Starting phenix.real_space_refine on Mon Sep 14 20:18:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6psq_20460/09_2026/6psq_20460_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6psq_20460/09_2026/6psq_20460.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6psq_20460/09_2026/6psq_20460.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6psq_20460/09_2026/6psq_20460.map" model { file = "/net/cci-nas-00/data/ceres_data/6psq_20460/09_2026/6psq_20460_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6psq_20460/09_2026/6psq_20460_trim.cif" } resolution = 3.4 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: 7 Type Number sf(0) Gaussians Zn 3 6.06 5 P 100 5.49 5 Mg 1 5.21 5 S 139 5.16 5 C 20260 2.51 5 N 5780 2.21 5 O 6494 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 82 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32777 Number of models: 1 Model: "" Number of chains: 13 Chain: "J" Number of atoms: 10466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1345, 10466 Classifications: {'peptide': 1345} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 54, 'TRANS': 1288} Chain breaks: 2 Chain: "N" 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: "G" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1764 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'CIS': 1, 'PTRANS': 9, 'TRANS': 219} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "H" Number of atoms: 1682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1682 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 210} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 10549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1339, 10549 Classifications: {'peptide': 1339} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 3, 'PCIS': 2, 'PTRANS': 54, 'TRANS': 1279} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "K" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 600 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "L" Number of atoms: 4411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4411 Classifications: {'peptide': 551} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'CIS': 3, 'PTRANS': 16, 'TRANS': 531} Chain breaks: 3 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 3, 'ASN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "M" Number of atoms: 572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 572 Classifications: {'peptide': 73} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 68} Chain: "O" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1024 Classifications: {'DNA': 50} Link IDs: {'rna3p': 49} Chain: "P" Number of atoms: 1026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1026 Classifications: {'DNA': 50} Link IDs: {'rna3p': 49} Chain: "J" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {' MG': 1, ' ZN': 2, '1N7': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'1N7:plan-1': 3} Unresolved non-hydrogen planarities: 9 Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} 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 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 449 SG CYS J 70 72.194 102.418 115.202 1.00 52.73 S ATOM 463 SG CYS J 72 74.047 104.963 116.597 1.00 56.38 S ATOM 571 SG CYS J 85 71.379 104.485 118.786 1.00 52.65 S ATOM 595 SG CYS J 88 69.971 105.038 115.019 1.00 47.70 S ATOM 6283 SG CYS J 814 66.416 41.755 89.956 1.00 33.33 S ATOM 6848 SG CYS J 888 66.534 45.280 88.537 1.00 31.08 S ATOM 6899 SG CYS J 895 69.451 43.632 89.446 1.00 21.00 S ATOM 6920 SG CYS J 898 68.518 41.514 86.838 1.00 26.18 S ATOM 10747 SG CYS N 37 49.312 56.215 28.935 1.00 68.32 S ATOM 10767 SG CYS N 40 46.948 57.222 26.641 1.00 71.01 S ATOM 10904 SG CYS N 58 50.262 58.391 26.383 1.00 56.63 S ATOM 10926 SG CYS N 61 47.517 59.375 29.831 1.00 60.81 S Time building chain proxies: 6.79, per 1000 atoms: 0.21 Number of scatterers: 32777 At special positions: 0 Unit cell: (157.3, 154.7, 167.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 3 29.99 S 139 16.00 P 100 15.00 Mg 1 11.99 O 6494 8.00 N 5780 7.00 C 20260 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.91 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 70 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 85 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 88 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 72 " pdb=" ZN J1503 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 895 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 898 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 888 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 814 " pdb=" ZN N 101 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 58 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 40 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 61 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 37 " Number of angles added : 18 7752 Ramachandran restraints generated. 3876 Oldfield, 0 Emsley, 3876 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7258 Finding SS restraints... Secondary structure from input PDB file: 139 helices and 54 sheets defined 42.5% alpha, 11.9% beta 50 base pairs and 82 stacking pairs defined. Time for finding SS restraints: 4.12 Creating SS restraints... Processing helix chain 'J' and resid 26 through 34 Processing helix chain 'J' and resid 77 through 81 Processing helix chain 'J' and resid 96 through 100 Processing helix chain 'J' and resid 113 through 118 Processing helix chain 'J' and resid 124 through 129 Processing helix chain 'J' and resid 131 through 140 Processing helix chain 'J' and resid 161 through 172 Processing helix chain 'J' and resid 180 through 192 Processing helix chain 'J' and resid 193 through 207 Processing helix chain 'J' and resid 210 through 230 Processing helix chain 'J' and resid 233 through 236 Processing helix chain 'J' and resid 246 through 250 Processing helix chain 'J' and resid 263 through 286 removed outlier: 4.222A pdb=" N ASP J 267 " --> pdb=" O SER J 263 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG J 275 " --> pdb=" O ARG J 271 " (cutoff:3.500A) Processing helix chain 'J' and resid 288 through 308 removed outlier: 3.562A pdb=" N VAL J 292 " --> pdb=" O PRO J 288 " (cutoff:3.500A) Processing helix chain 'J' and resid 326 through 332 Processing helix chain 'J' and resid 370 through 377 Processing helix chain 'J' and resid 377 through 388 Processing helix chain 'J' and resid 393 through 404 removed outlier: 3.569A pdb=" N ALA J 397 " --> pdb=" O THR J 393 " (cutoff:3.500A) Processing helix chain 'J' and resid 405 through 417 removed outlier: 3.594A pdb=" N TRP J 409 " --> pdb=" O GLU J 405 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ASP J 410 " --> pdb=" O ALA J 406 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ARG J 417 " --> pdb=" O ASP J 413 " (cutoff:3.500A) Processing helix chain 'J' and resid 430 through 432 No H-bonds generated for 'chain 'J' and resid 430 through 432' Processing helix chain 'J' and resid 450 through 452 No H-bonds generated for 'chain 'J' and resid 450 through 452' Processing helix chain 'J' and resid 453 through 458 Processing helix chain 'J' and resid 473 through 484 Processing helix chain 'J' and resid 504 through 514 removed outlier: 3.506A pdb=" N LEU J 508 " --> pdb=" O GLN J 504 " (cutoff:3.500A) Processing helix chain 'J' and resid 529 through 538 Processing helix chain 'J' and resid 573 through 580 Processing helix chain 'J' and resid 581 through 583 No H-bonds generated for 'chain 'J' and resid 581 through 583' Processing helix chain 'J' and resid 588 through 592 Processing helix chain 'J' and resid 597 through 613 removed outlier: 3.713A pdb=" N ILE J 601 " --> pdb=" O GLY J 597 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LEU J 605 " --> pdb=" O ILE J 601 " (cutoff:3.500A) Processing helix chain 'J' and resid 614 through 636 removed outlier: 3.688A pdb=" N GLY J 636 " --> pdb=" O ALA J 632 " (cutoff:3.500A) Processing helix chain 'J' and resid 649 through 670 Processing helix chain 'J' and resid 674 through 703 removed outlier: 4.206A pdb=" N THR J 703 " --> pdb=" O ASP J 699 " (cutoff:3.500A) Processing helix chain 'J' and resid 720 through 728 Processing helix chain 'J' and resid 733 through 741 removed outlier: 3.672A pdb=" N ILE J 737 " --> pdb=" O SER J 733 " (cutoff:3.500A) Processing helix chain 'J' and resid 768 through 792 removed outlier: 4.130A pdb=" N HIS J 777 " --> pdb=" O PHE J 773 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N GLY J 778 " --> pdb=" O ILE J 774 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ALA J 791 " --> pdb=" O ALA J 787 " (cutoff:3.500A) Processing helix chain 'J' and resid 794 through 805 removed outlier: 3.838A pdb=" N VAL J 803 " --> pdb=" O ARG J 799 " (cutoff:3.500A) Processing helix chain 'J' and resid 834 through 840 removed outlier: 3.861A pdb=" N ARG J 838 " --> pdb=" O PRO J 834 " (cutoff:3.500A) Processing helix chain 'J' and resid 865 through 874 Processing helix chain 'J' and resid 914 through 925 Processing helix chain 'J' and resid 926 through 929 Processing helix chain 'J' and resid 1137 through 1147 Processing helix chain 'J' and resid 1216 through 1225 Processing helix chain 'J' and resid 1225 through 1243 Processing helix chain 'J' and resid 1250 through 1261 Processing helix chain 'J' and resid 1282 through 1295 Processing helix chain 'J' and resid 1308 through 1313 Processing helix chain 'J' and resid 1327 through 1338 Processing helix chain 'J' and resid 1348 through 1353 Processing helix chain 'J' and resid 1361 through 1373 removed outlier: 4.216A pdb=" N TYR J1365 " --> pdb=" O THR J1361 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 26 removed outlier: 3.596A pdb=" N GLU N 7 " --> pdb=" O ASP N 3 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER N 10 " --> pdb=" O ASP N 6 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ARG N 22 " --> pdb=" O THR N 18 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE N 23 " --> pdb=" O GLY N 19 " (cutoff:3.500A) Processing helix chain 'N' and resid 45 through 52 removed outlier: 4.214A pdb=" N PHE N 52 " --> pdb=" O ARG N 48 " (cutoff:3.500A) Processing helix chain 'N' and resid 58 through 70 Processing helix chain 'G' and resid 34 through 50 removed outlier: 3.714A pdb=" N THR G 38 " --> pdb=" O GLY G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 86 Processing helix chain 'G' and resid 155 through 159 Processing helix chain 'G' and resid 212 through 234 removed outlier: 3.640A pdb=" N LEU G 234 " --> pdb=" O ALA G 230 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 50 removed outlier: 3.610A pdb=" N THR H 38 " --> pdb=" O GLY H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 78 through 87 Processing helix chain 'H' and resid 154 through 158 removed outlier: 3.622A pdb=" N THR H 157 " --> pdb=" O PRO H 154 " (cutoff:3.500A) Processing helix chain 'H' and resid 212 through 228 removed outlier: 3.845A pdb=" N LEU H 228 " --> pdb=" O LEU H 224 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 39 Processing helix chain 'I' and resid 49 through 54 Processing helix chain 'I' and resid 81 through 89 Processing helix chain 'I' and resid 206 through 213 removed outlier: 4.101A pdb=" N LEU I 210 " --> pdb=" O ALA I 206 " (cutoff:3.500A) Processing helix chain 'I' and resid 216 through 225 Processing helix chain 'I' and resid 242 through 247 Processing helix chain 'I' and resid 270 through 281 Processing helix chain 'I' and resid 318 through 329 removed outlier: 3.789A pdb=" N LEU I 322 " --> pdb=" O SER I 318 " (cutoff:3.500A) Processing helix chain 'I' and resid 346 through 354 Processing helix chain 'I' and resid 358 through 371 Processing helix chain 'I' and resid 377 through 389 removed outlier: 3.817A pdb=" N PHE I 389 " --> pdb=" O PHE I 385 " (cutoff:3.500A) Processing helix chain 'I' and resid 398 through 409 Processing helix chain 'I' and resid 421 through 438 Processing helix chain 'I' and resid 455 through 481 removed outlier: 4.284A pdb=" N ASN I 462 " --> pdb=" O GLU I 458 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU I 481 " --> pdb=" O GLU I 477 " (cutoff:3.500A) Processing helix chain 'I' and resid 495 through 508 removed outlier: 3.700A pdb=" N SER I 499 " --> pdb=" O ALA I 495 " (cutoff:3.500A) Processing helix chain 'I' and resid 519 through 528 removed outlier: 3.695A pdb=" N ARG I 528 " --> pdb=" O ILE I 524 " (cutoff:3.500A) Processing helix chain 'I' and resid 607 through 612 removed outlier: 3.963A pdb=" N GLY I 612 " --> pdb=" O ALA I 608 " (cutoff:3.500A) Processing helix chain 'I' and resid 646 through 650 removed outlier: 3.682A pdb=" N GLN I 649 " --> pdb=" O SER I 646 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N VAL I 650 " --> pdb=" O ARG I 647 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 646 through 650' Processing helix chain 'I' and resid 656 through 660 removed outlier: 4.325A pdb=" N VAL I 660 " --> pdb=" O THR I 657 " (cutoff:3.500A) Processing helix chain 'I' and resid 663 through 667 removed outlier: 3.567A pdb=" N LEU I 667 " --> pdb=" O GLY I 664 " (cutoff:3.500A) Processing helix chain 'I' and resid 670 through 674 Processing helix chain 'I' and resid 675 through 687 Processing helix chain 'I' and resid 703 through 712 removed outlier: 4.554A pdb=" N ALA I 707 " --> pdb=" O GLY I 703 " (cutoff:3.500A) Processing helix chain 'I' and resid 820 through 825 Processing helix chain 'I' and resid 858 through 863 removed outlier: 3.806A pdb=" N SER I 863 " --> pdb=" O ALA I 860 " (cutoff:3.500A) Processing helix chain 'I' and resid 898 through 906 removed outlier: 3.519A pdb=" N PHE I 906 " --> pdb=" O LEU I 902 " (cutoff:3.500A) Processing helix chain 'I' and resid 942 through 979 Processing helix chain 'I' and resid 993 through 998 removed outlier: 3.986A pdb=" N LEU I 998 " --> pdb=" O ASP I 995 " (cutoff:3.500A) Processing helix chain 'I' and resid 1005 through 1037 Processing helix chain 'I' and resid 1099 through 1103 removed outlier: 3.590A pdb=" N GLY I1102 " --> pdb=" O ASN I1099 " (cutoff:3.500A) Processing helix chain 'I' and resid 1109 through 1134 Processing helix chain 'I' and resid 1137 through 1151 removed outlier: 3.606A pdb=" N LEU I1141 " --> pdb=" O GLU I1137 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU I1151 " --> pdb=" O ARG I1147 " (cutoff:3.500A) Processing helix chain 'I' and resid 1169 through 1176 Processing helix chain 'I' and resid 1191 through 1202 removed outlier: 3.565A pdb=" N GLY I1202 " --> pdb=" O LEU I1198 " (cutoff:3.500A) Processing helix chain 'I' and resid 1238 through 1242 Processing helix chain 'I' and resid 1272 through 1281 removed outlier: 3.632A pdb=" N TYR I1281 " --> pdb=" O ALA I1277 " (cutoff:3.500A) Processing helix chain 'I' and resid 1283 through 1292 removed outlier: 3.576A pdb=" N LEU I1287 " --> pdb=" O ALA I1283 " (cutoff:3.500A) Processing helix chain 'I' and resid 1299 through 1310 Processing helix chain 'I' and resid 1320 through 1331 Processing helix chain 'K' and resid 6 through 14 Processing helix chain 'K' and resid 16 through 32 removed outlier: 3.582A pdb=" N VAL K 20 " --> pdb=" O ARG K 16 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU K 21 " --> pdb=" O PHE K 17 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 57 Processing helix chain 'K' and resid 60 through 74 Processing helix chain 'L' and resid 8 through 20 Processing helix chain 'L' and resid 25 through 30 Processing helix chain 'L' and resid 37 through 51 removed outlier: 3.837A pdb=" N ILE L 41 " --> pdb=" O ASP L 37 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET L 51 " --> pdb=" O MET L 47 " (cutoff:3.500A) Processing helix chain 'L' and resid 74 through 88 removed outlier: 4.165A pdb=" N GLU L 78 " --> pdb=" O GLU L 74 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA L 79 " --> pdb=" O ASP L 75 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLU L 88 " --> pdb=" O LEU L 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 96 through 108 removed outlier: 4.010A pdb=" N VAL L 108 " --> pdb=" O GLU L 104 " (cutoff:3.500A) Processing helix chain 'L' and resid 115 through 125 Processing helix chain 'L' and resid 128 through 136 Processing helix chain 'L' and resid 137 through 152 Processing helix chain 'L' and resid 157 through 162 removed outlier: 3.645A pdb=" N LEU L 161 " --> pdb=" O LEU L 158 " (cutoff:3.500A) Processing helix chain 'L' and resid 214 through 233 Processing helix chain 'L' and resid 234 through 235 No H-bonds generated for 'chain 'L' and resid 234 through 235' Processing helix chain 'L' and resid 243 through 243 No H-bonds generated for 'chain 'L' and resid 243 through 243' Processing helix chain 'L' and resid 244 through 257 removed outlier: 3.832A pdb=" N GLU L 248 " --> pdb=" O THR L 244 " (cutoff:3.500A) Processing helix chain 'L' and resid 262 through 289 Processing helix chain 'L' and resid 298 through 305 Processing helix chain 'L' and resid 305 through 310 removed outlier: 4.143A pdb=" N ASN L 309 " --> pdb=" O LEU L 305 " (cutoff:3.500A) Processing helix chain 'L' and resid 319 through 323 removed outlier: 3.568A pdb=" N MET L 322 " --> pdb=" O ALA L 319 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASN L 323 " --> pdb=" O ILE L 320 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 319 through 323' Processing helix chain 'L' and resid 326 through 330 removed outlier: 3.502A pdb=" N LYS L 329 " --> pdb=" O TRP L 326 " (cutoff:3.500A) Processing helix chain 'L' and resid 333 through 352 removed outlier: 3.677A pdb=" N VAL L 337 " --> pdb=" O VAL L 333 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN L 342 " --> pdb=" O HIS L 338 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLU L 349 " --> pdb=" O GLN L 345 " (cutoff:3.500A) Processing helix chain 'L' and resid 354 through 392 removed outlier: 3.951A pdb=" N VAL L 358 " --> pdb=" O THR L 354 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA L 375 " --> pdb=" O LYS L 371 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLU L 378 " --> pdb=" O ARG L 374 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N LEU L 386 " --> pdb=" O ALA L 382 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N SER L 389 " --> pdb=" O ARG L 385 " (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 417 Processing helix chain 'L' and resid 426 through 446 removed outlier: 4.212A pdb=" N TYR L 430 " --> pdb=" O LYS L 426 " (cutoff:3.500A) Processing helix chain 'L' and resid 453 through 474 Processing helix chain 'L' and resid 479 through 487 removed outlier: 3.791A pdb=" N GLU L 485 " --> pdb=" O GLU L 481 " (cutoff:3.500A) Processing helix chain 'L' and resid 492 through 502 removed outlier: 4.006A pdb=" N LYS L 502 " --> pdb=" O LEU L 498 " (cutoff:3.500A) Processing helix chain 'L' and resid 518 through 522 removed outlier: 3.879A pdb=" N ASP L 521 " --> pdb=" O HIS L 518 " (cutoff:3.500A) Processing helix chain 'L' and resid 530 through 550 removed outlier: 3.623A pdb=" N SER L 539 " --> pdb=" O ALA L 535 " (cutoff:3.500A) Processing helix chain 'L' and resid 552 through 563 Processing helix chain 'L' and resid 572 through 581 Processing helix chain 'L' and resid 583 through 600 removed outlier: 3.848A pdb=" N HIS L 600 " --> pdb=" O ARG L 596 " (cutoff:3.500A) Processing helix chain 'L' and resid 604 through 611 removed outlier: 3.756A pdb=" N LEU L 611 " --> pdb=" O LEU L 607 " (cutoff:3.500A) Processing helix chain 'M' and resid 256 through 261 removed outlier: 3.808A pdb=" N GLU M 261 " --> pdb=" O ASP M 258 " (cutoff:3.500A) Processing helix chain 'M' and resid 263 through 274 Processing helix chain 'M' and resid 285 through 290 Processing helix chain 'M' and resid 296 through 310 removed outlier: 3.507A pdb=" N LEU M 300 " --> pdb=" O GLY M 296 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG M 310 " --> pdb=" O VAL M 306 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'J' and resid 20 through 24 Processing sheet with id=AA2, first strand: chain 'J' and resid 103 through 112 removed outlier: 6.952A pdb=" N THR J 240 " --> pdb=" O LEU J 107 " (cutoff:3.500A) removed outlier: 10.129A pdb=" N SER J 109 " --> pdb=" O ILE J 238 " (cutoff:3.500A) removed outlier: 9.938A pdb=" N ILE J 238 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'J' and resid 159 through 160 Processing sheet with id=AA4, first strand: chain 'J' and resid 261 through 262 Processing sheet with id=AA5, first strand: chain 'J' and resid 345 through 347 Processing sheet with id=AA6, first strand: chain 'J' and resid 365 through 369 removed outlier: 5.963A pdb=" N CYS J 366 " --> pdb=" O VAL J 440 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ILE J 442 " --> pdb=" O CYS J 366 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N LEU J 368 " --> pdb=" O ILE J 442 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ILE J 447 " --> pdb=" O ARG J 352 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N VAL J 354 " --> pdb=" O ILE J 447 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'J' and resid 526 through 527 Processing sheet with id=AA8, first strand: chain 'J' and resid 706 through 707 Processing sheet with id=AA9, first strand: chain 'J' and resid 809 through 811 removed outlier: 5.820A pdb=" N VAL J 894 " --> pdb=" O VAL J 809 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU J 811 " --> pdb=" O VAL J 894 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'J' and resid 820 through 822 Processing sheet with id=AB2, first strand: chain 'J' and resid 825 through 826 removed outlier: 6.667A pdb=" N VAL J 825 " --> pdb=" O LYS J 832 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 848 through 849 Processing sheet with id=AB4, first strand: chain 'J' and resid 956 through 957 removed outlier: 4.343A pdb=" N GLY J 956 " --> pdb=" O VAL J1011 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL J1011 " --> pdb=" O GLY J 956 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'J' and resid 960 through 961 removed outlier: 7.062A pdb=" N LEU J 982 " --> pdb=" O SER J 994 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N SER J 994 " --> pdb=" O LEU J 982 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N LEU J 984 " --> pdb=" O LYS J 992 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'J' and resid 965 through 966 Processing sheet with id=AB7, first strand: chain 'J' and resid 1002 through 1003 Processing sheet with id=AB8, first strand: chain 'J' and resid 1034 through 1038 Processing sheet with id=AB9, first strand: chain 'J' and resid 1047 through 1051 Processing sheet with id=AC1, first strand: chain 'J' and resid 1106 through 1107 Processing sheet with id=AC2, first strand: chain 'J' and resid 1187 through 1191 Processing sheet with id=AC3, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 6.458A pdb=" N THR J1301 " --> pdb=" O VAL J1267 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 13 through 18 removed outlier: 8.850A pdb=" N LEU G 13 " --> pdb=" O GLU G 29 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N GLU G 29 " --> pdb=" O LEU G 13 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N ASP G 15 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N THR G 27 " --> pdb=" O ASP G 15 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU G 17 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ASP G 199 " --> pdb=" O PRO G 30 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 52 through 53 Processing sheet with id=AC6, first strand: chain 'G' and resid 115 through 116 removed outlier: 4.437A pdb=" N THR G 101 " --> pdb=" O THR G 116 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ARG G 143 " --> pdb=" O VAL G 59 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N VAL G 59 " --> pdb=" O ARG G 143 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N LYS G 145 " --> pdb=" O THR G 57 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 90 through 92 Processing sheet with id=AC8, first strand: chain 'G' and resid 108 through 111 removed outlier: 6.075A pdb=" N GLY G 108 " --> pdb=" O HIS G 132 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N HIS G 132 " --> pdb=" O GLY G 108 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL G 110 " --> pdb=" O ILE G 130 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 180 through 182 removed outlier: 6.610A pdb=" N GLU G 206 " --> pdb=" O GLU G 181 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 23 through 31 removed outlier: 5.816A pdb=" N HIS H 23 " --> pdb=" O THR H 207 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N THR H 207 " --> pdb=" O HIS H 23 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N LYS H 25 " --> pdb=" O MET H 205 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N MET H 205 " --> pdb=" O LYS H 25 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N THR H 27 " --> pdb=" O ILE H 203 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N ILE H 203 " --> pdb=" O THR H 27 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N GLU H 29 " --> pdb=" O LEU H 201 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N LEU H 201 " --> pdb=" O GLU H 29 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N GLU H 206 " --> pdb=" O GLU H 181 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 53 through 61 removed outlier: 6.689A pdb=" N LYS H 145 " --> pdb=" O THR H 57 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N VAL H 59 " --> pdb=" O ARG H 143 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ARG H 143 " --> pdb=" O VAL H 59 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 90 through 91 Processing sheet with id=AD4, first strand: chain 'H' and resid 104 through 105 Processing sheet with id=AD5, first strand: chain 'H' and resid 109 through 110 removed outlier: 3.844A pdb=" N CYS H 131 " --> pdb=" O VAL H 110 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 152 through 153 Processing sheet with id=AD7, first strand: chain 'I' and resid 13 through 14 removed outlier: 6.853A pdb=" N LYS I 13 " --> pdb=" O ALA I1183 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'I' and resid 59 through 60 removed outlier: 5.202A pdb=" N SER I 66 " --> pdb=" O TYR I 105 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N TYR I 105 " --> pdb=" O SER I 66 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N LEU I 68 " --> pdb=" O VAL I 103 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N VAL I 103 " --> pdb=" O LEU I 68 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N TYR I 70 " --> pdb=" O ARG I 101 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ARG I 101 " --> pdb=" O TYR I 70 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N SER I 72 " --> pdb=" O LYS I 99 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU I 102 " --> pdb=" O ILE I 117 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ILE I 117 " --> pdb=" O LEU I 102 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE I 104 " --> pdb=" O LYS I 115 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 59 through 60 removed outlier: 5.202A pdb=" N SER I 66 " --> pdb=" O TYR I 105 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N TYR I 105 " --> pdb=" O SER I 66 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N LEU I 68 " --> pdb=" O VAL I 103 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N VAL I 103 " --> pdb=" O LEU I 68 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N TYR I 70 " --> pdb=" O ARG I 101 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ARG I 101 " --> pdb=" O TYR I 70 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N SER I 72 " --> pdb=" O LYS I 99 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ALA I 94 " --> pdb=" O GLU I 126 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N GLU I 126 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N LEU I 96 " --> pdb=" O MET I 124 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 136 through 137 Processing sheet with id=AE2, first strand: chain 'I' and resid 147 through 148 removed outlier: 6.357A pdb=" N SER I 147 " --> pdb=" O SER I 531 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'I' and resid 154 through 157 Processing sheet with id=AE4, first strand: chain 'I' and resid 184 through 187 Processing sheet with id=AE5, first strand: chain 'I' and resid 284 through 285 removed outlier: 5.249A pdb=" N ILE I 229 " --> pdb=" O GLU I 240 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 255 through 257 removed outlier: 6.666A pdb=" N ILE I 255 " --> pdb=" O TYR I 262 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 296 through 297 removed outlier: 3.716A pdb=" N MET I 315 " --> pdb=" O VAL I 297 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 580 through 581 removed outlier: 5.397A pdb=" N GLU I 602 " --> pdb=" O LYS I 593 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 580 through 581 Processing sheet with id=AF1, first strand: chain 'I' and resid 634 through 637 Processing sheet with id=AF2, first strand: chain 'I' and resid 749 through 752 removed outlier: 6.957A pdb=" N VAL I 733 " --> pdb=" O GLN I 725 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 757 through 758 Processing sheet with id=AF4, first strand: chain 'I' and resid 768 through 769 Processing sheet with id=AF5, first strand: chain 'I' and resid 1065 through 1067 removed outlier: 7.271A pdb=" N ILE I 816 " --> pdb=" O SER I1077 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ILE I1079 " --> pdb=" O ILE I 816 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N VAL I 818 " --> pdb=" O ILE I1079 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'I' and resid 830 through 841 removed outlier: 5.885A pdb=" N THR I 830 " --> pdb=" O LYS I1057 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N LYS I1057 " --> pdb=" O THR I 830 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N HIS I 832 " --> pdb=" O ALA I1055 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ALA I1055 " --> pdb=" O HIS I 832 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N GLN I 834 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N TYR I1053 " --> pdb=" O GLN I 834 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LEU I 836 " --> pdb=" O LYS I1051 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N LYS I1051 " --> pdb=" O LEU I 836 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N CYS I 838 " --> pdb=" O ILE I1049 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ILE I1049 " --> pdb=" O CYS I 838 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N SER I 840 " --> pdb=" O LEU I1047 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ALA I1055 " --> pdb=" O VAL I 928 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N VAL I 928 " --> pdb=" O ALA I1055 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N LYS I1057 " --> pdb=" O GLY I 926 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N GLY I 926 " --> pdb=" O LYS I1057 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'I' and resid 882 through 884 removed outlier: 6.456A pdb=" N LEU I 918 " --> pdb=" O LEU I 883 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'I' and resid 887 through 889 Processing sheet with id=AF9, first strand: chain 'I' and resid 1087 through 1088 1279 hydrogen bonds defined for protein. 3597 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 120 hydrogen bonds 236 hydrogen bond angles 0 basepair planarities 50 basepair parallelities 82 stacking parallelities Total time for adding SS restraints: 9.00 Time building geometry restraints manager: 3.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.26: 5483 1.26 - 1.40: 7646 1.40 - 1.55: 19837 1.55 - 1.69: 257 1.69 - 1.83: 252 Bond restraints: 33475 Sorted by residual: bond pdb=" C19 1N7 J1504 " pdb=" C3 1N7 J1504 " ideal model delta sigma weight residual 1.532 1.827 -0.295 2.00e-02 2.50e+03 2.18e+02 bond pdb=" C19 1N7 J1506 " pdb=" C3 1N7 J1506 " ideal model delta sigma weight residual 1.532 1.824 -0.292 2.00e-02 2.50e+03 2.13e+02 bond pdb=" C19 1N7 J1505 " pdb=" C3 1N7 J1505 " ideal model delta sigma weight residual 1.532 1.821 -0.289 2.00e-02 2.50e+03 2.09e+02 bond pdb=" C19 1N7 I1401 " pdb=" C3 1N7 I1401 " ideal model delta sigma weight residual 1.532 1.819 -0.287 2.00e-02 2.50e+03 2.06e+02 bond pdb=" C3 1N7 J1504 " pdb=" C4 1N7 J1504 " ideal model delta sigma weight residual 1.532 1.730 -0.198 2.00e-02 2.50e+03 9.76e+01 ... (remaining 33470 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.12: 44919 3.12 - 6.23: 682 6.23 - 9.35: 56 9.35 - 12.47: 4 12.47 - 15.58: 1 Bond angle restraints: 45662 Sorted by residual: angle pdb=" C ARG J 362 " pdb=" N LEU J 363 " pdb=" CA LEU J 363 " ideal model delta sigma weight residual 122.56 106.98 15.58 1.72e+00 3.38e-01 8.21e+01 angle pdb=" C ILE I1082 " pdb=" CA ILE I1082 " pdb=" CB ILE I1082 " ideal model delta sigma weight residual 112.04 102.96 9.08 1.31e+00 5.83e-01 4.80e+01 angle pdb=" N ILE I1079 " pdb=" CA ILE I1079 " pdb=" C ILE I1079 " ideal model delta sigma weight residual 106.53 97.39 9.14 1.41e+00 5.03e-01 4.21e+01 angle pdb=" N PRO I1081 " pdb=" CA PRO I1081 " pdb=" CB PRO I1081 " ideal model delta sigma weight residual 103.25 96.55 6.70 1.05e+00 9.07e-01 4.07e+01 angle pdb=" N PRO I1081 " pdb=" CD PRO I1081 " pdb=" CG PRO I1081 " ideal model delta sigma weight residual 103.20 94.21 8.99 1.50e+00 4.44e-01 3.59e+01 ... (remaining 45657 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.18: 18754 30.18 - 60.37: 1761 60.37 - 90.55: 87 90.55 - 120.74: 3 120.74 - 150.92: 4 Dihedral angle restraints: 20609 sinusoidal: 9359 harmonic: 11250 Sorted by residual: 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 -135.04 -44.96 0 5.00e+00 4.00e-02 8.08e+01 dihedral pdb=" CA PRO I 897 " pdb=" C PRO I 897 " pdb=" N GLU I 898 " pdb=" CA GLU I 898 " ideal model delta harmonic sigma weight residual 180.00 -143.30 -36.70 0 5.00e+00 4.00e-02 5.39e+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 -143.67 -36.33 0 5.00e+00 4.00e-02 5.28e+01 ... (remaining 20606 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 4344 0.069 - 0.137: 827 0.137 - 0.206: 59 0.206 - 0.275: 8 0.275 - 0.344: 2 Chirality restraints: 5240 Sorted by residual: chirality pdb=" CA ILE I1079 " pdb=" N ILE I1079 " pdb=" C ILE I1079 " pdb=" CB ILE I1079 " both_signs ideal model delta sigma weight residual False 2.43 2.78 -0.34 2.00e-01 2.50e+01 2.95e+00 chirality pdb=" C19 1N7 J1506 " pdb=" C18 1N7 J1506 " pdb=" C2 1N7 J1506 " pdb=" C3 1N7 J1506 " both_signs ideal model delta sigma weight residual False -2.53 -2.87 0.33 2.00e-01 2.50e+01 2.79e+00 chirality pdb=" C19 1N7 J1504 " pdb=" C18 1N7 J1504 " pdb=" C2 1N7 J1504 " pdb=" C3 1N7 J1504 " both_signs ideal model delta sigma weight residual False -2.53 -2.78 0.25 2.00e-01 2.50e+01 1.58e+00 ... (remaining 5237 not shown) Planarity restraints: 5595 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN I1080 " -0.044 5.00e-02 4.00e+02 7.12e-02 8.12e+00 pdb=" N PRO I1081 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO I1081 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO I1081 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS J 850 " 0.042 5.00e-02 4.00e+02 6.36e-02 6.48e+00 pdb=" N PRO J 851 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO J 851 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO J 851 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN I 519 " 0.042 5.00e-02 4.00e+02 6.33e-02 6.41e+00 pdb=" N PRO I 520 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO I 520 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO I 520 " 0.035 5.00e-02 4.00e+02 ... (remaining 5592 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.58: 447 2.58 - 3.16: 29614 3.16 - 3.74: 51970 3.74 - 4.32: 73445 4.32 - 4.90: 118149 Nonbonded interactions: 273625 Sorted by model distance: nonbonded pdb=" OD1 ASP J 464 " pdb="MG MG J1501 " model vdw 1.995 2.170 nonbonded pdb=" OH TYR I 301 " pdb=" O ARG I 332 " model vdw 2.001 3.040 nonbonded pdb=" O LEU J 361 " pdb=" OH TYR J 626 " model vdw 2.007 3.040 nonbonded pdb=" O ILE I 11 " pdb=" OH TYR I1149 " model vdw 2.034 3.040 nonbonded pdb=" O ARG G 45 " pdb=" OG SER G 49 " model vdw 2.034 3.040 ... (remaining 273620 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 5 and (name N or name CA or name C or name O or name CB ) \ ) or resid 6 through 158 or resid 171 through 233 or (resid 234 and (name N or n \ ame CA or name C or name O or name CB )))) selection = (chain 'H' and (resid 5 through 232 or (resid 233 through 234 and (name N or nam \ e CA or name C or name O or name CB )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 1.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.540 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 39.090 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 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 : 0.011 0.295 33487 Z= 0.539 Angle : 1.075 38.859 45680 Z= 0.628 Chirality : 0.052 0.344 5240 Planarity : 0.005 0.071 5595 Dihedral : 20.449 150.923 13351 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 40.39 Ramachandran Plot: Outliers : 0.28 % Allowed : 10.24 % Favored : 89.47 % Rotamer: Outliers : 13.45 % Allowed : 21.69 % Favored : 64.86 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 3.25 % Cis-general : 0.21 % Twisted Proline : 1.30 % Twisted General : 0.21 % 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: -4.43 (0.11), residues: 3876 helix: -2.34 (0.10), residues: 1545 sheet: -3.38 (0.21), residues: 429 loop : -3.38 (0.12), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG J 576 TYR 0.022 0.003 TYR G 177 PHE 0.026 0.003 PHE I 514 TRP 0.012 0.002 TRP L 434 HIS 0.009 0.002 HIS J 430 Details of bonding type rmsd/Z covalent geometry : bond 0.01069 / 0.54 (33475) covalent geometry : angle 1.01355 / 0.62 (45662) hydrogen bonds : bond 0.14886 / 9.79 ( 1392) hydrogen bonds : angle 6.86284 / 4.76 ( 3833) metal coordination : bond 0.04984 / 2.85 ( 12) metal coordination : angle 18.01242 / 9.30 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7752 Ramachandran restraints generated. 3876 Oldfield, 0 Emsley, 3876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7752 Ramachandran restraints generated. 3876 Oldfield, 0 Emsley, 3876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 930 residues out of total 3346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 447 poor density : 483 time to evaluate : 1.241 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: J 69 GLU cc_start: 0.7698 (tt0) cc_final: 0.7411 (mt-10) REVERT: J 77 ARG cc_start: 0.7398 (mpp-170) cc_final: 0.6725 (mpt180) REVERT: J 86 GLU cc_start: 0.7908 (pm20) cc_final: 0.7684 (pm20) REVERT: J 137 ARG cc_start: 0.7552 (mtp180) cc_final: 0.7080 (mtm-85) REVERT: J 306 LEU cc_start: 0.9403 (OUTLIER) cc_final: 0.9124 (tp) REVERT: J 339 ARG cc_start: 0.4934 (mmm160) cc_final: 0.3917 (mmt-90) REVERT: J 375 GLU cc_start: 0.8372 (tp30) cc_final: 0.7943 (tp30) REVERT: J 400 MET cc_start: 0.8237 (mtp) cc_final: 0.7992 (ttm) REVERT: J 557 LYS cc_start: 0.7748 (OUTLIER) cc_final: 0.7032 (pttt) REVERT: J 591 ILE cc_start: 0.8969 (OUTLIER) cc_final: 0.8647 (tp) REVERT: J 661 VAL cc_start: 0.8607 (OUTLIER) cc_final: 0.8351 (t) REVERT: J 1101 LEU cc_start: 0.5654 (OUTLIER) cc_final: 0.5427 (mp) REVERT: J 1144 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8656 (tt) REVERT: J 1194 ARG cc_start: 0.5649 (mpt180) cc_final: 0.4333 (mmm-85) REVERT: J 1236 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.7039 (mp0) REVERT: J 1304 ARG cc_start: 0.7140 (OUTLIER) cc_final: 0.6199 (tpt90) REVERT: J 1310 THR cc_start: 0.8875 (OUTLIER) cc_final: 0.8558 (m) REVERT: N 17 MET cc_start: 0.6730 (OUTLIER) cc_final: 0.6472 (mtt) REVERT: N 21 ASN cc_start: 0.7912 (OUTLIER) cc_final: 0.7411 (m-40) REVERT: G 15 ASP cc_start: 0.6907 (OUTLIER) cc_final: 0.6554 (m-30) REVERT: G 33 ARG cc_start: 0.7063 (OUTLIER) cc_final: 0.6138 (ttp-170) REVERT: G 157 THR cc_start: 0.7739 (m) cc_final: 0.7386 (m) REVERT: G 158 ARG cc_start: 0.7720 (OUTLIER) cc_final: 0.6652 (ttm-80) REVERT: I 200 ARG cc_start: 0.7071 (mmm160) cc_final: 0.6816 (ptt90) REVERT: I 268 ARG cc_start: 0.4424 (OUTLIER) cc_final: 0.4182 (ttm170) REVERT: I 284 LEU cc_start: 0.6834 (OUTLIER) cc_final: 0.6571 (mp) REVERT: I 301 TYR cc_start: 0.5044 (OUTLIER) cc_final: 0.3824 (m-10) REVERT: I 503 LYS cc_start: 0.8447 (ttpp) cc_final: 0.8196 (ptmm) REVERT: I 514 PHE cc_start: 0.8169 (OUTLIER) cc_final: 0.7596 (m-10) REVERT: I 892 GLU cc_start: 0.6287 (tt0) cc_final: 0.6085 (pm20) REVERT: I 1016 GLU cc_start: 0.6653 (OUTLIER) cc_final: 0.6225 (tm-30) REVERT: I 1041 ASP cc_start: 0.7638 (OUTLIER) cc_final: 0.7247 (m-30) REVERT: K 42 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.6399 (pp20) REVERT: K 74 GLU cc_start: 0.6279 (mt-10) cc_final: 0.6059 (mt-10) REVERT: L 24 TYR cc_start: 0.7014 (OUTLIER) cc_final: 0.5009 (t80) REVERT: L 144 LEU cc_start: 0.4461 (OUTLIER) cc_final: 0.4222 (pp) REVERT: L 273 MET cc_start: 0.4296 (OUTLIER) cc_final: 0.2663 (tpp) REVERT: L 379 MET cc_start: 0.7237 (tpp) cc_final: 0.6562 (tpp) REVERT: L 559 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8432 (mp) REVERT: L 561 MET cc_start: 0.7922 (ttm) cc_final: 0.7559 (mtp) REVERT: M 297 LYS cc_start: 0.6093 (OUTLIER) cc_final: 0.5754 (pttp) outliers start: 447 outliers final: 309 residues processed: 874 average time/residue: 0.2298 time to fit residues: 316.6845 Evaluate side-chains 698 residues out of total 3346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 335 poor density : 363 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 37 GLU Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 56 LEU Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 95 THR Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain J residue 199 GLU Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 212 THR Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain J residue 241 VAL Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 289 ASP Chi-restraints excluded: chain J residue 292 VAL Chi-restraints excluded: chain J residue 306 LEU Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 326 SER Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 365 GLN Chi-restraints excluded: chain J residue 374 LEU Chi-restraints excluded: chain J residue 393 THR Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 442 ILE Chi-restraints excluded: chain J residue 466 MET Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 473 THR Chi-restraints excluded: chain J residue 474 LEU Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 489 ASN Chi-restraints excluded: chain J residue 492 SER Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 517 CYS Chi-restraints excluded: chain J residue 526 VAL Chi-restraints excluded: chain J residue 543 SER Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 548 VAL Chi-restraints excluded: chain J residue 550 VAL Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 557 LYS Chi-restraints excluded: chain J residue 558 ASP Chi-restraints excluded: chain J residue 571 ASP Chi-restraints excluded: chain J residue 572 THR Chi-restraints excluded: chain J residue 576 ARG Chi-restraints excluded: chain J residue 578 ILE Chi-restraints excluded: chain J residue 591 ILE Chi-restraints excluded: chain J residue 592 VAL Chi-restraints excluded: chain J residue 601 ILE Chi-restraints excluded: chain J residue 638 SER Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 683 ILE Chi-restraints excluded: chain J residue 685 ILE Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 722 ILE Chi-restraints excluded: chain J residue 744 ARG Chi-restraints excluded: chain J residue 762 ASN Chi-restraints excluded: chain J residue 770 LEU Chi-restraints excluded: chain J residue 783 LEU Chi-restraints excluded: chain J residue 788 LEU Chi-restraints excluded: chain J residue 796 LEU Chi-restraints excluded: chain J residue 797 THR Chi-restraints excluded: chain J residue 801 VAL Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 816 THR Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 835 LEU Chi-restraints excluded: chain J residue 869 CYS Chi-restraints excluded: chain J residue 878 ASP Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 903 LEU Chi-restraints excluded: chain J residue 909 ILE Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 928 THR Chi-restraints excluded: chain J residue 931 THR Chi-restraints excluded: chain J residue 952 VAL Chi-restraints excluded: chain J residue 968 ASN Chi-restraints excluded: chain J residue 1028 ILE Chi-restraints excluded: chain J residue 1060 VAL Chi-restraints excluded: chain J residue 1081 VAL Chi-restraints excluded: chain J residue 1101 LEU Chi-restraints excluded: chain J residue 1116 SER Chi-restraints excluded: chain J residue 1120 THR Chi-restraints excluded: chain J residue 1144 LEU Chi-restraints excluded: chain J residue 1148 ARG Chi-restraints excluded: chain J residue 1155 ILE Chi-restraints excluded: chain J residue 1164 SER Chi-restraints excluded: chain J residue 1177 ILE Chi-restraints excluded: chain J residue 1181 ASP Chi-restraints excluded: chain J residue 1196 LEU Chi-restraints excluded: chain J residue 1198 VAL Chi-restraints excluded: chain J residue 1206 ARG Chi-restraints excluded: chain J residue 1220 ILE Chi-restraints excluded: chain J residue 1223 LEU Chi-restraints excluded: chain J residue 1230 THR Chi-restraints excluded: chain J residue 1236 GLU Chi-restraints excluded: chain J residue 1240 VAL Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain J residue 1256 ILE Chi-restraints excluded: chain J residue 1257 VAL Chi-restraints excluded: chain J residue 1258 ARG Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1262 ARG Chi-restraints excluded: chain J residue 1266 ILE Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain J residue 1273 ASP Chi-restraints excluded: chain J residue 1304 ARG Chi-restraints excluded: chain J residue 1307 LEU Chi-restraints excluded: chain J residue 1310 THR Chi-restraints excluded: chain J residue 1332 LEU Chi-restraints excluded: chain J residue 1333 THR Chi-restraints excluded: chain J residue 1342 ASP Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain J residue 1356 LEU Chi-restraints excluded: chain N residue 10 SER Chi-restraints excluded: chain N residue 15 LEU Chi-restraints excluded: chain N residue 17 MET Chi-restraints excluded: chain N residue 21 ASN Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 61 CYS Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 15 ASP Chi-restraints excluded: chain G residue 29 GLU Chi-restraints excluded: chain G residue 33 ARG Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 75 GLN Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 158 ARG Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 182 ARG Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 200 LYS Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 214 GLU Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain H residue 140 ILE Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 172 LEU Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 203 ILE Chi-restraints excluded: chain H residue 217 ILE Chi-restraints excluded: chain I residue 33 ASP Chi-restraints excluded: chain I residue 37 LYS Chi-restraints excluded: chain I residue 67 GLU Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 133 ASN Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain I residue 147 SER Chi-restraints excluded: chain I residue 177 ILE Chi-restraints excluded: chain I residue 220 ILE Chi-restraints excluded: chain I residue 256 GLU Chi-restraints excluded: chain I residue 268 ARG Chi-restraints excluded: chain I residue 284 LEU Chi-restraints excluded: chain I residue 286 GLU Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain I residue 296 VAL Chi-restraints excluded: chain I residue 301 TYR Chi-restraints excluded: chain I residue 317 LEU Chi-restraints excluded: chain I residue 319 LEU Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 391 SER Chi-restraints excluded: chain I residue 398 SER Chi-restraints excluded: chain I residue 417 SER Chi-restraints excluded: chain I residue 435 ILE Chi-restraints excluded: chain I residue 466 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 475 VAL Chi-restraints excluded: chain I residue 487 LEU Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 521 LEU Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 525 THR Chi-restraints excluded: chain I residue 531 SER Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 553 THR Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 573 ASN Chi-restraints excluded: chain I residue 576 SER Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 583 GLU Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 596 ASP Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 602 GLU Chi-restraints excluded: chain I residue 604 HIS Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 633 LEU Chi-restraints excluded: chain I residue 634 VAL Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 643 SER Chi-restraints excluded: chain I residue 658 GLN Chi-restraints excluded: chain I residue 659 GLN Chi-restraints excluded: chain I residue 662 SER Chi-restraints excluded: chain I residue 690 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 750 ILE Chi-restraints excluded: chain I residue 754 THR Chi-restraints excluded: chain I residue 764 CYS Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 773 LEU Chi-restraints excluded: chain I residue 777 VAL Chi-restraints excluded: chain I residue 783 LEU Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 816 ILE Chi-restraints excluded: chain I residue 819 SER Chi-restraints excluded: chain I residue 839 VAL Chi-restraints excluded: chain I residue 843 THR Chi-restraints excluded: chain I residue 905 ILE Chi-restraints excluded: chain I residue 911 SER Chi-restraints excluded: chain I residue 919 ARG Chi-restraints excluded: chain I residue 935 THR Chi-restraints excluded: chain I residue 939 VAL Chi-restraints excluded: chain I residue 1003 THR Chi-restraints excluded: chain I residue 1014 LEU Chi-restraints excluded: chain I residue 1016 GLU Chi-restraints excluded: chain I residue 1041 ASP Chi-restraints excluded: chain I residue 1073 LYS Chi-restraints excluded: chain I residue 1083 GLU Chi-restraints excluded: chain I residue 1092 THR Chi-restraints excluded: chain I residue 1096 ILE Chi-restraints excluded: chain I residue 1097 VAL Chi-restraints excluded: chain I residue 1107 MET Chi-restraints excluded: chain I residue 1135 GLN Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1165 SER Chi-restraints excluded: chain I residue 1182 ILE Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1198 LEU Chi-restraints excluded: chain I residue 1201 LEU Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain I residue 1210 ILE Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1247 SER Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1295 SER Chi-restraints excluded: chain I residue 1296 ASP Chi-restraints excluded: chain I residue 1322 SER Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 42 GLU Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 52 ARG Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 24 TYR Chi-restraints excluded: chain L residue 41 ILE Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 118 ASP Chi-restraints excluded: chain L residue 127 ILE Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 162 ILE Chi-restraints excluded: chain L residue 229 VAL Chi-restraints excluded: chain L residue 231 THR Chi-restraints excluded: chain L residue 235 ILE Chi-restraints excluded: chain L residue 255 VAL Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 273 MET Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 314 THR Chi-restraints excluded: chain L residue 330 LEU Chi-restraints excluded: chain L residue 337 VAL Chi-restraints excluded: chain L residue 338 HIS Chi-restraints excluded: chain L residue 366 SER Chi-restraints excluded: chain L residue 386 LEU Chi-restraints excluded: chain L residue 389 SER Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 405 ILE Chi-restraints excluded: chain L residue 439 ILE Chi-restraints excluded: chain L residue 442 SER Chi-restraints excluded: chain L residue 454 VAL Chi-restraints excluded: chain L residue 467 SER Chi-restraints excluded: chain L residue 494 ILE Chi-restraints excluded: chain L residue 498 LEU Chi-restraints excluded: chain L residue 511 ILE Chi-restraints excluded: chain L residue 517 SER Chi-restraints excluded: chain L residue 519 LEU Chi-restraints excluded: chain L residue 530 LEU Chi-restraints excluded: chain L residue 547 VAL Chi-restraints excluded: chain L residue 559 LEU Chi-restraints excluded: chain L residue 587 ILE Chi-restraints excluded: chain M residue 262 LEU Chi-restraints excluded: chain M residue 285 THR Chi-restraints excluded: chain M residue 289 LEU Chi-restraints excluded: chain M residue 297 LYS Chi-restraints excluded: chain M residue 306 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 30.0000 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 80 HIS J 450 HIS J 477 GLN ** J 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 680 ASN ** J 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 777 HIS ** J 962 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1218 HIS J1227 HIS ** J1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1249 ASN ** J1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1366 HIS N 71 HIS G 23 HIS G 132 HIS H 37 HIS I 31 GLN I 276 GLN I 330 HIS I 357 ASN ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 618 GLN ** I 798 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 799 ASN I 811 ASN I 834 GLN I1116 HIS I1134 GLN I1136 GLN I1209 GLN I1237 HIS I1264 GLN I1314 GLN K 29 GLN K 61 ASN L 323 ASN ** L 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 406 GLN L 409 ASN L 446 GLN L 518 HIS M 268 ASN M 283 GLN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.155280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.114941 restraints weight = 50562.958| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 2.05 r_work: 0.3126 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 33487 Z= 0.191 Angle : 0.808 25.950 45680 Z= 0.414 Chirality : 0.049 0.253 5240 Planarity : 0.005 0.070 5595 Dihedral : 19.149 151.067 6259 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.89 % Favored : 91.98 % Rotamer: Outliers : 8.48 % Allowed : 24.58 % Favored : 66.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.25 % Cis-general : 0.21 % Twisted Proline : 1.30 % 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: -3.12 (0.12), residues: 3876 helix: -1.05 (0.12), residues: 1566 sheet: -2.96 (0.22), residues: 408 loop : -2.79 (0.13), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 486 TYR 0.020 0.002 TYR G 177 PHE 0.018 0.002 PHE I 906 TRP 0.012 0.001 TRP I 807 HIS 0.010 0.001 HIS I 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.19 (33475) covalent geometry : angle 0.78463 / 0.41 (45662) hydrogen bonds : bond 0.05680 / 3.72 ( 1392) hydrogen bonds : angle 5.39483 / 3.73 ( 3833) metal coordination : bond 0.01555 / 0.83 ( 12) metal coordination : angle 9.85096 / 6.03 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7752 Ramachandran restraints generated. 3876 Oldfield, 0 Emsley, 3876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7752 Ramachandran restraints generated. 3876 Oldfield, 0 Emsley, 3876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 707 residues out of total 3346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 282 poor density : 425 time to evaluate : 1.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 69 GLU cc_start: 0.8533 (tt0) cc_final: 0.7737 (mt-10) REVERT: J 77 ARG cc_start: 0.7526 (mpp-170) cc_final: 0.7168 (mtp85) REVERT: J 133 ARG cc_start: 0.7524 (tpt170) cc_final: 0.7222 (tpp-160) REVERT: J 137 ARG cc_start: 0.7860 (mtp180) cc_final: 0.7168 (mtt90) REVERT: J 290 ILE cc_start: 0.7661 (OUTLIER) cc_final: 0.7451 (mt) REVERT: J 306 LEU cc_start: 0.9441 (OUTLIER) cc_final: 0.9126 (tp) REVERT: J 375 GLU cc_start: 0.8702 (tp30) cc_final: 0.8190 (tp30) REVERT: J 610 ARG cc_start: 0.8291 (mmt-90) cc_final: 0.8023 (ptt90) REVERT: J 625 MET cc_start: 0.9242 (ttp) cc_final: 0.8938 (ttp) REVERT: J 1081 VAL cc_start: 0.1062 (OUTLIER) cc_final: 0.0640 (t) REVERT: J 1134 ILE cc_start: 0.7931 (OUTLIER) cc_final: 0.7704 (pt) REVERT: J 1194 ARG cc_start: 0.5486 (mpt180) cc_final: 0.4449 (mmm-85) REVERT: J 1239 ASP cc_start: 0.8263 (p0) cc_final: 0.8026 (t0) REVERT: J 1266 ILE cc_start: 0.7135 (OUTLIER) cc_final: 0.6896 (mm) REVERT: J 1310 THR cc_start: 0.9261 (OUTLIER) cc_final: 0.9044 (m) REVERT: J 1311 LYS cc_start: 0.8854 (OUTLIER) cc_final: 0.8529 (mmtp) REVERT: J 1334 GLU cc_start: 0.8349 (tt0) cc_final: 0.7799 (tp30) REVERT: N 4 GLU cc_start: 0.8497 (mp0) cc_final: 0.8280 (mp0) REVERT: N 21 ASN cc_start: 0.8393 (OUTLIER) cc_final: 0.7856 (m-40) REVERT: N 48 ARG cc_start: 0.8816 (OUTLIER) cc_final: 0.8526 (tpt-90) REVERT: G 33 ARG cc_start: 0.7860 (OUTLIER) cc_final: 0.7395 (ttp-170) REVERT: G 215 GLU cc_start: 0.7542 (tp30) cc_final: 0.7338 (tp30) REVERT: G 231 PHE cc_start: 0.8470 (OUTLIER) cc_final: 0.7935 (t80) REVERT: H 195 ARG cc_start: 0.6261 (mtp180) cc_final: 0.5999 (mtp180) REVERT: I 11 ILE cc_start: 0.8693 (OUTLIER) cc_final: 0.8400 (tp) REVERT: I 200 ARG cc_start: 0.7159 (mmm160) cc_final: 0.6551 (ptt90) REVERT: I 240 GLU cc_start: 0.6793 (tm-30) cc_final: 0.6545 (tm-30) REVERT: I 278 GLU cc_start: 0.7283 (OUTLIER) cc_final: 0.6737 (mt-10) REVERT: I 304 GLU cc_start: 0.6900 (mm-30) cc_final: 0.6603 (pm20) REVERT: I 315 MET cc_start: 0.6154 (mmm) cc_final: 0.5851 (mmt) REVERT: I 503 LYS cc_start: 0.8777 (ttpp) cc_final: 0.8488 (ptmm) REVERT: I 514 PHE cc_start: 0.8613 (OUTLIER) cc_final: 0.8248 (m-10) REVERT: I 563 THR cc_start: 0.9018 (OUTLIER) cc_final: 0.8666 (p) REVERT: I 643 SER cc_start: 0.7911 (OUTLIER) cc_final: 0.7244 (m) REVERT: I 652 TYR cc_start: 0.8949 (m-80) cc_final: 0.8724 (m-80) REVERT: I 659 GLN cc_start: 0.9208 (OUTLIER) cc_final: 0.8882 (tt0) REVERT: I 800 MET cc_start: 0.8886 (OUTLIER) cc_final: 0.8439 (mtm) REVERT: I 892 GLU cc_start: 0.7089 (tt0) cc_final: 0.6301 (pm20) REVERT: I 919 ARG cc_start: 0.8851 (OUTLIER) cc_final: 0.8650 (mtt-85) REVERT: I 1016 GLU cc_start: 0.7105 (tm-30) cc_final: 0.6790 (tm-30) REVERT: I 1041 ASP cc_start: 0.8171 (OUTLIER) cc_final: 0.7796 (m-30) REVERT: I 1106 ARG cc_start: 0.7477 (OUTLIER) cc_final: 0.7038 (mtt180) REVERT: I 1253 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.8907 (tp) REVERT: K 30 MET cc_start: 0.8980 (mtm) cc_final: 0.8647 (mtp) REVERT: K 42 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.6356 (pp20) REVERT: K 74 GLU cc_start: 0.6435 (mt-10) cc_final: 0.6169 (mt-10) REVERT: L 144 LEU cc_start: 0.4949 (OUTLIER) cc_final: 0.4650 (pp) REVERT: L 273 MET cc_start: 0.3748 (OUTLIER) cc_final: 0.2725 (tpp) REVERT: L 392 LYS cc_start: 0.8543 (mtmt) cc_final: 0.8290 (tttm) REVERT: L 561 MET cc_start: 0.8709 (ttm) cc_final: 0.8456 (mtp) REVERT: M 300 LEU cc_start: 0.5498 (OUTLIER) cc_final: 0.5233 (tp) REVERT: M 316 MET cc_start: 0.4043 (mmt) cc_final: 0.2590 (tmm) outliers start: 282 outliers final: 160 residues processed: 666 average time/residue: 0.2193 time to fit residues: 234.6886 Evaluate side-chains 550 residues out of total 3346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 186 poor density : 364 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 56 LEU Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 76 LYS Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 152 THR Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 199 GLU Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 212 THR Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 290 ILE Chi-restraints excluded: chain J residue 292 VAL Chi-restraints excluded: chain J residue 306 LEU Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 326 SER Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 442 ILE Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 489 ASN Chi-restraints excluded: chain J residue 492 SER Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 567 THR Chi-restraints excluded: chain J residue 601 ILE Chi-restraints excluded: chain J residue 698 MET Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 762 ASN Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 770 LEU Chi-restraints excluded: chain J residue 783 LEU Chi-restraints excluded: chain J residue 796 LEU Chi-restraints excluded: chain J residue 797 THR Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 835 LEU Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 903 LEU Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 928 THR Chi-restraints excluded: chain J residue 931 THR Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 1028 ILE Chi-restraints excluded: chain J residue 1081 VAL Chi-restraints excluded: chain J residue 1134 ILE Chi-restraints excluded: chain J residue 1135 THR Chi-restraints excluded: chain J residue 1148 ARG Chi-restraints excluded: chain J residue 1155 ILE Chi-restraints excluded: chain J residue 1181 ASP Chi-restraints excluded: chain J residue 1196 LEU Chi-restraints excluded: chain J residue 1198 VAL Chi-restraints excluded: chain J residue 1223 LEU Chi-restraints excluded: chain J residue 1249 ASN Chi-restraints excluded: chain J residue 1257 VAL Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1262 ARG Chi-restraints excluded: chain J residue 1266 ILE Chi-restraints excluded: chain J residue 1273 ASP Chi-restraints excluded: chain J residue 1301 THR Chi-restraints excluded: chain J residue 1307 LEU Chi-restraints excluded: chain J residue 1310 THR Chi-restraints excluded: chain J residue 1311 LYS Chi-restraints excluded: chain J residue 1332 LEU Chi-restraints excluded: chain J residue 1342 ASP Chi-restraints excluded: chain N residue 21 ASN Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 48 ARG Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 33 ARG Chi-restraints excluded: chain G residue 75 GLN Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 117 HIS Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain H residue 139 SER Chi-restraints excluded: chain H residue 141 SER Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 37 LYS Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 105 TYR Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 117 ILE Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain I residue 220 ILE Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 278 GLU Chi-restraints excluded: chain I residue 284 LEU Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 296 VAL Chi-restraints excluded: chain I residue 319 LEU Chi-restraints excluded: chain I residue 349 GLU Chi-restraints excluded: chain I residue 419 ILE Chi-restraints excluded: chain I residue 426 ILE Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 490 GLN Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 521 LEU Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 573 ASN Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 604 HIS Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 633 LEU Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 643 SER Chi-restraints excluded: chain I residue 659 GLN Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 699 LEU Chi-restraints excluded: chain I residue 750 ILE Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 839 VAL Chi-restraints excluded: chain I residue 913 VAL Chi-restraints excluded: chain I residue 919 ARG Chi-restraints excluded: chain I residue 939 VAL Chi-restraints excluded: chain I residue 973 SER Chi-restraints excluded: chain I residue 1003 THR Chi-restraints excluded: chain I residue 1014 LEU Chi-restraints excluded: chain I residue 1041 ASP Chi-restraints excluded: chain I residue 1073 LYS Chi-restraints excluded: chain I residue 1083 GLU Chi-restraints excluded: chain I residue 1092 THR Chi-restraints excluded: chain I residue 1106 ARG Chi-restraints excluded: chain I residue 1135 GLN Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1198 LEU Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1296 ASP Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 42 GLU Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 96 ASP Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 148 TYR Chi-restraints excluded: chain L residue 231 THR Chi-restraints excluded: chain L residue 235 ILE Chi-restraints excluded: chain L residue 246 GLN Chi-restraints excluded: chain L residue 255 VAL Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 273 MET Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 330 LEU Chi-restraints excluded: chain L residue 386 LEU Chi-restraints excluded: chain L residue 388 ILE Chi-restraints excluded: chain L residue 389 SER Chi-restraints excluded: chain L residue 405 ILE Chi-restraints excluded: chain L residue 429 THR Chi-restraints excluded: chain L residue 547 VAL Chi-restraints excluded: chain L residue 587 ILE Chi-restraints excluded: chain M residue 262 LEU Chi-restraints excluded: chain M residue 268 ASN Chi-restraints excluded: chain M residue 289 LEU Chi-restraints excluded: chain M residue 300 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 305 optimal weight: 0.0670 chunk 240 optimal weight: 4.9990 chunk 129 optimal weight: 0.6980 chunk 333 optimal weight: 10.0000 chunk 116 optimal weight: 8.9990 chunk 302 optimal weight: 0.0980 chunk 275 optimal weight: 3.9990 chunk 183 optimal weight: 4.9990 chunk 197 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 96 optimal weight: 9.9990 overall best weight: 0.5520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 45 ASN J 320 ASN ** J 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 962 ASN ** J1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 46 GLN I 766 ASN ** I 798 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 811 ASN I1314 GLN ** L 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.160042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.122239 restraints weight = 50196.411| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 2.21 r_work: 0.3196 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 33487 Z= 0.139 Angle : 0.702 16.189 45680 Z= 0.366 Chirality : 0.045 0.241 5240 Planarity : 0.005 0.078 5595 Dihedral : 18.333 152.953 5916 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.91 % Favored : 92.96 % Rotamer: Outliers : 7.13 % Allowed : 24.97 % Favored : 67.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.25 % Cis-general : 0.21 % Twisted Proline : 0.65 % 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: -2.39 (0.13), residues: 3876 helix: -0.37 (0.12), residues: 1580 sheet: -2.62 (0.22), residues: 413 loop : -2.43 (0.13), residues: 1883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 841 TYR 0.017 0.001 TYR J 589 PHE 0.021 0.002 PHE I 972 TRP 0.009 0.001 TRP I 807 HIS 0.006 0.001 HIS I 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 (33475) covalent geometry : angle 0.69417 / 0.37 (45662) hydrogen bonds : bond 0.04892 / 3.20 ( 1392) hydrogen bonds : angle 4.94634 / 3.43 ( 3833) metal coordination : bond 0.00786 / 0.41 ( 12) metal coordination : angle 5.30154 / 3.14 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7752 Ramachandran restraints generated. 3876 Oldfield, 0 Emsley, 3876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7752 Ramachandran restraints generated. 3876 Oldfield, 0 Emsley, 3876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 659 residues out of total 3346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 237 poor density : 422 time to evaluate : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 69 GLU cc_start: 0.8542 (tt0) cc_final: 0.7648 (mt-10) REVERT: J 77 ARG cc_start: 0.7618 (mpp-170) cc_final: 0.7295 (mtp85) REVERT: J 133 ARG cc_start: 0.7530 (tpt170) cc_final: 0.7249 (tpp-160) REVERT: J 137 ARG cc_start: 0.7864 (mtp180) cc_final: 0.7185 (mtt90) REVERT: J 375 GLU cc_start: 0.8762 (tp30) cc_final: 0.8256 (tp30) REVERT: J 625 MET cc_start: 0.9231 (ttp) cc_final: 0.8863 (ttp) REVERT: J 1095 MET cc_start: 0.2362 (ttp) cc_final: 0.1145 (ttp) REVERT: J 1135 THR cc_start: 0.8067 (OUTLIER) cc_final: 0.7848 (m) REVERT: J 1187 GLU cc_start: 0.5880 (OUTLIER) cc_final: 0.5428 (mm-30) REVERT: J 1188 GLU cc_start: 0.6758 (tm-30) cc_final: 0.6492 (tp30) REVERT: J 1194 ARG cc_start: 0.5148 (mpt180) cc_final: 0.4272 (mmm-85) REVERT: J 1195 GLN cc_start: 0.6870 (OUTLIER) cc_final: 0.6482 (pp30) REVERT: J 1262 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.8120 (ptt180) REVERT: J 1266 ILE cc_start: 0.7125 (OUTLIER) cc_final: 0.6696 (mm) REVERT: J 1334 GLU cc_start: 0.8160 (tt0) cc_final: 0.7882 (tp30) REVERT: N 48 ARG cc_start: 0.8670 (OUTLIER) cc_final: 0.8339 (tpt-90) REVERT: G 93 GLN cc_start: 0.7677 (mp10) cc_final: 0.7435 (mp10) REVERT: G 158 ARG cc_start: 0.7628 (OUTLIER) cc_final: 0.6663 (ttm-80) REVERT: G 200 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7889 (ptmt) REVERT: G 231 PHE cc_start: 0.8323 (OUTLIER) cc_final: 0.7980 (t80) REVERT: H 195 ARG cc_start: 0.6265 (mtp180) cc_final: 0.5931 (mtp180) REVERT: H 206 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8474 (mt-10) REVERT: I 200 ARG cc_start: 0.7019 (mmm160) cc_final: 0.6443 (ptt90) REVERT: I 240 GLU cc_start: 0.6573 (tm-30) cc_final: 0.6281 (tm-30) REVERT: I 278 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.6829 (mt-10) REVERT: I 304 GLU cc_start: 0.6905 (mm-30) cc_final: 0.6603 (pm20) REVERT: I 315 MET cc_start: 0.6090 (mmm) cc_final: 0.5800 (mmt) REVERT: I 386 GLU cc_start: 0.7089 (mm-30) cc_final: 0.6832 (tp30) REVERT: I 514 PHE cc_start: 0.8504 (OUTLIER) cc_final: 0.8118 (m-10) REVERT: I 538 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8519 (pp) REVERT: I 563 THR cc_start: 0.8922 (OUTLIER) cc_final: 0.8588 (p) REVERT: I 652 TYR cc_start: 0.8961 (m-80) cc_final: 0.8745 (m-80) REVERT: I 800 MET cc_start: 0.8697 (OUTLIER) cc_final: 0.8309 (mtm) REVERT: I 892 GLU cc_start: 0.7063 (tt0) cc_final: 0.6257 (pm20) REVERT: I 919 ARG cc_start: 0.8854 (OUTLIER) cc_final: 0.8613 (mtt-85) REVERT: I 1016 GLU cc_start: 0.7080 (tm-30) cc_final: 0.6754 (tm-30) REVERT: I 1106 ARG cc_start: 0.7309 (OUTLIER) cc_final: 0.6806 (mtt180) REVERT: I 1198 LEU cc_start: 0.9399 (OUTLIER) cc_final: 0.9165 (mt) REVERT: I 1253 LEU cc_start: 0.9281 (OUTLIER) cc_final: 0.8841 (tp) REVERT: K 30 MET cc_start: 0.8756 (mtm) cc_final: 0.8493 (mtp) REVERT: K 42 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.6323 (pp20) REVERT: L 116 GLU cc_start: 0.7139 (mm-30) cc_final: 0.5949 (pt0) REVERT: L 118 ASP cc_start: 0.7135 (m-30) cc_final: 0.6322 (t0) REVERT: L 273 MET cc_start: 0.3275 (OUTLIER) cc_final: 0.2938 (tpp) REVERT: L 277 MET cc_start: 0.4638 (OUTLIER) cc_final: 0.3717 (mmt) REVERT: L 379 MET cc_start: 0.8567 (mmm) cc_final: 0.8276 (tpp) REVERT: L 417 ASP cc_start: 0.7531 (m-30) cc_final: 0.7162 (m-30) REVERT: L 474 MET cc_start: 0.7329 (tmm) cc_final: 0.6460 (tmm) REVERT: L 545 HIS cc_start: 0.7798 (t70) cc_final: 0.7529 (t-90) REVERT: M 300 LEU cc_start: 0.5797 (OUTLIER) cc_final: 0.5517 (tp) REVERT: M 316 MET cc_start: 0.4140 (mmt) cc_final: 0.2812 (tmm) outliers start: 237 outliers final: 131 residues processed: 621 average time/residue: 0.2164 time to fit residues: 217.3664 Evaluate side-chains 520 residues out of total 3346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 366 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 56 LEU Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 76 LYS Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 199 GLU Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 292 VAL Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 363 LEU Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 442 ILE Chi-restraints excluded: chain J residue 489 ASN Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 508 LEU Chi-restraints excluded: chain J residue 513 MET Chi-restraints excluded: chain J residue 517 CYS Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 667 GLN Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 722 ILE Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 762 ASN Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 770 LEU Chi-restraints excluded: chain J residue 783 LEU Chi-restraints excluded: chain J residue 796 LEU Chi-restraints excluded: chain J residue 797 THR Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 903 LEU Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 928 THR Chi-restraints excluded: chain J residue 991 THR Chi-restraints excluded: chain J residue 1028 ILE Chi-restraints excluded: chain J residue 1135 THR Chi-restraints excluded: chain J residue 1148 ARG Chi-restraints excluded: chain J residue 1160 SER Chi-restraints excluded: chain J residue 1180 VAL Chi-restraints excluded: chain J residue 1181 ASP Chi-restraints excluded: chain J residue 1187 GLU Chi-restraints excluded: chain J residue 1195 GLN Chi-restraints excluded: chain J residue 1196 LEU Chi-restraints excluded: chain J residue 1257 VAL Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1262 ARG Chi-restraints excluded: chain J residue 1266 ILE Chi-restraints excluded: chain J residue 1273 ASP Chi-restraints excluded: chain J residue 1301 THR Chi-restraints excluded: chain J residue 1307 LEU Chi-restraints excluded: chain J residue 1332 LEU Chi-restraints excluded: chain J residue 1342 ASP Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 48 ARG Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 117 HIS Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 158 ARG Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 200 LYS Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 139 SER Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 206 GLU Chi-restraints excluded: chain I residue 37 LYS Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 117 ILE Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain I residue 203 LYS Chi-restraints excluded: chain I residue 278 GLU Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain I residue 292 ILE Chi-restraints excluded: chain I residue 319 LEU Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 490 GLN Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 521 LEU Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 573 ASN Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 594 VAL Chi-restraints excluded: chain I residue 602 GLU Chi-restraints excluded: chain I residue 606 LEU Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 633 LEU Chi-restraints excluded: chain I residue 699 LEU Chi-restraints excluded: chain I residue 750 ILE Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 768 MET Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 811 ASN Chi-restraints excluded: chain I residue 913 VAL Chi-restraints excluded: chain I residue 919 ARG Chi-restraints excluded: chain I residue 939 VAL Chi-restraints excluded: chain I residue 973 SER Chi-restraints excluded: chain I residue 1014 LEU Chi-restraints excluded: chain I residue 1083 GLU Chi-restraints excluded: chain I residue 1092 THR Chi-restraints excluded: chain I residue 1096 ILE Chi-restraints excluded: chain I residue 1106 ARG Chi-restraints excluded: chain I residue 1135 GLN Chi-restraints excluded: chain I residue 1162 SER Chi-restraints excluded: chain I residue 1198 LEU Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1296 ASP Chi-restraints excluded: chain I residue 1315 MET Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 42 GLU Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 96 ASP Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 231 THR Chi-restraints excluded: chain L residue 246 GLN Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 273 MET Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 277 MET Chi-restraints excluded: chain L residue 386 LEU Chi-restraints excluded: chain L residue 389 SER Chi-restraints excluded: chain L residue 511 ILE Chi-restraints excluded: chain M residue 262 LEU Chi-restraints excluded: chain M residue 268 ASN Chi-restraints excluded: chain M residue 289 LEU Chi-restraints excluded: chain M residue 300 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 315 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 245 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 48 optimal weight: 4.9990 chunk 15 optimal weight: 9.9990 chunk 203 optimal weight: 5.9990 chunk 103 optimal weight: 6.9990 chunk 269 optimal weight: 9.9990 chunk 350 optimal weight: 9.9990 chunk 372 optimal weight: 7.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 320 ASN J 495 ASN J 951 GLN ** J1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1249 ASN ** J1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 21 ASN ** I 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 766 ASN I 811 ASN ** L 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.157381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.119700 restraints weight = 50487.568| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.38 r_work: 0.3124 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 33487 Z= 0.232 Angle : 0.738 13.943 45680 Z= 0.380 Chirality : 0.047 0.251 5240 Planarity : 0.005 0.066 5595 Dihedral : 18.084 154.589 5832 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.30 % Favored : 92.57 % Rotamer: Outliers : 7.40 % Allowed : 25.18 % Favored : 67.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.25 % Cis-general : 0.21 % 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: -2.24 (0.13), residues: 3876 helix: -0.28 (0.12), residues: 1598 sheet: -2.36 (0.23), residues: 420 loop : -2.38 (0.13), residues: 1858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 170 TYR 0.021 0.002 TYR I 105 PHE 0.017 0.002 PHE J 620 TRP 0.010 0.001 TRP I 807 HIS 0.006 0.001 HIS J 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00542 / 0.23 (33475) covalent geometry : angle 0.73239 / 0.38 (45662) hydrogen bonds : bond 0.05080 / 3.31 ( 1392) hydrogen bonds : angle 4.87320 / 3.37 ( 3833) metal coordination : bond 0.01174 / 0.61 ( 12) metal coordination : angle 4.49517 / 2.60 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7752 Ramachandran restraints generated. 3876 Oldfield, 0 Emsley, 3876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7752 Ramachandran restraints generated. 3876 Oldfield, 0 Emsley, 3876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 605 residues out of total 3346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 246 poor density : 359 time to evaluate : 1.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 69 GLU cc_start: 0.8406 (tt0) cc_final: 0.7652 (mt-10) REVERT: J 133 ARG cc_start: 0.7533 (tpt170) cc_final: 0.7272 (tpp-160) REVERT: J 137 ARG cc_start: 0.7630 (mtp180) cc_final: 0.7183 (mtt90) REVERT: J 306 LEU cc_start: 0.9452 (OUTLIER) cc_final: 0.9211 (tp) REVERT: J 375 GLU cc_start: 0.8530 (tp30) cc_final: 0.8025 (tp30) REVERT: J 557 LYS cc_start: 0.7455 (ptmt) cc_final: 0.6783 (pttt) REVERT: J 625 MET cc_start: 0.9094 (ttp) cc_final: 0.8740 (ttp) REVERT: J 796 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8767 (tm) REVERT: J 985 ILE cc_start: 0.4231 (OUTLIER) cc_final: 0.3809 (tt) REVERT: J 1095 MET cc_start: 0.2750 (ttp) cc_final: 0.1657 (tpp) REVERT: J 1194 ARG cc_start: 0.5146 (mpt180) cc_final: 0.4252 (mmm-85) REVERT: J 1258 ARG cc_start: 0.8888 (OUTLIER) cc_final: 0.8623 (ttt180) REVERT: J 1266 ILE cc_start: 0.7078 (OUTLIER) cc_final: 0.6684 (mm) REVERT: J 1311 LYS cc_start: 0.8777 (OUTLIER) cc_final: 0.8518 (mmtp) REVERT: J 1334 GLU cc_start: 0.8105 (tt0) cc_final: 0.7786 (tp30) REVERT: N 48 ARG cc_start: 0.8711 (OUTLIER) cc_final: 0.8446 (tpt-90) REVERT: G 93 GLN cc_start: 0.7677 (mp10) cc_final: 0.7363 (mp10) REVERT: G 158 ARG cc_start: 0.7752 (OUTLIER) cc_final: 0.6532 (ttm-80) REVERT: G 200 LYS cc_start: 0.8115 (OUTLIER) cc_final: 0.7799 (ptmt) REVERT: G 231 PHE cc_start: 0.8336 (OUTLIER) cc_final: 0.7935 (t80) REVERT: H 206 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.8361 (mt-10) REVERT: I 200 ARG cc_start: 0.7051 (mmm160) cc_final: 0.6487 (ptt90) REVERT: I 240 GLU cc_start: 0.6584 (tm-30) cc_final: 0.6241 (tm-30) REVERT: I 278 GLU cc_start: 0.7453 (OUTLIER) cc_final: 0.6791 (mt-10) REVERT: I 315 MET cc_start: 0.6057 (mmm) cc_final: 0.5734 (mmt) REVERT: I 330 HIS cc_start: 0.5699 (m90) cc_final: 0.5483 (m170) REVERT: I 386 GLU cc_start: 0.7252 (mm-30) cc_final: 0.6852 (tp30) REVERT: I 412 GLU cc_start: 0.6315 (OUTLIER) cc_final: 0.6096 (tp30) REVERT: I 514 PHE cc_start: 0.8517 (OUTLIER) cc_final: 0.8062 (m-10) REVERT: I 557 ARG cc_start: 0.9269 (OUTLIER) cc_final: 0.8417 (mtt90) REVERT: I 637 ARG cc_start: 0.8639 (OUTLIER) cc_final: 0.8218 (ptt-90) REVERT: I 659 GLN cc_start: 0.9220 (OUTLIER) cc_final: 0.8807 (tt0) REVERT: I 826 ASP cc_start: 0.8503 (OUTLIER) cc_final: 0.8082 (t0) REVERT: I 1016 GLU cc_start: 0.7199 (tm-30) cc_final: 0.6853 (tm-30) REVERT: I 1041 ASP cc_start: 0.8095 (OUTLIER) cc_final: 0.7721 (m-30) REVERT: I 1188 ASP cc_start: 0.8094 (t0) cc_final: 0.7885 (t0) REVERT: I 1253 LEU cc_start: 0.9309 (OUTLIER) cc_final: 0.8912 (tp) REVERT: K 42 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.6412 (pp20) REVERT: L 116 GLU cc_start: 0.7034 (mm-30) cc_final: 0.6264 (pt0) REVERT: L 273 MET cc_start: 0.3305 (OUTLIER) cc_final: 0.2374 (tpp) REVERT: L 277 MET cc_start: 0.4663 (OUTLIER) cc_final: 0.3794 (ptp) REVERT: L 474 MET cc_start: 0.7465 (tmm) cc_final: 0.6845 (tmm) REVERT: L 545 HIS cc_start: 0.7650 (t70) cc_final: 0.7360 (t-90) REVERT: M 297 LYS cc_start: 0.5751 (OUTLIER) cc_final: 0.5548 (pptt) REVERT: M 300 LEU cc_start: 0.5219 (OUTLIER) cc_final: 0.4968 (tp) outliers start: 246 outliers final: 165 residues processed: 564 average time/residue: 0.2188 time to fit residues: 200.2673 Evaluate side-chains 533 residues out of total 3346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 190 poor density : 343 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 56 LEU Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 76 LYS Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 199 GLU Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 292 VAL Chi-restraints excluded: chain J residue 306 LEU Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 363 LEU Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 442 ILE Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 489 ASN Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 508 LEU Chi-restraints excluded: chain J residue 513 MET Chi-restraints excluded: chain J residue 517 CYS Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 567 THR Chi-restraints excluded: chain J residue 571 ASP Chi-restraints excluded: chain J residue 667 GLN Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 722 ILE Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 762 ASN Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 770 LEU Chi-restraints excluded: chain J residue 783 LEU Chi-restraints excluded: chain J residue 786 THR Chi-restraints excluded: chain J residue 796 LEU Chi-restraints excluded: chain J residue 797 THR Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 835 LEU Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 869 CYS Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 903 LEU Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 928 THR Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 985 ILE Chi-restraints excluded: chain J residue 991 THR Chi-restraints excluded: chain J residue 1028 ILE Chi-restraints excluded: chain J residue 1045 THR Chi-restraints excluded: chain J residue 1054 THR Chi-restraints excluded: chain J residue 1135 THR Chi-restraints excluded: chain J residue 1160 SER Chi-restraints excluded: chain J residue 1180 VAL Chi-restraints excluded: chain J residue 1181 ASP Chi-restraints excluded: chain J residue 1196 LEU Chi-restraints excluded: chain J residue 1257 VAL Chi-restraints excluded: chain J residue 1258 ARG Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1262 ARG Chi-restraints excluded: chain J residue 1266 ILE Chi-restraints excluded: chain J residue 1301 THR Chi-restraints excluded: chain J residue 1307 LEU Chi-restraints excluded: chain J residue 1311 LYS Chi-restraints excluded: chain J residue 1332 LEU Chi-restraints excluded: chain J residue 1342 ASP Chi-restraints excluded: chain N residue 10 SER Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 48 ARG Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 29 GLU Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 117 HIS Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 158 ARG Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 200 LYS Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 139 SER Chi-restraints excluded: chain H residue 141 SER Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 206 GLU Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 37 LYS Chi-restraints excluded: chain I residue 105 TYR Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 117 ILE Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain I residue 203 LYS Chi-restraints excluded: chain I residue 278 GLU Chi-restraints excluded: chain I residue 284 LEU Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain I residue 297 VAL Chi-restraints excluded: chain I residue 319 LEU Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 412 GLU Chi-restraints excluded: chain I residue 426 ILE Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 475 VAL Chi-restraints excluded: chain I residue 490 GLN Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 521 LEU Chi-restraints excluded: chain I residue 557 ARG Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 573 ASN Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 594 VAL Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 606 LEU Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 633 LEU Chi-restraints excluded: chain I residue 637 ARG Chi-restraints excluded: chain I residue 659 GLN Chi-restraints excluded: chain I residue 699 LEU Chi-restraints excluded: chain I residue 717 VAL Chi-restraints excluded: chain I residue 750 ILE Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 768 MET Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 826 ASP Chi-restraints excluded: chain I residue 839 VAL Chi-restraints excluded: chain I residue 843 THR Chi-restraints excluded: chain I residue 913 VAL Chi-restraints excluded: chain I residue 939 VAL Chi-restraints excluded: chain I residue 960 LEU Chi-restraints excluded: chain I residue 1014 LEU Chi-restraints excluded: chain I residue 1041 ASP Chi-restraints excluded: chain I residue 1083 GLU Chi-restraints excluded: chain I residue 1092 THR Chi-restraints excluded: chain I residue 1135 GLN Chi-restraints excluded: chain I residue 1167 GLU Chi-restraints excluded: chain I residue 1198 LEU Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1296 ASP Chi-restraints excluded: chain I residue 1315 MET Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 42 GLU Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 96 ASP Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 231 THR Chi-restraints excluded: chain L residue 235 ILE Chi-restraints excluded: chain L residue 246 GLN Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 273 MET Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 277 MET Chi-restraints excluded: chain L residue 337 VAL Chi-restraints excluded: chain L residue 358 VAL Chi-restraints excluded: chain L residue 386 LEU Chi-restraints excluded: chain L residue 389 SER Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain M residue 262 LEU Chi-restraints excluded: chain M residue 263 THR Chi-restraints excluded: chain M residue 297 LYS Chi-restraints excluded: chain M residue 300 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 33 optimal weight: 0.9990 chunk 107 optimal weight: 0.8980 chunk 118 optimal weight: 7.9990 chunk 138 optimal weight: 0.9980 chunk 237 optimal weight: 0.7980 chunk 179 optimal weight: 0.9990 chunk 351 optimal weight: 9.9990 chunk 132 optimal weight: 0.0010 chunk 39 optimal weight: 0.2980 chunk 80 optimal weight: 9.9990 chunk 8 optimal weight: 5.9990 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 294 ASN J 320 ASN ** J1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1249 ASN ** J1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 21 ASN I 811 ASN I 894 GLN I1264 GLN L 28 ASN ** L 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 406 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.161064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.123686 restraints weight = 50337.597| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 2.30 r_work: 0.3192 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 33487 Z= 0.129 Angle : 0.658 9.809 45680 Z= 0.343 Chirality : 0.044 0.244 5240 Planarity : 0.004 0.065 5595 Dihedral : 17.811 155.017 5814 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.35 % Favored : 93.52 % Rotamer: Outliers : 6.77 % Allowed : 25.54 % Favored : 67.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.25 % Cis-general : 0.21 % 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: -1.84 (0.13), residues: 3876 helix: 0.07 (0.13), residues: 1609 sheet: -2.22 (0.22), residues: 455 loop : -2.15 (0.14), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG I 478 TYR 0.028 0.001 TYR L 143 PHE 0.015 0.001 PHE I1323 TRP 0.014 0.001 TRP L 434 HIS 0.006 0.001 HIS G 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 (33475) covalent geometry : angle 0.65530 / 0.34 (45662) hydrogen bonds : bond 0.04483 / 2.94 ( 1392) hydrogen bonds : angle 4.62804 / 3.21 ( 3833) metal coordination : bond 0.00502 / 0.27 ( 12) metal coordination : angle 3.15896 / 1.78 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7752 Ramachandran restraints generated. 3876 Oldfield, 0 Emsley, 3876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7752 Ramachandran restraints generated. 3876 Oldfield, 0 Emsley, 3876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 627 residues out of total 3346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 225 poor density : 402 time to evaluate : 1.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 69 GLU cc_start: 0.8203 (tt0) cc_final: 0.7586 (mt-10) REVERT: J 133 ARG cc_start: 0.7499 (tpt170) cc_final: 0.7226 (tpp-160) REVERT: J 137 ARG cc_start: 0.7471 (mtp180) cc_final: 0.7208 (ttm-80) REVERT: J 169 LEU cc_start: 0.7725 (tt) cc_final: 0.7450 (tt) REVERT: J 192 MET cc_start: 0.7973 (OUTLIER) cc_final: 0.7656 (ppp) REVERT: J 290 ILE cc_start: 0.7412 (mt) cc_final: 0.7191 (mt) REVERT: J 375 GLU cc_start: 0.8409 (tp30) cc_final: 0.7906 (tp30) REVERT: J 532 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7710 (tt0) REVERT: J 625 MET cc_start: 0.9061 (ttp) cc_final: 0.8685 (ttp) REVERT: J 667 GLN cc_start: 0.8551 (OUTLIER) cc_final: 0.8190 (tt0) REVERT: J 796 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8708 (tm) REVERT: J 985 ILE cc_start: 0.4257 (OUTLIER) cc_final: 0.3795 (tt) REVERT: J 1095 MET cc_start: 0.2097 (ttp) cc_final: 0.1645 (tpp) REVERT: J 1101 LEU cc_start: 0.5190 (OUTLIER) cc_final: 0.4935 (mt) REVERT: J 1187 GLU cc_start: 0.5784 (OUTLIER) cc_final: 0.5383 (mm-30) REVERT: J 1188 GLU cc_start: 0.6760 (tm-30) cc_final: 0.6533 (tp30) REVERT: J 1194 ARG cc_start: 0.4959 (mpt180) cc_final: 0.4273 (mmm-85) REVERT: J 1195 GLN cc_start: 0.6876 (OUTLIER) cc_final: 0.6504 (pp30) REVERT: J 1258 ARG cc_start: 0.8851 (OUTLIER) cc_final: 0.8584 (ttt180) REVERT: J 1266 ILE cc_start: 0.7072 (OUTLIER) cc_final: 0.6695 (mm) REVERT: J 1334 GLU cc_start: 0.8081 (tt0) cc_final: 0.7723 (tp30) REVERT: J 1370 MET cc_start: 0.7710 (ttp) cc_final: 0.7498 (ttt) REVERT: N 21 ASN cc_start: 0.8309 (OUTLIER) cc_final: 0.7880 (m-40) REVERT: G 93 GLN cc_start: 0.7689 (mp10) cc_final: 0.7410 (mp10) REVERT: G 158 ARG cc_start: 0.7703 (OUTLIER) cc_final: 0.6656 (ttm-80) REVERT: G 231 PHE cc_start: 0.8196 (OUTLIER) cc_final: 0.7993 (t80) REVERT: H 206 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.8278 (mt-10) REVERT: I 200 ARG cc_start: 0.6928 (mmm160) cc_final: 0.6101 (ptt90) REVERT: I 240 GLU cc_start: 0.6501 (tm-30) cc_final: 0.6153 (tm-30) REVERT: I 241 LEU cc_start: 0.7870 (tp) cc_final: 0.7591 (tp) REVERT: I 278 GLU cc_start: 0.7302 (OUTLIER) cc_final: 0.6835 (mt-10) REVERT: I 315 MET cc_start: 0.6002 (mmm) cc_final: 0.5732 (mmt) REVERT: I 330 HIS cc_start: 0.5776 (m90) cc_final: 0.5538 (m170) REVERT: I 475 VAL cc_start: 0.7507 (t) cc_final: 0.7143 (t) REVERT: I 514 PHE cc_start: 0.8415 (OUTLIER) cc_final: 0.7972 (m-10) REVERT: I 521 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8921 (tp) REVERT: I 541 GLU cc_start: 0.6269 (OUTLIER) cc_final: 0.5876 (mp0) REVERT: I 572 ILE cc_start: 0.9270 (OUTLIER) cc_final: 0.8880 (mt) REVERT: I 637 ARG cc_start: 0.8339 (OUTLIER) cc_final: 0.7958 (ptt-90) REVERT: I 659 GLN cc_start: 0.9093 (OUTLIER) cc_final: 0.8856 (tt0) REVERT: I 826 ASP cc_start: 0.8394 (OUTLIER) cc_final: 0.8187 (t0) REVERT: I 922 ASN cc_start: 0.8097 (OUTLIER) cc_final: 0.7748 (m-40) REVERT: I 1016 GLU cc_start: 0.7174 (tm-30) cc_final: 0.6805 (tm-30) REVERT: I 1085 MET cc_start: 0.9069 (mmm) cc_final: 0.8534 (mmt) REVERT: I 1106 ARG cc_start: 0.7071 (OUTLIER) cc_final: 0.6659 (mtt180) REVERT: I 1188 ASP cc_start: 0.7878 (t0) cc_final: 0.7670 (t0) REVERT: I 1197 GLU cc_start: 0.7915 (tt0) cc_final: 0.7665 (mt-10) REVERT: K 42 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.6318 (pp20) REVERT: L 111 LEU cc_start: 0.6071 (OUTLIER) cc_final: 0.5563 (tt) REVERT: L 118 ASP cc_start: 0.6824 (m-30) cc_final: 0.6061 (t0) REVERT: L 277 MET cc_start: 0.4780 (OUTLIER) cc_final: 0.3846 (mmt) REVERT: L 379 MET cc_start: 0.8348 (mmm) cc_final: 0.7894 (tpp) REVERT: L 436 ARG cc_start: 0.7991 (ptp-110) cc_final: 0.7430 (ptp-110) REVERT: L 474 MET cc_start: 0.7386 (tmm) cc_final: 0.6904 (tmm) REVERT: L 545 HIS cc_start: 0.7923 (t70) cc_final: 0.7629 (t-90) outliers start: 225 outliers final: 129 residues processed: 594 average time/residue: 0.2089 time to fit residues: 202.4995 Evaluate side-chains 521 residues out of total 3346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 365 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 56 LEU Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 76 LYS Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 199 GLU Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 292 VAL Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 442 ILE Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 508 LEU Chi-restraints excluded: chain J residue 513 MET Chi-restraints excluded: chain J residue 517 CYS Chi-restraints excluded: chain J residue 532 GLU Chi-restraints excluded: chain J residue 543 SER Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 596 LEU Chi-restraints excluded: chain J residue 667 GLN Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 713 GLU Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 722 ILE Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 762 ASN Chi-restraints excluded: chain J residue 770 LEU Chi-restraints excluded: chain J residue 788 LEU Chi-restraints excluded: chain J residue 796 LEU Chi-restraints excluded: chain J residue 797 THR Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 835 LEU Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 903 LEU Chi-restraints excluded: chain J residue 928 THR Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 985 ILE Chi-restraints excluded: chain J residue 1054 THR Chi-restraints excluded: chain J residue 1098 GLN Chi-restraints excluded: chain J residue 1101 LEU Chi-restraints excluded: chain J residue 1180 VAL Chi-restraints excluded: chain J residue 1181 ASP Chi-restraints excluded: chain J residue 1187 GLU Chi-restraints excluded: chain J residue 1195 GLN Chi-restraints excluded: chain J residue 1196 LEU Chi-restraints excluded: chain J residue 1249 ASN Chi-restraints excluded: chain J residue 1258 ARG Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1266 ILE Chi-restraints excluded: chain J residue 1280 VAL Chi-restraints excluded: chain J residue 1332 LEU Chi-restraints excluded: chain J residue 1342 ASP Chi-restraints excluded: chain N residue 10 SER Chi-restraints excluded: chain N residue 15 LEU Chi-restraints excluded: chain N residue 21 ASN Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain G residue 29 GLU Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 117 HIS Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 158 ARG Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 139 SER Chi-restraints excluded: chain H residue 141 SER Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 206 GLU Chi-restraints excluded: chain I residue 37 LYS Chi-restraints excluded: chain I residue 105 TYR Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 117 ILE Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain I residue 147 SER Chi-restraints excluded: chain I residue 203 LYS Chi-restraints excluded: chain I residue 278 GLU Chi-restraints excluded: chain I residue 282 VAL Chi-restraints excluded: chain I residue 297 VAL Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 521 LEU Chi-restraints excluded: chain I residue 541 GLU Chi-restraints excluded: chain I residue 572 ILE Chi-restraints excluded: chain I residue 573 ASN Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 594 VAL Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 602 GLU Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 633 LEU Chi-restraints excluded: chain I residue 637 ARG Chi-restraints excluded: chain I residue 659 GLN Chi-restraints excluded: chain I residue 699 LEU Chi-restraints excluded: chain I residue 750 ILE Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 768 MET Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 826 ASP Chi-restraints excluded: chain I residue 913 VAL Chi-restraints excluded: chain I residue 922 ASN Chi-restraints excluded: chain I residue 939 VAL Chi-restraints excluded: chain I residue 1014 LEU Chi-restraints excluded: chain I residue 1083 GLU Chi-restraints excluded: chain I residue 1092 THR Chi-restraints excluded: chain I residue 1106 ARG Chi-restraints excluded: chain I residue 1135 GLN Chi-restraints excluded: chain I residue 1162 SER Chi-restraints excluded: chain I residue 1167 GLU Chi-restraints excluded: chain I residue 1198 LEU Chi-restraints excluded: chain I residue 1247 SER Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1296 ASP Chi-restraints excluded: chain I residue 1315 MET Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 42 GLU Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 231 THR Chi-restraints excluded: chain L residue 235 ILE Chi-restraints excluded: chain L residue 246 GLN Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 277 MET Chi-restraints excluded: chain L residue 337 VAL Chi-restraints excluded: chain L residue 386 LEU Chi-restraints excluded: chain L residue 429 THR Chi-restraints excluded: chain L residue 537 THR Chi-restraints excluded: chain L residue 547 VAL Chi-restraints excluded: chain M residue 262 LEU Chi-restraints excluded: chain M residue 263 THR Chi-restraints excluded: chain M residue 289 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 324 optimal weight: 6.9990 chunk 85 optimal weight: 6.9990 chunk 136 optimal weight: 5.9990 chunk 307 optimal weight: 2.9990 chunk 352 optimal weight: 9.9990 chunk 237 optimal weight: 4.9990 chunk 163 optimal weight: 5.9990 chunk 332 optimal weight: 5.9990 chunk 241 optimal weight: 5.9990 chunk 150 optimal weight: 0.5980 chunk 387 optimal weight: 50.0000 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** J 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1010 GLN ** J1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 766 ASN I 811 ASN I 894 GLN I1017 GLN I1134 GLN L 28 ASN L 362 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.156009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.116797 restraints weight = 50068.510| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 2.06 r_work: 0.3130 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 33487 Z= 0.289 Angle : 0.757 10.605 45680 Z= 0.389 Chirality : 0.048 0.247 5240 Planarity : 0.005 0.061 5595 Dihedral : 17.753 156.511 5782 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.66 % Favored : 92.21 % Rotamer: Outliers : 7.46 % Allowed : 25.57 % Favored : 66.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.25 % Cis-general : 0.21 % 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: -1.97 (0.13), residues: 3876 helix: -0.07 (0.13), residues: 1603 sheet: -2.21 (0.22), residues: 457 loop : -2.20 (0.14), residues: 1816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 44 TYR 0.028 0.002 TYR L 143 PHE 0.022 0.002 PHE I 464 TRP 0.012 0.002 TRP I 807 HIS 0.008 0.002 HIS J 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00686 / 0.29 (33475) covalent geometry : angle 0.75303 / 0.39 (45662) hydrogen bonds : bond 0.05103 / 3.32 ( 1392) hydrogen bonds : angle 4.75941 / 3.30 ( 3833) metal coordination : bond 0.01196 / 0.64 ( 12) metal coordination : angle 3.72343 / 2.06 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7752 Ramachandran restraints generated. 3876 Oldfield, 0 Emsley, 3876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7752 Ramachandran restraints generated. 3876 Oldfield, 0 Emsley, 3876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 3346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 248 poor density : 352 time to evaluate : 1.100 Fit side-chains revert: symmetry clash REVERT: J 69 GLU cc_start: 0.8532 (tt0) cc_final: 0.7862 (mt-10) REVERT: J 133 ARG cc_start: 0.7712 (tpt170) cc_final: 0.7473 (tpp-160) REVERT: J 137 ARG cc_start: 0.7625 (mtp180) cc_final: 0.7263 (mtt90) REVERT: J 290 ILE cc_start: 0.7723 (mt) cc_final: 0.7476 (mt) REVERT: J 375 GLU cc_start: 0.8672 (tp30) cc_final: 0.8130 (tp30) REVERT: J 625 MET cc_start: 0.9171 (ttp) cc_final: 0.8859 (ttp) REVERT: J 796 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8914 (tm) REVERT: J 985 ILE cc_start: 0.4329 (OUTLIER) cc_final: 0.3739 (tt) REVERT: J 1095 MET cc_start: 0.2129 (ttp) cc_final: 0.1732 (ttm) REVERT: J 1194 ARG cc_start: 0.5076 (OUTLIER) cc_final: 0.4247 (mmm-85) REVERT: J 1258 ARG cc_start: 0.9028 (OUTLIER) cc_final: 0.8754 (ttt180) REVERT: J 1311 LYS cc_start: 0.8927 (OUTLIER) cc_final: 0.8593 (mmtp) REVERT: J 1334 GLU cc_start: 0.8302 (tt0) cc_final: 0.7964 (tp30) REVERT: G 93 GLN cc_start: 0.7909 (mp10) cc_final: 0.7686 (mp10) REVERT: G 231 PHE cc_start: 0.8324 (OUTLIER) cc_final: 0.7967 (t80) REVERT: H 206 GLU cc_start: 0.8802 (OUTLIER) cc_final: 0.8513 (mt-10) REVERT: I 124 MET cc_start: 0.7942 (mtp) cc_final: 0.7689 (mtm) REVERT: I 200 ARG cc_start: 0.7106 (mmm160) cc_final: 0.6256 (ptt90) REVERT: I 240 GLU cc_start: 0.6716 (tm-30) cc_final: 0.6381 (tm-30) REVERT: I 241 LEU cc_start: 0.8081 (tp) cc_final: 0.7654 (tp) REVERT: I 278 GLU cc_start: 0.7350 (OUTLIER) cc_final: 0.6806 (mt-10) REVERT: I 315 MET cc_start: 0.6056 (mmm) cc_final: 0.5772 (mmt) REVERT: I 330 HIS cc_start: 0.5846 (m90) cc_final: 0.5611 (m170) REVERT: I 412 GLU cc_start: 0.6536 (OUTLIER) cc_final: 0.6326 (tp30) REVERT: I 488 MET cc_start: 0.6330 (tpp) cc_final: 0.6104 (tpp) REVERT: I 492 MET cc_start: 0.6572 (pmm) cc_final: 0.5240 (pmm) REVERT: I 514 PHE cc_start: 0.8706 (OUTLIER) cc_final: 0.8167 (m-10) REVERT: I 541 GLU cc_start: 0.6361 (OUTLIER) cc_final: 0.5949 (mp0) REVERT: I 584 TYR cc_start: 0.8609 (m-80) cc_final: 0.8393 (m-80) REVERT: I 637 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.8265 (ptt-90) REVERT: I 826 ASP cc_start: 0.8761 (OUTLIER) cc_final: 0.8407 (t70) REVERT: I 1016 GLU cc_start: 0.7119 (tm-30) cc_final: 0.6741 (tm-30) REVERT: I 1041 ASP cc_start: 0.8346 (OUTLIER) cc_final: 0.7954 (m-30) REVERT: I 1073 LYS cc_start: 0.8716 (OUTLIER) cc_final: 0.8412 (ptpt) REVERT: I 1197 GLU cc_start: 0.8342 (tt0) cc_final: 0.8073 (mt-10) REVERT: I 1253 LEU cc_start: 0.9379 (OUTLIER) cc_final: 0.9075 (tp) REVERT: L 28 ASN cc_start: 0.8759 (OUTLIER) cc_final: 0.8338 (m110) REVERT: L 51 MET cc_start: 0.5287 (ptt) cc_final: 0.5007 (ptt) REVERT: L 116 GLU cc_start: 0.7106 (mm-30) cc_final: 0.6075 (pt0) REVERT: L 131 GLN cc_start: 0.5960 (mt0) cc_final: 0.5354 (tp40) REVERT: L 379 MET cc_start: 0.8491 (mmm) cc_final: 0.8188 (tpp) REVERT: L 434 TRP cc_start: 0.8428 (m100) cc_final: 0.8141 (m100) REVERT: L 474 MET cc_start: 0.7665 (tmm) cc_final: 0.7071 (tmm) REVERT: L 545 HIS cc_start: 0.7956 (t70) cc_final: 0.7709 (t-90) outliers start: 248 outliers final: 179 residues processed: 563 average time/residue: 0.2058 time to fit residues: 190.7806 Evaluate side-chains 542 residues out of total 3346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 196 poor density : 346 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 56 LEU Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 76 LYS Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 212 THR Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 292 VAL Chi-restraints excluded: chain J residue 363 LEU Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 442 ILE Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 489 ASN Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 508 LEU Chi-restraints excluded: chain J residue 513 MET Chi-restraints excluded: chain J residue 543 SER Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 569 LEU Chi-restraints excluded: chain J residue 571 ASP Chi-restraints excluded: chain J residue 596 LEU Chi-restraints excluded: chain J residue 667 GLN Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 722 ILE Chi-restraints excluded: chain J residue 762 ASN Chi-restraints excluded: chain J residue 770 LEU Chi-restraints excluded: chain J residue 786 THR Chi-restraints excluded: chain J residue 788 LEU Chi-restraints excluded: chain J residue 796 LEU Chi-restraints excluded: chain J residue 797 THR Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 835 LEU Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 869 CYS Chi-restraints excluded: chain J residue 903 LEU Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 928 THR Chi-restraints excluded: chain J residue 967 VAL Chi-restraints excluded: chain J residue 968 ASN Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 985 ILE Chi-restraints excluded: chain J residue 1054 THR Chi-restraints excluded: chain J residue 1078 LEU Chi-restraints excluded: chain J residue 1180 VAL Chi-restraints excluded: chain J residue 1181 ASP Chi-restraints excluded: chain J residue 1194 ARG Chi-restraints excluded: chain J residue 1196 LEU Chi-restraints excluded: chain J residue 1198 VAL Chi-restraints excluded: chain J residue 1258 ARG Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1266 ILE Chi-restraints excluded: chain J residue 1273 ASP Chi-restraints excluded: chain J residue 1280 VAL Chi-restraints excluded: chain J residue 1307 LEU Chi-restraints excluded: chain J residue 1311 LYS Chi-restraints excluded: chain J residue 1342 ASP Chi-restraints excluded: chain N residue 10 SER Chi-restraints excluded: chain N residue 15 LEU Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 75 GLN Chi-restraints excluded: chain G residue 117 HIS Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 139 SER Chi-restraints excluded: chain H residue 141 SER Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 203 ILE Chi-restraints excluded: chain H residue 206 GLU Chi-restraints excluded: chain I residue 37 LYS Chi-restraints excluded: chain I residue 105 TYR Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 117 ILE Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain I residue 147 SER Chi-restraints excluded: chain I residue 187 GLU Chi-restraints excluded: chain I residue 203 LYS Chi-restraints excluded: chain I residue 278 GLU Chi-restraints excluded: chain I residue 282 VAL Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain I residue 296 VAL Chi-restraints excluded: chain I residue 297 VAL Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 412 GLU Chi-restraints excluded: chain I residue 426 ILE Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 490 GLN Chi-restraints excluded: chain I residue 502 VAL Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 521 LEU Chi-restraints excluded: chain I residue 541 GLU Chi-restraints excluded: chain I residue 573 ASN Chi-restraints excluded: chain I residue 576 SER Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 594 VAL Chi-restraints excluded: chain I residue 596 ASP Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 602 GLU Chi-restraints excluded: chain I residue 606 LEU Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 633 LEU Chi-restraints excluded: chain I residue 637 ARG Chi-restraints excluded: chain I residue 699 LEU Chi-restraints excluded: chain I residue 717 VAL Chi-restraints excluded: chain I residue 750 ILE Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 768 MET Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 811 ASN Chi-restraints excluded: chain I residue 826 ASP Chi-restraints excluded: chain I residue 829 THR Chi-restraints excluded: chain I residue 839 VAL Chi-restraints excluded: chain I residue 843 THR Chi-restraints excluded: chain I residue 913 VAL Chi-restraints excluded: chain I residue 939 VAL Chi-restraints excluded: chain I residue 960 LEU Chi-restraints excluded: chain I residue 973 SER Chi-restraints excluded: chain I residue 1000 LEU Chi-restraints excluded: chain I residue 1014 LEU Chi-restraints excluded: chain I residue 1041 ASP Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1073 LYS Chi-restraints excluded: chain I residue 1075 VAL Chi-restraints excluded: chain I residue 1083 GLU Chi-restraints excluded: chain I residue 1092 THR Chi-restraints excluded: chain I residue 1096 ILE Chi-restraints excluded: chain I residue 1135 GLN Chi-restraints excluded: chain I residue 1162 SER Chi-restraints excluded: chain I residue 1167 GLU Chi-restraints excluded: chain I residue 1182 ILE Chi-restraints excluded: chain I residue 1198 LEU Chi-restraints excluded: chain I residue 1247 SER Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1315 MET Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain L residue 28 ASN Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 231 THR Chi-restraints excluded: chain L residue 235 ILE Chi-restraints excluded: chain L residue 246 GLN Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 314 THR Chi-restraints excluded: chain L residue 330 LEU Chi-restraints excluded: chain L residue 337 VAL Chi-restraints excluded: chain L residue 386 LEU Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 429 THR Chi-restraints excluded: chain L residue 537 THR Chi-restraints excluded: chain L residue 547 VAL Chi-restraints excluded: chain M residue 262 LEU Chi-restraints excluded: chain M residue 289 LEU Chi-restraints excluded: chain M residue 297 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 132 optimal weight: 0.5980 chunk 124 optimal weight: 5.9990 chunk 66 optimal weight: 0.8980 chunk 98 optimal weight: 9.9990 chunk 247 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 134 optimal weight: 1.9990 chunk 68 optimal weight: 0.4980 chunk 145 optimal weight: 0.7980 chunk 306 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 320 ASN ** J1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 965 GLN L 28 ASN ** L 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.160733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.122726 restraints weight = 50576.824| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 2.29 r_work: 0.3171 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 33487 Z= 0.134 Angle : 0.656 10.255 45680 Z= 0.342 Chirality : 0.044 0.284 5240 Planarity : 0.004 0.063 5595 Dihedral : 17.529 156.182 5772 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.24 % Favored : 93.63 % Rotamer: Outliers : 5.90 % Allowed : 26.99 % Favored : 67.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.25 % Cis-general : 0.21 % 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: -1.62 (0.13), residues: 3876 helix: 0.24 (0.13), residues: 1592 sheet: -2.13 (0.23), residues: 447 loop : -2.01 (0.14), residues: 1837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J1373 TYR 0.029 0.001 TYR I 810 PHE 0.015 0.001 PHE I1323 TRP 0.016 0.001 TRP I 807 HIS 0.009 0.001 HIS L 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (33475) covalent geometry : angle 0.65379 / 0.34 (45662) hydrogen bonds : bond 0.04462 / 2.92 ( 1392) hydrogen bonds : angle 4.53468 / 3.15 ( 3833) metal coordination : bond 0.00429 / 0.23 ( 12) metal coordination : angle 2.68707 / 1.43 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7752 Ramachandran restraints generated. 3876 Oldfield, 0 Emsley, 3876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7752 Ramachandran restraints generated. 3876 Oldfield, 0 Emsley, 3876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 3346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 196 poor density : 367 time to evaluate : 1.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 69 GLU cc_start: 0.8281 (tt0) cc_final: 0.7720 (mt-10) REVERT: J 133 ARG cc_start: 0.7508 (tpt170) cc_final: 0.7279 (tpp-160) REVERT: J 137 ARG cc_start: 0.7391 (mtp180) cc_final: 0.6996 (mtt90) REVERT: J 375 GLU cc_start: 0.8462 (tp30) cc_final: 0.7939 (tp30) REVERT: J 625 MET cc_start: 0.9015 (ttp) cc_final: 0.8735 (ttp) REVERT: J 667 GLN cc_start: 0.8577 (OUTLIER) cc_final: 0.8200 (tt0) REVERT: J 796 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8718 (tm) REVERT: J 985 ILE cc_start: 0.4188 (OUTLIER) cc_final: 0.3656 (tt) REVERT: J 1101 LEU cc_start: 0.5265 (OUTLIER) cc_final: 0.5020 (mt) REVERT: J 1188 GLU cc_start: 0.6867 (tm-30) cc_final: 0.6530 (tp30) REVERT: J 1194 ARG cc_start: 0.5058 (mpt180) cc_final: 0.4246 (mmm-85) REVERT: J 1197 ASN cc_start: 0.7373 (m-40) cc_final: 0.6758 (m110) REVERT: J 1258 ARG cc_start: 0.8861 (OUTLIER) cc_final: 0.8591 (ttt180) REVERT: J 1266 ILE cc_start: 0.7478 (OUTLIER) cc_final: 0.7023 (mm) REVERT: J 1334 GLU cc_start: 0.8040 (tt0) cc_final: 0.7729 (tp30) REVERT: N 3 ASP cc_start: 0.7926 (t0) cc_final: 0.7696 (t0) REVERT: G 93 GLN cc_start: 0.7781 (mp10) cc_final: 0.7580 (mp10) REVERT: G 158 ARG cc_start: 0.7757 (OUTLIER) cc_final: 0.6722 (ttm-80) REVERT: G 231 PHE cc_start: 0.8102 (OUTLIER) cc_final: 0.7886 (t80) REVERT: H 206 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.8336 (mt-10) REVERT: I 124 MET cc_start: 0.7926 (mtp) cc_final: 0.7712 (mtm) REVERT: I 200 ARG cc_start: 0.6900 (mmm160) cc_final: 0.6089 (ptt90) REVERT: I 240 GLU cc_start: 0.6644 (tm-30) cc_final: 0.6221 (tm-30) REVERT: I 241 LEU cc_start: 0.7936 (tp) cc_final: 0.7655 (tp) REVERT: I 278 GLU cc_start: 0.7224 (OUTLIER) cc_final: 0.6886 (mt-10) REVERT: I 315 MET cc_start: 0.5957 (mmm) cc_final: 0.5714 (mmt) REVERT: I 434 ASP cc_start: 0.7807 (m-30) cc_final: 0.7536 (m-30) REVERT: I 488 MET cc_start: 0.6176 (tpp) cc_final: 0.4966 (mtm) REVERT: I 514 PHE cc_start: 0.8509 (OUTLIER) cc_final: 0.7981 (m-10) REVERT: I 521 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8906 (tp) REVERT: I 541 GLU cc_start: 0.6239 (OUTLIER) cc_final: 0.5833 (mp0) REVERT: I 637 ARG cc_start: 0.8394 (OUTLIER) cc_final: 0.7938 (ptt-90) REVERT: I 659 GLN cc_start: 0.9174 (OUTLIER) cc_final: 0.8813 (tt0) REVERT: I 922 ASN cc_start: 0.8093 (OUTLIER) cc_final: 0.7716 (m-40) REVERT: I 1016 GLU cc_start: 0.7081 (tm-30) cc_final: 0.6678 (tm-30) REVERT: I 1073 LYS cc_start: 0.8476 (OUTLIER) cc_final: 0.8115 (ptpt) REVERT: I 1085 MET cc_start: 0.9075 (mmm) cc_final: 0.8792 (mmm) REVERT: I 1106 ARG cc_start: 0.7130 (OUTLIER) cc_final: 0.6751 (mtt180) REVERT: I 1197 GLU cc_start: 0.7937 (tt0) cc_final: 0.7707 (mt-10) REVERT: L 17 LYS cc_start: 0.7363 (pttt) cc_final: 0.6762 (tptt) REVERT: L 118 ASP cc_start: 0.6920 (m-30) cc_final: 0.6165 (t0) REVERT: L 131 GLN cc_start: 0.6065 (mt0) cc_final: 0.5462 (tp40) REVERT: L 435 ILE cc_start: 0.7777 (OUTLIER) cc_final: 0.7476 (mt) REVERT: L 436 ARG cc_start: 0.8029 (ptp-110) cc_final: 0.7454 (ptp-170) REVERT: L 474 MET cc_start: 0.7602 (tmm) cc_final: 0.7049 (tmm) REVERT: L 545 HIS cc_start: 0.7789 (t70) cc_final: 0.7527 (t-90) REVERT: M 316 MET cc_start: 0.3826 (mpp) cc_final: 0.2306 (tpp) outliers start: 196 outliers final: 145 residues processed: 536 average time/residue: 0.2221 time to fit residues: 193.8788 Evaluate side-chains 512 residues out of total 3346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 348 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 56 LEU Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 76 LYS Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 292 VAL Chi-restraints excluded: chain J residue 363 LEU Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 442 ILE Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 508 LEU Chi-restraints excluded: chain J residue 513 MET Chi-restraints excluded: chain J residue 543 SER Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 596 LEU Chi-restraints excluded: chain J residue 667 GLN Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 722 ILE Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 762 ASN Chi-restraints excluded: chain J residue 770 LEU Chi-restraints excluded: chain J residue 788 LEU Chi-restraints excluded: chain J residue 796 LEU Chi-restraints excluded: chain J residue 797 THR Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 835 LEU Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 903 LEU Chi-restraints excluded: chain J residue 928 THR Chi-restraints excluded: chain J residue 967 VAL Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 985 ILE Chi-restraints excluded: chain J residue 1017 VAL Chi-restraints excluded: chain J residue 1045 THR Chi-restraints excluded: chain J residue 1054 THR Chi-restraints excluded: chain J residue 1078 LEU Chi-restraints excluded: chain J residue 1098 GLN Chi-restraints excluded: chain J residue 1101 LEU Chi-restraints excluded: chain J residue 1180 VAL Chi-restraints excluded: chain J residue 1181 ASP Chi-restraints excluded: chain J residue 1196 LEU Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain J residue 1258 ARG Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1262 ARG Chi-restraints excluded: chain J residue 1266 ILE Chi-restraints excluded: chain J residue 1273 ASP Chi-restraints excluded: chain J residue 1280 VAL Chi-restraints excluded: chain J residue 1342 ASP Chi-restraints excluded: chain N residue 10 SER Chi-restraints excluded: chain N residue 15 LEU Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 75 GLN Chi-restraints excluded: chain G residue 117 HIS Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 158 ARG Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain H residue 139 SER Chi-restraints excluded: chain H residue 141 SER Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 206 GLU Chi-restraints excluded: chain I residue 37 LYS Chi-restraints excluded: chain I residue 105 TYR Chi-restraints excluded: chain I residue 107 ARG Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 117 ILE Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain I residue 147 SER Chi-restraints excluded: chain I residue 187 GLU Chi-restraints excluded: chain I residue 203 LYS Chi-restraints excluded: chain I residue 278 GLU Chi-restraints excluded: chain I residue 282 VAL Chi-restraints excluded: chain I residue 297 VAL Chi-restraints excluded: chain I residue 426 ILE Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 521 LEU Chi-restraints excluded: chain I residue 541 GLU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 573 ASN Chi-restraints excluded: chain I residue 594 VAL Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 602 GLU Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 633 LEU Chi-restraints excluded: chain I residue 637 ARG Chi-restraints excluded: chain I residue 659 GLN Chi-restraints excluded: chain I residue 699 LEU Chi-restraints excluded: chain I residue 750 ILE Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 768 MET Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 829 THR Chi-restraints excluded: chain I residue 913 VAL Chi-restraints excluded: chain I residue 922 ASN Chi-restraints excluded: chain I residue 939 VAL Chi-restraints excluded: chain I residue 960 LEU Chi-restraints excluded: chain I residue 973 SER Chi-restraints excluded: chain I residue 1014 LEU Chi-restraints excluded: chain I residue 1073 LYS Chi-restraints excluded: chain I residue 1083 GLU Chi-restraints excluded: chain I residue 1092 THR Chi-restraints excluded: chain I residue 1106 ARG Chi-restraints excluded: chain I residue 1162 SER Chi-restraints excluded: chain I residue 1167 GLU Chi-restraints excluded: chain I residue 1198 LEU Chi-restraints excluded: chain I residue 1247 SER Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1315 MET Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 105 MET Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 231 THR Chi-restraints excluded: chain L residue 235 ILE Chi-restraints excluded: chain L residue 246 GLN Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 337 VAL Chi-restraints excluded: chain L residue 386 LEU Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 429 THR Chi-restraints excluded: chain L residue 435 ILE Chi-restraints excluded: chain L residue 537 THR Chi-restraints excluded: chain L residue 547 VAL Chi-restraints excluded: chain M residue 262 LEU Chi-restraints excluded: chain M residue 289 LEU Chi-restraints excluded: chain M residue 297 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 264 optimal weight: 3.9990 chunk 89 optimal weight: 6.9990 chunk 263 optimal weight: 0.5980 chunk 316 optimal weight: 0.9980 chunk 322 optimal weight: 0.9990 chunk 209 optimal weight: 8.9990 chunk 161 optimal weight: 0.7980 chunk 217 optimal weight: 0.9980 chunk 101 optimal weight: 5.9990 chunk 273 optimal weight: 0.5980 chunk 174 optimal weight: 10.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 320 ASN J 477 GLN J1049 GLN ** J1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 811 ASN I 965 GLN I1313 HIS ** L 362 ASN ** 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 = 0.3982 r_free = 0.3982 target = 0.160758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.123453 restraints weight = 50418.939| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.35 r_work: 0.3190 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.3321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 33487 Z= 0.130 Angle : 0.639 9.631 45680 Z= 0.333 Chirality : 0.043 0.246 5240 Planarity : 0.004 0.062 5595 Dihedral : 17.296 157.436 5768 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.55 % Favored : 93.32 % Rotamer: Outliers : 5.81 % Allowed : 27.20 % Favored : 67.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.25 % Cis-general : 0.21 % 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: -1.36 (0.13), residues: 3876 helix: 0.46 (0.13), residues: 1591 sheet: -1.96 (0.23), residues: 431 loop : -1.87 (0.14), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG L 113 TYR 0.028 0.001 TYR L 143 PHE 0.019 0.001 PHE I 464 TRP 0.011 0.001 TRP L 434 HIS 0.008 0.001 HIS G 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (33475) covalent geometry : angle 0.63721 / 0.33 (45662) hydrogen bonds : bond 0.04259 / 2.79 ( 1392) hydrogen bonds : angle 4.40539 / 3.06 ( 3833) metal coordination : bond 0.00433 / 0.23 ( 12) metal coordination : angle 2.56614 / 1.43 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7752 Ramachandran restraints generated. 3876 Oldfield, 0 Emsley, 3876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7752 Ramachandran restraints generated. 3876 Oldfield, 0 Emsley, 3876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 3346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 193 poor density : 384 time to evaluate : 1.254 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 69 GLU cc_start: 0.8251 (tt0) cc_final: 0.7768 (mt-10) REVERT: J 133 ARG cc_start: 0.7483 (tpt170) cc_final: 0.7258 (tpp-160) REVERT: J 137 ARG cc_start: 0.7401 (mtp180) cc_final: 0.6962 (mtt90) REVERT: J 148 GLU cc_start: 0.7620 (mt-10) cc_final: 0.7155 (tt0) REVERT: J 299 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8818 (tt) REVERT: J 375 GLU cc_start: 0.8329 (tp30) cc_final: 0.7937 (tp30) REVERT: J 443 GLU cc_start: 0.7478 (OUTLIER) cc_final: 0.7186 (tp30) REVERT: J 625 MET cc_start: 0.8987 (ttp) cc_final: 0.8703 (ttp) REVERT: J 796 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8727 (tm) REVERT: J 830 ASP cc_start: 0.5138 (OUTLIER) cc_final: 0.4889 (m-30) REVERT: J 985 ILE cc_start: 0.4313 (OUTLIER) cc_final: 0.3760 (tt) REVERT: J 1101 LEU cc_start: 0.5344 (OUTLIER) cc_final: 0.5124 (mt) REVERT: J 1187 GLU cc_start: 0.5541 (OUTLIER) cc_final: 0.5209 (mm-30) REVERT: J 1188 GLU cc_start: 0.6919 (tm-30) cc_final: 0.6651 (tp30) REVERT: J 1194 ARG cc_start: 0.4948 (mpt180) cc_final: 0.4213 (mmm-85) REVERT: J 1197 ASN cc_start: 0.7372 (m-40) cc_final: 0.6765 (m110) REVERT: J 1215 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7495 (mp0) REVERT: J 1258 ARG cc_start: 0.8834 (OUTLIER) cc_final: 0.8600 (ttt180) REVERT: J 1334 GLU cc_start: 0.8033 (tt0) cc_final: 0.7765 (tp30) REVERT: N 3 ASP cc_start: 0.7895 (t0) cc_final: 0.7694 (t0) REVERT: G 158 ARG cc_start: 0.7712 (OUTLIER) cc_final: 0.6631 (ttm-80) REVERT: H 206 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.8362 (mt-10) REVERT: I 240 GLU cc_start: 0.6576 (tm-30) cc_final: 0.6170 (tm-30) REVERT: I 241 LEU cc_start: 0.7914 (tp) cc_final: 0.7669 (tp) REVERT: I 278 GLU cc_start: 0.7220 (OUTLIER) cc_final: 0.6763 (mt-10) REVERT: I 315 MET cc_start: 0.6031 (mmm) cc_final: 0.5795 (mmt) REVERT: I 434 ASP cc_start: 0.7854 (m-30) cc_final: 0.7588 (m-30) REVERT: I 488 MET cc_start: 0.5483 (tpp) cc_final: 0.4648 (mpp) REVERT: I 514 PHE cc_start: 0.8496 (OUTLIER) cc_final: 0.8061 (m-10) REVERT: I 521 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.8985 (tp) REVERT: I 541 GLU cc_start: 0.6139 (OUTLIER) cc_final: 0.5708 (mp0) REVERT: I 572 ILE cc_start: 0.9210 (OUTLIER) cc_final: 0.8833 (mt) REVERT: I 637 ARG cc_start: 0.8489 (OUTLIER) cc_final: 0.8067 (ptt-90) REVERT: I 965 GLN cc_start: 0.7746 (tt0) cc_final: 0.7518 (tt0) REVERT: I 1016 GLU cc_start: 0.7079 (tm-30) cc_final: 0.6668 (tm-30) REVERT: I 1073 LYS cc_start: 0.8407 (OUTLIER) cc_final: 0.8012 (ptpt) REVERT: I 1085 MET cc_start: 0.9031 (mmm) cc_final: 0.8709 (mmm) REVERT: I 1106 ARG cc_start: 0.7125 (OUTLIER) cc_final: 0.6720 (mtt180) REVERT: I 1167 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7900 (tm-30) REVERT: K 13 ILE cc_start: 0.8084 (tt) cc_final: 0.7783 (tt) REVERT: L 17 LYS cc_start: 0.7655 (pttt) cc_final: 0.6968 (tptt) REVERT: L 118 ASP cc_start: 0.6738 (m-30) cc_final: 0.6101 (t0) REVERT: L 131 GLN cc_start: 0.5961 (mt0) cc_final: 0.5457 (tp40) REVERT: L 246 GLN cc_start: 0.2290 (OUTLIER) cc_final: 0.1251 (pp30) REVERT: L 251 LYS cc_start: 0.4908 (mmtm) cc_final: 0.4001 (ptmm) REVERT: L 271 ASN cc_start: 0.7664 (t0) cc_final: 0.7141 (t0) REVERT: L 379 MET cc_start: 0.8360 (mmm) cc_final: 0.7926 (tpp) REVERT: L 436 ARG cc_start: 0.7981 (ptp-110) cc_final: 0.7342 (ptp-110) REVERT: L 474 MET cc_start: 0.7610 (tmm) cc_final: 0.6723 (tmm) REVERT: L 545 HIS cc_start: 0.7821 (t70) cc_final: 0.7527 (t-90) outliers start: 193 outliers final: 137 residues processed: 552 average time/residue: 0.2126 time to fit residues: 193.5681 Evaluate side-chains 511 residues out of total 3346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 353 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 56 LEU Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 76 LYS Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 292 VAL Chi-restraints excluded: chain J residue 299 LEU Chi-restraints excluded: chain J residue 363 LEU Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 442 ILE Chi-restraints excluded: chain J residue 443 GLU Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 508 LEU Chi-restraints excluded: chain J residue 513 MET Chi-restraints excluded: chain J residue 543 SER Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 571 ASP Chi-restraints excluded: chain J residue 596 LEU Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 770 LEU Chi-restraints excluded: chain J residue 788 LEU Chi-restraints excluded: chain J residue 796 LEU Chi-restraints excluded: chain J residue 797 THR Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 830 ASP Chi-restraints excluded: chain J residue 835 LEU Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 869 CYS Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 903 LEU Chi-restraints excluded: chain J residue 928 THR Chi-restraints excluded: chain J residue 967 VAL Chi-restraints excluded: chain J residue 968 ASN Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 985 ILE Chi-restraints excluded: chain J residue 1017 VAL Chi-restraints excluded: chain J residue 1045 THR Chi-restraints excluded: chain J residue 1078 LEU Chi-restraints excluded: chain J residue 1101 LEU Chi-restraints excluded: chain J residue 1160 SER Chi-restraints excluded: chain J residue 1180 VAL Chi-restraints excluded: chain J residue 1181 ASP Chi-restraints excluded: chain J residue 1187 GLU Chi-restraints excluded: chain J residue 1196 LEU Chi-restraints excluded: chain J residue 1215 GLU Chi-restraints excluded: chain J residue 1258 ARG Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1266 ILE Chi-restraints excluded: chain J residue 1273 ASP Chi-restraints excluded: chain J residue 1280 VAL Chi-restraints excluded: chain J residue 1301 THR Chi-restraints excluded: chain J residue 1307 LEU Chi-restraints excluded: chain J residue 1342 ASP Chi-restraints excluded: chain N residue 10 SER Chi-restraints excluded: chain N residue 15 LEU Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 158 ARG Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain H residue 139 SER Chi-restraints excluded: chain H residue 141 SER Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 206 GLU Chi-restraints excluded: chain I residue 37 LYS Chi-restraints excluded: chain I residue 105 TYR Chi-restraints excluded: chain I residue 107 ARG Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 117 ILE Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain I residue 147 SER Chi-restraints excluded: chain I residue 187 GLU Chi-restraints excluded: chain I residue 203 LYS Chi-restraints excluded: chain I residue 278 GLU Chi-restraints excluded: chain I residue 282 VAL Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain I residue 297 VAL Chi-restraints excluded: chain I residue 426 ILE Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 490 GLN Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 521 LEU Chi-restraints excluded: chain I residue 541 GLU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 572 ILE Chi-restraints excluded: chain I residue 573 ASN Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 594 VAL Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 602 GLU Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 633 LEU Chi-restraints excluded: chain I residue 637 ARG Chi-restraints excluded: chain I residue 699 LEU Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 768 MET Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 843 THR Chi-restraints excluded: chain I residue 913 VAL Chi-restraints excluded: chain I residue 939 VAL Chi-restraints excluded: chain I residue 960 LEU Chi-restraints excluded: chain I residue 1014 LEU Chi-restraints excluded: chain I residue 1073 LYS Chi-restraints excluded: chain I residue 1083 GLU Chi-restraints excluded: chain I residue 1092 THR Chi-restraints excluded: chain I residue 1096 ILE Chi-restraints excluded: chain I residue 1106 ARG Chi-restraints excluded: chain I residue 1162 SER Chi-restraints excluded: chain I residue 1167 GLU Chi-restraints excluded: chain I residue 1198 LEU Chi-restraints excluded: chain I residue 1247 SER Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 105 MET Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 235 ILE Chi-restraints excluded: chain L residue 246 GLN Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 337 VAL Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 537 THR Chi-restraints excluded: chain L residue 547 VAL Chi-restraints excluded: chain M residue 262 LEU Chi-restraints excluded: chain M residue 297 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 159 optimal weight: 9.9990 chunk 43 optimal weight: 1.9990 chunk 314 optimal weight: 1.9990 chunk 210 optimal weight: 0.1980 chunk 303 optimal weight: 0.2980 chunk 199 optimal weight: 0.9990 chunk 164 optimal weight: 1.9990 chunk 133 optimal weight: 10.0000 chunk 358 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 376 optimal weight: 0.8980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 320 ASN ** J1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 21 ASN I1134 GLN L 28 ASN ** L 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.161619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.124418 restraints weight = 50498.345| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 2.38 r_work: 0.3201 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.3514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 33487 Z= 0.125 Angle : 0.639 10.092 45680 Z= 0.332 Chirality : 0.043 0.249 5240 Planarity : 0.004 0.063 5595 Dihedral : 17.132 157.816 5754 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.04 % Favored : 93.83 % Rotamer: Outliers : 5.14 % Allowed : 28.31 % Favored : 66.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.25 % Cis-general : 0.21 % 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: -1.25 (0.13), residues: 3876 helix: 0.56 (0.13), residues: 1587 sheet: -1.96 (0.23), residues: 461 loop : -1.79 (0.14), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG L 113 TYR 0.025 0.001 TYR L 143 PHE 0.014 0.001 PHE I 464 TRP 0.010 0.001 TRP L 434 HIS 0.009 0.001 HIS G 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 (33475) covalent geometry : angle 0.63737 / 0.33 (45662) hydrogen bonds : bond 0.04157 / 2.73 ( 1392) hydrogen bonds : angle 4.35056 / 3.02 ( 3833) metal coordination : bond 0.00360 / 0.19 ( 12) metal coordination : angle 2.32496 / 1.24 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7752 Ramachandran restraints generated. 3876 Oldfield, 0 Emsley, 3876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7752 Ramachandran restraints generated. 3876 Oldfield, 0 Emsley, 3876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 3346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 379 time to evaluate : 1.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 69 GLU cc_start: 0.8224 (tt0) cc_final: 0.7776 (mt-10) REVERT: J 133 ARG cc_start: 0.7474 (tpt170) cc_final: 0.7209 (tpp-160) REVERT: J 332 LYS cc_start: 0.8075 (OUTLIER) cc_final: 0.7663 (pttp) REVERT: J 375 GLU cc_start: 0.8319 (tp30) cc_final: 0.7929 (tp30) REVERT: J 443 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.7342 (tp30) REVERT: J 532 GLU cc_start: 0.7979 (tt0) cc_final: 0.7775 (tp30) REVERT: J 625 MET cc_start: 0.8982 (ttp) cc_final: 0.8725 (ttp) REVERT: J 796 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8702 (tm) REVERT: J 918 ILE cc_start: 0.9024 (pt) cc_final: 0.8424 (mt) REVERT: J 985 ILE cc_start: 0.4301 (OUTLIER) cc_final: 0.3760 (tt) REVERT: J 1101 LEU cc_start: 0.5180 (OUTLIER) cc_final: 0.4961 (mt) REVERT: J 1187 GLU cc_start: 0.5522 (OUTLIER) cc_final: 0.5185 (mm-30) REVERT: J 1188 GLU cc_start: 0.6832 (tm-30) cc_final: 0.6589 (tp30) REVERT: J 1194 ARG cc_start: 0.4919 (mpt180) cc_final: 0.4202 (mmm-85) REVERT: J 1197 ASN cc_start: 0.7350 (m-40) cc_final: 0.6751 (m110) REVERT: J 1215 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7531 (mp0) REVERT: J 1258 ARG cc_start: 0.8791 (OUTLIER) cc_final: 0.8588 (ttt180) REVERT: J 1334 GLU cc_start: 0.8065 (tt0) cc_final: 0.7758 (tp30) REVERT: G 215 GLU cc_start: 0.7594 (tp30) cc_final: 0.7388 (tp30) REVERT: H 15 ASP cc_start: 0.6609 (t0) cc_final: 0.6353 (t0) REVERT: H 27 THR cc_start: 0.8879 (m) cc_final: 0.8500 (p) REVERT: H 206 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.8341 (mt-10) REVERT: I 240 GLU cc_start: 0.6575 (tm-30) cc_final: 0.6179 (tm-30) REVERT: I 241 LEU cc_start: 0.7885 (tp) cc_final: 0.7645 (tp) REVERT: I 278 GLU cc_start: 0.7222 (OUTLIER) cc_final: 0.6715 (mt-10) REVERT: I 315 MET cc_start: 0.6048 (mmm) cc_final: 0.5768 (mmt) REVERT: I 330 HIS cc_start: 0.5752 (m170) cc_final: 0.4842 (m170) REVERT: I 434 ASP cc_start: 0.7863 (m-30) cc_final: 0.7596 (m-30) REVERT: I 488 MET cc_start: 0.5542 (tpp) cc_final: 0.4668 (mpp) REVERT: I 514 PHE cc_start: 0.8462 (OUTLIER) cc_final: 0.8114 (m-10) REVERT: I 541 GLU cc_start: 0.6204 (OUTLIER) cc_final: 0.5868 (mp0) REVERT: I 637 ARG cc_start: 0.8426 (OUTLIER) cc_final: 0.7945 (ptt-90) REVERT: I 765 ILE cc_start: 0.8991 (OUTLIER) cc_final: 0.8632 (pt) REVERT: I 899 GLU cc_start: 0.7947 (tm-30) cc_final: 0.7552 (tt0) REVERT: I 965 GLN cc_start: 0.7730 (tt0) cc_final: 0.7507 (tt0) REVERT: I 1016 GLU cc_start: 0.6824 (tm-30) cc_final: 0.6503 (tm-30) REVERT: I 1073 LYS cc_start: 0.8344 (OUTLIER) cc_final: 0.7961 (ptpt) REVERT: I 1085 MET cc_start: 0.8991 (mmm) cc_final: 0.8688 (mmm) REVERT: I 1106 ARG cc_start: 0.7161 (OUTLIER) cc_final: 0.6826 (mtt180) REVERT: I 1167 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7957 (tm-30) REVERT: I 1253 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.8912 (tp) REVERT: I 1319 MET cc_start: 0.8392 (tpp) cc_final: 0.7974 (tpp) REVERT: K 13 ILE cc_start: 0.8013 (tt) cc_final: 0.7724 (tt) REVERT: K 42 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.6319 (pp20) REVERT: L 17 LYS cc_start: 0.7701 (pttt) cc_final: 0.6995 (tptt) REVERT: L 28 ASN cc_start: 0.8745 (OUTLIER) cc_final: 0.8328 (m110) REVERT: L 118 ASP cc_start: 0.6532 (m-30) cc_final: 0.5981 (t0) REVERT: L 131 GLN cc_start: 0.5884 (mt0) cc_final: 0.5388 (tp40) REVERT: L 246 GLN cc_start: 0.2193 (OUTLIER) cc_final: 0.1217 (pp30) REVERT: L 251 LYS cc_start: 0.4901 (mmtm) cc_final: 0.3986 (ptmm) REVERT: L 271 ASN cc_start: 0.7528 (t0) cc_final: 0.6910 (t0) REVERT: L 379 MET cc_start: 0.8390 (mmm) cc_final: 0.8183 (tpp) REVERT: L 436 ARG cc_start: 0.7879 (ptp-110) cc_final: 0.7351 (ptp-170) REVERT: L 474 MET cc_start: 0.7725 (tmm) cc_final: 0.6839 (tmm) REVERT: L 545 HIS cc_start: 0.7861 (t70) cc_final: 0.7554 (t-90) outliers start: 171 outliers final: 125 residues processed: 526 average time/residue: 0.2109 time to fit residues: 181.7983 Evaluate side-chains 503 residues out of total 3346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 357 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 56 LEU Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 76 LYS Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 292 VAL Chi-restraints excluded: chain J residue 332 LYS Chi-restraints excluded: chain J residue 363 LEU Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 442 ILE Chi-restraints excluded: chain J residue 443 GLU Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 508 LEU Chi-restraints excluded: chain J residue 543 SER Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 571 ASP Chi-restraints excluded: chain J residue 596 LEU Chi-restraints excluded: chain J residue 648 GLU Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 770 LEU Chi-restraints excluded: chain J residue 788 LEU Chi-restraints excluded: chain J residue 796 LEU Chi-restraints excluded: chain J residue 797 THR Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 835 LEU Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 869 CYS Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 903 LEU Chi-restraints excluded: chain J residue 928 THR Chi-restraints excluded: chain J residue 967 VAL Chi-restraints excluded: chain J residue 968 ASN Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 985 ILE Chi-restraints excluded: chain J residue 1017 VAL Chi-restraints excluded: chain J residue 1045 THR Chi-restraints excluded: chain J residue 1098 GLN Chi-restraints excluded: chain J residue 1101 LEU Chi-restraints excluded: chain J residue 1180 VAL Chi-restraints excluded: chain J residue 1181 ASP Chi-restraints excluded: chain J residue 1187 GLU Chi-restraints excluded: chain J residue 1196 LEU Chi-restraints excluded: chain J residue 1215 GLU Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain J residue 1258 ARG Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1266 ILE Chi-restraints excluded: chain J residue 1273 ASP Chi-restraints excluded: chain J residue 1280 VAL Chi-restraints excluded: chain J residue 1301 THR Chi-restraints excluded: chain J residue 1342 ASP Chi-restraints excluded: chain N residue 10 SER Chi-restraints excluded: chain N residue 15 LEU Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 206 GLU Chi-restraints excluded: chain I residue 37 LYS Chi-restraints excluded: chain I residue 105 TYR Chi-restraints excluded: chain I residue 107 ARG Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 117 ILE Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 147 SER Chi-restraints excluded: chain I residue 187 GLU Chi-restraints excluded: chain I residue 278 GLU Chi-restraints excluded: chain I residue 282 VAL Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain I residue 297 VAL Chi-restraints excluded: chain I residue 319 LEU Chi-restraints excluded: chain I residue 426 ILE Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 541 GLU Chi-restraints excluded: chain I residue 573 ASN Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 594 VAL Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 633 LEU Chi-restraints excluded: chain I residue 637 ARG Chi-restraints excluded: chain I residue 750 ILE Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 768 MET Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 843 THR Chi-restraints excluded: chain I residue 913 VAL Chi-restraints excluded: chain I residue 939 VAL Chi-restraints excluded: chain I residue 960 LEU Chi-restraints excluded: chain I residue 1014 LEU Chi-restraints excluded: chain I residue 1073 LYS Chi-restraints excluded: chain I residue 1083 GLU Chi-restraints excluded: chain I residue 1092 THR Chi-restraints excluded: chain I residue 1106 ARG Chi-restraints excluded: chain I residue 1162 SER Chi-restraints excluded: chain I residue 1167 GLU Chi-restraints excluded: chain I residue 1198 LEU Chi-restraints excluded: chain I residue 1247 SER Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain K residue 42 GLU Chi-restraints excluded: chain L residue 28 ASN Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 105 MET Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 235 ILE Chi-restraints excluded: chain L residue 246 GLN Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 337 VAL Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 429 THR Chi-restraints excluded: chain L residue 537 THR Chi-restraints excluded: chain L residue 547 VAL Chi-restraints excluded: chain M residue 262 LEU Chi-restraints excluded: chain M residue 297 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 308 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 3 optimal weight: 0.0980 chunk 108 optimal weight: 7.9990 chunk 358 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 369 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 142 optimal weight: 5.9990 chunk 267 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 320 ASN ** J1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1249 ASN ** J1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 117 HIS H 41 ASN I 766 ASN I1134 GLN L 28 ASN ** L 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.160284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.123130 restraints weight = 50503.271| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 2.43 r_work: 0.3170 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.3500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 33487 Z= 0.166 Angle : 0.656 9.666 45680 Z= 0.340 Chirality : 0.044 0.252 5240 Planarity : 0.004 0.069 5595 Dihedral : 17.093 158.333 5748 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.55 % Favored : 93.32 % Rotamer: Outliers : 5.08 % Allowed : 28.46 % Favored : 66.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.25 % Cis-general : 0.21 % 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: -1.26 (0.13), residues: 3876 helix: 0.54 (0.13), residues: 1592 sheet: -1.95 (0.23), residues: 450 loop : -1.80 (0.14), residues: 1834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG L 113 TYR 0.026 0.002 TYR L 143 PHE 0.027 0.002 PHE J 172 TRP 0.009 0.001 TRP L 434 HIS 0.011 0.001 HIS G 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.17 (33475) covalent geometry : angle 0.65439 / 0.34 (45662) hydrogen bonds : bond 0.04268 / 2.80 ( 1392) hydrogen bonds : angle 4.36820 / 3.03 ( 3833) metal coordination : bond 0.00610 / 0.33 ( 12) metal coordination : angle 2.59208 / 1.41 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7752 Ramachandran restraints generated. 3876 Oldfield, 0 Emsley, 3876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7752 Ramachandran restraints generated. 3876 Oldfield, 0 Emsley, 3876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 3346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 362 time to evaluate : 1.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 69 GLU cc_start: 0.8229 (tt0) cc_final: 0.7776 (mt-10) REVERT: J 332 LYS cc_start: 0.8083 (OUTLIER) cc_final: 0.7663 (pttp) REVERT: J 375 GLU cc_start: 0.8371 (tp30) cc_final: 0.7926 (tp30) REVERT: J 443 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7321 (tp30) REVERT: J 532 GLU cc_start: 0.8041 (tt0) cc_final: 0.7819 (tp30) REVERT: J 625 MET cc_start: 0.9041 (ttp) cc_final: 0.8803 (ttp) REVERT: J 796 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8849 (tm) REVERT: J 870 ASP cc_start: 0.6784 (m-30) cc_final: 0.6494 (m-30) REVERT: J 985 ILE cc_start: 0.4255 (OUTLIER) cc_final: 0.3722 (tt) REVERT: J 1187 GLU cc_start: 0.5528 (OUTLIER) cc_final: 0.5191 (mm-30) REVERT: J 1188 GLU cc_start: 0.6949 (tm-30) cc_final: 0.6652 (tp30) REVERT: J 1194 ARG cc_start: 0.4918 (mpt180) cc_final: 0.4212 (mmm-85) REVERT: J 1197 ASN cc_start: 0.7360 (m-40) cc_final: 0.6764 (m110) REVERT: J 1258 ARG cc_start: 0.8869 (OUTLIER) cc_final: 0.8623 (ttt180) REVERT: J 1334 GLU cc_start: 0.8065 (tt0) cc_final: 0.7730 (tp30) REVERT: H 15 ASP cc_start: 0.6722 (t0) cc_final: 0.6479 (t0) REVERT: H 27 THR cc_start: 0.8829 (m) cc_final: 0.8462 (p) REVERT: H 206 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.8340 (mt-10) REVERT: I 240 GLU cc_start: 0.6504 (tm-30) cc_final: 0.6190 (tm-30) REVERT: I 241 LEU cc_start: 0.7905 (tp) cc_final: 0.7640 (tp) REVERT: I 278 GLU cc_start: 0.7267 (OUTLIER) cc_final: 0.6750 (mt-10) REVERT: I 315 MET cc_start: 0.6071 (mmm) cc_final: 0.5787 (mmt) REVERT: I 434 ASP cc_start: 0.7883 (m-30) cc_final: 0.7596 (m-30) REVERT: I 488 MET cc_start: 0.5726 (tpp) cc_final: 0.4918 (mpp) REVERT: I 514 PHE cc_start: 0.8421 (OUTLIER) cc_final: 0.8032 (m-10) REVERT: I 541 GLU cc_start: 0.6212 (OUTLIER) cc_final: 0.5900 (mp0) REVERT: I 572 ILE cc_start: 0.9196 (OUTLIER) cc_final: 0.8801 (mt) REVERT: I 637 ARG cc_start: 0.8522 (OUTLIER) cc_final: 0.8047 (ptt-90) REVERT: I 765 ILE cc_start: 0.9100 (OUTLIER) cc_final: 0.8717 (pt) REVERT: I 965 GLN cc_start: 0.7766 (tt0) cc_final: 0.7524 (tt0) REVERT: I 1016 GLU cc_start: 0.6826 (tm-30) cc_final: 0.6493 (tm-30) REVERT: I 1073 LYS cc_start: 0.8419 (OUTLIER) cc_final: 0.8030 (ptpt) REVERT: I 1167 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.8024 (tm-30) REVERT: I 1253 LEU cc_start: 0.9299 (OUTLIER) cc_final: 0.8893 (tp) REVERT: I 1319 MET cc_start: 0.8411 (tpp) cc_final: 0.7986 (tpp) REVERT: K 42 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.6329 (pp20) REVERT: L 17 LYS cc_start: 0.7515 (pttt) cc_final: 0.6916 (tptt) REVERT: L 28 ASN cc_start: 0.8566 (OUTLIER) cc_final: 0.8361 (m-40) REVERT: L 51 MET cc_start: 0.5229 (ptt) cc_final: 0.5003 (ptt) REVERT: L 118 ASP cc_start: 0.6650 (m-30) cc_final: 0.6062 (t0) REVERT: L 131 GLN cc_start: 0.6020 (mt0) cc_final: 0.5534 (tp40) REVERT: L 246 GLN cc_start: 0.2161 (OUTLIER) cc_final: 0.1193 (pp30) REVERT: L 251 LYS cc_start: 0.4988 (mmtm) cc_final: 0.4101 (ptmm) REVERT: L 271 ASN cc_start: 0.7444 (t0) cc_final: 0.6829 (t0) REVERT: L 281 ARG cc_start: 0.4552 (mtt180) cc_final: 0.4126 (mtp180) REVERT: L 379 MET cc_start: 0.8412 (mmm) cc_final: 0.8199 (tpp) REVERT: L 436 ARG cc_start: 0.7925 (ptp-110) cc_final: 0.7416 (ptp-170) REVERT: L 474 MET cc_start: 0.7796 (tmm) cc_final: 0.6793 (tmm) REVERT: L 545 HIS cc_start: 0.7898 (t70) cc_final: 0.7618 (t-90) outliers start: 169 outliers final: 136 residues processed: 508 average time/residue: 0.2039 time to fit residues: 171.2646 Evaluate side-chains 512 residues out of total 3346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 357 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 56 LEU Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 76 LYS Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 292 VAL Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 332 LYS Chi-restraints excluded: chain J residue 363 LEU Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 442 ILE Chi-restraints excluded: chain J residue 443 GLU Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 508 LEU Chi-restraints excluded: chain J residue 543 SER Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 571 ASP Chi-restraints excluded: chain J residue 596 LEU Chi-restraints excluded: chain J residue 648 GLU Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 770 LEU Chi-restraints excluded: chain J residue 786 THR Chi-restraints excluded: chain J residue 788 LEU Chi-restraints excluded: chain J residue 796 LEU Chi-restraints excluded: chain J residue 797 THR Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 835 LEU Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 869 CYS Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 903 LEU Chi-restraints excluded: chain J residue 928 THR Chi-restraints excluded: chain J residue 967 VAL Chi-restraints excluded: chain J residue 968 ASN Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 985 ILE Chi-restraints excluded: chain J residue 1017 VAL Chi-restraints excluded: chain J residue 1045 THR Chi-restraints excluded: chain J residue 1098 GLN Chi-restraints excluded: chain J residue 1160 SER Chi-restraints excluded: chain J residue 1180 VAL Chi-restraints excluded: chain J residue 1181 ASP Chi-restraints excluded: chain J residue 1187 GLU Chi-restraints excluded: chain J residue 1196 LEU Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain J residue 1258 ARG Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1266 ILE Chi-restraints excluded: chain J residue 1273 ASP Chi-restraints excluded: chain J residue 1280 VAL Chi-restraints excluded: chain J residue 1301 THR Chi-restraints excluded: chain J residue 1307 LEU Chi-restraints excluded: chain J residue 1342 ASP Chi-restraints excluded: chain N residue 10 SER Chi-restraints excluded: chain N residue 15 LEU Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 32 ILE Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 206 GLU Chi-restraints excluded: chain I residue 37 LYS Chi-restraints excluded: chain I residue 105 TYR Chi-restraints excluded: chain I residue 107 ARG Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 117 ILE Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 147 SER Chi-restraints excluded: chain I residue 278 GLU Chi-restraints excluded: chain I residue 282 VAL Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain I residue 297 VAL Chi-restraints excluded: chain I residue 319 LEU Chi-restraints excluded: chain I residue 426 ILE Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 490 GLN Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 541 GLU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 572 ILE Chi-restraints excluded: chain I residue 573 ASN Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 594 VAL Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 633 LEU Chi-restraints excluded: chain I residue 637 ARG Chi-restraints excluded: chain I residue 750 ILE Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 768 MET Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 843 THR Chi-restraints excluded: chain I residue 913 VAL Chi-restraints excluded: chain I residue 939 VAL Chi-restraints excluded: chain I residue 960 LEU Chi-restraints excluded: chain I residue 1014 LEU Chi-restraints excluded: chain I residue 1073 LYS Chi-restraints excluded: chain I residue 1083 GLU Chi-restraints excluded: chain I residue 1092 THR Chi-restraints excluded: chain I residue 1162 SER Chi-restraints excluded: chain I residue 1167 GLU Chi-restraints excluded: chain I residue 1182 ILE Chi-restraints excluded: chain I residue 1198 LEU Chi-restraints excluded: chain I residue 1244 HIS Chi-restraints excluded: chain I residue 1247 SER Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain K residue 42 GLU Chi-restraints excluded: chain L residue 28 ASN Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 105 MET Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 235 ILE Chi-restraints excluded: chain L residue 246 GLN Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 288 MET Chi-restraints excluded: chain L residue 337 VAL Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 429 THR Chi-restraints excluded: chain L residue 537 THR Chi-restraints excluded: chain L residue 547 VAL Chi-restraints excluded: chain M residue 262 LEU Chi-restraints excluded: chain M residue 297 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 9 optimal weight: 2.9990 chunk 216 optimal weight: 10.0000 chunk 371 optimal weight: 0.0060 chunk 122 optimal weight: 0.9980 chunk 82 optimal weight: 8.9990 chunk 121 optimal weight: 0.0970 chunk 301 optimal weight: 0.3980 chunk 70 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 312 optimal weight: 0.7980 chunk 211 optimal weight: 8.9990 overall best weight: 0.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 320 ASN ** J1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1249 ASN ** J1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 117 HIS I1134 GLN L 28 ASN ** L 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.162670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.125512 restraints weight = 50764.081| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 2.36 r_work: 0.3217 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.3731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 33487 Z= 0.121 Angle : 0.640 10.737 45680 Z= 0.332 Chirality : 0.043 0.251 5240 Planarity : 0.004 0.068 5595 Dihedral : 16.975 158.233 5748 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.96 % Favored : 93.91 % Rotamer: Outliers : 4.42 % Allowed : 29.15 % Favored : 66.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.25 % Cis-general : 0.21 % 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: -1.08 (0.13), residues: 3876 helix: 0.71 (0.13), residues: 1594 sheet: -1.83 (0.23), residues: 451 loop : -1.72 (0.14), residues: 1831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG L 113 TYR 0.028 0.001 TYR L 143 PHE 0.018 0.001 PHE N 52 TRP 0.012 0.001 TRP L 434 HIS 0.010 0.001 HIS G 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (33475) covalent geometry : angle 0.63916 / 0.33 (45662) hydrogen bonds : bond 0.04049 / 2.67 ( 1392) hydrogen bonds : angle 4.29787 / 2.98 ( 3833) metal coordination : bond 0.00304 / 0.16 ( 12) metal coordination : angle 2.08765 / 1.09 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8465.88 seconds wall clock time: 145 minutes 35.21 seconds (8735.21 seconds total)