Starting phenix.real_space_refine on Thu Nov 20 07:03:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5vt0_8732/11_2025/5vt0_8732.cif Found real_map, /net/cci-nas-00/data/ceres_data/5vt0_8732/11_2025/5vt0_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 { model { file = "/net/cci-nas-00/data/ceres_data/5vt0_8732/11_2025/5vt0_8732.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5vt0_8732/11_2025/5vt0_8732.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5vt0_8732/11_2025/5vt0_8732.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5vt0_8732/11_2025/5vt0_8732.map" } 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/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: {'RNA': 112} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 6, 'rna3p_pur': 48, 'rna3p_pyr': 48} Link IDs: {'rna2p': 16, 'rna3p': 95} Chain breaks: 1 Chain: "J" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14432 SG CYS J 70 58.491 56.126 71.464 1.00 77.06 S ATOM 14446 SG CYS J 72 57.241 52.809 71.980 1.00 88.00 S ATOM 14554 SG CYS J 85 54.534 55.209 71.781 1.00 92.38 S ATOM 14578 SG CYS J 88 57.781 55.434 75.190 1.00 98.30 S ATOM 20831 SG CYS J 888 86.178 113.277 63.751 1.00 70.73 S ATOM 20882 SG CYS J 895 86.921 113.212 60.191 1.00 62.13 S ATOM 20903 SG CYS J 898 90.524 114.624 63.033 1.00 67.65 S Time building chain proxies: 7.08, per 1000 atoms: 0.23 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: 2.68 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: 4.29 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: 7.47 Time building geometry restraints manager: 3.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 5364 1.32 - 1.44: 8165 1.44 - 1.57: 17937 1.57 - 1.69: 221 1.69 - 1.81: 225 Bond restraints: 31912 Sorted by residual: bond pdb=" C ILE I1079 " pdb=" N ASN I1080 " ideal model delta sigma weight residual 1.330 1.404 -0.074 1.47e-02 4.63e+03 2.52e+01 bond pdb=" P G R 88 " pdb=" OP1 G R 88 " ideal model delta sigma weight residual 1.485 1.424 0.061 2.00e-02 2.50e+03 9.32e+00 bond pdb=" C4' G R 97 " pdb=" C3' G R 97 " ideal model delta sigma weight residual 1.527 1.482 0.045 1.50e-02 4.44e+03 8.88e+00 bond pdb=" C4 C R 85 " pdb=" N4 C R 85 " ideal model delta sigma weight residual 1.335 1.279 0.056 2.00e-02 2.50e+03 7.75e+00 bond pdb=" P G R 88 " pdb=" O5' G R 88 " ideal model delta sigma weight residual 1.593 1.553 0.040 1.50e-02 4.44e+03 7.13e+00 ... (remaining 31907 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 41805 2.41 - 4.83: 1539 4.83 - 7.24: 213 7.24 - 9.65: 50 9.65 - 12.07: 18 Bond angle restraints: 43625 Sorted by residual: angle pdb=" N ASP I 516 " pdb=" CA ASP I 516 " pdb=" C ASP I 516 " ideal model delta sigma weight residual 109.25 97.27 11.98 1.53e+00 4.27e-01 6.13e+01 angle pdb=" C4' U R 94 " pdb=" C3' U R 94 " pdb=" O3' U R 94 " ideal model delta sigma weight residual 113.00 102.75 10.25 1.50e+00 4.44e-01 4.67e+01 angle pdb=" P G R 97 " pdb=" O5' G R 97 " pdb=" C5' G R 97 " ideal model delta sigma weight residual 120.90 111.12 9.78 1.50e+00 4.44e-01 4.25e+01 angle pdb=" O5' G R 97 " pdb=" C5' G R 97 " pdb=" C4' G R 97 " ideal model delta sigma weight residual 111.70 120.85 -9.15 1.50e+00 4.44e-01 3.72e+01 angle pdb=" C4' C R 96 " pdb=" C3' C R 96 " pdb=" O3' C R 96 " ideal model delta sigma weight residual 113.00 104.01 8.99 1.50e+00 4.44e-01 3.59e+01 ... (remaining 43620 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.10: 19105 26.10 - 52.21: 521 52.21 - 78.31: 204 78.31 - 104.42: 3 104.42 - 130.52: 1 Dihedral angle restraints: 19834 sinusoidal: 9266 harmonic: 10568 Sorted by residual: dihedral pdb=" CA LEU J1344 " pdb=" C LEU J1344 " pdb=" N ARG J1345 " pdb=" CA ARG J1345 " ideal model delta harmonic sigma weight residual 180.00 129.17 50.83 0 5.00e+00 4.00e-02 1.03e+02 dihedral pdb=" O4' U R 109 " pdb=" C1' U R 109 " pdb=" N1 U R 109 " pdb=" C2 U R 109 " ideal model delta sinusoidal sigma weight residual 200.00 69.48 130.52 1 1.50e+01 4.44e-03 7.04e+01 dihedral pdb=" CA PRO I1185 " pdb=" C PRO I1185 " pdb=" N VAL I1186 " pdb=" CA VAL I1186 " ideal model delta harmonic sigma weight residual -180.00 -142.99 -37.01 0 5.00e+00 4.00e-02 5.48e+01 ... (remaining 19831 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 4681 0.109 - 0.218: 353 0.218 - 0.327: 23 0.327 - 0.437: 3 0.437 - 0.546: 2 Chirality restraints: 5062 Sorted by residual: chirality pdb=" CB ILE I1079 " pdb=" CA ILE I1079 " pdb=" CG1 ILE I1079 " pdb=" CG2 ILE I1079 " both_signs ideal model delta sigma weight residual False 2.64 2.10 0.55 2.00e-01 2.50e+01 7.45e+00 chirality pdb=" C4' G R 97 " pdb=" C5' G R 97 " pdb=" O4' G R 97 " pdb=" C3' G R 97 " both_signs ideal model delta sigma weight residual False -2.50 -1.98 -0.52 2.00e-01 2.50e+01 6.76e+00 chirality pdb=" CB ILE G 159 " pdb=" CA ILE G 159 " pdb=" CG1 ILE G 159 " pdb=" CG2 ILE G 159 " both_signs ideal model delta sigma weight residual False 2.64 2.22 0.42 2.00e-01 2.50e+01 4.45e+00 ... (remaining 5059 not shown) Planarity restraints: 5287 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO I 897 " -0.027 2.00e-02 2.50e+03 5.41e-02 2.92e+01 pdb=" C PRO I 897 " 0.094 2.00e-02 2.50e+03 pdb=" O PRO I 897 " -0.035 2.00e-02 2.50e+03 pdb=" N GLU I 898 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G R 68 " -0.046 2.00e-02 2.50e+03 3.11e-02 2.91e+01 pdb=" N9 G R 68 " 0.018 2.00e-02 2.50e+03 pdb=" C8 G R 68 " -0.003 2.00e-02 2.50e+03 pdb=" N7 G R 68 " 0.006 2.00e-02 2.50e+03 pdb=" C5 G R 68 " 0.002 2.00e-02 2.50e+03 pdb=" C6 G R 68 " -0.011 2.00e-02 2.50e+03 pdb=" O6 G R 68 " 0.001 2.00e-02 2.50e+03 pdb=" N1 G R 68 " -0.016 2.00e-02 2.50e+03 pdb=" C2 G R 68 " -0.019 2.00e-02 2.50e+03 pdb=" N2 G R 68 " -0.020 2.00e-02 2.50e+03 pdb=" N3 G R 68 " 0.089 2.00e-02 2.50e+03 pdb=" C4 G R 68 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C R 85 " -0.062 2.00e-02 2.50e+03 3.00e-02 2.02e+01 pdb=" N1 C R 85 " 0.018 2.00e-02 2.50e+03 pdb=" C2 C R 85 " 0.018 2.00e-02 2.50e+03 pdb=" O2 C R 85 " 0.013 2.00e-02 2.50e+03 pdb=" N3 C R 85 " 0.006 2.00e-02 2.50e+03 pdb=" C4 C R 85 " -0.004 2.00e-02 2.50e+03 pdb=" N4 C R 85 " -0.034 2.00e-02 2.50e+03 pdb=" C5 C R 85 " -0.002 2.00e-02 2.50e+03 pdb=" C6 C R 85 " 0.047 2.00e-02 2.50e+03 ... (remaining 5284 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 668 2.67 - 3.23: 28178 3.23 - 3.78: 48931 3.78 - 4.34: 63343 4.34 - 4.90: 103101 Nonbonded interactions: 244221 Sorted by model distance: nonbonded pdb=" OD2 ASP J 464 " pdb="MG MG J1501 " model vdw 2.110 2.170 nonbonded pdb=" O2' C R 96 " pdb=" O4' G R 97 " model vdw 2.150 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: 1.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.340 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 36.450 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.601 31919 Z= 0.369 Angle : 1.112 28.854 43631 Z= 0.613 Chirality : 0.061 0.546 5062 Planarity : 0.007 0.072 5287 Dihedral : 13.281 130.523 13020 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.35 % Favored : 92.57 % Rotamer: Outliers : 0.57 % Allowed : 2.30 % Favored : 97.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.11 % Twisted Proline : 0.69 % Twisted General : 0.14 % Rama-Z 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 covalent geometry : bond 0.00749 (31912) covalent geometry : angle 1.09613 (43625) hydrogen bonds : bond 0.15806 ( 1310) hydrogen bonds : angle 6.93995 ( 3648) metal coordination : bond 0.28149 ( 7) metal coordination : angle 15.75986 ( 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 : 1.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 25 LYS cc_start: 0.8763 (mtpt) cc_final: 0.8464 (mttt) REVERT: G 111 THR cc_start: 0.9049 (p) cc_final: 0.8843 (t) REVERT: G 118 ASP cc_start: 0.7948 (t70) cc_final: 0.6482 (t0) REVERT: G 137 ASN cc_start: 0.8482 (m-40) cc_final: 0.7950 (m-40) REVERT: G 186 ASN cc_start: 0.8550 (m-40) cc_final: 0.8340 (m-40) REVERT: H 47 LEU cc_start: 0.9002 (mt) cc_final: 0.8780 (mt) REVERT: H 51 MET cc_start: 0.9217 (mmp) cc_final: 0.8879 (mmp) REVERT: H 57 THR cc_start: 0.4639 (m) cc_final: 0.3873 (m) REVERT: H 85 LEU cc_start: 0.8156 (mt) cc_final: 0.7956 (mt) REVERT: H 86 LYS cc_start: 0.7895 (ttmt) cc_final: 0.7558 (tttt) REVERT: H 104 LYS cc_start: 0.4891 (tptm) cc_final: 0.4249 (tptp) REVERT: H 107 ILE cc_start: 0.7928 (mt) cc_final: 0.7544 (tt) REVERT: H 129 VAL cc_start: 0.9153 (t) cc_final: 0.8831 (m) REVERT: H 185 TYR cc_start: 0.9066 (p90) cc_final: 0.8759 (p90) REVERT: I 37 LYS cc_start: 0.8009 (mmtt) cc_final: 0.7603 (mmmm) REVERT: I 218 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7311 (tt0) REVERT: I 272 ARG cc_start: 0.8171 (ttt180) cc_final: 0.7677 (tpm170) REVERT: I 327 GLN cc_start: 0.8250 (pt0) cc_final: 0.7745 (mm-40) REVERT: I 461 GLU cc_start: 0.8535 (tt0) cc_final: 0.8143 (tt0) REVERT: I 488 MET cc_start: 0.8348 (mmp) cc_final: 0.8104 (mmp) REVERT: I 549 ASP cc_start: 0.8540 (t0) cc_final: 0.8270 (m-30) REVERT: I 684 ASN cc_start: 0.8518 (t0) cc_final: 0.8269 (t0) REVERT: I 741 MET cc_start: 0.8476 (ttp) cc_final: 0.8138 (ttm) REVERT: I 765 ILE cc_start: 0.9525 (tt) cc_final: 0.9281 (mt) REVERT: I 788 SER cc_start: 0.9184 (m) cc_final: 0.8617 (p) REVERT: I 829 THR cc_start: 0.9298 (m) cc_final: 0.8893 (p) REVERT: I 844 LYS cc_start: 0.8205 (mttm) cc_final: 0.7920 (pttm) REVERT: I 898 GLU cc_start: 0.7553 (mp0) cc_final: 0.7336 (mp0) REVERT: I 1230 MET cc_start: 0.8655 (ttm) cc_final: 0.8368 (ttp) REVERT: J 133 ARG cc_start: 0.6709 (tpt170) cc_final: 0.6373 (tpt170) REVERT: J 151 MET cc_start: 0.6666 (mtp) cc_final: 0.6234 (tpt) REVERT: J 176 PHE cc_start: 0.7082 (t80) cc_final: 0.6544 (t80) REVERT: J 295 GLU cc_start: 0.8664 (tp30) cc_final: 0.8161 (tp30) REVERT: J 304 ASP cc_start: 0.7428 (m-30) cc_final: 0.7066 (m-30) REVERT: J 434 ILE cc_start: 0.9217 (mt) cc_final: 0.8971 (tt) REVERT: J 523 GLU cc_start: 0.7868 (tp30) cc_final: 0.7328 (tp30) REVERT: J 625 MET cc_start: 0.9054 (ttp) cc_final: 0.8793 (ttp) REVERT: J 707 ILE cc_start: 0.8585 (pt) cc_final: 0.8308 (pt) REVERT: J 753 SER cc_start: 0.8210 (m) cc_final: 0.7751 (p) REVERT: J 754 ILE cc_start: 0.8505 (tt) cc_final: 0.8283 (mt) REVERT: J 870 ASP cc_start: 0.8286 (m-30) cc_final: 0.7961 (m-30) REVERT: J 922 SER cc_start: 0.9189 (m) cc_final: 0.8814 (p) REVERT: J 1317 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7448 (tm-30) REVERT: J 1368 ASP cc_start: 0.7024 (t70) cc_final: 0.5678 (m-30) REVERT: K 43 ASN cc_start: 0.8410 (m-40) cc_final: 0.8135 (m-40) REVERT: K 62 GLN cc_start: 0.8441 (tp-100) cc_final: 0.7936 (tp-100) REVERT: K 63 ILE cc_start: 0.9073 (OUTLIER) cc_final: 0.8618 (mp) REVERT: K 75 GLN cc_start: 0.7844 (mt0) cc_final: 0.7502 (tp40) REVERT: L 322 MET cc_start: 0.3571 (mtp) cc_final: 0.3210 (mtt) REVERT: L 365 MET cc_start: 0.9026 (ttp) cc_final: 0.8684 (ttt) REVERT: L 366 SER cc_start: 0.8388 (m) cc_final: 0.8119 (p) REVERT: L 468 ARG cc_start: 0.7312 (ttp80) cc_final: 0.7060 (ttm170) REVERT: L 514 ASP cc_start: 0.7941 (t0) cc_final: 0.7595 (p0) REVERT: L 524 GLU cc_start: 0.7826 (pt0) cc_final: 0.7540 (pm20) REVERT: L 561 MET cc_start: 0.8145 (ttm) cc_final: 0.7925 (ttm) REVERT: L 578 LYS cc_start: 0.7267 (mmtm) cc_final: 0.7016 (tttm) outliers start: 18 outliers final: 5 residues processed: 737 average time/residue: 0.2421 time to fit residues: 270.5417 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 : 1.212 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: G 66 HIS G 147 GLN H 23 HIS H 227 GLN I 69 GLN I 273 HIS I 327 GLN I 513 GLN I 604 HIS I 952 GLN I1010 GLN I1080 ASN I1209 GLN 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 = 0.3859 r_free = 0.3859 target = 0.136295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.100281 restraints weight = 62018.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.100657 restraints weight = 35251.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.100957 restraints weight = 26267.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.101566 restraints weight = 24793.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.101636 restraints weight = 20980.425| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 31919 Z= 0.129 Angle : 0.639 8.375 43631 Z= 0.332 Chirality : 0.042 0.349 5062 Planarity : 0.005 0.068 5287 Dihedral : 14.615 116.429 5779 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.54 % Favored : 94.41 % Rotamer: Outliers : 2.17 % Allowed : 8.65 % Favored : 89.18 % 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: -2.15 (0.13), residues: 3647 helix: -0.49 (0.13), residues: 1418 sheet: -1.55 (0.25), residues: 390 loop : -2.19 (0.13), residues: 1839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 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 covalent geometry : bond 0.00280 (31912) covalent geometry : angle 0.63770 (43625) hydrogen bonds : bond 0.04300 ( 1310) hydrogen bonds : angle 5.01092 ( 3648) metal coordination : bond 0.00536 ( 7) metal coordination : angle 3.87695 ( 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 529 residues out of total 3142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 461 time to evaluate : 1.037 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: G 25 LYS cc_start: 0.8652 (mtpt) cc_final: 0.8404 (mttt) REVERT: H 16 ILE cc_start: 0.8761 (mt) cc_final: 0.8392 (tt) REVERT: H 81 ILE cc_start: 0.8536 (mm) cc_final: 0.8216 (mm) REVERT: H 84 ASN cc_start: 0.8510 (t0) cc_final: 0.8271 (t0) REVERT: H 85 LEU cc_start: 0.8365 (mt) cc_final: 0.8049 (mt) REVERT: H 86 LYS cc_start: 0.8066 (ttmt) cc_final: 0.7129 (tttt) REVERT: H 185 TYR cc_start: 0.9080 (p90) cc_final: 0.8775 (p90) REVERT: H 200 LYS cc_start: 0.8522 (ttmt) cc_final: 0.8316 (tttt) REVERT: I 37 LYS cc_start: 0.7994 (mmtt) cc_final: 0.7710 (mmmm) REVERT: I 315 MET cc_start: 0.8070 (mtp) cc_final: 0.7581 (mtt) REVERT: I 327 GLN cc_start: 0.8519 (pt0) cc_final: 0.8146 (mm-40) REVERT: I 391 SER cc_start: 0.8839 (t) cc_final: 0.8524 (m) REVERT: I 461 GLU cc_start: 0.8441 (tt0) cc_final: 0.8216 (tt0) REVERT: I 484 LEU cc_start: 0.7717 (OUTLIER) cc_final: 0.7469 (mt) REVERT: I 510 GLN cc_start: 0.8338 (mt0) cc_final: 0.8098 (mt0) REVERT: I 515 MET cc_start: 0.8917 (ttp) cc_final: 0.8512 (ttp) REVERT: I 549 ASP cc_start: 0.8606 (t0) cc_final: 0.8267 (m-30) REVERT: I 741 MET cc_start: 0.8207 (ttp) cc_final: 0.7890 (ttt) REVERT: I 768 MET cc_start: 0.7895 (mtm) cc_final: 0.7629 (mtp) REVERT: I 788 SER cc_start: 0.9228 (m) cc_final: 0.8642 (p) REVERT: I 813 GLU cc_start: 0.8049 (mm-30) cc_final: 0.7764 (tp30) REVERT: I 844 LYS cc_start: 0.8196 (mttm) cc_final: 0.7870 (pttm) REVERT: I 898 GLU cc_start: 0.7510 (mp0) cc_final: 0.7298 (mp0) REVERT: I 902 LEU cc_start: 0.9119 (tt) cc_final: 0.8870 (tp) REVERT: I 913 VAL cc_start: 0.9165 (OUTLIER) cc_final: 0.8867 (m) REVERT: I 992 LEU cc_start: 0.6456 (OUTLIER) cc_final: 0.6110 (tp) REVERT: I 1027 LYS cc_start: 0.8681 (pttt) cc_final: 0.8226 (ptpp) REVERT: I 1111 GLN cc_start: 0.7951 (pt0) cc_final: 0.7676 (pt0) REVERT: I 1119 MET cc_start: 0.8827 (tpp) cc_final: 0.7830 (tpp) REVERT: I 1230 MET cc_start: 0.8580 (ttm) cc_final: 0.8121 (ttp) REVERT: I 1236 ASN cc_start: 0.7911 (p0) cc_final: 0.7639 (t0) REVERT: J 151 MET cc_start: 0.6488 (mtp) cc_final: 0.6071 (tpt) REVERT: J 162 GLU cc_start: 0.8266 (pm20) cc_final: 0.7457 (pm20) REVERT: J 163 GLU cc_start: 0.8311 (mp0) cc_final: 0.7557 (mp0) REVERT: J 295 GLU cc_start: 0.8657 (tp30) cc_final: 0.8281 (tp30) REVERT: J 304 ASP cc_start: 0.7517 (m-30) cc_final: 0.7217 (m-30) REVERT: J 314 ARG cc_start: 0.7385 (ttt180) cc_final: 0.6894 (ttp80) REVERT: J 718 SER cc_start: 0.8856 (t) cc_final: 0.8622 (m) REVERT: J 737 ILE cc_start: 0.9161 (OUTLIER) cc_final: 0.8821 (pt) REVERT: J 870 ASP cc_start: 0.8329 (m-30) cc_final: 0.7928 (m-30) REVERT: J 890 THR cc_start: 0.8483 (m) cc_final: 0.8151 (p) REVERT: J 922 SER cc_start: 0.9186 (m) cc_final: 0.8906 (p) REVERT: J 1021 ASP cc_start: 0.5754 (p0) cc_final: 0.5450 (p0) REVERT: J 1275 LEU cc_start: 0.8062 (mp) cc_final: 0.7542 (tp) REVERT: J 1345 ARG cc_start: 0.6848 (mmp80) cc_final: 0.6531 (mmt180) REVERT: K 42 GLU cc_start: 0.8170 (mp0) cc_final: 0.7763 (mp0) REVERT: K 53 GLU cc_start: 0.8848 (mt-10) cc_final: 0.8424 (mt-10) REVERT: L 105 MET cc_start: 0.8995 (tmm) cc_final: 0.8610 (tmm) REVERT: L 276 MET cc_start: 0.7980 (ttt) cc_final: 0.7634 (ttp) REVERT: L 322 MET cc_start: 0.3421 (mtp) cc_final: 0.3083 (mtt) REVERT: L 468 ARG cc_start: 0.7621 (ttp80) cc_final: 0.7313 (ttm170) REVERT: L 474 MET cc_start: 0.7557 (mmm) cc_final: 0.7173 (mmm) REVERT: L 513 ASP cc_start: 0.8307 (m-30) cc_final: 0.8083 (m-30) REVERT: L 514 ASP cc_start: 0.7969 (t0) cc_final: 0.7490 (p0) REVERT: L 524 GLU cc_start: 0.7735 (pt0) cc_final: 0.7386 (pm20) outliers start: 68 outliers final: 32 residues processed: 509 average time/residue: 0.2017 time to fit residues: 165.4432 Evaluate side-chains 359 residues out of total 3142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 323 time to evaluate : 1.176 ------------------------------------------------------------------------------- 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 569 ILE Chi-restraints excluded: chain I residue 653 MET Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 773 LEU Chi-restraints excluded: chain I residue 903 ARG Chi-restraints excluded: chain I residue 913 VAL 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 635 SER 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 1017 VAL 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: 7.9990 chunk 88 optimal weight: 2.9990 chunk 253 optimal weight: 2.9990 chunk 282 optimal weight: 40.0000 chunk 182 optimal weight: 0.9990 chunk 136 optimal weight: 7.9990 chunk 99 optimal weight: 2.9990 chunk 180 optimal weight: 6.9990 chunk 75 optimal weight: 9.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 84 ASN ** I 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 273 HIS I 513 GLN 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 = 0.3771 r_free = 0.3771 target = 0.129821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.094646 restraints weight = 62710.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.094858 restraints weight = 39157.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.095579 restraints weight = 28036.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.095974 restraints weight = 24759.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.096048 restraints weight = 22325.033| |-----------------------------------------------------------------------------| r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 31919 Z= 0.232 Angle : 0.677 10.637 43631 Z= 0.350 Chirality : 0.044 0.348 5062 Planarity : 0.005 0.069 5287 Dihedral : 14.438 115.218 5777 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.55 % Favored : 93.39 % Rotamer: Outliers : 2.90 % Allowed : 11.52 % Favored : 85.57 % 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: -1.63 (0.13), residues: 3647 helix: 0.12 (0.13), residues: 1434 sheet: -1.48 (0.25), residues: 392 loop : -2.02 (0.13), residues: 1821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I1246 TYR 0.022 0.002 TYR L 228 PHE 0.019 0.002 PHE I 545 TRP 0.015 0.002 TRP L 326 HIS 0.009 0.001 HIS H 23 Details of bonding type rmsd covalent geometry : bond 0.00531 (31912) covalent geometry : angle 0.67628 (43625) hydrogen bonds : bond 0.04362 ( 1310) hydrogen bonds : angle 4.89002 ( 3648) metal coordination : bond 0.00800 ( 7) metal coordination : angle 3.05748 ( 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 426 residues out of total 3142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 335 time to evaluate : 1.209 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 16 ILE cc_start: 0.8836 (mt) cc_final: 0.8451 (tt) REVERT: H 86 LYS cc_start: 0.8524 (ttmt) cc_final: 0.7870 (ttmm) REVERT: H 185 TYR cc_start: 0.9165 (p90) cc_final: 0.8943 (p90) REVERT: I 37 LYS cc_start: 0.8025 (mmtt) cc_final: 0.7738 (mmmm) REVERT: I 295 LYS cc_start: 0.8570 (OUTLIER) cc_final: 0.8368 (mptt) REVERT: I 315 MET cc_start: 0.8334 (mtp) cc_final: 0.7889 (mtt) REVERT: I 327 GLN cc_start: 0.8277 (pt0) cc_final: 0.7982 (mm-40) REVERT: I 484 LEU cc_start: 0.7827 (OUTLIER) cc_final: 0.7562 (mt) REVERT: I 549 ASP cc_start: 0.8810 (t0) cc_final: 0.8411 (m-30) REVERT: I 672 GLU cc_start: 0.8174 (pm20) cc_final: 0.7820 (pm20) REVERT: I 704 MET cc_start: 0.8639 (tpp) cc_final: 0.8393 (tpp) REVERT: I 741 MET cc_start: 0.8284 (ttp) cc_final: 0.7914 (ttt) REVERT: I 788 SER cc_start: 0.9229 (m) cc_final: 0.8579 (p) REVERT: I 844 LYS cc_start: 0.8340 (mttm) cc_final: 0.8072 (pttp) REVERT: I 992 LEU cc_start: 0.6709 (OUTLIER) cc_final: 0.6187 (tp) REVERT: I 1027 LYS cc_start: 0.8771 (pttt) cc_final: 0.8264 (ptpp) REVERT: I 1040 ASP cc_start: 0.7733 (p0) cc_final: 0.7350 (m-30) REVERT: I 1111 GLN cc_start: 0.8214 (pt0) cc_final: 0.7611 (pt0) REVERT: I 1119 MET cc_start: 0.8974 (tpp) cc_final: 0.8294 (tpp) REVERT: I 1151 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8204 (tt) REVERT: I 1230 MET cc_start: 0.8770 (ttm) cc_final: 0.8505 (ttp) REVERT: I 1327 LEU cc_start: 0.9434 (OUTLIER) cc_final: 0.9085 (mp) REVERT: J 151 MET cc_start: 0.6634 (mtp) cc_final: 0.6394 (tpt) REVERT: J 304 ASP cc_start: 0.7562 (m-30) cc_final: 0.7263 (m-30) REVERT: J 652 GLU cc_start: 0.8437 (tm-30) cc_final: 0.8101 (pp20) REVERT: J 718 SER cc_start: 0.8771 (t) cc_final: 0.8542 (m) REVERT: J 870 ASP cc_start: 0.8294 (m-30) cc_final: 0.7847 (m-30) REVERT: J 922 SER cc_start: 0.9223 (m) cc_final: 0.8941 (p) REVERT: J 1021 ASP cc_start: 0.6210 (p0) cc_final: 0.5915 (p0) REVERT: J 1345 ARG cc_start: 0.7217 (mmp80) cc_final: 0.6696 (mmt180) REVERT: J 1352 ILE cc_start: 0.9536 (mm) cc_final: 0.9335 (mm) REVERT: K 11 GLU cc_start: 0.8218 (tp30) cc_final: 0.7752 (pt0) REVERT: K 53 GLU cc_start: 0.8839 (mt-10) cc_final: 0.8507 (mt-10) REVERT: K 59 ILE cc_start: 0.8884 (mt) cc_final: 0.8484 (tt) REVERT: K 76 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7375 (mm-30) REVERT: L 276 MET cc_start: 0.7542 (ttt) cc_final: 0.7181 (ttp) REVERT: L 322 MET cc_start: 0.3423 (mtp) cc_final: 0.2860 (mtt) REVERT: L 365 MET cc_start: 0.8807 (ttt) cc_final: 0.8435 (ttp) REVERT: L 413 MET cc_start: 0.8768 (mtp) cc_final: 0.8467 (mtm) REVERT: L 468 ARG cc_start: 0.7504 (ttp80) cc_final: 0.7110 (ttm170) REVERT: L 524 GLU cc_start: 0.7704 (pt0) cc_final: 0.7389 (pm20) REVERT: L 561 MET cc_start: 0.8137 (ttm) cc_final: 0.7835 (ttp) outliers start: 91 outliers final: 56 residues processed: 401 average time/residue: 0.1919 time to fit residues: 126.4216 Evaluate side-chains 351 residues out of total 3142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 290 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain H residue 23 HIS Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 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 295 LYS Chi-restraints excluded: chain I residue 410 LEU Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 770 CYS Chi-restraints excluded: chain I residue 863 SER 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 1254 VAL 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 I residue 1327 LEU Chi-restraints excluded: chain I residue 1332 SER Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 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 803 VAL 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 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 224 LEU Chi-restraints excluded: chain L residue 267 ASP Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 338 HIS Chi-restraints excluded: chain L residue 367 ILE Chi-restraints excluded: chain L residue 387 VAL Chi-restraints excluded: chain L residue 488 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 290 optimal weight: 3.9990 chunk 175 optimal weight: 0.9990 chunk 123 optimal weight: 0.7980 chunk 91 optimal weight: 10.0000 chunk 256 optimal weight: 3.9990 chunk 284 optimal weight: 8.9990 chunk 76 optimal weight: 7.9990 chunk 278 optimal weight: 30.0000 chunk 114 optimal weight: 6.9990 chunk 53 optimal weight: 10.0000 chunk 271 optimal weight: 6.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 219 GLN I 273 HIS ** I 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 832 HIS J 560 ASN J1244 GLN ** L 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.128625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.093665 restraints weight = 62127.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.094030 restraints weight = 37583.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.094527 restraints weight = 27527.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.094834 restraints weight = 24574.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.094981 restraints weight = 22225.352| |-----------------------------------------------------------------------------| r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 31919 Z= 0.227 Angle : 0.666 9.940 43631 Z= 0.343 Chirality : 0.044 0.311 5062 Planarity : 0.005 0.070 5287 Dihedral : 14.338 115.278 5777 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.24 % Favored : 92.71 % Rotamer: Outliers : 3.45 % Allowed : 13.41 % Favored : 83.15 % 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: -1.31 (0.14), residues: 3647 helix: 0.44 (0.14), residues: 1429 sheet: -1.43 (0.25), residues: 400 loop : -1.85 (0.14), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG I 996 TYR 0.020 0.002 TYR L 228 PHE 0.019 0.002 PHE I 545 TRP 0.016 0.002 TRP L 326 HIS 0.008 0.001 HIS J 777 Details of bonding type rmsd covalent geometry : bond 0.00522 (31912) covalent geometry : angle 0.66538 (43625) hydrogen bonds : bond 0.04206 ( 1310) hydrogen bonds : angle 4.77751 ( 3648) metal coordination : bond 0.00843 ( 7) metal coordination : angle 2.79552 ( 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 446 residues out of total 3142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 338 time to evaluate : 1.188 Fit side-chains revert: symmetry clash REVERT: G 10 LYS cc_start: 0.8917 (ptmt) cc_final: 0.8653 (mtpt) REVERT: G 50 SER cc_start: 0.9328 (m) cc_final: 0.8707 (p) REVERT: H 16 ILE cc_start: 0.8887 (mt) cc_final: 0.8484 (tt) REVERT: H 86 LYS cc_start: 0.8629 (ttmt) cc_final: 0.7989 (tttp) REVERT: H 185 TYR cc_start: 0.9205 (p90) cc_final: 0.8977 (p90) REVERT: I 37 LYS cc_start: 0.8054 (mmtt) cc_final: 0.7748 (mmmm) REVERT: I 315 MET cc_start: 0.8174 (mtp) cc_final: 0.7825 (mtt) REVERT: I 327 GLN cc_start: 0.8153 (pt0) cc_final: 0.7902 (mm-40) REVERT: I 461 GLU cc_start: 0.8412 (tt0) cc_final: 0.8048 (tt0) REVERT: I 484 LEU cc_start: 0.7880 (OUTLIER) cc_final: 0.7620 (mt) REVERT: I 549 ASP cc_start: 0.8809 (t0) cc_final: 0.8593 (m-30) REVERT: I 633 LEU cc_start: 0.7829 (OUTLIER) cc_final: 0.7570 (pp) REVERT: I 672 GLU cc_start: 0.8182 (pm20) cc_final: 0.7828 (pm20) REVERT: I 741 MET cc_start: 0.8198 (ttp) cc_final: 0.7785 (ttt) REVERT: I 788 SER cc_start: 0.9257 (m) cc_final: 0.8717 (p) REVERT: I 828 PHE cc_start: 0.9305 (OUTLIER) cc_final: 0.8928 (m-10) REVERT: I 844 LYS cc_start: 0.8298 (mttm) cc_final: 0.8003 (pttp) REVERT: I 971 LEU cc_start: 0.7801 (OUTLIER) cc_final: 0.7475 (tt) REVERT: I 992 LEU cc_start: 0.6755 (OUTLIER) cc_final: 0.6172 (tp) REVERT: I 1027 LYS cc_start: 0.8730 (pttt) cc_final: 0.8497 (ptpt) REVERT: I 1111 GLN cc_start: 0.8110 (pt0) cc_final: 0.7490 (pt0) REVERT: I 1119 MET cc_start: 0.8985 (tpp) cc_final: 0.8229 (tpp) REVERT: I 1230 MET cc_start: 0.8829 (ttm) cc_final: 0.8536 (ttp) REVERT: J 96 LYS cc_start: 0.8519 (ptmm) cc_final: 0.8133 (tmtt) REVERT: J 151 MET cc_start: 0.6737 (mtp) cc_final: 0.6397 (tpt) REVERT: J 298 MET cc_start: 0.8370 (OUTLIER) cc_final: 0.7985 (mtm) REVERT: J 304 ASP cc_start: 0.7592 (m-30) cc_final: 0.7340 (m-30) REVERT: J 652 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.8074 (pp20) REVERT: J 707 ILE cc_start: 0.8618 (tp) cc_final: 0.8256 (tt) REVERT: J 870 ASP cc_start: 0.8183 (m-30) cc_final: 0.7780 (m-30) REVERT: J 922 SER cc_start: 0.9248 (m) cc_final: 0.8976 (p) REVERT: J 1021 ASP cc_start: 0.6230 (p0) cc_final: 0.5949 (p0) REVERT: J 1175 LEU cc_start: 0.8076 (tt) cc_final: 0.7747 (mm) REVERT: J 1372 ARG cc_start: 0.7820 (ttp-170) cc_final: 0.6830 (ttm-80) REVERT: J 1373 ARG cc_start: 0.7593 (tpm170) cc_final: 0.7202 (tpp-160) REVERT: K 42 GLU cc_start: 0.8085 (mp0) cc_final: 0.7821 (mp0) REVERT: K 53 GLU cc_start: 0.8892 (mt-10) cc_final: 0.8547 (mt-10) REVERT: K 55 GLU cc_start: 0.7830 (tm-30) cc_final: 0.7617 (tm-30) REVERT: K 59 ILE cc_start: 0.8767 (mt) cc_final: 0.8450 (tt) REVERT: K 76 GLU cc_start: 0.7879 (mm-30) cc_final: 0.7297 (mm-30) REVERT: L 276 MET cc_start: 0.7510 (ttt) cc_final: 0.7161 (ttp) REVERT: L 322 MET cc_start: 0.3095 (mtp) cc_final: 0.2784 (tpt) REVERT: L 365 MET cc_start: 0.8802 (ttt) cc_final: 0.8532 (ttp) REVERT: L 468 ARG cc_start: 0.7416 (ttp80) cc_final: 0.7010 (ttm170) REVERT: L 514 ASP cc_start: 0.8025 (t0) cc_final: 0.7415 (p0) REVERT: L 524 GLU cc_start: 0.7757 (pt0) cc_final: 0.7418 (pm20) REVERT: L 561 MET cc_start: 0.8131 (ttm) cc_final: 0.7812 (ptm) outliers start: 108 outliers final: 70 residues processed: 411 average time/residue: 0.1866 time to fit residues: 127.5269 Evaluate side-chains 382 residues out of total 3142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 305 time to evaluate : 1.408 ------------------------------------------------------------------------------- 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 178 SER Chi-restraints excluded: chain H residue 23 HIS Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain I residue 60 GLN Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 124 MET Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 341 LEU Chi-restraints excluded: chain I residue 410 LEU Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 633 LEU Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 770 CYS 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 971 LEU Chi-restraints excluded: chain I residue 992 LEU Chi-restraints excluded: chain I residue 1042 LEU Chi-restraints excluded: chain I residue 1145 ILE Chi-restraints excluded: chain I residue 1170 MET Chi-restraints excluded: chain I residue 1292 THR Chi-restraints excluded: chain I residue 1295 SER Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain I residue 1315 MET Chi-restraints excluded: chain I residue 1332 SER Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 237 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 416 ILE Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 539 SER 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 803 VAL 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 1233 ILE Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain J residue 1283 SER Chi-restraints excluded: chain J residue 1324 SER Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 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 387 VAL Chi-restraints excluded: chain L residue 410 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: 5.9990 chunk 341 optimal weight: 5.9990 chunk 69 optimal weight: 20.0000 chunk 126 optimal weight: 8.9990 chunk 276 optimal weight: 9.9990 chunk 65 optimal weight: 8.9990 chunk 155 optimal weight: 1.9990 chunk 299 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 174 optimal weight: 0.9990 chunk 324 optimal weight: 20.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 132 HIS H 227 GLN I 219 GLN I 273 HIS J 489 ASN J 560 ASN J 910 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.127822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.092704 restraints weight = 62561.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.093554 restraints weight = 37875.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.093837 restraints weight = 26459.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.094179 restraints weight = 23950.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.094313 restraints weight = 21529.832| |-----------------------------------------------------------------------------| r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 31919 Z= 0.239 Angle : 0.677 9.812 43631 Z= 0.347 Chirality : 0.044 0.281 5062 Planarity : 0.005 0.067 5287 Dihedral : 14.305 116.975 5777 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.54 % Favored : 92.40 % Rotamer: Outliers : 3.86 % Allowed : 13.92 % Favored : 82.22 % 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: -1.22 (0.14), residues: 3647 helix: 0.57 (0.14), residues: 1426 sheet: -1.42 (0.25), residues: 413 loop : -1.83 (0.14), residues: 1808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG J1258 TYR 0.022 0.002 TYR I 62 PHE 0.018 0.002 PHE I 545 TRP 0.019 0.002 TRP L 326 HIS 0.008 0.001 HIS J 777 Details of bonding type rmsd covalent geometry : bond 0.00553 (31912) covalent geometry : angle 0.67676 (43625) hydrogen bonds : bond 0.04223 ( 1310) hydrogen bonds : angle 4.76854 ( 3648) metal coordination : bond 0.00927 ( 7) metal coordination : angle 2.59863 ( 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 437 residues out of total 3142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 316 time to evaluate : 1.254 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 10 LYS cc_start: 0.8865 (ptmt) cc_final: 0.8664 (mtpt) REVERT: G 50 SER cc_start: 0.9353 (m) cc_final: 0.8855 (p) REVERT: G 75 GLN cc_start: 0.8946 (pt0) cc_final: 0.8531 (tt0) REVERT: H 16 ILE cc_start: 0.8825 (mt) cc_final: 0.8459 (tt) REVERT: H 58 GLU cc_start: 0.6926 (mp0) cc_final: 0.6707 (mp0) REVERT: H 86 LYS cc_start: 0.8600 (ttmt) cc_final: 0.7873 (tptt) REVERT: H 136 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.6978 (mp0) REVERT: I 37 LYS cc_start: 0.8048 (mmtt) cc_final: 0.7780 (mmmm) REVERT: I 260 LYS cc_start: 0.7427 (tptt) cc_final: 0.7158 (tptp) REVERT: I 315 MET cc_start: 0.8246 (mtp) cc_final: 0.8018 (mtt) REVERT: I 484 LEU cc_start: 0.7901 (OUTLIER) cc_final: 0.7639 (mt) REVERT: I 549 ASP cc_start: 0.8804 (t0) cc_final: 0.8513 (m-30) REVERT: I 633 LEU cc_start: 0.7765 (OUTLIER) cc_final: 0.7542 (pp) REVERT: I 672 GLU cc_start: 0.8270 (pm20) cc_final: 0.7931 (pm20) REVERT: I 741 MET cc_start: 0.8188 (ttp) cc_final: 0.7531 (ttm) REVERT: I 788 SER cc_start: 0.9269 (m) cc_final: 0.8735 (p) REVERT: I 828 PHE cc_start: 0.9357 (OUTLIER) cc_final: 0.9066 (m-10) REVERT: I 844 LYS cc_start: 0.8316 (mttm) cc_final: 0.8005 (pttp) REVERT: I 992 LEU cc_start: 0.6822 (OUTLIER) cc_final: 0.6201 (tp) REVERT: I 1025 PHE cc_start: 0.7745 (t80) cc_final: 0.6877 (t80) REVERT: I 1027 LYS cc_start: 0.8727 (pttt) cc_final: 0.8480 (ptpt) REVERT: I 1111 GLN cc_start: 0.8160 (pt0) cc_final: 0.7506 (pt0) REVERT: I 1119 MET cc_start: 0.8995 (tpp) cc_final: 0.8270 (tpp) REVERT: I 1230 MET cc_start: 0.8840 (ttm) cc_final: 0.8524 (ttp) REVERT: J 151 MET cc_start: 0.6639 (mtp) cc_final: 0.6411 (tpt) REVERT: J 298 MET cc_start: 0.8285 (OUTLIER) cc_final: 0.7751 (mtm) REVERT: J 304 ASP cc_start: 0.7643 (m-30) cc_final: 0.7349 (m-30) REVERT: J 652 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.8124 (pp20) REVERT: J 707 ILE cc_start: 0.8598 (tp) cc_final: 0.8315 (tt) REVERT: J 870 ASP cc_start: 0.8161 (m-30) cc_final: 0.7813 (m-30) REVERT: J 922 SER cc_start: 0.9276 (m) cc_final: 0.8989 (p) REVERT: J 1021 ASP cc_start: 0.6207 (p0) cc_final: 0.5919 (p0) REVERT: J 1175 LEU cc_start: 0.8245 (tt) cc_final: 0.7959 (mm) REVERT: J 1372 ARG cc_start: 0.7810 (ttp-170) cc_final: 0.6620 (ttm-80) REVERT: J 1373 ARG cc_start: 0.7630 (tpm170) cc_final: 0.7272 (tpp-160) REVERT: K 53 GLU cc_start: 0.8919 (mt-10) cc_final: 0.8540 (mt-10) REVERT: K 55 GLU cc_start: 0.7917 (tm-30) cc_final: 0.7484 (tm-30) REVERT: K 56 GLU cc_start: 0.8476 (mm-30) cc_final: 0.7954 (mm-30) REVERT: K 59 ILE cc_start: 0.8783 (mt) cc_final: 0.8559 (tt) REVERT: L 144 LEU cc_start: 0.8243 (tt) cc_final: 0.7830 (mp) REVERT: L 276 MET cc_start: 0.7456 (ttt) cc_final: 0.7121 (ttp) REVERT: L 322 MET cc_start: 0.3209 (mtp) cc_final: 0.2786 (tpt) REVERT: L 365 MET cc_start: 0.8858 (ttt) cc_final: 0.8547 (ttp) REVERT: L 468 ARG cc_start: 0.7409 (ttp80) cc_final: 0.6991 (ttm170) REVERT: L 524 GLU cc_start: 0.7713 (pt0) cc_final: 0.7438 (pm20) REVERT: L 603 ARG cc_start: 0.8683 (OUTLIER) cc_final: 0.8101 (mtt180) outliers start: 121 outliers final: 79 residues processed: 407 average time/residue: 0.1863 time to fit residues: 125.3649 Evaluate side-chains 383 residues out of total 3142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 296 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 15 ASP Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain H residue 23 HIS Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 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 136 GLU 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 219 GLN Chi-restraints excluded: chain I residue 410 LEU Chi-restraints excluded: chain I residue 420 LEU Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 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 770 CYS Chi-restraints excluded: chain I residue 828 PHE Chi-restraints excluded: chain I residue 829 THR Chi-restraints excluded: chain I residue 863 SER Chi-restraints excluded: chain I residue 903 ARG Chi-restraints excluded: chain I residue 992 LEU Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1145 ILE Chi-restraints excluded: chain I residue 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 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 803 VAL Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 897 HIS Chi-restraints excluded: chain J residue 909 ILE Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 1189 MET Chi-restraints excluded: chain J residue 1233 ILE Chi-restraints excluded: chain J residue 1283 SER Chi-restraints excluded: chain J residue 1324 SER Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 64 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 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: 0.0670 chunk 180 optimal weight: 0.9990 chunk 369 optimal weight: 30.0000 chunk 34 optimal weight: 0.0270 chunk 263 optimal weight: 9.9990 chunk 225 optimal weight: 0.0970 chunk 28 optimal weight: 5.9990 chunk 114 optimal weight: 7.9990 chunk 167 optimal weight: 4.9990 chunk 255 optimal weight: 0.8980 chunk 101 optimal weight: 0.2980 overall best weight: 0.2774 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 23 HIS H 37 HIS ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 219 GLN I 273 HIS I 808 ASN I1010 GLN I1013 GLN J 560 ASN K 72 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.133248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.098292 restraints weight = 61908.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.099366 restraints weight = 35758.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.099476 restraints weight = 25614.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.099931 restraints weight = 23769.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.100049 restraints weight = 20868.626| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.3769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 31919 Z= 0.107 Angle : 0.567 7.863 43631 Z= 0.292 Chirality : 0.041 0.261 5062 Planarity : 0.004 0.069 5287 Dihedral : 14.064 118.026 5777 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.65 % Favored : 94.30 % Rotamer: Outliers : 2.90 % Allowed : 14.81 % Favored : 82.29 % 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: -0.74 (0.14), residues: 3647 helix: 1.08 (0.14), residues: 1420 sheet: -1.24 (0.25), residues: 404 loop : -1.62 (0.14), residues: 1823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 44 TYR 0.027 0.001 TYR I 62 PHE 0.015 0.001 PHE I1164 TRP 0.014 0.001 TRP L 326 HIS 0.004 0.001 HIS L 600 Details of bonding type rmsd covalent geometry : bond 0.00232 (31912) covalent geometry : angle 0.56703 (43625) hydrogen bonds : bond 0.03499 ( 1310) hydrogen bonds : angle 4.35364 ( 3648) metal coordination : bond 0.00218 ( 7) metal coordination : angle 1.96589 ( 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 468 residues out of total 3142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 377 time to evaluate : 1.193 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 50 SER cc_start: 0.9252 (m) cc_final: 0.8727 (p) REVERT: H 86 LYS cc_start: 0.8367 (ttmt) cc_final: 0.7793 (tttp) REVERT: H 136 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.6737 (mp0) REVERT: H 185 TYR cc_start: 0.8607 (p90) cc_final: 0.8275 (p90) REVERT: I 37 LYS cc_start: 0.7953 (mmtt) cc_final: 0.7687 (mmmm) REVERT: I 62 TYR cc_start: 0.6930 (OUTLIER) cc_final: 0.6702 (m-80) REVERT: I 219 GLN cc_start: 0.7881 (OUTLIER) cc_final: 0.7676 (mt0) REVERT: I 291 TYR cc_start: 0.6956 (t80) cc_final: 0.6715 (t80) REVERT: I 315 MET cc_start: 0.8218 (mtp) cc_final: 0.7838 (mtt) REVERT: I 391 SER cc_start: 0.8814 (t) cc_final: 0.8464 (m) REVERT: I 530 ILE cc_start: 0.9709 (mm) cc_final: 0.9471 (mm) REVERT: I 549 ASP cc_start: 0.8645 (t0) cc_final: 0.8300 (m-30) REVERT: I 672 GLU cc_start: 0.8186 (pm20) cc_final: 0.7785 (pm20) REVERT: I 684 ASN cc_start: 0.8755 (t0) cc_final: 0.8511 (t0) REVERT: I 741 MET cc_start: 0.8059 (ttp) cc_final: 0.7531 (ttm) REVERT: I 788 SER cc_start: 0.9008 (m) cc_final: 0.8232 (p) REVERT: I 828 PHE cc_start: 0.9228 (OUTLIER) cc_final: 0.8816 (m-10) REVERT: I 844 LYS cc_start: 0.8248 (mttm) cc_final: 0.7946 (pttp) REVERT: I 992 LEU cc_start: 0.6372 (OUTLIER) cc_final: 0.5814 (tp) REVERT: I 1027 LYS cc_start: 0.8758 (pttt) cc_final: 0.8490 (ptpt) REVERT: I 1111 GLN cc_start: 0.8020 (pt0) cc_final: 0.7645 (pt0) REVERT: I 1119 MET cc_start: 0.8934 (tpp) cc_final: 0.8222 (tpp) REVERT: I 1230 MET cc_start: 0.8601 (ttm) cc_final: 0.8194 (ttp) REVERT: J 298 MET cc_start: 0.8126 (OUTLIER) cc_final: 0.7622 (mtm) REVERT: J 304 ASP cc_start: 0.7677 (m-30) cc_final: 0.7432 (m-30) REVERT: J 581 MET cc_start: 0.8345 (mtm) cc_final: 0.7987 (mtp) REVERT: J 652 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.8062 (pp20) REVERT: J 707 ILE cc_start: 0.8543 (tp) cc_final: 0.8189 (tt) REVERT: J 840 LEU cc_start: 0.8765 (tt) cc_final: 0.8553 (tt) REVERT: J 1021 ASP cc_start: 0.6200 (p0) cc_final: 0.5969 (p0) REVERT: J 1175 LEU cc_start: 0.8367 (tt) cc_final: 0.8109 (mm) REVERT: J 1189 MET cc_start: 0.8273 (OUTLIER) cc_final: 0.7838 (mmm) REVERT: K 53 GLU cc_start: 0.8896 (mt-10) cc_final: 0.8457 (mt-10) REVERT: K 56 GLU cc_start: 0.8609 (mm-30) cc_final: 0.8396 (mm-30) REVERT: L 100 MET cc_start: 0.7938 (mtt) cc_final: 0.7647 (mtt) REVERT: L 144 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7930 (mt) REVERT: L 276 MET cc_start: 0.7414 (ttt) cc_final: 0.7082 (ttp) REVERT: L 288 MET cc_start: 0.3604 (mtt) cc_final: 0.3334 (ptp) REVERT: L 322 MET cc_start: 0.3239 (mtp) cc_final: 0.2484 (tpt) REVERT: L 365 MET cc_start: 0.8817 (ttt) cc_final: 0.8485 (ttp) REVERT: L 468 ARG cc_start: 0.7344 (ttp80) cc_final: 0.7044 (ttp-170) REVERT: L 474 MET cc_start: 0.7614 (mmm) cc_final: 0.7357 (mmm) REVERT: L 514 ASP cc_start: 0.8091 (t70) cc_final: 0.7693 (m-30) REVERT: L 524 GLU cc_start: 0.7652 (pt0) cc_final: 0.7368 (pm20) outliers start: 91 outliers final: 46 residues processed: 441 average time/residue: 0.1906 time to fit residues: 138.7650 Evaluate side-chains 371 residues out of total 3142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 316 time to evaluate : 1.133 ------------------------------------------------------------------------------- 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 H residue 23 HIS Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 136 GLU Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain I residue 62 TYR Chi-restraints excluded: chain I residue 124 MET Chi-restraints excluded: chain I residue 219 GLN 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 690 VAL Chi-restraints excluded: chain I residue 773 LEU 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 992 LEU Chi-restraints excluded: chain I residue 1151 LEU 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 298 MET 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 567 THR 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 918 ILE Chi-restraints excluded: chain J residue 950 ILE Chi-restraints excluded: chain J residue 1189 MET Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain J residue 1357 ILE Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 41 GLU Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain L residue 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 203 optimal weight: 5.9990 chunk 129 optimal weight: 0.5980 chunk 19 optimal weight: 10.0000 chunk 144 optimal weight: 10.0000 chunk 66 optimal weight: 7.9990 chunk 362 optimal weight: 10.0000 chunk 333 optimal weight: 20.0000 chunk 65 optimal weight: 5.9990 chunk 269 optimal weight: 7.9990 chunk 243 optimal weight: 2.9990 chunk 318 optimal weight: 8.9990 overall best weight: 4.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 219 GLN ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 560 ASN K 72 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.126628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.091512 restraints weight = 62590.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.091581 restraints weight = 38889.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.092280 restraints weight = 27684.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.092643 restraints weight = 24762.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.092718 restraints weight = 22254.086| |-----------------------------------------------------------------------------| r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.3904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 31919 Z= 0.296 Angle : 0.720 10.381 43631 Z= 0.368 Chirality : 0.045 0.249 5062 Planarity : 0.005 0.071 5287 Dihedral : 14.222 115.530 5777 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.70 % Favored : 92.24 % Rotamer: Outliers : 3.48 % Allowed : 15.38 % Favored : 81.14 % 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: -1.02 (0.14), residues: 3647 helix: 0.74 (0.14), residues: 1432 sheet: -1.26 (0.25), residues: 411 loop : -1.74 (0.14), residues: 1804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I1246 TYR 0.025 0.002 TYR I 62 PHE 0.028 0.002 PHE L 221 TRP 0.015 0.002 TRP L 326 HIS 0.007 0.001 HIS G 23 Details of bonding type rmsd covalent geometry : bond 0.00681 (31912) covalent geometry : angle 0.71912 (43625) hydrogen bonds : bond 0.04352 ( 1310) hydrogen bonds : angle 4.76686 ( 3648) metal coordination : bond 0.01130 ( 7) metal coordination : angle 2.16058 ( 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 408 residues out of total 3142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 299 time to evaluate : 1.112 Fit side-chains revert: symmetry clash REVERT: G 50 SER cc_start: 0.9410 (m) cc_final: 0.8920 (p) REVERT: G 75 GLN cc_start: 0.9032 (pt0) cc_final: 0.8627 (tt0) REVERT: G 163 GLU cc_start: 0.5992 (OUTLIER) cc_final: 0.5524 (mp0) REVERT: H 136 GLU cc_start: 0.7157 (OUTLIER) cc_final: 0.6574 (mp0) REVERT: I 37 LYS cc_start: 0.8107 (mmtt) cc_final: 0.7820 (mmmm) REVERT: I 315 MET cc_start: 0.8256 (mtp) cc_final: 0.7982 (mtt) REVERT: I 475 VAL cc_start: 0.9435 (OUTLIER) cc_final: 0.9174 (p) REVERT: I 549 ASP cc_start: 0.8818 (t0) cc_final: 0.8563 (m-30) REVERT: I 588 GLU cc_start: 0.8051 (mp0) cc_final: 0.7850 (mp0) REVERT: I 672 GLU cc_start: 0.8264 (pm20) cc_final: 0.7917 (pm20) REVERT: I 741 MET cc_start: 0.8153 (ttp) cc_final: 0.7453 (ttm) REVERT: I 828 PHE cc_start: 0.9362 (OUTLIER) cc_final: 0.9072 (m-10) REVERT: I 844 LYS cc_start: 0.8298 (mttm) cc_final: 0.7953 (pttm) REVERT: I 992 LEU cc_start: 0.7005 (OUTLIER) cc_final: 0.6026 (tp) REVERT: I 1025 PHE cc_start: 0.7903 (t80) cc_final: 0.6958 (t80) REVERT: I 1027 LYS cc_start: 0.8742 (pttt) cc_final: 0.8474 (ptpt) REVERT: I 1111 GLN cc_start: 0.8256 (pt0) cc_final: 0.7593 (pt0) REVERT: I 1119 MET cc_start: 0.8942 (tpp) cc_final: 0.8285 (tpp) REVERT: I 1230 MET cc_start: 0.8849 (ttm) cc_final: 0.8528 (ttp) REVERT: J 144 TYR cc_start: 0.9015 (m-80) cc_final: 0.8419 (m-10) REVERT: J 298 MET cc_start: 0.8311 (OUTLIER) cc_final: 0.7786 (mtm) REVERT: J 304 ASP cc_start: 0.7681 (m-30) cc_final: 0.7387 (m-30) REVERT: J 505 ASP cc_start: 0.9208 (OUTLIER) cc_final: 0.8735 (t0) REVERT: J 581 MET cc_start: 0.8489 (mtm) cc_final: 0.8060 (mtp) REVERT: J 652 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.8182 (pp20) REVERT: J 658 GLU cc_start: 0.8054 (mt-10) cc_final: 0.7763 (mt-10) REVERT: J 707 ILE cc_start: 0.8639 (tp) cc_final: 0.8400 (tt) REVERT: J 870 ASP cc_start: 0.8091 (m-30) cc_final: 0.7794 (m-30) REVERT: J 1021 ASP cc_start: 0.6459 (p0) cc_final: 0.6151 (p0) REVERT: J 1175 LEU cc_start: 0.8295 (tt) cc_final: 0.7964 (mm) REVERT: K 53 GLU cc_start: 0.8889 (mt-10) cc_final: 0.8462 (mt-10) REVERT: L 276 MET cc_start: 0.7327 (ttt) cc_final: 0.7116 (ttp) REVERT: L 288 MET cc_start: 0.3742 (mtt) cc_final: 0.3468 (ptp) REVERT: L 322 MET cc_start: 0.3414 (mtp) cc_final: 0.2619 (tpt) REVERT: L 365 MET cc_start: 0.8877 (ttt) cc_final: 0.8630 (ttp) REVERT: L 468 ARG cc_start: 0.7369 (ttp80) cc_final: 0.6884 (ttm170) REVERT: L 514 ASP cc_start: 0.8056 (t70) cc_final: 0.7579 (p0) REVERT: L 524 GLU cc_start: 0.7797 (pt0) cc_final: 0.7463 (pm20) REVERT: L 603 ARG cc_start: 0.8726 (OUTLIER) cc_final: 0.8208 (mtt180) outliers start: 109 outliers final: 72 residues processed: 384 average time/residue: 0.1952 time to fit residues: 123.3912 Evaluate side-chains 367 residues out of total 3142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 286 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 15 ASP Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 163 GLU Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 136 GLU Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 302 ILE Chi-restraints excluded: chain I residue 336 LEU Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain I residue 410 LEU Chi-restraints excluded: chain I residue 453 ILE 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 690 VAL Chi-restraints excluded: chain I residue 693 LEU Chi-restraints excluded: chain I residue 717 VAL Chi-restraints excluded: chain I residue 802 VAL 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 992 LEU Chi-restraints excluded: chain I residue 1145 ILE Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1170 MET Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1295 SER Chi-restraints excluded: chain I residue 1332 SER Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 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 408 VAL Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 505 ASP Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 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 743 MET Chi-restraints excluded: chain J residue 797 THR Chi-restraints excluded: chain J residue 802 ASP Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 857 LEU Chi-restraints excluded: chain J residue 890 THR Chi-restraints excluded: chain J residue 897 HIS Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 950 ILE Chi-restraints excluded: chain J residue 1189 MET Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 39 VAL 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 410 ILE Chi-restraints excluded: chain L residue 488 LEU Chi-restraints excluded: chain L residue 603 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 309 optimal weight: 0.9990 chunk 313 optimal weight: 7.9990 chunk 207 optimal weight: 0.8980 chunk 266 optimal weight: 4.9990 chunk 344 optimal weight: 1.9990 chunk 67 optimal weight: 0.2980 chunk 10 optimal weight: 10.0000 chunk 315 optimal weight: 0.5980 chunk 85 optimal weight: 0.9980 chunk 277 optimal weight: 20.0000 chunk 133 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 23 HIS H 227 GLN ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 219 GLN I 618 GLN J 560 ASN K 31 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.131492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.096505 restraints weight = 62070.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.097165 restraints weight = 34606.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.097467 restraints weight = 25915.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.097825 restraints weight = 25143.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.098150 restraints weight = 21399.513| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.4044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 31919 Z= 0.114 Angle : 0.589 8.634 43631 Z= 0.300 Chirality : 0.041 0.244 5062 Planarity : 0.004 0.073 5287 Dihedral : 14.060 119.047 5777 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.81 % Favored : 94.13 % Rotamer: Outliers : 2.39 % Allowed : 16.79 % 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: -0.65 (0.14), residues: 3647 helix: 1.10 (0.14), residues: 1433 sheet: -1.09 (0.25), residues: 406 loop : -1.57 (0.14), residues: 1808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 436 TYR 0.029 0.001 TYR H 185 PHE 0.031 0.001 PHE L 256 TRP 0.017 0.001 TRP L 326 HIS 0.006 0.001 HIS J 450 Details of bonding type rmsd covalent geometry : bond 0.00255 (31912) covalent geometry : angle 0.58846 (43625) hydrogen bonds : bond 0.03587 ( 1310) hydrogen bonds : angle 4.36973 ( 3648) metal coordination : bond 0.00262 ( 7) metal coordination : angle 1.93080 ( 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 393 residues out of total 3142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 318 time to evaluate : 1.406 Fit side-chains revert: symmetry clash REVERT: G 50 SER cc_start: 0.9297 (m) cc_final: 0.8806 (p) REVERT: G 163 GLU cc_start: 0.5869 (OUTLIER) cc_final: 0.5537 (mp0) REVERT: H 16 ILE cc_start: 0.8757 (mt) cc_final: 0.8338 (tt) REVERT: H 136 GLU cc_start: 0.7356 (OUTLIER) cc_final: 0.6591 (mp0) REVERT: I 37 LYS cc_start: 0.8114 (mmtt) cc_final: 0.7835 (mmmm) REVERT: I 315 MET cc_start: 0.8274 (mtp) cc_final: 0.7997 (mtt) REVERT: I 391 SER cc_start: 0.8851 (t) cc_final: 0.8475 (m) REVERT: I 549 ASP cc_start: 0.8678 (t0) cc_final: 0.8320 (m-30) REVERT: I 672 GLU cc_start: 0.8180 (pm20) cc_final: 0.7809 (pm20) REVERT: I 741 MET cc_start: 0.7930 (ttp) cc_final: 0.7360 (ttm) REVERT: I 788 SER cc_start: 0.9113 (m) cc_final: 0.8489 (p) REVERT: I 828 PHE cc_start: 0.9269 (OUTLIER) cc_final: 0.8910 (m-10) REVERT: I 844 LYS cc_start: 0.8238 (mttm) cc_final: 0.7974 (pttp) REVERT: I 936 ARG cc_start: 0.7400 (ttm-80) cc_final: 0.7140 (ttm170) REVERT: I 992 LEU cc_start: 0.6786 (OUTLIER) cc_final: 0.5831 (tp) REVERT: I 1027 LYS cc_start: 0.8775 (pttt) cc_final: 0.8504 (ptpt) REVERT: I 1111 GLN cc_start: 0.7969 (pt0) cc_final: 0.7560 (pt0) REVERT: I 1119 MET cc_start: 0.8715 (tpp) cc_final: 0.8148 (tpp) REVERT: I 1230 MET cc_start: 0.8591 (ttm) cc_final: 0.8081 (ttp) REVERT: J 144 TYR cc_start: 0.8982 (m-80) cc_final: 0.8460 (m-10) REVERT: J 298 MET cc_start: 0.8109 (OUTLIER) cc_final: 0.7615 (mtm) REVERT: J 304 ASP cc_start: 0.7705 (m-30) cc_final: 0.7446 (m-30) REVERT: J 581 MET cc_start: 0.8431 (mtm) cc_final: 0.8149 (mtp) REVERT: J 652 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.8070 (pp20) REVERT: J 707 ILE cc_start: 0.8633 (tp) cc_final: 0.8366 (tt) REVERT: J 835 LEU cc_start: 0.8556 (tp) cc_final: 0.8340 (tp) REVERT: J 1021 ASP cc_start: 0.6352 (p0) cc_final: 0.6057 (p0) REVERT: J 1175 LEU cc_start: 0.8479 (tt) cc_final: 0.8132 (mm) REVERT: J 1251 LYS cc_start: 0.9192 (OUTLIER) cc_final: 0.8961 (mtpp) REVERT: K 53 GLU cc_start: 0.8641 (mt-10) cc_final: 0.8263 (mt-10) REVERT: L 100 MET cc_start: 0.7912 (mtt) cc_final: 0.7597 (mtt) REVERT: L 276 MET cc_start: 0.7504 (ttt) cc_final: 0.7191 (ttp) REVERT: L 288 MET cc_start: 0.4092 (mtt) cc_final: 0.3750 (ptp) REVERT: L 322 MET cc_start: 0.3183 (mtp) cc_final: 0.2433 (tpt) REVERT: L 365 MET cc_start: 0.8895 (ttt) cc_final: 0.8625 (ttp) REVERT: L 468 ARG cc_start: 0.7276 (ttp80) cc_final: 0.6913 (ttp-170) REVERT: L 514 ASP cc_start: 0.8019 (t70) cc_final: 0.7538 (m-30) REVERT: L 524 GLU cc_start: 0.7657 (pt0) cc_final: 0.7369 (pm20) REVERT: L 561 MET cc_start: 0.8487 (OUTLIER) cc_final: 0.8236 (tmm) outliers start: 75 outliers final: 50 residues processed: 375 average time/residue: 0.1989 time to fit residues: 123.5115 Evaluate side-chains 350 residues out of total 3142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 292 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 15 ASP Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 163 GLU Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain H residue 23 HIS Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 136 GLU Chi-restraints excluded: chain H residue 198 LEU 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 778 GLU 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 1151 LEU Chi-restraints excluded: chain J residue 93 THR 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 357 VAL Chi-restraints excluded: chain J residue 368 LEU Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 539 SER Chi-restraints excluded: chain J residue 567 THR Chi-restraints excluded: chain J residue 587 LEU Chi-restraints excluded: chain J residue 652 GLU Chi-restraints excluded: chain J residue 800 LEU 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 918 ILE 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 1267 VAL Chi-restraints excluded: chain K residue 39 VAL 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 Chi-restraints excluded: chain L residue 561 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 317 optimal weight: 7.9990 chunk 202 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 249 optimal weight: 0.8980 chunk 368 optimal weight: 20.0000 chunk 91 optimal weight: 0.9990 chunk 328 optimal weight: 9.9990 chunk 293 optimal weight: 10.0000 chunk 70 optimal weight: 6.9990 chunk 366 optimal weight: 20.0000 chunk 139 optimal weight: 10.0000 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 219 GLN J 560 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.127771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.092652 restraints weight = 62157.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.092896 restraints weight = 37806.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.093599 restraints weight = 28929.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.093730 restraints weight = 26403.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.093896 restraints weight = 22399.856| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.4093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 31919 Z= 0.239 Angle : 0.678 9.735 43631 Z= 0.344 Chirality : 0.044 0.241 5062 Planarity : 0.005 0.070 5287 Dihedral : 14.141 117.545 5777 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.40 % Favored : 92.54 % Rotamer: Outliers : 2.71 % Allowed : 16.88 % Favored : 80.40 % 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: 0.92 (0.14), residues: 1437 sheet: -1.23 (0.25), residues: 412 loop : -1.63 (0.14), residues: 1798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 436 TYR 0.026 0.002 TYR H 185 PHE 0.023 0.002 PHE L 221 TRP 0.017 0.001 TRP L 326 HIS 0.006 0.001 HIS G 23 Details of bonding type rmsd covalent geometry : bond 0.00556 (31912) covalent geometry : angle 0.67734 (43625) hydrogen bonds : bond 0.04061 ( 1310) hydrogen bonds : angle 4.59622 ( 3648) metal coordination : bond 0.00891 ( 7) metal coordination : angle 1.72662 ( 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 373 residues out of total 3142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 288 time to evaluate : 1.151 Fit side-chains revert: symmetry clash REVERT: G 50 SER cc_start: 0.9370 (m) cc_final: 0.8894 (p) REVERT: G 163 GLU cc_start: 0.6034 (OUTLIER) cc_final: 0.5547 (mp0) REVERT: H 16 ILE cc_start: 0.8809 (mt) cc_final: 0.8390 (tt) REVERT: H 136 GLU cc_start: 0.7272 (OUTLIER) cc_final: 0.6662 (mp0) REVERT: I 37 LYS cc_start: 0.8071 (mmtt) cc_final: 0.7830 (mmmm) REVERT: I 315 MET cc_start: 0.8201 (mtp) cc_final: 0.7939 (mtt) REVERT: I 549 ASP cc_start: 0.8785 (t0) cc_final: 0.8520 (m-30) REVERT: I 672 GLU cc_start: 0.8194 (pm20) cc_final: 0.7839 (pm20) REVERT: I 741 MET cc_start: 0.8087 (ttp) cc_final: 0.7555 (ttm) REVERT: I 828 PHE cc_start: 0.9338 (OUTLIER) cc_final: 0.9039 (m-10) REVERT: I 844 LYS cc_start: 0.8238 (mttm) cc_final: 0.7944 (pttm) REVERT: I 936 ARG cc_start: 0.7371 (ttm-80) cc_final: 0.7034 (ttm170) REVERT: I 992 LEU cc_start: 0.6913 (OUTLIER) cc_final: 0.5878 (tp) REVERT: I 1027 LYS cc_start: 0.8692 (pttt) cc_final: 0.8411 (ptpt) REVERT: I 1111 GLN cc_start: 0.8115 (pt0) cc_final: 0.7452 (pt0) REVERT: I 1119 MET cc_start: 0.8865 (tpp) cc_final: 0.8250 (tpp) REVERT: I 1230 MET cc_start: 0.8832 (ttm) cc_final: 0.8469 (ttp) REVERT: J 144 TYR cc_start: 0.9015 (m-80) cc_final: 0.8504 (m-10) REVERT: J 298 MET cc_start: 0.8253 (OUTLIER) cc_final: 0.7704 (mtm) REVERT: J 304 ASP cc_start: 0.7691 (m-30) cc_final: 0.7432 (m-30) REVERT: J 581 MET cc_start: 0.8539 (mtm) cc_final: 0.8122 (mtp) REVERT: J 652 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.8164 (pp20) REVERT: J 707 ILE cc_start: 0.8718 (tp) cc_final: 0.8454 (tt) REVERT: J 870 ASP cc_start: 0.8041 (m-30) cc_final: 0.7790 (m-30) REVERT: J 1175 LEU cc_start: 0.8359 (tt) cc_final: 0.7977 (mm) REVERT: J 1251 LYS cc_start: 0.9292 (OUTLIER) cc_final: 0.8965 (mtpp) REVERT: L 100 MET cc_start: 0.8179 (mtt) cc_final: 0.7829 (mtt) REVERT: L 276 MET cc_start: 0.7409 (ttt) cc_final: 0.7208 (ttp) REVERT: L 288 MET cc_start: 0.4081 (mtt) cc_final: 0.3774 (ptp) REVERT: L 322 MET cc_start: 0.3395 (mtp) cc_final: 0.2485 (tpt) REVERT: L 365 MET cc_start: 0.8934 (ttt) cc_final: 0.8678 (ttp) REVERT: L 468 ARG cc_start: 0.7372 (ttp80) cc_final: 0.6903 (ttm170) REVERT: L 524 GLU cc_start: 0.7670 (pt0) cc_final: 0.7348 (pm20) outliers start: 85 outliers final: 60 residues processed: 355 average time/residue: 0.1968 time to fit residues: 115.6587 Evaluate side-chains 353 residues out of total 3142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 286 time to evaluate : 1.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 15 ASP Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 163 GLU Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 136 GLU Chi-restraints excluded: chain H residue 198 LEU 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 538 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 778 GLU Chi-restraints excluded: chain I residue 819 SER Chi-restraints excluded: chain I residue 828 PHE Chi-restraints excluded: chain I residue 829 THR 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 1046 VAL Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1170 MET 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 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 408 VAL Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 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 857 LEU Chi-restraints excluded: chain J residue 890 THR Chi-restraints excluded: chain J residue 897 HIS Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 950 ILE Chi-restraints excluded: chain J residue 1189 MET Chi-restraints excluded: chain J residue 1251 LYS Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain J residue 1324 SER Chi-restraints excluded: chain K residue 39 VAL 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 387 VAL Chi-restraints excluded: chain L residue 488 LEU Chi-restraints excluded: chain L residue 561 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 75 optimal weight: 10.0000 chunk 17 optimal weight: 0.9980 chunk 316 optimal weight: 5.9990 chunk 231 optimal weight: 10.0000 chunk 171 optimal weight: 0.7980 chunk 313 optimal weight: 3.9990 chunk 5 optimal weight: 7.9990 chunk 113 optimal weight: 4.9990 chunk 158 optimal weight: 0.3980 chunk 224 optimal weight: 3.9990 chunk 242 optimal weight: 8.9990 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 23 HIS ** H 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 219 GLN J 560 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.129529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.094733 restraints weight = 62172.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.094668 restraints weight = 33799.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.095103 restraints weight = 28155.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.095475 restraints weight = 25108.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.095614 restraints weight = 22345.666| |-----------------------------------------------------------------------------| r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.4171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 31919 Z= 0.159 Angle : 0.622 9.993 43631 Z= 0.316 Chirality : 0.042 0.238 5062 Planarity : 0.004 0.070 5287 Dihedral : 14.107 119.585 5777 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.61 % Favored : 93.34 % Rotamer: Outliers : 2.14 % Allowed : 17.52 % Favored : 80.34 % 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: -0.68 (0.14), residues: 3647 helix: 1.09 (0.14), residues: 1428 sheet: -1.19 (0.24), residues: 428 loop : -1.58 (0.14), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 143 TYR 0.025 0.001 TYR H 185 PHE 0.022 0.001 PHE L 221 TRP 0.018 0.001 TRP L 326 HIS 0.006 0.001 HIS J 450 Details of bonding type rmsd covalent geometry : bond 0.00370 (31912) covalent geometry : angle 0.62148 (43625) hydrogen bonds : bond 0.03785 ( 1310) hydrogen bonds : angle 4.45597 ( 3648) metal coordination : bond 0.00536 ( 7) metal coordination : angle 1.96891 ( 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 364 residues out of total 3142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 297 time to evaluate : 1.222 Fit side-chains revert: symmetry clash REVERT: G 50 SER cc_start: 0.9364 (m) cc_final: 0.8878 (p) REVERT: G 163 GLU cc_start: 0.6125 (OUTLIER) cc_final: 0.5662 (mp0) REVERT: H 16 ILE cc_start: 0.8746 (mt) cc_final: 0.8348 (tt) REVERT: H 136 GLU cc_start: 0.7354 (OUTLIER) cc_final: 0.6661 (mp0) REVERT: I 37 LYS cc_start: 0.7977 (mmtt) cc_final: 0.7649 (mmmm) REVERT: I 272 ARG cc_start: 0.8345 (ttt180) cc_final: 0.7965 (ttp-110) REVERT: I 315 MET cc_start: 0.8350 (mtp) cc_final: 0.8030 (mtt) REVERT: I 515 MET cc_start: 0.8774 (ttp) cc_final: 0.8550 (ttp) REVERT: I 549 ASP cc_start: 0.8907 (t0) cc_final: 0.8630 (m-30) REVERT: I 672 GLU cc_start: 0.8326 (pm20) cc_final: 0.7848 (pm20) REVERT: I 741 MET cc_start: 0.8011 (ttp) cc_final: 0.7427 (ttm) REVERT: I 788 SER cc_start: 0.9293 (m) cc_final: 0.8679 (p) REVERT: I 828 PHE cc_start: 0.9368 (OUTLIER) cc_final: 0.9023 (m-10) REVERT: I 844 LYS cc_start: 0.8252 (mttm) cc_final: 0.7908 (pttm) REVERT: I 936 ARG cc_start: 0.7403 (ttm-80) cc_final: 0.6996 (ttm170) REVERT: I 992 LEU cc_start: 0.6911 (OUTLIER) cc_final: 0.5945 (tp) REVERT: I 1027 LYS cc_start: 0.8727 (pttt) cc_final: 0.8449 (ptpt) REVERT: I 1111 GLN cc_start: 0.8131 (pt0) cc_final: 0.7471 (pt0) REVERT: I 1119 MET cc_start: 0.8890 (tpp) cc_final: 0.8327 (tpp) REVERT: I 1230 MET cc_start: 0.8771 (ttm) cc_final: 0.8454 (ttp) REVERT: J 144 TYR cc_start: 0.8912 (m-80) cc_final: 0.8449 (m-10) REVERT: J 298 MET cc_start: 0.8298 (OUTLIER) cc_final: 0.7804 (mtm) REVERT: J 304 ASP cc_start: 0.7784 (m-30) cc_final: 0.7463 (m-30) REVERT: J 581 MET cc_start: 0.8606 (mtm) cc_final: 0.8221 (mtp) REVERT: J 652 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.8100 (pp20) REVERT: J 707 ILE cc_start: 0.8664 (tp) cc_final: 0.8423 (tt) REVERT: J 870 ASP cc_start: 0.8128 (m-30) cc_final: 0.7837 (m-30) REVERT: J 1175 LEU cc_start: 0.8417 (tt) cc_final: 0.8034 (mm) REVERT: J 1251 LYS cc_start: 0.9255 (OUTLIER) cc_final: 0.8903 (mtpp) REVERT: K 53 GLU cc_start: 0.8865 (mt-10) cc_final: 0.8471 (mt-10) REVERT: L 100 MET cc_start: 0.8106 (mtt) cc_final: 0.7721 (mtt) REVERT: L 276 MET cc_start: 0.7475 (ttt) cc_final: 0.7261 (ttp) REVERT: L 288 MET cc_start: 0.4114 (mtt) cc_final: 0.3757 (ptp) REVERT: L 322 MET cc_start: 0.3367 (mtp) cc_final: 0.2460 (tpt) REVERT: L 365 MET cc_start: 0.9043 (ttt) cc_final: 0.8782 (ttp) REVERT: L 468 ARG cc_start: 0.7281 (ttp80) cc_final: 0.6821 (ttp-170) REVERT: L 524 GLU cc_start: 0.7747 (pt0) cc_final: 0.7381 (pm20) REVERT: L 603 ARG cc_start: 0.8717 (OUTLIER) cc_final: 0.8215 (mtt180) outliers start: 67 outliers final: 52 residues processed: 350 average time/residue: 0.1996 time to fit residues: 114.9353 Evaluate side-chains 344 residues out of total 3142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 284 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 15 ASP Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 163 GLU Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain H residue 23 HIS Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 136 GLU Chi-restraints excluded: chain H residue 198 LEU 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 778 GLU Chi-restraints excluded: chain I residue 828 PHE Chi-restraints excluded: chain I residue 829 THR 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 1145 ILE Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1170 MET Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 241 VAL Chi-restraints excluded: chain J residue 244 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 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 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 918 ILE 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 1267 VAL Chi-restraints excluded: chain K residue 39 VAL 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 Chi-restraints excluded: chain L residue 603 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 94 optimal weight: 0.7980 chunk 277 optimal weight: 20.0000 chunk 329 optimal weight: 4.9990 chunk 172 optimal weight: 0.9990 chunk 237 optimal weight: 2.9990 chunk 224 optimal weight: 4.9990 chunk 215 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 169 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 23 HIS H 227 GLN ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3778 r_free = 0.3778 target = 0.130475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.095262 restraints weight = 61974.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.095940 restraints weight = 36292.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.096500 restraints weight = 27232.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.096690 restraints weight = 25065.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.096946 restraints weight = 21225.228| |-----------------------------------------------------------------------------| r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.4260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 31919 Z= 0.133 Angle : 0.601 14.041 43631 Z= 0.305 Chirality : 0.042 0.239 5062 Planarity : 0.004 0.071 5287 Dihedral : 14.052 120.566 5777 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.88 % Favored : 93.06 % Rotamer: Outliers : 2.14 % Allowed : 17.56 % Favored : 80.31 % 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: -0.57 (0.14), residues: 3647 helix: 1.22 (0.14), residues: 1426 sheet: -1.19 (0.25), residues: 419 loop : -1.54 (0.15), residues: 1802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 436 TYR 0.024 0.001 TYR H 185 PHE 0.021 0.001 PHE L 221 TRP 0.019 0.001 TRP L 326 HIS 0.015 0.001 HIS H 23 Details of bonding type rmsd covalent geometry : bond 0.00307 (31912) covalent geometry : angle 0.60030 (43625) hydrogen bonds : bond 0.03628 ( 1310) hydrogen bonds : angle 4.35086 ( 3648) metal coordination : bond 0.00424 ( 7) metal coordination : angle 1.83815 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5005.60 seconds wall clock time: 87 minutes 27.26 seconds (5247.26 seconds total)