt) cc_final: 0.7333 (tpt) REVERT: B 1009 TYR cc_start: 0.8465 (m-80) cc_final: 0.8102 (m-80) REVERT: B 1050 MET cc_start: 0.7102 (pmm) cc_final: 0.6496 (pmm) REVERT: C 56 MET cc_start: 0.8628 (tmm) cc_final: 0.8020 (tmm) REVERT: C 83 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7862 (mt-10) REVERT: C 87 MET cc_start: 0.8546 (mmm) cc_final: 0.8269 (mmm) REVERT: C 103 ASP cc_start: 0.8507 (m-30) cc_final: 0.8033 (m-30) REVERT: D 26 GLN cc_start: 0.8633 (tp40) cc_final: 0.8188 (tp-100) REVERT: D 60 HIS cc_start: 0.6953 (m90) cc_final: 0.6273 (p-80) REVERT: D 90 ARG cc_start: 0.3878 (mtm-85) cc_final: 0.1848 (tpt170) REVERT: E 14 ARG cc_start: 0.8745 (ttt90) cc_final: 0.8110 (ttt180) REVERT: E 27 LEU cc_start: 0.8307 (mt) cc_final: 0.7970 (mt) REVERT: E 94 MET cc_start: 0.6618 (mmp) cc_final: 0.6284 (mmp) REVERT: G 73 ARG cc_start: 0.8188 (mtm-85) cc_final: 0.7655 (mtm-85) REVERT: G 106 ASP cc_start: 0.8182 (p0) cc_final: 0.6959 (t70) REVERT: H 64 LEU cc_start: 0.8633 (tp) cc_final: 0.8140 (tt) REVERT: H 74 GLU cc_start: 0.7681 (pp20) cc_final: 0.7422 (pp20) REVERT: H 123 MET cc_start: 0.8493 (tmm) cc_final: 0.8142 (tmm) REVERT: I 12 LEU cc_start: 0.8679 (mt) cc_final: 0.8300 (mp) REVERT: I 15 GLU cc_start: 0.7800 (tp30) cc_final: 0.6963 (tp30) REVERT: K 46 GLU cc_start: 0.8104 (tm-30) cc_final: 0.7789 (tm-30) REVERT: L 28 ILE cc_start: 0.8168 (pt) cc_final: 0.7757 (mp) REVERT: L 38 GLU cc_start: 0.8172 (tm-30) cc_final: 0.7707 (tm-30) REVERT: L 44 MET cc_start: 0.8938 (mmm) cc_final: 0.8287 (mmm) REVERT: L 52 LEU cc_start: 0.8382 (tt) cc_final: 0.8110 (pp) REVERT: M 12 GLU cc_start: 0.8200 (tt0) cc_final: 0.7895 (mp0) REVERT: M 286 MET cc_start: 0.8897 (mmm) cc_final: 0.8579 (mmm) REVERT: M 292 MET cc_start: 0.8533 (tpt) cc_final: 0.8110 (tpt) REVERT: M 383 LYS cc_start: 0.7479 (tttm) cc_final: 0.7160 (tptp) REVERT: N 157 MET cc_start: 0.0450 (ptp) cc_final: 0.0043 (ptp) REVERT: N 256 ARG cc_start: 0.8500 (tmm160) cc_final: 0.8144 (mtt180) REVERT: N 341 LEU cc_start: 0.8994 (tp) cc_final: 0.8739 (tt) REVERT: N 373 MET cc_start: 0.6512 (mpp) cc_final: 0.5610 (mpp) REVERT: O 8 LEU cc_start: 0.9401 (tp) cc_final: 0.9178 (tp) REVERT: O 85 MET cc_start: 0.8321 (ptt) cc_final: 0.8002 (ptp) REVERT: O 133 MET cc_start: 0.6496 (ppp) cc_final: 0.6133 (ppp) REVERT: O 338 LEU cc_start: 0.8697 (mm) cc_final: 0.8349 (mp) REVERT: O 398 MET cc_start: 0.8154 (ttm) cc_final: 0.7693 (ttp) REVERT: O 404 MET cc_start: 0.8438 (mtm) cc_final: 0.7997 (mtm) REVERT: O 512 SER cc_start: 0.9403 (m) cc_final: 0.9191 (p) REVERT: P 85 MET cc_start: 0.3653 (mmp) cc_final: 0.3239 (mpp) REVERT: P 125 LYS cc_start: 0.7166 (tppt) cc_final: 0.6861 (mmtm) REVERT: P 159 ARG cc_start: 0.6417 (ttt-90) cc_final: 0.5682 (mmp-170) REVERT: P 297 HIS cc_start: 0.7492 (t-90) cc_final: 0.7239 (t-90) REVERT: P 310 MET cc_start: 0.8780 (mmm) cc_final: 0.8326 (mpp) REVERT: Q 92 MET cc_start: 0.0097 (ppp) cc_final: -0.0138 (ptt) REVERT: Q 111 MET cc_start: 0.7763 (mpp) cc_final: 0.7351 (mpp) REVERT: 1 33 TRP cc_start: 0.3161 (t-100) cc_final: 0.2232 (t-100) REVERT: 1 46 MET cc_start: 0.3787 (ptm) cc_final: 0.3390 (tmm) REVERT: 3 136 PHE cc_start: 0.6279 (m-80) cc_final: 0.5563 (t80) REVERT: 3 159 MET cc_start: 0.1905 (mmp) cc_final: 0.1503 (mtp) REVERT: 3 314 GLN cc_start: 0.5082 (mt0) cc_final: 0.4505 (tt0) REVERT: 3 316 ASP cc_start: 0.5315 (p0) cc_final: 0.4977 (t0) REVERT: 3 368 ASN cc_start: 0.5523 (m110) cc_final: 0.4783 (p0) REVERT: 4 348 GLU cc_start: 0.5096 (tp30) cc_final: 0.4464 (mm-30) REVERT: 4 364 MET cc_start: 0.2361 (tmm) cc_final: 0.1800 (mmt) REVERT: 4 375 ILE cc_start: 0.2070 (mp) cc_final: 0.1786 (mm) REVERT: 4 377 TYR cc_start: 0.4203 (t80) cc_final: 0.3627 (t80) REVERT: 4 385 MET cc_start: 0.1166 (tmm) cc_final: 0.0252 (mmm) REVERT: 4 389 TYR cc_start: 0.1629 (m-10) cc_final: 0.1257 (m-80) REVERT: U 178 LEU cc_start: 0.7061 (mp) cc_final: 0.6735 (tp) REVERT: U 186 ARG cc_start: 0.8010 (mtt-85) cc_final: 0.7410 (ttt90) REVERT: U 192 TYR cc_start: 0.8097 (t80) cc_final: 0.7868 (t80) REVERT: U 212 LEU cc_start: 0.6958 (mm) cc_final: 0.6453 (tp) REVERT: U 246 PHE cc_start: 0.5232 (m-80) cc_final: 0.4964 (m-80) REVERT: V 130 ASN cc_start: 0.8225 (m-40) cc_final: 0.7803 (m-40) REVERT: V 135 MET cc_start: 0.9213 (mtt) cc_final: 0.8004 (mtt) REVERT: V 273 LEU cc_start: 0.8426 (mt) cc_final: 0.8164 (mt) REVERT: V 404 ARG cc_start: 0.6253 (tmm-80) cc_final: 0.5979 (tmm160) REVERT: W 307 GLU cc_start: 0.7208 (tt0) cc_final: 0.6910 (tt0) REVERT: W 375 LEU cc_start: 0.6759 (mt) cc_final: 0.6264 (tt) outliers start: 1 outliers final: 1 residues processed: 531 average time/residue: 0.5417 time to fit residues: 492.2768 Evaluate side-chains 394 residues out of total 6068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 393 time to evaluate : 4.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 690 random chunks: chunk 620 optimal weight: 40.0000 chunk 471 optimal weight: 3.9990 chunk 325 optimal weight: 7.9990 chunk 69 optimal weight: 0.8980 chunk 299 optimal weight: 5.9990 chunk 421 optimal weight: 7.9990 chunk 629 optimal weight: 6.9990 chunk 666 optimal weight: 8.9990 chunk 329 optimal weight: 9.9990 chunk 597 optimal weight: 20.0000 chunk 179 optimal weight: 4.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 ASN ** A 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1039 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 GLN B 273 GLN ** C 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 61 GLN ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 GLN ** I 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 184 GLN N 282 GLN O 60 HIS O 377 GLN 3 388 HIS ** 4 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.3967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 59344 Z= 0.333 Angle : 0.640 11.308 80728 Z= 0.332 Chirality : 0.044 0.273 8984 Planarity : 0.005 0.055 9896 Dihedral : 15.241 177.992 9118 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.02 % Allowed : 3.31 % Favored : 96.67 % 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: -0.46 (0.10), residues: 6809 helix: 0.82 (0.10), residues: 2748 sheet: -0.94 (0.18), residues: 748 loop : -1.08 (0.11), residues: 3313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP M 398 HIS 0.010 0.001 HIS D 60 PHE 0.030 0.002 PHE 1 66 TYR 0.024 0.002 TYR U 322 ARG 0.009 0.001 ARG V 291 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13618 Ramachandran restraints generated. 6809 Oldfield, 0 Emsley, 6809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13618 Ramachandran restraints generated. 6809 Oldfield, 0 Emsley, 6809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 6068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 492 time to evaluate : 4.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLN cc_start: 0.7851 (tt0) cc_final: 0.7509 (tp-100) REVERT: A 332 MET cc_start: 0.5923 (mmp) cc_final: 0.5715 (mmp) REVERT: A 474 MET cc_start: 0.7687 (mtp) cc_final: 0.7169 (mtp) REVERT: A 505 MET cc_start: 0.7854 (tpt) cc_final: 0.6856 (tpt) REVERT: A 724 CYS cc_start: 0.9117 (m) cc_final: 0.8846 (m) REVERT: A 912 MET cc_start: 0.8593 (mmp) cc_final: 0.8199 (mmp) REVERT: A 1236 MET cc_start: 0.7587 (ptp) cc_final: 0.6973 (mtm) REVERT: A 1327 HIS cc_start: 0.7230 (m90) cc_final: 0.6439 (t70) REVERT: A 1349 MET cc_start: 0.8908 (mpp) cc_final: 0.8658 (mpp) REVERT: B 79 ASN cc_start: 0.8006 (t0) cc_final: 0.7668 (m-40) REVERT: B 107 MET cc_start: 0.8959 (ptm) cc_final: 0.8687 (ptm) REVERT: B 243 MET cc_start: 0.7704 (ttm) cc_final: 0.7102 (ttm) REVERT: B 499 MET cc_start: 0.8745 (ttp) cc_final: 0.8538 (ttp) REVERT: B 689 MET cc_start: 0.5949 (mmt) cc_final: 0.5474 (mmt) REVERT: B 719 MET cc_start: 0.9137 (mmm) cc_final: 0.8728 (mmm) REVERT: B 763 ASP cc_start: 0.8413 (m-30) cc_final: 0.7986 (m-30) REVERT: B 794 MET cc_start: 0.8030 (tmm) cc_final: 0.7754 (mmt) REVERT: B 883 MET cc_start: 0.8088 (mpp) cc_final: 0.7716 (mpp) REVERT: B 916 MET cc_start: 0.9196 (mmt) cc_final: 0.8670 (mmm) REVERT: B 929 MET cc_start: 0.7836 (tpt) cc_final: 0.7557 (tpt) REVERT: B 1050 MET cc_start: 0.7264 (pmm) cc_final: 0.6560 (pmm) REVERT: C 56 MET cc_start: 0.8642 (tmm) cc_final: 0.7998 (tmm) REVERT: C 87 MET cc_start: 0.8681 (mmm) cc_final: 0.8417 (mmt) REVERT: C 103 ASP cc_start: 0.8493 (m-30) cc_final: 0.8133 (m-30) REVERT: C 256 CYS cc_start: 0.7759 (m) cc_final: 0.7493 (m) REVERT: D 22 ASP cc_start: 0.7149 (m-30) cc_final: 0.6934 (m-30) REVERT: D 26 GLN cc_start: 0.8637 (tp40) cc_final: 0.8210 (tp-100) REVERT: D 60 HIS cc_start: 0.7239 (m90) cc_final: 0.6172 (p-80) REVERT: D 90 ARG cc_start: 0.4533 (mtm-85) cc_final: 0.2353 (tpt170) REVERT: E 27 LEU cc_start: 0.8544 (mt) cc_final: 0.8268 (mt) REVERT: E 94 MET cc_start: 0.6905 (mmp) cc_final: 0.6590 (mmp) REVERT: G 73 ARG cc_start: 0.8365 (mtm-85) cc_final: 0.7650 (mtm-85) REVERT: G 90 LYS cc_start: 0.6045 (mmtm) cc_final: 0.4618 (ttpt) REVERT: G 106 ASP cc_start: 0.8222 (p0) cc_final: 0.6904 (t70) REVERT: H 64 LEU cc_start: 0.8673 (tp) cc_final: 0.7985 (tt) REVERT: H 74 GLU cc_start: 0.7737 (pp20) cc_final: 0.7417 (pp20) REVERT: H 92 MET cc_start: 0.8835 (mtp) cc_final: 0.7535 (mtp) REVERT: H 107 GLU cc_start: 0.5917 (mp0) cc_final: 0.5034 (pt0) REVERT: H 118 TYR cc_start: 0.8075 (m-80) cc_final: 0.7613 (m-80) REVERT: H 123 MET cc_start: 0.8733 (tmm) cc_final: 0.8473 (tmm) REVERT: I 12 LEU cc_start: 0.8676 (mt) cc_final: 0.8289 (mt) REVERT: I 15 GLU cc_start: 0.7739 (tp30) cc_final: 0.6956 (tp30) REVERT: K 46 GLU cc_start: 0.8051 (tm-30) cc_final: 0.7614 (tm-30) REVERT: K 47 GLU cc_start: 0.8954 (tp30) cc_final: 0.8573 (tp30) REVERT: K 60 MET cc_start: 0.9201 (tpp) cc_final: 0.8975 (mmm) REVERT: L 28 ILE cc_start: 0.8754 (pt) cc_final: 0.8457 (mp) REVERT: L 44 MET cc_start: 0.8914 (mmm) cc_final: 0.8297 (mmm) REVERT: M 12 GLU cc_start: 0.8249 (tt0) cc_final: 0.7901 (mp0) REVERT: M 286 MET cc_start: 0.8886 (mmm) cc_final: 0.8661 (mmm) REVERT: M 292 MET cc_start: 0.8739 (tpt) cc_final: 0.7943 (tmm) REVERT: M 357 MET cc_start: 0.8786 (mtm) cc_final: 0.8577 (mtt) REVERT: M 383 LYS cc_start: 0.7445 (tttm) cc_final: 0.7080 (tptp) REVERT: N 341 LEU cc_start: 0.8957 (tp) cc_final: 0.8747 (tt) REVERT: O 8 LEU cc_start: 0.9403 (tp) cc_final: 0.9171 (tp) REVERT: O 85 MET cc_start: 0.8309 (ptt) cc_final: 0.8036 (ptp) REVERT: O 133 MET cc_start: 0.6336 (ppp) cc_final: 0.5951 (ppp) REVERT: O 338 LEU cc_start: 0.8726 (mm) cc_final: 0.8345 (mp) REVERT: O 394 MET cc_start: 0.8700 (mmp) cc_final: 0.8060 (mmt) REVERT: O 398 MET cc_start: 0.8169 (ttm) cc_final: 0.7665 (ttp) REVERT: O 404 MET cc_start: 0.8499 (mtm) cc_final: 0.8075 (mtm) REVERT: P 85 MET cc_start: 0.2736 (mmp) cc_final: 0.2522 (mpp) REVERT: P 122 GLU cc_start: 0.6294 (mp0) cc_final: 0.5968 (tp30) REVERT: P 125 LYS cc_start: 0.7241 (tppt) cc_final: 0.6927 (mmtm) REVERT: P 159 ARG cc_start: 0.6570 (ttt-90) cc_final: 0.5660 (mmp-170) REVERT: P 204 ILE cc_start: 0.8168 (mm) cc_final: 0.7802 (tt) REVERT: P 214 HIS cc_start: 0.8335 (t-170) cc_final: 0.8041 (t-170) REVERT: P 297 HIS cc_start: 0.7525 (t-90) cc_final: 0.7285 (t-90) REVERT: P 310 MET cc_start: 0.8649 (mmm) cc_final: 0.8184 (mpp) REVERT: Q 68 MET cc_start: 0.8497 (tpp) cc_final: 0.8296 (tpp) REVERT: Q 71 MET cc_start: 0.8847 (ttp) cc_final: 0.8240 (ttm) REVERT: Q 111 MET cc_start: 0.7280 (mpp) cc_final: 0.6827 (mpp) REVERT: 1 33 TRP cc_start: 0.3190 (t-100) cc_final: 0.2353 (t-100) REVERT: 1 46 MET cc_start: 0.3903 (ptm) cc_final: 0.3386 (tmm) REVERT: 3 136 PHE cc_start: 0.6439 (m-80) cc_final: 0.5744 (t80) REVERT: 3 174 MET cc_start: 0.3689 (ppp) cc_final: 0.2996 (mmt) REVERT: 3 368 ASN cc_start: 0.5562 (m110) cc_final: 0.4947 (p0) REVERT: 4 348 GLU cc_start: 0.5433 (tp30) cc_final: 0.4773 (mm-30) REVERT: 4 377 TYR cc_start: 0.4413 (t80) cc_final: 0.3941 (t80) REVERT: 4 385 MET cc_start: 0.1243 (tmm) cc_final: 0.0466 (mmm) REVERT: 4 389 TYR cc_start: 0.1424 (m-10) cc_final: 0.1174 (m-80) REVERT: U 178 LEU cc_start: 0.6579 (mp) cc_final: 0.6356 (tp) REVERT: U 189 ASN cc_start: 0.2688 (p0) cc_final: 0.2375 (p0) REVERT: U 202 MET cc_start: 0.7770 (mtp) cc_final: 0.7482 (mmm) REVERT: U 212 LEU cc_start: 0.6510 (mm) cc_final: 0.6290 (tp) REVERT: U 214 PHE cc_start: 0.3527 (m-80) cc_final: 0.2761 (m-80) REVERT: U 258 MET cc_start: 0.5444 (ptp) cc_final: 0.4973 (mtp) REVERT: V 273 LEU cc_start: 0.8364 (mt) cc_final: 0.8146 (mt) REVERT: W 285 ARG cc_start: 0.7047 (tpt170) cc_final: 0.6222 (tpt90) REVERT: W 307 GLU cc_start: 0.7255 (tt0) cc_final: 0.6795 (tt0) REVERT: W 375 LEU cc_start: 0.6539 (mt) cc_final: 0.6028 (tt) outliers start: 1 outliers final: 0 residues processed: 493 average time/residue: 0.5432 time to fit residues: 457.2796 Evaluate side-chains 380 residues out of total 6068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 380 time to evaluate : 4.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 690 random chunks: chunk 555 optimal weight: 40.0000 chunk 378 optimal weight: 5.9990 chunk 9 optimal weight: 0.1980 chunk 496 optimal weight: 20.0000 chunk 275 optimal weight: 2.9990 chunk 569 optimal weight: 7.9990 chunk 461 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 340 optimal weight: 3.9990 chunk 598 optimal weight: 20.0000 chunk 168 optimal weight: 5.9990 overall best weight: 3.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 801 GLN ** A 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1039 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 959 HIS ** C 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 245 HIS 1 111 GLN ** 4 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.4225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 59344 Z= 0.277 Angle : 0.592 12.969 80728 Z= 0.308 Chirality : 0.043 0.305 8984 Planarity : 0.004 0.052 9896 Dihedral : 15.242 178.673 9118 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % 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: -0.34 (0.10), residues: 6809 helix: 0.91 (0.10), residues: 2743 sheet: -0.94 (0.18), residues: 758 loop : -1.00 (0.11), residues: 3308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP M 398 HIS 0.015 0.001 HIS M 44 PHE 0.022 0.002 PHE M 360 TYR 0.030 0.002 TYR U 322 ARG 0.015 0.001 ARG O 90 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13618 Ramachandran restraints generated. 6809 Oldfield, 0 Emsley, 6809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13618 Ramachandran restraints generated. 6809 Oldfield, 0 Emsley, 6809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 6068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 490 time to evaluate : 4.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLN cc_start: 0.7895 (tt0) cc_final: 0.7399 (tp-100) REVERT: A 332 MET cc_start: 0.5861 (mmp) cc_final: 0.5597 (mmp) REVERT: A 474 MET cc_start: 0.7570 (mtp) cc_final: 0.7047 (mtp) REVERT: A 505 MET cc_start: 0.7825 (tpt) cc_final: 0.6804 (tpt) REVERT: A 724 CYS cc_start: 0.9128 (m) cc_final: 0.8875 (m) REVERT: A 912 MET cc_start: 0.8532 (mmp) cc_final: 0.8129 (mmp) REVERT: A 1027 MET cc_start: 0.8124 (tpt) cc_final: 0.7767 (tpt) REVERT: A 1236 MET cc_start: 0.7603 (ptp) cc_final: 0.6959 (mtm) REVERT: A 1327 HIS cc_start: 0.7460 (m90) cc_final: 0.6421 (t70) REVERT: B 107 MET cc_start: 0.8973 (ptm) cc_final: 0.8610 (ptm) REVERT: B 243 MET cc_start: 0.8019 (ttm) cc_final: 0.7325 (ttm) REVERT: B 689 MET cc_start: 0.5935 (mmt) cc_final: 0.5433 (mmt) REVERT: B 719 MET cc_start: 0.9112 (mmm) cc_final: 0.8689 (mmm) REVERT: B 763 ASP cc_start: 0.8435 (m-30) cc_final: 0.8030 (m-30) REVERT: B 794 MET cc_start: 0.8060 (tmm) cc_final: 0.7756 (mmt) REVERT: B 883 MET cc_start: 0.8063 (mpp) cc_final: 0.7674 (mpp) REVERT: B 916 MET cc_start: 0.9178 (mmt) cc_final: 0.8640 (mmm) REVERT: B 929 MET cc_start: 0.7944 (tpt) cc_final: 0.7632 (tpt) REVERT: B 1015 MET cc_start: 0.8278 (mtp) cc_final: 0.7071 (mmt) REVERT: B 1050 MET cc_start: 0.6765 (pmm) cc_final: 0.6254 (pmm) REVERT: C 56 MET cc_start: 0.8633 (tmm) cc_final: 0.7939 (tmm) REVERT: C 87 MET cc_start: 0.8689 (mmm) cc_final: 0.8305 (mmm) REVERT: C 256 CYS cc_start: 0.7672 (m) cc_final: 0.7421 (m) REVERT: D 22 ASP cc_start: 0.7152 (m-30) cc_final: 0.6949 (m-30) REVERT: D 26 GLN cc_start: 0.8345 (tp40) cc_final: 0.7932 (tp-100) REVERT: D 60 HIS cc_start: 0.6982 (m90) cc_final: 0.6263 (p-80) REVERT: D 90 ARG cc_start: 0.4212 (mtm-85) cc_final: 0.1926 (tpt170) REVERT: E 27 LEU cc_start: 0.8588 (mt) cc_final: 0.8310 (mt) REVERT: E 94 MET cc_start: 0.6856 (mmp) cc_final: 0.6536 (mmp) REVERT: G 7 MET cc_start: 0.6555 (tpt) cc_final: 0.6277 (tpt) REVERT: G 73 ARG cc_start: 0.8430 (mtm-85) cc_final: 0.7564 (mtm-85) REVERT: G 90 LYS cc_start: 0.5987 (mmtm) cc_final: 0.4603 (ttpt) REVERT: G 106 ASP cc_start: 0.8219 (p0) cc_final: 0.6857 (t70) REVERT: G 201 TRP cc_start: 0.6974 (p-90) cc_final: 0.6460 (p-90) REVERT: H 64 LEU cc_start: 0.8617 (tp) cc_final: 0.7882 (tt) REVERT: H 74 GLU cc_start: 0.7728 (pp20) cc_final: 0.7395 (pp20) REVERT: H 118 TYR cc_start: 0.8171 (m-80) cc_final: 0.7632 (m-80) REVERT: H 123 MET cc_start: 0.8610 (tmm) cc_final: 0.8360 (tmm) REVERT: I 12 LEU cc_start: 0.8654 (mt) cc_final: 0.8337 (mt) REVERT: I 15 GLU cc_start: 0.7719 (tp30) cc_final: 0.6971 (tp30) REVERT: K 38 HIS cc_start: 0.8000 (m90) cc_final: 0.7782 (m-70) REVERT: K 46 GLU cc_start: 0.8015 (tm-30) cc_final: 0.7740 (tm-30) REVERT: K 47 GLU cc_start: 0.8910 (tp30) cc_final: 0.8665 (tp30) REVERT: L 28 ILE cc_start: 0.8780 (pt) cc_final: 0.8491 (mp) REVERT: L 44 MET cc_start: 0.9092 (mmm) cc_final: 0.8317 (mmm) REVERT: M 12 GLU cc_start: 0.8195 (tt0) cc_final: 0.7866 (mp0) REVERT: M 286 MET cc_start: 0.8877 (mmm) cc_final: 0.8607 (mmm) REVERT: M 292 MET cc_start: 0.8784 (tpt) cc_final: 0.8014 (mmm) REVERT: M 357 MET cc_start: 0.8864 (mtm) cc_final: 0.8583 (mtt) REVERT: M 383 LYS cc_start: 0.7455 (tttm) cc_final: 0.7037 (tptp) REVERT: N 341 LEU cc_start: 0.8998 (tp) cc_final: 0.8763 (tt) REVERT: N 373 MET cc_start: 0.6821 (mpp) cc_final: 0.5976 (mpp) REVERT: O 8 LEU cc_start: 0.9387 (tp) cc_final: 0.9150 (tp) REVERT: O 85 MET cc_start: 0.8362 (ptt) cc_final: 0.8054 (ptp) REVERT: O 133 MET cc_start: 0.6593 (ppp) cc_final: 0.5942 (ppp) REVERT: O 338 LEU cc_start: 0.8718 (mm) cc_final: 0.8326 (mp) REVERT: O 398 MET cc_start: 0.8164 (ttm) cc_final: 0.7649 (ttp) REVERT: O 404 MET cc_start: 0.8478 (mtm) cc_final: 0.8046 (mtm) REVERT: P 85 MET cc_start: 0.2569 (mmp) cc_final: 0.2367 (mpp) REVERT: P 125 LYS cc_start: 0.7225 (tppt) cc_final: 0.6903 (mmtm) REVERT: P 159 ARG cc_start: 0.6243 (ttt-90) cc_final: 0.5469 (mmp-170) REVERT: P 204 ILE cc_start: 0.8032 (mm) cc_final: 0.7685 (tt) REVERT: P 214 HIS cc_start: 0.8340 (t-170) cc_final: 0.8062 (t-170) REVERT: P 297 HIS cc_start: 0.7528 (t-90) cc_final: 0.7283 (t-90) REVERT: P 310 MET cc_start: 0.8727 (mmm) cc_final: 0.8216 (mpp) REVERT: Q 68 MET cc_start: 0.8529 (tpp) cc_final: 0.8318 (tpp) REVERT: Q 71 MET cc_start: 0.8779 (ttp) cc_final: 0.8203 (ttm) REVERT: Q 111 MET cc_start: 0.7296 (mpp) cc_final: 0.6869 (mpp) REVERT: 1 33 TRP cc_start: 0.3216 (t-100) cc_final: 0.2513 (t-100) REVERT: 1 46 MET cc_start: 0.3956 (ptm) cc_final: 0.3344 (tmm) REVERT: 3 136 PHE cc_start: 0.6441 (m-80) cc_final: 0.5676 (t80) REVERT: 3 179 GLU cc_start: 0.5673 (tm-30) cc_final: 0.5381 (tm-30) REVERT: 3 368 ASN cc_start: 0.5564 (m110) cc_final: 0.4919 (p0) REVERT: 4 348 GLU cc_start: 0.5434 (tp30) cc_final: 0.4768 (mm-30) REVERT: 4 377 TYR cc_start: 0.4437 (t80) cc_final: 0.3950 (t80) REVERT: 4 385 MET cc_start: 0.1324 (tmm) cc_final: 0.0941 (mmm) REVERT: 4 389 TYR cc_start: 0.1479 (m-10) cc_final: 0.1158 (m-80) REVERT: U 178 LEU cc_start: 0.6853 (mp) cc_final: 0.6564 (tp) REVERT: U 212 LEU cc_start: 0.6870 (mm) cc_final: 0.6664 (tp) REVERT: U 214 PHE cc_start: 0.3479 (m-80) cc_final: 0.2758 (m-80) REVERT: V 130 ASN cc_start: 0.8312 (m-40) cc_final: 0.7915 (m-40) REVERT: V 135 MET cc_start: 0.9210 (mtt) cc_final: 0.8177 (mtt) REVERT: W 285 ARG cc_start: 0.6813 (tpt170) cc_final: 0.5949 (tpt90) REVERT: W 307 GLU cc_start: 0.7261 (tt0) cc_final: 0.6877 (tt0) REVERT: W 375 LEU cc_start: 0.6444 (mt) cc_final: 0.5940 (tt) outliers start: 0 outliers final: 0 residues processed: 490 average time/residue: 0.5948 time to fit residues: 500.7922 Evaluate side-chains 383 residues out of total 6068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 383 time to evaluate : 4.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 690 random chunks: chunk 224 optimal weight: 7.9990 chunk 600 optimal weight: 10.0000 chunk 131 optimal weight: 6.9990 chunk 391 optimal weight: 10.0000 chunk 164 optimal weight: 0.0470 chunk 667 optimal weight: 10.0000 chunk 554 optimal weight: 6.9990 chunk 309 optimal weight: 7.9990 chunk 55 optimal weight: 5.9990 chunk 220 optimal weight: 7.9990 chunk 350 optimal weight: 0.9980 overall best weight: 4.2084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 HIS ** A 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1039 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 677 HIS B1093 HIS ** C 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.4581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 59344 Z= 0.307 Angle : 0.616 13.301 80728 Z= 0.319 Chirality : 0.043 0.284 8984 Planarity : 0.005 0.055 9896 Dihedral : 15.313 178.252 9118 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.10), residues: 6809 helix: 0.90 (0.10), residues: 2737 sheet: -0.92 (0.18), residues: 748 loop : -1.04 (0.11), residues: 3324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP G 200 HIS 0.014 0.001 HIS M 44 PHE 0.017 0.002 PHE C 336 TYR 0.037 0.002 TYR U 322 ARG 0.007 0.001 ARG 4 365 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13618 Ramachandran restraints generated. 6809 Oldfield, 0 Emsley, 6809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13618 Ramachandran restraints generated. 6809 Oldfield, 0 Emsley, 6809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 6068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 463 time to evaluate : 5.015 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: A 35 GLN cc_start: 0.7842 (tt0) cc_final: 0.7323 (tp-100) REVERT: A 474 MET cc_start: 0.7677 (mtp) cc_final: 0.7170 (mtp) REVERT: A 505 MET cc_start: 0.7901 (tpt) cc_final: 0.6895 (tpt) REVERT: A 724 CYS cc_start: 0.9082 (m) cc_final: 0.8866 (m) REVERT: A 912 MET cc_start: 0.8542 (mmp) cc_final: 0.8135 (mmp) REVERT: A 1027 MET cc_start: 0.8109 (tpt) cc_final: 0.7843 (tpt) REVERT: A 1236 MET cc_start: 0.7677 (ptp) cc_final: 0.6993 (mtm) REVERT: A 1327 HIS cc_start: 0.7575 (m90) cc_final: 0.6496 (t-90) REVERT: B 107 MET cc_start: 0.8889 (ptm) cc_final: 0.8528 (ptm) REVERT: B 243 MET cc_start: 0.7904 (ttm) cc_final: 0.7186 (ttm) REVERT: B 641 CYS cc_start: 0.8792 (m) cc_final: 0.8093 (p) REVERT: B 689 MET cc_start: 0.5978 (mmt) cc_final: 0.5467 (mmt) REVERT: B 719 MET cc_start: 0.9113 (mmm) cc_final: 0.8793 (mmm) REVERT: B 763 ASP cc_start: 0.8379 (m-30) cc_final: 0.8041 (m-30) REVERT: B 794 MET cc_start: 0.8120 (tmm) cc_final: 0.7744 (mmt) REVERT: B 883 MET cc_start: 0.8050 (mpp) cc_final: 0.7677 (mpp) REVERT: B 916 MET cc_start: 0.9227 (mmt) cc_final: 0.8824 (mmm) REVERT: B 1015 MET cc_start: 0.8404 (mtp) cc_final: 0.7112 (mmt) REVERT: B 1050 MET cc_start: 0.6985 (pmm) cc_final: 0.6417 (pmm) REVERT: C 56 MET cc_start: 0.8627 (tmm) cc_final: 0.7545 (tmm) REVERT: C 87 MET cc_start: 0.8595 (mmm) cc_final: 0.8298 (mmt) REVERT: D 26 GLN cc_start: 0.8370 (tp40) cc_final: 0.7974 (tp-100) REVERT: D 60 HIS cc_start: 0.7209 (m90) cc_final: 0.6931 (m170) REVERT: D 90 ARG cc_start: 0.4065 (mtm-85) cc_final: 0.1840 (tpt170) REVERT: E 27 LEU cc_start: 0.8612 (mt) cc_final: 0.8338 (mt) REVERT: E 94 MET cc_start: 0.6877 (mmp) cc_final: 0.6534 (mmp) REVERT: G 7 MET cc_start: 0.6982 (tpt) cc_final: 0.6414 (tpt) REVERT: G 90 LYS cc_start: 0.5932 (mmtm) cc_final: 0.4501 (ttpt) REVERT: G 106 ASP cc_start: 0.8216 (p0) cc_final: 0.6868 (t70) REVERT: G 201 TRP cc_start: 0.7122 (p-90) cc_final: 0.6337 (p-90) REVERT: H 64 LEU cc_start: 0.8603 (tp) cc_final: 0.7760 (tt) REVERT: H 74 GLU cc_start: 0.7751 (pp20) cc_final: 0.7404 (pp20) REVERT: H 107 GLU cc_start: 0.6125 (mp0) cc_final: 0.5166 (pm20) REVERT: H 118 TYR cc_start: 0.8193 (m-80) cc_final: 0.7672 (m-80) REVERT: H 123 MET cc_start: 0.8628 (tmm) cc_final: 0.8420 (tmm) REVERT: I 12 LEU cc_start: 0.8609 (mt) cc_final: 0.8347 (mt) REVERT: I 15 GLU cc_start: 0.7704 (tp30) cc_final: 0.6973 (tp30) REVERT: K 60 MET cc_start: 0.9197 (tpp) cc_final: 0.8936 (mmm) REVERT: L 28 ILE cc_start: 0.8838 (pt) cc_final: 0.8561 (mp) REVERT: L 44 MET cc_start: 0.9110 (mmm) cc_final: 0.8496 (mmm) REVERT: M 12 GLU cc_start: 0.8251 (tt0) cc_final: 0.7918 (mp0) REVERT: M 286 MET cc_start: 0.8880 (mmm) cc_final: 0.8574 (mmm) REVERT: M 292 MET cc_start: 0.8902 (tpt) cc_final: 0.8454 (tpp) REVERT: M 357 MET cc_start: 0.8857 (mtm) cc_final: 0.8603 (mtt) REVERT: M 383 LYS cc_start: 0.7514 (tttm) cc_final: 0.7190 (tptp) REVERT: N 341 LEU cc_start: 0.9011 (tp) cc_final: 0.8747 (tt) REVERT: N 373 MET cc_start: 0.6779 (mpp) cc_final: 0.5929 (mpp) REVERT: O 8 LEU cc_start: 0.9382 (tp) cc_final: 0.9133 (tp) REVERT: O 85 MET cc_start: 0.8381 (ptt) cc_final: 0.8137 (ptp) REVERT: O 338 LEU cc_start: 0.8724 (mm) cc_final: 0.8307 (mp) REVERT: O 398 MET cc_start: 0.8139 (ttm) cc_final: 0.7617 (ttp) REVERT: O 404 MET cc_start: 0.8494 (mtm) cc_final: 0.8054 (mtm) REVERT: P 125 LYS cc_start: 0.7227 (tppt) cc_final: 0.6847 (mmtm) REVERT: P 159 ARG cc_start: 0.6359 (ttt-90) cc_final: 0.5509 (mmp-170) REVERT: P 204 ILE cc_start: 0.8094 (mm) cc_final: 0.7744 (tt) REVERT: P 214 HIS cc_start: 0.8359 (t-170) cc_final: 0.8109 (t-170) REVERT: P 297 HIS cc_start: 0.7542 (t-90) cc_final: 0.7290 (t-90) REVERT: P 310 MET cc_start: 0.8678 (mmm) cc_final: 0.8173 (mpp) REVERT: Q 68 MET cc_start: 0.8501 (tpp) cc_final: 0.8257 (tpp) REVERT: Q 71 MET cc_start: 0.8758 (ttp) cc_final: 0.8145 (ttm) REVERT: Q 111 MET cc_start: 0.7390 (mpp) cc_final: 0.6869 (mpp) REVERT: 1 33 TRP cc_start: 0.3198 (t-100) cc_final: 0.2446 (t-100) REVERT: 1 46 MET cc_start: 0.3748 (ptm) cc_final: 0.3175 (tmm) REVERT: 3 136 PHE cc_start: 0.6336 (m-80) cc_final: 0.5575 (t80) REVERT: 3 179 GLU cc_start: 0.5760 (tm-30) cc_final: 0.5246 (pp20) REVERT: 3 368 ASN cc_start: 0.5465 (m110) cc_final: 0.4786 (p0) REVERT: 4 348 GLU cc_start: 0.5287 (tp30) cc_final: 0.4710 (mm-30) REVERT: 4 377 TYR cc_start: 0.4407 (t80) cc_final: 0.4011 (t80) REVERT: 4 389 TYR cc_start: 0.1640 (m-10) cc_final: 0.1305 (m-80) REVERT: U 179 ASP cc_start: 0.8038 (t0) cc_final: 0.7202 (m-30) REVERT: U 214 PHE cc_start: 0.3455 (m-80) cc_final: 0.2750 (m-80) REVERT: U 284 GLU cc_start: 0.8242 (mm-30) cc_final: 0.8039 (mm-30) REVERT: W 285 ARG cc_start: 0.6914 (tpt170) cc_final: 0.6003 (tpt90) REVERT: W 307 GLU cc_start: 0.7295 (tt0) cc_final: 0.6800 (tt0) REVERT: W 375 LEU cc_start: 0.6300 (mt) cc_final: 0.5882 (tt) outliers start: 0 outliers final: 0 residues processed: 463 average time/residue: 0.5330 time to fit residues: 424.7015 Evaluate side-chains 383 residues out of total 6068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 383 time to evaluate : 4.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 690 random chunks: chunk 643 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 380 optimal weight: 2.9990 chunk 487 optimal weight: 1.9990 chunk 377 optimal weight: 7.9990 chunk 561 optimal weight: 6.9990 chunk 372 optimal weight: 1.9990 chunk 665 optimal weight: 1.9990 chunk 416 optimal weight: 9.9990 chunk 405 optimal weight: 0.3980 chunk 307 optimal weight: 3.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 872 GLN ** A1039 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 84 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.4591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 59344 Z= 0.188 Angle : 0.562 11.704 80728 Z= 0.290 Chirality : 0.042 0.290 8984 Planarity : 0.004 0.057 9896 Dihedral : 15.260 179.090 9118 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.10), residues: 6809 helix: 1.06 (0.10), residues: 2741 sheet: -0.83 (0.19), residues: 747 loop : -0.92 (0.11), residues: 3321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP G 201 HIS 0.012 0.001 HIS M 44 PHE 0.018 0.001 PHE V 402 TYR 0.038 0.001 TYR U 322 ARG 0.008 0.000 ARG L 42 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13618 Ramachandran restraints generated. 6809 Oldfield, 0 Emsley, 6809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13618 Ramachandran restraints generated. 6809 Oldfield, 0 Emsley, 6809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 6068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 472 time to evaluate : 4.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLN cc_start: 0.7820 (tt0) cc_final: 0.7384 (tp-100) REVERT: A 505 MET cc_start: 0.7854 (tpt) cc_final: 0.6843 (tpt) REVERT: A 724 CYS cc_start: 0.9112 (m) cc_final: 0.8843 (m) REVERT: A 912 MET cc_start: 0.8431 (mmp) cc_final: 0.8072 (mmp) REVERT: A 953 MET cc_start: 0.8656 (tpp) cc_final: 0.8204 (tpt) REVERT: A 1027 MET cc_start: 0.8050 (tpt) cc_final: 0.7550 (tpt) REVERT: A 1236 MET cc_start: 0.7647 (ptp) cc_final: 0.6969 (mtm) REVERT: A 1327 HIS cc_start: 0.7487 (m90) cc_final: 0.6244 (t70) REVERT: B 107 MET cc_start: 0.8947 (ptm) cc_final: 0.8629 (ptm) REVERT: B 243 MET cc_start: 0.8042 (ttm) cc_final: 0.7309 (ttm) REVERT: B 641 CYS cc_start: 0.8746 (m) cc_final: 0.7859 (p) REVERT: B 689 MET cc_start: 0.5921 (mmt) cc_final: 0.5359 (mmt) REVERT: B 719 MET cc_start: 0.9052 (mmm) cc_final: 0.8781 (mmm) REVERT: B 763 ASP cc_start: 0.8393 (m-30) cc_final: 0.8017 (m-30) REVERT: B 794 MET cc_start: 0.8220 (tmm) cc_final: 0.7822 (mmt) REVERT: B 883 MET cc_start: 0.8010 (mpp) cc_final: 0.7631 (mpp) REVERT: B 916 MET cc_start: 0.9208 (mmt) cc_final: 0.8887 (mmm) REVERT: B 929 MET cc_start: 0.7909 (tpt) cc_final: 0.7550 (tpt) REVERT: B 1015 MET cc_start: 0.8315 (mtp) cc_final: 0.7170 (mmt) REVERT: B 1050 MET cc_start: 0.7027 (pmm) cc_final: 0.6419 (pmm) REVERT: C 56 MET cc_start: 0.8729 (tmm) cc_final: 0.7643 (tmm) REVERT: C 65 MET cc_start: 0.8591 (mtp) cc_final: 0.8073 (ttm) REVERT: C 68 ILE cc_start: 0.9395 (tp) cc_final: 0.9087 (tp) REVERT: C 87 MET cc_start: 0.8564 (mmm) cc_final: 0.8231 (mmm) REVERT: C 255 ARG cc_start: 0.8555 (mmt-90) cc_final: 0.7818 (mtm110) REVERT: D 22 ASP cc_start: 0.7251 (m-30) cc_final: 0.7017 (m-30) REVERT: D 26 GLN cc_start: 0.8331 (tp40) cc_final: 0.7913 (tp-100) REVERT: D 90 ARG cc_start: 0.3944 (mtm-85) cc_final: 0.1674 (tpt170) REVERT: E 27 LEU cc_start: 0.8614 (mt) cc_final: 0.8326 (mt) REVERT: E 94 MET cc_start: 0.6729 (mmp) cc_final: 0.6305 (mmp) REVERT: G 90 LYS cc_start: 0.5920 (mmtm) cc_final: 0.4522 (ttpt) REVERT: G 106 ASP cc_start: 0.8183 (p0) cc_final: 0.6932 (t70) REVERT: G 201 TRP cc_start: 0.6871 (p-90) cc_final: 0.6306 (p-90) REVERT: H 8 ASP cc_start: 0.6956 (t0) cc_final: 0.6615 (t0) REVERT: H 64 LEU cc_start: 0.8567 (tp) cc_final: 0.8273 (tp) REVERT: H 74 GLU cc_start: 0.7775 (pp20) cc_final: 0.7437 (pp20) REVERT: H 107 GLU cc_start: 0.6116 (mp0) cc_final: 0.5131 (pt0) REVERT: H 118 TYR cc_start: 0.7979 (m-80) cc_final: 0.7433 (m-80) REVERT: H 123 MET cc_start: 0.8512 (tmm) cc_final: 0.8211 (tmm) REVERT: I 12 LEU cc_start: 0.8622 (mt) cc_final: 0.8360 (mt) REVERT: I 15 GLU cc_start: 0.7682 (tp30) cc_final: 0.6911 (tp30) REVERT: I 79 PHE cc_start: 0.5006 (m-80) cc_final: 0.4263 (m-10) REVERT: K 46 GLU cc_start: 0.7861 (tm-30) cc_final: 0.7536 (tm-30) REVERT: K 60 MET cc_start: 0.9237 (tpp) cc_final: 0.8901 (mmm) REVERT: L 44 MET cc_start: 0.9073 (mmm) cc_final: 0.8603 (mmt) REVERT: M 12 GLU cc_start: 0.8160 (tt0) cc_final: 0.7831 (tm-30) REVERT: M 292 MET cc_start: 0.8893 (tpt) cc_final: 0.8437 (tpt) REVERT: M 357 MET cc_start: 0.8833 (mtm) cc_final: 0.8524 (mtt) REVERT: M 383 LYS cc_start: 0.7378 (tttm) cc_final: 0.7143 (tptp) REVERT: N 256 ARG cc_start: 0.8521 (tmm160) cc_final: 0.8293 (mtt180) REVERT: N 341 LEU cc_start: 0.9001 (tp) cc_final: 0.8731 (tt) REVERT: N 350 MET cc_start: 0.8417 (tpp) cc_final: 0.7635 (mpp) REVERT: N 373 MET cc_start: 0.6732 (mpp) cc_final: 0.5891 (mpp) REVERT: O 8 LEU cc_start: 0.9391 (tp) cc_final: 0.9174 (tp) REVERT: O 85 MET cc_start: 0.8328 (ptt) cc_final: 0.8086 (ptp) REVERT: O 338 LEU cc_start: 0.8695 (mm) cc_final: 0.8300 (mp) REVERT: O 398 MET cc_start: 0.8156 (ttm) cc_final: 0.7603 (ttp) REVERT: O 404 MET cc_start: 0.8464 (mtm) cc_final: 0.8011 (mtm) REVERT: P 159 ARG cc_start: 0.6256 (ttt-90) cc_final: 0.5442 (mmp-170) REVERT: P 204 ILE cc_start: 0.8054 (mm) cc_final: 0.7722 (tt) REVERT: P 210 PHE cc_start: 0.7759 (m-10) cc_final: 0.7519 (m-10) REVERT: P 214 HIS cc_start: 0.8277 (t-170) cc_final: 0.8051 (t-170) REVERT: P 297 HIS cc_start: 0.7583 (t-90) cc_final: 0.7271 (t-90) REVERT: P 310 MET cc_start: 0.8652 (mmm) cc_final: 0.8188 (mpp) REVERT: Q 111 MET cc_start: 0.7432 (mpp) cc_final: 0.6817 (mpp) REVERT: 1 33 TRP cc_start: 0.3341 (t-100) cc_final: 0.2557 (t-100) REVERT: 1 46 MET cc_start: 0.3739 (ptm) cc_final: 0.3156 (tmm) REVERT: 1 96 LYS cc_start: 0.0020 (mtmm) cc_final: -0.0346 (mttt) REVERT: 3 136 PHE cc_start: 0.6331 (m-80) cc_final: 0.5560 (t80) REVERT: 3 179 GLU cc_start: 0.5696 (tm-30) cc_final: 0.5401 (pp20) REVERT: 3 293 MET cc_start: 0.1629 (ptp) cc_final: 0.1314 (ptm) REVERT: 4 348 GLU cc_start: 0.5246 (tp30) cc_final: 0.4686 (mm-30) REVERT: 4 377 TYR cc_start: 0.4436 (t80) cc_final: 0.4041 (t80) REVERT: 4 389 TYR cc_start: 0.1327 (m-10) cc_final: 0.0935 (m-80) REVERT: U 214 PHE cc_start: 0.3207 (m-80) cc_final: 0.2672 (m-80) REVERT: W 285 ARG cc_start: 0.6948 (tpt170) cc_final: 0.6012 (tpm170) REVERT: W 307 GLU cc_start: 0.7202 (tt0) cc_final: 0.6816 (tt0) REVERT: W 375 LEU cc_start: 0.6417 (mt) cc_final: 0.5918 (tt) outliers start: 0 outliers final: 0 residues processed: 472 average time/residue: 0.5537 time to fit residues: 449.5443 Evaluate side-chains 386 residues out of total 6068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 386 time to evaluate : 4.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 690 random chunks: chunk 411 optimal weight: 10.0000 chunk 265 optimal weight: 1.9990 chunk 397 optimal weight: 20.0000 chunk 200 optimal weight: 0.0020 chunk 130 optimal weight: 0.0570 chunk 128 optimal weight: 2.9990 chunk 422 optimal weight: 0.0670 chunk 453 optimal weight: 0.0270 chunk 328 optimal weight: 20.0000 chunk 61 optimal weight: 4.9990 chunk 522 optimal weight: 0.6980 overall best weight: 0.1702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 HIS ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 463 ASN A 872 GLN ** A1039 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 273 GLN B 979 HIS ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.4491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 59344 Z= 0.143 Angle : 0.540 12.705 80728 Z= 0.278 Chirality : 0.041 0.296 8984 Planarity : 0.004 0.088 9896 Dihedral : 15.191 179.947 9118 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % 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: 0.02 (0.10), residues: 6809 helix: 1.25 (0.10), residues: 2733 sheet: -0.69 (0.19), residues: 742 loop : -0.84 (0.11), residues: 3334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP G 200 HIS 0.008 0.001 HIS M 44 PHE 0.020 0.001 PHE E 73 TYR 0.033 0.001 TYR U 322 ARG 0.016 0.000 ARG E 101 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13618 Ramachandran restraints generated. 6809 Oldfield, 0 Emsley, 6809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13618 Ramachandran restraints generated. 6809 Oldfield, 0 Emsley, 6809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 6068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 493 time to evaluate : 5.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLN cc_start: 0.7754 (tt0) cc_final: 0.7381 (tp-100) REVERT: A 724 CYS cc_start: 0.9116 (m) cc_final: 0.8828 (m) REVERT: A 912 MET cc_start: 0.8469 (mmp) cc_final: 0.8143 (mmp) REVERT: A 953 MET cc_start: 0.8490 (tpp) cc_final: 0.8195 (tpt) REVERT: A 1027 MET cc_start: 0.8048 (tpt) cc_final: 0.7777 (tpt) REVERT: A 1236 MET cc_start: 0.7598 (ptp) cc_final: 0.7004 (mtm) REVERT: A 1327 HIS cc_start: 0.7221 (m90) cc_final: 0.6294 (t70) REVERT: B 68 ASP cc_start: 0.6843 (p0) cc_final: 0.6049 (t0) REVERT: B 136 MET cc_start: 0.8557 (ttt) cc_final: 0.8155 (tpp) REVERT: B 243 MET cc_start: 0.8002 (ttm) cc_final: 0.7223 (ttm) REVERT: B 689 MET cc_start: 0.6001 (mmt) cc_final: 0.5369 (mmt) REVERT: B 719 MET cc_start: 0.8944 (mmm) cc_final: 0.8654 (mmm) REVERT: B 763 ASP cc_start: 0.8346 (m-30) cc_final: 0.7890 (m-30) REVERT: B 794 MET cc_start: 0.8160 (tmm) cc_final: 0.7816 (mmt) REVERT: B 883 MET cc_start: 0.8094 (mpp) cc_final: 0.7758 (mpp) REVERT: B 916 MET cc_start: 0.9117 (mmt) cc_final: 0.8860 (mmm) REVERT: B 929 MET cc_start: 0.7766 (tpt) cc_final: 0.7511 (tpt) REVERT: B 1020 MET cc_start: 0.7295 (ttm) cc_final: 0.7035 (ttm) REVERT: B 1050 MET cc_start: 0.7176 (pmm) cc_final: 0.6558 (pmm) REVERT: C 56 MET cc_start: 0.8807 (tmm) cc_final: 0.7690 (tmm) REVERT: C 65 MET cc_start: 0.8460 (mtp) cc_final: 0.7938 (ttm) REVERT: C 68 ILE cc_start: 0.9380 (tp) cc_final: 0.9114 (tp) REVERT: C 212 MET cc_start: 0.8293 (mtp) cc_final: 0.7760 (mtp) REVERT: C 255 ARG cc_start: 0.8494 (mmt-90) cc_final: 0.7826 (ttm110) REVERT: D 22 ASP cc_start: 0.7269 (m-30) cc_final: 0.6436 (t0) REVERT: D 26 GLN cc_start: 0.8497 (tp40) cc_final: 0.8089 (tp-100) REVERT: D 90 ARG cc_start: 0.3819 (mtm-85) cc_final: 0.1548 (tpt170) REVERT: E 27 LEU cc_start: 0.8509 (mt) cc_final: 0.8225 (mt) REVERT: E 94 MET cc_start: 0.6673 (mmp) cc_final: 0.6359 (mmp) REVERT: G 90 LYS cc_start: 0.5709 (mmtm) cc_final: 0.4649 (ttpt) REVERT: G 106 ASP cc_start: 0.8141 (p0) cc_final: 0.6863 (t70) REVERT: G 201 TRP cc_start: 0.6875 (p-90) cc_final: 0.6292 (p-90) REVERT: H 64 LEU cc_start: 0.8567 (tp) cc_final: 0.8275 (tp) REVERT: H 74 GLU cc_start: 0.7755 (pp20) cc_final: 0.7449 (pp20) REVERT: H 107 GLU cc_start: 0.5971 (mp0) cc_final: 0.5035 (pt0) REVERT: H 118 TYR cc_start: 0.7597 (m-80) cc_final: 0.7048 (m-80) REVERT: H 123 MET cc_start: 0.8495 (tmm) cc_final: 0.8068 (tmm) REVERT: I 15 GLU cc_start: 0.7623 (tp30) cc_final: 0.6876 (tp30) REVERT: I 79 PHE cc_start: 0.4672 (m-80) cc_final: 0.4370 (m-10) REVERT: J 19 GLU cc_start: 0.8394 (mt-10) cc_final: 0.8027 (tt0) REVERT: J 48 MET cc_start: 0.9047 (tpp) cc_final: 0.7619 (tpp) REVERT: K 46 GLU cc_start: 0.7767 (tm-30) cc_final: 0.7412 (tm-30) REVERT: L 44 MET cc_start: 0.9182 (mmm) cc_final: 0.8771 (mmt) REVERT: M 12 GLU cc_start: 0.8116 (tt0) cc_final: 0.7912 (tm-30) REVERT: M 119 TYR cc_start: 0.7247 (t80) cc_final: 0.6843 (t80) REVERT: M 250 MET cc_start: 0.9026 (tpp) cc_final: 0.8815 (tpp) REVERT: M 292 MET cc_start: 0.8902 (tpt) cc_final: 0.8346 (tpt) REVERT: M 357 MET cc_start: 0.8802 (mtm) cc_final: 0.8490 (mtt) REVERT: M 383 LYS cc_start: 0.7346 (tttm) cc_final: 0.7126 (tptp) REVERT: N 341 LEU cc_start: 0.8994 (tp) cc_final: 0.8730 (tt) REVERT: N 350 MET cc_start: 0.8377 (tpp) cc_final: 0.7650 (mpp) REVERT: N 373 MET cc_start: 0.6726 (mpp) cc_final: 0.5780 (mpp) REVERT: O 8 LEU cc_start: 0.9363 (tp) cc_final: 0.9149 (tp) REVERT: O 20 ILE cc_start: 0.8910 (pt) cc_final: 0.8649 (tt) REVERT: O 85 MET cc_start: 0.8282 (ptt) cc_final: 0.8015 (ptp) REVERT: O 133 MET cc_start: 0.5245 (ptt) cc_final: 0.4819 (ppp) REVERT: O 240 ASP cc_start: 0.9222 (m-30) cc_final: 0.9020 (m-30) REVERT: O 338 LEU cc_start: 0.8694 (mm) cc_final: 0.8272 (mp) REVERT: O 398 MET cc_start: 0.8167 (ttm) cc_final: 0.7663 (ttp) REVERT: O 404 MET cc_start: 0.8442 (mtm) cc_final: 0.7950 (mtm) REVERT: P 159 ARG cc_start: 0.6236 (ttt-90) cc_final: 0.5474 (mmp-170) REVERT: P 204 ILE cc_start: 0.7992 (mm) cc_final: 0.7701 (tt) REVERT: P 210 PHE cc_start: 0.7826 (m-10) cc_final: 0.7581 (m-10) REVERT: P 297 HIS cc_start: 0.7510 (t-90) cc_final: 0.7196 (t-90) REVERT: Q 111 MET cc_start: 0.7679 (mpp) cc_final: 0.7458 (mpp) REVERT: 1 33 TRP cc_start: 0.3206 (t-100) cc_final: 0.2441 (t-100) REVERT: 1 46 MET cc_start: 0.3907 (ptm) cc_final: 0.3261 (tmm) REVERT: 3 136 PHE cc_start: 0.6310 (m-80) cc_final: 0.5543 (t80) REVERT: 3 272 ARG cc_start: 0.6119 (mpt90) cc_final: 0.5227 (mmt180) REVERT: 4 348 GLU cc_start: 0.5207 (tp30) cc_final: 0.4660 (mm-30) REVERT: 4 377 TYR cc_start: 0.4466 (t80) cc_final: 0.4008 (t80) REVERT: 4 389 TYR cc_start: 0.1111 (m-10) cc_final: 0.0773 (m-80) REVERT: U 214 PHE cc_start: 0.3067 (m-80) cc_final: 0.2628 (m-80) REVERT: V 135 MET cc_start: 0.8889 (mtt) cc_final: 0.8468 (mtt) REVERT: W 307 GLU cc_start: 0.7207 (tt0) cc_final: 0.6820 (tt0) REVERT: W 375 LEU cc_start: 0.6271 (mt) cc_final: 0.5784 (tt) outliers start: 0 outliers final: 0 residues processed: 493 average time/residue: 0.5402 time to fit residues: 457.1026 Evaluate side-chains 391 residues out of total 6068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 391 time to evaluate : 4.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 690 random chunks: chunk 604 optimal weight: 3.9990 chunk 637 optimal weight: 8.9990 chunk 581 optimal weight: 10.0000 chunk 619 optimal weight: 9.9990 chunk 636 optimal weight: 1.9990 chunk 373 optimal weight: 1.9990 chunk 269 optimal weight: 6.9990 chunk 486 optimal weight: 0.8980 chunk 190 optimal weight: 4.9990 chunk 560 optimal weight: 20.0000 chunk 586 optimal weight: 5.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1039 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 273 GLN ** C 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 GLN D 43 ASN ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 81 GLN ** I 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 327 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.4674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 59344 Z= 0.229 Angle : 0.574 11.788 80728 Z= 0.294 Chirality : 0.042 0.309 8984 Planarity : 0.004 0.056 9896 Dihedral : 15.237 179.939 9118 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % 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: -0.00 (0.10), residues: 6809 helix: 1.22 (0.10), residues: 2757 sheet: -0.72 (0.19), residues: 747 loop : -0.85 (0.11), residues: 3305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP G 201 HIS 0.011 0.001 HIS M 44 PHE 0.016 0.001 PHE C 336 TYR 0.026 0.001 TYR B1003 ARG 0.010 0.000 ARG N 256 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13618 Ramachandran restraints generated. 6809 Oldfield, 0 Emsley, 6809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13618 Ramachandran restraints generated. 6809 Oldfield, 0 Emsley, 6809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 6068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 453 time to evaluate : 4.920 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: A 35 GLN cc_start: 0.7844 (tt0) cc_final: 0.7378 (tm-30) REVERT: A 107 MET cc_start: 0.8007 (mtm) cc_final: 0.7668 (mtp) REVERT: A 724 CYS cc_start: 0.9089 (m) cc_final: 0.8852 (m) REVERT: A 912 MET cc_start: 0.8436 (mmp) cc_final: 0.8106 (mmp) REVERT: A 1027 MET cc_start: 0.8046 (tpt) cc_final: 0.7713 (tpt) REVERT: A 1236 MET cc_start: 0.7629 (ptp) cc_final: 0.6971 (mtm) REVERT: A 1327 HIS cc_start: 0.7320 (m90) cc_final: 0.6280 (t70) REVERT: B 68 ASP cc_start: 0.6924 (p0) cc_final: 0.6224 (t0) REVERT: B 243 MET cc_start: 0.7939 (ttm) cc_final: 0.7103 (ttm) REVERT: B 689 MET cc_start: 0.5944 (mmt) cc_final: 0.5373 (mmt) REVERT: B 719 MET cc_start: 0.9034 (mmm) cc_final: 0.8780 (mmm) REVERT: B 763 ASP cc_start: 0.8434 (m-30) cc_final: 0.8073 (m-30) REVERT: B 794 MET cc_start: 0.8149 (tmm) cc_final: 0.7825 (mmt) REVERT: B 883 MET cc_start: 0.8037 (mpp) cc_final: 0.7682 (mpp) REVERT: B 929 MET cc_start: 0.7747 (tpt) cc_final: 0.7428 (tpt) REVERT: B 1050 MET cc_start: 0.7164 (pmm) cc_final: 0.6534 (pmm) REVERT: C 56 MET cc_start: 0.8731 (tmm) cc_final: 0.7637 (tmm) REVERT: C 65 MET cc_start: 0.8607 (mtp) cc_final: 0.8077 (ttm) REVERT: C 68 ILE cc_start: 0.9405 (tp) cc_final: 0.9136 (tp) REVERT: C 255 ARG cc_start: 0.8490 (mmt-90) cc_final: 0.7822 (ttm110) REVERT: C 330 MET cc_start: 0.8308 (mmm) cc_final: 0.7769 (mmm) REVERT: D 22 ASP cc_start: 0.7248 (m-30) cc_final: 0.7010 (m-30) REVERT: D 26 GLN cc_start: 0.8302 (tp40) cc_final: 0.7914 (tp-100) REVERT: D 90 ARG cc_start: 0.3951 (mtm-85) cc_final: 0.1623 (tpt170) REVERT: E 27 LEU cc_start: 0.8548 (mt) cc_final: 0.8251 (mt) REVERT: E 94 MET cc_start: 0.6819 (mmp) cc_final: 0.6559 (mmp) REVERT: G 90 LYS cc_start: 0.5723 (mmtm) cc_final: 0.4633 (ttpt) REVERT: G 106 ASP cc_start: 0.8156 (p0) cc_final: 0.6974 (t70) REVERT: G 201 TRP cc_start: 0.6928 (p-90) cc_final: 0.6349 (p-90) REVERT: H 64 LEU cc_start: 0.8597 (tp) cc_final: 0.8389 (tp) REVERT: H 74 GLU cc_start: 0.7751 (pp20) cc_final: 0.7425 (pp20) REVERT: H 107 GLU cc_start: 0.6001 (mp0) cc_final: 0.5043 (pt0) REVERT: H 118 TYR cc_start: 0.7758 (m-80) cc_final: 0.7142 (m-80) REVERT: H 123 MET cc_start: 0.8503 (tmm) cc_final: 0.8092 (tmm) REVERT: I 15 GLU cc_start: 0.7669 (tp30) cc_final: 0.6935 (tp30) REVERT: J 19 GLU cc_start: 0.8479 (mt-10) cc_final: 0.8165 (tt0) REVERT: J 48 MET cc_start: 0.9070 (tpp) cc_final: 0.7668 (tpp) REVERT: K 46 GLU cc_start: 0.7873 (tm-30) cc_final: 0.7458 (tm-30) REVERT: K 60 MET cc_start: 0.9123 (mmm) cc_final: 0.8651 (mmm) REVERT: L 44 MET cc_start: 0.8943 (mmm) cc_final: 0.8250 (mmm) REVERT: M 292 MET cc_start: 0.8938 (tpt) cc_final: 0.8056 (mmm) REVERT: M 357 MET cc_start: 0.8783 (mtm) cc_final: 0.8512 (mtt) REVERT: M 383 LYS cc_start: 0.7356 (tttm) cc_final: 0.7122 (tptp) REVERT: N 341 LEU cc_start: 0.9011 (tp) cc_final: 0.8746 (tt) REVERT: N 350 MET cc_start: 0.8459 (tpp) cc_final: 0.7581 (mpp) REVERT: N 373 MET cc_start: 0.6712 (mpp) cc_final: 0.5804 (mpp) REVERT: O 8 LEU cc_start: 0.9397 (tp) cc_final: 0.9166 (tp) REVERT: O 20 ILE cc_start: 0.8982 (pt) cc_final: 0.8738 (tt) REVERT: O 85 MET cc_start: 0.8344 (ptt) cc_final: 0.8085 (ptp) REVERT: O 338 LEU cc_start: 0.8701 (mm) cc_final: 0.8300 (mp) REVERT: O 398 MET cc_start: 0.8141 (ttm) cc_final: 0.7502 (ttp) REVERT: O 404 MET cc_start: 0.8477 (mtm) cc_final: 0.7970 (mtm) REVERT: P 159 ARG cc_start: 0.6235 (ttt-90) cc_final: 0.5400 (mmp-170) REVERT: P 204 ILE cc_start: 0.7999 (mm) cc_final: 0.7711 (tt) REVERT: P 210 PHE cc_start: 0.7814 (m-10) cc_final: 0.7556 (m-10) REVERT: P 297 HIS cc_start: 0.7558 (t-90) cc_final: 0.7228 (t-90) REVERT: P 310 MET cc_start: 0.8514 (tpp) cc_final: 0.7734 (mpp) REVERT: Q 111 MET cc_start: 0.7710 (mpp) cc_final: 0.7382 (tpt) REVERT: 1 33 TRP cc_start: 0.3208 (t-100) cc_final: 0.2436 (t-100) REVERT: 1 46 MET cc_start: 0.3650 (ptm) cc_final: 0.3108 (tmm) REVERT: 3 136 PHE cc_start: 0.6343 (m-80) cc_final: 0.5575 (t80) REVERT: 3 204 MET cc_start: 0.6136 (mtt) cc_final: 0.5846 (mtp) REVERT: 4 348 GLU cc_start: 0.4970 (tp30) cc_final: 0.4591 (mm-30) REVERT: 4 377 TYR cc_start: 0.4349 (t80) cc_final: 0.3939 (t80) REVERT: 4 389 TYR cc_start: 0.1314 (m-10) cc_final: 0.0885 (m-80) REVERT: U 214 PHE cc_start: 0.3027 (m-80) cc_final: 0.2652 (m-80) REVERT: V 130 ASN cc_start: 0.7901 (m-40) cc_final: 0.7615 (m-40) REVERT: V 135 MET cc_start: 0.8907 (mtt) cc_final: 0.8342 (mtp) REVERT: W 307 GLU cc_start: 0.7212 (tt0) cc_final: 0.6830 (tt0) REVERT: W 375 LEU cc_start: 0.6269 (mt) cc_final: 0.5772 (tt) outliers start: 0 outliers final: 0 residues processed: 453 average time/residue: 0.5569 time to fit residues: 438.3405 Evaluate side-chains 379 residues out of total 6068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 379 time to evaluate : 5.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 690 random chunks: chunk 617 optimal weight: 20.0000 chunk 406 optimal weight: 5.9990 chunk 655 optimal weight: 4.9990 chunk 399 optimal weight: 5.9990 chunk 310 optimal weight: 0.9990 chunk 455 optimal weight: 5.9990 chunk 687 optimal weight: 0.5980 chunk 632 optimal weight: 10.0000 chunk 547 optimal weight: 10.0000 chunk 56 optimal weight: 7.9990 chunk 422 optimal weight: 8.9990 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 HIS ** A1039 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1062 ASN ** C 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 81 GLN ** I 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 314 GLN ** 4 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 303 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.4991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 59344 Z= 0.271 Angle : 0.606 11.763 80728 Z= 0.312 Chirality : 0.043 0.315 8984 Planarity : 0.004 0.110 9896 Dihedral : 15.308 179.422 9118 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 0.03 % Allowed : 0.21 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.10), residues: 6809 helix: 1.11 (0.10), residues: 2739 sheet: -0.84 (0.19), residues: 751 loop : -0.92 (0.11), residues: 3319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP G 201 HIS 0.010 0.001 HIS M 44 PHE 0.018 0.002 PHE V 402 TYR 0.031 0.002 TYR B1003 ARG 0.006 0.000 ARG L 42 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13618 Ramachandran restraints generated. 6809 Oldfield, 0 Emsley, 6809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13618 Ramachandran restraints generated. 6809 Oldfield, 0 Emsley, 6809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 6068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 447 time to evaluate : 5.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLN cc_start: 0.7892 (tt0) cc_final: 0.7408 (tm-30) REVERT: A 474 MET cc_start: 0.7407 (mtp) cc_final: 0.6931 (mtp) REVERT: A 724 CYS cc_start: 0.9100 (m) cc_final: 0.8869 (m) REVERT: A 912 MET cc_start: 0.8546 (mmp) cc_final: 0.8182 (mmp) REVERT: A 1027 MET cc_start: 0.8062 (tpt) cc_final: 0.7705 (tpt) REVERT: A 1236 MET cc_start: 0.7673 (ptp) cc_final: 0.6876 (mtm) REVERT: A 1327 HIS cc_start: 0.7464 (m90) cc_final: 0.6390 (t70) REVERT: B 68 ASP cc_start: 0.7109 (p0) cc_final: 0.6427 (t0) REVERT: B 243 MET cc_start: 0.7933 (ttm) cc_final: 0.7197 (ttm) REVERT: B 689 MET cc_start: 0.5762 (mmt) cc_final: 0.5271 (mmt) REVERT: B 719 MET cc_start: 0.9013 (mmm) cc_final: 0.8624 (tpp) REVERT: B 763 ASP cc_start: 0.8334 (m-30) cc_final: 0.7964 (m-30) REVERT: B 794 MET cc_start: 0.8202 (tmm) cc_final: 0.7827 (mmt) REVERT: B 883 MET cc_start: 0.8060 (mpp) cc_final: 0.7708 (mpp) REVERT: B 926 ASP cc_start: 0.8414 (m-30) cc_final: 0.8112 (m-30) REVERT: B 929 MET cc_start: 0.7670 (tpt) cc_final: 0.7371 (tpt) REVERT: B 1015 MET cc_start: 0.8152 (mtp) cc_final: 0.7736 (mmm) REVERT: B 1050 MET cc_start: 0.7412 (pmm) cc_final: 0.6995 (pmm) REVERT: C 56 MET cc_start: 0.8678 (tmm) cc_final: 0.7637 (tmm) REVERT: C 255 ARG cc_start: 0.8484 (mmt-90) cc_final: 0.7893 (ttm110) REVERT: D 22 ASP cc_start: 0.7266 (m-30) cc_final: 0.7012 (m-30) REVERT: D 26 GLN cc_start: 0.8300 (tp40) cc_final: 0.7949 (tp-100) REVERT: D 90 ARG cc_start: 0.4070 (mtm-85) cc_final: 0.1606 (tpt170) REVERT: E 27 LEU cc_start: 0.8533 (mt) cc_final: 0.8218 (mt) REVERT: G 90 LYS cc_start: 0.5670 (mmtm) cc_final: 0.4632 (ttpt) REVERT: G 106 ASP cc_start: 0.8191 (p0) cc_final: 0.7082 (t70) REVERT: G 119 LYS cc_start: 0.3200 (mttt) cc_final: 0.2520 (tmtt) REVERT: G 201 TRP cc_start: 0.6878 (p-90) cc_final: 0.6351 (p-90) REVERT: H 48 TYR cc_start: 0.8815 (t80) cc_final: 0.8585 (t80) REVERT: H 64 LEU cc_start: 0.8583 (tp) cc_final: 0.8335 (tt) REVERT: H 74 GLU cc_start: 0.7667 (pp20) cc_final: 0.7352 (pp20) REVERT: H 107 GLU cc_start: 0.6143 (mp0) cc_final: 0.5088 (pt0) REVERT: H 118 TYR cc_start: 0.7861 (m-80) cc_final: 0.7182 (m-80) REVERT: H 123 MET cc_start: 0.8524 (tmm) cc_final: 0.8046 (tmm) REVERT: I 15 GLU cc_start: 0.7687 (tp30) cc_final: 0.7014 (tp30) REVERT: K 46 GLU cc_start: 0.7736 (tm-30) cc_final: 0.7335 (tm-30) REVERT: K 102 GLU cc_start: 0.7738 (tp30) cc_final: 0.6957 (tp30) REVERT: L 44 MET cc_start: 0.8901 (mmm) cc_final: 0.8529 (mmt) REVERT: M 292 MET cc_start: 0.8965 (tpt) cc_final: 0.8085 (mmm) REVERT: M 357 MET cc_start: 0.8810 (mtm) cc_final: 0.8492 (mtt) REVERT: M 383 LYS cc_start: 0.7421 (tttm) cc_final: 0.7178 (tptp) REVERT: N 256 ARG cc_start: 0.8610 (mtt180) cc_final: 0.8286 (ttp80) REVERT: N 341 LEU cc_start: 0.9037 (tp) cc_final: 0.8765 (tt) REVERT: N 373 MET cc_start: 0.6909 (mpp) cc_final: 0.6064 (mpp) REVERT: O 8 LEU cc_start: 0.9371 (tp) cc_final: 0.9133 (tp) REVERT: O 20 ILE cc_start: 0.9022 (pt) cc_final: 0.8769 (tt) REVERT: O 85 MET cc_start: 0.8414 (ptt) cc_final: 0.8165 (ptp) REVERT: O 338 LEU cc_start: 0.8710 (mm) cc_final: 0.8296 (mp) REVERT: O 398 MET cc_start: 0.8142 (ttm) cc_final: 0.7518 (ttp) REVERT: O 404 MET cc_start: 0.8485 (mtm) cc_final: 0.7986 (mtm) REVERT: P 90 ASN cc_start: 0.5940 (p0) cc_final: 0.5455 (m110) REVERT: P 203 MET cc_start: 0.7590 (mtt) cc_final: 0.7337 (ptm) REVERT: P 210 PHE cc_start: 0.7877 (m-10) cc_final: 0.7532 (m-10) REVERT: P 297 HIS cc_start: 0.7597 (t-90) cc_final: 0.7262 (t-90) REVERT: Q 111 MET cc_start: 0.7452 (mpp) cc_final: 0.7191 (tpt) REVERT: 1 46 MET cc_start: 0.3735 (ptm) cc_final: 0.3250 (tmm) REVERT: 3 49 GLU cc_start: 0.4482 (mp0) cc_final: 0.4155 (pp20) REVERT: 3 136 PHE cc_start: 0.6240 (m-80) cc_final: 0.5459 (t80) REVERT: 3 204 MET cc_start: 0.5875 (mtt) cc_final: 0.5593 (mtp) REVERT: 4 348 GLU cc_start: 0.5008 (tp30) cc_final: 0.4783 (mm-30) REVERT: 4 377 TYR cc_start: 0.4712 (t80) cc_final: 0.4201 (t80) REVERT: 4 389 TYR cc_start: 0.0880 (m-10) cc_final: 0.0523 (m-80) REVERT: U 214 PHE cc_start: 0.3041 (m-80) cc_final: 0.2663 (m-80) REVERT: V 130 ASN cc_start: 0.7941 (m-40) cc_final: 0.7674 (m-40) REVERT: V 135 MET cc_start: 0.8955 (mtt) cc_final: 0.8453 (mtt) REVERT: W 307 GLU cc_start: 0.7277 (tt0) cc_final: 0.6891 (tt0) REVERT: W 345 GLU cc_start: 0.7393 (mt-10) cc_final: 0.7151 (mt-10) REVERT: W 375 LEU cc_start: 0.6291 (mt) cc_final: 0.5784 (tt) outliers start: 2 outliers final: 0 residues processed: 449 average time/residue: 0.5648 time to fit residues: 439.7870 Evaluate side-chains 372 residues out of total 6068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 372 time to evaluate : 5.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 690 random chunks: chunk 335 optimal weight: 20.0000 chunk 434 optimal weight: 8.9990 chunk 583 optimal weight: 20.0000 chunk 167 optimal weight: 10.0000 chunk 504 optimal weight: 10.0000 chunk 80 optimal weight: 0.9990 chunk 152 optimal weight: 0.9990 chunk 548 optimal weight: 0.0470 chunk 229 optimal weight: 1.9990 chunk 562 optimal weight: 10.0000 chunk 69 optimal weight: 0.8980 overall best weight: 0.9884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1039 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1062 ASN ** C 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 81 GLN ** I 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.092829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.069827 restraints weight = 216905.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.069087 restraints weight = 154601.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.069115 restraints weight = 129069.468| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3225 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3225 r_free = 0.3225 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 83 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3225 r_free = 0.3225 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 83 | |-----------------------------------------------------------------------------| r_final: 0.3225 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.4933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 59344 Z= 0.158 Angle : 0.553 12.575 80728 Z= 0.284 Chirality : 0.042 0.315 8984 Planarity : 0.004 0.064 9896 Dihedral : 15.247 179.671 9118 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 0.02 % Allowed : 0.18 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.10), residues: 6809 helix: 1.21 (0.10), residues: 2745 sheet: -0.73 (0.19), residues: 742 loop : -0.84 (0.11), residues: 3322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP G 201 HIS 0.008 0.001 HIS M 44 PHE 0.016 0.001 PHE V 402 TYR 0.026 0.001 TYR B1003 ARG 0.013 0.000 ARG N 369 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10037.16 seconds wall clock time: 179 minutes 54.28 seconds (10794.28 seconds total)