Starting phenix.real_space_refine on Fri Mar 6 11:23:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6n58_0349/03_2026/6n58_0349_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6n58_0349/03_2026/6n58_0349.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6n58_0349/03_2026/6n58_0349.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6n58_0349/03_2026/6n58_0349.map" model { file = "/net/cci-nas-00/data/ceres_data/6n58_0349/03_2026/6n58_0349_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6n58_0349/03_2026/6n58_0349_trim.cif" } resolution = 3.78 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 3 6.06 5 Mg 1 5.21 5 S 137 5.16 5 C 18938 2.51 5 N 5317 2.21 5 O 5793 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30189 Number of models: 1 Model: "" Number of chains: 11 Chain: "G" Number of atoms: 1766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1766 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 218} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 1678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1678 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 210} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 10577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1341, 10577 Classifications: {'peptide': 1341} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 55, 'TRANS': 1283} Chain: "J" Number of atoms: 10479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1347, 10479 Classifications: {'peptide': 1347} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 54, 'TRANS': 1290} 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: 4379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 547, 4379 Classifications: {'peptide': 547} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'CIS': 3, 'PTRANS': 16, 'TRANS': 527} Chain breaks: 3 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 3, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "M" Number of atoms: 571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 571 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 4, 'TRANS': 67} Chain: "I" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'1N7': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'1N7:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "J" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "L" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'1N7': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'1N7:plan-1': 2} Unresolved non-hydrogen planarities: 6 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' ZN': 1, '1N7': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'1N7:plan-1': 1} Unresolved non-hydrogen planarities: 3 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14479 SG CYS J 70 50.636 39.118 118.330 1.00 42.49 S ATOM 14493 SG CYS J 72 52.456 36.933 120.146 1.00 40.35 S ATOM 14601 SG CYS J 85 49.125 37.546 121.088 1.00 45.47 S ATOM 14625 SG CYS J 88 52.028 41.325 120.599 1.00 44.20 S ATOM 20313 SG CYS J 814 25.028 89.891 83.027 1.00 30.79 S ATOM 20878 SG CYS J 888 28.202 88.922 84.710 1.00 35.98 S ATOM 20929 SG CYS J 895 27.227 87.732 81.641 1.00 21.07 S ATOM 20950 SG CYS J 898 27.929 90.922 80.740 1.00 20.11 S ATOM 29787 SG CYS M 37 75.580 130.033 82.388 1.00 48.55 S ATOM 29807 SG CYS M 40 78.608 131.974 83.105 1.00 49.34 S ATOM 29944 SG CYS M 58 80.141 129.281 81.623 1.00 45.33 S ATOM 29966 SG CYS M 61 78.215 128.768 84.493 1.00 42.90 S Time building chain proxies: 6.22, per 1000 atoms: 0.21 Number of scatterers: 30189 At special positions: 0 Unit cell: (153.4, 159.9, 193.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 3 29.99 S 137 16.00 Mg 1 11.99 O 5793 8.00 N 5317 7.00 C 18938 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.66 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 85 " 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 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 814 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 898 " pdb=" ZN M 101 " pdb="ZN ZN M 101 " - pdb=" SG CYS M 40 " pdb="ZN ZN M 101 " - pdb=" SG CYS M 58 " pdb="ZN ZN M 101 " - pdb=" SG CYS M 37 " pdb="ZN ZN M 101 " - pdb=" SG CYS M 61 " Number of angles added : 18 7614 Ramachandran restraints generated. 3807 Oldfield, 0 Emsley, 3807 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7122 Finding SS restraints... Secondary structure from input PDB file: 137 helices and 47 sheets defined 43.2% alpha, 10.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.26 Creating SS restraints... Processing helix chain 'G' and resid 34 through 50 Processing helix chain 'G' and resid 77 through 86 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 Processing helix chain 'G' and resid 212 through 234 removed outlier: 3.881A pdb=" N LEU G 234 " --> pdb=" O ALA G 230 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 50 removed outlier: 3.637A pdb=" N THR H 38 " --> pdb=" O GLY H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 86 Processing helix chain 'H' and resid 111 through 115 removed outlier: 3.671A pdb=" N ASP H 114 " --> pdb=" O THR H 111 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE H 115 " --> pdb=" O ALA H 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 111 through 115' Processing helix chain 'H' and resid 212 through 228 removed outlier: 4.402A pdb=" N ARG H 218 " --> pdb=" O GLU H 214 " (cutoff:3.500A) Processing helix chain 'I' and resid 6 through 10 removed outlier: 4.130A pdb=" N ARG I 10 " --> pdb=" O GLU I 7 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 39 Processing helix chain 'I' and resid 48 through 57 removed outlier: 3.814A pdb=" N ALA I 52 " --> pdb=" O GLY I 48 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 89 Processing helix chain 'I' and resid 206 through 213 removed outlier: 4.130A pdb=" N LEU I 210 " --> pdb=" O ALA I 206 " (cutoff:3.500A) Processing helix chain 'I' and resid 216 through 224 Processing helix chain 'I' and resid 242 through 247 removed outlier: 3.529A pdb=" N LEU I 246 " --> pdb=" O PRO I 243 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG I 247 " --> pdb=" O GLU I 244 " (cutoff:3.500A) Processing helix chain 'I' and resid 270 through 281 Processing helix chain 'I' and resid 291 through 294 removed outlier: 4.089A pdb=" N GLY I 294 " --> pdb=" O TYR I 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 291 through 294' Processing helix chain 'I' and resid 318 through 327 removed outlier: 3.520A pdb=" N GLN I 327 " --> pdb=" O ALA I 323 " (cutoff:3.500A) Processing helix chain 'I' and resid 346 through 354 Processing helix chain 'I' and resid 358 through 371 removed outlier: 3.536A pdb=" N ARG I 371 " --> pdb=" O TYR I 367 " (cutoff:3.500A) Processing helix chain 'I' and resid 377 through 390 removed outlier: 3.873A 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 438 Processing helix chain 'I' and resid 447 through 451 removed outlier: 3.560A pdb=" N ARG I 451 " --> pdb=" O LEU I 448 " (cutoff:3.500A) Processing helix chain 'I' and resid 455 through 481 removed outlier: 4.016A pdb=" N ALA I 474 " --> pdb=" O ARG I 470 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU I 481 " --> pdb=" O GLU I 477 " (cutoff:3.500A) Processing helix chain 'I' and resid 495 through 508 Processing helix chain 'I' and resid 519 through 527 Processing helix chain 'I' and resid 544 through 549 removed outlier: 4.078A pdb=" N ARG I 548 " --> pdb=" O GLY I 544 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ASP I 549 " --> pdb=" O PHE I 545 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 544 through 549' Processing helix chain 'I' and resid 551 through 555 removed outlier: 4.021A pdb=" N TYR I 555 " --> pdb=" O PRO I 552 " (cutoff:3.500A) Processing helix chain 'I' and resid 670 through 674 Processing helix chain 'I' and resid 675 through 687 Processing helix chain 'I' and resid 703 through 712 removed outlier: 4.585A pdb=" N ALA I 707 " --> pdb=" O GLY I 703 " (cutoff:3.500A) Processing helix chain 'I' and resid 820 through 825 removed outlier: 4.019A pdb=" N GLU I 825 " --> pdb=" O ARG I 821 " (cutoff:3.500A) Processing helix chain 'I' and resid 898 through 907 Processing helix chain 'I' and resid 942 through 981 removed outlier: 3.634A pdb=" N ILE I 966 " --> pdb=" O GLU I 962 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ALA I 981 " --> pdb=" O ALA I 977 " (cutoff:3.500A) Processing helix chain 'I' and resid 1005 through 1038 Processing helix chain 'I' and resid 1099 through 1103 removed outlier: 3.791A pdb=" N GLY I1102 " --> pdb=" O ASN I1099 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL I1103 " --> pdb=" O PRO I1100 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 1099 through 1103' Processing helix chain 'I' and resid 1109 through 1134 Processing helix chain 'I' and resid 1138 through 1151 removed outlier: 3.515A pdb=" N LEU I1151 " --> pdb=" O ARG I1147 " (cutoff:3.500A) Processing helix chain 'I' and resid 1160 through 1164 Processing helix chain 'I' and resid 1165 through 1177 removed outlier: 3.764A pdb=" N MET I1170 " --> pdb=" O ASP I1166 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG I1171 " --> pdb=" O GLU I1167 " (cutoff:3.500A) Processing helix chain 'I' and resid 1185 through 1189 removed outlier: 3.783A pdb=" N GLY I1189 " --> pdb=" O VAL I1186 " (cutoff:3.500A) Processing helix chain 'I' and resid 1191 through 1202 removed outlier: 3.537A pdb=" N ILE I1195 " --> pdb=" O LYS I1191 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY I1202 " --> pdb=" O LEU I1198 " (cutoff:3.500A) Processing helix chain 'I' and resid 1238 through 1243 removed outlier: 3.532A pdb=" N LYS I1242 " --> pdb=" O LEU I1238 " (cutoff:3.500A) Processing helix chain 'I' and resid 1272 through 1281 Processing helix chain 'I' and resid 1284 through 1291 Processing helix chain 'I' and resid 1299 through 1310 Processing helix chain 'I' and resid 1320 through 1333 removed outlier: 3.903A pdb=" N LEU I1333 " --> pdb=" O GLU I1329 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 34 removed outlier: 3.713A pdb=" N SER J 34 " --> pdb=" O ILE J 30 " (cutoff:3.500A) Processing helix chain 'J' and resid 77 through 81 removed outlier: 3.558A pdb=" N ARG J 81 " --> pdb=" O LEU J 78 " (cutoff:3.500A) Processing helix chain 'J' and resid 94 through 100 removed outlier: 3.501A pdb=" N ARG J 99 " --> pdb=" O LYS J 96 " (cutoff:3.500A) Processing helix chain 'J' and resid 114 through 117 Processing helix chain 'J' and resid 122 through 129 Processing helix chain 'J' and resid 131 through 141 Processing helix chain 'J' and resid 161 through 172 removed outlier: 4.012A pdb=" N GLU J 170 " --> pdb=" O LEU J 166 " (cutoff:3.500A) Processing helix chain 'J' and resid 181 through 192 Processing helix chain 'J' and resid 193 through 207 removed outlier: 3.905A pdb=" N GLU J 197 " --> pdb=" O ASP J 193 " (cutoff:3.500A) Processing helix chain 'J' and resid 210 through 230 Processing helix chain 'J' and resid 234 through 236 No H-bonds generated for 'chain 'J' and resid 234 through 236' Processing helix chain 'J' and resid 264 through 286 Processing helix chain 'J' and resid 288 through 308 removed outlier: 3.553A pdb=" N VAL J 292 " --> pdb=" O PRO J 288 " (cutoff:3.500A) Processing helix chain 'J' and resid 326 through 330 Processing helix chain 'J' and resid 336 through 342 Processing helix chain 'J' and resid 370 through 377 Processing helix chain 'J' and resid 377 through 389 Processing helix chain 'J' and resid 393 through 404 Processing helix chain 'J' and resid 405 through 416 removed outlier: 4.251A pdb=" N TRP J 409 " --> pdb=" O GLU J 405 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ASP J 410 " --> pdb=" O ALA J 406 " (cutoff:3.500A) 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 485 through 489 Processing helix chain 'J' and resid 504 through 514 Processing helix chain 'J' and resid 529 through 538 Processing helix chain 'J' and resid 573 through 581 removed outlier: 4.007A pdb=" N MET J 581 " --> pdb=" O ALA J 577 " (cutoff:3.500A) Processing helix chain 'J' and resid 588 through 592 Processing helix chain 'J' and resid 598 through 613 removed outlier: 3.533A pdb=" N LEU J 605 " --> pdb=" O ILE J 601 " (cutoff:3.500A) Processing helix chain 'J' and resid 614 through 636 removed outlier: 3.506A pdb=" N GLY J 636 " --> pdb=" O ALA J 632 " (cutoff:3.500A) Processing helix chain 'J' and resid 640 through 644 removed outlier: 4.038A 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 Processing helix chain 'J' and resid 720 through 728 Processing helix chain 'J' and resid 733 through 741 Processing helix chain 'J' and resid 768 through 789 removed outlier: 4.192A pdb=" N HIS J 777 " --> pdb=" O PHE J 773 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLY J 778 " --> pdb=" O ILE J 774 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU J 788 " --> pdb=" O ALA J 784 " (cutoff:3.500A) Processing helix chain 'J' and resid 790 through 793 Processing helix chain 'J' and resid 794 through 802 Processing helix chain 'J' and resid 834 through 839 Processing helix chain 'J' and resid 865 through 875 Processing helix chain 'J' and resid 896 through 900 Processing helix chain 'J' and resid 914 through 925 removed outlier: 3.563A pdb=" N ILE J 918 " --> pdb=" O ALA J 914 " (cutoff:3.500A) Processing helix chain 'J' and resid 926 through 930 Processing helix chain 'J' and resid 1068 through 1072 removed outlier: 3.749A pdb=" N LYS J1072 " --> pdb=" O ALA J1069 " (cutoff:3.500A) Processing helix chain 'J' and resid 1138 through 1146 Processing helix chain 'J' and resid 1216 through 1224 removed outlier: 3.660A pdb=" N ILE J1220 " --> pdb=" O ALA J1216 " (cutoff:3.500A) Processing helix chain 'J' and resid 1225 through 1245 removed outlier: 4.273A pdb=" N GLN J1244 " --> pdb=" O VAL J1240 " (cutoff:3.500A) Processing helix chain 'J' and resid 1249 through 1261 removed outlier: 4.515A pdb=" N ILE J1253 " --> pdb=" O ASN J1249 " (cutoff:3.500A) Processing helix chain 'J' and resid 1282 through 1295 Processing helix chain 'J' and resid 1308 through 1313 Processing helix chain 'J' and resid 1318 through 1326 removed outlier: 3.601A pdb=" N ALA J1322 " --> pdb=" O SER J1318 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER J1324 " --> pdb=" O ILE J1320 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N PHE J1325 " --> pdb=" O SER J1321 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN J1326 " --> pdb=" O ALA J1322 " (cutoff:3.500A) Processing helix chain 'J' and resid 1327 through 1339 Processing helix chain 'J' and resid 1347 through 1353 Processing helix chain 'J' and resid 1361 through 1373 removed outlier: 4.385A 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 Processing helix chain 'K' and resid 45 through 56 Processing helix chain 'K' and resid 60 through 80 removed outlier: 3.790A pdb=" N LEU K 80 " --> pdb=" O GLU K 76 " (cutoff:3.500A) Processing helix chain 'L' and resid 8 through 20 Processing helix chain 'L' and resid 23 through 30 Processing helix chain 'L' and resid 37 through 52 removed outlier: 3.705A pdb=" N MET L 51 " --> pdb=" O MET L 47 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLY L 52 " --> pdb=" O ILE L 48 " (cutoff:3.500A) Processing helix chain 'L' and resid 76 through 90 removed outlier: 3.647A pdb=" N ALA L 80 " --> pdb=" O ALA L 76 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N SER L 89 " --> pdb=" O SER L 85 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLU L 90 " --> pdb=" O SER L 86 " (cutoff:3.500A) Processing helix chain 'L' and resid 96 through 107 removed outlier: 3.818A pdb=" N MET L 100 " --> pdb=" O ASP L 96 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR L 107 " --> pdb=" O ARG L 103 " (cutoff:3.500A) Processing helix chain 'L' and resid 115 through 136 Processing helix chain 'L' and resid 137 through 152 removed outlier: 3.565A pdb=" N ILE L 141 " --> pdb=" O TYR L 137 " (cutoff:3.500A) Processing helix chain 'L' and resid 214 through 233 Processing helix chain 'L' and resid 244 through 257 Processing helix chain 'L' and resid 262 through 292 removed outlier: 3.703A pdb=" N LEU L 290 " --> pdb=" O LEU L 286 " (cutoff:3.500A) Processing helix chain 'L' and resid 299 through 307 removed outlier: 3.728A pdb=" N LEU L 305 " --> pdb=" O ASN L 301 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N THR L 307 " --> pdb=" O ILE L 303 " (cutoff:3.500A) Processing helix chain 'L' and resid 316 through 321 removed outlier: 3.832A pdb=" N ALA L 321 " --> pdb=" O ASN L 317 " (cutoff:3.500A) Processing helix chain 'L' and resid 329 through 332 removed outlier: 3.763A pdb=" N ASP L 332 " --> pdb=" O LYS L 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 329 through 332' Processing helix chain 'L' and resid 333 through 352 removed outlier: 3.511A pdb=" N VAL L 337 " --> pdb=" O VAL L 333 " (cutoff:3.500A) Processing helix chain 'L' and resid 354 through 392 removed outlier: 5.335A pdb=" N ARG L 385 " --> pdb=" O GLU L 381 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N LEU L 386 " --> pdb=" O ALA L 382 " (cutoff:3.500A) Processing helix chain 'L' and resid 393 through 395 No H-bonds generated for 'chain 'L' and resid 393 through 395' Processing helix chain 'L' and resid 400 through 418 Processing helix chain 'L' and resid 419 through 424 removed outlier: 6.822A pdb=" N ARG L 422 " --> pdb=" O PHE L 419 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG L 423 " --> pdb=" O GLU L 420 " (cutoff:3.500A) Processing helix chain 'L' and resid 426 through 446 removed outlier: 4.413A pdb=" N TRP L 433 " --> pdb=" O THR L 429 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N TRP L 434 " --> pdb=" O TYR L 430 " (cutoff:3.500A) Processing helix chain 'L' and resid 453 through 474 removed outlier: 3.517A pdb=" N ILE L 457 " --> pdb=" O PRO L 453 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN L 472 " --> pdb=" O ARG L 468 " (cutoff:3.500A) Processing helix chain 'L' and resid 479 through 487 removed outlier: 4.075A pdb=" N GLU L 485 " --> pdb=" O GLU L 481 " (cutoff:3.500A) Processing helix chain 'L' and resid 492 through 501 Processing helix chain 'L' and resid 518 through 522 Processing helix chain 'L' and resid 530 through 550 Processing helix chain 'L' and resid 552 through 563 Processing helix chain 'L' and resid 572 through 580 Processing helix chain 'L' and resid 584 through 600 removed outlier: 3.679A pdb=" N ARG L 588 " --> pdb=" O ARG L 584 " (cutoff:3.500A) Processing helix chain 'L' and resid 604 through 610 Processing helix chain 'M' and resid 3 through 27 removed outlier: 3.950A pdb=" N GLU M 7 " --> pdb=" O ASP M 3 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA M 8 " --> pdb=" O GLU M 4 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE M 27 " --> pdb=" O ILE M 23 " (cutoff:3.500A) Processing helix chain 'M' and resid 45 through 52 Processing helix chain 'M' and resid 58 through 71 removed outlier: 3.851A pdb=" N HIS M 71 " --> pdb=" O ARG M 67 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 13 through 17 removed outlier: 4.329A pdb=" N THR G 27 " --> pdb=" O VAL G 14 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N ILE G 16 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LYS G 25 " --> pdb=" O ILE G 16 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N HIS G 23 " --> pdb=" O THR G 207 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N THR G 207 " --> pdb=" O HIS G 23 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N LYS G 25 " --> pdb=" O MET G 205 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N MET G 205 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N THR G 27 " --> pdb=" O ILE G 203 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N ILE G 203 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N GLU G 29 " --> pdb=" O LEU G 201 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LEU G 201 " --> pdb=" O GLU G 29 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ARG G 182 " --> pdb=" O GLU G 206 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 13 through 17 removed outlier: 4.329A pdb=" N THR G 27 " --> pdb=" O VAL G 14 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N ILE G 16 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LYS G 25 " --> pdb=" O ILE G 16 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N HIS G 23 " --> pdb=" O THR G 207 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N THR G 207 " --> pdb=" O HIS G 23 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N LYS G 25 " --> pdb=" O MET G 205 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N MET G 205 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N THR G 27 " --> pdb=" O ILE G 203 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N ILE G 203 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N GLU G 29 " --> pdb=" O LEU G 201 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LEU G 201 " --> pdb=" O GLU G 29 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 97 through 105 removed outlier: 6.280A pdb=" N ARG G 143 " --> pdb=" O VAL G 59 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N VAL G 59 " --> pdb=" O ARG G 143 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LYS G 145 " --> pdb=" O THR G 57 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 90 through 91 Processing sheet with id=AA5, first strand: chain 'G' and resid 108 through 111 removed outlier: 3.927A pdb=" N CYS G 131 " --> pdb=" O VAL G 110 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 23 through 24 removed outlier: 6.761A pdb=" N GLU H 206 " --> pdb=" O GLU H 181 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 27 through 31 removed outlier: 5.246A pdb=" N GLU H 29 " --> pdb=" O LEU H 201 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N LEU H 201 " --> pdb=" O GLU H 29 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU H 198 " --> pdb=" O ALA H 190 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU H 188 " --> pdb=" O LYS H 200 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL H 202 " --> pdb=" O ASN H 186 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 53 through 61 removed outlier: 3.794A pdb=" N GLY H 149 " --> pdb=" O GLY H 53 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LYS H 145 " --> pdb=" O THR H 57 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N VAL H 59 " --> pdb=" O ARG H 143 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ARG H 143 " --> pdb=" O VAL H 59 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 104 through 105 Processing sheet with id=AB1, first strand: chain 'I' and resid 59 through 60 Processing sheet with id=AB2, first strand: chain 'I' and resid 59 through 60 removed outlier: 5.944A pdb=" N VAL I 98 " --> pdb=" O GLU I 121 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N GLU I 121 " --> pdb=" O VAL I 98 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N LEU I 100 " --> pdb=" O GLU I 119 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N GLU I 119 " --> pdb=" O LEU I 100 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N LEU I 102 " --> pdb=" O ILE I 117 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ILE I 117 " --> pdb=" O LEU I 102 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ILE I 104 " --> pdb=" O LYS I 115 " (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 452 through 453 removed outlier: 6.540A pdb=" N SER I 147 " --> pdb=" O SER I 531 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 154 through 158 removed outlier: 3.810A pdb=" N LEU I 184 " --> pdb=" O ILE I 176 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 284 through 285 removed outlier: 5.664A pdb=" N ILE I 229 " --> pdb=" O GLU I 240 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 255 through 257 removed outlier: 7.224A pdb=" N ILE I 255 " --> pdb=" O TYR I 262 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 296 through 297 removed outlier: 3.619A pdb=" N MET I 315 " --> pdb=" O VAL I 297 " (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: 5.434A 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 616 through 617 Processing sheet with id=AC4, first strand: chain 'I' and resid 716 through 717 removed outlier: 3.720A pdb=" N ALA I 784 " --> pdb=" O ALA I 716 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 749 through 752 removed outlier: 6.894A pdb=" N VAL I 733 " --> pdb=" O GLN I 725 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 789 through 790 Processing sheet with id=AC7, first strand: chain 'I' and resid 798 through 804 removed outlier: 4.244A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 830 through 832 Processing sheet with id=AC9, first strand: chain 'I' and resid 835 through 838 removed outlier: 3.861A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 842 through 843 Processing sheet with id=AD2, first strand: chain 'I' and resid 882 through 884 removed outlier: 6.726A pdb=" N LEU I 918 " --> pdb=" O LEU I 883 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 887 through 889 Processing sheet with id=AD4, first strand: chain 'I' and resid 1065 through 1067 Processing sheet with id=AD5, first strand: chain 'I' and resid 1087 through 1088 Processing sheet with id=AD6, first strand: chain 'I' and resid 1244 through 1246 removed outlier: 6.607A pdb=" N CYS J 366 " --> pdb=" O VAL J 440 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N ILE J 442 " --> pdb=" O CYS J 366 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N LEU J 368 " --> pdb=" O ILE J 442 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 1335 through 1339 Processing sheet with id=AD8, first strand: chain 'J' and resid 103 through 112 removed outlier: 3.779A pdb=" N LEU J 242 " --> pdb=" O ILE J 105 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU J 107 " --> pdb=" O THR J 240 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N THR J 240 " --> pdb=" O LEU J 107 " (cutoff:3.500A) removed outlier: 10.541A pdb=" N SER J 109 " --> pdb=" O ILE J 238 " (cutoff:3.500A) removed outlier: 10.217A pdb=" N ILE J 238 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 145 through 146 Processing sheet with id=AE1, first strand: chain 'J' and resid 252 through 254 removed outlier: 3.868A pdb=" N VAL J 253 " --> pdb=" O ALA J 261 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N PHE J 260 " --> pdb=" O ILE L 505 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 548 through 550 Processing sheet with id=AE3, first strand: chain 'J' and resid 706 through 707 Processing sheet with id=AE4, first strand: chain 'J' and resid 820 through 822 Processing sheet with id=AE5, first strand: chain 'J' and resid 949 through 950 removed outlier: 3.945A pdb=" N ALA J1018 " --> pdb=" O ILE J 950 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 957 through 961 removed outlier: 6.684A pdb=" N LEU J 982 " --> pdb=" O SER J 994 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N SER J 994 " --> pdb=" O LEU J 982 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LEU J 984 " --> pdb=" O LYS J 992 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 966 through 967 Processing sheet with id=AE8, first strand: chain 'J' and resid 1025 through 1026 removed outlier: 3.648A pdb=" N ILE J1124 " --> pdb=" O MET J1025 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 1034 through 1038 Processing sheet with id=AF1, first strand: chain 'J' and resid 1161 through 1165 removed outlier: 4.160A 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: 6.639A pdb=" N THR J1301 " --> pdb=" O VAL J1267 " (cutoff:3.500A) 1274 hydrogen bonds defined for protein. 3582 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.39 Time building geometry restraints manager: 3.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 10273 1.34 - 1.46: 6173 1.46 - 1.59: 13925 1.59 - 1.71: 16 1.71 - 1.84: 247 Bond restraints: 30634 Sorted by residual: bond pdb=" C19 1N7 I1401 " pdb=" C3 1N7 I1401 " ideal model delta sigma weight residual 1.532 1.836 -0.304 2.00e-02 2.50e+03 2.32e+02 bond pdb=" C19 1N7 L 702 " pdb=" C3 1N7 L 702 " ideal model delta sigma weight residual 1.532 1.825 -0.293 2.00e-02 2.50e+03 2.14e+02 bond pdb=" C19 1N7 L 701 " pdb=" C3 1N7 L 701 " ideal model delta sigma weight residual 1.532 1.823 -0.291 2.00e-02 2.50e+03 2.12e+02 bond pdb=" C19 1N7 M 102 " pdb=" C3 1N7 M 102 " ideal model delta sigma weight residual 1.532 1.809 -0.277 2.00e-02 2.50e+03 1.92e+02 bond pdb=" C3 1N7 L 701 " pdb=" C4 1N7 L 701 " ideal model delta sigma weight residual 1.532 1.724 -0.192 2.00e-02 2.50e+03 9.25e+01 ... (remaining 30629 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.37: 40984 4.37 - 8.74: 368 8.74 - 13.11: 23 13.11 - 17.48: 6 17.48 - 21.86: 2 Bond angle restraints: 41383 Sorted by residual: angle pdb=" C THR J1024 " pdb=" N MET J1025 " pdb=" CA MET J1025 " ideal model delta sigma weight residual 121.80 143.66 -21.86 2.44e+00 1.68e-01 8.02e+01 angle pdb=" C LEU G 9 " pdb=" N LYS G 10 " pdb=" CA LYS G 10 " ideal model delta sigma weight residual 122.38 100.60 21.78 2.90e+00 1.19e-01 5.64e+01 angle pdb=" C ASP J1094 " pdb=" N MET J1095 " pdb=" CA MET J1095 " ideal model delta sigma weight residual 122.28 133.93 -11.65 1.77e+00 3.19e-01 4.33e+01 angle pdb=" C ILE I1079 " pdb=" N ASN I1080 " pdb=" CA ASN I1080 " ideal model delta sigma weight residual 120.86 131.33 -10.47 1.60e+00 3.91e-01 4.28e+01 angle pdb=" N VAL H 192 " pdb=" CA VAL H 192 " pdb=" C VAL H 192 " ideal model delta sigma weight residual 110.21 103.80 6.41 1.13e+00 7.83e-01 3.22e+01 ... (remaining 41378 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.48: 18392 19.48 - 38.96: 682 38.96 - 58.44: 47 58.44 - 77.91: 31 77.91 - 97.39: 3 Dihedral angle restraints: 19155 sinusoidal: 8111 harmonic: 11044 Sorted by residual: dihedral pdb=" CA THR J 853 " pdb=" C THR J 853 " pdb=" N ALA J 854 " pdb=" CA ALA J 854 " ideal model delta harmonic sigma weight residual 180.00 134.70 45.30 0 5.00e+00 4.00e-02 8.21e+01 dihedral pdb=" CA ASP I 199 " pdb=" C ASP I 199 " pdb=" N ARG I 200 " pdb=" CA ARG I 200 " ideal model delta harmonic sigma weight residual -180.00 -135.57 -44.43 0 5.00e+00 4.00e-02 7.89e+01 dihedral pdb=" CA GLN I1134 " pdb=" C GLN I1134 " pdb=" N GLN I1135 " pdb=" CA GLN I1135 " ideal model delta harmonic sigma weight residual -180.00 -138.86 -41.14 0 5.00e+00 4.00e-02 6.77e+01 ... (remaining 19152 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 3744 0.072 - 0.144: 911 0.144 - 0.216: 77 0.216 - 0.288: 8 0.288 - 0.360: 4 Chirality restraints: 4744 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 2.28 0.36 2.00e-01 2.50e+01 3.25e+00 chirality pdb=" C19 1N7 M 102 " pdb=" C18 1N7 M 102 " pdb=" C2 1N7 M 102 " pdb=" C3 1N7 M 102 " both_signs ideal model delta sigma weight residual False -2.53 -2.88 0.35 2.00e-01 2.50e+01 3.03e+00 chirality pdb=" C5 1N7 M 102 " pdb=" C4 1N7 M 102 " pdb=" C6 1N7 M 102 " pdb=" C9 1N7 M 102 " both_signs ideal model delta sigma weight residual False -2.85 -2.54 -0.31 2.00e-01 2.50e+01 2.35e+00 ... (remaining 4741 not shown) Planarity restraints: 5404 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO J 246 " 0.067 5.00e-02 4.00e+02 1.00e-01 1.61e+01 pdb=" N PRO J 247 " -0.174 5.00e-02 4.00e+02 pdb=" CA PRO J 247 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO J 247 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA L 59 " -0.057 5.00e-02 4.00e+02 8.67e-02 1.20e+01 pdb=" N PRO L 60 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO L 60 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO L 60 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS I 559 " 0.056 5.00e-02 4.00e+02 8.57e-02 1.18e+01 pdb=" N PRO I 560 " -0.148 5.00e-02 4.00e+02 pdb=" CA PRO I 560 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO I 560 " 0.047 5.00e-02 4.00e+02 ... (remaining 5401 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 216 2.49 - 3.10: 25219 3.10 - 3.70: 43439 3.70 - 4.30: 63813 4.30 - 4.90: 105617 Nonbonded interactions: 238304 Sorted by model distance: nonbonded pdb=" OD2 ASP J 464 " pdb="MG MG J1501 " model vdw 1.892 2.170 nonbonded pdb=" OD1 ASP I 516 " pdb=" OG SER I 522 " model vdw 1.918 3.040 nonbonded pdb=" OG SER J1057 " pdb=" OE2 GLU J1110 " model vdw 1.941 3.040 nonbonded pdb=" O LYS G 104 " pdb=" OG SER G 139 " model vdw 2.028 3.040 nonbonded pdb=" O GLU J 204 " pdb=" OG1 THR J 208 " model vdw 2.041 3.040 ... (remaining 238299 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 233 or (resid 234 and ( \ name N or name CA or name C or name O or name CB )))) selection = (chain 'H' and (resid 8 through 228 or (resid 229 through 230 and (name N or nam \ e CA or name C or name O or name CB )) or resid 231 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: 0.990 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: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 30.690 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.040 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 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 : 0.013 0.337 30647 Z= 0.602 Angle : 1.288 49.503 41401 Z= 0.665 Chirality : 0.060 0.360 4744 Planarity : 0.007 0.100 5404 Dihedral : 10.750 97.393 12033 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 38.56 Ramachandran Plot: Outliers : 0.39 % Allowed : 14.66 % Favored : 84.95 % Rotamer: Outliers : 0.37 % Allowed : 3.58 % Favored : 96.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.14 % Twisted Proline : 0.67 % Twisted General : 0.30 % 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: -4.74 (0.11), residues: 3807 helix: -2.38 (0.10), residues: 1489 sheet: -3.60 (0.20), residues: 397 loop : -3.76 (0.12), residues: 1921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.002 ARG J 270 TYR 0.040 0.004 TYR I1229 PHE 0.033 0.004 PHE H 231 TRP 0.048 0.005 TRP I 807 HIS 0.017 0.003 HIS I 673 Details of bonding type rmsd covalent geometry : bond 0.01330 (30634) covalent geometry : angle 1.21142 (41383) hydrogen bonds : bond 0.14572 ( 1263) hydrogen bonds : angle 7.70342 ( 3582) metal coordination : bond 0.10758 ( 12) metal coordination : angle 21.08484 ( 18) Misc. bond : bond 0.00260 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7614 Ramachandran restraints generated. 3807 Oldfield, 0 Emsley, 3807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7614 Ramachandran restraints generated. 3807 Oldfield, 0 Emsley, 3807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 788 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 776 time to evaluate : 1.072 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 29 GLU cc_start: 0.8129 (tp30) cc_final: 0.7688 (mm-30) REVERT: H 49 SER cc_start: 0.9126 (m) cc_final: 0.8868 (t) REVERT: H 51 MET cc_start: 0.7850 (mmm) cc_final: 0.7615 (tpp) REVERT: H 181 GLU cc_start: 0.7388 (mt-10) cc_final: 0.7121 (tt0) REVERT: I 97 ARG cc_start: 0.7904 (mmt180) cc_final: 0.7620 (mpt-90) REVERT: I 768 MET cc_start: 0.7715 (mtp) cc_final: 0.7427 (mtp) REVERT: I 906 PHE cc_start: 0.7639 (m-10) cc_final: 0.7400 (m-10) REVERT: I 1085 MET cc_start: 0.9042 (mmp) cc_final: 0.8479 (mmm) REVERT: J 26 SER cc_start: 0.8082 (t) cc_final: 0.7881 (m) REVERT: J 140 TYR cc_start: 0.8016 (m-10) cc_final: 0.7674 (m-10) REVERT: J 180 MET cc_start: 0.7999 (ptm) cc_final: 0.7739 (ptm) REVERT: J 232 ASN cc_start: 0.8586 (m-40) cc_final: 0.8047 (m-40) REVERT: J 332 LYS cc_start: 0.8454 (tmmt) cc_final: 0.8146 (ttpt) REVERT: J 387 LEU cc_start: 0.9075 (tp) cc_final: 0.8827 (tt) REVERT: J 513 MET cc_start: 0.9110 (ttp) cc_final: 0.8705 (ttp) REVERT: J 516 ASP cc_start: 0.8633 (p0) cc_final: 0.8302 (p0) REVERT: J 725 MET cc_start: 0.9022 (mtm) cc_final: 0.8771 (mtm) REVERT: J 796 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8559 (tm) REVERT: J 827 GLU cc_start: 0.6861 (tp30) cc_final: 0.6527 (tp30) REVERT: J 1020 TRP cc_start: 0.7105 (p90) cc_final: 0.6799 (p90) REVERT: J 1116 SER cc_start: 0.7508 (m) cc_final: 0.7235 (t) REVERT: J 1144 LEU cc_start: 0.9255 (mt) cc_final: 0.8941 (mt) REVERT: K 41 GLU cc_start: 0.7145 (pt0) cc_final: 0.6918 (pp20) REVERT: K 49 ILE cc_start: 0.8413 (mt) cc_final: 0.8195 (mt) REVERT: L 361 ILE cc_start: 0.6526 (mt) cc_final: 0.6317 (mm) REVERT: L 373 ARG cc_start: 0.7821 (mtm110) cc_final: 0.7315 (mtp85) REVERT: L 402 LEU cc_start: 0.8629 (mp) cc_final: 0.8094 (mp) REVERT: L 588 ARG cc_start: 0.6583 (mmm-85) cc_final: 0.6354 (mtt180) REVERT: L 595 LEU cc_start: 0.7821 (tp) cc_final: 0.7291 (mm) REVERT: L 596 ARG cc_start: 0.6693 (ttt-90) cc_final: 0.6483 (ttt90) REVERT: M 25 GLN cc_start: 0.8395 (mm110) cc_final: 0.8083 (mm-40) REVERT: M 44 ILE cc_start: 0.9036 (mt) cc_final: 0.8777 (mt) outliers start: 12 outliers final: 2 residues processed: 785 average time/residue: 0.2241 time to fit residues: 266.1551 Evaluate side-chains 433 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 430 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain J residue 421 VAL Chi-restraints excluded: chain J residue 796 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 23 HIS H 37 HIS I 69 GLN ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 330 HIS I 343 HIS I 628 HIS ** I 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 799 ASN I 808 ASN ** I1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1116 HIS I1220 GLN I1236 ASN I1237 HIS I1264 GLN J 341 ASN J 465 GLN J 680 ASN J 720 ASN J1197 ASN ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J1279 GLN J1295 ASN J1366 HIS ** L 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 383 ASN L 446 GLN L 518 HIS L 600 HIS M 21 ASN M 68 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.171416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.140861 restraints weight = 43978.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.139473 restraints weight = 65215.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.141011 restraints weight = 52272.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.141423 restraints weight = 35127.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.141527 restraints weight = 32838.034| |-----------------------------------------------------------------------------| r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 30647 Z= 0.154 Angle : 0.745 13.460 41401 Z= 0.377 Chirality : 0.046 0.183 4744 Planarity : 0.006 0.090 5404 Dihedral : 6.591 115.032 4492 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.35 % Favored : 92.51 % Rotamer: Outliers : 2.24 % Allowed : 9.53 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.14 % Twisted Proline : 0.67 % Twisted General : 0.16 % 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: -3.02 (0.12), residues: 3807 helix: -0.61 (0.13), residues: 1528 sheet: -2.89 (0.23), residues: 372 loop : -3.09 (0.12), residues: 1907 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG J1242 TYR 0.025 0.002 TYR G 185 PHE 0.019 0.002 PHE I 136 TRP 0.017 0.002 TRP J 115 HIS 0.023 0.001 HIS I 165 Details of bonding type rmsd covalent geometry : bond 0.00350 (30634) covalent geometry : angle 0.73492 (41383) hydrogen bonds : bond 0.04385 ( 1263) hydrogen bonds : angle 5.29844 ( 3582) metal coordination : bond 0.01053 ( 12) metal coordination : angle 5.95235 ( 18) Misc. bond : bond 0.00023 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7614 Ramachandran restraints generated. 3807 Oldfield, 0 Emsley, 3807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7614 Ramachandran restraints generated. 3807 Oldfield, 0 Emsley, 3807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 675 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 602 time to evaluate : 1.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 84 ASN cc_start: 0.7951 (m110) cc_final: 0.7233 (m110) REVERT: H 15 ASP cc_start: 0.7264 (t0) cc_final: 0.6990 (t0) REVERT: H 76 GLU cc_start: 0.6259 (mt-10) cc_final: 0.6045 (mt-10) REVERT: I 97 ARG cc_start: 0.7912 (mmt180) cc_final: 0.7660 (mmt90) REVERT: I 175 ARG cc_start: 0.7743 (mtp85) cc_final: 0.7484 (ttm110) REVERT: I 279 LYS cc_start: 0.8043 (ttpp) cc_final: 0.7282 (mppt) REVERT: I 374 GLU cc_start: 0.4636 (pt0) cc_final: 0.4296 (pt0) REVERT: I 490 GLN cc_start: 0.8488 (pm20) cc_final: 0.8159 (pm20) REVERT: I 542 ARG cc_start: 0.7576 (ptm160) cc_final: 0.6692 (ttm-80) REVERT: I 562 GLU cc_start: 0.8257 (tt0) cc_final: 0.7886 (tt0) REVERT: I 698 PRO cc_start: 0.8409 (Cg_exo) cc_final: 0.8174 (Cg_endo) REVERT: I 699 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8067 (tt) REVERT: I 702 THR cc_start: 0.9079 (p) cc_final: 0.8753 (m) REVERT: I 842 ASP cc_start: 0.8076 (t0) cc_final: 0.7418 (t0) REVERT: I 903 ARG cc_start: 0.7357 (mmt180) cc_final: 0.6711 (mmt180) REVERT: I 1119 MET cc_start: 0.8461 (tpp) cc_final: 0.8257 (tpp) REVERT: I 1170 MET cc_start: 0.8474 (mmm) cc_final: 0.8239 (mmm) REVERT: I 1180 MET cc_start: 0.8774 (ttm) cc_final: 0.8553 (ttm) REVERT: I 1290 MET cc_start: 0.8241 (tpp) cc_final: 0.7968 (tpp) REVERT: J 157 GLN cc_start: 0.7702 (tp40) cc_final: 0.7479 (tp40) REVERT: J 232 ASN cc_start: 0.8523 (m-40) cc_final: 0.8108 (m-40) REVERT: J 274 ASN cc_start: 0.7368 (m-40) cc_final: 0.7094 (m-40) REVERT: J 295 GLU cc_start: 0.7354 (tp30) cc_final: 0.7067 (tp30) REVERT: J 332 LYS cc_start: 0.8200 (tmmt) cc_final: 0.7910 (ttmt) REVERT: J 334 LYS cc_start: 0.6391 (tptt) cc_final: 0.6147 (mmtt) REVERT: J 349 TYR cc_start: 0.8753 (m-10) cc_final: 0.8518 (m-10) REVERT: J 387 LEU cc_start: 0.8884 (tp) cc_final: 0.8452 (tt) REVERT: J 513 MET cc_start: 0.8993 (ttp) cc_final: 0.8714 (ttp) REVERT: J 516 ASP cc_start: 0.8284 (p0) cc_final: 0.8073 (p0) REVERT: J 827 GLU cc_start: 0.6618 (tp30) cc_final: 0.6179 (tp30) REVERT: J 1158 GLU cc_start: 0.7117 (mm-30) cc_final: 0.6725 (mm-30) REVERT: J 1159 ILE cc_start: 0.7853 (tp) cc_final: 0.7618 (tt) REVERT: J 1200 GLU cc_start: 0.6000 (pm20) cc_final: 0.5570 (tm-30) REVERT: K 52 ARG cc_start: 0.8179 (mtm-85) cc_final: 0.7811 (mtm-85) REVERT: K 53 GLU cc_start: 0.8831 (mt-10) cc_final: 0.8597 (mt-10) REVERT: K 74 GLU cc_start: 0.6266 (mm-30) cc_final: 0.5138 (mt-10) REVERT: L 264 LYS cc_start: 0.6118 (tptp) cc_final: 0.5407 (pttt) REVERT: L 322 MET cc_start: 0.2531 (mtp) cc_final: 0.2271 (mtp) REVERT: L 499 LYS cc_start: 0.8029 (ttmp) cc_final: 0.7759 (mttm) REVERT: L 511 ILE cc_start: 0.7877 (tp) cc_final: 0.7495 (tp) REVERT: M 64 TYR cc_start: 0.8459 (t80) cc_final: 0.8235 (t80) outliers start: 73 outliers final: 29 residues processed: 647 average time/residue: 0.1934 time to fit residues: 199.2858 Evaluate side-chains 439 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 409 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 204 GLU Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 699 LEU Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 306 LEU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 754 ILE Chi-restraints excluded: chain J residue 913 GLU Chi-restraints excluded: chain J residue 1024 THR Chi-restraints excluded: chain J residue 1248 ILE Chi-restraints excluded: chain J residue 1313 SER Chi-restraints excluded: chain J residue 1349 GLU Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 43 ASP Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 270 VAL Chi-restraints excluded: chain L residue 379 MET Chi-restraints excluded: chain L residue 457 ILE Chi-restraints excluded: chain L residue 545 HIS Chi-restraints excluded: chain M residue 59 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 145 optimal weight: 0.9990 chunk 309 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 239 optimal weight: 3.9990 chunk 156 optimal weight: 5.9990 chunk 353 optimal weight: 20.0000 chunk 112 optimal weight: 0.3980 chunk 157 optimal weight: 0.7980 chunk 91 optimal weight: 0.9990 chunk 28 optimal weight: 7.9990 chunk 14 optimal weight: 0.7980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 219 GLN I 314 ASN I 450 ASN ** I 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 799 ASN I1157 GLN J 157 GLN J 594 GLN ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 15 ASN K 43 ASN ** L 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 301 ASN L 446 GLN L 568 ASN M 25 GLN M 71 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.171963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.139512 restraints weight = 43497.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.138251 restraints weight = 54583.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.139820 restraints weight = 44881.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.140468 restraints weight = 31218.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.140513 restraints weight = 28765.932| |-----------------------------------------------------------------------------| r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.3917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 30647 Z= 0.131 Angle : 0.659 12.252 41401 Z= 0.334 Chirality : 0.044 0.192 4744 Planarity : 0.005 0.087 5404 Dihedral : 5.889 88.731 4489 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.17 % Favored : 92.70 % Rotamer: Outliers : 3.22 % Allowed : 12.96 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.14 % Twisted Proline : 0.67 % Twisted General : 0.16 % 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: -2.18 (0.13), residues: 3807 helix: 0.20 (0.13), residues: 1528 sheet: -2.48 (0.24), residues: 357 loop : -2.73 (0.13), residues: 1922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 451 TYR 0.035 0.002 TYR H 177 PHE 0.016 0.001 PHE I 230 TRP 0.019 0.001 TRP I 807 HIS 0.013 0.001 HIS I 165 Details of bonding type rmsd covalent geometry : bond 0.00294 (30634) covalent geometry : angle 0.65466 (41383) hydrogen bonds : bond 0.03784 ( 1263) hydrogen bonds : angle 4.83438 ( 3582) metal coordination : bond 0.00637 ( 12) metal coordination : angle 3.70738 ( 18) Misc. bond : bond 0.00028 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7614 Ramachandran restraints generated. 3807 Oldfield, 0 Emsley, 3807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7614 Ramachandran restraints generated. 3807 Oldfield, 0 Emsley, 3807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 586 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 481 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 83 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8227 (tt) REVERT: G 84 ASN cc_start: 0.7935 (m110) cc_final: 0.7482 (m110) REVERT: H 47 LEU cc_start: 0.8288 (mt) cc_final: 0.8035 (mt) REVERT: H 102 LEU cc_start: 0.6795 (OUTLIER) cc_final: 0.5941 (tp) REVERT: H 144 ILE cc_start: 0.7494 (OUTLIER) cc_final: 0.7268 (mt) REVERT: I 28 LEU cc_start: 0.9009 (mt) cc_final: 0.8782 (mt) REVERT: I 175 ARG cc_start: 0.7708 (mtp85) cc_final: 0.7303 (mtm-85) REVERT: I 189 ASP cc_start: 0.8440 (p0) cc_final: 0.8032 (m-30) REVERT: I 279 LYS cc_start: 0.7997 (ttpp) cc_final: 0.7167 (mppt) REVERT: I 374 GLU cc_start: 0.4435 (pt0) cc_final: 0.4201 (pt0) REVERT: I 490 GLN cc_start: 0.8453 (pm20) cc_final: 0.8201 (pm20) REVERT: I 702 THR cc_start: 0.9194 (p) cc_final: 0.8720 (m) REVERT: I 704 MET cc_start: 0.8659 (mmm) cc_final: 0.8285 (tpt) REVERT: I 902 LEU cc_start: 0.8663 (tt) cc_final: 0.8405 (tt) REVERT: I 962 GLU cc_start: 0.6464 (mt-10) cc_final: 0.6254 (mt-10) REVERT: I 1085 MET cc_start: 0.9110 (mmm) cc_final: 0.8614 (mmm) REVERT: I 1119 MET cc_start: 0.8485 (tpp) cc_final: 0.8193 (tpp) REVERT: I 1290 MET cc_start: 0.8086 (tpp) cc_final: 0.7689 (tpp) REVERT: J 180 MET cc_start: 0.7673 (ttp) cc_final: 0.7003 (ttm) REVERT: J 274 ASN cc_start: 0.7388 (m-40) cc_final: 0.7085 (m110) REVERT: J 295 GLU cc_start: 0.7352 (tp30) cc_final: 0.7074 (tp30) REVERT: J 330 MET cc_start: 0.7001 (mtp) cc_final: 0.6785 (mtp) REVERT: J 387 LEU cc_start: 0.8734 (tp) cc_final: 0.8288 (mt) REVERT: J 513 MET cc_start: 0.8851 (ttp) cc_final: 0.8531 (ttp) REVERT: J 516 ASP cc_start: 0.8282 (p0) cc_final: 0.8046 (p0) REVERT: J 701 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.8990 (tt) REVERT: J 887 SER cc_start: 0.8521 (p) cc_final: 0.8293 (p) REVERT: J 1021 ASP cc_start: 0.7570 (OUTLIER) cc_final: 0.7251 (p0) REVERT: J 1143 ASP cc_start: 0.7755 (t0) cc_final: 0.7525 (t0) REVERT: J 1159 ILE cc_start: 0.7792 (tp) cc_final: 0.7579 (tt) REVERT: J 1332 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.8986 (mt) REVERT: K 15 ASN cc_start: 0.8272 (OUTLIER) cc_final: 0.7993 (m-40) REVERT: K 74 GLU cc_start: 0.6150 (mm-30) cc_final: 0.5379 (mt-10) REVERT: L 32 PRO cc_start: 0.7508 (Cg_exo) cc_final: 0.7257 (Cg_endo) REVERT: L 40 GLN cc_start: 0.6520 (tp40) cc_final: 0.6177 (tp40) REVERT: L 264 LYS cc_start: 0.5411 (tptp) cc_final: 0.4971 (ptmm) REVERT: L 384 LEU cc_start: 0.8608 (mt) cc_final: 0.8259 (mt) REVERT: M 66 GLU cc_start: 0.7956 (tp30) cc_final: 0.7706 (tp30) outliers start: 105 outliers final: 48 residues processed: 556 average time/residue: 0.1913 time to fit residues: 170.0276 Evaluate side-chains 445 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 390 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 136 GLU Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 120 ASP Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 161 LYS Chi-restraints excluded: chain I residue 239 MET Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 414 ILE Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 699 LEU Chi-restraints excluded: chain I residue 736 VAL Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 951 MET Chi-restraints excluded: chain I residue 1322 SER Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 306 LEU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 573 THR Chi-restraints excluded: chain J residue 664 ILE Chi-restraints excluded: chain J residue 701 LEU Chi-restraints excluded: chain J residue 724 MET Chi-restraints excluded: chain J residue 754 ILE Chi-restraints excluded: chain J residue 1021 ASP Chi-restraints excluded: chain J residue 1024 THR Chi-restraints excluded: chain J residue 1221 LEU Chi-restraints excluded: chain J residue 1248 ILE Chi-restraints excluded: chain J residue 1283 SER Chi-restraints excluded: chain J residue 1313 SER Chi-restraints excluded: chain J residue 1329 THR Chi-restraints excluded: chain J residue 1332 LEU Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 15 ASN Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 65 ASP Chi-restraints excluded: chain L residue 43 ASP Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 545 HIS Chi-restraints excluded: chain L residue 568 ASN Chi-restraints excluded: chain L residue 569 THR Chi-restraints excluded: chain L residue 590 ILE Chi-restraints excluded: chain M residue 59 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 156 optimal weight: 7.9990 chunk 244 optimal weight: 0.6980 chunk 164 optimal weight: 0.7980 chunk 310 optimal weight: 3.9990 chunk 174 optimal weight: 0.7980 chunk 254 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 54 optimal weight: 10.0000 chunk 82 optimal weight: 0.9980 chunk 334 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 103 ASN I 219 GLN ** I 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 799 ASN I1136 GLN ** I1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 45 ASN ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1289 ASN ** L 227 GLN ** 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 = 0.3975 r_free = 0.3975 target = 0.170735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.139012 restraints weight = 43294.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.136636 restraints weight = 62919.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.138612 restraints weight = 48664.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.138968 restraints weight = 33752.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.139162 restraints weight = 31110.444| |-----------------------------------------------------------------------------| r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.4220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 30647 Z= 0.143 Angle : 0.648 9.745 41401 Z= 0.326 Chirality : 0.043 0.189 4744 Planarity : 0.004 0.083 5404 Dihedral : 5.637 71.538 4489 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.22 % Favored : 92.65 % Rotamer: Outliers : 3.58 % Allowed : 14.40 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.14 % Twisted Proline : 0.67 % 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: -1.80 (0.13), residues: 3807 helix: 0.54 (0.13), residues: 1536 sheet: -2.27 (0.24), residues: 362 loop : -2.54 (0.13), residues: 1909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 417 TYR 0.026 0.002 TYR H 177 PHE 0.015 0.001 PHE J 338 TRP 0.017 0.001 TRP I 807 HIS 0.005 0.001 HIS J 430 Details of bonding type rmsd covalent geometry : bond 0.00334 (30634) covalent geometry : angle 0.64460 (41383) hydrogen bonds : bond 0.03634 ( 1263) hydrogen bonds : angle 4.66561 ( 3582) metal coordination : bond 0.00683 ( 12) metal coordination : angle 3.10877 ( 18) Misc. bond : bond 0.00041 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7614 Ramachandran restraints generated. 3807 Oldfield, 0 Emsley, 3807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7614 Ramachandran restraints generated. 3807 Oldfield, 0 Emsley, 3807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 419 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 83 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8215 (tt) REVERT: G 84 ASN cc_start: 0.8085 (m110) cc_final: 0.7732 (m110) REVERT: G 231 PHE cc_start: 0.8753 (OUTLIER) cc_final: 0.7651 (t80) REVERT: H 47 LEU cc_start: 0.8349 (mt) cc_final: 0.8055 (mt) REVERT: H 102 LEU cc_start: 0.6367 (OUTLIER) cc_final: 0.5565 (tt) REVERT: I 84 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7584 (mt-10) REVERT: I 239 MET cc_start: 0.3169 (OUTLIER) cc_final: 0.2919 (ppp) REVERT: I 699 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8079 (tt) REVERT: I 702 THR cc_start: 0.9261 (p) cc_final: 0.8810 (m) REVERT: I 704 MET cc_start: 0.8797 (mmm) cc_final: 0.8382 (tpt) REVERT: I 799 ASN cc_start: 0.8704 (OUTLIER) cc_final: 0.8408 (p0) REVERT: I 962 GLU cc_start: 0.6571 (mt-10) cc_final: 0.6348 (mt-10) REVERT: I 1085 MET cc_start: 0.9309 (mmm) cc_final: 0.8664 (mmm) REVERT: I 1119 MET cc_start: 0.8385 (tpp) cc_final: 0.7980 (tpp) REVERT: I 1290 MET cc_start: 0.8147 (tpp) cc_final: 0.7750 (tpp) REVERT: J 274 ASN cc_start: 0.7344 (m-40) cc_final: 0.7132 (m110) REVERT: J 330 MET cc_start: 0.7023 (mtp) cc_final: 0.6717 (mtp) REVERT: J 387 LEU cc_start: 0.8541 (tp) cc_final: 0.7924 (mp) REVERT: J 417 ARG cc_start: 0.7248 (ttt90) cc_final: 0.6895 (ttt90) REVERT: J 431 ARG cc_start: 0.9201 (OUTLIER) cc_final: 0.8921 (ptt180) REVERT: J 513 MET cc_start: 0.8854 (ttp) cc_final: 0.8532 (ttp) REVERT: J 697 MET cc_start: 0.8597 (tmm) cc_final: 0.8268 (tmm) REVERT: J 701 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.9018 (tt) REVERT: J 895 CYS cc_start: 0.8315 (OUTLIER) cc_final: 0.8095 (p) REVERT: J 1021 ASP cc_start: 0.7556 (OUTLIER) cc_final: 0.7215 (p0) REVERT: J 1143 ASP cc_start: 0.7885 (t0) cc_final: 0.7660 (t0) REVERT: J 1286 LYS cc_start: 0.8861 (OUTLIER) cc_final: 0.8611 (ttmm) REVERT: J 1332 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8998 (mt) REVERT: K 74 GLU cc_start: 0.6308 (mm-30) cc_final: 0.5685 (mt-10) REVERT: L 32 PRO cc_start: 0.7460 (Cg_exo) cc_final: 0.7251 (Cg_endo) REVERT: L 264 LYS cc_start: 0.5125 (tptp) cc_final: 0.4820 (ptmm) REVERT: L 384 LEU cc_start: 0.8636 (mt) cc_final: 0.8364 (mt) REVERT: L 561 MET cc_start: 0.7671 (mmt) cc_final: 0.7166 (mmt) REVERT: M 66 GLU cc_start: 0.8022 (tp30) cc_final: 0.7797 (tp30) outliers start: 117 outliers final: 66 residues processed: 506 average time/residue: 0.1845 time to fit residues: 150.0481 Evaluate side-chains 445 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 367 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 136 GLU Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 120 ASP Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 161 LYS Chi-restraints excluded: chain I residue 239 MET Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 414 ILE Chi-restraints excluded: chain I residue 435 ILE Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 699 LEU Chi-restraints excluded: chain I residue 717 VAL Chi-restraints excluded: chain I residue 736 VAL Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 818 VAL Chi-restraints excluded: chain I residue 901 LEU Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 951 MET Chi-restraints excluded: chain I residue 1155 VAL Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1322 SER Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 225 GLU Chi-restraints excluded: chain J residue 306 LEU Chi-restraints excluded: chain J residue 320 ASN Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 431 ARG Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 573 THR Chi-restraints excluded: chain J residue 664 ILE Chi-restraints excluded: chain J residue 701 LEU Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 754 ILE Chi-restraints excluded: chain J residue 776 THR Chi-restraints excluded: chain J residue 895 CYS Chi-restraints excluded: chain J residue 1021 ASP Chi-restraints excluded: chain J residue 1024 THR Chi-restraints excluded: chain J residue 1221 LEU Chi-restraints excluded: chain J residue 1248 ILE Chi-restraints excluded: chain J residue 1283 SER Chi-restraints excluded: chain J residue 1286 LYS Chi-restraints excluded: chain J residue 1332 LEU Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 65 ASP Chi-restraints excluded: chain L residue 43 ASP Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 387 VAL Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 457 ILE Chi-restraints excluded: chain L residue 466 ILE Chi-restraints excluded: chain L residue 545 HIS Chi-restraints excluded: chain L residue 569 THR Chi-restraints excluded: chain L residue 582 VAL Chi-restraints excluded: chain L residue 590 ILE Chi-restraints excluded: chain M residue 17 MET Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain M residue 59 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 216 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 141 optimal weight: 5.9990 chunk 324 optimal weight: 9.9990 chunk 126 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 230 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 chunk 68 optimal weight: 8.9990 chunk 327 optimal weight: 0.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 103 ASN ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 219 GLN I 450 ASN ** I 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 659 GLN I 673 HIS I1157 GLN I1209 GLN ** I1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 435 GLN J 594 GLN J 910 ASN J1227 HIS ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1289 ASN J1295 ASN K 43 ASN ** L 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.166818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.133513 restraints weight = 44021.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.132368 restraints weight = 51701.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.134357 restraints weight = 44800.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.134452 restraints weight = 30648.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.134726 restraints weight = 27538.658| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.4241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 30647 Z= 0.201 Angle : 0.684 10.533 41401 Z= 0.345 Chirality : 0.045 0.250 4744 Planarity : 0.005 0.081 5404 Dihedral : 5.672 64.184 4489 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.14 % Favored : 91.73 % Rotamer: Outliers : 3.95 % Allowed : 15.29 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % 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: -1.70 (0.13), residues: 3807 helix: 0.57 (0.13), residues: 1533 sheet: -2.16 (0.25), residues: 356 loop : -2.44 (0.13), residues: 1918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 175 TYR 0.025 0.002 TYR H 177 PHE 0.020 0.002 PHE L 256 TRP 0.018 0.001 TRP I 807 HIS 0.006 0.001 HIS J 430 Details of bonding type rmsd covalent geometry : bond 0.00478 (30634) covalent geometry : angle 0.67973 (41383) hydrogen bonds : bond 0.03878 ( 1263) hydrogen bonds : angle 4.72216 ( 3582) metal coordination : bond 0.00999 ( 12) metal coordination : angle 3.63834 ( 18) Misc. bond : bond 0.00072 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7614 Ramachandran restraints generated. 3807 Oldfield, 0 Emsley, 3807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7614 Ramachandran restraints generated. 3807 Oldfield, 0 Emsley, 3807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 391 time to evaluate : 1.245 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 84 ASN cc_start: 0.8258 (m110) cc_final: 0.7873 (m110) REVERT: G 101 THR cc_start: 0.8826 (OUTLIER) cc_final: 0.8361 (p) REVERT: G 207 THR cc_start: 0.9084 (m) cc_final: 0.8847 (p) REVERT: G 231 PHE cc_start: 0.8662 (OUTLIER) cc_final: 0.7489 (t80) REVERT: H 102 LEU cc_start: 0.6493 (OUTLIER) cc_final: 0.5600 (tt) REVERT: H 137 ASN cc_start: 0.4672 (m-40) cc_final: 0.4292 (p0) REVERT: H 144 ILE cc_start: 0.7322 (OUTLIER) cc_final: 0.7115 (mt) REVERT: I 239 MET cc_start: 0.3666 (OUTLIER) cc_final: 0.3435 (ppp) REVERT: I 699 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8130 (tt) REVERT: I 704 MET cc_start: 0.8770 (mmm) cc_final: 0.8260 (tpt) REVERT: I 892 GLU cc_start: 0.6218 (tt0) cc_final: 0.5794 (tt0) REVERT: I 902 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8621 (tt) REVERT: I 1085 MET cc_start: 0.9344 (mmm) cc_final: 0.8453 (mmm) REVERT: I 1119 MET cc_start: 0.8443 (tpp) cc_final: 0.8064 (tpp) REVERT: I 1290 MET cc_start: 0.8123 (tpp) cc_final: 0.7728 (tpp) REVERT: I 1291 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8527 (pp) REVERT: J 34 SER cc_start: 0.8721 (t) cc_final: 0.8176 (p) REVERT: J 190 LYS cc_start: 0.8716 (OUTLIER) cc_final: 0.8232 (ttpp) REVERT: J 274 ASN cc_start: 0.7503 (m-40) cc_final: 0.7156 (m110) REVERT: J 349 TYR cc_start: 0.8780 (m-10) cc_final: 0.8562 (m-10) REVERT: J 387 LEU cc_start: 0.8637 (tp) cc_final: 0.8159 (mt) REVERT: J 417 ARG cc_start: 0.7600 (ttt90) cc_final: 0.7279 (ttt90) REVERT: J 431 ARG cc_start: 0.9257 (OUTLIER) cc_final: 0.9047 (ptt180) REVERT: J 505 ASP cc_start: 0.8915 (m-30) cc_final: 0.8539 (t0) REVERT: J 532 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7634 (tt0) REVERT: J 604 MET cc_start: 0.8280 (ttm) cc_final: 0.7860 (ttm) REVERT: J 701 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.9006 (tt) REVERT: J 1021 ASP cc_start: 0.7481 (OUTLIER) cc_final: 0.7139 (p0) REVERT: J 1143 ASP cc_start: 0.8052 (t0) cc_final: 0.7767 (t0) REVERT: J 1286 LYS cc_start: 0.8837 (OUTLIER) cc_final: 0.8589 (ttmm) REVERT: J 1332 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.9035 (mt) REVERT: K 74 GLU cc_start: 0.6418 (mm-30) cc_final: 0.5675 (mt-10) REVERT: L 264 LYS cc_start: 0.5225 (tptp) cc_final: 0.4904 (ptmm) REVERT: L 384 LEU cc_start: 0.8764 (mt) cc_final: 0.8461 (mt) REVERT: L 561 MET cc_start: 0.7819 (mmt) cc_final: 0.7336 (mmt) REVERT: M 66 GLU cc_start: 0.8048 (tp30) cc_final: 0.7817 (tp30) outliers start: 129 outliers final: 85 residues processed: 485 average time/residue: 0.1773 time to fit residues: 140.7478 Evaluate side-chains 452 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 352 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 136 GLU Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 91 ARG Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 120 ASP Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 161 LYS Chi-restraints excluded: chain I residue 239 MET Chi-restraints excluded: chain I residue 296 VAL Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 414 ILE Chi-restraints excluded: chain I residue 435 ILE Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 699 LEU Chi-restraints excluded: chain I residue 717 VAL Chi-restraints excluded: chain I residue 736 VAL Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 818 VAL Chi-restraints excluded: chain I residue 901 LEU Chi-restraints excluded: chain I residue 902 LEU Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 951 MET Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1155 VAL Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1291 LEU Chi-restraints excluded: chain I residue 1295 SER Chi-restraints excluded: chain I residue 1322 SER Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 114 ILE Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 190 LYS Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 212 THR Chi-restraints excluded: chain J residue 225 GLU Chi-restraints excluded: chain J residue 306 LEU Chi-restraints excluded: chain J residue 320 ASN Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 431 ARG Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 532 GLU Chi-restraints excluded: chain J residue 573 THR Chi-restraints excluded: chain J residue 664 ILE Chi-restraints excluded: chain J residue 701 LEU Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 754 ILE Chi-restraints excluded: chain J residue 776 THR Chi-restraints excluded: chain J residue 950 ILE Chi-restraints excluded: chain J residue 1021 ASP Chi-restraints excluded: chain J residue 1024 THR Chi-restraints excluded: chain J residue 1095 MET Chi-restraints excluded: chain J residue 1221 LEU Chi-restraints excluded: chain J residue 1248 ILE Chi-restraints excluded: chain J residue 1260 MET Chi-restraints excluded: chain J residue 1283 SER Chi-restraints excluded: chain J residue 1286 LYS Chi-restraints excluded: chain J residue 1313 SER Chi-restraints excluded: chain J residue 1332 LEU Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 65 ASP Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 43 ASP Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 367 ILE Chi-restraints excluded: chain L residue 387 VAL Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 412 LEU Chi-restraints excluded: chain L residue 457 ILE Chi-restraints excluded: chain L residue 466 ILE Chi-restraints excluded: chain L residue 505 ILE Chi-restraints excluded: chain L residue 545 HIS Chi-restraints excluded: chain L residue 582 VAL Chi-restraints excluded: chain L residue 590 ILE Chi-restraints excluded: chain L residue 598 LEU Chi-restraints excluded: chain M residue 17 MET Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain M residue 59 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 136 optimal weight: 5.9990 chunk 324 optimal weight: 0.0770 chunk 61 optimal weight: 6.9990 chunk 54 optimal weight: 8.9990 chunk 320 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 84 optimal weight: 10.0000 chunk 224 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 95 optimal weight: 0.9980 chunk 377 optimal weight: 1.9990 overall best weight: 0.9742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 132 HIS I 219 GLN J 435 GLN J1249 ASN J1289 ASN K 43 ASN ** L 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 472 GLN ** 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 = 0.3976 r_free = 0.3976 target = 0.170747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.138990 restraints weight = 43314.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.137772 restraints weight = 54741.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.139311 restraints weight = 50923.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.139784 restraints weight = 33211.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.139947 restraints weight = 29028.947| |-----------------------------------------------------------------------------| r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.4610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 30647 Z= 0.127 Angle : 0.621 9.333 41401 Z= 0.312 Chirality : 0.043 0.355 4744 Planarity : 0.004 0.076 5404 Dihedral : 5.260 65.395 4489 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.72 % Favored : 93.14 % Rotamer: Outliers : 3.89 % Allowed : 15.93 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.43 (0.13), residues: 3807 helix: 0.81 (0.13), residues: 1537 sheet: -2.05 (0.25), residues: 360 loop : -2.30 (0.13), residues: 1910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 3 TYR 0.021 0.001 TYR H 177 PHE 0.013 0.001 PHE J 338 TRP 0.016 0.001 TRP I 807 HIS 0.005 0.001 HIS J 450 Details of bonding type rmsd covalent geometry : bond 0.00294 (30634) covalent geometry : angle 0.61425 (41383) hydrogen bonds : bond 0.03441 ( 1263) hydrogen bonds : angle 4.50777 ( 3582) metal coordination : bond 0.00854 ( 12) metal coordination : angle 4.39205 ( 18) Misc. bond : bond 0.00021 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7614 Ramachandran restraints generated. 3807 Oldfield, 0 Emsley, 3807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7614 Ramachandran restraints generated. 3807 Oldfield, 0 Emsley, 3807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 407 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 84 ASN cc_start: 0.8141 (m110) cc_final: 0.7754 (m110) REVERT: G 231 PHE cc_start: 0.8629 (OUTLIER) cc_final: 0.7658 (t80) REVERT: H 47 LEU cc_start: 0.8361 (mt) cc_final: 0.8054 (mt) REVERT: H 102 LEU cc_start: 0.6298 (OUTLIER) cc_final: 0.5483 (tt) REVERT: H 137 ASN cc_start: 0.4539 (m-40) cc_final: 0.4277 (p0) REVERT: I 239 MET cc_start: 0.3415 (OUTLIER) cc_final: 0.3196 (ppp) REVERT: I 378 ARG cc_start: 0.6705 (OUTLIER) cc_final: 0.6474 (tpt-90) REVERT: I 540 ARG cc_start: 0.7742 (mtm180) cc_final: 0.7482 (mtm-85) REVERT: I 699 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8117 (tt) REVERT: I 704 MET cc_start: 0.8723 (mmm) cc_final: 0.8174 (tpt) REVERT: I 899 GLU cc_start: 0.7785 (tm-30) cc_final: 0.7343 (tm-30) REVERT: I 1085 MET cc_start: 0.9414 (mmm) cc_final: 0.8528 (mmm) REVERT: I 1119 MET cc_start: 0.8452 (tpp) cc_final: 0.8111 (tpp) REVERT: I 1264 GLN cc_start: 0.8563 (tp-100) cc_final: 0.8206 (tp40) REVERT: I 1290 MET cc_start: 0.8113 (tpp) cc_final: 0.7748 (tpp) REVERT: I 1291 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8467 (pp) REVERT: J 274 ASN cc_start: 0.7387 (m-40) cc_final: 0.7035 (m110) REVERT: J 349 TYR cc_start: 0.8709 (m-10) cc_final: 0.8503 (m-10) REVERT: J 387 LEU cc_start: 0.8612 (tp) cc_final: 0.8065 (mp) REVERT: J 429 LEU cc_start: 0.9309 (OUTLIER) cc_final: 0.9061 (mt) REVERT: J 431 ARG cc_start: 0.9279 (OUTLIER) cc_final: 0.9014 (ptt180) REVERT: J 532 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7487 (tt0) REVERT: J 669 GLN cc_start: 0.8169 (OUTLIER) cc_final: 0.7951 (tt0) REVERT: J 701 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.9003 (tt) REVERT: J 739 GLN cc_start: 0.8022 (mt0) cc_final: 0.7727 (mt0) REVERT: J 1021 ASP cc_start: 0.7469 (OUTLIER) cc_final: 0.7176 (p0) REVERT: J 1143 ASP cc_start: 0.7856 (t0) cc_final: 0.7522 (t0) REVERT: J 1158 GLU cc_start: 0.7459 (mm-30) cc_final: 0.7128 (mm-30) REVERT: J 1249 ASN cc_start: 0.8506 (OUTLIER) cc_final: 0.8174 (t0) REVERT: J 1286 LYS cc_start: 0.8765 (OUTLIER) cc_final: 0.8544 (ttmm) REVERT: J 1332 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.9016 (mt) REVERT: K 68 GLU cc_start: 0.7812 (mm-30) cc_final: 0.7575 (mm-30) REVERT: K 74 GLU cc_start: 0.6271 (mm-30) cc_final: 0.5875 (mt-10) REVERT: L 264 LYS cc_start: 0.5126 (tptp) cc_final: 0.4917 (ptmm) REVERT: L 384 LEU cc_start: 0.8656 (mt) cc_final: 0.8339 (mt) REVERT: M 66 GLU cc_start: 0.7992 (tp30) cc_final: 0.7776 (tp30) outliers start: 127 outliers final: 75 residues processed: 495 average time/residue: 0.1823 time to fit residues: 146.5248 Evaluate side-chains 451 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 361 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 91 ARG Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 120 ASP Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 197 ASP Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 161 LYS Chi-restraints excluded: chain I residue 239 MET Chi-restraints excluded: chain I residue 296 VAL Chi-restraints excluded: chain I residue 378 ARG Chi-restraints excluded: chain I residue 414 ILE Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 699 LEU Chi-restraints excluded: chain I residue 717 VAL Chi-restraints excluded: chain I residue 736 VAL Chi-restraints excluded: chain I residue 818 VAL Chi-restraints excluded: chain I residue 901 LEU Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 951 MET Chi-restraints excluded: chain I residue 1061 GLN Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1291 LEU Chi-restraints excluded: chain I residue 1322 SER Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 114 ILE Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 212 THR Chi-restraints excluded: chain J residue 225 GLU Chi-restraints excluded: chain J residue 306 LEU Chi-restraints excluded: chain J residue 320 ASN Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 429 LEU Chi-restraints excluded: chain J residue 431 ARG Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 532 GLU Chi-restraints excluded: chain J residue 573 THR Chi-restraints excluded: chain J residue 618 VAL Chi-restraints excluded: chain J residue 664 ILE Chi-restraints excluded: chain J residue 669 GLN Chi-restraints excluded: chain J residue 701 LEU Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 754 ILE Chi-restraints excluded: chain J residue 776 THR Chi-restraints excluded: chain J residue 1021 ASP Chi-restraints excluded: chain J residue 1024 THR Chi-restraints excluded: chain J residue 1095 MET Chi-restraints excluded: chain J residue 1221 LEU Chi-restraints excluded: chain J residue 1248 ILE Chi-restraints excluded: chain J residue 1249 ASN Chi-restraints excluded: chain J residue 1260 MET Chi-restraints excluded: chain J residue 1283 SER Chi-restraints excluded: chain J residue 1286 LYS Chi-restraints excluded: chain J residue 1303 SER Chi-restraints excluded: chain J residue 1313 SER Chi-restraints excluded: chain J residue 1332 LEU Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 65 ASP Chi-restraints excluded: chain L residue 43 ASP Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain L residue 110 LEU Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 457 ILE Chi-restraints excluded: chain L residue 505 ILE Chi-restraints excluded: chain L residue 545 HIS Chi-restraints excluded: chain L residue 582 VAL Chi-restraints excluded: chain M residue 17 MET Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain M residue 59 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 107 optimal weight: 8.9990 chunk 271 optimal weight: 7.9990 chunk 4 optimal weight: 5.9990 chunk 134 optimal weight: 4.9990 chunk 221 optimal weight: 2.9990 chunk 203 optimal weight: 5.9990 chunk 123 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 229 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 83 optimal weight: 4.9990 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 132 HIS I 219 GLN I 450 ASN ** I 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 435 GLN J1249 ASN ** J1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J1289 ASN ** L 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 579 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.163919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.132961 restraints weight = 44129.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.131744 restraints weight = 59316.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.133253 restraints weight = 52029.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.133445 restraints weight = 33744.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.133852 restraints weight = 31525.751| |-----------------------------------------------------------------------------| r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.4406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 30647 Z= 0.267 Angle : 0.751 12.049 41401 Z= 0.376 Chirality : 0.047 0.305 4744 Planarity : 0.005 0.075 5404 Dihedral : 5.723 65.652 4489 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.06 % Favored : 90.81 % Rotamer: Outliers : 4.20 % Allowed : 16.54 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % 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: -1.62 (0.13), residues: 3807 helix: 0.59 (0.13), residues: 1529 sheet: -2.16 (0.25), residues: 375 loop : -2.33 (0.13), residues: 1903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 417 TYR 0.025 0.002 TYR H 177 PHE 0.026 0.002 PHE L 256 TRP 0.016 0.001 TRP I 807 HIS 0.014 0.002 HIS I1244 Details of bonding type rmsd covalent geometry : bond 0.00637 (30634) covalent geometry : angle 0.74111 (41383) hydrogen bonds : bond 0.04174 ( 1263) hydrogen bonds : angle 4.83589 ( 3582) metal coordination : bond 0.01545 ( 12) metal coordination : angle 5.73969 ( 18) Misc. bond : bond 0.00082 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7614 Ramachandran restraints generated. 3807 Oldfield, 0 Emsley, 3807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7614 Ramachandran restraints generated. 3807 Oldfield, 0 Emsley, 3807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 364 time to evaluate : 1.155 Fit side-chains revert: symmetry clash REVERT: G 84 ASN cc_start: 0.8412 (m110) cc_final: 0.8010 (m-40) REVERT: G 101 THR cc_start: 0.8886 (OUTLIER) cc_final: 0.8450 (p) REVERT: G 231 PHE cc_start: 0.8799 (OUTLIER) cc_final: 0.7602 (t80) REVERT: I 233 ARG cc_start: 0.6752 (mtp85) cc_final: 0.6111 (tmt170) REVERT: I 378 ARG cc_start: 0.6818 (OUTLIER) cc_final: 0.6570 (tpt-90) REVERT: I 429 MET cc_start: 0.8242 (mmt) cc_final: 0.7843 (mmt) REVERT: I 510 GLN cc_start: 0.7684 (tt0) cc_final: 0.7206 (tp-100) REVERT: I 704 MET cc_start: 0.8827 (mmm) cc_final: 0.8253 (tpt) REVERT: I 768 MET cc_start: 0.7773 (mtp) cc_final: 0.7468 (mtp) REVERT: I 1119 MET cc_start: 0.8455 (tpp) cc_final: 0.8108 (tpp) REVERT: I 1268 GLN cc_start: 0.8616 (mm-40) cc_final: 0.8350 (mm-40) REVERT: I 1290 MET cc_start: 0.8227 (tpp) cc_final: 0.7919 (tpp) REVERT: I 1291 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8633 (pp) REVERT: J 190 LYS cc_start: 0.8678 (OUTLIER) cc_final: 0.8137 (ttpp) REVERT: J 274 ASN cc_start: 0.7477 (m-40) cc_final: 0.7109 (m110) REVERT: J 387 LEU cc_start: 0.8747 (tp) cc_final: 0.8204 (mt) REVERT: J 417 ARG cc_start: 0.7848 (ttt90) cc_final: 0.7534 (ttt90) REVERT: J 429 LEU cc_start: 0.9388 (OUTLIER) cc_final: 0.9117 (mt) REVERT: J 431 ARG cc_start: 0.9321 (OUTLIER) cc_final: 0.9043 (ptt180) REVERT: J 532 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7713 (tt0) REVERT: J 697 MET cc_start: 0.8719 (tmm) cc_final: 0.8185 (tmm) REVERT: J 701 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8984 (tt) REVERT: J 1021 ASP cc_start: 0.7399 (OUTLIER) cc_final: 0.7140 (p0) REVERT: J 1143 ASP cc_start: 0.8204 (t0) cc_final: 0.7979 (t0) REVERT: J 1158 GLU cc_start: 0.7700 (mm-30) cc_final: 0.7390 (mm-30) REVERT: J 1249 ASN cc_start: 0.8640 (OUTLIER) cc_final: 0.8394 (t0) REVERT: J 1330 ARG cc_start: 0.8259 (ttp80) cc_final: 0.7950 (tmm-80) REVERT: J 1332 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.8677 (mm) REVERT: K 68 GLU cc_start: 0.7754 (mm-30) cc_final: 0.7512 (mm-30) REVERT: K 74 GLU cc_start: 0.6292 (mm-30) cc_final: 0.5857 (mt-10) REVERT: L 264 LYS cc_start: 0.5099 (tptp) cc_final: 0.4867 (ptmm) REVERT: M 66 GLU cc_start: 0.8075 (tp30) cc_final: 0.7836 (tp30) outliers start: 137 outliers final: 93 residues processed: 466 average time/residue: 0.1723 time to fit residues: 131.2701 Evaluate side-chains 452 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 347 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 120 ASP Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 197 ASP Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 161 LYS Chi-restraints excluded: chain I residue 292 ILE Chi-restraints excluded: chain I residue 296 VAL Chi-restraints excluded: chain I residue 378 ARG Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 414 ILE Chi-restraints excluded: chain I residue 420 LEU Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 717 VAL Chi-restraints excluded: chain I residue 736 VAL Chi-restraints excluded: chain I residue 818 VAL Chi-restraints excluded: chain I residue 819 SER Chi-restraints excluded: chain I residue 901 LEU Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 925 SER Chi-restraints excluded: chain I residue 951 MET Chi-restraints excluded: chain I residue 1061 GLN Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1169 VAL Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1291 LEU Chi-restraints excluded: chain I residue 1295 SER Chi-restraints excluded: chain I residue 1322 SER Chi-restraints excluded: chain I residue 1337 ILE Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 114 ILE Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 190 LYS Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 212 THR Chi-restraints excluded: chain J residue 306 LEU Chi-restraints excluded: chain J residue 320 ASN Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 429 LEU Chi-restraints excluded: chain J residue 431 ARG Chi-restraints excluded: chain J residue 453 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 532 GLU Chi-restraints excluded: chain J residue 573 THR Chi-restraints excluded: chain J residue 601 ILE Chi-restraints excluded: chain J residue 644 MET Chi-restraints excluded: chain J residue 664 ILE Chi-restraints excluded: chain J residue 669 GLN Chi-restraints excluded: chain J residue 701 LEU Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 754 ILE Chi-restraints excluded: chain J residue 776 THR Chi-restraints excluded: chain J residue 786 THR Chi-restraints excluded: chain J residue 885 VAL Chi-restraints excluded: chain J residue 950 ILE Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 1021 ASP Chi-restraints excluded: chain J residue 1024 THR Chi-restraints excluded: chain J residue 1095 MET Chi-restraints excluded: chain J residue 1221 LEU Chi-restraints excluded: chain J residue 1248 ILE Chi-restraints excluded: chain J residue 1249 ASN Chi-restraints excluded: chain J residue 1260 MET Chi-restraints excluded: chain J residue 1283 SER Chi-restraints excluded: chain J residue 1303 SER Chi-restraints excluded: chain J residue 1313 SER Chi-restraints excluded: chain J residue 1332 LEU Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 65 ASP Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 341 LEU Chi-restraints excluded: chain L residue 367 ILE Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 412 LEU Chi-restraints excluded: chain L residue 457 ILE Chi-restraints excluded: chain L residue 466 ILE Chi-restraints excluded: chain L residue 505 ILE Chi-restraints excluded: chain L residue 545 HIS Chi-restraints excluded: chain L residue 582 VAL Chi-restraints excluded: chain L residue 598 LEU Chi-restraints excluded: chain M residue 17 MET Chi-restraints excluded: chain M residue 27 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 244 optimal weight: 1.9990 chunk 145 optimal weight: 0.9990 chunk 319 optimal weight: 10.0000 chunk 220 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 99 optimal weight: 0.5980 chunk 179 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 chunk 301 optimal weight: 10.0000 chunk 277 optimal weight: 6.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 132 HIS I 120 GLN I 219 GLN ** I1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 435 GLN J1289 ASN ** L 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 472 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.166770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.136956 restraints weight = 43985.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.136132 restraints weight = 59935.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.137200 restraints weight = 54041.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.137418 restraints weight = 35141.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.137614 restraints weight = 32304.516| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.4627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 30647 Z= 0.174 Angle : 0.677 15.922 41401 Z= 0.337 Chirality : 0.045 0.237 4744 Planarity : 0.004 0.073 5404 Dihedral : 5.482 67.596 4489 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.41 % Favored : 92.46 % Rotamer: Outliers : 3.71 % Allowed : 17.19 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.46 (0.13), residues: 3807 helix: 0.70 (0.13), residues: 1538 sheet: -2.01 (0.26), residues: 349 loop : -2.25 (0.13), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 417 TYR 0.023 0.002 TYR H 177 PHE 0.015 0.002 PHE J 338 TRP 0.018 0.001 TRP I 807 HIS 0.011 0.001 HIS I1244 Details of bonding type rmsd covalent geometry : bond 0.00413 (30634) covalent geometry : angle 0.67158 (41383) hydrogen bonds : bond 0.03743 ( 1263) hydrogen bonds : angle 4.66461 ( 3582) metal coordination : bond 0.01057 ( 12) metal coordination : angle 4.30370 ( 18) Misc. bond : bond 0.00047 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7614 Ramachandran restraints generated. 3807 Oldfield, 0 Emsley, 3807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7614 Ramachandran restraints generated. 3807 Oldfield, 0 Emsley, 3807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 376 time to evaluate : 1.132 Fit side-chains revert: symmetry clash REVERT: G 84 ASN cc_start: 0.8319 (m110) cc_final: 0.7612 (m110) REVERT: G 101 THR cc_start: 0.8901 (m) cc_final: 0.8406 (p) REVERT: G 231 PHE cc_start: 0.8679 (OUTLIER) cc_final: 0.7624 (t80) REVERT: I 233 ARG cc_start: 0.6963 (mtp85) cc_final: 0.6221 (tmt170) REVERT: I 378 ARG cc_start: 0.6775 (OUTLIER) cc_final: 0.6536 (tpt-90) REVERT: I 429 MET cc_start: 0.8052 (mmt) cc_final: 0.7479 (mmt) REVERT: I 704 MET cc_start: 0.8789 (mmm) cc_final: 0.8496 (tpp) REVERT: I 751 TYR cc_start: 0.8731 (m-80) cc_final: 0.8497 (m-10) REVERT: I 768 MET cc_start: 0.7552 (mtp) cc_final: 0.7250 (mtp) REVERT: I 899 GLU cc_start: 0.8046 (tm-30) cc_final: 0.7723 (tm-30) REVERT: I 902 LEU cc_start: 0.8525 (tt) cc_final: 0.8218 (tt) REVERT: I 941 LYS cc_start: 0.8402 (OUTLIER) cc_final: 0.7996 (mtpp) REVERT: I 1085 MET cc_start: 0.9429 (mmm) cc_final: 0.8441 (mmm) REVERT: I 1119 MET cc_start: 0.8447 (tpp) cc_final: 0.8054 (tpp) REVERT: I 1138 VAL cc_start: 0.8987 (m) cc_final: 0.8494 (p) REVERT: I 1268 GLN cc_start: 0.8478 (mm-40) cc_final: 0.8257 (mm-40) REVERT: I 1290 MET cc_start: 0.8120 (tpp) cc_final: 0.7835 (tpp) REVERT: I 1291 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8549 (pp) REVERT: J 274 ASN cc_start: 0.7537 (m-40) cc_final: 0.7091 (m110) REVERT: J 387 LEU cc_start: 0.8568 (tp) cc_final: 0.7963 (mt) REVERT: J 429 LEU cc_start: 0.9396 (OUTLIER) cc_final: 0.9125 (mt) REVERT: J 431 ARG cc_start: 0.9343 (OUTLIER) cc_final: 0.9136 (ptt180) REVERT: J 532 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7654 (tt0) REVERT: J 697 MET cc_start: 0.8666 (tmm) cc_final: 0.8149 (tmm) REVERT: J 701 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8933 (tt) REVERT: J 840 LEU cc_start: 0.8965 (tp) cc_final: 0.8757 (tt) REVERT: J 1021 ASP cc_start: 0.7390 (OUTLIER) cc_final: 0.7153 (p0) REVERT: J 1143 ASP cc_start: 0.8076 (t0) cc_final: 0.7799 (t0) REVERT: J 1158 GLU cc_start: 0.7603 (mm-30) cc_final: 0.7353 (mm-30) REVERT: J 1330 ARG cc_start: 0.8161 (ttp80) cc_final: 0.7861 (tmm-80) REVERT: J 1332 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.9007 (mt) REVERT: K 55 GLU cc_start: 0.7076 (mt-10) cc_final: 0.6842 (mt-10) REVERT: K 68 GLU cc_start: 0.7851 (mm-30) cc_final: 0.7526 (mm-30) REVERT: K 74 GLU cc_start: 0.6193 (mm-30) cc_final: 0.5850 (mt-10) REVERT: L 264 LYS cc_start: 0.5156 (tptp) cc_final: 0.4947 (ptmm) REVERT: L 288 MET cc_start: 0.4592 (mpp) cc_final: 0.4383 (mpp) REVERT: M 66 GLU cc_start: 0.8119 (tp30) cc_final: 0.7858 (tp30) outliers start: 121 outliers final: 88 residues processed: 468 average time/residue: 0.1883 time to fit residues: 143.8031 Evaluate side-chains 456 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 358 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 91 ARG Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 120 ASP Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 197 ASP Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 47 TYR Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 161 LYS Chi-restraints excluded: chain I residue 296 VAL Chi-restraints excluded: chain I residue 378 ARG Chi-restraints excluded: chain I residue 393 ASP Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 414 ILE Chi-restraints excluded: chain I residue 420 LEU Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 717 VAL Chi-restraints excluded: chain I residue 736 VAL Chi-restraints excluded: chain I residue 818 VAL Chi-restraints excluded: chain I residue 901 LEU Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 925 SER Chi-restraints excluded: chain I residue 941 LYS Chi-restraints excluded: chain I residue 951 MET Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1061 GLN Chi-restraints excluded: chain I residue 1066 MET Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1291 LEU Chi-restraints excluded: chain I residue 1322 SER Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain I residue 1337 ILE Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 212 THR Chi-restraints excluded: chain J residue 306 LEU Chi-restraints excluded: chain J residue 320 ASN Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 429 LEU Chi-restraints excluded: chain J residue 431 ARG Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 532 GLU Chi-restraints excluded: chain J residue 573 THR Chi-restraints excluded: chain J residue 618 VAL Chi-restraints excluded: chain J residue 644 MET Chi-restraints excluded: chain J residue 664 ILE Chi-restraints excluded: chain J residue 669 GLN Chi-restraints excluded: chain J residue 683 ILE Chi-restraints excluded: chain J residue 701 LEU Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 754 ILE Chi-restraints excluded: chain J residue 776 THR Chi-restraints excluded: chain J residue 950 ILE Chi-restraints excluded: chain J residue 1021 ASP Chi-restraints excluded: chain J residue 1024 THR Chi-restraints excluded: chain J residue 1095 MET Chi-restraints excluded: chain J residue 1221 LEU Chi-restraints excluded: chain J residue 1260 MET Chi-restraints excluded: chain J residue 1283 SER Chi-restraints excluded: chain J residue 1303 SER Chi-restraints excluded: chain J residue 1313 SER Chi-restraints excluded: chain J residue 1332 LEU Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 65 ASP Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 341 LEU Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 412 LEU Chi-restraints excluded: chain L residue 457 ILE Chi-restraints excluded: chain L residue 466 ILE Chi-restraints excluded: chain L residue 505 ILE Chi-restraints excluded: chain L residue 545 HIS Chi-restraints excluded: chain L residue 582 VAL Chi-restraints excluded: chain M residue 17 MET Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain M residue 59 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 95 optimal weight: 0.5980 chunk 49 optimal weight: 10.0000 chunk 74 optimal weight: 0.0670 chunk 357 optimal weight: 4.9990 chunk 322 optimal weight: 0.8980 chunk 335 optimal weight: 0.7980 chunk 81 optimal weight: 5.9990 chunk 115 optimal weight: 2.9990 chunk 327 optimal weight: 8.9990 chunk 307 optimal weight: 3.9990 chunk 249 optimal weight: 0.7980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 219 GLN I 450 ASN ** I 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1289 ASN ** L 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 406 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.172084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.140668 restraints weight = 43468.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.139555 restraints weight = 54126.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.141271 restraints weight = 45997.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.141392 restraints weight = 32895.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.141613 restraints weight = 29639.264| |-----------------------------------------------------------------------------| r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.5058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 30647 Z= 0.114 Angle : 0.621 16.328 41401 Z= 0.309 Chirality : 0.043 0.217 4744 Planarity : 0.004 0.071 5404 Dihedral : 5.081 68.189 4489 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.04 % Favored : 92.86 % Rotamer: Outliers : 3.09 % Allowed : 17.98 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.15 (0.14), residues: 3807 helix: 1.01 (0.13), residues: 1540 sheet: -1.99 (0.25), residues: 383 loop : -2.09 (0.14), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 259 TYR 0.022 0.001 TYR H 177 PHE 0.031 0.001 PHE L 256 TRP 0.017 0.001 TRP I 807 HIS 0.011 0.001 HIS I1244 Details of bonding type rmsd covalent geometry : bond 0.00259 (30634) covalent geometry : angle 0.61816 (41383) hydrogen bonds : bond 0.03301 ( 1263) hydrogen bonds : angle 4.46566 ( 3582) metal coordination : bond 0.00558 ( 12) metal coordination : angle 2.73691 ( 18) Misc. bond : bond 0.00005 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7614 Ramachandran restraints generated. 3807 Oldfield, 0 Emsley, 3807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7614 Ramachandran restraints generated. 3807 Oldfield, 0 Emsley, 3807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 418 time to evaluate : 1.199 Fit side-chains REVERT: G 84 ASN cc_start: 0.8051 (m110) cc_final: 0.7675 (m110) REVERT: G 101 THR cc_start: 0.8809 (m) cc_final: 0.8274 (p) REVERT: G 170 ARG cc_start: 0.7290 (mtt-85) cc_final: 0.6904 (mtt90) REVERT: G 231 PHE cc_start: 0.8593 (OUTLIER) cc_final: 0.7831 (t80) REVERT: H 102 LEU cc_start: 0.6902 (tp) cc_final: 0.6414 (tp) REVERT: I 233 ARG cc_start: 0.6916 (mtp85) cc_final: 0.6192 (tmt170) REVERT: I 378 ARG cc_start: 0.6616 (OUTLIER) cc_final: 0.6358 (tpt-90) REVERT: I 704 MET cc_start: 0.8651 (mmm) cc_final: 0.7992 (tpt) REVERT: I 899 GLU cc_start: 0.8060 (tm-30) cc_final: 0.7663 (tm-30) REVERT: I 1085 MET cc_start: 0.9334 (mmm) cc_final: 0.8639 (mmm) REVERT: I 1119 MET cc_start: 0.8404 (tpp) cc_final: 0.7547 (ttp) REVERT: I 1268 GLN cc_start: 0.8304 (mm-40) cc_final: 0.8087 (mm-40) REVERT: I 1290 MET cc_start: 0.8004 (tpp) cc_final: 0.7678 (tpp) REVERT: I 1291 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8430 (pp) REVERT: J 274 ASN cc_start: 0.7669 (m-40) cc_final: 0.7190 (m-40) REVERT: J 387 LEU cc_start: 0.8526 (tp) cc_final: 0.7958 (mp) REVERT: J 429 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.9085 (mt) REVERT: J 431 ARG cc_start: 0.9260 (OUTLIER) cc_final: 0.9037 (ptt180) REVERT: J 532 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7429 (tt0) REVERT: J 623 GLN cc_start: 0.8461 (mm-40) cc_final: 0.8196 (mm-40) REVERT: J 701 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8947 (tt) REVERT: J 840 LEU cc_start: 0.8978 (tp) cc_final: 0.8773 (tt) REVERT: J 1021 ASP cc_start: 0.7455 (OUTLIER) cc_final: 0.7217 (p0) REVERT: J 1143 ASP cc_start: 0.7889 (t0) cc_final: 0.7495 (t0) REVERT: J 1158 GLU cc_start: 0.7329 (mm-30) cc_final: 0.7097 (mm-30) REVERT: J 1330 ARG cc_start: 0.8062 (ttp80) cc_final: 0.7765 (tmm-80) REVERT: J 1349 GLU cc_start: 0.7426 (tt0) cc_final: 0.7043 (pt0) REVERT: K 55 GLU cc_start: 0.6947 (mt-10) cc_final: 0.6709 (mt-10) REVERT: K 68 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7432 (mm-30) REVERT: K 74 GLU cc_start: 0.6299 (mm-30) cc_final: 0.5930 (mt-10) REVERT: L 53 ILE cc_start: 0.6992 (mp) cc_final: 0.6730 (mm) REVERT: L 384 LEU cc_start: 0.8294 (mt) cc_final: 0.7906 (mt) REVERT: L 500 ILE cc_start: 0.8377 (tp) cc_final: 0.8146 (tp) REVERT: L 540 LEU cc_start: 0.8459 (tt) cc_final: 0.7978 (tp) REVERT: L 561 MET cc_start: 0.7927 (mmt) cc_final: 0.7476 (mmt) REVERT: M 66 GLU cc_start: 0.8007 (tp30) cc_final: 0.7740 (tp30) outliers start: 101 outliers final: 70 residues processed: 493 average time/residue: 0.1820 time to fit residues: 146.0292 Evaluate side-chains 448 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 370 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 91 ARG Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 120 ASP Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 197 ASP Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 161 LYS Chi-restraints excluded: chain I residue 292 ILE Chi-restraints excluded: chain I residue 378 ARG Chi-restraints excluded: chain I residue 420 LEU Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 717 VAL Chi-restraints excluded: chain I residue 736 VAL Chi-restraints excluded: chain I residue 901 LEU Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1161 LEU Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1291 LEU Chi-restraints excluded: chain I residue 1322 SER Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 212 THR Chi-restraints excluded: chain J residue 306 LEU Chi-restraints excluded: chain J residue 320 ASN Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 429 LEU Chi-restraints excluded: chain J residue 431 ARG Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 532 GLU Chi-restraints excluded: chain J residue 573 THR Chi-restraints excluded: chain J residue 618 VAL Chi-restraints excluded: chain J residue 701 LEU Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 754 ILE Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 776 THR Chi-restraints excluded: chain J residue 950 ILE Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 1021 ASP Chi-restraints excluded: chain J residue 1024 THR Chi-restraints excluded: chain J residue 1095 MET Chi-restraints excluded: chain J residue 1221 LEU Chi-restraints excluded: chain J residue 1248 ILE Chi-restraints excluded: chain J residue 1283 SER Chi-restraints excluded: chain J residue 1303 SER Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 65 ASP Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 314 THR Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 457 ILE Chi-restraints excluded: chain L residue 466 ILE Chi-restraints excluded: chain L residue 545 HIS Chi-restraints excluded: chain L residue 582 VAL Chi-restraints excluded: chain M residue 17 MET Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain M residue 59 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 363 optimal weight: 0.1980 chunk 150 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 51 optimal weight: 0.0570 chunk 185 optimal weight: 2.9990 chunk 76 optimal weight: 8.9990 chunk 63 optimal weight: 0.9980 chunk 100 optimal weight: 0.0270 chunk 203 optimal weight: 2.9990 chunk 219 optimal weight: 0.0370 chunk 138 optimal weight: 4.9990 overall best weight: 0.2634 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 120 GLN I 219 GLN J 153 ASN J 157 GLN ** L 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 14 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.175630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.145798 restraints weight = 43283.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.145198 restraints weight = 51403.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.146816 restraints weight = 45092.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.146786 restraints weight = 29960.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.147055 restraints weight = 27331.572| |-----------------------------------------------------------------------------| r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.5421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 30647 Z= 0.108 Angle : 0.621 16.056 41401 Z= 0.309 Chirality : 0.042 0.202 4744 Planarity : 0.004 0.067 5404 Dihedral : 4.868 66.011 4488 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.83 % Favored : 94.06 % Rotamer: Outliers : 2.36 % Allowed : 19.06 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.87 (0.14), residues: 3807 helix: 1.26 (0.13), residues: 1533 sheet: -1.80 (0.25), residues: 376 loop : -1.95 (0.14), residues: 1898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J 275 TYR 0.022 0.001 TYR H 177 PHE 0.014 0.001 PHE I 225 TRP 0.012 0.001 TRP I 807 HIS 0.008 0.001 HIS I1244 Details of bonding type rmsd covalent geometry : bond 0.00239 (30634) covalent geometry : angle 0.61890 (41383) hydrogen bonds : bond 0.03101 ( 1263) hydrogen bonds : angle 4.35715 ( 3582) metal coordination : bond 0.00483 ( 12) metal coordination : angle 2.25271 ( 18) Misc. bond : bond 0.00007 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7614 Ramachandran restraints generated. 3807 Oldfield, 0 Emsley, 3807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7614 Ramachandran restraints generated. 3807 Oldfield, 0 Emsley, 3807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 434 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 84 ASN cc_start: 0.8065 (m110) cc_final: 0.7725 (m-40) REVERT: G 101 THR cc_start: 0.8830 (m) cc_final: 0.8308 (p) REVERT: G 170 ARG cc_start: 0.7221 (mtt-85) cc_final: 0.6965 (mtt90) REVERT: G 231 PHE cc_start: 0.8605 (OUTLIER) cc_final: 0.8023 (t80) REVERT: H 102 LEU cc_start: 0.6480 (tp) cc_final: 0.5960 (tp) REVERT: I 210 LEU cc_start: 0.8374 (tp) cc_final: 0.8145 (tp) REVERT: I 704 MET cc_start: 0.8628 (mmm) cc_final: 0.7942 (tpt) REVERT: I 899 GLU cc_start: 0.7915 (tm-30) cc_final: 0.7537 (tm-30) REVERT: I 1085 MET cc_start: 0.9350 (mmm) cc_final: 0.8675 (mmm) REVERT: I 1129 ASN cc_start: 0.8659 (t0) cc_final: 0.8212 (t0) REVERT: I 1268 GLN cc_start: 0.8267 (mm-40) cc_final: 0.7956 (mm-40) REVERT: I 1290 MET cc_start: 0.7940 (tpp) cc_final: 0.7622 (tpp) REVERT: J 130 MET cc_start: 0.7495 (ttm) cc_final: 0.7120 (ttp) REVERT: J 172 PHE cc_start: 0.6260 (m-10) cc_final: 0.5984 (m-10) REVERT: J 274 ASN cc_start: 0.7663 (m-40) cc_final: 0.7286 (m-40) REVERT: J 387 LEU cc_start: 0.8496 (tp) cc_final: 0.7951 (mp) REVERT: J 429 LEU cc_start: 0.9241 (mm) cc_final: 0.9026 (mt) REVERT: J 431 ARG cc_start: 0.9288 (OUTLIER) cc_final: 0.9057 (ptt180) REVERT: J 532 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7416 (tt0) REVERT: J 623 GLN cc_start: 0.8258 (mm-40) cc_final: 0.7937 (mm-40) REVERT: J 840 LEU cc_start: 0.8930 (tp) cc_final: 0.8727 (tt) REVERT: J 1021 ASP cc_start: 0.7447 (OUTLIER) cc_final: 0.6977 (p0) REVERT: J 1143 ASP cc_start: 0.7833 (t0) cc_final: 0.7422 (t0) REVERT: J 1158 GLU cc_start: 0.6786 (mm-30) cc_final: 0.6385 (mm-30) REVERT: J 1330 ARG cc_start: 0.8116 (ttp80) cc_final: 0.7844 (tmm-80) REVERT: L 113 ARG cc_start: 0.5443 (tpm170) cc_final: 0.2228 (ttm-80) REVERT: L 277 MET cc_start: 0.4078 (tpt) cc_final: 0.3833 (tpt) REVERT: L 322 MET cc_start: 0.1199 (mtp) cc_final: -0.1733 (tpt) REVERT: L 495 ARG cc_start: 0.7143 (mmm160) cc_final: 0.6834 (tpm170) REVERT: L 500 ILE cc_start: 0.8244 (tp) cc_final: 0.8023 (tp) REVERT: L 561 MET cc_start: 0.7710 (mmt) cc_final: 0.7332 (mmt) REVERT: M 66 GLU cc_start: 0.8106 (tp30) cc_final: 0.7905 (tp30) outliers start: 77 outliers final: 59 residues processed: 491 average time/residue: 0.1819 time to fit residues: 145.4643 Evaluate side-chains 444 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 381 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 91 ARG Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 197 ASP Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 161 LYS Chi-restraints excluded: chain I residue 292 ILE Chi-restraints excluded: chain I residue 296 VAL Chi-restraints excluded: chain I residue 420 LEU Chi-restraints excluded: chain I residue 435 ILE Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 736 VAL Chi-restraints excluded: chain I residue 901 LEU Chi-restraints excluded: chain I residue 1066 MET Chi-restraints excluded: chain I residue 1161 LEU Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1322 SER Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 431 ARG Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 532 GLU Chi-restraints excluded: chain J residue 618 VAL Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 754 ILE Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 885 VAL Chi-restraints excluded: chain J residue 950 ILE Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 1021 ASP Chi-restraints excluded: chain J residue 1024 THR Chi-restraints excluded: chain J residue 1095 MET Chi-restraints excluded: chain J residue 1221 LEU Chi-restraints excluded: chain J residue 1248 ILE Chi-restraints excluded: chain J residue 1283 SER Chi-restraints excluded: chain J residue 1303 SER Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 65 ASP Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 314 THR Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 457 ILE Chi-restraints excluded: chain L residue 466 ILE Chi-restraints excluded: chain L residue 545 HIS Chi-restraints excluded: chain L residue 582 VAL Chi-restraints excluded: chain M residue 17 MET Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain M residue 59 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 287 optimal weight: 5.9990 chunk 66 optimal weight: 10.0000 chunk 28 optimal weight: 0.0170 chunk 183 optimal weight: 6.9990 chunk 131 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 333 optimal weight: 0.5980 chunk 22 optimal weight: 7.9990 chunk 156 optimal weight: 5.9990 chunk 106 optimal weight: 10.0000 overall best weight: 1.7222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 219 GLN ** I1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 708 ASN ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 30 HIS L 265 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.169738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.139560 restraints weight = 43480.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.138873 restraints weight = 53761.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.140064 restraints weight = 48235.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.140276 restraints weight = 31745.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.140430 restraints weight = 28956.448| |-----------------------------------------------------------------------------| r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.5216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 30647 Z= 0.165 Angle : 0.673 15.600 41401 Z= 0.334 Chirality : 0.044 0.246 4744 Planarity : 0.005 0.089 5404 Dihedral : 5.062 65.105 4488 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.54 % Favored : 92.36 % Rotamer: Outliers : 2.33 % Allowed : 19.06 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.93 (0.14), residues: 3807 helix: 1.15 (0.13), residues: 1538 sheet: -1.83 (0.25), residues: 378 loop : -1.94 (0.14), residues: 1891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 275 TYR 0.021 0.002 TYR H 177 PHE 0.017 0.002 PHE I 186 TRP 0.016 0.001 TRP I 807 HIS 0.014 0.001 HIS I1244 Details of bonding type rmsd covalent geometry : bond 0.00392 (30634) covalent geometry : angle 0.67042 (41383) hydrogen bonds : bond 0.03467 ( 1263) hydrogen bonds : angle 4.45973 ( 3582) metal coordination : bond 0.00886 ( 12) metal coordination : angle 2.84492 ( 18) Misc. bond : bond 0.00031 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4630.80 seconds wall clock time: 80 minutes 58.84 seconds (4858.84 seconds total)