Starting phenix.real_space_refine on Thu Mar 21 21:04:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vt0_8732/03_2024/5vt0_8732.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vt0_8732/03_2024/5vt0_8732.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vt0_8732/03_2024/5vt0_8732.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vt0_8732/03_2024/5vt0_8732.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vt0_8732/03_2024/5vt0_8732.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vt0_8732/03_2024/5vt0_8732.pdb" } resolution = 3.78 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 112 5.49 5 Mg 1 5.21 5 S 128 5.16 5 C 19130 2.51 5 N 5525 2.21 5 O 6317 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "I ARG 268": "NH1" <-> "NH2" Residue "I ARG 332": "NH1" <-> "NH2" Residue "I PHE 1187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 1229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 1302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 31215 Number of models: 1 Model: "" Number of chains: 8 Chain: "G" Number of atoms: 1750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1750 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 9, 'TRANS': 218} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "H" Number of atoms: 1667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1667 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 8, 'TRANS': 208} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "I" Number of atoms: 10566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1340, 10566 Classifications: {'peptide': 1340} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 55, 'TRANS': 1280} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "J" Number of atoms: 10375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1334, 10375 Classifications: {'peptide': 1334} Link IDs: {'CIS': 1, 'PTRANS': 55, 'TRANS': 1277} Chain breaks: 2 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: "L" Number of atoms: 3839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3839 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 14, 'TRANS': 456} Chain breaks: 2 Chain: "R" Number of atoms: 2388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 2388 Classifications: {'RNA': 112} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 6, 'rna3p_pur': 48, 'rna3p_pyr': 48} Link IDs: {'rna2p': 16, 'rna3p': 95} Chain breaks: 1 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14432 SG CYS J 70 58.491 56.126 71.464 1.00 77.06 S ATOM 14446 SG CYS J 72 57.241 52.809 71.980 1.00 88.00 S ATOM 14554 SG CYS J 85 54.534 55.209 71.781 1.00 92.38 S ATOM 14578 SG CYS J 88 57.781 55.434 75.190 1.00 98.30 S ATOM 20831 SG CYS J 888 86.178 113.277 63.751 1.00 70.73 S ATOM 20882 SG CYS J 895 86.921 113.212 60.191 1.00 62.13 S ATOM 20903 SG CYS J 898 90.524 114.624 63.033 1.00 67.65 S Time building chain proxies: 16.50, per 1000 atoms: 0.53 Number of scatterers: 31215 At special positions: 0 Unit cell: (170.3, 170.3, 166.4, 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 128 16.00 P 112 15.00 Mg 1 11.99 O 6317 8.00 N 5525 7.00 C 19130 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.23 Conformation dependent library (CDL) restraints added in 5.3 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 72 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 88 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 85 " pdb=" ZN J1503 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 888 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 895 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 898 " Number of angles added : 6 7294 Ramachandran restraints generated. 3647 Oldfield, 0 Emsley, 3647 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6814 Finding SS restraints... Secondary structure from input PDB file: 127 helices and 48 sheets defined 42.0% alpha, 13.7% beta 31 base pairs and 54 stacking pairs defined. Time for finding SS restraints: 10.95 Creating SS restraints... Processing helix chain 'G' and resid 34 through 50 Processing helix chain 'G' and resid 77 through 87 removed outlier: 3.792A 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 154 through 159 removed outlier: 3.720A pdb=" N ARG G 158 " --> pdb=" O PRO G 154 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ILE G 159 " --> pdb=" O ALA G 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 154 through 159' Processing helix chain 'G' and resid 212 through 229 Processing helix chain 'H' and resid 34 through 50 removed outlier: 3.648A pdb=" N THR H 38 " --> pdb=" O GLY H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 86 removed outlier: 3.580A pdb=" N ILE H 81 " --> pdb=" O ASP H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 212 through 228 Processing helix chain 'I' and resid 28 through 39 Processing helix chain 'I' and resid 48 through 57 Processing helix chain 'I' and resid 81 through 89 Processing helix chain 'I' and resid 206 through 212 removed outlier: 4.082A 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 Processing helix chain 'I' and resid 270 through 280 removed outlier: 3.603A pdb=" N ILE I 274 " --> pdb=" O THR I 270 " (cutoff:3.500A) Processing helix chain 'I' and resid 290 through 294 removed outlier: 3.922A pdb=" N GLY I 294 " --> pdb=" O TYR I 291 " (cutoff:3.500A) Processing helix chain 'I' and resid 318 through 329 removed outlier: 3.738A pdb=" N GLY I 329 " --> pdb=" O LEU I 325 " (cutoff:3.500A) Processing helix chain 'I' and resid 345 through 354 Processing helix chain 'I' and resid 358 through 369 Processing helix chain 'I' and resid 377 through 390 removed outlier: 4.211A pdb=" N PHE I 389 " --> pdb=" O PHE I 385 " (cutoff:3.500A) Processing helix chain 'I' and resid 398 through 408 Processing helix chain 'I' and resid 421 through 437 Processing helix chain 'I' and resid 455 through 481 removed outlier: 4.234A pdb=" N ALA I 474 " --> pdb=" O ARG I 470 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU I 481 " --> pdb=" O GLU I 477 " (cutoff:3.500A) Processing helix chain 'I' and resid 495 through 508 removed outlier: 3.521A pdb=" N SER I 499 " --> pdb=" O ALA I 495 " (cutoff:3.500A) Processing helix chain 'I' and resid 519 through 527 Processing helix chain 'I' and resid 551 through 555 removed outlier: 3.773A pdb=" N TYR I 555 " --> pdb=" O PRO I 552 " (cutoff:3.500A) Processing helix chain 'I' and resid 662 through 667 removed outlier: 3.898A pdb=" N LEU I 667 " --> pdb=" O VAL I 663 " (cutoff:3.500A) Processing helix chain 'I' and resid 670 through 674 Processing helix chain 'I' and resid 675 through 686 Processing helix chain 'I' and resid 704 through 711 removed outlier: 3.532A pdb=" N VAL I 708 " --> pdb=" O MET I 704 " (cutoff:3.500A) Processing helix chain 'I' and resid 820 through 826 Processing helix chain 'I' and resid 858 through 863 Processing helix chain 'I' and resid 897 through 907 Processing helix chain 'I' and resid 942 through 981 removed outlier: 4.146A pdb=" N ALA I 981 " --> pdb=" O ALA I 977 " (cutoff:3.500A) Processing helix chain 'I' and resid 994 through 998 removed outlier: 3.589A pdb=" N LEU I 998 " --> pdb=" O ASP I 995 " (cutoff:3.500A) Processing helix chain 'I' and resid 1005 through 1038 removed outlier: 3.626A pdb=" N GLN I1038 " --> pdb=" O ARG I1034 " (cutoff:3.500A) Processing helix chain 'I' and resid 1081 through 1085 Processing helix chain 'I' and resid 1101 through 1106 removed outlier: 4.077A pdb=" N SER I1105 " --> pdb=" O LEU I1101 " (cutoff:3.500A) Processing helix chain 'I' and resid 1109 through 1134 removed outlier: 3.589A pdb=" N LEU I1113 " --> pdb=" O ILE I1109 " (cutoff:3.500A) Processing helix chain 'I' and resid 1137 through 1151 removed outlier: 3.705A pdb=" N LEU I1151 " --> pdb=" O ARG I1147 " (cutoff:3.500A) Processing helix chain 'I' and resid 1168 through 1177 Processing helix chain 'I' and resid 1191 through 1202 removed outlier: 3.550A pdb=" N ILE I1195 " --> pdb=" O LYS I1191 " (cutoff:3.500A) Processing helix chain 'I' and resid 1238 through 1243 removed outlier: 3.673A pdb=" N LYS I1242 " --> pdb=" O LEU I1238 " (cutoff:3.500A) Processing helix chain 'I' and resid 1271 through 1281 Processing helix chain 'I' and resid 1284 through 1292 Processing helix chain 'I' and resid 1299 through 1310 Processing helix chain 'I' and resid 1320 through 1332 removed outlier: 3.775A pdb=" N ASN I1324 " --> pdb=" O PRO I1320 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 34 Processing helix chain 'J' and resid 94 through 100 removed outlier: 3.539A pdb=" N VAL J 97 " --> pdb=" O GLN J 94 " (cutoff:3.500A) Processing helix chain 'J' and resid 114 through 119 removed outlier: 4.111A pdb=" N SER J 119 " --> pdb=" O TRP J 115 " (cutoff:3.500A) Processing helix chain 'J' and resid 122 through 128 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 192 Processing helix chain 'J' and resid 193 through 207 removed outlier: 3.849A pdb=" N GLU J 197 " --> pdb=" O ASP J 193 " (cutoff:3.500A) Processing helix chain 'J' and resid 210 through 228 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 285 removed outlier: 4.040A pdb=" N ASP J 267 " --> pdb=" O SER J 263 " (cutoff:3.500A) 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 341 Processing helix chain 'J' and resid 370 through 377 Processing helix chain 'J' and resid 377 through 388 Processing helix chain 'J' and resid 393 through 404 removed outlier: 3.532A pdb=" N ALA J 397 " --> pdb=" O THR J 393 " (cutoff:3.500A) Processing helix chain 'J' and resid 407 through 417 removed outlier: 3.751A pdb=" N ILE J 411 " --> pdb=" O VAL J 407 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG J 417 " --> pdb=" O ASP J 413 " (cutoff:3.500A) 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 Processing helix chain 'J' and resid 473 through 483 Processing helix chain 'J' and resid 504 through 514 Processing helix chain 'J' and resid 529 through 539 Processing helix chain 'J' and resid 574 through 581 removed outlier: 3.895A pdb=" N MET J 581 " --> pdb=" O ALA J 577 " (cutoff:3.500A) Processing helix chain 'J' and resid 588 through 592 removed outlier: 3.609A pdb=" N ILE J 591 " --> pdb=" O PRO J 588 " (cutoff:3.500A) Processing helix chain 'J' and resid 597 through 613 Processing helix chain 'J' and resid 614 through 636 removed outlier: 3.509A pdb=" N GLY J 636 " --> pdb=" O ALA J 632 " (cutoff:3.500A) Processing helix chain 'J' and resid 640 through 644 removed outlier: 3.879A pdb=" N MET J 644 " --> pdb=" O ILE J 641 " (cutoff:3.500A) Processing helix chain 'J' and resid 649 through 670 Processing helix chain 'J' and resid 674 through 702 removed outlier: 3.568A pdb=" N ARG J 678 " --> pdb=" O THR J 674 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASP J 699 " --> pdb=" O LYS J 695 " (cutoff:3.500A) Processing helix chain 'J' and resid 720 through 728 Processing helix chain 'J' and resid 733 through 742 Processing helix chain 'J' and resid 768 through 804 removed outlier: 4.012A pdb=" N HIS J 777 " --> pdb=" O PHE J 773 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLY J 778 " --> pdb=" O ILE J 774 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA J 804 " --> pdb=" O LEU J 800 " (cutoff:3.500A) Processing helix chain 'J' and resid 835 through 840 Processing helix chain 'J' and resid 865 through 875 Processing helix chain 'J' and resid 884 through 888 removed outlier: 3.654A pdb=" N CYS J 888 " --> pdb=" O VAL J 885 " (cutoff:3.500A) Processing helix chain 'J' and resid 895 through 900 removed outlier: 3.863A pdb=" N GLY J 900 " --> pdb=" O ALA J 896 " (cutoff:3.500A) Processing helix chain 'J' and resid 915 through 925 Processing helix chain 'J' and resid 926 through 928 No H-bonds generated for 'chain 'J' and resid 926 through 928' Processing helix chain 'J' and resid 1138 through 1145 Processing helix chain 'J' and resid 1216 through 1224 removed outlier: 3.606A pdb=" N ILE J1220 " --> pdb=" O ALA J1216 " (cutoff:3.500A) Processing helix chain 'J' and resid 1225 through 1245 removed outlier: 3.966A pdb=" N GLN J1244 " --> pdb=" O VAL J1240 " (cutoff:3.500A) Processing helix chain 'J' and resid 1249 through 1261 removed outlier: 4.413A pdb=" N ILE J1253 " --> pdb=" O ASN J1249 " (cutoff:3.500A) Processing helix chain 'J' and resid 1282 through 1293 removed outlier: 3.537A pdb=" N GLU J1291 " --> pdb=" O ILE J1287 " (cutoff:3.500A) Processing helix chain 'J' and resid 1327 through 1338 removed outlier: 3.971A pdb=" N VAL J1331 " --> pdb=" O GLU J1327 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA J1338 " --> pdb=" O GLU J1334 " (cutoff:3.500A) Processing helix chain 'J' and resid 1347 through 1354 Processing helix chain 'J' and resid 1361 through 1373 removed outlier: 4.337A pdb=" N TYR J1365 " --> pdb=" O THR J1361 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 13 Processing helix chain 'K' and resid 17 through 32 removed outlier: 3.584A pdb=" N LEU K 21 " --> pdb=" O PHE K 17 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 56 Processing helix chain 'K' and resid 60 through 78 Processing helix chain 'L' and resid 96 through 106 removed outlier: 3.557A pdb=" N MET L 100 " --> pdb=" O ASP L 96 " (cutoff:3.500A) Processing helix chain 'L' and resid 114 through 135 Processing helix chain 'L' and resid 137 through 153 removed outlier: 3.808A pdb=" N ILE L 141 " --> pdb=" O TYR L 137 " (cutoff:3.500A) Processing helix chain 'L' and resid 213 through 232 removed outlier: 3.955A pdb=" N ARG L 232 " --> pdb=" O TYR L 228 " (cutoff:3.500A) Processing helix chain 'L' and resid 233 through 235 No H-bonds generated for 'chain 'L' and resid 233 through 235' Processing helix chain 'L' and resid 243 through 258 removed outlier: 4.493A pdb=" N GLU L 247 " --> pdb=" O ALA L 243 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N GLU L 248 " --> pdb=" O THR L 244 " (cutoff:3.500A) Processing helix chain 'L' and resid 262 through 292 Processing helix chain 'L' and resid 298 through 307 removed outlier: 4.744A pdb=" N LEU L 305 " --> pdb=" O ASN L 301 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE L 306 " --> pdb=" O PHE L 302 " (cutoff:3.500A) Processing helix chain 'L' and resid 315 through 322 removed outlier: 3.861A pdb=" N ALA L 319 " --> pdb=" O TRP L 315 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE L 320 " --> pdb=" O PHE L 316 " (cutoff:3.500A) Processing helix chain 'L' and resid 327 through 332 removed outlier: 3.850A pdb=" N ASP L 332 " --> pdb=" O LYS L 329 " (cutoff:3.500A) Processing helix chain 'L' and resid 333 through 352 Processing helix chain 'L' and resid 354 through 383 removed outlier: 4.290A pdb=" N ASP L 360 " --> pdb=" O GLU L 356 " (cutoff:3.500A) Processing helix chain 'L' and resid 383 through 392 removed outlier: 3.785A pdb=" N VAL L 387 " --> pdb=" O ASN L 383 " (cutoff:3.500A) Processing helix chain 'L' and resid 394 through 398 removed outlier: 4.175A pdb=" N GLY L 398 " --> pdb=" O THR L 395 " (cutoff:3.500A) Processing helix chain 'L' and resid 400 through 418 Processing helix chain 'L' and resid 420 through 424 removed outlier: 3.983A pdb=" N ARG L 423 " --> pdb=" O GLU L 420 " (cutoff:3.500A) Processing helix chain 'L' and resid 426 through 447 removed outlier: 3.763A pdb=" N TYR L 430 " --> pdb=" O LYS L 426 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N TRP L 433 " --> pdb=" O THR L 429 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N TRP L 434 " --> pdb=" O TYR L 430 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA L 447 " --> pdb=" O ILE L 443 " (cutoff:3.500A) Processing helix chain 'L' and resid 453 through 472 removed outlier: 3.576A pdb=" N LEU L 471 " --> pdb=" O SER L 467 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLN L 472 " --> pdb=" O ARG L 468 " (cutoff:3.500A) Processing helix chain 'L' and resid 479 through 487 removed outlier: 3.929A pdb=" N GLU L 485 " --> pdb=" O GLU L 481 " (cutoff:3.500A) Processing helix chain 'L' and resid 491 through 501 removed outlier: 3.879A pdb=" N ARG L 495 " --> pdb=" O GLU L 491 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LYS L 496 " --> pdb=" O ASP L 492 " (cutoff:3.500A) Processing helix chain 'L' and resid 511 through 515 removed outlier: 3.894A pdb=" N ASP L 514 " --> pdb=" O ILE L 511 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N GLU L 515 " --> pdb=" O GLY L 512 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 511 through 515' Processing helix chain 'L' and resid 518 through 522 removed outlier: 3.631A pdb=" N ASP L 521 " --> pdb=" O HIS L 518 " (cutoff:3.500A) Processing helix chain 'L' and resid 530 through 550 removed outlier: 3.530A pdb=" N GLY L 550 " --> pdb=" O ASP L 546 " (cutoff:3.500A) Processing helix chain 'L' and resid 552 through 563 removed outlier: 3.632A pdb=" N PHE L 563 " --> pdb=" O LEU L 559 " (cutoff:3.500A) Processing helix chain 'L' and resid 572 through 581 Processing helix chain 'L' and resid 583 through 600 removed outlier: 3.961A pdb=" N HIS L 600 " --> pdb=" O ARG L 596 " (cutoff:3.500A) Processing helix chain 'L' and resid 603 through 609 removed outlier: 4.159A pdb=" N LEU L 607 " --> pdb=" O ARG L 603 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 13 through 18 removed outlier: 8.449A pdb=" N LEU G 13 " --> pdb=" O GLU G 29 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N GLU G 29 " --> pdb=" O LEU G 13 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N ASP G 15 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ASP G 199 " --> pdb=" O PRO G 30 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU G 198 " --> pdb=" O ALA G 190 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 97 through 104 removed outlier: 7.407A pdb=" N SER G 141 " --> pdb=" O ILE G 61 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N ILE G 61 " --> pdb=" O SER G 141 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ARG G 143 " --> pdb=" O VAL G 59 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N VAL G 59 " --> pdb=" O ARG G 143 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LYS G 145 " --> pdb=" O THR G 57 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 90 through 92 Processing sheet with id=AA4, first strand: chain 'G' and resid 108 through 111 removed outlier: 6.533A pdb=" N GLY G 108 " --> pdb=" O HIS G 132 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N HIS G 132 " --> pdb=" O GLY G 108 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N VAL G 110 " --> pdb=" O ILE G 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 152 through 153 removed outlier: 3.549A pdb=" N ALA G 175 " --> pdb=" O VAL G 153 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 17 through 18 removed outlier: 7.033A pdb=" N ASP H 199 " --> pdb=" O PRO H 30 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU H 198 " --> pdb=" O ALA H 189 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ALA H 189 " --> pdb=" O LEU H 198 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N LYS H 200 " --> pdb=" O VAL H 187 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N VAL H 187 " --> pdb=" O LYS H 200 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N VAL H 202 " --> pdb=" O TYR H 185 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N TYR H 185 " --> pdb=" O VAL H 202 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLU H 204 " --> pdb=" O ILE H 183 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ILE H 183 " --> pdb=" O GLU H 204 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N GLU H 206 " --> pdb=" O GLU H 181 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 53 through 61 removed outlier: 4.818A pdb=" N CYS H 54 " --> pdb=" O GLY H 149 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLY H 149 " --> pdb=" O CYS H 54 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N VAL H 56 " --> pdb=" O GLN H 147 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N GLN H 147 " --> pdb=" O VAL H 56 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N VAL H 146 " --> pdb=" O VAL H 98 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N VAL H 98 " --> pdb=" O VAL H 146 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 90 through 91 Processing sheet with id=AA9, first strand: chain 'H' and resid 109 through 110 removed outlier: 3.906A pdb=" N CYS H 131 " --> pdb=" O VAL H 110 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 13 through 14 removed outlier: 6.514A pdb=" N LYS I 13 " --> pdb=" O ALA I1183 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 59 through 60 removed outlier: 6.780A pdb=" N LYS I 99 " --> pdb=" O VAL I 71 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N TYR I 73 " --> pdb=" O ARG I 97 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ARG I 97 " --> pdb=" O TYR I 73 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N LEU I 75 " --> pdb=" O PRO I 95 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N ALA I 94 " --> pdb=" O GLU I 126 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N GLU I 126 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N LEU I 96 " --> pdb=" O MET I 124 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 136 through 137 Processing sheet with id=AB4, first strand: chain 'I' and resid 451 through 453 removed outlier: 6.424A pdb=" N SER I 147 " --> pdb=" O SER I 531 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N SER I 574 " --> pdb=" O CYS I 559 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 154 through 158 Processing sheet with id=AB6, first strand: chain 'I' and resid 227 through 231 Processing sheet with id=AB7, first strand: chain 'I' and resid 239 through 240 Processing sheet with id=AB8, first strand: chain 'I' and resid 255 through 257 removed outlier: 6.747A pdb=" N ALA I 257 " --> pdb=" O VAL I 261 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N VAL I 261 " --> pdb=" O ALA I 257 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 301 through 302 Processing sheet with id=AC1, first strand: chain 'I' and resid 580 through 581 removed outlier: 5.658A pdb=" N GLU I 602 " --> pdb=" O LYS I 593 " (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 633 through 637 Processing sheet with id=AC4, first strand: chain 'I' and resid 716 through 717 removed outlier: 6.815A pdb=" N ALA I 716 " --> pdb=" O LEU I 783 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 749 through 752 removed outlier: 5.947A pdb=" N LYS I 735 " --> pdb=" O VAL I 724 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N VAL I 724 " --> pdb=" O LYS I 735 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 757 through 758 removed outlier: 3.521A pdb=" N THR I 757 " --> pdb=" O ILE I 765 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 1209 through 1210 removed outlier: 8.133A pdb=" N ILE I 816 " --> pdb=" O SER I1077 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ILE I1079 " --> pdb=" O ILE I 816 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL I 818 " --> pdb=" O ILE I1079 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU I 817 " --> pdb=" O VAL I1097 " (cutoff:3.500A) removed outlier: 8.867A pdb=" N ILE I1096 " --> pdb=" O ASN I 799 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ARG I 801 " --> pdb=" O ILE I1096 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N LEU I1098 " --> pdb=" O ARG I 801 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ALA I 803 " --> pdb=" O LEU I1098 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 846 through 847 removed outlier: 6.411A pdb=" N ASP I 842 " --> pdb=" O VAL I1046 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VAL I1046 " --> pdb=" O ASP I 842 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ALA I1055 " --> pdb=" O VAL I 928 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N VAL I 928 " --> pdb=" O ALA I1055 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 882 through 884 removed outlier: 3.627A pdb=" N VAL I 884 " --> pdb=" O LEU I 918 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 887 through 889 Processing sheet with id=AD2, first strand: chain 'I' and resid 1087 through 1088 Processing sheet with id=AD3, first strand: chain 'I' and resid 1244 through 1246 removed outlier: 6.467A pdb=" N CYS J 366 " --> pdb=" O VAL J 440 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ILE J 442 " --> pdb=" O CYS J 366 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LEU J 368 " --> pdb=" O ILE J 442 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 1244 through 1246 Processing sheet with id=AD5, first strand: chain 'I' and resid 1269 through 1270 removed outlier: 3.574A pdb=" N LYS J 345 " --> pdb=" O PHE I1270 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 1335 through 1338 removed outlier: 3.554A pdb=" N LYS J 21 " --> pdb=" O GLU I1338 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 103 through 112 removed outlier: 9.860A pdb=" N LEU J 107 " --> pdb=" O PRO J 243 " (cutoff:3.500A) removed outlier: 11.307A pdb=" N SER J 109 " --> pdb=" O VAL J 241 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N VAL J 241 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 159 through 160 removed outlier: 3.741A pdb=" N TYR J 144 " --> pdb=" O LEU J 160 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS J 179 " --> pdb=" O VAL J 145 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 252 through 254 removed outlier: 3.533A pdb=" N VAL J 253 " --> pdb=" O ALA J 261 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 526 through 527 Processing sheet with id=AE2, first strand: chain 'J' and resid 706 through 707 Processing sheet with id=AE3, first strand: chain 'J' and resid 820 through 822 Processing sheet with id=AE4, first strand: chain 'J' and resid 991 through 996 removed outlier: 6.578A pdb=" N LEU J 984 " --> pdb=" O LYS J 992 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N SER J 994 " --> pdb=" O LEU J 982 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LEU J 982 " --> pdb=" O SER J 994 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLY J 956 " --> pdb=" O VAL J1011 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 965 through 967 Processing sheet with id=AE6, first strand: chain 'J' and resid 1025 through 1026 removed outlier: 3.670A pdb=" N ILE J1124 " --> pdb=" O MET J1025 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 1080 through 1081 Processing sheet with id=AE8, first strand: chain 'J' and resid 1046 through 1049 Processing sheet with id=AE9, first strand: chain 'J' and resid 1077 through 1078 Processing sheet with id=AF1, first strand: chain 'J' and resid 1186 through 1191 removed outlier: 4.554A pdb=" N TYR J1186 " --> pdb=" O ILE J1177 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 3.557A pdb=" N VAL J1280 " --> pdb=" O ALA J1264 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 162 through 165 removed outlier: 4.779A pdb=" N ARG L 260 " --> pdb=" O THR L 163 " (cutoff:3.500A) 1235 hydrogen bonds defined for protein. 3498 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 81 hydrogen bonds 150 hydrogen bond angles 0 basepair planarities 31 basepair parallelities 54 stacking parallelities Total time for adding SS restraints: 14.28 Time building geometry restraints manager: 13.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 5364 1.32 - 1.44: 8165 1.44 - 1.57: 17937 1.57 - 1.69: 221 1.69 - 1.81: 225 Bond restraints: 31912 Sorted by residual: bond pdb=" C ILE I1079 " pdb=" N ASN I1080 " ideal model delta sigma weight residual 1.330 1.404 -0.074 1.47e-02 4.63e+03 2.52e+01 bond pdb=" P G R 88 " pdb=" OP1 G R 88 " ideal model delta sigma weight residual 1.485 1.424 0.061 2.00e-02 2.50e+03 9.32e+00 bond pdb=" C4' G R 97 " pdb=" C3' G R 97 " ideal model delta sigma weight residual 1.527 1.482 0.045 1.50e-02 4.44e+03 8.88e+00 bond pdb=" C4 C R 85 " pdb=" N4 C R 85 " ideal model delta sigma weight residual 1.335 1.279 0.056 2.00e-02 2.50e+03 7.75e+00 bond pdb=" P G R 88 " pdb=" O5' G R 88 " ideal model delta sigma weight residual 1.593 1.553 0.040 1.50e-02 4.44e+03 7.13e+00 ... (remaining 31907 not shown) Histogram of bond angle deviations from ideal: 93.79 - 101.94: 201 101.94 - 110.09: 7261 110.09 - 118.25: 18026 118.25 - 126.40: 17527 126.40 - 134.55: 610 Bond angle restraints: 43625 Sorted by residual: angle pdb=" N ASP I 516 " pdb=" CA ASP I 516 " pdb=" C ASP I 516 " ideal model delta sigma weight residual 109.25 97.27 11.98 1.53e+00 4.27e-01 6.13e+01 angle pdb=" C4' U R 94 " pdb=" C3' U R 94 " pdb=" O3' U R 94 " ideal model delta sigma weight residual 113.00 102.75 10.25 1.50e+00 4.44e-01 4.67e+01 angle pdb=" P G R 97 " pdb=" O5' G R 97 " pdb=" C5' G R 97 " ideal model delta sigma weight residual 120.90 111.12 9.78 1.50e+00 4.44e-01 4.25e+01 angle pdb=" O5' G R 97 " pdb=" C5' G R 97 " pdb=" C4' G R 97 " ideal model delta sigma weight residual 111.70 120.85 -9.15 1.50e+00 4.44e-01 3.72e+01 angle pdb=" C4' C R 96 " pdb=" C3' C R 96 " pdb=" O3' C R 96 " ideal model delta sigma weight residual 113.00 104.01 8.99 1.50e+00 4.44e-01 3.59e+01 ... (remaining 43620 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.10: 19105 26.10 - 52.21: 521 52.21 - 78.31: 204 78.31 - 104.42: 3 104.42 - 130.52: 1 Dihedral angle restraints: 19834 sinusoidal: 9266 harmonic: 10568 Sorted by residual: dihedral pdb=" CA LEU J1344 " pdb=" C LEU J1344 " pdb=" N ARG J1345 " pdb=" CA ARG J1345 " ideal model delta harmonic sigma weight residual 180.00 129.17 50.83 0 5.00e+00 4.00e-02 1.03e+02 dihedral pdb=" O4' U R 109 " pdb=" C1' U R 109 " pdb=" N1 U R 109 " pdb=" C2 U R 109 " ideal model delta sinusoidal sigma weight residual 200.00 69.48 130.52 1 1.50e+01 4.44e-03 7.04e+01 dihedral pdb=" CA PRO I1185 " pdb=" C PRO I1185 " pdb=" N VAL I1186 " pdb=" CA VAL I1186 " ideal model delta harmonic sigma weight residual -180.00 -142.99 -37.01 0 5.00e+00 4.00e-02 5.48e+01 ... (remaining 19831 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 4681 0.109 - 0.218: 353 0.218 - 0.327: 23 0.327 - 0.437: 3 0.437 - 0.546: 2 Chirality restraints: 5062 Sorted by residual: chirality pdb=" CB ILE I1079 " pdb=" CA ILE I1079 " pdb=" CG1 ILE I1079 " pdb=" CG2 ILE I1079 " both_signs ideal model delta sigma weight residual False 2.64 2.10 0.55 2.00e-01 2.50e+01 7.45e+00 chirality pdb=" C4' G R 97 " pdb=" C5' G R 97 " pdb=" O4' G R 97 " pdb=" C3' G R 97 " both_signs ideal model delta sigma weight residual False -2.50 -1.98 -0.52 2.00e-01 2.50e+01 6.76e+00 chirality pdb=" CB ILE G 159 " pdb=" CA ILE G 159 " pdb=" CG1 ILE G 159 " pdb=" CG2 ILE G 159 " both_signs ideal model delta sigma weight residual False 2.64 2.22 0.42 2.00e-01 2.50e+01 4.45e+00 ... (remaining 5059 not shown) Planarity restraints: 5287 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO I 897 " -0.027 2.00e-02 2.50e+03 5.41e-02 2.92e+01 pdb=" C PRO I 897 " 0.094 2.00e-02 2.50e+03 pdb=" O PRO I 897 " -0.035 2.00e-02 2.50e+03 pdb=" N GLU I 898 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G R 68 " -0.046 2.00e-02 2.50e+03 3.11e-02 2.91e+01 pdb=" N9 G R 68 " 0.018 2.00e-02 2.50e+03 pdb=" C8 G R 68 " -0.003 2.00e-02 2.50e+03 pdb=" N7 G R 68 " 0.006 2.00e-02 2.50e+03 pdb=" C5 G R 68 " 0.002 2.00e-02 2.50e+03 pdb=" C6 G R 68 " -0.011 2.00e-02 2.50e+03 pdb=" O6 G R 68 " 0.001 2.00e-02 2.50e+03 pdb=" N1 G R 68 " -0.016 2.00e-02 2.50e+03 pdb=" C2 G R 68 " -0.019 2.00e-02 2.50e+03 pdb=" N2 G R 68 " -0.020 2.00e-02 2.50e+03 pdb=" N3 G R 68 " 0.089 2.00e-02 2.50e+03 pdb=" C4 G R 68 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C R 85 " -0.062 2.00e-02 2.50e+03 3.00e-02 2.02e+01 pdb=" N1 C R 85 " 0.018 2.00e-02 2.50e+03 pdb=" C2 C R 85 " 0.018 2.00e-02 2.50e+03 pdb=" O2 C R 85 " 0.013 2.00e-02 2.50e+03 pdb=" N3 C R 85 " 0.006 2.00e-02 2.50e+03 pdb=" C4 C R 85 " -0.004 2.00e-02 2.50e+03 pdb=" N4 C R 85 " -0.034 2.00e-02 2.50e+03 pdb=" C5 C R 85 " -0.002 2.00e-02 2.50e+03 pdb=" C6 C R 85 " 0.047 2.00e-02 2.50e+03 ... (remaining 5284 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 668 2.67 - 3.23: 28178 3.23 - 3.78: 48931 3.78 - 4.34: 63343 4.34 - 4.90: 103101 Nonbonded interactions: 244221 Sorted by model distance: nonbonded pdb=" OD2 ASP J 464 " pdb="MG MG J1501 " model vdw 2.110 2.170 nonbonded pdb=" O2' C R 96 " pdb=" O4' G R 97 " model vdw 2.150 2.440 nonbonded pdb=" NH2 ARG I 903 " pdb=" O6 G R 82 " model vdw 2.248 2.520 nonbonded pdb=" O GLN L 227 " pdb=" OG1 THR L 231 " model vdw 2.256 2.440 nonbonded pdb=" N2 G R 84 " pdb=" O2 C R 107 " model vdw 2.260 2.520 ... (remaining 244216 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'G' and (resid 8 through 158 or resid 171 through 234)) selection = (chain 'H' and ((resid 8 and (name N or name CA or name C or name O or name CB ) \ ) or resid 9 through 234)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 5.400 Check model and map are aligned: 0.370 Set scattering table: 0.300 Process input model: 93.150 Find NCS groups from input model: 1.210 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 104.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 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 : 0.007 0.094 31912 Z= 0.486 Angle : 1.096 12.068 43625 Z= 0.612 Chirality : 0.061 0.546 5062 Planarity : 0.007 0.072 5287 Dihedral : 13.281 130.523 13020 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.35 % Favored : 92.57 % Rotamer: Outliers : 0.57 % Allowed : 2.30 % Favored : 97.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.11 % Twisted Proline : 0.69 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.69 (0.11), residues: 3647 helix: -2.41 (0.11), residues: 1370 sheet: -1.97 (0.24), residues: 389 loop : -2.58 (0.12), residues: 1888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.004 TRP J 115 HIS 0.013 0.002 HIS I1116 PHE 0.036 0.003 PHE J 620 TYR 0.028 0.003 TYR J 457 ARG 0.018 0.001 ARG J 538 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7294 Ramachandran restraints generated. 3647 Oldfield, 0 Emsley, 3647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7294 Ramachandran restraints generated. 3647 Oldfield, 0 Emsley, 3647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 741 residues out of total 3142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 723 time to evaluate : 3.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 25 LYS cc_start: 0.8763 (mtpt) cc_final: 0.8464 (mttt) REVERT: G 111 THR cc_start: 0.9049 (p) cc_final: 0.8843 (t) REVERT: G 118 ASP cc_start: 0.7948 (t70) cc_final: 0.6482 (t0) REVERT: G 137 ASN cc_start: 0.8482 (m-40) cc_final: 0.7950 (m-40) REVERT: G 186 ASN cc_start: 0.8550 (m-40) cc_final: 0.8340 (m-40) REVERT: H 47 LEU cc_start: 0.9002 (mt) cc_final: 0.8780 (mt) REVERT: H 51 MET cc_start: 0.9217 (mmp) cc_final: 0.8879 (mmp) REVERT: H 57 THR cc_start: 0.4639 (m) cc_final: 0.3873 (m) REVERT: H 85 LEU cc_start: 0.8156 (mt) cc_final: 0.7956 (mt) REVERT: H 86 LYS cc_start: 0.7895 (ttmt) cc_final: 0.7558 (tttt) REVERT: H 104 LYS cc_start: 0.4891 (tptm) cc_final: 0.4249 (tptp) REVERT: H 107 ILE cc_start: 0.7928 (mt) cc_final: 0.7544 (tt) REVERT: H 129 VAL cc_start: 0.9153 (t) cc_final: 0.8831 (m) REVERT: H 185 TYR cc_start: 0.9066 (p90) cc_final: 0.8759 (p90) REVERT: I 37 LYS cc_start: 0.8009 (mmtt) cc_final: 0.7603 (mmmm) REVERT: I 218 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7311 (tt0) REVERT: I 272 ARG cc_start: 0.8171 (ttt180) cc_final: 0.7677 (tpm170) REVERT: I 327 GLN cc_start: 0.8250 (pt0) cc_final: 0.7745 (mm-40) REVERT: I 461 GLU cc_start: 0.8535 (tt0) cc_final: 0.8143 (tt0) REVERT: I 488 MET cc_start: 0.8348 (mmp) cc_final: 0.8104 (mmp) REVERT: I 549 ASP cc_start: 0.8540 (t0) cc_final: 0.8270 (m-30) REVERT: I 684 ASN cc_start: 0.8518 (t0) cc_final: 0.8269 (t0) REVERT: I 741 MET cc_start: 0.8476 (ttp) cc_final: 0.8138 (ttm) REVERT: I 765 ILE cc_start: 0.9525 (tt) cc_final: 0.9281 (mt) REVERT: I 788 SER cc_start: 0.9184 (m) cc_final: 0.8617 (p) REVERT: I 829 THR cc_start: 0.9298 (m) cc_final: 0.8893 (p) REVERT: I 844 LYS cc_start: 0.8205 (mttm) cc_final: 0.7920 (pttm) REVERT: I 898 GLU cc_start: 0.7553 (mp0) cc_final: 0.7336 (mp0) REVERT: I 1230 MET cc_start: 0.8655 (ttm) cc_final: 0.8368 (ttp) REVERT: J 133 ARG cc_start: 0.6709 (tpt170) cc_final: 0.6373 (tpt170) REVERT: J 151 MET cc_start: 0.6666 (mtp) cc_final: 0.6234 (tpt) REVERT: J 176 PHE cc_start: 0.7082 (t80) cc_final: 0.6544 (t80) REVERT: J 295 GLU cc_start: 0.8664 (tp30) cc_final: 0.8161 (tp30) REVERT: J 304 ASP cc_start: 0.7428 (m-30) cc_final: 0.7066 (m-30) REVERT: J 434 ILE cc_start: 0.9217 (mt) cc_final: 0.8971 (tt) REVERT: J 523 GLU cc_start: 0.7868 (tp30) cc_final: 0.7328 (tp30) REVERT: J 625 MET cc_start: 0.9054 (ttp) cc_final: 0.8793 (ttp) REVERT: J 707 ILE cc_start: 0.8585 (pt) cc_final: 0.8308 (pt) REVERT: J 753 SER cc_start: 0.8210 (m) cc_final: 0.7751 (p) REVERT: J 754 ILE cc_start: 0.8505 (tt) cc_final: 0.8283 (mt) REVERT: J 870 ASP cc_start: 0.8286 (m-30) cc_final: 0.7961 (m-30) REVERT: J 922 SER cc_start: 0.9189 (m) cc_final: 0.8814 (p) REVERT: J 1317 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7448 (tm-30) REVERT: J 1368 ASP cc_start: 0.7024 (t70) cc_final: 0.5678 (m-30) REVERT: K 43 ASN cc_start: 0.8410 (m-40) cc_final: 0.8135 (m-40) REVERT: K 62 GLN cc_start: 0.8441 (tp-100) cc_final: 0.7936 (tp-100) REVERT: K 63 ILE cc_start: 0.9073 (OUTLIER) cc_final: 0.8618 (mp) REVERT: K 75 GLN cc_start: 0.7844 (mt0) cc_final: 0.7502 (tp40) REVERT: L 322 MET cc_start: 0.3571 (mtp) cc_final: 0.3210 (mtt) REVERT: L 365 MET cc_start: 0.9026 (ttp) cc_final: 0.8684 (ttt) REVERT: L 366 SER cc_start: 0.8388 (m) cc_final: 0.8119 (p) REVERT: L 468 ARG cc_start: 0.7312 (ttp80) cc_final: 0.7060 (ttm170) REVERT: L 514 ASP cc_start: 0.7941 (t0) cc_final: 0.7595 (p0) REVERT: L 524 GLU cc_start: 0.7826 (pt0) cc_final: 0.7540 (pm20) REVERT: L 561 MET cc_start: 0.8145 (ttm) cc_final: 0.7925 (ttm) REVERT: L 578 LYS cc_start: 0.7267 (mmtm) cc_final: 0.7016 (tttm) outliers start: 18 outliers final: 5 residues processed: 737 average time/residue: 0.4895 time to fit residues: 543.7088 Evaluate side-chains 358 residues out of total 3142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 352 time to evaluate : 3.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 903 ARG Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain K residue 63 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 316 optimal weight: 8.9990 chunk 284 optimal weight: 9.9990 chunk 157 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 191 optimal weight: 7.9990 chunk 151 optimal weight: 0.9990 chunk 293 optimal weight: 10.0000 chunk 113 optimal weight: 0.8980 chunk 178 optimal weight: 4.9990 chunk 218 optimal weight: 1.9990 chunk 340 optimal weight: 10.0000 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 66 HIS G 147 GLN H 23 HIS H 227 GLN I 69 GLN I 273 HIS I 327 GLN I 513 GLN I 604 HIS I 952 GLN I1010 GLN I1080 ASN I1209 GLN J 232 ASN J 489 ASN J 560 ASN J1108 GLN J1259 GLN L 283 GLN L 600 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 31912 Z= 0.246 Angle : 0.657 9.798 43625 Z= 0.342 Chirality : 0.043 0.347 5062 Planarity : 0.005 0.070 5287 Dihedral : 14.710 116.703 5779 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.25 % Favored : 93.69 % Rotamer: Outliers : 2.59 % Allowed : 8.65 % Favored : 88.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.13), residues: 3647 helix: -0.51 (0.13), residues: 1423 sheet: -1.55 (0.25), residues: 377 loop : -2.22 (0.13), residues: 1847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP L 326 HIS 0.013 0.001 HIS L 331 PHE 0.021 0.001 PHE I1164 TYR 0.026 0.001 TYR L 228 ARG 0.006 0.000 ARG I 996 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7294 Ramachandran restraints generated. 3647 Oldfield, 0 Emsley, 3647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7294 Ramachandran restraints generated. 3647 Oldfield, 0 Emsley, 3647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 3142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 421 time to evaluate : 3.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 25 LYS cc_start: 0.8719 (mtpt) cc_final: 0.8392 (mttt) REVERT: G 111 THR cc_start: 0.9125 (p) cc_final: 0.8750 (t) REVERT: H 16 ILE cc_start: 0.8843 (mt) cc_final: 0.8469 (tt) REVERT: H 85 LEU cc_start: 0.8529 (mt) cc_final: 0.8303 (mt) REVERT: H 86 LYS cc_start: 0.8147 (ttmt) cc_final: 0.7421 (tttt) REVERT: H 185 TYR cc_start: 0.9142 (p90) cc_final: 0.8829 (p90) REVERT: I 37 LYS cc_start: 0.8095 (mmtt) cc_final: 0.7828 (mmmm) REVERT: I 59 ILE cc_start: 0.8000 (mt) cc_final: 0.7759 (tp) REVERT: I 156 PHE cc_start: 0.8279 (m-10) cc_final: 0.8027 (m-10) REVERT: I 315 MET cc_start: 0.7778 (mtp) cc_final: 0.7467 (mtt) REVERT: I 327 GLN cc_start: 0.8397 (pt0) cc_final: 0.8073 (mm-40) REVERT: I 461 GLU cc_start: 0.8515 (tt0) cc_final: 0.8264 (tt0) REVERT: I 484 LEU cc_start: 0.7767 (OUTLIER) cc_final: 0.7497 (mt) REVERT: I 549 ASP cc_start: 0.8566 (t0) cc_final: 0.8305 (m-30) REVERT: I 684 ASN cc_start: 0.8430 (t0) cc_final: 0.8163 (t0) REVERT: I 741 MET cc_start: 0.8214 (ttp) cc_final: 0.7898 (ttt) REVERT: I 788 SER cc_start: 0.9161 (m) cc_final: 0.8690 (p) REVERT: I 813 GLU cc_start: 0.8168 (mm-30) cc_final: 0.7809 (tp30) REVERT: I 844 LYS cc_start: 0.8201 (mttm) cc_final: 0.7889 (pttm) REVERT: I 898 GLU cc_start: 0.7606 (mp0) cc_final: 0.7385 (mp0) REVERT: I 902 LEU cc_start: 0.9155 (tt) cc_final: 0.8893 (tp) REVERT: I 992 LEU cc_start: 0.6769 (OUTLIER) cc_final: 0.6265 (tp) REVERT: I 1027 LYS cc_start: 0.8631 (pttt) cc_final: 0.8135 (ptpp) REVERT: I 1119 MET cc_start: 0.8755 (tpp) cc_final: 0.7691 (tpp) REVERT: I 1151 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8165 (tt) REVERT: I 1230 MET cc_start: 0.8657 (ttm) cc_final: 0.8300 (ttp) REVERT: J 151 MET cc_start: 0.6634 (mtp) cc_final: 0.6378 (tpt) REVERT: J 295 GLU cc_start: 0.8798 (tp30) cc_final: 0.8392 (tp30) REVERT: J 304 ASP cc_start: 0.7475 (m-30) cc_final: 0.7114 (m-30) REVERT: J 523 GLU cc_start: 0.7832 (tp30) cc_final: 0.7321 (tp30) REVERT: J 652 GLU cc_start: 0.8355 (tm-30) cc_final: 0.7991 (pp20) REVERT: J 718 SER cc_start: 0.8840 (t) cc_final: 0.8326 (m) REVERT: J 737 ILE cc_start: 0.9219 (OUTLIER) cc_final: 0.8820 (pt) REVERT: J 870 ASP cc_start: 0.8401 (m-30) cc_final: 0.7998 (m-30) REVERT: J 922 SER cc_start: 0.9239 (m) cc_final: 0.8855 (p) REVERT: J 1317 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7589 (tm-30) REVERT: J 1345 ARG cc_start: 0.7243 (mmp80) cc_final: 0.6719 (mmt180) REVERT: K 42 GLU cc_start: 0.8270 (mp0) cc_final: 0.7861 (mp0) REVERT: K 43 ASN cc_start: 0.8315 (m-40) cc_final: 0.8035 (m-40) REVERT: K 53 GLU cc_start: 0.8759 (mt-10) cc_final: 0.8533 (mt-10) REVERT: K 63 ILE cc_start: 0.9048 (OUTLIER) cc_final: 0.8786 (mp) REVERT: L 105 MET cc_start: 0.9045 (tmm) cc_final: 0.8629 (tmm) REVERT: L 322 MET cc_start: 0.3437 (mtp) cc_final: 0.2936 (mtt) REVERT: L 381 GLU cc_start: 0.7981 (mt-10) cc_final: 0.7773 (mt-10) REVERT: L 468 ARG cc_start: 0.7347 (ttp80) cc_final: 0.7050 (ttm170) REVERT: L 513 ASP cc_start: 0.8331 (m-30) cc_final: 0.8116 (m-30) REVERT: L 514 ASP cc_start: 0.7938 (t0) cc_final: 0.7462 (p0) REVERT: L 524 GLU cc_start: 0.7734 (pt0) cc_final: 0.7397 (pm20) outliers start: 81 outliers final: 45 residues processed: 478 average time/residue: 0.4266 time to fit residues: 325.5891 Evaluate side-chains 367 residues out of total 3142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 317 time to evaluate : 3.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain H residue 23 HIS Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 205 MET Chi-restraints excluded: chain I residue 124 MET Chi-restraints excluded: chain I residue 295 LYS Chi-restraints excluded: chain I residue 410 LEU Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 770 CYS Chi-restraints excluded: chain I residue 903 ARG Chi-restraints excluded: chain I residue 992 LEU Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain I residue 1315 MET Chi-restraints excluded: chain I residue 1332 SER Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 237 MET Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 393 THR Chi-restraints excluded: chain J residue 452 LEU Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 514 THR Chi-restraints excluded: chain J residue 517 CYS Chi-restraints excluded: chain J residue 582 ILE Chi-restraints excluded: chain J residue 641 ILE Chi-restraints excluded: chain J residue 737 ILE Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 869 CYS Chi-restraints excluded: chain J residue 897 HIS Chi-restraints excluded: chain J residue 1324 SER Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 36 ASP Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 63 ILE Chi-restraints excluded: chain L residue 224 LEU Chi-restraints excluded: chain L residue 267 ASP Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 338 HIS Chi-restraints excluded: chain L residue 346 GLN Chi-restraints excluded: chain L residue 367 ILE Chi-restraints excluded: chain L residue 488 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 189 optimal weight: 7.9990 chunk 105 optimal weight: 0.8980 chunk 283 optimal weight: 0.8980 chunk 231 optimal weight: 7.9990 chunk 93 optimal weight: 4.9990 chunk 341 optimal weight: 8.9990 chunk 368 optimal weight: 20.0000 chunk 303 optimal weight: 9.9990 chunk 338 optimal weight: 5.9990 chunk 116 optimal weight: 5.9990 chunk 273 optimal weight: 8.9990 overall best weight: 3.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 273 HIS I 513 GLN I1010 GLN J 560 ASN K 72 GLN ** L 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 31912 Z= 0.381 Angle : 0.697 11.399 43625 Z= 0.359 Chirality : 0.045 0.335 5062 Planarity : 0.005 0.070 5287 Dihedral : 14.530 114.554 5779 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.57 % Favored : 92.38 % Rotamer: Outliers : 3.45 % Allowed : 11.27 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.11 % Twisted Proline : 0.69 % Twisted General : 0.09 % 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: -1.69 (0.13), residues: 3647 helix: 0.08 (0.13), residues: 1425 sheet: -1.50 (0.25), residues: 398 loop : -2.06 (0.13), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP L 326 HIS 0.008 0.001 HIS L 331 PHE 0.022 0.002 PHE I1164 TYR 0.023 0.002 TYR L 228 ARG 0.010 0.001 ARG H 143 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7294 Ramachandran restraints generated. 3647 Oldfield, 0 Emsley, 3647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7294 Ramachandran restraints generated. 3647 Oldfield, 0 Emsley, 3647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 3142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 336 time to evaluate : 3.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 16 ILE cc_start: 0.8862 (mt) cc_final: 0.8460 (tt) REVERT: H 85 LEU cc_start: 0.8641 (mt) cc_final: 0.8425 (mt) REVERT: H 86 LYS cc_start: 0.8460 (ttmt) cc_final: 0.7763 (tttt) REVERT: H 185 TYR cc_start: 0.9217 (p90) cc_final: 0.8991 (p90) REVERT: I 37 LYS cc_start: 0.8075 (mmtt) cc_final: 0.7785 (mmmm) REVERT: I 239 MET cc_start: 0.6053 (ttp) cc_final: 0.5811 (ttm) REVERT: I 370 MET cc_start: 0.8961 (mmm) cc_final: 0.8671 (tpp) REVERT: I 461 GLU cc_start: 0.8599 (tt0) cc_final: 0.8376 (tt0) REVERT: I 484 LEU cc_start: 0.7850 (OUTLIER) cc_final: 0.7537 (mt) REVERT: I 741 MET cc_start: 0.8261 (ttp) cc_final: 0.7782 (ttm) REVERT: I 788 SER cc_start: 0.9282 (m) cc_final: 0.8805 (p) REVERT: I 844 LYS cc_start: 0.8234 (mttm) cc_final: 0.7971 (pttp) REVERT: I 992 LEU cc_start: 0.6871 (OUTLIER) cc_final: 0.6296 (tp) REVERT: I 1027 LYS cc_start: 0.8754 (pttt) cc_final: 0.8242 (ptpp) REVERT: I 1119 MET cc_start: 0.8958 (tpp) cc_final: 0.8025 (tpp) REVERT: I 1329 GLU cc_start: 0.7660 (mt-10) cc_final: 0.7156 (mt-10) REVERT: J 151 MET cc_start: 0.6869 (mtp) cc_final: 0.6410 (tpt) REVERT: J 180 MET cc_start: 0.8355 (ttp) cc_final: 0.8132 (ttm) REVERT: J 215 LYS cc_start: 0.6930 (OUTLIER) cc_final: 0.6697 (mmtm) REVERT: J 523 GLU cc_start: 0.7865 (tp30) cc_final: 0.7420 (tp30) REVERT: J 652 GLU cc_start: 0.8511 (tm-30) cc_final: 0.8163 (pp20) REVERT: J 870 ASP cc_start: 0.8377 (m-30) cc_final: 0.7899 (m-30) REVERT: J 922 SER cc_start: 0.9305 (m) cc_final: 0.8997 (p) REVERT: J 1021 ASP cc_start: 0.6134 (p0) cc_final: 0.5744 (p0) REVERT: J 1175 LEU cc_start: 0.8032 (tt) cc_final: 0.7748 (mm) REVERT: J 1317 GLU cc_start: 0.7918 (mm-30) cc_final: 0.7614 (tm-30) REVERT: J 1345 ARG cc_start: 0.7343 (mmp80) cc_final: 0.6892 (mmt180) REVERT: K 11 GLU cc_start: 0.8326 (tp30) cc_final: 0.7744 (pt0) REVERT: K 42 GLU cc_start: 0.8415 (mp0) cc_final: 0.7708 (mp0) REVERT: K 43 ASN cc_start: 0.8562 (m-40) cc_final: 0.8233 (m-40) REVERT: K 55 GLU cc_start: 0.7937 (tm-30) cc_final: 0.7694 (tm-30) REVERT: K 56 GLU cc_start: 0.8593 (mm-30) cc_final: 0.8362 (mm-30) REVERT: K 76 GLU cc_start: 0.7911 (mm-30) cc_final: 0.7441 (mm-30) REVERT: L 276 MET cc_start: 0.7647 (ttt) cc_final: 0.7289 (ttp) REVERT: L 322 MET cc_start: 0.3005 (mtp) cc_final: 0.2735 (tpt) REVERT: L 365 MET cc_start: 0.9026 (ttt) cc_final: 0.8739 (ttp) REVERT: L 413 MET cc_start: 0.8566 (mtp) cc_final: 0.8361 (mtm) REVERT: L 456 MET cc_start: 0.8558 (tpp) cc_final: 0.8303 (tpp) REVERT: L 468 ARG cc_start: 0.7406 (ttp80) cc_final: 0.7006 (ttm170) REVERT: L 524 GLU cc_start: 0.7758 (pt0) cc_final: 0.7435 (pm20) REVERT: L 561 MET cc_start: 0.8196 (OUTLIER) cc_final: 0.7854 (ptm) outliers start: 108 outliers final: 74 residues processed: 413 average time/residue: 0.4001 time to fit residues: 272.1114 Evaluate side-chains 370 residues out of total 3142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 292 time to evaluate : 3.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain H residue 174 ASP Chi-restraints excluded: chain H residue 200 LYS Chi-restraints excluded: chain I residue 60 GLN Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 124 MET Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 341 LEU Chi-restraints excluded: chain I residue 410 LEU Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 693 LEU Chi-restraints excluded: chain I residue 702 THR Chi-restraints excluded: chain I residue 770 CYS Chi-restraints excluded: chain I residue 903 ARG Chi-restraints excluded: chain I residue 942 ASP Chi-restraints excluded: chain I residue 992 LEU Chi-restraints excluded: chain I residue 1145 ILE Chi-restraints excluded: chain I residue 1170 MET Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1295 SER Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain I residue 1315 MET Chi-restraints excluded: chain I residue 1322 SER Chi-restraints excluded: chain I residue 1332 SER Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 215 LYS Chi-restraints excluded: chain J residue 237 MET Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 368 LEU Chi-restraints excluded: chain J residue 393 THR Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 514 THR Chi-restraints excluded: chain J residue 532 GLU Chi-restraints excluded: chain J residue 539 SER Chi-restraints excluded: chain J residue 582 ILE Chi-restraints excluded: chain J residue 635 SER Chi-restraints excluded: chain J residue 641 ILE Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 802 ASP Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 840 LEU Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 869 CYS Chi-restraints excluded: chain J residue 897 HIS Chi-restraints excluded: chain J residue 1178 THR Chi-restraints excluded: chain J residue 1189 MET Chi-restraints excluded: chain J residue 1233 ILE Chi-restraints excluded: chain J residue 1283 SER Chi-restraints excluded: chain J residue 1324 SER Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 36 ASP Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 41 GLU Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain L residue 224 LEU Chi-restraints excluded: chain L residue 267 ASP Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 338 HIS Chi-restraints excluded: chain L residue 346 GLN Chi-restraints excluded: chain L residue 367 ILE Chi-restraints excluded: chain L residue 387 VAL Chi-restraints excluded: chain L residue 410 ILE Chi-restraints excluded: chain L residue 488 LEU Chi-restraints excluded: chain L residue 561 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 337 optimal weight: 20.0000 chunk 256 optimal weight: 3.9990 chunk 177 optimal weight: 2.9990 chunk 37 optimal weight: 20.0000 chunk 162 optimal weight: 0.9990 chunk 229 optimal weight: 0.9980 chunk 342 optimal weight: 9.9990 chunk 362 optimal weight: 1.9990 chunk 178 optimal weight: 4.9990 chunk 324 optimal weight: 20.0000 chunk 97 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 23 HIS H 132 HIS H 227 GLN ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 273 HIS J 560 ASN J 910 ASN ** L 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 31912 Z= 0.246 Angle : 0.602 9.226 43625 Z= 0.310 Chirality : 0.042 0.302 5062 Planarity : 0.004 0.072 5287 Dihedral : 14.317 115.867 5777 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.44 % Favored : 93.50 % Rotamer: Outliers : 3.64 % Allowed : 13.53 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.21 (0.14), residues: 3647 helix: 0.59 (0.14), residues: 1415 sheet: -1.39 (0.25), residues: 410 loop : -1.83 (0.14), residues: 1822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP L 326 HIS 0.011 0.001 HIS J 777 PHE 0.014 0.001 PHE J 620 TYR 0.021 0.001 TYR L 228 ARG 0.007 0.000 ARG H 143 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7294 Ramachandran restraints generated. 3647 Oldfield, 0 Emsley, 3647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7294 Ramachandran restraints generated. 3647 Oldfield, 0 Emsley, 3647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 3142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 336 time to evaluate : 3.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 50 SER cc_start: 0.9308 (m) cc_final: 0.8729 (p) REVERT: H 16 ILE cc_start: 0.8754 (mt) cc_final: 0.8345 (tt) REVERT: H 85 LEU cc_start: 0.8626 (mt) cc_final: 0.8396 (mt) REVERT: H 86 LYS cc_start: 0.8406 (ttmt) cc_final: 0.7605 (tptt) REVERT: H 185 TYR cc_start: 0.9215 (p90) cc_final: 0.8992 (p90) REVERT: I 33 ASP cc_start: 0.7877 (t0) cc_final: 0.7581 (t0) REVERT: I 37 LYS cc_start: 0.8009 (mmtt) cc_final: 0.7692 (mmmm) REVERT: I 315 MET cc_start: 0.7847 (mtt) cc_final: 0.7503 (mtt) REVERT: I 370 MET cc_start: 0.8986 (mmm) cc_final: 0.8617 (tpp) REVERT: I 391 SER cc_start: 0.8896 (t) cc_final: 0.8613 (m) REVERT: I 484 LEU cc_start: 0.7943 (OUTLIER) cc_final: 0.7707 (mt) REVERT: I 633 LEU cc_start: 0.7812 (OUTLIER) cc_final: 0.7572 (pp) REVERT: I 672 GLU cc_start: 0.8154 (pm20) cc_final: 0.7866 (pm20) REVERT: I 741 MET cc_start: 0.8190 (ttp) cc_final: 0.7759 (ttt) REVERT: I 788 SER cc_start: 0.9215 (m) cc_final: 0.8624 (p) REVERT: I 828 PHE cc_start: 0.9265 (OUTLIER) cc_final: 0.8826 (m-80) REVERT: I 844 LYS cc_start: 0.8245 (mttm) cc_final: 0.7991 (pttp) REVERT: I 898 GLU cc_start: 0.7488 (mp0) cc_final: 0.7255 (mp0) REVERT: I 971 LEU cc_start: 0.7679 (OUTLIER) cc_final: 0.7341 (tt) REVERT: I 992 LEU cc_start: 0.6830 (OUTLIER) cc_final: 0.6242 (tp) REVERT: I 1027 LYS cc_start: 0.8708 (pttt) cc_final: 0.8236 (ptpp) REVERT: I 1119 MET cc_start: 0.8964 (tpp) cc_final: 0.8220 (tpp) REVERT: I 1329 GLU cc_start: 0.7595 (mt-10) cc_final: 0.7128 (mt-10) REVERT: J 96 LYS cc_start: 0.8330 (ptmm) cc_final: 0.7927 (tmtt) REVERT: J 151 MET cc_start: 0.6643 (mtp) cc_final: 0.6300 (tpt) REVERT: J 215 LYS cc_start: 0.7021 (OUTLIER) cc_final: 0.6801 (mmtm) REVERT: J 652 GLU cc_start: 0.8503 (tm-30) cc_final: 0.8167 (pp20) REVERT: J 707 ILE cc_start: 0.8561 (tp) cc_final: 0.8284 (tt) REVERT: J 725 MET cc_start: 0.8713 (mtm) cc_final: 0.8355 (mtp) REVERT: J 870 ASP cc_start: 0.8252 (m-30) cc_final: 0.7975 (m-30) REVERT: J 922 SER cc_start: 0.9259 (m) cc_final: 0.8972 (p) REVERT: J 1021 ASP cc_start: 0.6420 (p0) cc_final: 0.6119 (p0) REVERT: J 1175 LEU cc_start: 0.8057 (tt) cc_final: 0.7722 (mm) REVERT: J 1317 GLU cc_start: 0.7891 (mm-30) cc_final: 0.7405 (tm-30) REVERT: J 1372 ARG cc_start: 0.7729 (ttp-170) cc_final: 0.6604 (ttm-80) REVERT: J 1373 ARG cc_start: 0.7559 (tpm170) cc_final: 0.7255 (tpp-160) REVERT: K 43 ASN cc_start: 0.8494 (m-40) cc_final: 0.8153 (m-40) REVERT: K 53 GLU cc_start: 0.8622 (mt-10) cc_final: 0.8287 (mt-10) REVERT: K 76 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7297 (mm-30) REVERT: L 276 MET cc_start: 0.7624 (ttt) cc_final: 0.7269 (ttp) REVERT: L 322 MET cc_start: 0.3001 (mtp) cc_final: 0.2600 (tpt) REVERT: L 365 MET cc_start: 0.9079 (ttt) cc_final: 0.8849 (ttp) REVERT: L 468 ARG cc_start: 0.7362 (ttp80) cc_final: 0.6984 (ttm170) REVERT: L 514 ASP cc_start: 0.8040 (t0) cc_final: 0.7400 (p0) REVERT: L 561 MET cc_start: 0.8188 (OUTLIER) cc_final: 0.7839 (ptm) outliers start: 114 outliers final: 63 residues processed: 417 average time/residue: 0.3871 time to fit residues: 267.3698 Evaluate side-chains 373 residues out of total 3142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 303 time to evaluate : 3.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 15 ASP Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain H residue 23 HIS Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain I residue 60 GLN Chi-restraints excluded: chain I residue 124 MET Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 295 LYS Chi-restraints excluded: chain I residue 410 LEU Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 633 LEU Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 702 THR Chi-restraints excluded: chain I residue 714 VAL Chi-restraints excluded: chain I residue 773 LEU Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 811 ASN Chi-restraints excluded: chain I residue 828 PHE Chi-restraints excluded: chain I residue 903 ARG Chi-restraints excluded: chain I residue 971 LEU Chi-restraints excluded: chain I residue 992 LEU Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1145 ILE Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain I residue 1315 MET Chi-restraints excluded: chain I residue 1332 SER Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 215 LYS Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 368 LEU Chi-restraints excluded: chain J residue 393 THR Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 532 GLU Chi-restraints excluded: chain J residue 539 SER Chi-restraints excluded: chain J residue 802 ASP Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 869 CYS Chi-restraints excluded: chain J residue 897 HIS Chi-restraints excluded: chain J residue 1178 THR Chi-restraints excluded: chain J residue 1189 MET Chi-restraints excluded: chain J residue 1283 SER Chi-restraints excluded: chain J residue 1324 SER Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 36 ASP Chi-restraints excluded: chain K residue 41 GLU Chi-restraints excluded: chain L residue 224 LEU Chi-restraints excluded: chain L residue 267 ASP Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 338 HIS Chi-restraints excluded: chain L residue 367 ILE Chi-restraints excluded: chain L residue 387 VAL Chi-restraints excluded: chain L residue 561 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 301 optimal weight: 1.9990 chunk 205 optimal weight: 6.9990 chunk 5 optimal weight: 0.2980 chunk 269 optimal weight: 9.9990 chunk 149 optimal weight: 6.9990 chunk 309 optimal weight: 8.9990 chunk 250 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 185 optimal weight: 6.9990 chunk 325 optimal weight: 20.0000 chunk 91 optimal weight: 6.9990 overall best weight: 4.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 23 HIS ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 684 ASN J 489 ASN J 560 ASN L 342 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.3527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.085 31912 Z= 0.451 Angle : 0.731 11.656 43625 Z= 0.374 Chirality : 0.046 0.277 5062 Planarity : 0.005 0.072 5287 Dihedral : 14.389 115.824 5777 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.72 % Favored : 91.23 % Rotamer: Outliers : 4.31 % Allowed : 13.60 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.32 (0.14), residues: 3647 helix: 0.51 (0.14), residues: 1417 sheet: -1.38 (0.25), residues: 402 loop : -1.92 (0.14), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP L 326 HIS 0.009 0.001 HIS J 777 PHE 0.017 0.002 PHE I 545 TYR 0.035 0.002 TYR J 144 ARG 0.007 0.001 ARG H 143 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7294 Ramachandran restraints generated. 3647 Oldfield, 0 Emsley, 3647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7294 Ramachandran restraints generated. 3647 Oldfield, 0 Emsley, 3647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 3142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 307 time to evaluate : 3.297 Fit side-chains revert: symmetry clash REVERT: G 50 SER cc_start: 0.9260 (m) cc_final: 0.8844 (p) REVERT: G 75 GLN cc_start: 0.9108 (pt0) cc_final: 0.8738 (tt0) REVERT: G 163 GLU cc_start: 0.6051 (OUTLIER) cc_final: 0.5585 (mp0) REVERT: H 16 ILE cc_start: 0.8838 (mt) cc_final: 0.8438 (tt) REVERT: H 86 LYS cc_start: 0.8554 (ttmt) cc_final: 0.7579 (tptt) REVERT: I 33 ASP cc_start: 0.7996 (t0) cc_final: 0.7638 (t0) REVERT: I 37 LYS cc_start: 0.8158 (mmtt) cc_final: 0.7882 (mmmm) REVERT: I 60 GLN cc_start: 0.8137 (OUTLIER) cc_final: 0.7696 (pm20) REVERT: I 370 MET cc_start: 0.9069 (mmm) cc_final: 0.8599 (tpp) REVERT: I 484 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7785 (mt) REVERT: I 633 LEU cc_start: 0.7669 (OUTLIER) cc_final: 0.7411 (pp) REVERT: I 672 GLU cc_start: 0.8220 (pm20) cc_final: 0.7978 (pm20) REVERT: I 741 MET cc_start: 0.8219 (ttp) cc_final: 0.7761 (ttt) REVERT: I 788 SER cc_start: 0.9278 (m) cc_final: 0.8804 (p) REVERT: I 828 PHE cc_start: 0.9363 (OUTLIER) cc_final: 0.9000 (m-10) REVERT: I 844 LYS cc_start: 0.8307 (mttm) cc_final: 0.7964 (pttm) REVERT: I 898 GLU cc_start: 0.7655 (mp0) cc_final: 0.7310 (mp0) REVERT: I 971 LEU cc_start: 0.7742 (OUTLIER) cc_final: 0.7404 (tt) REVERT: I 1027 LYS cc_start: 0.8732 (pttt) cc_final: 0.8497 (ptpt) REVERT: I 1119 MET cc_start: 0.9019 (tpp) cc_final: 0.8280 (tpp) REVERT: I 1321 GLU cc_start: 0.8376 (tp30) cc_final: 0.8054 (tp30) REVERT: J 151 MET cc_start: 0.6732 (mtp) cc_final: 0.6483 (tpt) REVERT: J 180 MET cc_start: 0.8400 (ttp) cc_final: 0.8145 (ttm) REVERT: J 298 MET cc_start: 0.8552 (OUTLIER) cc_final: 0.8153 (mtm) REVERT: J 652 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.8205 (pp20) REVERT: J 707 ILE cc_start: 0.8588 (tp) cc_final: 0.8358 (tt) REVERT: J 725 MET cc_start: 0.8672 (mtm) cc_final: 0.8341 (mtp) REVERT: J 805 GLN cc_start: 0.9111 (pm20) cc_final: 0.8212 (pp30) REVERT: J 870 ASP cc_start: 0.8262 (m-30) cc_final: 0.7825 (m-30) REVERT: J 922 SER cc_start: 0.9369 (m) cc_final: 0.9116 (p) REVERT: J 1021 ASP cc_start: 0.6716 (p0) cc_final: 0.6303 (p0) REVERT: J 1175 LEU cc_start: 0.8192 (tt) cc_final: 0.7821 (mm) REVERT: J 1317 GLU cc_start: 0.7885 (mm-30) cc_final: 0.7320 (tm-30) REVERT: K 15 ASN cc_start: 0.7825 (t0) cc_final: 0.7539 (t0) REVERT: K 42 GLU cc_start: 0.8569 (mp0) cc_final: 0.8172 (mp0) REVERT: K 43 ASN cc_start: 0.8554 (m-40) cc_final: 0.8191 (m-40) REVERT: L 276 MET cc_start: 0.7565 (ttt) cc_final: 0.7324 (ttp) REVERT: L 322 MET cc_start: 0.3130 (mtp) cc_final: 0.2734 (tpt) REVERT: L 365 MET cc_start: 0.9120 (ttt) cc_final: 0.8895 (ttp) REVERT: L 468 ARG cc_start: 0.7308 (ttp80) cc_final: 0.6880 (ttm170) REVERT: L 524 GLU cc_start: 0.7759 (pt0) cc_final: 0.7460 (pm20) REVERT: L 561 MET cc_start: 0.8194 (OUTLIER) cc_final: 0.7844 (ptm) REVERT: L 603 ARG cc_start: 0.8761 (OUTLIER) cc_final: 0.7638 (mtt180) outliers start: 135 outliers final: 83 residues processed: 405 average time/residue: 0.4051 time to fit residues: 268.8904 Evaluate side-chains 373 residues out of total 3142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 280 time to evaluate : 3.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 15 ASP Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 163 GLU Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 174 ASP Chi-restraints excluded: chain I residue 60 GLN Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 124 MET Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 295 LYS Chi-restraints excluded: chain I residue 341 LEU Chi-restraints excluded: chain I residue 410 LEU Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 633 LEU Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 693 LEU Chi-restraints excluded: chain I residue 702 THR Chi-restraints excluded: chain I residue 714 VAL Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 828 PHE Chi-restraints excluded: chain I residue 903 ARG Chi-restraints excluded: chain I residue 942 ASP Chi-restraints excluded: chain I residue 971 LEU Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1145 ILE Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1170 MET Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1292 THR Chi-restraints excluded: chain I residue 1295 SER Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain I residue 1315 MET Chi-restraints excluded: chain I residue 1332 SER Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 241 VAL Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 290 ILE Chi-restraints excluded: chain J residue 298 MET Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 368 LEU Chi-restraints excluded: chain J residue 393 THR Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 532 GLU Chi-restraints excluded: chain J residue 539 SER Chi-restraints excluded: chain J residue 567 THR Chi-restraints excluded: chain J residue 652 GLU Chi-restraints excluded: chain J residue 802 ASP Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 840 LEU Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 869 CYS Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 897 HIS Chi-restraints excluded: chain J residue 909 ILE Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 1178 THR Chi-restraints excluded: chain J residue 1189 MET Chi-restraints excluded: chain J residue 1233 ILE Chi-restraints excluded: chain J residue 1283 SER Chi-restraints excluded: chain J residue 1324 SER Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 36 ASP Chi-restraints excluded: chain K residue 41 GLU Chi-restraints excluded: chain L residue 143 TYR Chi-restraints excluded: chain L residue 224 LEU Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 338 HIS Chi-restraints excluded: chain L residue 367 ILE Chi-restraints excluded: chain L residue 387 VAL Chi-restraints excluded: chain L residue 410 ILE Chi-restraints excluded: chain L residue 488 LEU Chi-restraints excluded: chain L residue 561 MET Chi-restraints excluded: chain L residue 603 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 121 optimal weight: 2.9990 chunk 326 optimal weight: 9.9990 chunk 71 optimal weight: 20.0000 chunk 212 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 362 optimal weight: 9.9990 chunk 301 optimal weight: 2.9990 chunk 167 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 120 optimal weight: 0.7980 chunk 190 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 227 GLN ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 560 ASN K 31 GLN K 72 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.3677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 31912 Z= 0.242 Angle : 0.603 9.361 43625 Z= 0.309 Chirality : 0.042 0.266 5062 Planarity : 0.004 0.072 5287 Dihedral : 14.238 117.381 5777 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.80 % Favored : 93.15 % Rotamer: Outliers : 3.86 % Allowed : 14.43 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.95 (0.14), residues: 3647 helix: 0.85 (0.14), residues: 1414 sheet: -1.25 (0.25), residues: 408 loop : -1.72 (0.14), residues: 1825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP L 326 HIS 0.010 0.001 HIS H 23 PHE 0.016 0.001 PHE I1164 TYR 0.024 0.001 TYR H 185 ARG 0.006 0.000 ARG H 143 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7294 Ramachandran restraints generated. 3647 Oldfield, 0 Emsley, 3647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7294 Ramachandran restraints generated. 3647 Oldfield, 0 Emsley, 3647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 3142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 322 time to evaluate : 3.374 Fit side-chains revert: symmetry clash REVERT: G 50 SER cc_start: 0.9268 (m) cc_final: 0.8876 (p) REVERT: H 16 ILE cc_start: 0.8799 (mt) cc_final: 0.8378 (tt) REVERT: H 86 LYS cc_start: 0.8454 (ttmt) cc_final: 0.7447 (tptt) REVERT: H 174 ASP cc_start: 0.5890 (OUTLIER) cc_final: 0.5372 (p0) REVERT: H 185 TYR cc_start: 0.8955 (p90) cc_final: 0.8713 (p90) REVERT: I 33 ASP cc_start: 0.7921 (t0) cc_final: 0.7609 (t0) REVERT: I 37 LYS cc_start: 0.8035 (mmtt) cc_final: 0.7691 (mmmm) REVERT: I 138 ILE cc_start: 0.9375 (mm) cc_final: 0.8987 (mm) REVERT: I 315 MET cc_start: 0.7903 (mtt) cc_final: 0.7577 (mtt) REVERT: I 370 MET cc_start: 0.9054 (mmm) cc_final: 0.8600 (tpp) REVERT: I 391 SER cc_start: 0.8888 (t) cc_final: 0.8566 (m) REVERT: I 484 LEU cc_start: 0.7942 (OUTLIER) cc_final: 0.7735 (mt) REVERT: I 633 LEU cc_start: 0.7724 (OUTLIER) cc_final: 0.7497 (pp) REVERT: I 672 GLU cc_start: 0.8191 (pm20) cc_final: 0.7923 (pm20) REVERT: I 741 MET cc_start: 0.8134 (ttp) cc_final: 0.7665 (ttt) REVERT: I 788 SER cc_start: 0.9192 (m) cc_final: 0.8608 (p) REVERT: I 826 ASP cc_start: 0.8351 (OUTLIER) cc_final: 0.8078 (t0) REVERT: I 828 PHE cc_start: 0.9306 (OUTLIER) cc_final: 0.8909 (m-80) REVERT: I 844 LYS cc_start: 0.8245 (mttm) cc_final: 0.7991 (pttp) REVERT: I 898 GLU cc_start: 0.7532 (mp0) cc_final: 0.7298 (mp0) REVERT: I 971 LEU cc_start: 0.7771 (OUTLIER) cc_final: 0.7418 (tt) REVERT: I 992 LEU cc_start: 0.6855 (OUTLIER) cc_final: 0.6514 (tp) REVERT: I 1027 LYS cc_start: 0.8683 (pttt) cc_final: 0.8453 (ptpt) REVERT: I 1119 MET cc_start: 0.8915 (tpp) cc_final: 0.8205 (tpp) REVERT: J 151 MET cc_start: 0.6615 (mtp) cc_final: 0.6384 (tpt) REVERT: J 298 MET cc_start: 0.8325 (OUTLIER) cc_final: 0.7856 (mtm) REVERT: J 652 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.8167 (pp20) REVERT: J 707 ILE cc_start: 0.8651 (tp) cc_final: 0.8437 (tt) REVERT: J 725 MET cc_start: 0.8344 (mtm) cc_final: 0.8051 (mtp) REVERT: J 870 ASP cc_start: 0.8171 (m-30) cc_final: 0.7818 (m-30) REVERT: J 922 SER cc_start: 0.9270 (m) cc_final: 0.8989 (p) REVERT: J 1021 ASP cc_start: 0.6627 (p0) cc_final: 0.6161 (p0) REVERT: J 1146 GLU cc_start: 0.8187 (tt0) cc_final: 0.7985 (mt-10) REVERT: J 1175 LEU cc_start: 0.8294 (tt) cc_final: 0.8010 (mm) REVERT: J 1317 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7499 (tm-30) REVERT: K 43 ASN cc_start: 0.8530 (m-40) cc_final: 0.8172 (m110) REVERT: K 53 GLU cc_start: 0.8808 (mt-10) cc_final: 0.8328 (mt-10) REVERT: L 144 LEU cc_start: 0.8221 (tt) cc_final: 0.7990 (mt) REVERT: L 276 MET cc_start: 0.7642 (ttt) cc_final: 0.7296 (ttp) REVERT: L 288 MET cc_start: 0.4068 (mtt) cc_final: 0.3654 (ptp) REVERT: L 322 MET cc_start: 0.3198 (mtp) cc_final: 0.2450 (tpt) REVERT: L 365 MET cc_start: 0.9106 (ttt) cc_final: 0.8878 (ttp) REVERT: L 468 ARG cc_start: 0.7265 (ttp80) cc_final: 0.6852 (ttm170) REVERT: L 514 ASP cc_start: 0.8023 (t70) cc_final: 0.7512 (p0) REVERT: L 524 GLU cc_start: 0.7717 (pt0) cc_final: 0.7432 (pm20) REVERT: L 561 MET cc_start: 0.8165 (OUTLIER) cc_final: 0.7855 (ptm) REVERT: L 603 ARG cc_start: 0.8649 (OUTLIER) cc_final: 0.8222 (mtt180) outliers start: 121 outliers final: 79 residues processed: 408 average time/residue: 0.3884 time to fit residues: 264.6893 Evaluate side-chains 381 residues out of total 3142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 291 time to evaluate : 3.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 15 ASP Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain H residue 23 HIS Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 174 ASP Chi-restraints excluded: chain I residue 62 TYR Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 124 MET Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 295 LYS Chi-restraints excluded: chain I residue 398 SER Chi-restraints excluded: chain I residue 410 LEU Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 633 LEU Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 702 THR Chi-restraints excluded: chain I residue 826 ASP Chi-restraints excluded: chain I residue 828 PHE Chi-restraints excluded: chain I residue 903 ARG Chi-restraints excluded: chain I residue 942 ASP Chi-restraints excluded: chain I residue 971 LEU Chi-restraints excluded: chain I residue 992 LEU Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1145 ILE Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1170 MET Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain I residue 1315 MET Chi-restraints excluded: chain I residue 1332 SER Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 290 ILE Chi-restraints excluded: chain J residue 298 MET Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 368 LEU Chi-restraints excluded: chain J residue 393 THR Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 532 GLU Chi-restraints excluded: chain J residue 539 SER Chi-restraints excluded: chain J residue 567 THR Chi-restraints excluded: chain J residue 582 ILE Chi-restraints excluded: chain J residue 617 THR Chi-restraints excluded: chain J residue 641 ILE Chi-restraints excluded: chain J residue 652 GLU Chi-restraints excluded: chain J residue 743 MET Chi-restraints excluded: chain J residue 762 ASN Chi-restraints excluded: chain J residue 802 ASP Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 857 LEU Chi-restraints excluded: chain J residue 869 CYS Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 890 THR Chi-restraints excluded: chain J residue 897 HIS Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 1178 THR Chi-restraints excluded: chain J residue 1189 MET Chi-restraints excluded: chain J residue 1283 SER Chi-restraints excluded: chain J residue 1324 SER Chi-restraints excluded: chain J residue 1357 ILE Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 36 ASP Chi-restraints excluded: chain K residue 41 GLU Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain L residue 143 TYR Chi-restraints excluded: chain L residue 224 LEU Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 338 HIS Chi-restraints excluded: chain L residue 367 ILE Chi-restraints excluded: chain L residue 387 VAL Chi-restraints excluded: chain L residue 488 LEU Chi-restraints excluded: chain L residue 561 MET Chi-restraints excluded: chain L residue 603 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 349 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 chunk 206 optimal weight: 5.9990 chunk 264 optimal weight: 4.9990 chunk 205 optimal weight: 1.9990 chunk 305 optimal weight: 1.9990 chunk 202 optimal weight: 0.6980 chunk 361 optimal weight: 0.9980 chunk 226 optimal weight: 0.8980 chunk 220 optimal weight: 4.9990 chunk 166 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 132 HIS ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1220 GLN ** J 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 560 ASN K 72 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.3876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 31912 Z= 0.165 Angle : 0.559 8.150 43625 Z= 0.286 Chirality : 0.041 0.245 5062 Planarity : 0.004 0.074 5287 Dihedral : 14.048 116.999 5777 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.85 % Favored : 93.09 % Rotamer: Outliers : 2.87 % Allowed : 15.86 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.65 (0.14), residues: 3647 helix: 1.16 (0.14), residues: 1414 sheet: -1.14 (0.24), residues: 426 loop : -1.59 (0.14), residues: 1807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP L 326 HIS 0.010 0.001 HIS H 23 PHE 0.029 0.001 PHE L 221 TYR 0.026 0.001 TYR J 144 ARG 0.003 0.000 ARG H 143 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7294 Ramachandran restraints generated. 3647 Oldfield, 0 Emsley, 3647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7294 Ramachandran restraints generated. 3647 Oldfield, 0 Emsley, 3647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 3142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 339 time to evaluate : 3.520 Fit side-chains revert: symmetry clash REVERT: G 50 SER cc_start: 0.9221 (m) cc_final: 0.8825 (p) REVERT: H 16 ILE cc_start: 0.8780 (mt) cc_final: 0.8329 (tt) REVERT: H 86 LYS cc_start: 0.8431 (ttmt) cc_final: 0.7366 (tptt) REVERT: H 174 ASP cc_start: 0.6413 (OUTLIER) cc_final: 0.5916 (p0) REVERT: H 185 TYR cc_start: 0.8938 (p90) cc_final: 0.8633 (p90) REVERT: I 33 ASP cc_start: 0.7857 (t0) cc_final: 0.7500 (t0) REVERT: I 37 LYS cc_start: 0.8070 (mmtt) cc_final: 0.7756 (mmmm) REVERT: I 391 SER cc_start: 0.8823 (t) cc_final: 0.8487 (m) REVERT: I 530 ILE cc_start: 0.9725 (mm) cc_final: 0.9480 (mm) REVERT: I 672 GLU cc_start: 0.8202 (pm20) cc_final: 0.7816 (pm20) REVERT: I 741 MET cc_start: 0.8077 (ttp) cc_final: 0.7541 (ttm) REVERT: I 788 SER cc_start: 0.9086 (m) cc_final: 0.8530 (p) REVERT: I 826 ASP cc_start: 0.8256 (OUTLIER) cc_final: 0.7996 (t0) REVERT: I 828 PHE cc_start: 0.9201 (OUTLIER) cc_final: 0.8726 (m-10) REVERT: I 844 LYS cc_start: 0.8225 (mttm) cc_final: 0.7997 (pttp) REVERT: I 992 LEU cc_start: 0.6641 (OUTLIER) cc_final: 0.6278 (tp) REVERT: I 1025 PHE cc_start: 0.7786 (t80) cc_final: 0.7026 (t80) REVERT: I 1027 LYS cc_start: 0.8744 (pttt) cc_final: 0.8461 (ptpt) REVERT: I 1119 MET cc_start: 0.8841 (tpp) cc_final: 0.8116 (tpp) REVERT: I 1278 LEU cc_start: 0.9568 (OUTLIER) cc_final: 0.9350 (mp) REVERT: J 298 MET cc_start: 0.8219 (OUTLIER) cc_final: 0.7783 (mtm) REVERT: J 652 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.8161 (pp20) REVERT: J 707 ILE cc_start: 0.8566 (tp) cc_final: 0.8334 (tt) REVERT: J 718 SER cc_start: 0.8694 (t) cc_final: 0.8159 (m) REVERT: J 725 MET cc_start: 0.8027 (mtm) cc_final: 0.7816 (mtp) REVERT: J 922 SER cc_start: 0.9180 (m) cc_final: 0.8943 (p) REVERT: J 978 ARG cc_start: 0.7199 (OUTLIER) cc_final: 0.6547 (ptp-170) REVERT: J 1021 ASP cc_start: 0.6650 (p0) cc_final: 0.6007 (p0) REVERT: J 1040 MET cc_start: 0.2350 (ttt) cc_final: 0.2045 (ttt) REVERT: J 1175 LEU cc_start: 0.8308 (tt) cc_final: 0.8005 (mm) REVERT: J 1317 GLU cc_start: 0.7853 (mm-30) cc_final: 0.7573 (tm-30) REVERT: K 42 GLU cc_start: 0.8459 (mp0) cc_final: 0.7887 (mp0) REVERT: K 43 ASN cc_start: 0.8456 (m-40) cc_final: 0.8109 (m110) REVERT: L 144 LEU cc_start: 0.8142 (tt) cc_final: 0.7882 (mt) REVERT: L 276 MET cc_start: 0.7595 (ttt) cc_final: 0.7248 (ttp) REVERT: L 288 MET cc_start: 0.3960 (mtt) cc_final: 0.3545 (ptp) REVERT: L 322 MET cc_start: 0.3181 (mtp) cc_final: 0.2421 (tpt) REVERT: L 365 MET cc_start: 0.9044 (ttt) cc_final: 0.8807 (ttp) REVERT: L 468 ARG cc_start: 0.7232 (ttp80) cc_final: 0.6857 (ttm170) REVERT: L 474 MET cc_start: 0.7822 (mmm) cc_final: 0.7561 (mmm) REVERT: L 514 ASP cc_start: 0.8062 (t70) cc_final: 0.7583 (m-30) REVERT: L 524 GLU cc_start: 0.7709 (pt0) cc_final: 0.7395 (pm20) REVERT: L 561 MET cc_start: 0.8199 (ttm) cc_final: 0.7845 (ptm) REVERT: L 603 ARG cc_start: 0.8612 (OUTLIER) cc_final: 0.8232 (mtt180) outliers start: 90 outliers final: 54 residues processed: 406 average time/residue: 0.3975 time to fit residues: 265.3067 Evaluate side-chains 368 residues out of total 3142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 305 time to evaluate : 3.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 15 ASP Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain H residue 23 HIS Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain H residue 174 ASP Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 295 LYS Chi-restraints excluded: chain I residue 336 LEU Chi-restraints excluded: chain I residue 398 SER Chi-restraints excluded: chain I residue 410 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 773 LEU Chi-restraints excluded: chain I residue 826 ASP Chi-restraints excluded: chain I residue 828 PHE Chi-restraints excluded: chain I residue 863 SER Chi-restraints excluded: chain I residue 903 ARG Chi-restraints excluded: chain I residue 942 ASP Chi-restraints excluded: chain I residue 992 LEU Chi-restraints excluded: chain I residue 1124 ILE Chi-restraints excluded: chain I residue 1145 ILE Chi-restraints excluded: chain I residue 1278 LEU Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 298 MET Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 393 THR Chi-restraints excluded: chain J residue 452 LEU Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 532 GLU Chi-restraints excluded: chain J residue 539 SER Chi-restraints excluded: chain J residue 567 THR Chi-restraints excluded: chain J residue 617 THR Chi-restraints excluded: chain J residue 641 ILE Chi-restraints excluded: chain J residue 652 GLU Chi-restraints excluded: chain J residue 665 GLN Chi-restraints excluded: chain J residue 762 ASN Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 857 LEU Chi-restraints excluded: chain J residue 869 CYS Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 978 ARG Chi-restraints excluded: chain J residue 1178 THR Chi-restraints excluded: chain J residue 1189 MET Chi-restraints excluded: chain J residue 1324 SER Chi-restraints excluded: chain J residue 1357 ILE Chi-restraints excluded: chain K residue 41 GLU Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain L residue 224 LEU Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 338 HIS Chi-restraints excluded: chain L residue 367 ILE Chi-restraints excluded: chain L residue 387 VAL Chi-restraints excluded: chain L residue 488 LEU Chi-restraints excluded: chain L residue 603 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 223 optimal weight: 0.8980 chunk 144 optimal weight: 10.0000 chunk 215 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 chunk 71 optimal weight: 0.5980 chunk 70 optimal weight: 7.9990 chunk 229 optimal weight: 0.8980 chunk 246 optimal weight: 2.9990 chunk 178 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 284 optimal weight: 7.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 560 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.4063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 31912 Z= 0.160 Angle : 0.555 11.211 43625 Z= 0.282 Chirality : 0.040 0.232 5062 Planarity : 0.004 0.070 5287 Dihedral : 13.960 116.917 5777 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.50 % Favored : 93.45 % Rotamer: Outliers : 2.81 % Allowed : 16.31 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 3647 helix: 1.30 (0.14), residues: 1421 sheet: -1.06 (0.25), residues: 416 loop : -1.53 (0.14), residues: 1810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP L 326 HIS 0.011 0.001 HIS H 23 PHE 0.024 0.001 PHE L 221 TYR 0.020 0.001 TYR I 62 ARG 0.008 0.000 ARG H 44 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7294 Ramachandran restraints generated. 3647 Oldfield, 0 Emsley, 3647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7294 Ramachandran restraints generated. 3647 Oldfield, 0 Emsley, 3647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 3142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 319 time to evaluate : 3.258 Fit side-chains REVERT: G 10 LYS cc_start: 0.8760 (mtpt) cc_final: 0.8541 (mmmt) REVERT: G 50 SER cc_start: 0.9226 (m) cc_final: 0.8818 (p) REVERT: H 16 ILE cc_start: 0.8754 (mt) cc_final: 0.8320 (tt) REVERT: H 51 MET cc_start: 0.9148 (tpt) cc_final: 0.8809 (tpt) REVERT: H 86 LYS cc_start: 0.8421 (ttmt) cc_final: 0.7378 (ttmm) REVERT: H 174 ASP cc_start: 0.5672 (p0) cc_final: 0.5039 (p0) REVERT: H 185 TYR cc_start: 0.8903 (p90) cc_final: 0.8655 (p90) REVERT: I 33 ASP cc_start: 0.7669 (t0) cc_final: 0.7358 (t0) REVERT: I 37 LYS cc_start: 0.8159 (mmtt) cc_final: 0.7824 (mmmm) REVERT: I 315 MET cc_start: 0.7940 (mtt) cc_final: 0.7641 (mtt) REVERT: I 391 SER cc_start: 0.8822 (t) cc_final: 0.8383 (m) REVERT: I 499 SER cc_start: 0.8381 (t) cc_final: 0.7884 (p) REVERT: I 530 ILE cc_start: 0.9683 (mm) cc_final: 0.9456 (mm) REVERT: I 588 GLU cc_start: 0.7715 (mp0) cc_final: 0.7447 (mp0) REVERT: I 672 GLU cc_start: 0.8232 (pm20) cc_final: 0.7738 (pm20) REVERT: I 704 MET cc_start: 0.8607 (tpp) cc_final: 0.8250 (tpp) REVERT: I 741 MET cc_start: 0.7918 (ttp) cc_final: 0.7359 (ttm) REVERT: I 788 SER cc_start: 0.9051 (m) cc_final: 0.8480 (p) REVERT: I 826 ASP cc_start: 0.8117 (OUTLIER) cc_final: 0.7868 (t0) REVERT: I 828 PHE cc_start: 0.9194 (OUTLIER) cc_final: 0.8734 (m-10) REVERT: I 844 LYS cc_start: 0.8158 (mttm) cc_final: 0.7916 (pttm) REVERT: I 992 LEU cc_start: 0.6625 (OUTLIER) cc_final: 0.6243 (tp) REVERT: I 1027 LYS cc_start: 0.8774 (pttt) cc_final: 0.8521 (ptpt) REVERT: I 1119 MET cc_start: 0.8685 (tpp) cc_final: 0.8128 (tpp) REVERT: I 1278 LEU cc_start: 0.9530 (OUTLIER) cc_final: 0.9323 (mp) REVERT: J 505 ASP cc_start: 0.9102 (OUTLIER) cc_final: 0.8739 (t0) REVERT: J 652 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.8187 (pp20) REVERT: J 707 ILE cc_start: 0.8537 (tp) cc_final: 0.8295 (tt) REVERT: J 718 SER cc_start: 0.8812 (t) cc_final: 0.8278 (m) REVERT: J 870 ASP cc_start: 0.8041 (m-30) cc_final: 0.7703 (m-30) REVERT: J 922 SER cc_start: 0.9204 (m) cc_final: 0.8955 (p) REVERT: J 978 ARG cc_start: 0.7191 (OUTLIER) cc_final: 0.6525 (ptp-170) REVERT: J 1144 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.9065 (mm) REVERT: J 1175 LEU cc_start: 0.8343 (tt) cc_final: 0.8035 (mm) REVERT: J 1373 ARG cc_start: 0.7421 (OUTLIER) cc_final: 0.6897 (tpm170) REVERT: K 43 ASN cc_start: 0.8477 (m-40) cc_final: 0.8134 (m110) REVERT: K 53 GLU cc_start: 0.8572 (mt-10) cc_final: 0.8102 (mt-10) REVERT: K 76 GLU cc_start: 0.7926 (mm-30) cc_final: 0.7289 (mm-30) REVERT: L 102 MET cc_start: 0.8843 (mmm) cc_final: 0.8450 (mmm) REVERT: L 144 LEU cc_start: 0.8116 (OUTLIER) cc_final: 0.7891 (mp) REVERT: L 276 MET cc_start: 0.7558 (ttt) cc_final: 0.7220 (ttp) REVERT: L 288 MET cc_start: 0.4168 (mtt) cc_final: 0.3783 (ptp) REVERT: L 322 MET cc_start: 0.3353 (mtp) cc_final: 0.2403 (tpt) REVERT: L 365 MET cc_start: 0.9032 (ttt) cc_final: 0.8785 (ttp) REVERT: L 468 ARG cc_start: 0.7243 (ttp80) cc_final: 0.6867 (ttm170) REVERT: L 514 ASP cc_start: 0.8219 (t70) cc_final: 0.7793 (m-30) REVERT: L 524 GLU cc_start: 0.7689 (pt0) cc_final: 0.7391 (pm20) REVERT: L 561 MET cc_start: 0.8079 (ttm) cc_final: 0.7709 (ptm) outliers start: 88 outliers final: 55 residues processed: 386 average time/residue: 0.3831 time to fit residues: 245.2355 Evaluate side-chains 360 residues out of total 3142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 295 time to evaluate : 3.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 15 ASP Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain H residue 23 HIS Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 295 LYS Chi-restraints excluded: chain I residue 336 LEU Chi-restraints excluded: chain I residue 410 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 770 CYS Chi-restraints excluded: chain I residue 773 LEU Chi-restraints excluded: chain I residue 778 GLU Chi-restraints excluded: chain I residue 826 ASP Chi-restraints excluded: chain I residue 828 PHE Chi-restraints excluded: chain I residue 903 ARG Chi-restraints excluded: chain I residue 942 ASP Chi-restraints excluded: chain I residue 992 LEU Chi-restraints excluded: chain I residue 1278 LEU Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 241 VAL Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 368 LEU Chi-restraints excluded: chain J residue 393 THR Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 505 ASP Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 532 GLU Chi-restraints excluded: chain J residue 567 THR Chi-restraints excluded: chain J residue 587 LEU Chi-restraints excluded: chain J residue 652 GLU Chi-restraints excluded: chain J residue 665 GLN Chi-restraints excluded: chain J residue 762 ASN Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 857 LEU Chi-restraints excluded: chain J residue 869 CYS Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 950 ILE Chi-restraints excluded: chain J residue 978 ARG Chi-restraints excluded: chain J residue 1144 LEU Chi-restraints excluded: chain J residue 1178 THR Chi-restraints excluded: chain J residue 1189 MET Chi-restraints excluded: chain J residue 1283 SER Chi-restraints excluded: chain J residue 1324 SER Chi-restraints excluded: chain J residue 1357 ILE Chi-restraints excluded: chain J residue 1373 ARG Chi-restraints excluded: chain K residue 36 ASP Chi-restraints excluded: chain K residue 41 GLU Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 224 LEU Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 338 HIS Chi-restraints excluded: chain L residue 367 ILE Chi-restraints excluded: chain L residue 488 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 328 optimal weight: 9.9990 chunk 346 optimal weight: 6.9990 chunk 315 optimal weight: 3.9990 chunk 336 optimal weight: 5.9990 chunk 202 optimal weight: 2.9990 chunk 146 optimal weight: 9.9990 chunk 264 optimal weight: 5.9990 chunk 103 optimal weight: 7.9990 chunk 304 optimal weight: 0.9990 chunk 318 optimal weight: 8.9990 chunk 335 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 560 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.4121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 31912 Z= 0.394 Angle : 0.698 10.797 43625 Z= 0.355 Chirality : 0.044 0.231 5062 Planarity : 0.005 0.072 5287 Dihedral : 14.165 116.066 5777 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.34 % Favored : 91.61 % Rotamer: Outliers : 3.29 % Allowed : 16.15 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.71 (0.14), residues: 3647 helix: 1.02 (0.14), residues: 1417 sheet: -1.01 (0.25), residues: 417 loop : -1.60 (0.14), residues: 1813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP L 326 HIS 0.011 0.001 HIS H 23 PHE 0.034 0.002 PHE I 389 TYR 0.021 0.002 TYR J1186 ARG 0.008 0.001 ARG H 143 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7294 Ramachandran restraints generated. 3647 Oldfield, 0 Emsley, 3647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7294 Ramachandran restraints generated. 3647 Oldfield, 0 Emsley, 3647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 3142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 289 time to evaluate : 3.196 Fit side-chains revert: symmetry clash REVERT: G 50 SER cc_start: 0.9265 (m) cc_final: 0.8889 (p) REVERT: G 163 GLU cc_start: 0.6149 (OUTLIER) cc_final: 0.5546 (mp0) REVERT: H 16 ILE cc_start: 0.8809 (mt) cc_final: 0.8383 (tt) REVERT: H 86 LYS cc_start: 0.8551 (ttmt) cc_final: 0.7709 (ttmm) REVERT: H 174 ASP cc_start: 0.5837 (OUTLIER) cc_final: 0.5082 (p0) REVERT: I 33 ASP cc_start: 0.7890 (t0) cc_final: 0.7509 (t0) REVERT: I 37 LYS cc_start: 0.8334 (mmtt) cc_final: 0.7942 (mmmm) REVERT: I 515 MET cc_start: 0.8841 (ttp) cc_final: 0.8597 (ttp) REVERT: I 588 GLU cc_start: 0.8115 (mp0) cc_final: 0.7852 (mp0) REVERT: I 672 GLU cc_start: 0.8265 (pm20) cc_final: 0.7951 (pm20) REVERT: I 741 MET cc_start: 0.8153 (ttp) cc_final: 0.7435 (ttm) REVERT: I 788 SER cc_start: 0.9287 (m) cc_final: 0.8840 (p) REVERT: I 826 ASP cc_start: 0.8308 (OUTLIER) cc_final: 0.8068 (t0) REVERT: I 828 PHE cc_start: 0.9295 (OUTLIER) cc_final: 0.8983 (m-10) REVERT: I 844 LYS cc_start: 0.8193 (mttm) cc_final: 0.7925 (pttm) REVERT: I 992 LEU cc_start: 0.6829 (OUTLIER) cc_final: 0.6539 (tp) REVERT: I 1027 LYS cc_start: 0.8686 (pttt) cc_final: 0.8406 (ptpt) REVERT: I 1119 MET cc_start: 0.8888 (tpp) cc_final: 0.8260 (tpp) REVERT: I 1329 GLU cc_start: 0.7760 (mt-10) cc_final: 0.7200 (mt-10) REVERT: J 505 ASP cc_start: 0.9208 (OUTLIER) cc_final: 0.8764 (t0) REVERT: J 652 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.8182 (pp20) REVERT: J 658 GLU cc_start: 0.8087 (mt-10) cc_final: 0.7802 (mt-10) REVERT: J 707 ILE cc_start: 0.8675 (tp) cc_final: 0.8440 (tt) REVERT: J 870 ASP cc_start: 0.8074 (m-30) cc_final: 0.7738 (m-30) REVERT: J 978 ARG cc_start: 0.7283 (OUTLIER) cc_final: 0.6604 (ptp-170) REVERT: J 1144 LEU cc_start: 0.9439 (OUTLIER) cc_final: 0.9229 (mm) REVERT: J 1175 LEU cc_start: 0.8343 (tt) cc_final: 0.7960 (mm) REVERT: J 1372 ARG cc_start: 0.7729 (ttp80) cc_final: 0.7477 (ttp80) REVERT: K 15 ASN cc_start: 0.7883 (t0) cc_final: 0.7652 (t0) REVERT: K 43 ASN cc_start: 0.8550 (m-40) cc_final: 0.8233 (m110) REVERT: L 144 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7908 (pp) REVERT: L 276 MET cc_start: 0.7471 (ttt) cc_final: 0.7241 (ttp) REVERT: L 288 MET cc_start: 0.4243 (mtt) cc_final: 0.3841 (ptp) REVERT: L 322 MET cc_start: 0.3432 (mtp) cc_final: 0.2479 (tpt) REVERT: L 365 MET cc_start: 0.9106 (ttt) cc_final: 0.8865 (ttp) REVERT: L 379 MET cc_start: 0.8953 (tpt) cc_final: 0.8553 (tpt) REVERT: L 468 ARG cc_start: 0.7333 (ttp80) cc_final: 0.6831 (ttm170) REVERT: L 514 ASP cc_start: 0.8125 (t70) cc_final: 0.7667 (p0) REVERT: L 524 GLU cc_start: 0.7708 (pt0) cc_final: 0.7390 (pm20) REVERT: L 561 MET cc_start: 0.8126 (ttm) cc_final: 0.7846 (ptm) REVERT: L 603 ARG cc_start: 0.8720 (OUTLIER) cc_final: 0.8305 (mtt180) outliers start: 103 outliers final: 74 residues processed: 369 average time/residue: 0.3951 time to fit residues: 241.2959 Evaluate side-chains 367 residues out of total 3142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 282 time to evaluate : 3.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 15 ASP Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 163 GLU Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain H residue 23 HIS Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 174 ASP Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain H residue 205 MET Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 295 LYS Chi-restraints excluded: chain I residue 336 LEU Chi-restraints excluded: chain I residue 398 SER Chi-restraints excluded: chain I residue 410 LEU Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 717 VAL Chi-restraints excluded: chain I residue 770 CYS Chi-restraints excluded: chain I residue 773 LEU Chi-restraints excluded: chain I residue 778 GLU Chi-restraints excluded: chain I residue 826 ASP Chi-restraints excluded: chain I residue 828 PHE Chi-restraints excluded: chain I residue 903 ARG Chi-restraints excluded: chain I residue 942 ASP Chi-restraints excluded: chain I residue 992 LEU Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1170 MET Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 241 VAL Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 368 LEU Chi-restraints excluded: chain J residue 393 THR Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 505 ASP Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 532 GLU Chi-restraints excluded: chain J residue 567 THR Chi-restraints excluded: chain J residue 582 ILE Chi-restraints excluded: chain J residue 587 LEU Chi-restraints excluded: chain J residue 617 THR Chi-restraints excluded: chain J residue 641 ILE Chi-restraints excluded: chain J residue 652 GLU Chi-restraints excluded: chain J residue 762 ASN Chi-restraints excluded: chain J residue 802 ASP Chi-restraints excluded: chain J residue 840 LEU Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 857 LEU Chi-restraints excluded: chain J residue 863 LEU Chi-restraints excluded: chain J residue 869 CYS Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 897 HIS Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 950 ILE Chi-restraints excluded: chain J residue 978 ARG Chi-restraints excluded: chain J residue 1144 LEU Chi-restraints excluded: chain J residue 1178 THR Chi-restraints excluded: chain J residue 1189 MET Chi-restraints excluded: chain J residue 1283 SER Chi-restraints excluded: chain J residue 1324 SER Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain K residue 36 ASP Chi-restraints excluded: chain K residue 41 GLU Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 224 LEU Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 338 HIS Chi-restraints excluded: chain L residue 367 ILE Chi-restraints excluded: chain L residue 410 ILE Chi-restraints excluded: chain L residue 488 LEU Chi-restraints excluded: chain L residue 603 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 221 optimal weight: 0.9980 chunk 356 optimal weight: 4.9990 chunk 217 optimal weight: 0.8980 chunk 168 optimal weight: 4.9990 chunk 247 optimal weight: 0.6980 chunk 373 optimal weight: 10.0000 chunk 343 optimal weight: 0.9990 chunk 297 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 chunk 229 optimal weight: 0.5980 chunk 182 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 560 ASN ** K 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.4259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 31912 Z= 0.163 Angle : 0.580 11.044 43625 Z= 0.294 Chirality : 0.041 0.228 5062 Planarity : 0.004 0.072 5287 Dihedral : 14.021 119.447 5777 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.11 % Favored : 93.83 % Rotamer: Outliers : 2.17 % Allowed : 17.46 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.14), residues: 3647 helix: 1.29 (0.14), residues: 1427 sheet: -1.04 (0.25), residues: 418 loop : -1.48 (0.15), residues: 1802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP L 326 HIS 0.011 0.001 HIS H 23 PHE 0.021 0.001 PHE I1164 TYR 0.020 0.001 TYR H 185 ARG 0.009 0.000 ARG H 44 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7294 Ramachandran restraints generated. 3647 Oldfield, 0 Emsley, 3647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7294 Ramachandran restraints generated. 3647 Oldfield, 0 Emsley, 3647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 3142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 313 time to evaluate : 3.412 Fit side-chains REVERT: G 50 SER cc_start: 0.9221 (m) cc_final: 0.8847 (p) REVERT: H 16 ILE cc_start: 0.8732 (mt) cc_final: 0.8301 (tt) REVERT: H 51 MET cc_start: 0.9240 (tpt) cc_final: 0.8822 (tpt) REVERT: H 86 LYS cc_start: 0.8480 (ttmt) cc_final: 0.7571 (ttmm) REVERT: H 174 ASP cc_start: 0.5312 (p0) cc_final: 0.5088 (p0) REVERT: H 186 ASN cc_start: 0.8672 (m-40) cc_final: 0.8430 (m-40) REVERT: I 33 ASP cc_start: 0.7829 (t0) cc_final: 0.7527 (t0) REVERT: I 37 LYS cc_start: 0.8202 (mmtt) cc_final: 0.7834 (mmmm) REVERT: I 138 ILE cc_start: 0.9383 (mm) cc_final: 0.8944 (mm) REVERT: I 315 MET cc_start: 0.7987 (mtt) cc_final: 0.7493 (mtt) REVERT: I 364 VAL cc_start: 0.8730 (t) cc_final: 0.8427 (t) REVERT: I 391 SER cc_start: 0.8799 (t) cc_final: 0.8335 (m) REVERT: I 499 SER cc_start: 0.8393 (t) cc_final: 0.7869 (p) REVERT: I 515 MET cc_start: 0.8749 (ttp) cc_final: 0.8537 (ttp) REVERT: I 672 GLU cc_start: 0.8178 (pm20) cc_final: 0.7695 (pm20) REVERT: I 741 MET cc_start: 0.8017 (ttp) cc_final: 0.7447 (ttm) REVERT: I 788 SER cc_start: 0.9103 (m) cc_final: 0.8535 (p) REVERT: I 826 ASP cc_start: 0.8252 (OUTLIER) cc_final: 0.7977 (t0) REVERT: I 828 PHE cc_start: 0.9172 (OUTLIER) cc_final: 0.8727 (m-80) REVERT: I 992 LEU cc_start: 0.6486 (OUTLIER) cc_final: 0.6092 (tp) REVERT: I 1027 LYS cc_start: 0.8578 (pttt) cc_final: 0.8294 (ptpt) REVERT: I 1085 MET cc_start: 0.9414 (mmm) cc_final: 0.9147 (mmm) REVERT: I 1119 MET cc_start: 0.8658 (tpp) cc_final: 0.8125 (tpp) REVERT: J 163 GLU cc_start: 0.8371 (mp0) cc_final: 0.8059 (mp0) REVERT: J 169 LEU cc_start: 0.8474 (pp) cc_final: 0.8236 (tp) REVERT: J 582 ILE cc_start: 0.9396 (OUTLIER) cc_final: 0.9034 (tp) REVERT: J 652 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.8134 (pp20) REVERT: J 707 ILE cc_start: 0.8615 (tp) cc_final: 0.8383 (tt) REVERT: J 718 SER cc_start: 0.8702 (t) cc_final: 0.8141 (m) REVERT: J 870 ASP cc_start: 0.7944 (m-30) cc_final: 0.7616 (m-30) REVERT: J 978 ARG cc_start: 0.7254 (OUTLIER) cc_final: 0.6556 (ptp-170) REVERT: J 1144 LEU cc_start: 0.9315 (OUTLIER) cc_final: 0.9099 (mm) REVERT: J 1175 LEU cc_start: 0.8308 (tt) cc_final: 0.7962 (mm) REVERT: J 1189 MET cc_start: 0.8203 (OUTLIER) cc_final: 0.7593 (mmm) REVERT: J 1372 ARG cc_start: 0.7619 (ttp80) cc_final: 0.7401 (ttp80) REVERT: K 30 MET cc_start: 0.8594 (mtm) cc_final: 0.8309 (mtt) REVERT: K 53 GLU cc_start: 0.8634 (mt-10) cc_final: 0.7990 (mt-10) REVERT: L 102 MET cc_start: 0.8819 (mmm) cc_final: 0.8433 (mmm) REVERT: L 144 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7890 (pp) REVERT: L 276 MET cc_start: 0.7528 (ttt) cc_final: 0.7199 (ttp) REVERT: L 288 MET cc_start: 0.4144 (mtt) cc_final: 0.3771 (ptp) REVERT: L 322 MET cc_start: 0.3371 (mtp) cc_final: 0.2406 (tpt) REVERT: L 365 MET cc_start: 0.8943 (ttt) cc_final: 0.8685 (ttp) REVERT: L 468 ARG cc_start: 0.7226 (ttp80) cc_final: 0.6858 (ttm170) REVERT: L 514 ASP cc_start: 0.7928 (t70) cc_final: 0.7433 (m-30) REVERT: L 515 GLU cc_start: 0.5752 (mm-30) cc_final: 0.5543 (mm-30) REVERT: L 524 GLU cc_start: 0.7721 (pt0) cc_final: 0.7422 (pm20) REVERT: L 561 MET cc_start: 0.8109 (ttm) cc_final: 0.7776 (ptm) REVERT: L 603 ARG cc_start: 0.8622 (OUTLIER) cc_final: 0.7648 (mtm-85) outliers start: 68 outliers final: 50 residues processed: 368 average time/residue: 0.4004 time to fit residues: 241.7703 Evaluate side-chains 349 residues out of total 3142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 289 time to evaluate : 3.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 15 ASP Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain H residue 23 HIS Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 295 LYS Chi-restraints excluded: chain I residue 336 LEU Chi-restraints excluded: chain I residue 398 SER Chi-restraints excluded: chain I residue 410 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 773 LEU Chi-restraints excluded: chain I residue 826 ASP Chi-restraints excluded: chain I residue 828 PHE Chi-restraints excluded: chain I residue 903 ARG Chi-restraints excluded: chain I residue 992 LEU Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 241 VAL Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 368 LEU Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 532 GLU Chi-restraints excluded: chain J residue 567 THR Chi-restraints excluded: chain J residue 582 ILE Chi-restraints excluded: chain J residue 587 LEU Chi-restraints excluded: chain J residue 617 THR Chi-restraints excluded: chain J residue 641 ILE Chi-restraints excluded: chain J residue 652 GLU Chi-restraints excluded: chain J residue 762 ASN Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 857 LEU Chi-restraints excluded: chain J residue 869 CYS Chi-restraints excluded: chain J residue 950 ILE Chi-restraints excluded: chain J residue 978 ARG Chi-restraints excluded: chain J residue 1144 LEU Chi-restraints excluded: chain J residue 1178 THR Chi-restraints excluded: chain J residue 1189 MET Chi-restraints excluded: chain J residue 1250 ASP Chi-restraints excluded: chain J residue 1283 SER Chi-restraints excluded: chain K residue 36 ASP Chi-restraints excluded: chain K residue 41 GLU Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 224 LEU Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 338 HIS Chi-restraints excluded: chain L residue 367 ILE Chi-restraints excluded: chain L residue 488 LEU Chi-restraints excluded: chain L residue 603 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 236 optimal weight: 6.9990 chunk 316 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 274 optimal weight: 30.0000 chunk 43 optimal weight: 2.9990 chunk 82 optimal weight: 10.0000 chunk 297 optimal weight: 6.9990 chunk 124 optimal weight: 0.8980 chunk 305 optimal weight: 4.9990 chunk 37 optimal weight: 9.9990 chunk 54 optimal weight: 0.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 560 ASN K 43 ASN ** K 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.130734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.096287 restraints weight = 62433.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.096327 restraints weight = 42555.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.096592 restraints weight = 32856.987| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.4310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 31912 Z= 0.218 Angle : 0.599 12.412 43625 Z= 0.301 Chirality : 0.042 0.233 5062 Planarity : 0.004 0.072 5287 Dihedral : 13.997 118.103 5777 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.99 % Favored : 92.95 % Rotamer: Outliers : 2.23 % Allowed : 17.84 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.42 (0.14), residues: 3647 helix: 1.35 (0.14), residues: 1420 sheet: -0.99 (0.25), residues: 417 loop : -1.47 (0.15), residues: 1810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP L 326 HIS 0.011 0.001 HIS H 23 PHE 0.041 0.001 PHE L 256 TYR 0.024 0.001 TYR H 185 ARG 0.007 0.000 ARG H 44 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6037.52 seconds wall clock time: 109 minutes 58.28 seconds (6598.28 seconds total)