Starting phenix.real_space_refine on Mon Sep 14 15:38:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/5vt0_8732/09_2026/5vt0_8732.cif Found real_map, /net/cci-nas-00/data/ceres_data/5vt0_8732/09_2026/5vt0_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/cci-nas-00/data/ceres_data/5vt0_8732/09_2026/5vt0_8732.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5vt0_8732/09_2026/5vt0_8732.map" restraint_files = "/net/cci-nas-00/data/ceres_data/5vt0_8732/09_2026/5vt0_8732.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/5vt0_8732/09_2026/5vt0_8732.cif" model { file = "/net/cci-nas-00/data/ceres_data/5vt0_8732/09_2026/5vt0_8732.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5vt0_8732/09_2026/5vt0_8732.cif" } resolution = 3.78 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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. Time to flip 8 residue(s): 0.21s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/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, 'ASP:plan': 1, 'GLU: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: {'RNAv2': 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: 6.44, per 1000 atoms: 0.21 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.64 Conformation dependent library (CDL) restraints added in 1.3 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: 3.88 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: 7.93 Time building geometry restraints manager: 3.54 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 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=" CG ARG G 45 " pdb=" CD ARG G 45 " ideal model delta sigma weight residual 1.520 1.441 0.079 3.00e-02 1.11e+03 6.99e+00 bond pdb=" C2 G R 80 " pdb=" N2 G R 80 " ideal model delta sigma weight residual 1.341 1.291 0.050 2.00e-02 2.50e+03 6.24e+00 ... (remaining 31907 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 41605 2.41 - 4.83: 1719 4.83 - 7.24: 233 7.24 - 9.65: 46 9.65 - 12.07: 22 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=" C ILE L 565 " pdb=" N ASP L 566 " pdb=" CA ASP L 566 " ideal model delta sigma weight residual 121.54 131.99 -10.45 1.91e+00 2.74e-01 2.99e+01 angle pdb=" N TRP I 997 " pdb=" CA TRP I 997 " pdb=" C TRP I 997 " ideal model delta sigma weight residual 114.04 107.32 6.72 1.24e+00 6.50e-01 2.94e+01 angle pdb=" C4' G R 97 " pdb=" C3' G R 97 " pdb=" O3' G R 97 " ideal model delta sigma weight residual 112.50 102.02 10.48 2.00e+00 2.50e-01 2.74e+01 angle pdb=" N GLU J 211 " pdb=" CA GLU J 211 " pdb=" C GLU J 211 " ideal model delta sigma weight residual 111.02 117.37 -6.35 1.22e+00 6.72e-01 2.71e+01 ... (remaining 43620 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.03: 18145 16.03 - 32.06: 860 32.06 - 48.09: 270 48.09 - 64.12: 105 64.12 - 80.14: 46 Dihedral angle restraints: 19426 sinusoidal: 8858 harmonic: 10568 Sorted by residual: dihedral pdb=" C4' G R 97 " pdb=" C3' G R 97 " pdb=" C2' G R 97 " pdb=" C1' G R 97 " ideal model delta sinusoidal sigma weight residual 36.34 -37.53 73.87 1 3.10e+00 1.04e-01 7.21e+02 dihedral pdb=" C4' U R 81 " pdb=" C3' U R 81 " pdb=" C2' U R 81 " pdb=" C1' U R 81 " ideal model delta sinusoidal sigma weight residual 36.34 -36.78 73.12 1 3.10e+00 1.04e-01 7.09e+02 dihedral pdb=" C4' A R 142 " pdb=" C3' A R 142 " pdb=" C2' A R 142 " pdb=" C1' A R 142 " ideal model delta sinusoidal sigma weight residual 36.35 -35.61 71.96 1 3.10e+00 1.04e-01 6.90e+02 ... (remaining 19423 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 4552 0.109 - 0.218: 393 0.218 - 0.327: 106 0.327 - 0.437: 9 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 -2.49 -1.98 -0.51 2.00e-01 2.50e+01 6.52e+00 chirality pdb=" C2' C R 95 " pdb=" C3' C R 95 " pdb=" O2' C R 95 " pdb=" C1' C R 95 " both_signs ideal model delta sigma weight residual False -2.79 -2.36 -0.43 2.00e-01 2.50e+01 4.70e+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 3.040 nonbonded pdb=" NH2 ARG I 903 " pdb=" O6 G R 82 " model vdw 2.248 3.120 nonbonded pdb=" O GLN L 227 " pdb=" OG1 THR L 231 " model vdw 2.256 3.040 nonbonded pdb=" N2 G R 84 " pdb=" O2 C R 107 " model vdw 2.260 3.120 ... (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 Time spend for trying shortcut: 0.00 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: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.380 Check model and map are aligned: 0.100 Set scattering table: 0.050 Process input model: 35.870 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 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 : 0.009 0.601 31919 Z= 0.366 Angle : 1.142 28.854 43631 Z= 0.607 Chirality : 0.073 0.546 5062 Planarity : 0.007 0.072 5287 Dihedral : 12.173 80.144 12612 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.018 0.001 ARG J 538 TYR 0.028 0.003 TYR J 457 PHE 0.036 0.003 PHE J 620 TRP 0.040 0.004 TRP J 115 HIS 0.013 0.002 HIS I1116 Details of bonding type rmsd/Z covalent geometry : bond 0.00751 / 0.34 (31912) covalent geometry : angle 1.12743 / 0.61 (43625) hydrogen bonds : bond 0.15806 / 11.01 ( 1310) hydrogen bonds : angle 6.93995 / 4.80 ( 3648) metal coordination : bond 0.28149 / 19.70 ( 7) metal coordination : angle 15.75986 / 8.43 ( 6) *********************** 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 to be fit. rotamer outliers: 18 poor density : 723 time to evaluate : 1.142 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: 0.8656 (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: 0.7427 (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: 0.8504 (tt) cc_final: 0.8282 (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: 0.7449 (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: 0.2312 time to fit residues: 261.6763 Evaluate side-chains 358 residues out of total 3142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 352 time to evaluate : 1.281 ------------------------------------------------------------------------------- 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 197 optimal weight: 3.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 0.2980 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 0.4980 chunk 298 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 I1220 GLN ** J 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 489 ASN J 560 ASN J1108 GLN J1259 GLN L 283 GLN L 600 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.136306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.100605 restraints weight = 62281.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.101191 restraints weight = 37293.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.101826 restraints weight = 25373.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.102231 restraints weight = 24327.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.102384 restraints weight = 20840.203| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 31919 Z= 0.145 Angle : 0.781 15.666 43631 Z= 0.375 Chirality : 0.056 0.686 5062 Planarity : 0.005 0.066 5287 Dihedral : 11.048 153.572 5371 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.57 % Favored : 94.38 % Rotamer: Outliers : 2.01 % Allowed : 8.71 % Favored : 89.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.13 (0.13), residues: 3647 helix: -0.44 (0.13), residues: 1419 sheet: -1.55 (0.25), residues: 390 loop : -2.20 (0.13), residues: 1838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 996 TYR 0.025 0.001 TYR L 228 PHE 0.016 0.001 PHE J 620 TRP 0.019 0.002 TRP L 326 HIS 0.009 0.001 HIS L 600 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (31912) covalent geometry : angle 0.78027 / 0.37 (43625) hydrogen bonds : bond 0.04250 / 2.90 ( 1310) hydrogen bonds : angle 5.01403 / 3.44 ( 3648) metal coordination : bond 0.00778 / 0.57 ( 7) metal coordination : angle 3.62698 / 2.01 ( 6) *********************** 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 522 residues out of total 3142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 459 time to evaluate : 1.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 25 LYS cc_start: 0.8654 (mtpt) cc_final: 0.8408 (mttt) REVERT: G 111 THR cc_start: 0.9036 (p) cc_final: 0.8692 (t) REVERT: H 16 ILE cc_start: 0.8767 (mt) cc_final: 0.8404 (tt) REVERT: H 81 ILE cc_start: 0.8543 (mm) cc_final: 0.8287 (mm) REVERT: H 84 ASN cc_start: 0.8483 (t0) cc_final: 0.8249 (t0) REVERT: H 85 LEU cc_start: 0.8334 (mt) cc_final: 0.8054 (mt) REVERT: H 86 LYS cc_start: 0.8116 (ttmt) cc_final: 0.7597 (tttt) REVERT: H 185 TYR cc_start: 0.9075 (p90) cc_final: 0.8754 (p90) REVERT: H 200 LYS cc_start: 0.8531 (ttmt) cc_final: 0.8327 (tttt) REVERT: I 37 LYS cc_start: 0.7990 (mmtt) cc_final: 0.7737 (mmmm) REVERT: I 260 LYS cc_start: 0.8243 (tppt) cc_final: 0.8005 (tptp) REVERT: I 315 MET cc_start: 0.8041 (mtp) cc_final: 0.7583 (mtt) REVERT: I 327 GLN cc_start: 0.8517 (pt0) cc_final: 0.8173 (mm-40) REVERT: I 391 SER cc_start: 0.8825 (t) cc_final: 0.8540 (m) REVERT: I 461 GLU cc_start: 0.8438 (tt0) cc_final: 0.8225 (tt0) REVERT: I 484 LEU cc_start: 0.7594 (OUTLIER) cc_final: 0.7375 (mt) REVERT: I 510 GLN cc_start: 0.8327 (mt0) cc_final: 0.8098 (mt0) REVERT: I 515 MET cc_start: 0.8913 (ttp) cc_final: 0.8663 (ttp) REVERT: I 549 ASP cc_start: 0.8594 (t0) cc_final: 0.8262 (m-30) REVERT: I 741 MET cc_start: 0.8205 (ttp) cc_final: 0.7897 (ttt) REVERT: I 768 MET cc_start: 0.7899 (mtm) cc_final: 0.7633 (mtp) REVERT: I 788 SER cc_start: 0.9212 (m) cc_final: 0.8623 (p) REVERT: I 813 GLU cc_start: 0.8067 (mm-30) cc_final: 0.7786 (tp30) REVERT: I 844 LYS cc_start: 0.8176 (mttm) cc_final: 0.7828 (pttm) REVERT: I 902 LEU cc_start: 0.9136 (tt) cc_final: 0.8877 (tp) REVERT: I 992 LEU cc_start: 0.6431 (OUTLIER) cc_final: 0.6065 (tp) REVERT: I 1027 LYS cc_start: 0.8687 (pttt) cc_final: 0.8220 (ptpp) REVERT: I 1111 GLN cc_start: 0.8001 (pt0) cc_final: 0.7643 (pt0) REVERT: I 1119 MET cc_start: 0.8836 (tpp) cc_final: 0.7703 (tpp) REVERT: I 1230 MET cc_start: 0.8626 (ttm) cc_final: 0.8157 (ttp) REVERT: J 151 MET cc_start: 0.6399 (mtp) cc_final: 0.6065 (tpt) REVERT: J 162 GLU cc_start: 0.8201 (pm20) cc_final: 0.7350 (pm20) REVERT: J 163 GLU cc_start: 0.8246 (mp0) cc_final: 0.7482 (mp0) REVERT: J 295 GLU cc_start: 0.8628 (tp30) cc_final: 0.8259 (tp30) REVERT: J 304 ASP cc_start: 0.7508 (m-30) cc_final: 0.7227 (m-30) REVERT: J 314 ARG cc_start: 0.7395 (ttt180) cc_final: 0.6906 (ttp80) REVERT: J 718 SER cc_start: 0.8838 (t) cc_final: 0.8619 (m) REVERT: J 737 ILE cc_start: 0.9163 (OUTLIER) cc_final: 0.8804 (pt) REVERT: J 870 ASP cc_start: 0.8306 (m-30) cc_final: 0.7923 (m-30) REVERT: J 890 THR cc_start: 0.8489 (m) cc_final: 0.8163 (p) REVERT: J 922 SER cc_start: 0.9187 (m) cc_final: 0.8909 (p) REVERT: J 1021 ASP cc_start: 0.5644 (p0) cc_final: 0.5399 (p0) REVERT: J 1275 LEU cc_start: 0.8049 (mp) cc_final: 0.7797 (tp) REVERT: J 1283 SER cc_start: 0.8705 (OUTLIER) cc_final: 0.8333 (p) REVERT: J 1345 ARG cc_start: 0.6839 (mmp80) cc_final: 0.6521 (mmt180) REVERT: K 42 GLU cc_start: 0.8171 (mp0) cc_final: 0.7735 (mp0) REVERT: K 53 GLU cc_start: 0.8833 (mt-10) cc_final: 0.8433 (mt-10) REVERT: L 105 MET cc_start: 0.8952 (tmm) cc_final: 0.8609 (tmm) REVERT: L 276 MET cc_start: 0.7845 (ttt) cc_final: 0.7504 (ttp) REVERT: L 322 MET cc_start: 0.3508 (mtp) cc_final: 0.3149 (mtt) REVERT: L 381 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7720 (mt-10) REVERT: L 468 ARG cc_start: 0.7635 (ttp80) cc_final: 0.7186 (ttm170) REVERT: L 474 MET cc_start: 0.7527 (mmm) cc_final: 0.7141 (mmm) REVERT: L 524 GLU cc_start: 0.7719 (pt0) cc_final: 0.7373 (pm20) outliers start: 63 outliers final: 28 residues processed: 503 average time/residue: 0.1998 time to fit residues: 162.7963 Evaluate side-chains 355 residues out of total 3142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 323 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 23 HIS 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 653 MET Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 903 ARG Chi-restraints excluded: chain I residue 992 LEU Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain I residue 1315 MET Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 452 LEU Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 641 ILE Chi-restraints excluded: chain J residue 737 ILE Chi-restraints excluded: chain J residue 897 HIS Chi-restraints excluded: chain J residue 1283 SER Chi-restraints excluded: chain K residue 39 VAL 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 189 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 198 optimal weight: 6.9990 chunk 88 optimal weight: 2.9990 chunk 253 optimal weight: 2.9990 chunk 282 optimal weight: 40.0000 chunk 182 optimal weight: 0.0270 chunk 136 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 chunk 180 optimal weight: 0.5980 chunk 75 optimal weight: 8.9990 overall best weight: 2.1244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 84 ASN I 219 GLN I 273 HIS J 560 ASN J1244 GLN K 72 GLN ** L 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.132243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.097177 restraints weight = 62652.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.097662 restraints weight = 35303.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.098114 restraints weight = 25522.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.098529 restraints weight = 24343.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.098662 restraints weight = 20921.412| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 31919 Z= 0.174 Angle : 0.705 11.521 43631 Z= 0.343 Chirality : 0.052 0.392 5062 Planarity : 0.005 0.069 5287 Dihedral : 10.863 157.572 5369 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.20 % Favored : 93.75 % Rotamer: Outliers : 2.55 % Allowed : 11.33 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.13), residues: 3647 helix: 0.24 (0.14), residues: 1432 sheet: -1.43 (0.25), residues: 393 loop : -1.99 (0.13), residues: 1822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 44 TYR 0.021 0.001 TYR L 228 PHE 0.017 0.001 PHE J 620 TRP 0.015 0.002 TRP L 326 HIS 0.012 0.001 HIS H 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.17 (31912) covalent geometry : angle 0.70447 / 0.34 (43625) hydrogen bonds : bond 0.04085 / 2.79 ( 1310) hydrogen bonds : angle 4.72813 / 3.24 ( 3648) metal coordination : bond 0.00529 / 0.28 ( 7) metal coordination : angle 2.69917 / 1.52 ( 6) *********************** 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 434 residues out of total 3142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 354 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 16 ILE cc_start: 0.8753 (mt) cc_final: 0.8400 (tt) REVERT: H 81 ILE cc_start: 0.8781 (mm) cc_final: 0.8462 (mm) REVERT: H 85 LEU cc_start: 0.8493 (mt) cc_final: 0.8265 (mt) REVERT: H 86 LYS cc_start: 0.8237 (ttmt) cc_final: 0.7514 (tttt) REVERT: H 185 TYR cc_start: 0.9100 (p90) cc_final: 0.8789 (p90) REVERT: I 33 ASP cc_start: 0.7719 (t0) cc_final: 0.7493 (t0) REVERT: I 37 LYS cc_start: 0.8010 (mmtt) cc_final: 0.7733 (mmmm) REVERT: I 130 MET cc_start: 0.8780 (ttp) cc_final: 0.8520 (ttm) REVERT: I 315 MET cc_start: 0.8315 (mtp) cc_final: 0.7879 (mtt) REVERT: I 327 GLN cc_start: 0.8472 (pt0) cc_final: 0.8136 (mm-40) REVERT: I 391 SER cc_start: 0.8826 (t) cc_final: 0.8544 (m) REVERT: I 484 LEU cc_start: 0.7734 (OUTLIER) cc_final: 0.7508 (mt) REVERT: I 549 ASP cc_start: 0.8722 (t0) cc_final: 0.8322 (m-30) REVERT: I 672 GLU cc_start: 0.8092 (pm20) cc_final: 0.7695 (pm20) REVERT: I 681 MET cc_start: 0.8202 (mtt) cc_final: 0.7793 (mtm) REVERT: I 741 MET cc_start: 0.8234 (ttp) cc_final: 0.7870 (ttt) REVERT: I 788 SER cc_start: 0.9223 (m) cc_final: 0.8530 (p) REVERT: I 828 PHE cc_start: 0.9293 (OUTLIER) cc_final: 0.8769 (m-80) REVERT: I 844 LYS cc_start: 0.8260 (mttm) cc_final: 0.8031 (pttp) REVERT: I 992 LEU cc_start: 0.6611 (OUTLIER) cc_final: 0.6102 (tp) REVERT: I 1008 GLN cc_start: 0.6057 (tp40) cc_final: 0.5655 (tp40) REVERT: I 1027 LYS cc_start: 0.8766 (pttt) cc_final: 0.8253 (ptpp) REVERT: I 1040 ASP cc_start: 0.7751 (p0) cc_final: 0.7463 (m-30) REVERT: I 1111 GLN cc_start: 0.8120 (pt0) cc_final: 0.7561 (pt0) REVERT: I 1119 MET cc_start: 0.8950 (tpp) cc_final: 0.8284 (tpp) REVERT: I 1151 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8083 (tt) REVERT: I 1230 MET cc_start: 0.8714 (ttm) cc_final: 0.8154 (ttp) REVERT: I 1329 GLU cc_start: 0.7429 (mt-10) cc_final: 0.6975 (mt-10) REVERT: J 151 MET cc_start: 0.6541 (mtp) cc_final: 0.6321 (tpt) REVERT: J 180 MET cc_start: 0.8287 (ttp) cc_final: 0.8086 (ttm) REVERT: J 295 GLU cc_start: 0.8737 (tp30) cc_final: 0.8344 (tp30) REVERT: J 304 ASP cc_start: 0.7487 (m-30) cc_final: 0.7190 (m-30) REVERT: J 652 GLU cc_start: 0.8382 (tm-30) cc_final: 0.8069 (pp20) REVERT: J 870 ASP cc_start: 0.8294 (m-30) cc_final: 0.8040 (m-30) REVERT: J 922 SER cc_start: 0.9173 (m) cc_final: 0.8918 (p) REVERT: J 1021 ASP cc_start: 0.6147 (p0) cc_final: 0.5802 (p0) REVERT: J 1345 ARG cc_start: 0.6936 (mmp80) cc_final: 0.6431 (mmt180) REVERT: J 1352 ILE cc_start: 0.9486 (mm) cc_final: 0.9278 (mm) REVERT: K 42 GLU cc_start: 0.8162 (mp0) cc_final: 0.7884 (mp0) REVERT: K 53 GLU cc_start: 0.8780 (mt-10) cc_final: 0.8456 (mt-10) REVERT: K 56 GLU cc_start: 0.8435 (mm-30) cc_final: 0.8235 (mm-30) REVERT: K 76 GLU cc_start: 0.7967 (mm-30) cc_final: 0.7468 (mm-30) REVERT: L 276 MET cc_start: 0.7504 (ttt) cc_final: 0.7144 (ttp) REVERT: L 322 MET cc_start: 0.3652 (mtp) cc_final: 0.3083 (mtt) REVERT: L 365 MET cc_start: 0.8768 (ttt) cc_final: 0.8389 (ttp) REVERT: L 413 MET cc_start: 0.8716 (mtp) cc_final: 0.8495 (mtm) REVERT: L 468 ARG cc_start: 0.7584 (ttp80) cc_final: 0.7184 (ttm170) REVERT: L 474 MET cc_start: 0.7517 (mmm) cc_final: 0.7170 (mmm) REVERT: L 514 ASP cc_start: 0.8108 (t0) cc_final: 0.7418 (p0) REVERT: L 524 GLU cc_start: 0.7661 (pt0) cc_final: 0.7412 (pm20) REVERT: L 561 MET cc_start: 0.8077 (ttm) cc_final: 0.7817 (ptm) outliers start: 80 outliers final: 48 residues processed: 417 average time/residue: 0.1879 time to fit residues: 130.3939 Evaluate side-chains 360 residues out of total 3142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 308 time to evaluate : 1.087 ------------------------------------------------------------------------------- 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 27 THR Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 107 ILE 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 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 773 LEU 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 1145 ILE Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1289 GLU 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 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 253 VAL Chi-restraints excluded: chain J residue 350 SER Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 539 SER Chi-restraints excluded: chain J residue 802 ASP Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 897 HIS 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 39 VAL 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 367 ILE Chi-restraints excluded: chain L residue 488 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 290 optimal weight: 5.9990 chunk 175 optimal weight: 1.9990 chunk 123 optimal weight: 0.0770 chunk 91 optimal weight: 0.0040 chunk 256 optimal weight: 0.5980 chunk 284 optimal weight: 5.9990 chunk 76 optimal weight: 7.9990 chunk 278 optimal weight: 30.0000 chunk 114 optimal weight: 7.9990 chunk 53 optimal weight: 9.9990 chunk 271 optimal weight: 6.9990 overall best weight: 1.7354 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 23 HIS H 227 GLN I 219 GLN I 273 HIS I 513 GLN I 832 HIS I1010 GLN I1013 GLN J 560 ASN J1244 GLN L 331 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.132384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.097101 restraints weight = 62062.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.098444 restraints weight = 34861.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.098542 restraints weight = 24076.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.098933 restraints weight = 23608.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.099033 restraints weight = 20664.161| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 31919 Z= 0.148 Angle : 0.660 10.066 43631 Z= 0.320 Chirality : 0.049 0.324 5062 Planarity : 0.004 0.070 5287 Dihedral : 10.583 163.883 5369 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.92 % Favored : 94.02 % Rotamer: Outliers : 2.84 % Allowed : 12.74 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.14), residues: 3647 helix: 0.68 (0.14), residues: 1430 sheet: -1.37 (0.25), residues: 393 loop : -1.75 (0.14), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J1258 TYR 0.020 0.001 TYR L 228 PHE 0.015 0.001 PHE J 620 TRP 0.016 0.001 TRP L 326 HIS 0.006 0.001 HIS L 600 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (31912) covalent geometry : angle 0.65983 / 0.32 (43625) hydrogen bonds : bond 0.03783 / 2.59 ( 1310) hydrogen bonds : angle 4.48473 / 3.07 ( 3648) metal coordination : bond 0.00442 / 0.24 ( 7) metal coordination : angle 1.99758 / 1.13 ( 6) *********************** 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 460 residues out of total 3142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 371 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 10 LYS cc_start: 0.8890 (ptmt) cc_final: 0.8368 (mtpt) REVERT: G 50 SER cc_start: 0.9326 (m) cc_final: 0.8660 (p) REVERT: H 16 ILE cc_start: 0.8775 (mt) cc_final: 0.8336 (tt) REVERT: H 85 LEU cc_start: 0.8497 (mt) cc_final: 0.8282 (mt) REVERT: H 86 LYS cc_start: 0.8434 (ttmt) cc_final: 0.7674 (tttt) REVERT: H 185 TYR cc_start: 0.9110 (p90) cc_final: 0.8812 (p90) REVERT: I 33 ASP cc_start: 0.7729 (t0) cc_final: 0.7494 (t0) REVERT: I 37 LYS cc_start: 0.8129 (mmtt) cc_final: 0.7812 (mmmm) REVERT: I 130 MET cc_start: 0.8728 (ttp) cc_final: 0.8514 (ttm) REVERT: I 315 MET cc_start: 0.8145 (mtp) cc_final: 0.7797 (mtt) REVERT: I 327 GLN cc_start: 0.8332 (pt0) cc_final: 0.8046 (mm-40) REVERT: I 391 SER cc_start: 0.8779 (t) cc_final: 0.8468 (m) REVERT: I 407 ARG cc_start: 0.7894 (tpp80) cc_final: 0.7430 (ttm-80) REVERT: I 530 ILE cc_start: 0.9700 (mm) cc_final: 0.9479 (mm) REVERT: I 549 ASP cc_start: 0.8757 (t0) cc_final: 0.8488 (m-30) REVERT: I 633 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7581 (pp) REVERT: I 672 GLU cc_start: 0.8155 (pm20) cc_final: 0.7783 (pm20) REVERT: I 681 MET cc_start: 0.8145 (mtt) cc_final: 0.7767 (mtm) REVERT: I 741 MET cc_start: 0.8128 (ttp) cc_final: 0.7745 (ttt) REVERT: I 788 SER cc_start: 0.9135 (m) cc_final: 0.8377 (p) REVERT: I 828 PHE cc_start: 0.9245 (OUTLIER) cc_final: 0.8833 (m-80) REVERT: I 971 LEU cc_start: 0.7749 (OUTLIER) cc_final: 0.7429 (tt) REVERT: I 992 LEU cc_start: 0.6481 (OUTLIER) cc_final: 0.5987 (tp) REVERT: I 1027 LYS cc_start: 0.8749 (pttt) cc_final: 0.8503 (ptpt) REVERT: I 1040 ASP cc_start: 0.7783 (p0) cc_final: 0.7250 (m-30) REVERT: I 1111 GLN cc_start: 0.8066 (pt0) cc_final: 0.7668 (pt0) REVERT: I 1119 MET cc_start: 0.8962 (tpp) cc_final: 0.8547 (tpp) REVERT: I 1230 MET cc_start: 0.8683 (ttm) cc_final: 0.8175 (ttp) REVERT: I 1329 GLU cc_start: 0.7452 (mt-10) cc_final: 0.7048 (mt-10) REVERT: J 163 GLU cc_start: 0.8377 (mp0) cc_final: 0.8130 (mp0) REVERT: J 295 GLU cc_start: 0.8783 (tp30) cc_final: 0.8258 (tp30) REVERT: J 304 ASP cc_start: 0.7639 (m-30) cc_final: 0.7391 (m-30) REVERT: J 652 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.8082 (pp20) REVERT: J 707 ILE cc_start: 0.8473 (tp) cc_final: 0.8112 (tt) REVERT: J 870 ASP cc_start: 0.8115 (m-30) cc_final: 0.7784 (m-30) REVERT: J 922 SER cc_start: 0.9194 (m) cc_final: 0.8981 (p) REVERT: J 1021 ASP cc_start: 0.6296 (p0) cc_final: 0.5941 (p0) REVERT: J 1040 MET cc_start: 0.2018 (ttt) cc_final: 0.1777 (ttt) REVERT: J 1175 LEU cc_start: 0.8188 (tt) cc_final: 0.7941 (mm) REVERT: K 53 GLU cc_start: 0.8913 (mt-10) cc_final: 0.8515 (mt-10) REVERT: K 76 GLU cc_start: 0.7856 (mm-30) cc_final: 0.7214 (mm-30) REVERT: L 276 MET cc_start: 0.7446 (ttt) cc_final: 0.7116 (ttp) REVERT: L 288 MET cc_start: 0.3902 (mtt) cc_final: 0.3592 (ptp) REVERT: L 322 MET cc_start: 0.2952 (mtp) cc_final: 0.2632 (tpt) REVERT: L 365 MET cc_start: 0.8788 (ttt) cc_final: 0.8431 (ttp) REVERT: L 413 MET cc_start: 0.8761 (mtp) cc_final: 0.8520 (mtm) REVERT: L 468 ARG cc_start: 0.7630 (ttp80) cc_final: 0.7181 (ttm170) REVERT: L 514 ASP cc_start: 0.8135 (t0) cc_final: 0.7571 (m-30) REVERT: L 524 GLU cc_start: 0.7713 (pt0) cc_final: 0.7391 (pm20) REVERT: L 561 MET cc_start: 0.8063 (ttm) cc_final: 0.7791 (ptm) outliers start: 89 outliers final: 55 residues processed: 436 average time/residue: 0.1877 time to fit residues: 135.5625 Evaluate side-chains 377 residues out of total 3142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 317 time to evaluate : 1.094 ------------------------------------------------------------------------------- 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 129 VAL 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 174 ASP Chi-restraints excluded: chain H residue 198 LEU 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 219 GLN Chi-restraints excluded: chain I residue 410 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 633 LEU Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 773 LEU Chi-restraints excluded: chain I residue 828 PHE Chi-restraints excluded: chain I residue 903 ARG Chi-restraints excluded: chain I residue 913 VAL Chi-restraints excluded: chain I residue 971 LEU Chi-restraints excluded: chain I residue 992 LEU Chi-restraints excluded: chain I residue 1042 LEU 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 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 237 MET Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 350 SER Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 368 LEU Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 539 SER Chi-restraints excluded: chain J residue 587 LEU Chi-restraints excluded: chain J residue 652 GLU Chi-restraints excluded: chain J residue 802 ASP Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 897 HIS Chi-restraints excluded: chain J residue 980 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 39 VAL Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain L residue 98 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 58 optimal weight: 6.9990 chunk 341 optimal weight: 10.0000 chunk 69 optimal weight: 10.0000 chunk 126 optimal weight: 4.9990 chunk 276 optimal weight: 6.9990 chunk 65 optimal weight: 9.9990 chunk 155 optimal weight: 1.9990 chunk 299 optimal weight: 8.9990 chunk 93 optimal weight: 1.9990 chunk 174 optimal weight: 7.9990 chunk 324 optimal weight: 20.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 23 HIS I 219 GLN I 343 HIS J 560 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.127541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.092367 restraints weight = 62722.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.092730 restraints weight = 41993.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.093065 restraints weight = 30527.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.093682 restraints weight = 25758.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.093740 restraints weight = 22976.409| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.3616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.079 31919 Z= 0.299 Angle : 0.799 10.701 43631 Z= 0.389 Chirality : 0.053 0.376 5062 Planarity : 0.005 0.069 5287 Dihedral : 10.740 165.837 5369 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.49 % Favored : 92.46 % Rotamer: Outliers : 3.99 % Allowed : 13.21 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.14), residues: 3647 helix: 0.52 (0.14), residues: 1435 sheet: -1.39 (0.25), residues: 400 loop : -1.82 (0.14), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 996 TYR 0.026 0.002 TYR I 62 PHE 0.022 0.002 PHE I 545 TRP 0.016 0.002 TRP L 326 HIS 0.026 0.002 HIS H 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00691 / 0.30 (31912) covalent geometry : angle 0.79830 / 0.39 (43625) hydrogen bonds : bond 0.04464 / 3.06 ( 1310) hydrogen bonds : angle 4.83571 / 3.32 ( 3648) metal coordination : bond 0.01125 / 0.62 ( 7) metal coordination : angle 2.64876 / 1.48 ( 6) *********************** 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 441 residues out of total 3142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 316 time to evaluate : 1.127 Fit side-chains revert: symmetry clash REVERT: G 50 SER cc_start: 0.9336 (m) cc_final: 0.8784 (p) REVERT: G 75 GLN cc_start: 0.8965 (pt0) cc_final: 0.8533 (tt0) REVERT: H 16 ILE cc_start: 0.8843 (mt) cc_final: 0.8435 (tt) REVERT: H 86 LYS cc_start: 0.8612 (ttmt) cc_final: 0.7830 (ttmm) REVERT: H 185 TYR cc_start: 0.9241 (p90) cc_final: 0.9018 (p90) REVERT: I 33 ASP cc_start: 0.7919 (t0) cc_final: 0.7662 (t0) REVERT: I 37 LYS cc_start: 0.8060 (mmtt) cc_final: 0.7734 (mmmm) REVERT: I 315 MET cc_start: 0.8154 (mtp) cc_final: 0.7938 (mtt) REVERT: I 475 VAL cc_start: 0.9500 (OUTLIER) cc_final: 0.9282 (p) REVERT: I 549 ASP cc_start: 0.8819 (t0) cc_final: 0.8610 (m-30) REVERT: I 633 LEU cc_start: 0.7780 (OUTLIER) cc_final: 0.7523 (pp) REVERT: I 672 GLU cc_start: 0.8282 (pm20) cc_final: 0.7889 (pm20) REVERT: I 741 MET cc_start: 0.8214 (ttp) cc_final: 0.7601 (ttm) REVERT: I 788 SER cc_start: 0.9275 (m) cc_final: 0.8764 (p) REVERT: I 828 PHE cc_start: 0.9353 (OUTLIER) cc_final: 0.9067 (m-10) REVERT: I 992 LEU cc_start: 0.6736 (OUTLIER) cc_final: 0.6180 (tp) REVERT: I 1025 PHE cc_start: 0.7617 (t80) cc_final: 0.6778 (t80) REVERT: I 1027 LYS cc_start: 0.8742 (pttt) cc_final: 0.8491 (ptpt) REVERT: I 1111 GLN cc_start: 0.8327 (pt0) cc_final: 0.7688 (pt0) REVERT: I 1119 MET cc_start: 0.9023 (tpp) cc_final: 0.8331 (tpp) REVERT: I 1230 MET cc_start: 0.8839 (ttm) cc_final: 0.8543 (ttp) REVERT: J 304 ASP cc_start: 0.7617 (m-30) cc_final: 0.7316 (m-30) REVERT: J 652 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.8140 (pp20) REVERT: J 870 ASP cc_start: 0.8181 (m-30) cc_final: 0.7879 (m-30) REVERT: J 922 SER cc_start: 0.9300 (m) cc_final: 0.9041 (p) REVERT: J 1175 LEU cc_start: 0.8240 (tt) cc_final: 0.7957 (mm) REVERT: K 3 ARG cc_start: 0.8631 (mmm-85) cc_final: 0.8336 (mmm-85) REVERT: K 42 GLU cc_start: 0.8202 (mp0) cc_final: 0.7874 (mp0) REVERT: K 53 GLU cc_start: 0.8862 (mt-10) cc_final: 0.8452 (mt-10) REVERT: K 76 GLU cc_start: 0.7904 (mm-30) cc_final: 0.7275 (mm-30) REVERT: L 276 MET cc_start: 0.7238 (ttt) cc_final: 0.7035 (ttp) REVERT: L 322 MET cc_start: 0.3308 (mtp) cc_final: 0.2833 (tpt) REVERT: L 365 MET cc_start: 0.8719 (ttt) cc_final: 0.8397 (ttp) REVERT: L 379 MET cc_start: 0.8742 (tpt) cc_final: 0.8370 (tpt) REVERT: L 468 ARG cc_start: 0.7441 (ttp80) cc_final: 0.7055 (ttm170) REVERT: L 524 GLU cc_start: 0.7785 (pt0) cc_final: 0.7454 (pm20) REVERT: L 561 MET cc_start: 0.8058 (ttm) cc_final: 0.7805 (ptm) REVERT: L 603 ARG cc_start: 0.8745 (OUTLIER) cc_final: 0.8281 (mtt180) outliers start: 125 outliers final: 82 residues processed: 410 average time/residue: 0.1875 time to fit residues: 128.0647 Evaluate side-chains 372 residues out of total 3142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 284 time to evaluate : 1.183 ------------------------------------------------------------------------------- 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 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 155 VAL Chi-restraints excluded: chain I residue 164 THR Chi-restraints excluded: chain I residue 302 ILE Chi-restraints excluded: chain I residue 336 LEU Chi-restraints excluded: chain I residue 410 LEU Chi-restraints excluded: chain I residue 420 LEU Chi-restraints excluded: chain I residue 475 VAL 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 633 LEU Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 693 LEU Chi-restraints excluded: chain I residue 773 LEU Chi-restraints excluded: chain I residue 828 PHE Chi-restraints excluded: chain I residue 829 THR Chi-restraints excluded: chain I residue 845 LEU Chi-restraints excluded: chain I residue 903 ARG Chi-restraints excluded: chain I residue 927 THR Chi-restraints excluded: chain I residue 992 LEU Chi-restraints excluded: chain I residue 1042 LEU Chi-restraints excluded: chain I residue 1170 MET Chi-restraints excluded: chain I residue 1254 VAL 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 132 LEU Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 192 MET 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 350 SER 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 539 SER Chi-restraints excluded: chain J residue 587 LEU 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 840 LEU Chi-restraints excluded: chain J residue 849 LEU 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 950 ILE Chi-restraints excluded: chain J residue 980 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 4 VAL Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain L residue 133 SER 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 603 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 17 optimal weight: 2.9990 chunk 180 optimal weight: 1.9990 chunk 369 optimal weight: 20.0000 chunk 34 optimal weight: 3.9990 chunk 263 optimal weight: 7.9990 chunk 225 optimal weight: 0.4980 chunk 28 optimal weight: 1.9990 chunk 114 optimal weight: 4.9990 chunk 167 optimal weight: 2.9990 chunk 255 optimal weight: 0.7980 chunk 101 optimal weight: 0.7980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 23 HIS H 132 HIS ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 219 GLN I 808 ASN J 560 ASN J 910 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.131878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.097127 restraints weight = 62050.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.097425 restraints weight = 40172.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.097761 restraints weight = 29058.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.098042 restraints weight = 27695.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.098427 restraints weight = 23397.344| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.3831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 31919 Z= 0.130 Angle : 0.654 8.883 43631 Z= 0.317 Chirality : 0.048 0.302 5062 Planarity : 0.004 0.070 5287 Dihedral : 10.498 166.935 5369 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.98 % Favored : 93.97 % Rotamer: Outliers : 2.84 % Allowed : 14.75 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.14), residues: 3647 helix: 0.95 (0.14), residues: 1431 sheet: -1.23 (0.25), residues: 401 loop : -1.65 (0.14), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 996 TYR 0.018 0.001 TYR J 679 PHE 0.016 0.001 PHE L 256 TRP 0.015 0.001 TRP L 326 HIS 0.006 0.001 HIS J 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (31912) covalent geometry : angle 0.65333 / 0.32 (43625) hydrogen bonds : bond 0.03718 / 2.55 ( 1310) hydrogen bonds : angle 4.41562 / 3.02 ( 3648) metal coordination : bond 0.00358 / 0.19 ( 7) metal coordination : angle 1.98655 / 1.15 ( 6) *********************** 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 430 residues out of total 3142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 341 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 50 SER cc_start: 0.9278 (m) cc_final: 0.8771 (p) REVERT: G 163 GLU cc_start: 0.5723 (OUTLIER) cc_final: 0.5459 (mp0) REVERT: H 16 ILE cc_start: 0.8754 (mt) cc_final: 0.8315 (tt) REVERT: H 86 LYS cc_start: 0.8514 (ttmt) cc_final: 0.7397 (tptt) REVERT: H 174 ASP cc_start: 0.5438 (OUTLIER) cc_final: 0.5096 (p0) REVERT: H 185 TYR cc_start: 0.9173 (p90) cc_final: 0.8933 (p90) REVERT: I 33 ASP cc_start: 0.7678 (t0) cc_final: 0.7447 (t0) REVERT: I 37 LYS cc_start: 0.8089 (mmtt) cc_final: 0.7785 (mmmm) REVERT: I 315 MET cc_start: 0.8201 (mtp) cc_final: 0.7992 (mtt) REVERT: I 391 SER cc_start: 0.8850 (t) cc_final: 0.8530 (m) REVERT: I 549 ASP cc_start: 0.8768 (t0) cc_final: 0.8479 (m-30) REVERT: I 672 GLU cc_start: 0.8091 (pm20) cc_final: 0.7743 (pm20) REVERT: I 741 MET cc_start: 0.8128 (ttp) cc_final: 0.7620 (ttm) REVERT: I 788 SER cc_start: 0.9089 (m) cc_final: 0.8433 (p) REVERT: I 828 PHE cc_start: 0.9267 (OUTLIER) cc_final: 0.8892 (m-10) REVERT: I 992 LEU cc_start: 0.6346 (OUTLIER) cc_final: 0.5825 (tp) REVERT: I 1027 LYS cc_start: 0.8701 (pttt) cc_final: 0.8445 (ptpt) REVERT: I 1111 GLN cc_start: 0.8157 (pt0) cc_final: 0.7633 (pt0) REVERT: I 1119 MET cc_start: 0.8920 (tpp) cc_final: 0.8229 (tpp) REVERT: I 1230 MET cc_start: 0.8683 (ttm) cc_final: 0.8195 (ttp) REVERT: J 163 GLU cc_start: 0.8113 (mp0) cc_final: 0.7835 (mp0) REVERT: J 298 MET cc_start: 0.8174 (OUTLIER) cc_final: 0.7857 (mtm) REVERT: J 304 ASP cc_start: 0.7630 (m-30) cc_final: 0.7358 (m-30) REVERT: J 652 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.8073 (pp20) REVERT: J 658 GLU cc_start: 0.8023 (mt-10) cc_final: 0.7794 (mt-10) REVERT: J 725 MET cc_start: 0.8451 (mtm) cc_final: 0.8088 (mtp) REVERT: J 922 SER cc_start: 0.9144 (m) cc_final: 0.8942 (p) REVERT: J 1175 LEU cc_start: 0.8370 (tt) cc_final: 0.8118 (mm) REVERT: J 1189 MET cc_start: 0.8201 (OUTLIER) cc_final: 0.7788 (mmm) REVERT: K 3 ARG cc_start: 0.8623 (mmm-85) cc_final: 0.8357 (mmm-85) REVERT: K 42 GLU cc_start: 0.8133 (mp0) cc_final: 0.7874 (mp0) REVERT: K 53 GLU cc_start: 0.8806 (mt-10) cc_final: 0.8364 (mt-10) REVERT: L 100 MET cc_start: 0.7967 (mtt) cc_final: 0.7666 (mtt) REVERT: L 288 MET cc_start: 0.3542 (mtt) cc_final: 0.3321 (ptp) REVERT: L 322 MET cc_start: 0.3344 (mtp) cc_final: 0.2541 (tpt) REVERT: L 365 MET cc_start: 0.8723 (ttt) cc_final: 0.8449 (ttp) REVERT: L 468 ARG cc_start: 0.7457 (ttp80) cc_final: 0.7127 (ttm170) REVERT: L 474 MET cc_start: 0.7610 (mmm) cc_final: 0.7318 (mmm) REVERT: L 524 GLU cc_start: 0.7699 (pt0) cc_final: 0.7400 (pm20) REVERT: L 561 MET cc_start: 0.8053 (ttm) cc_final: 0.7729 (ptm) outliers start: 89 outliers final: 49 residues processed: 398 average time/residue: 0.1840 time to fit residues: 122.6750 Evaluate side-chains 361 residues out of total 3142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 305 time to evaluate : 1.139 ------------------------------------------------------------------------------- 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 163 GLU 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 48 LEU Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 124 VAL 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 62 TYR Chi-restraints excluded: chain I residue 410 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 773 LEU 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 1295 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 298 MET Chi-restraints excluded: chain J residue 350 SER Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 368 LEU Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 518 VAL 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 587 LEU Chi-restraints excluded: chain J residue 652 GLU Chi-restraints excluded: chain J residue 802 ASP Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 890 THR Chi-restraints excluded: chain J residue 897 HIS Chi-restraints excluded: chain J residue 950 ILE Chi-restraints excluded: chain J residue 1189 MET 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 133 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 203 optimal weight: 0.9980 chunk 129 optimal weight: 0.7980 chunk 19 optimal weight: 9.9990 chunk 144 optimal weight: 9.9990 chunk 66 optimal weight: 0.9980 chunk 362 optimal weight: 4.9990 chunk 333 optimal weight: 20.0000 chunk 65 optimal weight: 5.9990 chunk 269 optimal weight: 20.0000 chunk 243 optimal weight: 0.8980 chunk 318 optimal weight: 10.0000 overall best weight: 1.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 23 HIS H 37 HIS H 227 GLN I 219 GLN ** I 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 560 ASN K 72 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.132085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.096076 restraints weight = 61995.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.097033 restraints weight = 37642.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.097548 restraints weight = 24957.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.097915 restraints weight = 22806.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.097979 restraints weight = 20641.114| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.3970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 31919 Z= 0.149 Angle : 0.662 9.156 43631 Z= 0.321 Chirality : 0.048 0.308 5062 Planarity : 0.004 0.071 5287 Dihedral : 10.391 167.620 5369 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.53 % Favored : 93.42 % Rotamer: Outliers : 2.74 % Allowed : 15.42 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.14), residues: 3647 helix: 1.05 (0.14), residues: 1432 sheet: -1.24 (0.25), residues: 411 loop : -1.63 (0.14), residues: 1804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J1372 TYR 0.021 0.001 TYR I 73 PHE 0.027 0.001 PHE L 221 TRP 0.015 0.001 TRP L 326 HIS 0.005 0.001 HIS L 600 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (31912) covalent geometry : angle 0.66131 / 0.32 (43625) hydrogen bonds : bond 0.03767 / 2.58 ( 1310) hydrogen bonds : angle 4.40284 / 3.02 ( 3648) metal coordination : bond 0.00491 / 0.26 ( 7) metal coordination : angle 1.69995 / 0.98 ( 6) *********************** 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 404 residues out of total 3142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 318 time to evaluate : 1.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 50 SER cc_start: 0.9374 (m) cc_final: 0.8848 (p) REVERT: G 163 GLU cc_start: 0.5789 (OUTLIER) cc_final: 0.5467 (mp0) REVERT: H 16 ILE cc_start: 0.8758 (mt) cc_final: 0.8304 (tt) REVERT: H 86 LYS cc_start: 0.8534 (ttmt) cc_final: 0.7606 (tptt) REVERT: H 174 ASP cc_start: 0.5318 (OUTLIER) cc_final: 0.4976 (p0) REVERT: H 185 TYR cc_start: 0.9181 (p90) cc_final: 0.8949 (p90) REVERT: I 33 ASP cc_start: 0.7844 (t0) cc_final: 0.7546 (t0) REVERT: I 37 LYS cc_start: 0.8118 (mmtt) cc_final: 0.7782 (mmmm) REVERT: I 295 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.8283 (mppt) REVERT: I 315 MET cc_start: 0.8217 (mtp) cc_final: 0.7991 (mtt) REVERT: I 549 ASP cc_start: 0.8797 (t0) cc_final: 0.8448 (m-30) REVERT: I 672 GLU cc_start: 0.8194 (pm20) cc_final: 0.7809 (pm20) REVERT: I 741 MET cc_start: 0.8101 (ttp) cc_final: 0.7598 (ttm) REVERT: I 788 SER cc_start: 0.9230 (m) cc_final: 0.8606 (p) REVERT: I 828 PHE cc_start: 0.9292 (OUTLIER) cc_final: 0.8938 (m-10) REVERT: I 992 LEU cc_start: 0.6686 (OUTLIER) cc_final: 0.5758 (tp) REVERT: I 1025 PHE cc_start: 0.7765 (t80) cc_final: 0.6887 (t80) REVERT: I 1027 LYS cc_start: 0.8741 (pttt) cc_final: 0.8469 (ptpt) REVERT: I 1111 GLN cc_start: 0.8101 (pt0) cc_final: 0.7485 (pt0) REVERT: I 1119 MET cc_start: 0.8930 (tpp) cc_final: 0.8220 (tpp) REVERT: I 1230 MET cc_start: 0.8662 (ttm) cc_final: 0.8180 (ttp) REVERT: I 1278 LEU cc_start: 0.9530 (OUTLIER) cc_final: 0.9326 (mp) REVERT: J 298 MET cc_start: 0.8239 (OUTLIER) cc_final: 0.7879 (mtm) REVERT: J 304 ASP cc_start: 0.7693 (m-30) cc_final: 0.7384 (m-30) REVERT: J 652 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.8162 (pp20) REVERT: J 725 MET cc_start: 0.8480 (mtm) cc_final: 0.7960 (mtp) REVERT: J 922 SER cc_start: 0.9203 (m) cc_final: 0.8977 (p) REVERT: J 1040 MET cc_start: 0.2063 (ttt) cc_final: 0.1724 (ttt) REVERT: J 1175 LEU cc_start: 0.8434 (tt) cc_final: 0.8162 (mm) REVERT: J 1251 LYS cc_start: 0.9103 (OUTLIER) cc_final: 0.8855 (mtpp) REVERT: K 42 GLU cc_start: 0.8225 (mp0) cc_final: 0.7936 (mp0) REVERT: K 53 GLU cc_start: 0.8748 (mt-10) cc_final: 0.8301 (mt-10) REVERT: K 76 GLU cc_start: 0.7872 (mm-30) cc_final: 0.7247 (mm-30) REVERT: L 288 MET cc_start: 0.3985 (mtt) cc_final: 0.3757 (ptp) REVERT: L 322 MET cc_start: 0.3354 (mtp) cc_final: 0.2534 (tpt) REVERT: L 365 MET cc_start: 0.8737 (ttt) cc_final: 0.8467 (ttp) REVERT: L 468 ARG cc_start: 0.7334 (ttp80) cc_final: 0.7014 (ttm170) REVERT: L 514 ASP cc_start: 0.8124 (t0) cc_final: 0.7493 (m-30) REVERT: L 524 GLU cc_start: 0.7740 (pt0) cc_final: 0.7411 (pm20) REVERT: L 561 MET cc_start: 0.8084 (ttm) cc_final: 0.7755 (ptm) outliers start: 86 outliers final: 58 residues processed: 379 average time/residue: 0.1861 time to fit residues: 117.9836 Evaluate side-chains 365 residues out of total 3142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 298 time to evaluate : 1.170 ------------------------------------------------------------------------------- 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 129 VAL Chi-restraints excluded: chain G residue 163 GLU Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 124 VAL 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 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 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 773 LEU Chi-restraints excluded: chain I residue 819 SER 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 927 THR Chi-restraints excluded: chain I residue 992 LEU Chi-restraints excluded: chain I residue 1170 MET Chi-restraints excluded: chain I residue 1278 LEU Chi-restraints excluded: chain I residue 1295 SER Chi-restraints excluded: chain I residue 1298 VAL 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 241 VAL Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 298 MET Chi-restraints excluded: chain J residue 350 SER 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 434 ILE Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 518 VAL 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 652 GLU Chi-restraints excluded: chain J residue 802 ASP Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 857 LEU Chi-restraints excluded: chain J residue 890 THR Chi-restraints excluded: chain J residue 897 HIS Chi-restraints excluded: chain J residue 950 ILE Chi-restraints excluded: chain J residue 1189 MET Chi-restraints excluded: chain J residue 1251 LYS Chi-restraints excluded: chain J residue 1352 ILE 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 133 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 309 optimal weight: 10.0000 chunk 313 optimal weight: 5.9990 chunk 207 optimal weight: 0.0570 chunk 266 optimal weight: 7.9990 chunk 344 optimal weight: 0.4980 chunk 67 optimal weight: 7.9990 chunk 10 optimal weight: 0.0270 chunk 315 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 277 optimal weight: 20.0000 chunk 133 optimal weight: 0.9980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 219 GLN I 273 HIS I 760 ASN J 560 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.134813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.100308 restraints weight = 62118.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.101159 restraints weight = 36768.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.101261 restraints weight = 28012.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.101679 restraints weight = 25388.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.101840 restraints weight = 21990.857| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.4287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 31919 Z= 0.108 Angle : 0.623 8.519 43631 Z= 0.302 Chirality : 0.047 0.265 5062 Planarity : 0.004 0.073 5287 Dihedral : 10.124 169.010 5369 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.57 % Favored : 94.38 % Rotamer: Outliers : 2.33 % Allowed : 16.09 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.14), residues: 3647 helix: 1.25 (0.14), residues: 1440 sheet: -1.08 (0.26), residues: 393 loop : -1.53 (0.14), residues: 1814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 202 TYR 0.019 0.001 TYR J 144 PHE 0.036 0.001 PHE J 380 TRP 0.020 0.001 TRP L 326 HIS 0.005 0.001 HIS J 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (31912) covalent geometry : angle 0.62305 / 0.30 (43625) hydrogen bonds : bond 0.03434 / 2.35 ( 1310) hydrogen bonds : angle 4.22105 / 2.88 ( 3648) metal coordination : bond 0.00178 / 0.09 ( 7) metal coordination : angle 1.53983 / 0.71 ( 6) *********************** 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 439 residues out of total 3142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 366 time to evaluate : 1.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 50 SER cc_start: 0.9286 (m) cc_final: 0.8755 (p) REVERT: H 16 ILE cc_start: 0.8714 (mt) cc_final: 0.8252 (tt) REVERT: H 86 LYS cc_start: 0.8448 (ttmt) cc_final: 0.7556 (tttt) REVERT: H 174 ASP cc_start: 0.5180 (OUTLIER) cc_final: 0.4697 (p0) REVERT: H 185 TYR cc_start: 0.9117 (p90) cc_final: 0.8844 (p90) REVERT: I 33 ASP cc_start: 0.7660 (t0) cc_final: 0.7361 (t0) REVERT: I 37 LYS cc_start: 0.7989 (mmtt) cc_final: 0.7759 (mmmm) REVERT: I 192 ASP cc_start: 0.7596 (m-30) cc_final: 0.7231 (p0) REVERT: I 241 LEU cc_start: 0.8307 (mm) cc_final: 0.7983 (tt) REVERT: I 295 LYS cc_start: 0.8399 (OUTLIER) cc_final: 0.8052 (mmtm) REVERT: I 391 SER cc_start: 0.8755 (t) cc_final: 0.8403 (m) REVERT: I 499 SER cc_start: 0.8271 (t) cc_final: 0.7948 (p) REVERT: I 672 GLU cc_start: 0.8090 (pm20) cc_final: 0.7776 (pm20) REVERT: I 741 MET cc_start: 0.7932 (ttp) cc_final: 0.7410 (ttm) REVERT: I 788 SER cc_start: 0.9017 (m) cc_final: 0.8263 (p) REVERT: I 828 PHE cc_start: 0.9228 (OUTLIER) cc_final: 0.8811 (m-10) REVERT: I 992 LEU cc_start: 0.6675 (OUTLIER) cc_final: 0.5768 (tp) REVERT: I 1025 PHE cc_start: 0.7628 (t80) cc_final: 0.6839 (t80) REVERT: I 1027 LYS cc_start: 0.8622 (pttt) cc_final: 0.8342 (ptpt) REVERT: I 1111 GLN cc_start: 0.7854 (pt0) cc_final: 0.7462 (pt0) REVERT: I 1119 MET cc_start: 0.8691 (tpp) cc_final: 0.8121 (tpp) REVERT: I 1230 MET cc_start: 0.8596 (ttm) cc_final: 0.8206 (ttp) REVERT: J 304 ASP cc_start: 0.7701 (m-30) cc_final: 0.7430 (m-30) REVERT: J 314 ARG cc_start: 0.7270 (ttt180) cc_final: 0.6950 (ttp80) REVERT: J 652 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.8050 (pp20) REVERT: J 725 MET cc_start: 0.8238 (mtm) cc_final: 0.7993 (mtp) REVERT: J 870 ASP cc_start: 0.7942 (m-30) cc_final: 0.7722 (m-30) REVERT: J 1175 LEU cc_start: 0.8415 (tt) cc_final: 0.8100 (mm) REVERT: J 1189 MET cc_start: 0.8210 (OUTLIER) cc_final: 0.7726 (mmm) REVERT: J 1251 LYS cc_start: 0.8994 (OUTLIER) cc_final: 0.8700 (mtpp) REVERT: J 1317 GLU cc_start: 0.7595 (mm-30) cc_final: 0.7017 (tm-30) REVERT: K 42 GLU cc_start: 0.8117 (mp0) cc_final: 0.7850 (mp0) REVERT: K 53 GLU cc_start: 0.8662 (mt-10) cc_final: 0.8205 (mt-10) REVERT: K 61 ASN cc_start: 0.7189 (OUTLIER) cc_final: 0.6804 (m-40) REVERT: K 76 GLU cc_start: 0.7827 (mm-30) cc_final: 0.7159 (mm-30) REVERT: L 322 MET cc_start: 0.3558 (mtp) cc_final: 0.2579 (tpt) REVERT: L 365 MET cc_start: 0.8751 (ttt) cc_final: 0.8485 (ttp) REVERT: L 468 ARG cc_start: 0.7456 (ttp80) cc_final: 0.7090 (ttp-170) REVERT: L 474 MET cc_start: 0.7620 (mmm) cc_final: 0.7327 (mmm) REVERT: L 514 ASP cc_start: 0.7866 (t0) cc_final: 0.7350 (m-30) REVERT: L 524 GLU cc_start: 0.7616 (pt0) cc_final: 0.7380 (pm20) REVERT: L 561 MET cc_start: 0.8027 (ttm) cc_final: 0.7723 (ptm) REVERT: L 572 THR cc_start: 0.8821 (p) cc_final: 0.8591 (t) outliers start: 73 outliers final: 45 residues processed: 419 average time/residue: 0.1860 time to fit residues: 130.2905 Evaluate side-chains 358 residues out of total 3142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 305 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 623 LEU Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 717 VAL 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 927 THR Chi-restraints excluded: chain I residue 992 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 434 ILE Chi-restraints excluded: chain J residue 506 VAL 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 587 LEU Chi-restraints excluded: chain J residue 652 GLU Chi-restraints excluded: chain J residue 703 THR Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 857 LEU Chi-restraints excluded: chain J residue 890 THR Chi-restraints excluded: chain J residue 950 ILE Chi-restraints excluded: chain J residue 1189 MET Chi-restraints excluded: chain J residue 1251 LYS 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 K residue 61 ASN Chi-restraints excluded: chain L residue 133 SER 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 317 optimal weight: 0.9990 chunk 202 optimal weight: 3.9990 chunk 33 optimal weight: 10.0000 chunk 249 optimal weight: 0.8980 chunk 368 optimal weight: 20.0000 chunk 91 optimal weight: 0.3980 chunk 328 optimal weight: 7.9990 chunk 293 optimal weight: 8.9990 chunk 70 optimal weight: 5.9990 chunk 366 optimal weight: 20.0000 chunk 139 optimal weight: 7.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 273 HIS ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1157 GLN J 560 ASN K 31 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.130839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.096097 restraints weight = 62065.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.096144 restraints weight = 41754.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.096413 restraints weight = 31927.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.096763 restraints weight = 29036.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.097131 restraints weight = 24397.758| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.4294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 31919 Z= 0.179 Angle : 0.677 11.185 43631 Z= 0.328 Chirality : 0.048 0.277 5062 Planarity : 0.004 0.073 5287 Dihedral : 10.162 168.782 5369 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.66 % Favored : 93.28 % Rotamer: Outliers : 2.43 % Allowed : 16.60 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.14), residues: 3647 helix: 1.15 (0.14), residues: 1436 sheet: -0.99 (0.26), residues: 385 loop : -1.50 (0.14), residues: 1826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 143 TYR 0.019 0.001 TYR I 73 PHE 0.042 0.002 PHE L 256 TRP 0.020 0.001 TRP L 326 HIS 0.005 0.001 HIS L 600 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.18 (31912) covalent geometry : angle 0.67699 / 0.33 (43625) hydrogen bonds : bond 0.03770 / 2.57 ( 1310) hydrogen bonds : angle 4.37736 / 3.00 ( 3648) metal coordination : bond 0.00588 / 0.33 ( 7) metal coordination : angle 1.81896 / 0.87 ( 6) *********************** 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 394 residues out of total 3142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 318 time to evaluate : 1.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 50 SER cc_start: 0.9373 (m) cc_final: 0.8857 (p) REVERT: G 163 GLU cc_start: 0.5800 (OUTLIER) cc_final: 0.5185 (mp0) REVERT: H 16 ILE cc_start: 0.8754 (mt) cc_final: 0.8294 (tt) REVERT: H 86 LYS cc_start: 0.8625 (ttmt) cc_final: 0.7678 (tttt) REVERT: H 174 ASP cc_start: 0.5127 (p0) cc_final: 0.4775 (p0) REVERT: H 185 TYR cc_start: 0.9204 (p90) cc_final: 0.8974 (p90) REVERT: I 33 ASP cc_start: 0.7838 (t0) cc_final: 0.7564 (t0) REVERT: I 37 LYS cc_start: 0.8161 (mmtt) cc_final: 0.7820 (mmmm) REVERT: I 239 MET cc_start: 0.5973 (ttm) cc_final: 0.5735 (ttm) REVERT: I 241 LEU cc_start: 0.8370 (mm) cc_final: 0.7892 (tt) REVERT: I 499 SER cc_start: 0.8443 (t) cc_final: 0.8072 (p) REVERT: I 672 GLU cc_start: 0.8220 (pm20) cc_final: 0.7777 (pm20) REVERT: I 684 ASN cc_start: 0.8723 (t0) cc_final: 0.8470 (t0) REVERT: I 741 MET cc_start: 0.8110 (ttp) cc_final: 0.7610 (ttm) REVERT: I 788 SER cc_start: 0.9260 (m) cc_final: 0.8649 (p) REVERT: I 828 PHE cc_start: 0.9337 (OUTLIER) cc_final: 0.9045 (m-10) REVERT: I 992 LEU cc_start: 0.6756 (OUTLIER) cc_final: 0.5731 (tp) REVERT: I 1025 PHE cc_start: 0.7678 (t80) cc_final: 0.6879 (t80) REVERT: I 1027 LYS cc_start: 0.8691 (pttt) cc_final: 0.8409 (ptpt) REVERT: I 1111 GLN cc_start: 0.8170 (pt0) cc_final: 0.7647 (pt0) REVERT: I 1119 MET cc_start: 0.8857 (tpp) cc_final: 0.8308 (tpp) REVERT: I 1230 MET cc_start: 0.8797 (ttm) cc_final: 0.8425 (ttp) REVERT: J 304 ASP cc_start: 0.7690 (m-30) cc_final: 0.7406 (m-30) REVERT: J 652 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.8039 (pp20) REVERT: J 707 ILE cc_start: 0.8601 (tp) cc_final: 0.8290 (tt) REVERT: J 725 MET cc_start: 0.8426 (mtm) cc_final: 0.8050 (mtp) REVERT: J 870 ASP cc_start: 0.7983 (m-30) cc_final: 0.7725 (m-30) REVERT: J 1175 LEU cc_start: 0.8328 (tt) cc_final: 0.7984 (mm) REVERT: J 1189 MET cc_start: 0.8211 (OUTLIER) cc_final: 0.7740 (mmm) REVERT: K 42 GLU cc_start: 0.8244 (mp0) cc_final: 0.7919 (mp0) REVERT: K 49 ILE cc_start: 0.9257 (pt) cc_final: 0.8984 (pt) REVERT: K 53 GLU cc_start: 0.8701 (mt-10) cc_final: 0.8238 (mt-10) REVERT: K 76 GLU cc_start: 0.7856 (mm-30) cc_final: 0.7182 (mm-30) REVERT: L 273 MET cc_start: 0.8386 (mmm) cc_final: 0.8161 (mmm) REVERT: L 322 MET cc_start: 0.3640 (mtp) cc_final: 0.2617 (tpt) REVERT: L 365 MET cc_start: 0.8681 (ttt) cc_final: 0.8403 (ttp) REVERT: L 468 ARG cc_start: 0.7438 (ttp80) cc_final: 0.7042 (ttm170) REVERT: L 514 ASP cc_start: 0.8003 (t0) cc_final: 0.7347 (m-30) REVERT: L 524 GLU cc_start: 0.7702 (pt0) cc_final: 0.7420 (pm20) REVERT: L 561 MET cc_start: 0.8040 (ttm) cc_final: 0.7691 (ptm) outliers start: 76 outliers final: 59 residues processed: 374 average time/residue: 0.1916 time to fit residues: 119.0287 Evaluate side-chains 362 residues out of total 3142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 298 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 163 GLU Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain H residue 205 MET Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 155 VAL 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 717 VAL 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 927 THR Chi-restraints excluded: chain I residue 992 LEU Chi-restraints excluded: chain I residue 1170 MET Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1298 VAL 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 241 VAL Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 350 SER 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 434 ILE Chi-restraints excluded: chain J residue 506 VAL 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 587 LEU Chi-restraints excluded: chain J residue 652 GLU Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 857 LEU Chi-restraints excluded: chain J residue 890 THR Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 950 ILE 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 1352 ILE Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain J residue 1357 ILE Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain L residue 133 SER 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 75 optimal weight: 20.0000 chunk 17 optimal weight: 4.9990 chunk 316 optimal weight: 0.9980 chunk 231 optimal weight: 9.9990 chunk 171 optimal weight: 3.9990 chunk 313 optimal weight: 0.4980 chunk 5 optimal weight: 2.9990 chunk 113 optimal weight: 0.8980 chunk 158 optimal weight: 10.0000 chunk 224 optimal weight: 5.9990 chunk 242 optimal weight: 0.0980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 273 HIS ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 560 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.132829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.098097 restraints weight = 62050.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.098574 restraints weight = 37238.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.099222 restraints weight = 25925.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.099597 restraints weight = 23621.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.099644 restraints weight = 21118.511| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.4450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 31919 Z= 0.123 Angle : 0.655 12.373 43631 Z= 0.317 Chirality : 0.047 0.249 5062 Planarity : 0.004 0.073 5287 Dihedral : 10.094 169.029 5369 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.09 % Favored : 93.86 % Rotamer: Outliers : 1.88 % Allowed : 17.46 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.14), residues: 3647 helix: 1.26 (0.14), residues: 1427 sheet: -1.01 (0.25), residues: 411 loop : -1.47 (0.14), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 143 TYR 0.017 0.001 TYR J 679 PHE 0.030 0.001 PHE I 545 TRP 0.023 0.001 TRP L 326 HIS 0.005 0.001 HIS J 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (31912) covalent geometry : angle 0.65407 / 0.32 (43625) hydrogen bonds : bond 0.03557 / 2.42 ( 1310) hydrogen bonds : angle 4.29317 / 2.93 ( 3648) metal coordination : bond 0.00350 / 0.18 ( 7) metal coordination : angle 2.45538 / 1.08 ( 6) ********************** 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 to be fit. rotamer outliers: 59 poor density : 322 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 10 LYS cc_start: 0.9145 (mmmt) cc_final: 0.8699 (mmmt) REVERT: G 50 SER cc_start: 0.9329 (m) cc_final: 0.8819 (p) REVERT: H 16 ILE cc_start: 0.8705 (mt) cc_final: 0.8235 (tt) REVERT: H 86 LYS cc_start: 0.8587 (ttmt) cc_final: 0.7786 (tttp) REVERT: H 174 ASP cc_start: 0.5288 (p0) cc_final: 0.4958 (p0) REVERT: H 185 TYR cc_start: 0.9147 (p90) cc_final: 0.8868 (p90) REVERT: I 33 ASP cc_start: 0.7702 (t0) cc_final: 0.7389 (t0) REVERT: I 37 LYS cc_start: 0.8071 (mmtt) cc_final: 0.7764 (mmmm) REVERT: I 241 LEU cc_start: 0.8334 (mm) cc_final: 0.7935 (tt) REVERT: I 295 LYS cc_start: 0.8536 (OUTLIER) cc_final: 0.8261 (mmtm) REVERT: I 499 SER cc_start: 0.8327 (t) cc_final: 0.7973 (p) REVERT: I 515 MET cc_start: 0.8667 (ttp) cc_final: 0.8436 (ttp) REVERT: I 672 GLU cc_start: 0.8142 (pm20) cc_final: 0.7675 (pm20) REVERT: I 741 MET cc_start: 0.8048 (ttp) cc_final: 0.7558 (ttm) REVERT: I 788 SER cc_start: 0.9168 (m) cc_final: 0.8549 (p) REVERT: I 828 PHE cc_start: 0.9264 (OUTLIER) cc_final: 0.8925 (m-10) REVERT: I 992 LEU cc_start: 0.6692 (OUTLIER) cc_final: 0.5696 (tp) REVERT: I 1025 PHE cc_start: 0.7680 (t80) cc_final: 0.6854 (t80) REVERT: I 1027 LYS cc_start: 0.8713 (pttt) cc_final: 0.8459 (ptpt) REVERT: I 1111 GLN cc_start: 0.8100 (pt0) cc_final: 0.7592 (pt0) REVERT: I 1119 MET cc_start: 0.8766 (tpp) cc_final: 0.8245 (tpp) REVERT: I 1230 MET cc_start: 0.8637 (ttm) cc_final: 0.8180 (ttp) REVERT: I 1329 GLU cc_start: 0.7171 (mt-10) cc_final: 0.6922 (mp0) REVERT: J 304 ASP cc_start: 0.7640 (m-30) cc_final: 0.7347 (m-30) REVERT: J 412 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8859 (tp) REVERT: J 652 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.8027 (pp20) REVERT: J 707 ILE cc_start: 0.8529 (tp) cc_final: 0.8213 (tt) REVERT: J 725 MET cc_start: 0.8316 (mtm) cc_final: 0.7885 (mtp) REVERT: J 805 GLN cc_start: 0.8839 (pm20) cc_final: 0.8194 (pp30) REVERT: J 870 ASP cc_start: 0.7862 (m-30) cc_final: 0.7642 (m-30) REVERT: J 1175 LEU cc_start: 0.8297 (tt) cc_final: 0.7945 (mm) REVERT: J 1189 MET cc_start: 0.8241 (OUTLIER) cc_final: 0.7678 (mmm) REVERT: K 42 GLU cc_start: 0.8137 (mp0) cc_final: 0.7893 (mp0) REVERT: K 49 ILE cc_start: 0.9245 (pt) cc_final: 0.9002 (pt) REVERT: K 53 GLU cc_start: 0.8567 (mt-10) cc_final: 0.8147 (mt-10) REVERT: K 76 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7168 (mm-30) REVERT: L 322 MET cc_start: 0.3477 (mtp) cc_final: 0.2468 (tpt) REVERT: L 365 MET cc_start: 0.8684 (ttt) cc_final: 0.8399 (ttp) REVERT: L 468 ARG cc_start: 0.7396 (ttp80) cc_final: 0.7059 (ttm170) REVERT: L 514 ASP cc_start: 0.7891 (t0) cc_final: 0.7287 (m-30) REVERT: L 524 GLU cc_start: 0.7650 (pt0) cc_final: 0.7386 (pm20) REVERT: L 561 MET cc_start: 0.8012 (ttm) cc_final: 0.7704 (ptm) REVERT: L 572 THR cc_start: 0.8898 (p) cc_final: 0.8638 (t) outliers start: 59 outliers final: 49 residues processed: 365 average time/residue: 0.1896 time to fit residues: 115.0630 Evaluate side-chains 361 residues out of total 3142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 306 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 H residue 49 SER Chi-restraints excluded: chain H residue 124 VAL 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 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 717 VAL 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 927 THR Chi-restraints excluded: chain I residue 992 LEU Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 97 VAL 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 412 LEU Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 506 VAL 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 587 LEU Chi-restraints excluded: chain J residue 652 GLU Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 857 LEU Chi-restraints excluded: chain J residue 890 THR Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 950 ILE 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 54 ILE Chi-restraints excluded: chain L residue 133 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 94 optimal weight: 1.9990 chunk 277 optimal weight: 6.9990 chunk 329 optimal weight: 10.0000 chunk 172 optimal weight: 5.9990 chunk 237 optimal weight: 1.9990 chunk 224 optimal weight: 3.9990 chunk 215 optimal weight: 3.9990 chunk 56 optimal weight: 0.4980 chunk 16 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 169 optimal weight: 4.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 227 GLN ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 273 HIS ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 560 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.131006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.096050 restraints weight = 62278.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.096209 restraints weight = 39134.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.096716 restraints weight = 28043.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.097140 restraints weight = 25254.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.097224 restraints weight = 22596.371| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.4475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 31919 Z= 0.174 Angle : 0.686 11.655 43631 Z= 0.333 Chirality : 0.048 0.274 5062 Planarity : 0.004 0.073 5287 Dihedral : 10.143 168.977 5369 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.99 % Favored : 92.95 % Rotamer: Outliers : 2.30 % Allowed : 16.88 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.14), residues: 3647 helix: 1.13 (0.14), residues: 1436 sheet: -1.00 (0.25), residues: 410 loop : -1.46 (0.14), residues: 1801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 143 TYR 0.021 0.001 TYR I 73 PHE 0.029 0.002 PHE L 256 TRP 0.023 0.001 TRP L 326 HIS 0.005 0.001 HIS L 600 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.17 (31912) covalent geometry : angle 0.68571 / 0.33 (43625) hydrogen bonds : bond 0.03764 / 2.56 ( 1310) hydrogen bonds : angle 4.38994 / 3.00 ( 3648) metal coordination : bond 0.00623 / 0.34 ( 7) metal coordination : angle 2.15799 / 1.00 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4968.62 seconds wall clock time: 86 minutes 46.52 seconds (5206.52 seconds total)