Starting phenix.real_space_refine on Thu Jun 26 11:22:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f1i_28797/06_2025/8f1i_28797.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f1i_28797/06_2025/8f1i_28797.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8f1i_28797/06_2025/8f1i_28797.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f1i_28797/06_2025/8f1i_28797.map" model { file = "/net/cci-nas-00/data/ceres_data/8f1i_28797/06_2025/8f1i_28797.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f1i_28797/06_2025/8f1i_28797.cif" } resolution = 3.0 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= 0.006 sd= 1.056 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 91 5.49 5 Mg 1 5.21 5 S 119 5.16 5 C 18953 2.51 5 N 5402 2.21 5 O 6102 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 30670 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 679 Classifications: {'DNA': 33} Link IDs: {'rna3p': 32} Chain: "C" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 250 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Chain: "G" Number of atoms: 1718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1718 Classifications: {'peptide': 223} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 213} Chain breaks: 1 Chain: "H" Number of atoms: 2282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2282 Classifications: {'peptide': 295} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 281} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 10450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1327, 10450 Classifications: {'peptide': 1327} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1270} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 10498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1349, 10498 Classifications: {'peptide': 1349} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1293} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "K" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "M" Number of atoms: 3222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3222 Classifications: {'peptide': 405} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 387} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 671 Classifications: {'DNA': 33} Link IDs: {'rna3p': 32} Chain: "D" Number of atoms: 262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 262 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Chain: "J" 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: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 15935 SG CYS J 70 46.409 121.167 79.332 1.00 53.39 S ATOM 15949 SG CYS J 72 47.500 124.806 78.997 1.00 64.74 S ATOM 16057 SG CYS J 85 44.299 123.580 77.275 1.00 77.40 S ATOM 16081 SG CYS J 88 47.810 122.223 76.210 1.00 64.45 S ATOM 21769 SG CYS J 814 36.188 53.884 76.523 1.00 75.93 S ATOM 22334 SG CYS J 888 39.144 56.335 76.304 1.00 50.81 S ATOM 22385 SG CYS J 895 37.583 55.458 79.676 1.00 54.52 S ATOM 22406 SG CYS J 898 39.609 52.900 77.892 1.00 71.63 S Time building chain proxies: 16.77, per 1000 atoms: 0.55 Number of scatterers: 30670 At special positions: 0 Unit cell: (151.62, 174.363, 165.699, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 119 16.00 P 91 15.00 Mg 1 11.99 O 6102 8.00 N 5402 7.00 C 18953 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: 9.45 Conformation dependent library (CDL) restraints added in 4.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 70 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 88 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 72 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 85 " pdb=" ZN J1503 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 895 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 898 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 888 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 814 " Number of angles added : 12 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6830 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 49 sheets defined 40.0% alpha, 14.8% beta 42 base pairs and 75 stacking pairs defined. Time for finding SS restraints: 14.13 Creating SS restraints... Processing helix chain 'G' and resid 34 through 50 removed outlier: 3.610A pdb=" N ASN G 41 " --> pdb=" O HIS G 37 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA G 42 " --> pdb=" O THR G 38 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 87 removed outlier: 3.998A pdb=" N GLY G 87 " --> pdb=" O LEU G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'G' and resid 212 through 234 removed outlier: 4.651A pdb=" N ALA G 230 " --> pdb=" O GLU G 226 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N PHE G 231 " --> pdb=" O GLN G 227 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL G 232 " --> pdb=" O LEU G 228 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ASP G 233 " --> pdb=" O GLU G 229 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU G 234 " --> pdb=" O ALA G 230 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 50 removed outlier: 3.586A pdb=" N THR H 38 " --> pdb=" O GLY H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 87 Processing helix chain 'H' and resid 113 through 115 No H-bonds generated for 'chain 'H' and resid 113 through 115' Processing helix chain 'H' and resid 212 through 227 Processing helix chain 'H' and resid 250 through 255 removed outlier: 3.630A pdb=" N LEU H 254 " --> pdb=" O ASP H 250 " (cutoff:3.500A) Processing helix chain 'H' and resid 256 through 260 Processing helix chain 'H' and resid 263 through 273 Processing helix chain 'H' and resid 277 through 284 removed outlier: 3.694A pdb=" N GLN H 283 " --> pdb=" O GLY H 279 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG H 284 " --> pdb=" O ASP H 280 " (cutoff:3.500A) Processing helix chain 'H' and resid 285 through 291 Processing helix chain 'H' and resid 296 through 309 Processing helix chain 'I' and resid 6 through 10 Processing helix chain 'I' and resid 28 through 40 removed outlier: 3.740A pdb=" N LEU I 32 " --> pdb=" O LEU I 28 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS I 37 " --> pdb=" O ASP I 33 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE I 38 " --> pdb=" O SER I 34 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 55 Processing helix chain 'I' and resid 81 through 89 Processing helix chain 'I' and resid 206 through 213 removed outlier: 4.055A pdb=" N LEU I 210 " --> pdb=" O ALA I 206 " (cutoff:3.500A) Processing helix chain 'I' and resid 216 through 225 Processing helix chain 'I' and resid 242 through 247 removed outlier: 3.536A pdb=" N LEU I 246 " --> pdb=" O PRO I 243 " (cutoff:3.500A) Processing helix chain 'I' and resid 270 through 281 Processing helix chain 'I' and resid 288 through 294 removed outlier: 4.453A pdb=" N GLY I 294 " --> pdb=" O TYR I 291 " (cutoff:3.500A) Processing helix chain 'I' and resid 318 through 328 removed outlier: 3.834A pdb=" N SER I 328 " --> pdb=" O LYS I 324 " (cutoff:3.500A) Processing helix chain 'I' and resid 346 through 354 removed outlier: 3.568A pdb=" N ARG I 352 " --> pdb=" O SER I 348 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL I 353 " --> pdb=" O GLU I 349 " (cutoff:3.500A) Processing helix chain 'I' and resid 360 through 371 removed outlier: 3.540A pdb=" N VAL I 364 " --> pdb=" O LEU I 360 " (cutoff:3.500A) Processing helix chain 'I' and resid 377 through 390 removed outlier: 4.017A pdb=" N PHE I 389 " --> pdb=" O PHE I 385 " (cutoff:3.500A) Processing helix chain 'I' and resid 398 through 409 Processing helix chain 'I' and resid 421 through 438 Processing helix chain 'I' and resid 455 through 480 removed outlier: 3.735A pdb=" N ARG I 470 " --> pdb=" O VAL I 466 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER I 480 " --> pdb=" O LYS I 476 " (cutoff:3.500A) Processing helix chain 'I' and resid 488 through 493 removed outlier: 3.817A pdb=" N MET I 492 " --> pdb=" O MET I 488 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE I 493 " --> pdb=" O PRO I 489 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 488 through 493' Processing helix chain 'I' and resid 495 through 508 Processing helix chain 'I' and resid 519 through 527 removed outlier: 3.662A pdb=" N GLU I 523 " --> pdb=" O ASN I 519 " (cutoff:3.500A) Processing helix chain 'I' and resid 551 through 555 removed outlier: 3.878A pdb=" N TYR I 555 " --> pdb=" O PRO I 552 " (cutoff:3.500A) Processing helix chain 'I' and resid 608 through 612 removed outlier: 3.761A pdb=" N GLY I 612 " --> pdb=" O ALA I 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 608 through 612' Processing helix chain 'I' and resid 663 through 667 removed outlier: 3.690A pdb=" N LEU I 667 " --> pdb=" O GLY I 664 " (cutoff:3.500A) Processing helix chain 'I' and resid 670 through 674 Processing helix chain 'I' and resid 675 through 686 removed outlier: 3.614A pdb=" N LEU I 680 " --> pdb=" O ALA I 676 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N MET I 681 " --> pdb=" O ASN I 677 " (cutoff:3.500A) Processing helix chain 'I' and resid 704 through 712 Processing helix chain 'I' and resid 738 through 741 removed outlier: 3.900A pdb=" N MET I 741 " --> pdb=" O GLU I 738 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 738 through 741' Processing helix chain 'I' and resid 820 through 825 Processing helix chain 'I' and resid 896 through 907 removed outlier: 3.608A pdb=" N PHE I 906 " --> pdb=" O LEU I 902 " (cutoff:3.500A) Processing helix chain 'I' and resid 942 through 982 removed outlier: 3.532A pdb=" N GLU I 949 " --> pdb=" O ALA I 945 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLN I 955 " --> pdb=" O MET I 951 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ALA I 956 " --> pdb=" O GLN I 952 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS I 957 " --> pdb=" O LEU I 953 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS I 958 " --> pdb=" O LYS I 954 " (cutoff:3.500A) Processing helix chain 'I' and resid 987 through 992 removed outlier: 3.692A pdb=" N LYS I 991 " --> pdb=" O GLU I 987 " (cutoff:3.500A) Processing helix chain 'I' and resid 1011 through 1037 removed outlier: 3.646A pdb=" N TYR I1018 " --> pdb=" O LEU I1014 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASP I1019 " --> pdb=" O ALA I1015 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU I1029 " --> pdb=" O PHE I1025 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS I1035 " --> pdb=" O ALA I1031 " (cutoff:3.500A) Processing helix chain 'I' and resid 1081 through 1085 Processing helix chain 'I' and resid 1099 through 1101 No H-bonds generated for 'chain 'I' and resid 1099 through 1101' Processing helix chain 'I' and resid 1102 through 1107 removed outlier: 3.539A pdb=" N ARG I1106 " --> pdb=" O GLY I1102 " (cutoff:3.500A) Processing helix chain 'I' and resid 1109 through 1134 removed outlier: 3.532A pdb=" N ILE I1124 " --> pdb=" O ALA I1120 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS I1127 " --> pdb=" O GLY I1123 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLN I1134 " --> pdb=" O ALA I1130 " (cutoff:3.500A) Processing helix chain 'I' and resid 1137 through 1151 removed outlier: 3.515A pdb=" N LEU I1151 " --> pdb=" O ARG I1147 " (cutoff:3.500A) Processing helix chain 'I' and resid 1160 through 1164 removed outlier: 3.928A pdb=" N THR I1163 " --> pdb=" O ASP I1160 " (cutoff:3.500A) Processing helix chain 'I' and resid 1165 through 1176 Processing helix chain 'I' and resid 1191 through 1202 removed outlier: 3.578A pdb=" N LYS I1196 " --> pdb=" O GLU I1192 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU I1197 " --> pdb=" O ALA I1193 " (cutoff:3.500A) Processing helix chain 'I' and resid 1271 through 1282 Processing helix chain 'I' and resid 1283 through 1290 removed outlier: 3.537A pdb=" N LEU I1287 " --> pdb=" O ALA I1283 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N MET I1290 " --> pdb=" O THR I1286 " (cutoff:3.500A) Processing helix chain 'I' and resid 1297 through 1310 removed outlier: 4.133A pdb=" N THR I1302 " --> pdb=" O VAL I1298 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS I1303 " --> pdb=" O ASN I1299 " (cutoff:3.500A) Processing helix chain 'I' and resid 1320 through 1331 removed outlier: 4.238A pdb=" N ASN I1324 " --> pdb=" O PRO I1320 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL I1325 " --> pdb=" O GLU I1321 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU I1326 " --> pdb=" O SER I1322 " (cutoff:3.500A) Processing helix chain 'J' and resid 4 through 10 Processing helix chain 'J' and resid 26 through 33 Processing helix chain 'J' and resid 58 through 63 removed outlier: 3.808A pdb=" N PHE J 62 " --> pdb=" O CYS J 58 " (cutoff:3.500A) Processing helix chain 'J' and resid 77 through 81 Processing helix chain 'J' and resid 94 through 100 removed outlier: 3.682A pdb=" N VAL J 97 " --> pdb=" O GLN J 94 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG J 98 " --> pdb=" O THR J 95 " (cutoff:3.500A) Processing helix chain 'J' and resid 114 through 119 removed outlier: 3.677A pdb=" N SER J 119 " --> pdb=" O TRP J 115 " (cutoff:3.500A) Processing helix chain 'J' and resid 122 through 129 Processing helix chain 'J' and resid 131 through 140 Processing helix chain 'J' and resid 161 through 172 Processing helix chain 'J' and resid 181 through 191 removed outlier: 3.606A pdb=" N ILE J 185 " --> pdb=" O GLY J 181 " (cutoff:3.500A) Processing helix chain 'J' and resid 193 through 208 removed outlier: 3.607A pdb=" N GLU J 197 " --> pdb=" O ASP J 193 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR J 208 " --> pdb=" O GLU J 204 " (cutoff:3.500A) Processing helix chain 'J' and resid 211 through 230 removed outlier: 3.523A pdb=" N ARG J 220 " --> pdb=" O LYS J 216 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU J 223 " --> pdb=" O LYS J 219 " (cutoff:3.500A) Processing helix chain 'J' and resid 233 through 236 Processing helix chain 'J' and resid 246 through 250 Processing helix chain 'J' and resid 263 through 286 Processing helix chain 'J' and resid 288 through 308 Processing helix chain 'J' and resid 326 through 332 Processing helix chain 'J' and resid 336 through 342 removed outlier: 3.691A pdb=" N LEU J 342 " --> pdb=" O PHE J 338 " (cutoff:3.500A) Processing helix chain 'J' and resid 372 through 377 Processing helix chain 'J' and resid 377 through 388 removed outlier: 3.565A pdb=" N ARG J 388 " --> pdb=" O LYS J 384 " (cutoff:3.500A) Processing helix chain 'J' and resid 393 through 404 Processing helix chain 'J' and resid 407 through 416 Processing helix chain 'J' and resid 430 through 432 No H-bonds generated for 'chain 'J' and resid 430 through 432' Processing helix chain 'J' and resid 450 through 452 No H-bonds generated for 'chain 'J' and resid 450 through 452' Processing helix chain 'J' and resid 453 through 458 removed outlier: 3.546A pdb=" N TYR J 457 " --> pdb=" O VAL J 453 " (cutoff:3.500A) Processing helix chain 'J' and resid 475 through 483 removed outlier: 3.515A pdb=" N ARG J 481 " --> pdb=" O GLN J 477 " (cutoff:3.500A) Processing helix chain 'J' and resid 504 through 514 removed outlier: 3.757A pdb=" N GLY J 509 " --> pdb=" O ASP J 505 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU J 510 " --> pdb=" O VAL J 506 " (cutoff:3.500A) Processing helix chain 'J' and resid 529 through 539 Processing helix chain 'J' and resid 574 through 581 removed outlier: 3.772A pdb=" N MET J 581 " --> pdb=" O ALA J 577 " (cutoff:3.500A) Processing helix chain 'J' and resid 588 through 592 Processing helix chain 'J' and resid 598 through 612 removed outlier: 3.519A pdb=" N SER J 602 " --> pdb=" O LYS J 598 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N MET J 604 " --> pdb=" O ALA J 600 " (cutoff:3.500A) Processing helix chain 'J' and resid 614 through 636 removed outlier: 3.884A pdb=" N GLY J 636 " --> pdb=" O ALA J 632 " (cutoff:3.500A) Processing helix chain 'J' and resid 649 through 670 Processing helix chain 'J' and resid 674 through 702 Processing helix chain 'J' and resid 720 through 728 Processing helix chain 'J' and resid 733 through 742 removed outlier: 3.579A pdb=" N ILE J 737 " --> pdb=" O SER J 733 " (cutoff:3.500A) Processing helix chain 'J' and resid 774 through 804 removed outlier: 5.351A pdb=" N ALA J 791 " --> pdb=" O ALA J 787 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ASN J 792 " --> pdb=" O LEU J 788 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER J 793 " --> pdb=" O LYS J 789 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLY J 794 " --> pdb=" O THR J 790 " (cutoff:3.500A) Processing helix chain 'J' and resid 865 through 875 Processing helix chain 'J' and resid 896 through 900 removed outlier: 3.868A pdb=" N GLY J 900 " --> pdb=" O ALA J 896 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 896 through 900' Processing helix chain 'J' and resid 914 through 925 removed outlier: 3.814A pdb=" N ILE J 918 " --> pdb=" O ALA J 914 " (cutoff:3.500A) Processing helix chain 'J' and resid 926 through 930 removed outlier: 3.761A pdb=" N LEU J 930 " --> pdb=" O GLY J 927 " (cutoff:3.500A) Processing helix chain 'J' and resid 1137 through 1145 removed outlier: 3.610A pdb=" N VAL J1141 " --> pdb=" O GLY J1137 " (cutoff:3.500A) Processing helix chain 'J' and resid 1216 through 1225 Processing helix chain 'J' and resid 1228 through 1243 removed outlier: 4.090A pdb=" N VAL J1234 " --> pdb=" O THR J1230 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN J1238 " --> pdb=" O VAL J1234 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL J1240 " --> pdb=" O GLU J1236 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU J1243 " --> pdb=" O ASP J1239 " (cutoff:3.500A) Processing helix chain 'J' and resid 1250 through 1261 removed outlier: 3.787A pdb=" N ILE J1256 " --> pdb=" O HIS J1252 " (cutoff:3.500A) Processing helix chain 'J' and resid 1282 through 1294 removed outlier: 3.559A pdb=" N LEU J1292 " --> pdb=" O ALA J1288 " (cutoff:3.500A) Processing helix chain 'J' and resid 1319 through 1324 removed outlier: 3.594A pdb=" N SER J1324 " --> pdb=" O ILE J1320 " (cutoff:3.500A) Processing helix chain 'J' and resid 1327 through 1337 removed outlier: 3.775A pdb=" N GLU J1334 " --> pdb=" O ARG J1330 " (cutoff:3.500A) Processing helix chain 'J' and resid 1348 through 1354 Processing helix chain 'J' and resid 1362 through 1373 Processing helix chain 'K' and resid 6 through 14 Processing helix chain 'K' and resid 15 through 32 removed outlier: 4.085A pdb=" N VAL K 20 " --> pdb=" O ARG K 16 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU K 21 " --> pdb=" O PHE K 17 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 56 removed outlier: 3.625A pdb=" N GLU K 56 " --> pdb=" O ARG K 52 " (cutoff:3.500A) Processing helix chain 'K' and resid 60 through 80 Processing helix chain 'M' and resid 18 through 25 removed outlier: 3.638A pdb=" N ALA M 22 " --> pdb=" O GLN M 18 " (cutoff:3.500A) Processing helix chain 'M' and resid 29 through 43 removed outlier: 3.910A pdb=" N GLN M 39 " --> pdb=" O GLN M 35 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA M 40 " --> pdb=" O GLU M 36 " (cutoff:3.500A) Processing helix chain 'M' and resid 119 through 129 Processing helix chain 'M' and resid 134 through 147 Processing helix chain 'M' and resid 157 through 166 removed outlier: 4.008A pdb=" N GLY M 166 " --> pdb=" O LEU M 162 " (cutoff:3.500A) Processing helix chain 'M' and resid 171 through 183 removed outlier: 3.667A pdb=" N VAL M 175 " --> pdb=" O ASP M 171 " (cutoff:3.500A) Processing helix chain 'M' and resid 194 through 206 removed outlier: 3.521A pdb=" N GLN M 205 " --> pdb=" O ILE M 201 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE M 206 " --> pdb=" O GLN M 202 " (cutoff:3.500A) Processing helix chain 'M' and resid 212 through 222 removed outlier: 3.561A pdb=" N ILE M 219 " --> pdb=" O GLU M 215 " (cutoff:3.500A) Processing helix chain 'M' and resid 224 through 229 Processing helix chain 'M' and resid 231 through 240 Processing helix chain 'M' and resid 242 through 255 removed outlier: 3.887A pdb=" N VAL M 250 " --> pdb=" O LEU M 246 " (cutoff:3.500A) Processing helix chain 'M' and resid 259 through 263 removed outlier: 3.604A pdb=" N GLN M 262 " --> pdb=" O ARG M 259 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N SER M 263 " --> pdb=" O PRO M 260 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 259 through 263' Processing helix chain 'M' and resid 300 through 305 Processing helix chain 'M' and resid 313 through 351 removed outlier: 4.366A pdb=" N ILE M 319 " --> pdb=" O ASP M 315 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASP M 325 " --> pdb=" O SER M 321 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR M 339 " --> pdb=" O SER M 335 " (cutoff:3.500A) Processing helix chain 'M' and resid 351 through 357 removed outlier: 3.813A pdb=" N PHE M 355 " --> pdb=" O GLN M 351 " (cutoff:3.500A) Processing helix chain 'M' and resid 366 through 371 Processing helix chain 'M' and resid 377 through 385 Processing helix chain 'M' and resid 417 through 429 removed outlier: 3.779A pdb=" N ALA M 422 " --> pdb=" O THR M 418 " (cutoff:3.500A) Processing helix chain 'M' and resid 438 through 447 removed outlier: 3.502A pdb=" N LEU M 445 " --> pdb=" O LYS M 441 " (cutoff:3.500A) Processing helix chain 'M' and resid 454 through 465 Processing helix chain 'M' and resid 469 through 473 Processing sheet with id=AA1, first strand: chain 'G' and resid 12 through 20 removed outlier: 3.517A pdb=" N GLU G 29 " --> pdb=" O ARG G 12 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N THR G 27 " --> pdb=" O VAL G 14 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ILE G 16 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LYS G 25 " --> pdb=" O ILE G 16 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N GLN G 18 " --> pdb=" O HIS G 23 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N HIS G 23 " --> pdb=" O GLN G 18 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N LYS G 25 " --> pdb=" O MET G 205 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N MET G 205 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N THR G 27 " --> pdb=" O ILE G 203 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ILE G 203 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N GLU G 29 " --> pdb=" O LEU G 201 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N LEU G 201 " --> pdb=" O GLU G 29 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 97 through 105 removed outlier: 3.775A pdb=" N GLU G 58 " --> pdb=" O LYS G 145 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N GLN G 147 " --> pdb=" O VAL G 56 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N VAL G 56 " --> pdb=" O GLN G 147 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N GLY G 149 " --> pdb=" O CYS G 54 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N CYS G 54 " --> pdb=" O GLY G 149 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 90 through 91 Processing sheet with id=AA4, first strand: chain 'G' and resid 108 through 111 removed outlier: 3.689A pdb=" N CYS G 131 " --> pdb=" O VAL G 110 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 152 through 153 Processing sheet with id=AA6, first strand: chain 'H' and resid 17 through 18 removed outlier: 6.004A pdb=" N ASP H 199 " --> pdb=" O PRO H 30 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA H 190 " --> pdb=" O LEU H 198 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG H 182 " --> pdb=" O GLU H 206 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 97 through 101 removed outlier: 6.719A pdb=" N ARG H 143 " --> pdb=" O VAL H 59 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N VAL H 59 " --> pdb=" O ARG H 143 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N LYS H 145 " --> pdb=" O THR H 57 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 104 through 105 Processing sheet with id=AA9, first strand: chain 'H' and resid 109 through 111 Processing sheet with id=AB1, first strand: chain 'H' and resid 152 through 153 Processing sheet with id=AB2, first strand: chain 'I' and resid 13 through 14 removed outlier: 6.513A pdb=" N LYS I 13 " --> pdb=" O ALA I1183 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'I' and resid 59 through 60 removed outlier: 3.668A pdb=" N GLU I 67 " --> pdb=" O VAL I 103 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG I 101 " --> pdb=" O GLN I 69 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N LYS I 99 " --> pdb=" O VAL I 71 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N TYR I 73 " --> pdb=" O ARG I 97 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ARG I 97 " --> pdb=" O TYR I 73 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N LEU I 75 " --> pdb=" O PRO I 95 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N ALA I 94 " --> pdb=" O GLU I 126 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N GLU I 126 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N LEU I 96 " --> pdb=" O MET I 124 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASP I 116 " --> pdb=" O ILE I 104 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 136 through 137 Processing sheet with id=AB5, first strand: chain 'I' and resid 451 through 454 Processing sheet with id=AB6, first strand: chain 'I' and resid 154 through 155 removed outlier: 3.543A pdb=" N LEU I 184 " --> pdb=" O ILE I 176 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 284 through 286 removed outlier: 3.719A pdb=" N GLU I 240 " --> pdb=" O ILE I 229 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N ILE I 229 " --> pdb=" O GLU I 240 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 255 through 257 removed outlier: 7.348A pdb=" N ILE I 255 " --> pdb=" O TYR I 262 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR I 262 " --> pdb=" O ILE I 255 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 301 through 302 removed outlier: 7.301A pdb=" N TYR I 301 " --> pdb=" O ILE I 310 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 580 through 581 removed outlier: 4.948A pdb=" N GLU I 602 " --> pdb=" O LYS I 593 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N THR I 595 " --> pdb=" O THR I 600 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N THR I 600 " --> pdb=" O THR I 595 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 580 through 581 Processing sheet with id=AC3, first strand: chain 'I' and resid 616 through 617 Processing sheet with id=AC4, first strand: chain 'I' and resid 716 through 717 removed outlier: 6.405A pdb=" N ALA I 716 " --> pdb=" O LEU I 783 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 748 through 752 removed outlier: 6.814A pdb=" N ARG I 731 " --> pdb=" O VAL I 727 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N VAL I 727 " --> pdb=" O ARG I 731 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL I 733 " --> pdb=" O GLN I 725 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 757 through 758 Processing sheet with id=AC7, first strand: chain 'I' and resid 789 through 790 Processing sheet with id=AC8, first strand: chain 'I' and resid 1209 through 1210 removed outlier: 7.393A pdb=" N ILE I 816 " --> pdb=" O SER I1077 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ILE I1079 " --> pdb=" O ILE I 816 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N VAL I 818 " --> pdb=" O ILE I1079 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU I 817 " --> pdb=" O VAL I1097 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N ILE I1096 " --> pdb=" O ASN I 799 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ARG I 801 " --> pdb=" O ILE I1096 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N LEU I1098 " --> pdb=" O ARG I 801 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ALA I 803 " --> pdb=" O LEU I1098 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 830 through 841 removed outlier: 3.870A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ALA I1055 " --> pdb=" O VAL I 928 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N VAL I 928 " --> pdb=" O ALA I1055 " (cutoff:3.500A) removed outlier: 8.423A pdb=" N LYS I1057 " --> pdb=" O GLY I 926 " (cutoff:3.500A) removed outlier: 8.901A pdb=" N GLY I 926 " --> pdb=" O LYS I1057 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 849 through 850 Processing sheet with id=AD2, first strand: chain 'I' and resid 882 through 884 removed outlier: 6.748A pdb=" N LEU I 918 " --> pdb=" O LEU I 883 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 1268 through 1270 removed outlier: 3.748A pdb=" N GLN I1268 " --> pdb=" O VAL J 347 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 1335 through 1340 removed outlier: 3.873A pdb=" N ALA J 19 " --> pdb=" O GLU I1340 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 34 through 37 removed outlier: 7.695A pdb=" N HIS J 104 " --> pdb=" O PHE J 35 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N GLU J 37 " --> pdb=" O HIS J 104 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N GLU J 106 " --> pdb=" O GLU J 37 " (cutoff:3.500A) removed outlier: 10.013A pdb=" N LEU J 107 " --> pdb=" O PRO J 243 " (cutoff:3.500A) removed outlier: 10.455A pdb=" N SER J 109 " --> pdb=" O VAL J 241 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N VAL J 241 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 159 through 160 Processing sheet with id=AD7, first strand: chain 'J' and resid 253 through 255 removed outlier: 3.768A pdb=" N VAL J 253 " --> pdb=" O ALA J 261 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA J 261 " --> pdb=" O VAL J 253 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG J 259 " --> pdb=" O LEU J 255 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 350 through 357 removed outlier: 6.563A pdb=" N CYS J 366 " --> pdb=" O VAL J 440 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ILE J 442 " --> pdb=" O CYS J 366 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N LEU J 368 " --> pdb=" O ILE J 442 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 547 through 557 Processing sheet with id=AE1, first strand: chain 'J' and resid 703 through 707 Processing sheet with id=AE2, first strand: chain 'J' and resid 809 through 811 Processing sheet with id=AE3, first strand: chain 'J' and resid 820 through 822 removed outlier: 3.676A pdb=" N VAL J 880 " --> pdb=" O MET J 822 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 825 through 826 removed outlier: 7.155A pdb=" N VAL J 825 " --> pdb=" O LYS J 832 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 949 through 951 removed outlier: 3.921A pdb=" N ALA J1018 " --> pdb=" O ILE J 950 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU J 973 " --> pdb=" O LEU J1003 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 957 through 961 removed outlier: 3.539A pdb=" N LEU J 984 " --> pdb=" O GLU J 993 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLU J 993 " --> pdb=" O LEU J 984 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 1035 through 1038 removed outlier: 3.530A pdb=" N LYS J1079 " --> pdb=" O ARG J1036 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR J1038 " --> pdb=" O ALA J1077 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA J1077 " --> pdb=" O THR J1038 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 1046 through 1048 removed outlier: 5.118A pdb=" N LEU J1059 " --> pdb=" O VAL J1107 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL J1107 " --> pdb=" O LEU J1059 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 1187 through 1190 removed outlier: 3.627A pdb=" N GLU J1188 " --> pdb=" O LEU J1175 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 3.729A pdb=" N VAL J1267 " --> pdb=" O THR J1301 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N THR J1301 " --> pdb=" O VAL J1267 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'M' and resid 47 through 48 Processing sheet with id=AF3, first strand: chain 'M' and resid 284 through 289 removed outlier: 6.879A pdb=" N VAL M 276 " --> pdb=" O HIS M 391 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'M' and resid 406 through 408 1131 hydrogen bonds defined for protein. 3180 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 100 hydrogen bonds 200 hydrogen bond angles 0 basepair planarities 42 basepair parallelities 75 stacking parallelities Total time for adding SS restraints: 24.42 Time building geometry restraints manager: 9.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 9285 1.33 - 1.45: 4371 1.45 - 1.57: 17264 1.57 - 1.69: 178 1.69 - 1.81: 206 Bond restraints: 31304 Sorted by residual: bond pdb=" C LEU I1201 " pdb=" N GLY I1202 " ideal model delta sigma weight residual 1.332 1.348 -0.016 6.60e-03 2.30e+04 5.81e+00 bond pdb=" C GLU J 925 " pdb=" N PRO J 926 " ideal model delta sigma weight residual 1.334 1.351 -0.017 8.40e-03 1.42e+04 4.33e+00 bond pdb=" N PRO I 345 " pdb=" CA PRO I 345 " ideal model delta sigma weight residual 1.469 1.484 -0.016 1.28e-02 6.10e+03 1.48e+00 bond pdb=" C ASP J1184 " pdb=" N PRO J1185 " ideal model delta sigma weight residual 1.334 1.361 -0.028 2.34e-02 1.83e+03 1.39e+00 bond pdb=" C3' DC A 24 " pdb=" O3' DC A 24 " ideal model delta sigma weight residual 1.422 1.457 -0.035 3.00e-02 1.11e+03 1.36e+00 ... (remaining 31299 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 41679 1.41 - 2.81: 847 2.81 - 4.22: 126 4.22 - 5.63: 26 5.63 - 7.03: 4 Bond angle restraints: 42682 Sorted by residual: angle pdb=" N VAL I 21 " pdb=" CA VAL I 21 " pdb=" C VAL I 21 " ideal model delta sigma weight residual 113.53 109.48 4.05 9.80e-01 1.04e+00 1.71e+01 angle pdb=" N VAL J1226 " pdb=" CA VAL J1226 " pdb=" C VAL J1226 " ideal model delta sigma weight residual 111.90 108.95 2.95 8.10e-01 1.52e+00 1.33e+01 angle pdb=" C ASP J 902 " pdb=" N LEU J 903 " pdb=" CA LEU J 903 " ideal model delta sigma weight residual 121.54 128.49 -6.95 1.91e+00 2.74e-01 1.33e+01 angle pdb=" N ASN I 235 " pdb=" CA ASN I 235 " pdb=" C ASN I 235 " ideal model delta sigma weight residual 108.46 113.75 -5.29 1.51e+00 4.39e-01 1.23e+01 angle pdb=" N VAL J 253 " pdb=" CA VAL J 253 " pdb=" C VAL J 253 " ideal model delta sigma weight residual 107.56 110.69 -3.13 9.10e-01 1.21e+00 1.19e+01 ... (remaining 42677 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.04: 18465 35.04 - 70.08: 576 70.08 - 105.12: 14 105.12 - 140.16: 0 140.16 - 175.21: 1 Dihedral angle restraints: 19056 sinusoidal: 8466 harmonic: 10590 Sorted by residual: dihedral pdb=" CA ASP J1184 " pdb=" C ASP J1184 " pdb=" N PRO J1185 " pdb=" CA PRO J1185 " ideal model delta harmonic sigma weight residual -180.00 -152.89 -27.11 0 5.00e+00 4.00e-02 2.94e+01 dihedral pdb=" CA LYS I 236 " pdb=" C LYS I 236 " pdb=" N LEU I 237 " pdb=" CA LEU I 237 " ideal model delta harmonic sigma weight residual 180.00 154.89 25.11 0 5.00e+00 4.00e-02 2.52e+01 dihedral pdb=" CA SER I1295 " pdb=" C SER I1295 " pdb=" N ASP I1296 " pdb=" CA ASP I1296 " ideal model delta harmonic sigma weight residual 180.00 -156.41 -23.59 0 5.00e+00 4.00e-02 2.23e+01 ... (remaining 19053 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 3031 0.031 - 0.062: 1286 0.062 - 0.092: 343 0.092 - 0.123: 210 0.123 - 0.154: 24 Chirality restraints: 4894 Sorted by residual: chirality pdb=" CA GLN J 504 " pdb=" N GLN J 504 " pdb=" C GLN J 504 " pdb=" CB GLN J 504 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.94e-01 chirality pdb=" CA ILE J1090 " pdb=" N ILE J1090 " pdb=" C ILE J1090 " pdb=" CB ILE J1090 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.17e-01 chirality pdb=" CA ILE J 434 " pdb=" N ILE J 434 " pdb=" C ILE J 434 " pdb=" CB ILE J 434 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 5.00e-01 ... (remaining 4891 not shown) Planarity restraints: 5264 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS J 850 " 0.030 5.00e-02 4.00e+02 4.59e-02 3.37e+00 pdb=" N PRO J 851 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO J 851 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO J 851 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR I 896 " 0.029 5.00e-02 4.00e+02 4.41e-02 3.12e+00 pdb=" N PRO I 897 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO I 897 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO I 897 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU H 29 " -0.027 5.00e-02 4.00e+02 4.08e-02 2.66e+00 pdb=" N PRO H 30 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO H 30 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO H 30 " -0.021 5.00e-02 4.00e+02 ... (remaining 5261 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1074 2.72 - 3.26: 28799 3.26 - 3.81: 46423 3.81 - 4.35: 60634 4.35 - 4.90: 104191 Nonbonded interactions: 241121 Sorted by model distance: nonbonded pdb=" OD1 ASP J 462 " pdb="MG MG J1501 " model vdw 2.170 2.170 nonbonded pdb=" OG1 THR I 851 " pdb=" OD1 ASP I 853 " model vdw 2.187 3.040 nonbonded pdb=" OD1 ASN J1268 " pdb=" OG1 THR J1301 " model vdw 2.188 3.040 nonbonded pdb=" O GLY G 34 " pdb=" OG1 THR G 38 " model vdw 2.206 3.040 nonbonded pdb=" OH TYR I 179 " pdb=" OE2 GLU I 458 " model vdw 2.219 3.040 ... (remaining 241116 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.050 Check model and map are aligned: 0.200 Set scattering table: 0.260 Process input model: 98.850 Find NCS groups from input model: 1.220 Set up NCS constraints: 0.140 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:74.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 177.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 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 0.035 31312 Z= 0.126 Angle : 0.529 8.497 42694 Z= 0.306 Chirality : 0.041 0.154 4894 Planarity : 0.004 0.046 5264 Dihedral : 14.605 175.205 12226 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.89 % Allowed : 5.97 % Favored : 93.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % 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: -1.10 (0.14), residues: 3652 helix: 0.02 (0.15), residues: 1353 sheet: -0.32 (0.25), residues: 449 loop : -1.39 (0.13), residues: 1850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP J 409 HIS 0.004 0.001 HIS J 104 PHE 0.011 0.001 PHE I1164 TYR 0.011 0.001 TYR I 123 ARG 0.004 0.000 ARG J 860 Details of bonding type rmsd hydrogen bonds : bond 0.16820 ( 1229) hydrogen bonds : angle 5.97199 ( 3380) metal coordination : bond 0.00546 ( 8) metal coordination : angle 3.08021 ( 12) covalent geometry : bond 0.00252 (31304) covalent geometry : angle 0.52610 (42682) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 162 time to evaluate : 7.232 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 1085 MET cc_start: 0.8925 (mmm) cc_final: 0.8645 (mmm) REVERT: K 43 ASN cc_start: 0.7574 (t0) cc_final: 0.7330 (t0) REVERT: M 15 MET cc_start: 0.7941 (mmm) cc_final: 0.7713 (mmm) outliers start: 28 outliers final: 3 residues processed: 189 average time/residue: 2.2047 time to fit residues: 487.0327 Evaluate side-chains 129 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 126 time to evaluate : 3.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain M residue 203 LEU Chi-restraints excluded: chain M residue 254 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 314 optimal weight: 10.0000 chunk 281 optimal weight: 7.9990 chunk 156 optimal weight: 9.9990 chunk 96 optimal weight: 0.7980 chunk 190 optimal weight: 7.9990 chunk 150 optimal weight: 6.9990 chunk 291 optimal weight: 9.9990 chunk 112 optimal weight: 10.0000 chunk 177 optimal weight: 8.9990 chunk 217 optimal weight: 10.0000 chunk 337 optimal weight: 0.8980 overall best weight: 4.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 137 ASN H 147 GLN H 268 ASN M 262 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.066665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.041017 restraints weight = 102726.766| |-----------------------------------------------------------------------------| r_work (start): 0.2652 rms_B_bonded: 3.30 r_work: 0.2484 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 31312 Z= 0.252 Angle : 0.586 8.339 42694 Z= 0.313 Chirality : 0.043 0.160 4894 Planarity : 0.004 0.056 5264 Dihedral : 15.593 173.502 5026 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.46 % Allowed : 9.22 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % 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: -0.62 (0.14), residues: 3652 helix: 0.59 (0.15), residues: 1381 sheet: -0.21 (0.25), residues: 440 loop : -1.23 (0.14), residues: 1831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 328 HIS 0.005 0.001 HIS J1366 PHE 0.010 0.001 PHE I 405 TYR 0.012 0.001 TYR J 679 ARG 0.006 0.000 ARG I 272 Details of bonding type rmsd hydrogen bonds : bond 0.05061 ( 1229) hydrogen bonds : angle 4.42186 ( 3380) metal coordination : bond 0.01519 ( 8) metal coordination : angle 3.63877 ( 12) covalent geometry : bond 0.00580 (31304) covalent geometry : angle 0.58291 (42682) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 138 time to evaluate : 3.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 93 GLN cc_start: 0.8976 (tm-30) cc_final: 0.8748 (tm-30) REVERT: H 75 GLN cc_start: 0.8759 (tm-30) cc_final: 0.8326 (tm-30) REVERT: H 93 GLN cc_start: 0.7928 (mm110) cc_final: 0.7701 (mm110) REVERT: H 268 ASN cc_start: 0.9405 (m110) cc_final: 0.9141 (p0) REVERT: I 542 ARG cc_start: 0.8734 (OUTLIER) cc_final: 0.8314 (mtt-85) REVERT: J 393 THR cc_start: 0.8812 (OUTLIER) cc_final: 0.8386 (p) REVERT: J 999 TYR cc_start: 0.8937 (t80) cc_final: 0.8693 (t80) REVERT: J 1025 MET cc_start: 0.9067 (mpt) cc_final: 0.8587 (ppp) REVERT: J 1100 PHE cc_start: 0.8458 (m-10) cc_final: 0.8178 (m-80) REVERT: J 1189 MET cc_start: 0.6907 (tmm) cc_final: 0.6697 (tpt) REVERT: K 18 ASP cc_start: 0.9009 (m-30) cc_final: 0.8787 (m-30) REVERT: K 43 ASN cc_start: 0.8610 (t0) cc_final: 0.7952 (t0) REVERT: M 15 MET cc_start: 0.8271 (mmm) cc_final: 0.7905 (mmm) REVERT: M 376 MET cc_start: 0.9302 (mtp) cc_final: 0.9085 (mtp) outliers start: 46 outliers final: 10 residues processed: 171 average time/residue: 1.5714 time to fit residues: 315.7454 Evaluate side-chains 144 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 132 time to evaluate : 3.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain I residue 413 GLU Chi-restraints excluded: chain I residue 542 ARG Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 685 MET Chi-restraints excluded: chain I residue 896 THR Chi-restraints excluded: chain J residue 180 MET Chi-restraints excluded: chain J residue 393 THR Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain M residue 254 GLN Chi-restraints excluded: chain M residue 407 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 32 optimal weight: 20.0000 chunk 200 optimal weight: 3.9990 chunk 138 optimal weight: 6.9990 chunk 51 optimal weight: 7.9990 chunk 346 optimal weight: 3.9990 chunk 293 optimal weight: 8.9990 chunk 171 optimal weight: 6.9990 chunk 303 optimal weight: 7.9990 chunk 270 optimal weight: 3.9990 chunk 275 optimal weight: 10.0000 chunk 13 optimal weight: 0.9980 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 103 ASN H 147 GLN I1116 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.066572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.040998 restraints weight = 103172.539| |-----------------------------------------------------------------------------| r_work (start): 0.2654 rms_B_bonded: 3.31 r_work: 0.2485 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 31312 Z= 0.205 Angle : 0.540 7.380 42694 Z= 0.288 Chirality : 0.042 0.225 4894 Planarity : 0.004 0.045 5264 Dihedral : 15.514 174.609 5024 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.62 % Allowed : 10.45 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % 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: -0.31 (0.14), residues: 3652 helix: 0.95 (0.15), residues: 1385 sheet: -0.12 (0.25), residues: 447 loop : -1.14 (0.14), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 328 HIS 0.004 0.001 HIS I 273 PHE 0.010 0.001 PHE I 136 TYR 0.013 0.001 TYR M 112 ARG 0.012 0.000 ARG I 272 Details of bonding type rmsd hydrogen bonds : bond 0.04439 ( 1229) hydrogen bonds : angle 4.20922 ( 3380) metal coordination : bond 0.01292 ( 8) metal coordination : angle 3.34686 ( 12) covalent geometry : bond 0.00476 (31304) covalent geometry : angle 0.53718 (42682) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 139 time to evaluate : 4.451 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 93 GLN cc_start: 0.8994 (tm-30) cc_final: 0.8735 (tm-30) REVERT: H 75 GLN cc_start: 0.8825 (tm-30) cc_final: 0.8385 (tm-30) REVERT: H 93 GLN cc_start: 0.8031 (mm110) cc_final: 0.7757 (mm110) REVERT: H 117 HIS cc_start: 0.9316 (t-90) cc_final: 0.8686 (t-90) REVERT: H 142 MET cc_start: 0.9070 (pmm) cc_final: 0.8825 (pmm) REVERT: H 294 ASN cc_start: 0.9178 (m110) cc_final: 0.8669 (t0) REVERT: I 239 MET cc_start: 0.7308 (OUTLIER) cc_final: 0.7086 (tmm) REVERT: I 542 ARG cc_start: 0.8822 (OUTLIER) cc_final: 0.8583 (mtt-85) REVERT: I 1107 MET cc_start: 0.9187 (OUTLIER) cc_final: 0.8879 (mtp) REVERT: J 172 PHE cc_start: 0.6349 (m-80) cc_final: 0.6117 (m-80) REVERT: J 1100 PHE cc_start: 0.8457 (m-10) cc_final: 0.8134 (m-80) REVERT: K 18 ASP cc_start: 0.9025 (m-30) cc_final: 0.8801 (m-30) REVERT: K 43 ASN cc_start: 0.8637 (t0) cc_final: 0.8027 (t0) REVERT: M 15 MET cc_start: 0.8452 (mmm) cc_final: 0.7905 (mmm) REVERT: M 236 MET cc_start: 0.9332 (mtp) cc_final: 0.9118 (mmt) REVERT: M 376 MET cc_start: 0.9232 (mtp) cc_final: 0.8897 (mtp) outliers start: 51 outliers final: 12 residues processed: 180 average time/residue: 1.5530 time to fit residues: 334.8294 Evaluate side-chains 149 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 134 time to evaluate : 3.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain I residue 239 MET Chi-restraints excluded: chain I residue 413 GLU Chi-restraints excluded: chain I residue 542 ARG Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 685 MET Chi-restraints excluded: chain I residue 896 THR Chi-restraints excluded: chain I residue 1107 MET Chi-restraints excluded: chain J residue 88 CYS Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 1198 VAL Chi-restraints excluded: chain M residue 390 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 100 optimal weight: 1.9990 chunk 343 optimal weight: 7.9990 chunk 241 optimal weight: 9.9990 chunk 133 optimal weight: 8.9990 chunk 206 optimal weight: 6.9990 chunk 119 optimal weight: 8.9990 chunk 150 optimal weight: 8.9990 chunk 207 optimal weight: 9.9990 chunk 243 optimal weight: 5.9990 chunk 285 optimal weight: 20.0000 chunk 310 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 147 GLN H 268 ASN I 387 ASN J 489 ASN J1010 GLN J1023 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.065421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.039270 restraints weight = 105565.428| |-----------------------------------------------------------------------------| r_work (start): 0.2618 rms_B_bonded: 3.43 r_work: 0.2446 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 31312 Z= 0.289 Angle : 0.601 8.867 42694 Z= 0.317 Chirality : 0.044 0.204 4894 Planarity : 0.004 0.045 5264 Dihedral : 15.603 175.480 5021 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.91 % Allowed : 11.28 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % 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: -0.25 (0.14), residues: 3652 helix: 1.06 (0.15), residues: 1378 sheet: -0.21 (0.25), residues: 443 loop : -1.11 (0.14), residues: 1831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP M 328 HIS 0.004 0.001 HIS I 447 PHE 0.010 0.001 PHE J 172 TYR 0.020 0.001 TYR I 291 ARG 0.010 0.000 ARG I 272 Details of bonding type rmsd hydrogen bonds : bond 0.04959 ( 1229) hydrogen bonds : angle 4.30194 ( 3380) metal coordination : bond 0.01685 ( 8) metal coordination : angle 3.94378 ( 12) covalent geometry : bond 0.00673 (31304) covalent geometry : angle 0.59729 (42682) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 136 time to evaluate : 3.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 93 GLN cc_start: 0.9010 (tm-30) cc_final: 0.8650 (tm-30) REVERT: H 75 GLN cc_start: 0.8881 (tm-30) cc_final: 0.8425 (tm-30) REVERT: H 93 GLN cc_start: 0.8050 (mm110) cc_final: 0.7765 (mm110) REVERT: H 117 HIS cc_start: 0.9305 (t-90) cc_final: 0.8740 (t-90) REVERT: H 142 MET cc_start: 0.9046 (OUTLIER) cc_final: 0.8772 (pmm) REVERT: H 294 ASN cc_start: 0.9219 (m110) cc_final: 0.8714 (t0) REVERT: I 239 MET cc_start: 0.7389 (OUTLIER) cc_final: 0.7082 (tmm) REVERT: I 542 ARG cc_start: 0.8865 (OUTLIER) cc_final: 0.8625 (mtt-85) REVERT: I 1107 MET cc_start: 0.9242 (OUTLIER) cc_final: 0.9025 (mtp) REVERT: J 78 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8298 (tt) REVERT: J 161 THR cc_start: 0.8810 (OUTLIER) cc_final: 0.8518 (p) REVERT: J 180 MET cc_start: 0.8852 (OUTLIER) cc_final: 0.8502 (ttp) REVERT: J 1025 MET cc_start: 0.8887 (mmt) cc_final: 0.8087 (ppp) REVERT: J 1095 MET cc_start: 0.8882 (tmm) cc_final: 0.8665 (tpt) REVERT: K 18 ASP cc_start: 0.9051 (m-30) cc_final: 0.8831 (m-30) REVERT: K 43 ASN cc_start: 0.8741 (t0) cc_final: 0.8174 (t0) REVERT: M 15 MET cc_start: 0.8549 (mmm) cc_final: 0.7909 (mmm) REVERT: M 233 ARG cc_start: 0.8484 (tpm-80) cc_final: 0.8277 (tpm-80) REVERT: M 236 MET cc_start: 0.9325 (mtp) cc_final: 0.9118 (mmt) outliers start: 60 outliers final: 21 residues processed: 180 average time/residue: 1.4903 time to fit residues: 318.7309 Evaluate side-chains 161 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 133 time to evaluate : 3.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 142 MET Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain I residue 239 MET Chi-restraints excluded: chain I residue 413 GLU Chi-restraints excluded: chain I residue 542 ARG Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 643 SER Chi-restraints excluded: chain I residue 685 MET Chi-restraints excluded: chain I residue 896 THR Chi-restraints excluded: chain I residue 1107 MET Chi-restraints excluded: chain I residue 1138 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 88 CYS Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain J residue 180 MET Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 774 ILE Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 1173 ARG Chi-restraints excluded: chain J residue 1198 VAL Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain M residue 219 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 223 optimal weight: 0.8980 chunk 174 optimal weight: 3.9990 chunk 350 optimal weight: 3.9990 chunk 257 optimal weight: 9.9990 chunk 101 optimal weight: 2.9990 chunk 239 optimal weight: 2.9990 chunk 283 optimal weight: 30.0000 chunk 82 optimal weight: 10.0000 chunk 141 optimal weight: 1.9990 chunk 51 optimal weight: 8.9990 chunk 328 optimal weight: 9.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 127 GLN H 66 HIS H 103 ASN ** H 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 147 GLN I 628 HIS J 489 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.066752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.040671 restraints weight = 103052.987| |-----------------------------------------------------------------------------| r_work (start): 0.2665 rms_B_bonded: 3.42 r_work: 0.2495 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 31312 Z= 0.144 Angle : 0.514 10.765 42694 Z= 0.273 Chirality : 0.041 0.261 4894 Planarity : 0.003 0.047 5264 Dihedral : 15.435 175.253 5021 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.68 % Allowed : 12.27 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % 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 (0.14), residues: 3652 helix: 1.29 (0.15), residues: 1393 sheet: -0.03 (0.25), residues: 448 loop : -1.03 (0.14), residues: 1811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP M 328 HIS 0.003 0.001 HIS I 447 PHE 0.012 0.001 PHE J1100 TYR 0.026 0.001 TYR I 291 ARG 0.011 0.000 ARG I 272 Details of bonding type rmsd hydrogen bonds : bond 0.03888 ( 1229) hydrogen bonds : angle 4.02311 ( 3380) metal coordination : bond 0.00918 ( 8) metal coordination : angle 3.04240 ( 12) covalent geometry : bond 0.00333 (31304) covalent geometry : angle 0.51131 (42682) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 133 time to evaluate : 3.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 93 GLN cc_start: 0.9058 (tm-30) cc_final: 0.8821 (tm-30) REVERT: G 127 GLN cc_start: 0.9042 (OUTLIER) cc_final: 0.8809 (pm20) REVERT: H 93 GLN cc_start: 0.8223 (mm110) cc_final: 0.7945 (mm110) REVERT: H 117 HIS cc_start: 0.9297 (t-90) cc_final: 0.8723 (t-90) REVERT: H 142 MET cc_start: 0.9119 (OUTLIER) cc_final: 0.8914 (pmm) REVERT: H 294 ASN cc_start: 0.9237 (m110) cc_final: 0.8776 (t0) REVERT: I 239 MET cc_start: 0.7416 (tmm) cc_final: 0.7087 (tmm) REVERT: I 542 ARG cc_start: 0.8845 (OUTLIER) cc_final: 0.8592 (mtt-85) REVERT: I 1024 GLU cc_start: 0.9505 (OUTLIER) cc_final: 0.9114 (tp30) REVERT: I 1107 MET cc_start: 0.9182 (OUTLIER) cc_final: 0.8966 (mtp) REVERT: J 161 THR cc_start: 0.8749 (OUTLIER) cc_final: 0.8452 (p) REVERT: J 180 MET cc_start: 0.8831 (ptp) cc_final: 0.8528 (ttp) REVERT: J 740 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8621 (mp) REVERT: J 774 ILE cc_start: 0.7651 (OUTLIER) cc_final: 0.7333 (pt) REVERT: K 18 ASP cc_start: 0.9050 (m-30) cc_final: 0.8815 (m-30) REVERT: K 43 ASN cc_start: 0.8689 (t0) cc_final: 0.8176 (t0) REVERT: M 15 MET cc_start: 0.8514 (mmm) cc_final: 0.7919 (mmm) REVERT: M 236 MET cc_start: 0.9350 (mtp) cc_final: 0.9002 (mmt) outliers start: 53 outliers final: 13 residues processed: 178 average time/residue: 1.4976 time to fit residues: 316.8659 Evaluate side-chains 152 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 time to evaluate : 3.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 127 GLN Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 142 MET Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain I residue 542 ARG Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1024 GLU Chi-restraints excluded: chain I residue 1107 MET Chi-restraints excluded: chain J residue 88 CYS Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 774 ILE Chi-restraints excluded: chain J residue 862 THR Chi-restraints excluded: chain J residue 1173 ARG Chi-restraints excluded: chain J residue 1198 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 192 optimal weight: 0.5980 chunk 60 optimal weight: 0.9980 chunk 293 optimal weight: 40.0000 chunk 101 optimal weight: 0.9990 chunk 90 optimal weight: 9.9990 chunk 211 optimal weight: 0.6980 chunk 139 optimal weight: 6.9990 chunk 20 optimal weight: 9.9990 chunk 257 optimal weight: 9.9990 chunk 360 optimal weight: 3.9990 chunk 163 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 147 GLN ** I1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 489 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.067942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.042006 restraints weight = 103308.103| |-----------------------------------------------------------------------------| r_work (start): 0.2709 rms_B_bonded: 3.42 r_work: 0.2540 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 31312 Z= 0.095 Angle : 0.494 8.573 42694 Z= 0.260 Chirality : 0.040 0.190 4894 Planarity : 0.003 0.055 5264 Dihedral : 15.256 174.870 5021 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.40 % Allowed : 13.12 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % 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: 0.23 (0.14), residues: 3652 helix: 1.52 (0.15), residues: 1389 sheet: 0.05 (0.25), residues: 444 loop : -0.91 (0.14), residues: 1819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J1193 HIS 0.004 0.000 HIS G 128 PHE 0.010 0.001 PHE M 318 TYR 0.018 0.001 TYR H 68 ARG 0.010 0.000 ARG I 272 Details of bonding type rmsd hydrogen bonds : bond 0.03207 ( 1229) hydrogen bonds : angle 3.77823 ( 3380) metal coordination : bond 0.00462 ( 8) metal coordination : angle 2.21958 ( 12) covalent geometry : bond 0.00207 (31304) covalent geometry : angle 0.49282 (42682) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 134 time to evaluate : 3.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 93 GLN cc_start: 0.9073 (tm-30) cc_final: 0.8745 (tm-30) REVERT: H 93 GLN cc_start: 0.8207 (mm110) cc_final: 0.7915 (mm110) REVERT: H 117 HIS cc_start: 0.9325 (t-90) cc_final: 0.8791 (t-90) REVERT: H 142 MET cc_start: 0.9105 (OUTLIER) cc_final: 0.8872 (pmm) REVERT: H 294 ASN cc_start: 0.9204 (m110) cc_final: 0.8802 (t0) REVERT: I 239 MET cc_start: 0.7653 (OUTLIER) cc_final: 0.7402 (tmm) REVERT: I 542 ARG cc_start: 0.8788 (OUTLIER) cc_final: 0.8415 (mtt-85) REVERT: I 1024 GLU cc_start: 0.9493 (OUTLIER) cc_final: 0.9092 (tp30) REVERT: I 1107 MET cc_start: 0.9111 (OUTLIER) cc_final: 0.8883 (mtp) REVERT: J 161 THR cc_start: 0.8744 (OUTLIER) cc_final: 0.8451 (p) REVERT: J 180 MET cc_start: 0.8832 (ptp) cc_final: 0.8541 (ttp) REVERT: J 740 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8545 (mp) REVERT: J 774 ILE cc_start: 0.7366 (OUTLIER) cc_final: 0.7016 (pt) REVERT: J 1025 MET cc_start: 0.8854 (mmt) cc_final: 0.8197 (ppp) REVERT: J 1100 PHE cc_start: 0.8468 (m-80) cc_final: 0.8081 (t80) REVERT: K 18 ASP cc_start: 0.9091 (m-30) cc_final: 0.8857 (m-30) REVERT: K 43 ASN cc_start: 0.8663 (t0) cc_final: 0.8191 (t0) REVERT: K 72 GLN cc_start: 0.7994 (pp30) cc_final: 0.7473 (tm-30) REVERT: M 236 MET cc_start: 0.9312 (mtp) cc_final: 0.9025 (mmt) REVERT: M 254 GLN cc_start: 0.8971 (OUTLIER) cc_final: 0.8341 (mp10) outliers start: 44 outliers final: 14 residues processed: 170 average time/residue: 1.5194 time to fit residues: 303.1993 Evaluate side-chains 154 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 131 time to evaluate : 3.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 142 MET Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain I residue 62 TYR Chi-restraints excluded: chain I residue 239 MET Chi-restraints excluded: chain I residue 516 ASP Chi-restraints excluded: chain I residue 542 ARG Chi-restraints excluded: chain I residue 896 THR Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1024 GLU Chi-restraints excluded: chain I residue 1107 MET Chi-restraints excluded: chain J residue 88 CYS Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 774 ILE Chi-restraints excluded: chain J residue 862 THR Chi-restraints excluded: chain J residue 1173 ARG Chi-restraints excluded: chain J residue 1198 VAL Chi-restraints excluded: chain M residue 254 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 199 optimal weight: 0.5980 chunk 240 optimal weight: 9.9990 chunk 33 optimal weight: 0.9980 chunk 198 optimal weight: 0.9980 chunk 49 optimal weight: 8.9990 chunk 146 optimal weight: 9.9990 chunk 268 optimal weight: 8.9990 chunk 162 optimal weight: 1.9990 chunk 254 optimal weight: 5.9990 chunk 276 optimal weight: 5.9990 chunk 170 optimal weight: 3.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 147 GLN ** I1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 489 ASN J 805 GLN ** K 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.067580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.041741 restraints weight = 103187.500| |-----------------------------------------------------------------------------| r_work (start): 0.2697 rms_B_bonded: 3.41 r_work: 0.2529 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 31312 Z= 0.115 Angle : 0.502 11.191 42694 Z= 0.261 Chirality : 0.040 0.227 4894 Planarity : 0.003 0.048 5264 Dihedral : 15.264 174.705 5021 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.33 % Allowed : 13.31 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.14), residues: 3652 helix: 1.55 (0.15), residues: 1403 sheet: 0.06 (0.25), residues: 438 loop : -0.86 (0.14), residues: 1811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J1193 HIS 0.003 0.001 HIS J 865 PHE 0.015 0.001 PHE I 136 TYR 0.020 0.001 TYR M 112 ARG 0.008 0.000 ARG I 272 Details of bonding type rmsd hydrogen bonds : bond 0.03370 ( 1229) hydrogen bonds : angle 3.75519 ( 3380) metal coordination : bond 0.00668 ( 8) metal coordination : angle 2.37665 ( 12) covalent geometry : bond 0.00262 (31304) covalent geometry : angle 0.50044 (42682) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 136 time to evaluate : 3.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 93 GLN cc_start: 0.9113 (tm-30) cc_final: 0.8797 (tm-30) REVERT: H 66 HIS cc_start: 0.9057 (t-90) cc_final: 0.8442 (t70) REVERT: H 75 GLN cc_start: 0.8860 (pt0) cc_final: 0.8553 (pt0) REVERT: H 93 GLN cc_start: 0.8215 (mm110) cc_final: 0.7923 (mm110) REVERT: H 117 HIS cc_start: 0.9343 (t-90) cc_final: 0.8800 (t-90) REVERT: H 142 MET cc_start: 0.9142 (OUTLIER) cc_final: 0.8915 (pmm) REVERT: H 294 ASN cc_start: 0.9202 (m110) cc_final: 0.8809 (t0) REVERT: I 239 MET cc_start: 0.7701 (OUTLIER) cc_final: 0.7468 (tmm) REVERT: I 542 ARG cc_start: 0.8794 (OUTLIER) cc_final: 0.8424 (mtt-85) REVERT: I 1024 GLU cc_start: 0.9493 (OUTLIER) cc_final: 0.9129 (tm-30) REVERT: J 161 THR cc_start: 0.8787 (OUTLIER) cc_final: 0.8485 (p) REVERT: J 180 MET cc_start: 0.8822 (ptp) cc_final: 0.8519 (ttp) REVERT: J 740 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8575 (mp) REVERT: J 774 ILE cc_start: 0.7490 (OUTLIER) cc_final: 0.7171 (pt) REVERT: J 1025 MET cc_start: 0.8819 (mmt) cc_final: 0.8118 (ppp) REVERT: J 1100 PHE cc_start: 0.8459 (m-80) cc_final: 0.8014 (t80) REVERT: K 18 ASP cc_start: 0.9062 (m-30) cc_final: 0.8796 (m-30) REVERT: K 43 ASN cc_start: 0.8671 (t0) cc_final: 0.8172 (t0) REVERT: M 15 MET cc_start: 0.8347 (mmm) cc_final: 0.8146 (mmm) REVERT: M 112 TYR cc_start: 0.7034 (t80) cc_final: 0.6820 (t80) REVERT: M 236 MET cc_start: 0.9372 (mtp) cc_final: 0.9089 (mmt) outliers start: 42 outliers final: 19 residues processed: 169 average time/residue: 1.5971 time to fit residues: 319.7845 Evaluate side-chains 160 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 134 time to evaluate : 3.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 142 MET Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 239 MET Chi-restraints excluded: chain I residue 516 ASP Chi-restraints excluded: chain I residue 542 ARG Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 896 THR Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1024 GLU Chi-restraints excluded: chain I residue 1339 LEU Chi-restraints excluded: chain J residue 88 CYS Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 489 ASN Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 774 ILE Chi-restraints excluded: chain J residue 805 GLN Chi-restraints excluded: chain J residue 862 THR Chi-restraints excluded: chain J residue 1173 ARG Chi-restraints excluded: chain J residue 1198 VAL Chi-restraints excluded: chain K residue 75 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 73 optimal weight: 3.9990 chunk 310 optimal weight: 3.9990 chunk 227 optimal weight: 0.0770 chunk 260 optimal weight: 0.1980 chunk 160 optimal weight: 5.9990 chunk 270 optimal weight: 5.9990 chunk 306 optimal weight: 2.9990 chunk 355 optimal weight: 6.9990 chunk 56 optimal weight: 9.9990 chunk 197 optimal weight: 1.9990 chunk 181 optimal weight: 5.9990 overall best weight: 1.8544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1023 HIS J 489 ASN J 805 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.067572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.041667 restraints weight = 103668.242| |-----------------------------------------------------------------------------| r_work (start): 0.2696 rms_B_bonded: 3.40 r_work: 0.2527 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 31312 Z= 0.119 Angle : 0.514 11.148 42694 Z= 0.265 Chirality : 0.040 0.267 4894 Planarity : 0.003 0.053 5264 Dihedral : 15.257 174.878 5021 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.08 % Allowed : 13.89 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % 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: 0.35 (0.14), residues: 3652 helix: 1.60 (0.15), residues: 1404 sheet: 0.08 (0.25), residues: 438 loop : -0.83 (0.14), residues: 1810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J1193 HIS 0.002 0.000 HIS J 865 PHE 0.009 0.001 PHE I 405 TYR 0.015 0.001 TYR M 112 ARG 0.010 0.000 ARG M 233 Details of bonding type rmsd hydrogen bonds : bond 0.03348 ( 1229) hydrogen bonds : angle 3.72719 ( 3380) metal coordination : bond 0.00686 ( 8) metal coordination : angle 2.34994 ( 12) covalent geometry : bond 0.00273 (31304) covalent geometry : angle 0.51223 (42682) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 138 time to evaluate : 3.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 93 GLN cc_start: 0.9119 (tm-30) cc_final: 0.8800 (tm-30) REVERT: H 66 HIS cc_start: 0.9034 (t-90) cc_final: 0.8353 (t70) REVERT: H 75 GLN cc_start: 0.8895 (pt0) cc_final: 0.8544 (pt0) REVERT: H 93 GLN cc_start: 0.8231 (mm110) cc_final: 0.7912 (mm110) REVERT: H 117 HIS cc_start: 0.9344 (t-90) cc_final: 0.8782 (t-90) REVERT: H 142 MET cc_start: 0.9094 (OUTLIER) cc_final: 0.8851 (pmm) REVERT: H 250 ASP cc_start: 0.8361 (OUTLIER) cc_final: 0.7676 (t0) REVERT: H 294 ASN cc_start: 0.9234 (m110) cc_final: 0.8870 (t0) REVERT: I 239 MET cc_start: 0.7568 (OUTLIER) cc_final: 0.7203 (tmm) REVERT: I 542 ARG cc_start: 0.8804 (OUTLIER) cc_final: 0.8436 (mtt-85) REVERT: I 1024 GLU cc_start: 0.9481 (OUTLIER) cc_final: 0.9141 (tm-30) REVERT: J 161 THR cc_start: 0.8801 (OUTLIER) cc_final: 0.8501 (p) REVERT: J 180 MET cc_start: 0.8830 (ptp) cc_final: 0.8529 (ttp) REVERT: J 740 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8591 (mp) REVERT: J 762 ASN cc_start: 0.9336 (OUTLIER) cc_final: 0.9041 (p0) REVERT: J 774 ILE cc_start: 0.7516 (OUTLIER) cc_final: 0.7203 (pt) REVERT: J 1100 PHE cc_start: 0.8406 (m-80) cc_final: 0.8064 (t80) REVERT: K 18 ASP cc_start: 0.9051 (m-30) cc_final: 0.8792 (m-30) REVERT: K 43 ASN cc_start: 0.8680 (t0) cc_final: 0.8174 (t0) REVERT: M 112 TYR cc_start: 0.7066 (t80) cc_final: 0.6811 (t80) outliers start: 34 outliers final: 16 residues processed: 168 average time/residue: 1.6054 time to fit residues: 317.9270 Evaluate side-chains 159 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 134 time to evaluate : 3.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 142 MET Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 250 ASP Chi-restraints excluded: chain I residue 239 MET Chi-restraints excluded: chain I residue 516 ASP Chi-restraints excluded: chain I residue 542 ARG Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 896 THR Chi-restraints excluded: chain I residue 979 LEU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1024 GLU Chi-restraints excluded: chain I residue 1339 LEU Chi-restraints excluded: chain J residue 88 CYS Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 762 ASN Chi-restraints excluded: chain J residue 774 ILE Chi-restraints excluded: chain J residue 862 THR Chi-restraints excluded: chain J residue 1169 THR Chi-restraints excluded: chain J residue 1173 ARG Chi-restraints excluded: chain J residue 1198 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 150 optimal weight: 8.9990 chunk 97 optimal weight: 4.9990 chunk 71 optimal weight: 0.0770 chunk 120 optimal weight: 1.9990 chunk 355 optimal weight: 6.9990 chunk 325 optimal weight: 6.9990 chunk 273 optimal weight: 2.9990 chunk 370 optimal weight: 8.9990 chunk 238 optimal weight: 7.9990 chunk 343 optimal weight: 10.0000 chunk 324 optimal weight: 2.9990 overall best weight: 2.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 127 GLN G 132 HIS ** H 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 147 GLN I1023 HIS J 489 ASN J 805 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.067081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.041004 restraints weight = 103331.808| |-----------------------------------------------------------------------------| r_work (start): 0.2677 rms_B_bonded: 3.41 r_work: 0.2506 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 31312 Z= 0.147 Angle : 0.535 13.795 42694 Z= 0.275 Chirality : 0.041 0.304 4894 Planarity : 0.003 0.050 5264 Dihedral : 15.315 175.051 5021 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.14 % Allowed : 14.20 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % 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: 0.38 (0.14), residues: 3652 helix: 1.63 (0.15), residues: 1402 sheet: 0.07 (0.25), residues: 438 loop : -0.80 (0.14), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J1193 HIS 0.005 0.001 HIS I 273 PHE 0.011 0.001 PHE I 230 TYR 0.015 0.001 TYR M 112 ARG 0.011 0.000 ARG I 272 Details of bonding type rmsd hydrogen bonds : bond 0.03626 ( 1229) hydrogen bonds : angle 3.77165 ( 3380) metal coordination : bond 0.00897 ( 8) metal coordination : angle 2.66546 ( 12) covalent geometry : bond 0.00343 (31304) covalent geometry : angle 0.53354 (42682) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 136 time to evaluate : 3.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 93 GLN cc_start: 0.9125 (tm-30) cc_final: 0.8795 (tm-30) REVERT: H 66 HIS cc_start: 0.9056 (t-90) cc_final: 0.8357 (t70) REVERT: H 75 GLN cc_start: 0.8982 (pt0) cc_final: 0.8635 (pt0) REVERT: H 93 GLN cc_start: 0.8251 (mm110) cc_final: 0.7947 (mm110) REVERT: H 117 HIS cc_start: 0.9349 (t-90) cc_final: 0.8847 (t-90) REVERT: H 142 MET cc_start: 0.9087 (OUTLIER) cc_final: 0.8841 (pmm) REVERT: H 250 ASP cc_start: 0.8423 (OUTLIER) cc_final: 0.7766 (t0) REVERT: H 294 ASN cc_start: 0.9214 (m110) cc_final: 0.8860 (t0) REVERT: I 239 MET cc_start: 0.7346 (OUTLIER) cc_final: 0.6555 (tmt) REVERT: I 542 ARG cc_start: 0.8848 (OUTLIER) cc_final: 0.8469 (mtt-85) REVERT: I 1024 GLU cc_start: 0.9485 (OUTLIER) cc_final: 0.9157 (tm-30) REVERT: J 161 THR cc_start: 0.8827 (OUTLIER) cc_final: 0.8513 (p) REVERT: J 180 MET cc_start: 0.8851 (ptp) cc_final: 0.8531 (ttp) REVERT: J 740 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8605 (mp) REVERT: J 762 ASN cc_start: 0.9340 (OUTLIER) cc_final: 0.9072 (p0) REVERT: J 774 ILE cc_start: 0.7619 (OUTLIER) cc_final: 0.7281 (pt) REVERT: J 1025 MET cc_start: 0.9098 (mpm) cc_final: 0.8558 (ppp) REVERT: J 1100 PHE cc_start: 0.8396 (m-80) cc_final: 0.8092 (t80) REVERT: K 18 ASP cc_start: 0.9060 (m-30) cc_final: 0.8797 (m-30) REVERT: K 43 ASN cc_start: 0.8700 (t0) cc_final: 0.8198 (t0) REVERT: M 236 MET cc_start: 0.9349 (mtt) cc_final: 0.9066 (mmt) REVERT: M 306 MET cc_start: 0.9080 (mtt) cc_final: 0.8702 (mpt) outliers start: 36 outliers final: 18 residues processed: 166 average time/residue: 1.7073 time to fit residues: 335.4454 Evaluate side-chains 162 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 135 time to evaluate : 3.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 142 MET Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 250 ASP Chi-restraints excluded: chain I residue 239 MET Chi-restraints excluded: chain I residue 542 ARG Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 896 THR Chi-restraints excluded: chain I residue 979 LEU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1024 GLU Chi-restraints excluded: chain I residue 1339 LEU Chi-restraints excluded: chain J residue 88 CYS Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 762 ASN Chi-restraints excluded: chain J residue 774 ILE Chi-restraints excluded: chain J residue 862 THR Chi-restraints excluded: chain J residue 1169 THR Chi-restraints excluded: chain J residue 1173 ARG Chi-restraints excluded: chain J residue 1198 VAL Chi-restraints excluded: chain K residue 75 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 141 optimal weight: 0.9990 chunk 335 optimal weight: 0.9990 chunk 208 optimal weight: 8.9990 chunk 322 optimal weight: 1.9990 chunk 371 optimal weight: 20.0000 chunk 72 optimal weight: 9.9990 chunk 260 optimal weight: 7.9990 chunk 9 optimal weight: 0.0570 chunk 357 optimal weight: 0.7980 chunk 142 optimal weight: 2.9990 chunk 362 optimal weight: 0.9990 overall best weight: 0.7704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 147 GLN I1023 HIS J 489 ASN J 805 GLN M 262 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.068425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.042652 restraints weight = 104745.831| |-----------------------------------------------------------------------------| r_work (start): 0.2722 rms_B_bonded: 3.41 r_work: 0.2557 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 31312 Z= 0.094 Angle : 0.516 15.154 42694 Z= 0.262 Chirality : 0.040 0.262 4894 Planarity : 0.003 0.048 5264 Dihedral : 15.195 175.253 5021 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.02 % Allowed : 14.27 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.14), residues: 3652 helix: 1.72 (0.15), residues: 1402 sheet: 0.01 (0.25), residues: 475 loop : -0.73 (0.15), residues: 1775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP J1193 HIS 0.003 0.000 HIS J 450 PHE 0.016 0.001 PHE I 230 TYR 0.033 0.001 TYR M 112 ARG 0.009 0.000 ARG M 233 Details of bonding type rmsd hydrogen bonds : bond 0.02957 ( 1229) hydrogen bonds : angle 3.61281 ( 3380) metal coordination : bond 0.00430 ( 8) metal coordination : angle 1.90207 ( 12) covalent geometry : bond 0.00211 (31304) covalent geometry : angle 0.51476 (42682) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 137 time to evaluate : 4.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 93 GLN cc_start: 0.9122 (tm-30) cc_final: 0.8814 (tm-30) REVERT: H 66 HIS cc_start: 0.9059 (t-90) cc_final: 0.8363 (t70) REVERT: H 75 GLN cc_start: 0.9015 (pt0) cc_final: 0.8715 (pt0) REVERT: H 93 GLN cc_start: 0.8249 (mm110) cc_final: 0.7947 (mm110) REVERT: H 142 MET cc_start: 0.9092 (OUTLIER) cc_final: 0.8844 (pmm) REVERT: H 250 ASP cc_start: 0.8331 (OUTLIER) cc_final: 0.7638 (t0) REVERT: H 294 ASN cc_start: 0.9203 (m110) cc_final: 0.8877 (t0) REVERT: I 239 MET cc_start: 0.7509 (OUTLIER) cc_final: 0.7238 (tmm) REVERT: I 542 ARG cc_start: 0.8818 (OUTLIER) cc_final: 0.8397 (mtt-85) REVERT: I 1024 GLU cc_start: 0.9485 (OUTLIER) cc_final: 0.9209 (tm-30) REVERT: J 161 THR cc_start: 0.8727 (OUTLIER) cc_final: 0.8396 (p) REVERT: J 180 MET cc_start: 0.8801 (ptp) cc_final: 0.8527 (ttp) REVERT: J 774 ILE cc_start: 0.7306 (OUTLIER) cc_final: 0.6882 (pt) REVERT: J 958 ILE cc_start: 0.9408 (mp) cc_final: 0.9093 (tp) REVERT: J 1025 MET cc_start: 0.9051 (mpm) cc_final: 0.8561 (ppp) REVERT: J 1100 PHE cc_start: 0.8385 (m-80) cc_final: 0.8065 (t80) REVERT: J 1370 MET cc_start: 0.9100 (OUTLIER) cc_final: 0.8832 (mtm) REVERT: K 18 ASP cc_start: 0.9037 (m-30) cc_final: 0.8778 (m-30) REVERT: K 43 ASN cc_start: 0.8599 (t0) cc_final: 0.8102 (t0) REVERT: M 15 MET cc_start: 0.7837 (mmm) cc_final: 0.7625 (mmp) REVERT: M 112 TYR cc_start: 0.7096 (t80) cc_final: 0.6894 (t80) REVERT: M 236 MET cc_start: 0.9366 (mtt) cc_final: 0.9090 (mmt) REVERT: M 306 MET cc_start: 0.9096 (mtt) cc_final: 0.8720 (mpt) outliers start: 32 outliers final: 17 residues processed: 163 average time/residue: 1.6689 time to fit residues: 322.5289 Evaluate side-chains 159 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 134 time to evaluate : 3.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 142 MET Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 250 ASP Chi-restraints excluded: chain I residue 239 MET Chi-restraints excluded: chain I residue 542 ARG Chi-restraints excluded: chain I residue 896 THR Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1024 GLU Chi-restraints excluded: chain I residue 1339 LEU Chi-restraints excluded: chain J residue 88 CYS Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 489 ASN Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 774 ILE Chi-restraints excluded: chain J residue 862 THR Chi-restraints excluded: chain J residue 1169 THR Chi-restraints excluded: chain J residue 1173 ARG Chi-restraints excluded: chain J residue 1198 VAL Chi-restraints excluded: chain J residue 1370 MET Chi-restraints excluded: chain K residue 75 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 61 optimal weight: 10.0000 chunk 277 optimal weight: 8.9990 chunk 317 optimal weight: 0.9980 chunk 325 optimal weight: 6.9990 chunk 311 optimal weight: 7.9990 chunk 360 optimal weight: 1.9990 chunk 171 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 293 optimal weight: 9.9990 chunk 89 optimal weight: 6.9990 chunk 44 optimal weight: 8.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 127 GLN ** H 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 490 GLN I1023 HIS J 489 ASN J 805 GLN M 262 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.067367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.041338 restraints weight = 103710.227| |-----------------------------------------------------------------------------| r_work (start): 0.2690 rms_B_bonded: 3.41 r_work: 0.2521 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 31312 Z= 0.143 Angle : 0.534 15.009 42694 Z= 0.272 Chirality : 0.041 0.248 4894 Planarity : 0.003 0.050 5264 Dihedral : 15.288 174.646 5021 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.95 % Allowed : 14.59 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % 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: 0.50 (0.14), residues: 3652 helix: 1.73 (0.15), residues: 1399 sheet: 0.10 (0.25), residues: 456 loop : -0.72 (0.14), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP J1193 HIS 0.003 0.001 HIS J 817 PHE 0.014 0.001 PHE I 230 TYR 0.031 0.001 TYR M 112 ARG 0.012 0.000 ARG M 233 Details of bonding type rmsd hydrogen bonds : bond 0.03497 ( 1229) hydrogen bonds : angle 3.68235 ( 3380) metal coordination : bond 0.00862 ( 8) metal coordination : angle 2.46904 ( 12) covalent geometry : bond 0.00334 (31304) covalent geometry : angle 0.53210 (42682) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 25305.23 seconds wall clock time: 446 minutes 24.35 seconds (26784.35 seconds total)