Starting phenix.real_space_refine on Sat Aug 8 20:07:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9t5h_55583/08_2026/9t5h_55583.cif Found real_map, /net/cci-nas-00/data/ceres_data/9t5h_55583/08_2026/9t5h_55583.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9t5h_55583/08_2026/9t5h_55583.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9t5h_55583/08_2026/9t5h_55583.map" model { file = "/net/cci-nas-00/data/ceres_data/9t5h_55583/08_2026/9t5h_55583.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9t5h_55583/08_2026/9t5h_55583.cif" } resolution = 2.7 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= 0.003 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: 5 Type Number sf(0) Gaussians Zn 6 6.06 5 S 168 5.16 5 C 18569 2.51 5 N 5082 2.21 5 O 5490 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 29315 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 8296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8296 Classifications: {'peptide': 1040} Link IDs: {'PCIS': 2, 'PTRANS': 44, 'TRANS': 993} Chain breaks: 4 Chain: "B" Number of atoms: 8111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1013, 8111 Classifications: {'peptide': 1013} Link IDs: {'PTRANS': 48, 'TRANS': 964} Chain breaks: 4 Chain: "C" Number of atoms: 2073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2073 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 15, 'TRANS': 242} Chain breaks: 1 Chain: "D" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1013 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 3, 'TRANS': 124} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "E" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1721 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "F" Number of atoms: 659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 659 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "G" Number of atoms: 1334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1334 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 10, 'TRANS': 160} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "H" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1186 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain: "I" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 950 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 111} Chain: "J" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 534 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "K" Number of atoms: 912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 912 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 8, 'TRANS': 105} Chain: "L" Number of atoms: 380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 380 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "M" Number of atoms: 1048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1048 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 7, 'TRANS': 119} Chain breaks: 2 Chain: "N" Number of atoms: 1092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1092 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 125} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" 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: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 17102 SG CYS C 88 19.211 73.001 91.467 1.00 86.42 S ATOM 17115 SG CYS C 90 21.347 73.226 94.573 1.00 86.46 S ATOM 17150 SG CYS C 94 18.451 70.966 94.349 1.00 78.74 S ATOM 17172 SG CYS C 97 21.780 70.182 92.439 1.00 72.71 S ATOM 24462 SG CYS I 17 138.017 31.764 94.780 1.00 83.77 S ATOM 24486 SG CYS I 20 136.252 33.905 97.339 1.00 82.34 S ATOM 24647 SG CYS I 39 137.897 35.730 94.621 1.00 88.18 S ATOM 24672 SG CYS I 42 140.123 33.759 97.022 1.00 91.26 S ATOM 25024 SG CYS I 86 106.295 12.240 69.216 1.00 59.05 S ATOM 25048 SG CYS I 89 104.925 9.078 70.825 1.00 57.35 S ATOM 25252 SG CYS I 114 103.477 12.348 71.947 1.00 45.47 S ATOM 25287 SG CYS I 119 107.007 11.465 72.823 1.00 59.77 S ATOM 25398 SG CYS J 7 40.567 48.193 79.743 1.00 36.65 S ATOM 25422 SG CYS J 10 37.402 48.381 77.459 1.00 35.64 S ATOM 25686 SG CYS J 44 40.809 46.903 76.251 1.00 40.13 S ATOM 25692 SG CYS J 45 38.356 45.217 78.672 1.00 51.42 S ATOM 26838 SG CYS L 19 51.463 53.321 122.819 1.00 52.55 S ATOM 26857 SG CYS L 22 48.888 51.376 124.567 1.00 56.61 S ATOM 26974 SG CYS L 36 50.602 54.172 126.404 1.00 58.98 S ATOM 27000 SG CYS L 39 52.567 51.003 125.674 1.00 63.99 S ATOM 28708 SG CYS N 100 148.958 80.353 74.445 1.00478.86 S ATOM 28745 SG CYS N 105 151.601 80.390 76.917 1.00466.61 S ATOM 28998 SG CYS N 136 150.769 77.201 74.718 1.00494.89 S ATOM 29029 SG CYS N 140 148.968 78.001 77.846 1.00498.96 S Time building chain proxies: 6.16, per 1000 atoms: 0.21 Number of scatterers: 29315 At special positions: 0 Unit cell: (162.688, 174.496, 158.752, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 6 29.99 S 168 16.00 O 5490 8.00 N 5082 7.00 C 18569 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: 2.38 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 90 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 94 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 97 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 20 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 42 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 17 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 39 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 119 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 89 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 114 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 86 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 19 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 22 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 39 " pdb=" ZN N 701 " pdb="ZN ZN N 701 " - pdb=" SG CYS N 105 " pdb="ZN ZN N 701 " - pdb=" SG CYS N 136 " pdb="ZN ZN N 701 " - pdb=" SG CYS N 100 " pdb="ZN ZN N 701 " - pdb=" SG CYS N 140 " Number of angles added : 36 7202 Ramachandran restraints generated. 3601 Oldfield, 0 Emsley, 3601 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6922 Finding SS restraints... Secondary structure from input PDB file: 141 helices and 44 sheets defined 41.6% alpha, 20.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 382 through 386 Processing helix chain 'A' and resid 398 through 409 removed outlier: 3.995A pdb=" N GLU A 404 " --> pdb=" O ASP A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 439 removed outlier: 3.686A pdb=" N HIS A 439 " --> pdb=" O SER A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 467 No H-bonds generated for 'chain 'A' and resid 465 through 467' Processing helix chain 'A' and resid 488 through 493 Processing helix chain 'A' and resid 508 through 519 Processing helix chain 'A' and resid 520 through 524 Processing helix chain 'A' and resid 538 through 550 removed outlier: 3.528A pdb=" N LEU A 542 " --> pdb=" O VAL A 538 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG A 546 " --> pdb=" O LEU A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 565 Processing helix chain 'A' and resid 588 through 596 removed outlier: 3.957A pdb=" N LEU A 594 " --> pdb=" O GLN A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 616 removed outlier: 4.069A pdb=" N ASP A 614 " --> pdb=" O ASP A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 646 Processing helix chain 'A' and resid 651 through 684 removed outlier: 8.025A pdb=" N HIS A 662 " --> pdb=" O LEU A 658 " (cutoff:3.500A) removed outlier: 9.415A pdb=" N ASP A 663 " --> pdb=" O GLU A 659 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ILE A 664 " --> pdb=" O MET A 660 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU A 667 " --> pdb=" O ASP A 663 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASN A 678 " --> pdb=" O THR A 674 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ILE A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 693 removed outlier: 3.807A pdb=" N SER A 692 " --> pdb=" O GLY A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 722 Processing helix chain 'A' and resid 732 through 760 removed outlier: 3.686A pdb=" N LEU A 760 " --> pdb=" O ALA A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 772 Processing helix chain 'A' and resid 777 through 786 Processing helix chain 'A' and resid 832 through 869 removed outlier: 3.645A pdb=" N GLU A 845 " --> pdb=" O MET A 841 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLY A 846 " --> pdb=" O GLY A 842 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ALA A 855 " --> pdb=" O ALA A 851 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLY A 858 " --> pdb=" O THR A 854 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ARG A 862 " --> pdb=" O GLY A 858 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 894 Processing helix chain 'A' and resid 897 through 901 removed outlier: 4.068A pdb=" N VAL A 901 " --> pdb=" O GLY A 898 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 921 Processing helix chain 'A' and resid 926 through 934 Processing helix chain 'A' and resid 935 through 945 removed outlier: 3.594A pdb=" N LYS A 940 " --> pdb=" O GLU A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 970 Processing helix chain 'A' and resid 982 through 994 Processing helix chain 'A' and resid 1005 through 1020 Processing helix chain 'A' and resid 1027 through 1038 Processing helix chain 'A' and resid 1038 through 1049 Processing helix chain 'A' and resid 1050 through 1057 Processing helix chain 'A' and resid 1061 through 1080 removed outlier: 3.620A pdb=" N GLY A1070 " --> pdb=" O ASP A1066 " (cutoff:3.500A) Processing helix chain 'A' and resid 1086 through 1100 Proline residue: A1098 - end of helix Processing helix chain 'A' and resid 1120 through 1130 Processing helix chain 'A' and resid 1145 through 1149 Processing helix chain 'A' and resid 1150 through 1162 removed outlier: 3.514A pdb=" N ILE A1157 " --> pdb=" O ARG A1153 " (cutoff:3.500A) Processing helix chain 'A' and resid 1166 through 1169 No H-bonds generated for 'chain 'A' and resid 1166 through 1169' Processing helix chain 'A' and resid 1180 through 1184 removed outlier: 4.160A pdb=" N THR A1184 " --> pdb=" O PRO A1181 " (cutoff:3.500A) Processing helix chain 'A' and resid 1189 through 1199 removed outlier: 4.802A pdb=" N VAL A1195 " --> pdb=" O GLU A1191 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TYR A1196 " --> pdb=" O TRP A1192 " (cutoff:3.500A) Processing helix chain 'A' and resid 1203 through 1205 No H-bonds generated for 'chain 'A' and resid 1203 through 1205' Processing helix chain 'A' and resid 1217 through 1223 Processing helix chain 'A' and resid 1227 through 1240 removed outlier: 3.684A pdb=" N LYS A1234 " --> pdb=" O GLN A1230 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY A1238 " --> pdb=" O LYS A1234 " (cutoff:3.500A) Processing helix chain 'A' and resid 1280 through 1296 removed outlier: 3.758A pdb=" N LEU A1285 " --> pdb=" O ASP A1281 " (cutoff:3.500A) Processing helix chain 'A' and resid 1342 through 1347 Processing helix chain 'A' and resid 1361 through 1369 removed outlier: 3.623A pdb=" N ILE A1365 " --> pdb=" O ASP A1361 " (cutoff:3.500A) Processing helix chain 'A' and resid 1370 through 1389 removed outlier: 3.556A pdb=" N GLU A1379 " --> pdb=" O ARG A1375 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ASP A1389 " --> pdb=" O VAL A1385 " (cutoff:3.500A) Processing helix chain 'A' and resid 1394 through 1405 removed outlier: 3.573A pdb=" N LEU A1398 " --> pdb=" O ASN A1394 " (cutoff:3.500A) Processing helix chain 'A' and resid 1478 through 1482 Processing helix chain 'B' and resid 21 through 38 removed outlier: 3.978A pdb=" N TRP B 27 " --> pdb=" O GLN B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 53 removed outlier: 3.860A pdb=" N SER B 46 " --> pdb=" O GLN B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 61 Processing helix chain 'B' and resid 109 through 116 Processing helix chain 'B' and resid 167 through 174 Processing helix chain 'B' and resid 246 through 253 removed outlier: 4.106A pdb=" N ALA B 251 " --> pdb=" O ALA B 247 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ILE B 252 " --> pdb=" O LYS B 248 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N GLY B 253 " --> pdb=" O LYS B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 276 removed outlier: 3.659A pdb=" N VAL B 272 " --> pdb=" O PRO B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 286 Processing helix chain 'B' and resid 294 through 308 removed outlier: 3.886A pdb=" N MET B 300 " --> pdb=" O GLU B 296 " (cutoff:3.500A) Proline residue: B 303 - end of helix Processing helix chain 'B' and resid 313 through 323 Processing helix chain 'B' and resid 331 through 346 Processing helix chain 'B' and resid 348 through 352 Processing helix chain 'B' and resid 354 through 356 No H-bonds generated for 'chain 'B' and resid 354 through 356' Processing helix chain 'B' and resid 357 through 377 Processing helix chain 'B' and resid 387 through 389 No H-bonds generated for 'chain 'B' and resid 387 through 389' Processing helix chain 'B' and resid 395 through 424 removed outlier: 3.561A pdb=" N GLY B 406 " --> pdb=" O PHE B 402 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LYS B 421 " --> pdb=" O ILE B 417 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N PHE B 422 " --> pdb=" O TYR B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 435 removed outlier: 3.787A pdb=" N ALA B 434 " --> pdb=" O ASN B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 451 removed outlier: 3.509A pdb=" N SER B 441 " --> pdb=" O THR B 437 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER B 447 " --> pdb=" O GLY B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 482 Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 516 through 520 removed outlier: 4.143A pdb=" N ALA B 519 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 548 removed outlier: 3.520A pdb=" N GLU B 547 " --> pdb=" O GLU B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 594 Processing helix chain 'B' and resid 636 through 645 removed outlier: 3.605A pdb=" N ILE B 640 " --> pdb=" O LYS B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 646 through 648 No H-bonds generated for 'chain 'B' and resid 646 through 648' Processing helix chain 'B' and resid 652 through 659 Processing helix chain 'B' and resid 668 through 672 Processing helix chain 'B' and resid 699 through 704 removed outlier: 3.595A pdb=" N ILE B 703 " --> pdb=" O PRO B 700 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 710 removed outlier: 3.520A pdb=" N ILE B 710 " --> pdb=" O CYS B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 717 Processing helix chain 'B' and resid 718 through 729 removed outlier: 3.663A pdb=" N ASN B 722 " --> pdb=" O GLN B 718 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 766 Processing helix chain 'B' and resid 798 through 803 Processing helix chain 'B' and resid 969 through 972 Processing helix chain 'B' and resid 977 through 994 removed outlier: 3.756A pdb=" N LEU B 981 " --> pdb=" O THR B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 1007 through 1017 removed outlier: 3.623A pdb=" N ASP B1017 " --> pdb=" O ASN B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1054 through 1059 removed outlier: 3.571A pdb=" N LYS B1058 " --> pdb=" O MET B1054 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 41 removed outlier: 3.573A pdb=" N ILE C 39 " --> pdb=" O ARG C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 71 removed outlier: 3.598A pdb=" N HIS C 66 " --> pdb=" O GLU C 62 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU C 70 " --> pdb=" O HIS C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 82 removed outlier: 3.817A pdb=" N LYS C 81 " --> pdb=" O ASP C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 120 No H-bonds generated for 'chain 'C' and resid 118 through 120' Processing helix chain 'C' and resid 129 through 133 removed outlier: 3.724A pdb=" N ARG C 133 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 177 Processing helix chain 'C' and resid 199 through 203 Processing helix chain 'C' and resid 240 through 269 removed outlier: 3.746A pdb=" N VAL C 245 " --> pdb=" O PRO C 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 28 Processing helix chain 'D' and resid 33 through 50 Processing helix chain 'D' and resid 58 through 72 Processing helix chain 'D' and resid 76 through 89 removed outlier: 4.083A pdb=" N VAL D 83 " --> pdb=" O THR D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 104 Processing helix chain 'D' and resid 107 through 115 Processing helix chain 'D' and resid 116 through 119 Processing helix chain 'D' and resid 123 through 136 removed outlier: 4.203A pdb=" N GLN D 129 " --> pdb=" O GLU D 125 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ILE D 130 " --> pdb=" O GLU D 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 24 removed outlier: 4.276A pdb=" N THR E 7 " --> pdb=" O ASP E 3 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 34 Processing helix chain 'E' and resid 36 through 45 Processing helix chain 'E' and resid 54 through 59 Processing helix chain 'E' and resid 83 through 97 Processing helix chain 'E' and resid 111 through 120 Processing helix chain 'E' and resid 132 through 137 removed outlier: 3.576A pdb=" N LEU E 136 " --> pdb=" O GLN E 132 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ILE E 137 " --> pdb=" O GLN E 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 132 through 137' Processing helix chain 'E' and resid 138 through 142 Processing helix chain 'E' and resid 152 through 164 Processing helix chain 'E' and resid 166 through 170 Processing helix chain 'E' and resid 177 through 184 Processing helix chain 'F' and resid 58 through 75 Processing helix chain 'F' and resid 88 through 99 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 35 Processing helix chain 'H' and resid 83 through 88 Processing helix chain 'H' and resid 129 through 133 Processing helix chain 'I' and resid 63 through 67 Processing helix chain 'I' and resid 69 through 75 Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 30 through 38 Processing helix chain 'J' and resid 42 through 51 removed outlier: 3.973A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 60 Processing helix chain 'K' and resid 5 through 10 Processing helix chain 'K' and resid 39 through 51 removed outlier: 4.487A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 115 Processing helix chain 'M' and resid 15 through 19 Processing helix chain 'M' and resid 20 through 36 Processing helix chain 'M' and resid 37 through 42 Processing helix chain 'M' and resid 48 through 66 Processing helix chain 'M' and resid 229 through 240 removed outlier: 3.727A pdb=" N GLU M 233 " --> pdb=" O PRO M 229 " (cutoff:3.500A) Processing helix chain 'M' and resid 305 through 332 Processing helix chain 'M' and resid 333 through 335 No H-bonds generated for 'chain 'M' and resid 333 through 335' Processing helix chain 'N' and resid 42 through 47 Processing helix chain 'N' and resid 47 through 65 removed outlier: 3.869A pdb=" N LYS N 51 " --> pdb=" O ALA N 47 " (cutoff:3.500A) Processing helix chain 'N' and resid 71 through 79 Processing helix chain 'N' and resid 80 through 82 No H-bonds generated for 'chain 'N' and resid 80 through 82' Processing helix chain 'N' and resid 83 through 97 removed outlier: 3.801A pdb=" N VAL N 97 " --> pdb=" O GLU N 93 " (cutoff:3.500A) Processing helix chain 'N' and resid 131 through 135 removed outlier: 3.512A pdb=" N PHE N 135 " --> pdb=" O ARG N 132 " (cutoff:3.500A) Processing helix chain 'N' and resid 137 through 151 removed outlier: 3.582A pdb=" N TYR N 141 " --> pdb=" O SER N 137 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLN N 150 " --> pdb=" O PHE N 146 " (cutoff:3.500A) Processing helix chain 'N' and resid 155 through 162 removed outlier: 4.577A pdb=" N GLU N 160 " --> pdb=" O TRP N 157 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 364 through 369 removed outlier: 3.980A pdb=" N MET A 470 " --> pdb=" O PHE A 458 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN A 502 " --> pdb=" O ASN A 459 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N MET A 501 " --> pdb=" O THR A 365 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N THR A 365 " --> pdb=" O MET A 501 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 389 through 393 removed outlier: 3.879A pdb=" N TYR A 418 " --> pdb=" O GLU A 447 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N HIS A 449 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ALA A 416 " --> pdb=" O HIS A 449 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 526 through 527 removed outlier: 3.833A pdb=" N ARG A 532 " --> pdb=" O THR A 527 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 554 through 555 Processing sheet with id=AA5, first strand: chain 'A' and resid 579 through 581 removed outlier: 5.572A pdb=" N ILE A 579 " --> pdb=" O TYR H 93 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N TYR H 93 " --> pdb=" O ILE A 579 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS A 581 " --> pdb=" O VAL H 91 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N VAL H 12 " --> pdb=" O GLU H 31 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N GLU H 31 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 602 through 605 removed outlier: 6.666A pdb=" N VAL A 629 " --> pdb=" O ILE A 636 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 789 through 790 Processing sheet with id=AA8, first strand: chain 'A' and resid 792 through 793 Processing sheet with id=AA9, first strand: chain 'A' and resid 872 through 873 Processing sheet with id=AB1, first strand: chain 'A' and resid 902 through 905 Processing sheet with id=AB2, first strand: chain 'A' and resid 1306 through 1310 removed outlier: 3.661A pdb=" N LYS A1306 " --> pdb=" O ASP A1339 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU A1139 " --> pdb=" O THR A1338 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1164 through 1165 Processing sheet with id=AB4, first strand: chain 'A' and resid 1243 through 1247 removed outlier: 4.584A pdb=" N LEU A1255 " --> pdb=" O LEU A1216 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ILE A1261 " --> pdb=" O TRP A1210 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N TRP A1210 " --> pdb=" O ILE A1261 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N TYR A1177 " --> pdb=" O PRO A1209 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LEU A1211 " --> pdb=" O ILE A1175 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ILE A1175 " --> pdb=" O LEU A1211 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N ARG A1213 " --> pdb=" O THR A1173 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N THR A1173 " --> pdb=" O ARG A1213 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N GLU A1215 " --> pdb=" O ALA A1171 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR I 54 " --> pdb=" O ILE A1175 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N TYR A1177 " --> pdb=" O CYS I 52 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N CYS I 52 " --> pdb=" O TYR A1177 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1319 through 1322 Processing sheet with id=AB6, first strand: chain 'A' and resid 1471 through 1475 Processing sheet with id=AB7, first strand: chain 'B' and resid 65 through 67 removed outlier: 5.171A pdb=" N ASP B 127 " --> pdb=" O GLU B 89 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ILE B 91 " --> pdb=" O TYR B 125 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N TYR B 125 " --> pdb=" O ILE B 91 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N LEU B 93 " --> pdb=" O PRO B 123 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLY B 150 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL B 126 " --> pdb=" O PHE B 148 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N PHE B 148 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N ILE B 128 " --> pdb=" O LYS B 146 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LYS B 146 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N LYS B 130 " --> pdb=" O HIS B 144 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N HIS B 144 " --> pdb=" O LYS B 130 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N VAL B 132 " --> pdb=" O THR B 142 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N THR B 142 " --> pdb=" O VAL B 132 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 65 through 67 removed outlier: 3.615A pdb=" N GLN M 302 " --> pdb=" O ILE B 91 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AC1, first strand: chain 'B' and resid 185 through 187 Processing sheet with id=AC2, first strand: chain 'B' and resid 391 through 394 removed outlier: 6.591A pdb=" N ALA B 196 " --> pdb=" O ASN B 486 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 205 through 209 removed outlier: 3.642A pdb=" N TYR B 217 " --> pdb=" O MET B 239 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TRP B 236 " --> pdb=" O THR B 259 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=AC5, first strand: chain 'B' and resid 632 through 633 Processing sheet with id=AC6, first strand: chain 'B' and resid 551 through 552 removed outlier: 6.735A pdb=" N ILE B 567 " --> pdb=" O VAL B 574 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ILE B 576 " --> pdb=" O THR B 565 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N THR B 565 " --> pdb=" O ILE B 576 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU B 611 " --> pdb=" O ASP B 606 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 747 through 751 removed outlier: 3.613A pdb=" N SER B 808 " --> pdb=" O ARG B 927 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ARG B 924 " --> pdb=" O VAL B 904 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N VAL B 904 " --> pdb=" O ARG B 924 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N VAL B 926 " --> pdb=" O GLY B 902 " (cutoff:3.500A) removed outlier: 8.295A pdb=" N GLY B 902 " --> pdb=" O VAL B 926 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 747 through 751 removed outlier: 3.613A pdb=" N SER B 808 " --> pdb=" O ARG B 927 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ARG B 924 " --> pdb=" O VAL B 904 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N VAL B 904 " --> pdb=" O ARG B 924 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N VAL B 926 " --> pdb=" O GLY B 902 " (cutoff:3.500A) removed outlier: 8.295A pdb=" N GLY B 902 " --> pdb=" O VAL B 926 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N VAL B 907 " --> pdb=" O LYS L 46 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 759 through 760 Processing sheet with id=AD1, first strand: chain 'B' and resid 1025 through 1026 removed outlier: 7.300A pdb=" N VAL B 794 " --> pdb=" O GLY B 946 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N GLN B 948 " --> pdb=" O VAL B 794 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N MET B 796 " --> pdb=" O GLN B 948 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N PHE B1042 " --> pdb=" O ILE B 782 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 819 through 820 removed outlier: 3.765A pdb=" N SER B 819 " --> pdb=" O GLU B 827 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N GLU B 826 " --> pdb=" O THR B 872 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 865 through 867 removed outlier: 3.775A pdb=" N ILE B 867 " --> pdb=" O THR B 894 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 8 through 14 removed outlier: 6.468A pdb=" N LYS C 20 " --> pdb=" O THR C 12 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N LEU C 14 " --> pdb=" O ASN C 18 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ASN C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLY C 181 " --> pdb=" O GLU C 234 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 121 through 122 removed outlier: 6.653A pdb=" N GLU C 158 " --> pdb=" O ASN C 55 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ASN C 55 " --> pdb=" O GLU C 158 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ARG C 160 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N LYS C 166 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N ILE C 47 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N GLY C 168 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N ILE C 45 " --> pdb=" O GLY C 168 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 113 through 116 removed outlier: 6.665A pdb=" N ARG C 113 " --> pdb=" O LYS C 152 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N LYS C 152 " --> pdb=" O ARG C 113 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N VAL C 115 " --> pdb=" O ILE C 150 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 30 through 31 removed outlier: 4.911A pdb=" N ILE G 54 " --> pdb=" O PRO G 69 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LYS G 71 " --> pdb=" O ASP G 52 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR G 50 " --> pdb=" O LYS G 73 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ILE G 75 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N VAL G 48 " --> pdb=" O ILE G 75 " (cutoff:3.500A) removed outlier: 8.516A pdb=" N PHE G 77 " --> pdb=" O ILE G 46 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N ILE G 46 " --> pdb=" O PHE G 77 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 30 through 31 Processing sheet with id=AD9, first strand: chain 'E' and resid 60 through 63 removed outlier: 3.576A pdb=" N ARG E 101 " --> pdb=" O GLN E 71 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 81 through 82 removed outlier: 3.653A pdb=" N VAL E 82 " --> pdb=" O GLY E 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'E' and resid 147 through 150 removed outlier: 3.536A pdb=" N GLU E 147 " --> pdb=" O ILE E 194 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 169 through 170 removed outlier: 5.458A pdb=" N ILE G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N SER G 162 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N SER G 105 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N SER G 109 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N MET G 104 " --> pdb=" O ILE G 101 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N GLY G 96 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N VAL G 92 " --> pdb=" O GLY G 96 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N PHE G 98 " --> pdb=" O THR G 90 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 117 through 120 Processing sheet with id=AE5, first strand: chain 'I' and resid 25 through 29 Processing sheet with id=AE6, first strand: chain 'I' and resid 80 through 81 Processing sheet with id=AE7, first strand: chain 'K' and resid 19 through 23 Processing sheet with id=AE8, first strand: chain 'N' and resid 117 through 119 1343 hydrogen bonds defined for protein. 3672 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.75 Time building geometry restraints manager: 3.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9749 1.34 - 1.46: 5505 1.46 - 1.58: 14349 1.58 - 1.70: 0 1.70 - 1.82: 265 Bond restraints: 29868 Sorted by residual: bond pdb=" CB PRO L 14 " pdb=" CG PRO L 14 " ideal model delta sigma weight residual 1.492 1.565 -0.073 5.00e-02 4.00e+02 2.12e+00 bond pdb=" CB PRO C 2 " pdb=" CG PRO C 2 " ideal model delta sigma weight residual 1.492 1.552 -0.060 5.00e-02 4.00e+02 1.45e+00 bond pdb=" CB PRO I 9 " pdb=" CG PRO I 9 " ideal model delta sigma weight residual 1.492 1.548 -0.056 5.00e-02 4.00e+02 1.23e+00 bond pdb=" CB LYS N 153 " pdb=" CG LYS N 153 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.55e-01 bond pdb=" CB GLU B 600 " pdb=" CG GLU B 600 " ideal model delta sigma weight residual 1.520 1.491 0.029 3.00e-02 1.11e+03 9.37e-01 ... (remaining 29863 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 39188 1.81 - 3.62: 1031 3.62 - 5.44: 103 5.44 - 7.25: 15 7.25 - 9.06: 3 Bond angle restraints: 40340 Sorted by residual: angle pdb=" N LYS A 910 " pdb=" CA LYS A 910 " pdb=" C LYS A 910 " ideal model delta sigma weight residual 109.81 117.88 -8.07 2.21e+00 2.05e-01 1.33e+01 angle pdb=" N ARG E 52 " pdb=" CA ARG E 52 " pdb=" C ARG E 52 " ideal model delta sigma weight residual 109.81 116.70 -6.89 2.21e+00 2.05e-01 9.71e+00 angle pdb=" N THR B 616 " pdb=" CA THR B 616 " pdb=" C THR B 616 " ideal model delta sigma weight residual 112.88 108.93 3.95 1.29e+00 6.01e-01 9.37e+00 angle pdb=" C THR B 616 " pdb=" N ASP B 617 " pdb=" CA ASP B 617 " ideal model delta sigma weight residual 120.94 125.57 -4.63 1.57e+00 4.06e-01 8.71e+00 angle pdb=" C ASP A 876 " pdb=" N ALA A 877 " pdb=" CA ALA A 877 " ideal model delta sigma weight residual 121.54 127.12 -5.58 1.91e+00 2.74e-01 8.53e+00 ... (remaining 40335 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 16921 17.95 - 35.90: 1090 35.90 - 53.85: 229 53.85 - 71.79: 63 71.79 - 89.74: 47 Dihedral angle restraints: 18350 sinusoidal: 7675 harmonic: 10675 Sorted by residual: dihedral pdb=" CA ASN A1248 " pdb=" C ASN A1248 " pdb=" N ASP A1249 " pdb=" CA ASP A1249 " ideal model delta harmonic sigma weight residual 180.00 151.17 28.83 0 5.00e+00 4.00e-02 3.33e+01 dihedral pdb=" CA THR A1294 " pdb=" C THR A1294 " pdb=" N ASP A1295 " pdb=" CA ASP A1295 " ideal model delta harmonic sigma weight residual -180.00 -151.40 -28.60 0 5.00e+00 4.00e-02 3.27e+01 dihedral pdb=" CA GLY B 734 " pdb=" C GLY B 734 " pdb=" N VAL B 735 " pdb=" CA VAL B 735 " ideal model delta harmonic sigma weight residual 180.00 151.68 28.32 0 5.00e+00 4.00e-02 3.21e+01 ... (remaining 18347 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 3020 0.043 - 0.086: 1040 0.086 - 0.129: 402 0.129 - 0.172: 44 0.172 - 0.215: 4 Chirality restraints: 4510 Sorted by residual: chirality pdb=" CA ARG B 157 " pdb=" N ARG B 157 " pdb=" C ARG B 157 " pdb=" CB ARG B 157 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA ARG B 938 " pdb=" N ARG B 938 " pdb=" C ARG B 938 " pdb=" CB ARG B 938 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CB ILE A 621 " pdb=" CA ILE A 621 " pdb=" CG1 ILE A 621 " pdb=" CG2 ILE A 621 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.59e-01 ... (remaining 4507 not shown) Planarity restraints: 5224 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG J 47 " -0.359 9.50e-02 1.11e+02 1.62e-01 2.03e+01 pdb=" NE ARG J 47 " 0.034 2.00e-02 2.50e+03 pdb=" CZ ARG J 47 " -0.032 2.00e-02 2.50e+03 pdb=" NH1 ARG J 47 " 0.015 2.00e-02 2.50e+03 pdb=" NH2 ARG J 47 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 483 " -0.289 9.50e-02 1.11e+02 1.30e-01 1.35e+01 pdb=" NE ARG A 483 " 0.028 2.00e-02 2.50e+03 pdb=" CZ ARG A 483 " -0.028 2.00e-02 2.50e+03 pdb=" NH1 ARG A 483 " 0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG A 483 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 274 " -0.252 9.50e-02 1.11e+02 1.14e-01 1.10e+01 pdb=" NE ARG B 274 " 0.025 2.00e-02 2.50e+03 pdb=" CZ ARG B 274 " -0.028 2.00e-02 2.50e+03 pdb=" NH1 ARG B 274 " 0.012 2.00e-02 2.50e+03 pdb=" NH2 ARG B 274 " 0.001 2.00e-02 2.50e+03 ... (remaining 5221 not shown) Histogram of nonbonded interaction distances: 2.43 - 2.92: 11550 2.92 - 3.42: 28067 3.42 - 3.91: 48582 3.91 - 4.41: 56347 4.41 - 4.90: 93381 Nonbonded interactions: 237927 Sorted by model distance: nonbonded pdb=" NE2 GLN B 654 " pdb=" O ARG M 247 " model vdw 2.427 3.120 nonbonded pdb=" O GLY A1238 " pdb=" OE1 GLN N 115 " model vdw 2.530 3.040 nonbonded pdb=" O LEU A 486 " pdb=" OG1 THR A 489 " model vdw 2.558 3.040 nonbonded pdb=" OG1 THR K 77 " pdb=" O TYR K 81 " model vdw 2.564 3.040 nonbonded pdb=" O MET A1279 " pdb=" ND2 ASN N 124 " model vdw 2.565 3.120 ... (remaining 237922 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.000 Normalize map: mean=0, sd=1: 4.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.460 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 32.260 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 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 : 0.003 0.073 29892 Z= 0.139 Angle : 0.717 15.639 40376 Z= 0.406 Chirality : 0.049 0.215 4510 Planarity : 0.009 0.162 5224 Dihedral : 13.884 89.742 11428 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 1.65 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.94 % Favored : 97.03 % Rotamer: Outliers : 0.99 % Allowed : 3.76 % Favored : 95.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.13), residues: 3601 helix: -1.39 (0.12), residues: 1259 sheet: 0.21 (0.21), residues: 544 loop : -0.11 (0.14), residues: 1798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.036 0.004 ARG J 47 TYR 0.027 0.005 TYR A 669 PHE 0.026 0.002 PHE B 805 TRP 0.038 0.003 TRP B 453 HIS 0.007 0.001 HIS M 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (29868) covalent geometry : angle 0.69987 / 0.40 (40340) hydrogen bonds : bond 0.18834 / 12.44 ( 1306) hydrogen bonds : angle 7.78462 / 5.55 ( 3672) metal coordination : bond 0.00993 / 0.58 ( 24) metal coordination : angle 5.22718 / 3.26 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7202 Ramachandran restraints generated. 3601 Oldfield, 0 Emsley, 3601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7202 Ramachandran restraints generated. 3601 Oldfield, 0 Emsley, 3601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 3258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 528 time to evaluate : 0.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 467 MET cc_start: 0.2164 (OUTLIER) cc_final: 0.1362 (pp-130) REVERT: A 470 MET cc_start: 0.8870 (mtm) cc_final: 0.8323 (mtm) REVERT: A 862 ARG cc_start: 0.7474 (ttt-90) cc_final: 0.7118 (mtp-110) REVERT: A 868 MET cc_start: 0.8417 (mtm) cc_final: 0.8160 (mtm) REVERT: A 899 GLU cc_start: 0.8564 (pt0) cc_final: 0.8253 (pm20) REVERT: A 940 LYS cc_start: 0.8576 (ttpp) cc_final: 0.8335 (tmmt) REVERT: A 1199 MET cc_start: 0.5372 (ppp) cc_final: 0.4451 (mpm) REVERT: A 1243 LEU cc_start: 0.8299 (tp) cc_final: 0.7985 (mm) REVERT: A 1255 LEU cc_start: 0.8254 (tp) cc_final: 0.7782 (mt) REVERT: A 1262 MET cc_start: 0.6962 (ttp) cc_final: 0.6632 (ttt) REVERT: A 1292 MET cc_start: 0.7033 (mtm) cc_final: 0.6805 (mmp) REVERT: A 1344 MET cc_start: 0.8054 (tpt) cc_final: 0.7778 (ttt) REVERT: A 1388 PHE cc_start: 0.8587 (t80) cc_final: 0.8249 (t80) REVERT: A 1405 MET cc_start: 0.8951 (mtp) cc_final: 0.8715 (mtm) REVERT: B 155 MET cc_start: 0.8851 (ttm) cc_final: 0.8527 (ttm) REVERT: B 200 MET cc_start: 0.8821 (OUTLIER) cc_final: 0.8531 (tpt) REVERT: B 222 ARG cc_start: 0.8218 (mtp-110) cc_final: 0.7902 (mtp85) REVERT: B 234 THR cc_start: 0.9104 (t) cc_final: 0.8797 (m) REVERT: B 298 MET cc_start: 0.8704 (mmt) cc_final: 0.8490 (mmt) REVERT: B 307 GLU cc_start: 0.7835 (tp30) cc_final: 0.7473 (tm-30) REVERT: B 347 MET cc_start: 0.8463 (ptt) cc_final: 0.7884 (ttt) REVERT: B 381 GLU cc_start: 0.8384 (mt-10) cc_final: 0.8057 (mp0) REVERT: B 388 TYR cc_start: 0.8935 (OUTLIER) cc_final: 0.8096 (m-80) REVERT: B 525 ASN cc_start: 0.9058 (OUTLIER) cc_final: 0.8450 (t0) REVERT: B 550 MET cc_start: 0.9135 (ttp) cc_final: 0.8930 (ttm) REVERT: B 897 ARG cc_start: 0.7823 (ttm170) cc_final: 0.7507 (ttp-170) REVERT: C 19 VAL cc_start: 0.9060 (OUTLIER) cc_final: 0.8794 (p) REVERT: C 212 ASP cc_start: 0.7284 (OUTLIER) cc_final: 0.6830 (p0) REVERT: D 68 THR cc_start: 0.7941 (p) cc_final: 0.6873 (p) REVERT: D 104 CYS cc_start: 0.7667 (m) cc_final: 0.6422 (t) REVERT: E 8 TYR cc_start: 0.7682 (t80) cc_final: 0.7351 (t80) REVERT: E 72 MET cc_start: 0.8769 (ttp) cc_final: 0.8529 (ttm) REVERT: E 158 GLU cc_start: 0.8393 (tt0) cc_final: 0.8040 (mt-10) REVERT: G 97 LEU cc_start: 0.9245 (mt) cc_final: 0.8905 (tt) REVERT: H 65 TYR cc_start: 0.8418 (m-80) cc_final: 0.8203 (m-10) REVERT: H 92 MET cc_start: 0.9347 (mtm) cc_final: 0.9123 (mtm) REVERT: H 146 LYS cc_start: 0.8733 (tttt) cc_final: 0.8530 (ttmt) REVERT: I 50 ASN cc_start: 0.6670 (t0) cc_final: 0.6359 (p0) REVERT: I 56 ASN cc_start: 0.8188 (t0) cc_final: 0.7554 (p0) REVERT: J 58 LYS cc_start: 0.8733 (mmtt) cc_final: 0.8511 (mttp) REVERT: K 22 ASN cc_start: 0.8565 (m-40) cc_final: 0.8352 (m-40) REVERT: N 87 TYR cc_start: 0.9236 (t80) cc_final: 0.9034 (t80) REVERT: N 146 PHE cc_start: 0.8799 (t80) cc_final: 0.8498 (t80) outliers start: 32 outliers final: 9 residues processed: 555 average time/residue: 0.7799 time to fit residues: 498.6192 Evaluate side-chains 359 residues out of total 3258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 344 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 467 MET Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 1026 ASP Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 525 ASN Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain H residue 7 GLU Chi-restraints excluded: chain N residue 168 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.3980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.2980 chunk 207 optimal weight: 0.3980 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.0070 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 2.9990 overall best weight: 0.6200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 449 HIS A 472 HIS A 721 HIS A 723 ASN A 791 GLN A 861 GLN A1032 GLN ** A1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1220 HIS A1230 GLN B 471 ASN B 941 GLN B1007 ASN C 83 GLN C 177 ASN C 190 ASN C 268 GLN ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 122 ASN H 133 HIS J 26 GLN ** M 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 318 GLN ** N 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 86 HIS N 124 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.111769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.075181 restraints weight = 58479.135| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.24 r_work: 0.3055 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 29892 Z= 0.154 Angle : 0.651 12.175 40376 Z= 0.340 Chirality : 0.046 0.252 4510 Planarity : 0.004 0.045 5224 Dihedral : 6.185 83.850 4016 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.00 % Allowed : 10.36 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.14), residues: 3601 helix: 0.41 (0.14), residues: 1292 sheet: 0.36 (0.20), residues: 585 loop : 0.36 (0.15), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG G 16 TYR 0.033 0.002 TYR N 102 PHE 0.038 0.002 PHE M 52 TRP 0.019 0.002 TRP C 176 HIS 0.015 0.001 HIS N 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 (29868) covalent geometry : angle 0.64024 / 0.34 (40340) hydrogen bonds : bond 0.04990 / 3.31 ( 1306) hydrogen bonds : angle 5.24892 / 3.73 ( 3672) metal coordination : bond 0.00567 / 0.36 ( 24) metal coordination : angle 4.03345 / 2.54 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7202 Ramachandran restraints generated. 3601 Oldfield, 0 Emsley, 3601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7202 Ramachandran restraints generated. 3601 Oldfield, 0 Emsley, 3601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 3258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 386 time to evaluate : 1.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 467 MET cc_start: 0.2642 (OUTLIER) cc_final: 0.1930 (pp-130) REVERT: A 526 VAL cc_start: 0.8133 (t) cc_final: 0.7871 (p) REVERT: A 797 ARG cc_start: 0.9091 (OUTLIER) cc_final: 0.8848 (mtm180) REVERT: A 899 GLU cc_start: 0.8317 (pt0) cc_final: 0.8030 (pm20) REVERT: A 940 LYS cc_start: 0.8544 (ttpp) cc_final: 0.8331 (tmmt) REVERT: A 1199 MET cc_start: 0.5810 (ppp) cc_final: 0.5043 (mpm) REVERT: A 1292 MET cc_start: 0.6427 (mtm) cc_final: 0.6222 (mmp) REVERT: A 1296 MET cc_start: 0.7492 (tpp) cc_final: 0.7273 (tpp) REVERT: A 1362 ILE cc_start: 0.8262 (OUTLIER) cc_final: 0.8022 (mm) REVERT: B 169 ARG cc_start: 0.8224 (mtp-110) cc_final: 0.7974 (mmp-170) REVERT: B 200 MET cc_start: 0.8836 (OUTLIER) cc_final: 0.8526 (tpt) REVERT: B 222 ARG cc_start: 0.8422 (mtp-110) cc_final: 0.8137 (mmm-85) REVERT: B 234 THR cc_start: 0.9180 (OUTLIER) cc_final: 0.8965 (m) REVERT: B 307 GLU cc_start: 0.7906 (tp30) cc_final: 0.7590 (tm-30) REVERT: B 347 MET cc_start: 0.8702 (OUTLIER) cc_final: 0.8171 (ttt) REVERT: B 407 MET cc_start: 0.8325 (OUTLIER) cc_final: 0.7710 (mpp) REVERT: B 550 MET cc_start: 0.9180 (ttp) cc_final: 0.8932 (tmm) REVERT: B 798 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.8382 (tpm170) REVERT: C 109 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.7123 (mp0) REVERT: C 199 LYS cc_start: 0.9057 (mttt) cc_final: 0.8831 (mttm) REVERT: D 38 HIS cc_start: 0.8510 (t70) cc_final: 0.8158 (t70) REVERT: D 61 PHE cc_start: 0.9391 (t80) cc_final: 0.9094 (t80) REVERT: D 66 ASN cc_start: 0.9092 (m110) cc_final: 0.8869 (p0) REVERT: D 68 THR cc_start: 0.9482 (p) cc_final: 0.8967 (p) REVERT: D 104 CYS cc_start: 0.7495 (m) cc_final: 0.6535 (t) REVERT: E 8 TYR cc_start: 0.7326 (t80) cc_final: 0.6948 (t80) REVERT: F 64 ARG cc_start: 0.8402 (tpp80) cc_final: 0.8193 (ttt-90) REVERT: F 91 LEU cc_start: 0.8858 (mt) cc_final: 0.8607 (mm) REVERT: G 60 GLN cc_start: 0.8559 (mm110) cc_final: 0.8042 (mp10) REVERT: G 104 MET cc_start: 0.7933 (tpt) cc_final: 0.7418 (tpp) REVERT: G 108 ILE cc_start: 0.6561 (OUTLIER) cc_final: 0.6101 (mm) REVERT: G 128 TYR cc_start: 0.7202 (m-80) cc_final: 0.6737 (m-80) REVERT: G 140 ASP cc_start: 0.8368 (p0) cc_final: 0.7951 (p0) REVERT: G 141 ASP cc_start: 0.6033 (m-30) cc_final: 0.5084 (m-30) REVERT: G 142 GLU cc_start: 0.8681 (mp0) cc_final: 0.7643 (pm20) REVERT: H 92 MET cc_start: 0.9355 (mtm) cc_final: 0.9115 (mtm) REVERT: I 34 ILE cc_start: 0.8337 (tp) cc_final: 0.8069 (tp) REVERT: I 56 ASN cc_start: 0.8238 (t0) cc_final: 0.7419 (p0) REVERT: I 92 LYS cc_start: 0.8452 (mmmm) cc_final: 0.8131 (mmtp) REVERT: I 93 GLU cc_start: 0.8656 (tt0) cc_final: 0.8391 (tt0) REVERT: J 31 GLU cc_start: 0.8874 (OUTLIER) cc_final: 0.8598 (mt-10) REVERT: K 110 LYS cc_start: 0.8469 (mttt) cc_final: 0.8264 (mttt) REVERT: L 21 GLU cc_start: 0.8413 (tm-30) cc_final: 0.8138 (tm-30) REVERT: M 232 MET cc_start: 0.8767 (mmm) cc_final: 0.8488 (mmt) REVERT: M 237 MET cc_start: 0.8277 (mpt) cc_final: 0.8045 (mmm) REVERT: M 315 GLN cc_start: 0.8596 (tp40) cc_final: 0.8387 (tp40) REVERT: M 319 ASN cc_start: 0.8284 (m-40) cc_final: 0.7863 (m-40) REVERT: N 73 GLU cc_start: 0.8353 (tp30) cc_final: 0.8140 (tm-30) REVERT: N 74 PHE cc_start: 0.8941 (t80) cc_final: 0.8683 (t80) REVERT: N 146 PHE cc_start: 0.9030 (t80) cc_final: 0.8242 (t80) outliers start: 65 outliers final: 17 residues processed: 423 average time/residue: 0.7490 time to fit residues: 365.3369 Evaluate side-chains 367 residues out of total 3258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 339 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 467 MET Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 797 ARG Chi-restraints excluded: chain A residue 1345 ARG Chi-restraints excluded: chain A residue 1362 ILE Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 99 TRP Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 648 TYR Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 798 ARG Chi-restraints excluded: chain C residue 86 ARG Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 150 THR Chi-restraints excluded: chain H residue 7 GLU Chi-restraints excluded: chain J residue 31 GLU Chi-restraints excluded: chain M residue 243 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 108 optimal weight: 2.9990 chunk 338 optimal weight: 0.9990 chunk 280 optimal weight: 7.9990 chunk 248 optimal weight: 0.3980 chunk 209 optimal weight: 1.9990 chunk 133 optimal weight: 0.3980 chunk 17 optimal weight: 0.9990 chunk 170 optimal weight: 0.0060 chunk 346 optimal weight: 6.9990 chunk 116 optimal weight: 1.9990 chunk 291 optimal weight: 0.0770 overall best weight: 0.3756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 723 ASN ** A1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1310 HIS B 350 HIS C 268 GLN D 19 GLN D 47 GLN H 76 ASN I 50 ASN N 60 HIS N 86 HIS N 124 ASN N 138 ASN ** N 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.112317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.075963 restraints weight = 58580.175| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.41 r_work: 0.3061 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 29892 Z= 0.122 Angle : 0.579 10.898 40376 Z= 0.301 Chirality : 0.044 0.206 4510 Planarity : 0.004 0.047 5224 Dihedral : 5.448 82.285 4001 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.13 % Allowed : 12.00 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.14), residues: 3601 helix: 1.04 (0.15), residues: 1273 sheet: 0.43 (0.20), residues: 591 loop : 0.59 (0.15), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG M 19 TYR 0.025 0.001 TYR M 231 PHE 0.039 0.002 PHE M 52 TRP 0.016 0.002 TRP C 49 HIS 0.012 0.001 HIS N 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (29868) covalent geometry : angle 0.57153 / 0.30 (40340) hydrogen bonds : bond 0.04259 / 2.83 ( 1306) hydrogen bonds : angle 4.85967 / 3.45 ( 3672) metal coordination : bond 0.00396 / 0.26 ( 24) metal coordination : angle 3.14437 / 2.02 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7202 Ramachandran restraints generated. 3601 Oldfield, 0 Emsley, 3601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7202 Ramachandran restraints generated. 3601 Oldfield, 0 Emsley, 3601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 3258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 365 time to evaluate : 1.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 660 MET cc_start: 0.9179 (OUTLIER) cc_final: 0.7637 (mmt) REVERT: A 899 GLU cc_start: 0.8443 (pt0) cc_final: 0.8162 (pm20) REVERT: A 940 LYS cc_start: 0.8560 (ttpp) cc_final: 0.8345 (tmmt) REVERT: A 1199 MET cc_start: 0.5721 (ppp) cc_final: 0.4959 (mpm) REVERT: A 1292 MET cc_start: 0.6777 (mtm) cc_final: 0.6369 (mmp) REVERT: B 200 MET cc_start: 0.8789 (OUTLIER) cc_final: 0.8560 (tpt) REVERT: B 222 ARG cc_start: 0.8459 (mtp-110) cc_final: 0.8178 (mmm-85) REVERT: B 307 GLU cc_start: 0.7912 (tp30) cc_final: 0.7608 (tm-30) REVERT: B 347 MET cc_start: 0.8685 (OUTLIER) cc_final: 0.8184 (ttt) REVERT: B 410 ASN cc_start: 0.8329 (m-40) cc_final: 0.8028 (m110) REVERT: B 416 ARG cc_start: 0.7764 (mtp-110) cc_final: 0.7500 (mtt180) REVERT: B 785 TYR cc_start: 0.7925 (OUTLIER) cc_final: 0.4857 (m-80) REVERT: B 798 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.8381 (tpm170) REVERT: B 838 GLN cc_start: 0.7768 (tt0) cc_final: 0.7206 (tp40) REVERT: B 892 CYS cc_start: 0.7224 (m) cc_final: 0.6712 (p) REVERT: C 109 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7249 (mp0) REVERT: D 61 PHE cc_start: 0.9412 (t80) cc_final: 0.9170 (t80) REVERT: E 8 TYR cc_start: 0.7288 (t80) cc_final: 0.6883 (t80) REVERT: F 75 MET cc_start: 0.8087 (mtt) cc_final: 0.7879 (mtt) REVERT: G 3 TYR cc_start: 0.8286 (m-80) cc_final: 0.8061 (m-80) REVERT: G 29 LYS cc_start: 0.9518 (mtpt) cc_final: 0.8888 (tptp) REVERT: G 60 GLN cc_start: 0.8620 (mm110) cc_final: 0.8083 (mp10) REVERT: G 71 LYS cc_start: 0.7980 (mttt) cc_final: 0.7720 (mttt) REVERT: G 97 LEU cc_start: 0.8919 (mt) cc_final: 0.8651 (tp) REVERT: G 104 MET cc_start: 0.8021 (tpt) cc_final: 0.7743 (tpp) REVERT: G 108 ILE cc_start: 0.6937 (OUTLIER) cc_final: 0.6478 (mm) REVERT: G 140 ASP cc_start: 0.8352 (p0) cc_final: 0.7989 (p0) REVERT: G 141 ASP cc_start: 0.6266 (m-30) cc_final: 0.5389 (m-30) REVERT: G 142 GLU cc_start: 0.8696 (mp0) cc_final: 0.7605 (pm20) REVERT: H 92 MET cc_start: 0.9365 (mtm) cc_final: 0.9123 (mtm) REVERT: I 56 ASN cc_start: 0.8046 (t0) cc_final: 0.7113 (p0) REVERT: I 57 LYS cc_start: 0.7274 (mmtp) cc_final: 0.6777 (mtmt) REVERT: I 92 LYS cc_start: 0.8428 (mmmm) cc_final: 0.8166 (mmtp) REVERT: I 93 GLU cc_start: 0.8572 (tt0) cc_final: 0.8364 (tt0) REVERT: K 16 GLU cc_start: 0.7233 (mt-10) cc_final: 0.7024 (mt-10) REVERT: L 21 GLU cc_start: 0.8416 (tm-30) cc_final: 0.8134 (tm-30) REVERT: M 25 ARG cc_start: 0.9157 (ttm-80) cc_final: 0.8773 (mtm180) REVERT: M 232 MET cc_start: 0.8817 (mmm) cc_final: 0.8440 (mmt) REVERT: M 237 MET cc_start: 0.8324 (mpt) cc_final: 0.8077 (mmm) REVERT: N 102 TYR cc_start: 0.8397 (t80) cc_final: 0.8193 (t80) REVERT: N 146 PHE cc_start: 0.9106 (t80) cc_final: 0.8559 (t80) outliers start: 69 outliers final: 20 residues processed: 404 average time/residue: 0.7108 time to fit residues: 333.6872 Evaluate side-chains 355 residues out of total 3258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 328 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 467 MET Chi-restraints excluded: chain A residue 660 MET Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain A residue 1345 ARG Chi-restraints excluded: chain B residue 99 TRP Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 264 LYS Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 648 TYR Chi-restraints excluded: chain B residue 674 MET Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain B residue 798 ARG Chi-restraints excluded: chain C residue 86 ARG Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain D residue 16 ASP Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 156 ASP Chi-restraints excluded: chain G residue 158 PHE Chi-restraints excluded: chain H residue 7 GLU Chi-restraints excluded: chain H residue 146 LYS Chi-restraints excluded: chain N residue 70 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 189 optimal weight: 2.9990 chunk 230 optimal weight: 0.0030 chunk 123 optimal weight: 6.9990 chunk 109 optimal weight: 0.7980 chunk 304 optimal weight: 2.9990 chunk 331 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 199 optimal weight: 0.0470 chunk 97 optimal weight: 0.7980 chunk 201 optimal weight: 1.9990 chunk 176 optimal weight: 0.8980 overall best weight: 0.5088 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 144 HIS ** B 741 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 268 GLN D 43 HIS H 76 ASN N 124 ASN N 138 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.111714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.074287 restraints weight = 58647.396| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.29 r_work: 0.3031 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 29892 Z= 0.130 Angle : 0.586 11.579 40376 Z= 0.302 Chirality : 0.045 0.279 4510 Planarity : 0.004 0.045 5224 Dihedral : 5.182 81.809 3998 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.67 % Allowed : 13.36 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.07 (0.14), residues: 3601 helix: 1.19 (0.15), residues: 1275 sheet: 0.47 (0.21), residues: 582 loop : 0.62 (0.15), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 100 TYR 0.024 0.001 TYR M 231 PHE 0.041 0.002 PHE M 52 TRP 0.016 0.002 TRP C 49 HIS 0.005 0.001 HIS C 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (29868) covalent geometry : angle 0.57976 / 0.30 (40340) hydrogen bonds : bond 0.04025 / 2.68 ( 1306) hydrogen bonds : angle 4.74150 / 3.37 ( 3672) metal coordination : bond 0.00419 / 0.28 ( 24) metal coordination : angle 3.01253 / 1.92 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7202 Ramachandran restraints generated. 3601 Oldfield, 0 Emsley, 3601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7202 Ramachandran restraints generated. 3601 Oldfield, 0 Emsley, 3601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 3258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 344 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 467 MET cc_start: 0.2244 (OUTLIER) cc_final: 0.1738 (pp-130) REVERT: A 660 MET cc_start: 0.9152 (OUTLIER) cc_final: 0.7708 (mmt) REVERT: A 899 GLU cc_start: 0.8459 (pt0) cc_final: 0.8170 (pm20) REVERT: A 940 LYS cc_start: 0.8592 (ttpp) cc_final: 0.8354 (tmmt) REVERT: A 1199 MET cc_start: 0.5824 (ppp) cc_final: 0.5152 (mpm) REVERT: A 1292 MET cc_start: 0.6894 (mtm) cc_final: 0.6497 (mmp) REVERT: A 1344 MET cc_start: 0.8119 (tpp) cc_final: 0.7778 (ttt) REVERT: B 169 ARG cc_start: 0.8192 (mtp-110) cc_final: 0.7945 (mmp-170) REVERT: B 200 MET cc_start: 0.8717 (OUTLIER) cc_final: 0.8462 (tpt) REVERT: B 222 ARG cc_start: 0.8517 (mtp-110) cc_final: 0.8145 (mmm-85) REVERT: B 307 GLU cc_start: 0.8051 (tp30) cc_final: 0.7761 (tm-30) REVERT: B 347 MET cc_start: 0.8661 (OUTLIER) cc_final: 0.8158 (ttt) REVERT: B 410 ASN cc_start: 0.8215 (m-40) cc_final: 0.7912 (m110) REVERT: B 724 TYR cc_start: 0.8659 (m-10) cc_final: 0.8326 (t80) REVERT: B 785 TYR cc_start: 0.7884 (OUTLIER) cc_final: 0.4780 (m-80) REVERT: B 798 ARG cc_start: 0.8534 (OUTLIER) cc_final: 0.8323 (tpm170) REVERT: B 838 GLN cc_start: 0.7766 (tt0) cc_final: 0.7221 (tp40) REVERT: B 892 CYS cc_start: 0.7090 (m) cc_final: 0.6764 (p) REVERT: C 41 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.8116 (mt-10) REVERT: C 109 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7220 (mp0) REVERT: D 38 HIS cc_start: 0.8634 (t70) cc_final: 0.8427 (t70) REVERT: D 71 PHE cc_start: 0.8827 (m-10) cc_final: 0.8401 (m-10) REVERT: G 29 LYS cc_start: 0.9523 (mtpt) cc_final: 0.8913 (tptp) REVERT: G 60 GLN cc_start: 0.8743 (mm110) cc_final: 0.8134 (mp10) REVERT: G 97 LEU cc_start: 0.8958 (mt) cc_final: 0.8726 (tp) REVERT: G 104 MET cc_start: 0.8152 (tpt) cc_final: 0.7752 (tpp) REVERT: G 108 ILE cc_start: 0.6586 (OUTLIER) cc_final: 0.6152 (mm) REVERT: G 140 ASP cc_start: 0.8441 (p0) cc_final: 0.7996 (p0) REVERT: G 141 ASP cc_start: 0.6406 (m-30) cc_final: 0.5486 (m-30) REVERT: G 142 GLU cc_start: 0.8445 (mp0) cc_final: 0.7704 (pm20) REVERT: H 92 MET cc_start: 0.9354 (mtm) cc_final: 0.9123 (mtm) REVERT: I 56 ASN cc_start: 0.8051 (t0) cc_final: 0.7114 (p0) REVERT: I 57 LYS cc_start: 0.7284 (mmtp) cc_final: 0.6814 (mtmt) REVERT: I 69 ILE cc_start: 0.8239 (mt) cc_final: 0.7943 (mp) REVERT: I 92 LYS cc_start: 0.8436 (mmmm) cc_final: 0.8129 (mmtp) REVERT: I 93 GLU cc_start: 0.8547 (tt0) cc_final: 0.8339 (tt0) REVERT: J 28 GLU cc_start: 0.8038 (mm-30) cc_final: 0.7700 (mm-30) REVERT: K 13 PHE cc_start: 0.8190 (p90) cc_final: 0.7844 (p90) REVERT: K 16 GLU cc_start: 0.7184 (mt-10) cc_final: 0.6721 (mt-10) REVERT: L 21 GLU cc_start: 0.8413 (tm-30) cc_final: 0.8100 (tm-30) REVERT: M 27 MET cc_start: 0.8949 (mpm) cc_final: 0.8696 (mmp) REVERT: M 237 MET cc_start: 0.8353 (mpt) cc_final: 0.8136 (mmm) REVERT: M 299 MET cc_start: 0.6246 (OUTLIER) cc_final: 0.5978 (ptt) REVERT: M 315 GLN cc_start: 0.8744 (tp40) cc_final: 0.8395 (tp40) outliers start: 54 outliers final: 17 residues processed: 371 average time/residue: 0.6988 time to fit residues: 302.3212 Evaluate side-chains 348 residues out of total 3258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 321 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 467 MET Chi-restraints excluded: chain A residue 660 MET Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain B residue 99 TRP Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 264 LYS Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 648 TYR Chi-restraints excluded: chain B residue 674 MET Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain B residue 798 ARG Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 86 ARG Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain D residue 16 ASP Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 158 PHE Chi-restraints excluded: chain H residue 7 GLU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain M residue 299 MET Chi-restraints excluded: chain N residue 70 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 123 optimal weight: 6.9990 chunk 34 optimal weight: 0.7980 chunk 212 optimal weight: 0.6980 chunk 79 optimal weight: 8.9990 chunk 146 optimal weight: 3.9990 chunk 347 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 327 optimal weight: 0.5980 chunk 1 optimal weight: 0.7980 chunk 106 optimal weight: 1.9990 chunk 176 optimal weight: 0.2980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1163 HIS ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 HIS ** B 741 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1021 HIS C 111 GLN C 268 GLN G 28 GLN H 76 ASN I 67 GLN N 124 ASN N 138 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.111359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.073754 restraints weight = 59060.619| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 2.31 r_work: 0.3019 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 29892 Z= 0.140 Angle : 0.587 11.734 40376 Z= 0.301 Chirality : 0.045 0.296 4510 Planarity : 0.004 0.052 5224 Dihedral : 5.077 81.205 3998 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.00 % Allowed : 13.54 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 (0.14), residues: 3601 helix: 1.27 (0.15), residues: 1272 sheet: 0.49 (0.20), residues: 586 loop : 0.55 (0.15), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 416 TYR 0.019 0.002 TYR M 231 PHE 0.043 0.002 PHE M 52 TRP 0.016 0.002 TRP C 49 HIS 0.005 0.001 HIS C 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 (29868) covalent geometry : angle 0.57936 / 0.30 (40340) hydrogen bonds : bond 0.03974 / 2.65 ( 1306) hydrogen bonds : angle 4.65811 / 3.30 ( 3672) metal coordination : bond 0.00435 / 0.28 ( 24) metal coordination : angle 3.18379 / 2.01 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7202 Ramachandran restraints generated. 3601 Oldfield, 0 Emsley, 3601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7202 Ramachandran restraints generated. 3601 Oldfield, 0 Emsley, 3601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 3258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 340 time to evaluate : 1.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 467 MET cc_start: 0.2411 (OUTLIER) cc_final: 0.1886 (pp-130) REVERT: A 520 MET cc_start: 0.8839 (mmt) cc_final: 0.8516 (mmm) REVERT: A 660 MET cc_start: 0.9148 (OUTLIER) cc_final: 0.7652 (mmt) REVERT: A 899 GLU cc_start: 0.8507 (pt0) cc_final: 0.8226 (pm20) REVERT: A 940 LYS cc_start: 0.8612 (ttpp) cc_final: 0.8358 (tmmt) REVERT: A 1199 MET cc_start: 0.5765 (ppp) cc_final: 0.5154 (mpm) REVERT: A 1292 MET cc_start: 0.7141 (mtm) cc_final: 0.6563 (mmp) REVERT: A 1344 MET cc_start: 0.7984 (tpp) cc_final: 0.7619 (ttt) REVERT: B 200 MET cc_start: 0.8747 (OUTLIER) cc_final: 0.8478 (tpt) REVERT: B 222 ARG cc_start: 0.8517 (mtp-110) cc_final: 0.8158 (mmm-85) REVERT: B 307 GLU cc_start: 0.8057 (tp30) cc_final: 0.7791 (tm-30) REVERT: B 347 MET cc_start: 0.8669 (OUTLIER) cc_final: 0.8143 (ttt) REVERT: B 410 ASN cc_start: 0.8231 (m-40) cc_final: 0.7931 (m110) REVERT: B 525 ASN cc_start: 0.9013 (OUTLIER) cc_final: 0.8601 (t0) REVERT: B 724 TYR cc_start: 0.8671 (m-10) cc_final: 0.8319 (t80) REVERT: B 785 TYR cc_start: 0.7905 (OUTLIER) cc_final: 0.4777 (m-80) REVERT: B 798 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.8316 (tpm170) REVERT: B 838 GLN cc_start: 0.7773 (tt0) cc_final: 0.7212 (tp40) REVERT: B 892 CYS cc_start: 0.7081 (OUTLIER) cc_final: 0.6760 (p) REVERT: C 41 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.8158 (mt-10) REVERT: C 109 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7273 (mp0) REVERT: D 16 ASP cc_start: 0.8269 (t0) cc_final: 0.8039 (t0) REVERT: D 70 ARG cc_start: 0.8228 (ptp-110) cc_final: 0.7972 (ptp-110) REVERT: D 71 PHE cc_start: 0.8937 (m-10) cc_final: 0.8534 (m-10) REVERT: E 113 SER cc_start: 0.9012 (t) cc_final: 0.8783 (p) REVERT: F 62 ARG cc_start: 0.8660 (OUTLIER) cc_final: 0.7572 (ttp-170) REVERT: F 75 MET cc_start: 0.7997 (mtt) cc_final: 0.7737 (mtt) REVERT: G 24 ASN cc_start: 0.8802 (OUTLIER) cc_final: 0.8574 (p0) REVERT: G 29 LYS cc_start: 0.9521 (mtpt) cc_final: 0.8900 (tptp) REVERT: G 60 GLN cc_start: 0.8842 (mm110) cc_final: 0.8166 (mp10) REVERT: G 97 LEU cc_start: 0.8923 (mt) cc_final: 0.8689 (tp) REVERT: G 101 ILE cc_start: 0.8844 (mp) cc_final: 0.8598 (mm) REVERT: G 108 ILE cc_start: 0.6238 (OUTLIER) cc_final: 0.5780 (mm) REVERT: G 110 ARG cc_start: 0.7911 (tpm-80) cc_final: 0.7672 (mmm160) REVERT: G 140 ASP cc_start: 0.8471 (p0) cc_final: 0.8123 (p0) REVERT: G 141 ASP cc_start: 0.6757 (m-30) cc_final: 0.5935 (m-30) REVERT: G 142 GLU cc_start: 0.8906 (mp0) cc_final: 0.7873 (pm20) REVERT: I 32 ASN cc_start: 0.8378 (m-40) cc_final: 0.8137 (m-40) REVERT: I 56 ASN cc_start: 0.8069 (t0) cc_final: 0.7127 (p0) REVERT: I 57 LYS cc_start: 0.7473 (mmtp) cc_final: 0.6915 (mtmt) REVERT: I 69 ILE cc_start: 0.8247 (mt) cc_final: 0.7957 (mp) REVERT: J 1 MET cc_start: 0.8652 (OUTLIER) cc_final: 0.7912 (mmt) REVERT: J 28 GLU cc_start: 0.8141 (mm-30) cc_final: 0.7812 (mm-30) REVERT: K 13 PHE cc_start: 0.8149 (p90) cc_final: 0.7666 (p90) REVERT: K 16 GLU cc_start: 0.7203 (mt-10) cc_final: 0.6667 (mt-10) REVERT: M 25 ARG cc_start: 0.8934 (ptp-110) cc_final: 0.8675 (ptp-110) REVERT: M 232 MET cc_start: 0.8892 (mmm) cc_final: 0.8577 (mmt) REVERT: M 237 MET cc_start: 0.8334 (OUTLIER) cc_final: 0.7258 (tpp) REVERT: M 299 MET cc_start: 0.6517 (OUTLIER) cc_final: 0.6269 (ptt) outliers start: 65 outliers final: 26 residues processed: 373 average time/residue: 0.7389 time to fit residues: 321.1612 Evaluate side-chains 363 residues out of total 3258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 321 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 467 MET Chi-restraints excluded: chain A residue 660 MET Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain A residue 1345 ARG Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 99 TRP Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 264 LYS Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 427 LYS Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 525 ASN Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 648 TYR Chi-restraints excluded: chain B residue 674 MET Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain B residue 798 ARG Chi-restraints excluded: chain B residue 892 CYS Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 86 ARG Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain E residue 98 ASN Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 62 ARG Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 158 PHE Chi-restraints excluded: chain H residue 7 GLU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain M residue 237 MET Chi-restraints excluded: chain M residue 299 MET Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 153 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 193 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 297 optimal weight: 7.9990 chunk 207 optimal weight: 0.8980 chunk 13 optimal weight: 7.9990 chunk 47 optimal weight: 1.9990 chunk 210 optimal weight: 1.9990 chunk 163 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 264 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 144 HIS C 111 GLN C 190 ASN C 268 GLN ** E 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 26 ASN N 124 ASN N 138 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.109630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.071855 restraints weight = 58599.604| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 2.31 r_work: 0.2983 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 29892 Z= 0.229 Angle : 0.660 12.186 40376 Z= 0.337 Chirality : 0.048 0.283 4510 Planarity : 0.005 0.044 5224 Dihedral : 5.247 80.897 3998 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.53 % Allowed : 14.34 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.14), residues: 3601 helix: 1.14 (0.15), residues: 1270 sheet: 0.23 (0.20), residues: 608 loop : 0.41 (0.15), residues: 1723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG M 25 TYR 0.022 0.002 TYR M 231 PHE 0.031 0.002 PHE D 95 TRP 0.018 0.003 TRP C 49 HIS 0.008 0.001 HIS C 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00565 / 0.23 (29868) covalent geometry : angle 0.65336 / 0.34 (40340) hydrogen bonds : bond 0.04632 / 3.09 ( 1306) hydrogen bonds : angle 4.82246 / 3.41 ( 3672) metal coordination : bond 0.00653 / 0.42 ( 24) metal coordination : angle 3.30028 / 2.12 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7202 Ramachandran restraints generated. 3601 Oldfield, 0 Emsley, 3601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7202 Ramachandran restraints generated. 3601 Oldfield, 0 Emsley, 3601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 3258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 328 time to evaluate : 1.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 467 MET cc_start: 0.2519 (mmt) cc_final: 0.2130 (pp-130) REVERT: A 520 MET cc_start: 0.8982 (mmt) cc_final: 0.8678 (mmm) REVERT: A 660 MET cc_start: 0.9195 (OUTLIER) cc_final: 0.7782 (mmt) REVERT: A 899 GLU cc_start: 0.8528 (pt0) cc_final: 0.8292 (pm20) REVERT: A 940 LYS cc_start: 0.8614 (ttpp) cc_final: 0.8386 (tmmt) REVERT: A 1199 MET cc_start: 0.5675 (ppp) cc_final: 0.5167 (mpm) REVERT: A 1255 LEU cc_start: 0.8324 (mt) cc_final: 0.8109 (mt) REVERT: A 1287 CYS cc_start: 0.7268 (OUTLIER) cc_final: 0.7063 (t) REVERT: A 1292 MET cc_start: 0.7244 (mtm) cc_final: 0.6657 (mmp) REVERT: A 1482 TYR cc_start: 0.5372 (OUTLIER) cc_final: 0.4293 (m-10) REVERT: B 42 GLN cc_start: 0.9146 (OUTLIER) cc_final: 0.8251 (pm20) REVERT: B 222 ARG cc_start: 0.8528 (mtp-110) cc_final: 0.8261 (mmm-85) REVERT: B 307 GLU cc_start: 0.8053 (tp30) cc_final: 0.7826 (tm-30) REVERT: B 410 ASN cc_start: 0.8314 (m-40) cc_final: 0.7984 (m110) REVERT: B 431 LEU cc_start: 0.7849 (mp) cc_final: 0.7609 (pt) REVERT: B 525 ASN cc_start: 0.8997 (OUTLIER) cc_final: 0.8605 (t0) REVERT: B 724 TYR cc_start: 0.8698 (m-10) cc_final: 0.8462 (t80) REVERT: B 785 TYR cc_start: 0.8132 (OUTLIER) cc_final: 0.5027 (m-80) REVERT: B 838 GLN cc_start: 0.7812 (tt0) cc_final: 0.7290 (tp40) REVERT: B 1054 MET cc_start: 0.8945 (mtp) cc_final: 0.8557 (mtp) REVERT: C 41 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.8083 (mt-10) REVERT: C 109 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7308 (mp0) REVERT: D 41 LEU cc_start: 0.9598 (OUTLIER) cc_final: 0.9331 (pp) REVERT: E 113 SER cc_start: 0.9068 (t) cc_final: 0.8740 (p) REVERT: F 62 ARG cc_start: 0.8758 (OUTLIER) cc_final: 0.7725 (ttp-170) REVERT: F 75 MET cc_start: 0.8068 (mtt) cc_final: 0.7775 (mtt) REVERT: G 60 GLN cc_start: 0.8938 (mm110) cc_final: 0.8512 (mp10) REVERT: G 97 LEU cc_start: 0.8937 (mt) cc_final: 0.8662 (tp) REVERT: G 108 ILE cc_start: 0.6095 (OUTLIER) cc_final: 0.5575 (mm) REVERT: G 110 ARG cc_start: 0.7889 (tpm-80) cc_final: 0.7594 (mmm160) REVERT: G 140 ASP cc_start: 0.8468 (p0) cc_final: 0.8120 (p0) REVERT: G 141 ASP cc_start: 0.6879 (m-30) cc_final: 0.6124 (m-30) REVERT: G 142 GLU cc_start: 0.8910 (mp0) cc_final: 0.7750 (pm20) REVERT: H 92 MET cc_start: 0.9362 (mtm) cc_final: 0.9140 (mtm) REVERT: I 32 ASN cc_start: 0.8544 (m-40) cc_final: 0.8315 (m-40) REVERT: I 56 ASN cc_start: 0.7979 (t0) cc_final: 0.7127 (p0) REVERT: I 57 LYS cc_start: 0.7653 (mmtp) cc_final: 0.7046 (mtmt) REVERT: I 69 ILE cc_start: 0.8288 (mt) cc_final: 0.8015 (mp) REVERT: I 92 LYS cc_start: 0.8717 (mmmm) cc_final: 0.8459 (mmtp) REVERT: J 28 GLU cc_start: 0.8271 (mm-30) cc_final: 0.8000 (mm-30) REVERT: K 16 GLU cc_start: 0.7184 (mt-10) cc_final: 0.6909 (mt-10) REVERT: L 21 GLU cc_start: 0.8441 (tm-30) cc_final: 0.8127 (tm-30) REVERT: M 232 MET cc_start: 0.8811 (mmm) cc_final: 0.8476 (mmt) REVERT: M 237 MET cc_start: 0.8360 (OUTLIER) cc_final: 0.7392 (tpp) REVERT: M 315 GLN cc_start: 0.8691 (tp40) cc_final: 0.8376 (tp40) REVERT: M 323 MET cc_start: 0.7114 (ttm) cc_final: 0.6733 (ttm) REVERT: N 59 LEU cc_start: 0.9542 (tm) cc_final: 0.9290 (pp) outliers start: 82 outliers final: 36 residues processed: 378 average time/residue: 0.6876 time to fit residues: 304.7053 Evaluate side-chains 364 residues out of total 3258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 316 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 660 MET Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 1287 CYS Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain A residue 1482 TYR Chi-restraints excluded: chain B residue 42 GLN Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 99 TRP Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 214 LYS Chi-restraints excluded: chain B residue 264 LYS Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 309 PHE Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 525 ASN Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 648 TYR Chi-restraints excluded: chain B residue 674 MET Chi-restraints excluded: chain B residue 718 GLN Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain B residue 892 CYS Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 86 ARG Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 98 ASN Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 62 ARG Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 156 ASP Chi-restraints excluded: chain G residue 158 PHE Chi-restraints excluded: chain H residue 7 GLU Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain M residue 237 MET Chi-restraints excluded: chain N residue 94 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 177 optimal weight: 0.0870 chunk 345 optimal weight: 4.9990 chunk 217 optimal weight: 3.9990 chunk 210 optimal weight: 0.9990 chunk 224 optimal weight: 0.9980 chunk 270 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 65 optimal weight: 0.6980 chunk 124 optimal weight: 1.9990 chunk 152 optimal weight: 0.4980 chunk 236 optimal weight: 9.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 GLN H 76 ASN N 124 ASN N 138 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.110601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.073015 restraints weight = 58419.991| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 2.33 r_work: 0.3009 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 29892 Z= 0.142 Angle : 0.612 12.319 40376 Z= 0.313 Chirality : 0.045 0.289 4510 Planarity : 0.004 0.072 5224 Dihedral : 5.035 80.168 3995 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.85 % Allowed : 15.30 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.14), residues: 3601 helix: 1.27 (0.15), residues: 1273 sheet: 0.25 (0.20), residues: 597 loop : 0.43 (0.15), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 416 TYR 0.025 0.002 TYR M 231 PHE 0.044 0.002 PHE M 52 TRP 0.024 0.002 TRP N 157 HIS 0.006 0.001 HIS D 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.14 (29868) covalent geometry : angle 0.60481 / 0.31 (40340) hydrogen bonds : bond 0.04099 / 2.73 ( 1306) hydrogen bonds : angle 4.66529 / 3.29 ( 3672) metal coordination : bond 0.00474 / 0.33 ( 24) metal coordination : angle 3.15788 / 1.99 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7202 Ramachandran restraints generated. 3601 Oldfield, 0 Emsley, 3601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7202 Ramachandran restraints generated. 3601 Oldfield, 0 Emsley, 3601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 3258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 327 time to evaluate : 1.308 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: A 458 PHE cc_start: 0.8609 (OUTLIER) cc_final: 0.7986 (t80) REVERT: A 467 MET cc_start: 0.2567 (mmt) cc_final: 0.1849 (pp-130) REVERT: A 470 MET cc_start: 0.8009 (mtp) cc_final: 0.7597 (mtm) REVERT: A 501 MET cc_start: 0.6508 (OUTLIER) cc_final: 0.6273 (tpt) REVERT: A 520 MET cc_start: 0.8896 (mmt) cc_final: 0.8607 (mmm) REVERT: A 660 MET cc_start: 0.9152 (OUTLIER) cc_final: 0.7667 (mmt) REVERT: A 899 GLU cc_start: 0.8525 (pt0) cc_final: 0.8281 (pm20) REVERT: A 940 LYS cc_start: 0.8622 (ttpp) cc_final: 0.8399 (tmmt) REVERT: A 1199 MET cc_start: 0.5640 (ppp) cc_final: 0.5122 (mpm) REVERT: A 1255 LEU cc_start: 0.8443 (mt) cc_final: 0.8240 (mt) REVERT: A 1287 CYS cc_start: 0.7214 (OUTLIER) cc_final: 0.7006 (t) REVERT: A 1292 MET cc_start: 0.7094 (mtm) cc_final: 0.6528 (mmp) REVERT: A 1344 MET cc_start: 0.8050 (tpp) cc_final: 0.7775 (ttt) REVERT: B 200 MET cc_start: 0.8719 (OUTLIER) cc_final: 0.8415 (tpt) REVERT: B 222 ARG cc_start: 0.8526 (mtp-110) cc_final: 0.8255 (mmm-85) REVERT: B 410 ASN cc_start: 0.8321 (m-40) cc_final: 0.8004 (m110) REVERT: B 525 ASN cc_start: 0.8964 (OUTLIER) cc_final: 0.8587 (t0) REVERT: B 724 TYR cc_start: 0.8704 (m-10) cc_final: 0.8498 (t80) REVERT: B 785 TYR cc_start: 0.7914 (OUTLIER) cc_final: 0.4877 (m-80) REVERT: B 838 GLN cc_start: 0.7828 (tt0) cc_final: 0.7293 (tp40) REVERT: B 892 CYS cc_start: 0.7101 (OUTLIER) cc_final: 0.6848 (p) REVERT: C 41 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.8042 (mt-10) REVERT: C 109 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7310 (mp0) REVERT: D 38 HIS cc_start: 0.9246 (p-80) cc_final: 0.8765 (p-80) REVERT: D 67 TYR cc_start: 0.8984 (t80) cc_final: 0.8757 (t80) REVERT: D 68 THR cc_start: 0.9679 (p) cc_final: 0.9459 (t) REVERT: E 113 SER cc_start: 0.9011 (t) cc_final: 0.8671 (p) REVERT: F 62 ARG cc_start: 0.8718 (OUTLIER) cc_final: 0.7673 (ttp-170) REVERT: G 60 GLN cc_start: 0.8923 (mm110) cc_final: 0.8577 (mm-40) REVERT: G 104 MET cc_start: 0.7837 (mmm) cc_final: 0.7576 (tpp) REVERT: G 108 ILE cc_start: 0.6042 (OUTLIER) cc_final: 0.5581 (mm) REVERT: G 140 ASP cc_start: 0.8503 (p0) cc_final: 0.8209 (p0) REVERT: G 141 ASP cc_start: 0.6868 (m-30) cc_final: 0.6282 (m-30) REVERT: G 142 GLU cc_start: 0.8923 (mp0) cc_final: 0.7485 (pm20) REVERT: I 56 ASN cc_start: 0.7977 (t0) cc_final: 0.7127 (p0) REVERT: I 57 LYS cc_start: 0.7618 (mmtp) cc_final: 0.7020 (mtmt) REVERT: I 64 GLU cc_start: 0.7485 (tp30) cc_final: 0.7135 (tp30) REVERT: I 92 LYS cc_start: 0.8725 (mmmm) cc_final: 0.8458 (mmtp) REVERT: J 1 MET cc_start: 0.8716 (OUTLIER) cc_final: 0.7873 (mmt) REVERT: J 28 GLU cc_start: 0.8263 (mm-30) cc_final: 0.7986 (mm-30) REVERT: K 13 PHE cc_start: 0.8154 (p90) cc_final: 0.7755 (p90) REVERT: K 16 GLU cc_start: 0.7106 (mt-10) cc_final: 0.6542 (mt-10) REVERT: L 21 GLU cc_start: 0.8498 (tm-30) cc_final: 0.8125 (tm-30) REVERT: M 232 MET cc_start: 0.8827 (mmm) cc_final: 0.8581 (mmt) REVERT: M 237 MET cc_start: 0.8359 (OUTLIER) cc_final: 0.7387 (tpp) REVERT: M 315 GLN cc_start: 0.8687 (tp40) cc_final: 0.8387 (tp40) REVERT: M 323 MET cc_start: 0.7140 (ttm) cc_final: 0.6655 (ttm) REVERT: N 59 LEU cc_start: 0.9539 (tm) cc_final: 0.9291 (pp) outliers start: 60 outliers final: 27 residues processed: 357 average time/residue: 0.7785 time to fit residues: 323.5113 Evaluate side-chains 351 residues out of total 3258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 310 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 660 MET Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 1287 CYS Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 99 TRP Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 214 LYS Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 309 PHE Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 525 ASN Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 648 TYR Chi-restraints excluded: chain B residue 674 MET Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain B residue 796 MET Chi-restraints excluded: chain B residue 892 CYS Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 86 ARG Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 98 ASN Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 62 ARG Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 21 ASN Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 158 PHE Chi-restraints excluded: chain H residue 7 GLU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain M residue 237 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 178 optimal weight: 1.9990 chunk 177 optimal weight: 0.5980 chunk 49 optimal weight: 6.9990 chunk 71 optimal weight: 1.9990 chunk 282 optimal weight: 2.9990 chunk 264 optimal weight: 0.5980 chunk 130 optimal weight: 0.9990 chunk 132 optimal weight: 2.9990 chunk 280 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 111 GLN H 76 ASN I 32 ASN N 124 ASN N 138 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.110339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.073850 restraints weight = 58118.922| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.27 r_work: 0.3021 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 29892 Z= 0.191 Angle : 0.646 12.539 40376 Z= 0.329 Chirality : 0.047 0.275 4510 Planarity : 0.004 0.086 5224 Dihedral : 5.068 79.676 3995 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.13 % Allowed : 15.45 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.14), residues: 3601 helix: 1.21 (0.15), residues: 1273 sheet: 0.19 (0.20), residues: 600 loop : 0.38 (0.15), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG G 151 TYR 0.027 0.002 TYR M 231 PHE 0.038 0.002 PHE N 147 TRP 0.030 0.002 TRP N 157 HIS 0.007 0.001 HIS C 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.19 (29868) covalent geometry : angle 0.63885 / 0.33 (40340) hydrogen bonds : bond 0.04301 / 2.86 ( 1306) hydrogen bonds : angle 4.71142 / 3.32 ( 3672) metal coordination : bond 0.00549 / 0.36 ( 24) metal coordination : angle 3.26980 / 2.07 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7202 Ramachandran restraints generated. 3601 Oldfield, 0 Emsley, 3601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7202 Ramachandran restraints generated. 3601 Oldfield, 0 Emsley, 3601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 3258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 324 time to evaluate : 1.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 458 PHE cc_start: 0.8639 (OUTLIER) cc_final: 0.8069 (t80) REVERT: A 467 MET cc_start: 0.2546 (mmt) cc_final: 0.1888 (pp-130) REVERT: A 470 MET cc_start: 0.8069 (OUTLIER) cc_final: 0.7676 (mtm) REVERT: A 660 MET cc_start: 0.9148 (OUTLIER) cc_final: 0.7650 (mmt) REVERT: A 899 GLU cc_start: 0.8504 (pt0) cc_final: 0.8226 (pm20) REVERT: A 940 LYS cc_start: 0.8622 (ttpp) cc_final: 0.8383 (tmmt) REVERT: A 1199 MET cc_start: 0.5621 (ppp) cc_final: 0.5126 (mpm) REVERT: A 1262 MET cc_start: 0.7460 (mmm) cc_final: 0.7043 (mmm) REVERT: A 1287 CYS cc_start: 0.7218 (OUTLIER) cc_final: 0.6999 (t) REVERT: A 1292 MET cc_start: 0.7074 (mtm) cc_final: 0.6514 (mmp) REVERT: A 1344 MET cc_start: 0.8048 (tpp) cc_final: 0.7829 (ttt) REVERT: B 200 MET cc_start: 0.8870 (OUTLIER) cc_final: 0.8535 (tpt) REVERT: B 222 ARG cc_start: 0.8465 (mtp-110) cc_final: 0.8208 (mmm-85) REVERT: B 410 ASN cc_start: 0.8315 (m-40) cc_final: 0.7996 (m110) REVERT: B 525 ASN cc_start: 0.8964 (OUTLIER) cc_final: 0.8565 (t0) REVERT: B 724 TYR cc_start: 0.8707 (m-10) cc_final: 0.8421 (t80) REVERT: B 785 TYR cc_start: 0.8020 (OUTLIER) cc_final: 0.4917 (m-80) REVERT: B 838 GLN cc_start: 0.7829 (tt0) cc_final: 0.7292 (tp40) REVERT: B 892 CYS cc_start: 0.7197 (OUTLIER) cc_final: 0.6915 (p) REVERT: C 41 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8102 (mt-10) REVERT: C 109 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7304 (mp0) REVERT: D 38 HIS cc_start: 0.9202 (p-80) cc_final: 0.8767 (p-80) REVERT: D 48 ASN cc_start: 0.8955 (t0) cc_final: 0.8692 (m-40) REVERT: D 67 TYR cc_start: 0.9018 (OUTLIER) cc_final: 0.8794 (t80) REVERT: D 68 THR cc_start: 0.9683 (p) cc_final: 0.9395 (t) REVERT: E 113 SER cc_start: 0.8992 (t) cc_final: 0.8644 (p) REVERT: F 62 ARG cc_start: 0.8708 (OUTLIER) cc_final: 0.7650 (ttp-170) REVERT: G 41 LYS cc_start: 0.9229 (mppt) cc_final: 0.8228 (tptp) REVERT: G 60 GLN cc_start: 0.8839 (mm110) cc_final: 0.8516 (mp10) REVERT: G 104 MET cc_start: 0.7740 (mmm) cc_final: 0.7422 (tpp) REVERT: G 108 ILE cc_start: 0.6080 (OUTLIER) cc_final: 0.5139 (mm) REVERT: G 128 TYR cc_start: 0.7511 (m-80) cc_final: 0.6945 (m-80) REVERT: G 140 ASP cc_start: 0.8463 (p0) cc_final: 0.8131 (p0) REVERT: G 141 ASP cc_start: 0.6356 (m-30) cc_final: 0.5504 (m-30) REVERT: G 142 GLU cc_start: 0.8443 (mp0) cc_final: 0.7662 (pm20) REVERT: G 151 ARG cc_start: 0.8693 (tmm160) cc_final: 0.8331 (tmm-80) REVERT: G 156 ASP cc_start: 0.7650 (t0) cc_final: 0.7228 (t0) REVERT: I 34 ILE cc_start: 0.7661 (tp) cc_final: 0.7448 (tp) REVERT: I 56 ASN cc_start: 0.7968 (t0) cc_final: 0.7103 (p0) REVERT: I 57 LYS cc_start: 0.7471 (mmtp) cc_final: 0.6926 (mtmt) REVERT: I 64 GLU cc_start: 0.7639 (tp30) cc_final: 0.7298 (tp30) REVERT: I 69 ILE cc_start: 0.8221 (mt) cc_final: 0.7948 (mp) REVERT: I 92 LYS cc_start: 0.8747 (mmmm) cc_final: 0.8483 (mmtp) REVERT: J 1 MET cc_start: 0.8784 (OUTLIER) cc_final: 0.7916 (mmt) REVERT: J 28 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7939 (mm-30) REVERT: K 13 PHE cc_start: 0.8237 (p90) cc_final: 0.7902 (p90) REVERT: K 16 GLU cc_start: 0.7179 (mt-10) cc_final: 0.6576 (mt-10) REVERT: K 110 LYS cc_start: 0.8465 (OUTLIER) cc_final: 0.7997 (mptt) REVERT: L 21 GLU cc_start: 0.8431 (tm-30) cc_final: 0.8090 (tm-30) REVERT: M 25 ARG cc_start: 0.8899 (ptp-110) cc_final: 0.8582 (ptp-110) REVERT: M 232 MET cc_start: 0.8861 (mmm) cc_final: 0.8497 (mmt) REVERT: M 237 MET cc_start: 0.8340 (OUTLIER) cc_final: 0.7517 (tpp) REVERT: M 315 GLN cc_start: 0.8717 (tp40) cc_final: 0.8395 (tp40) REVERT: M 323 MET cc_start: 0.7200 (ttm) cc_final: 0.6669 (ttm) REVERT: N 59 LEU cc_start: 0.9552 (tm) cc_final: 0.9299 (pp) REVERT: N 94 ARG cc_start: 0.8481 (ttt180) cc_final: 0.7580 (ttt180) REVERT: N 132 ARG cc_start: 0.8992 (tpt90) cc_final: 0.8414 (tpp-160) REVERT: N 141 TYR cc_start: 0.7974 (t80) cc_final: 0.7715 (t80) outliers start: 69 outliers final: 28 residues processed: 362 average time/residue: 0.6957 time to fit residues: 294.5629 Evaluate side-chains 358 residues out of total 3258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 314 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 470 MET Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 660 MET Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 1287 CYS Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 214 LYS Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 309 PHE Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 525 ASN Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 648 TYR Chi-restraints excluded: chain B residue 674 MET Chi-restraints excluded: chain B residue 718 GLN Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain B residue 796 MET Chi-restraints excluded: chain B residue 892 CYS Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 86 ARG Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 67 TYR Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 98 ASN Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 62 ARG Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain H residue 7 GLU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 110 LYS Chi-restraints excluded: chain M residue 237 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 25 optimal weight: 0.6980 chunk 348 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 36 optimal weight: 0.0770 chunk 249 optimal weight: 1.9990 chunk 252 optimal weight: 3.9990 chunk 65 optimal weight: 0.5980 chunk 277 optimal weight: 5.9990 chunk 280 optimal weight: 7.9990 chunk 245 optimal weight: 4.9990 chunk 104 optimal weight: 0.6980 overall best weight: 0.8140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN ** N 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 124 ASN N 138 ASN N 150 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.110138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.072773 restraints weight = 58572.220| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 2.47 r_work: 0.2992 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.3397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 29892 Z= 0.162 Angle : 0.636 13.516 40376 Z= 0.323 Chirality : 0.046 0.280 4510 Planarity : 0.004 0.085 5224 Dihedral : 5.009 78.836 3995 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.51 % Allowed : 16.50 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.14), residues: 3601 helix: 1.26 (0.15), residues: 1274 sheet: 0.19 (0.20), residues: 588 loop : 0.40 (0.15), residues: 1739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 70 TYR 0.032 0.002 TYR E 125 PHE 0.045 0.002 PHE M 52 TRP 0.040 0.002 TRP N 157 HIS 0.008 0.001 HIS M 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.16 (29868) covalent geometry : angle 0.62843 / 0.32 (40340) hydrogen bonds : bond 0.04140 / 2.76 ( 1306) hydrogen bonds : angle 4.69513 / 3.31 ( 3672) metal coordination : bond 0.00528 / 0.36 ( 24) metal coordination : angle 3.33420 / 2.10 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7202 Ramachandran restraints generated. 3601 Oldfield, 0 Emsley, 3601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7202 Ramachandran restraints generated. 3601 Oldfield, 0 Emsley, 3601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 3258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 322 time to evaluate : 1.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 458 PHE cc_start: 0.8654 (OUTLIER) cc_final: 0.8111 (t80) REVERT: A 467 MET cc_start: 0.2474 (mmt) cc_final: 0.1817 (pp-130) REVERT: A 470 MET cc_start: 0.7990 (mtp) cc_final: 0.7654 (mtm) REVERT: A 501 MET cc_start: 0.6496 (OUTLIER) cc_final: 0.6156 (tpt) REVERT: A 520 MET cc_start: 0.8828 (mmt) cc_final: 0.8494 (mmm) REVERT: A 660 MET cc_start: 0.9109 (OUTLIER) cc_final: 0.7595 (mmt) REVERT: A 899 GLU cc_start: 0.8553 (pt0) cc_final: 0.8267 (pm20) REVERT: A 940 LYS cc_start: 0.8634 (ttpp) cc_final: 0.8368 (tmmt) REVERT: A 1199 MET cc_start: 0.5624 (ppp) cc_final: 0.5133 (mpm) REVERT: A 1262 MET cc_start: 0.7496 (mmm) cc_final: 0.7006 (mmm) REVERT: A 1287 CYS cc_start: 0.7127 (OUTLIER) cc_final: 0.6905 (t) REVERT: A 1292 MET cc_start: 0.6710 (mtm) cc_final: 0.6478 (mmp) REVERT: A 1344 MET cc_start: 0.8099 (tpp) cc_final: 0.7875 (ttt) REVERT: B 169 ARG cc_start: 0.8162 (mtp-110) cc_final: 0.7881 (mmp-170) REVERT: B 200 MET cc_start: 0.8793 (OUTLIER) cc_final: 0.8479 (tpt) REVERT: B 222 ARG cc_start: 0.8535 (mtp-110) cc_final: 0.8292 (mtp85) REVERT: B 381 GLU cc_start: 0.8441 (pt0) cc_final: 0.8209 (mp0) REVERT: B 410 ASN cc_start: 0.8269 (m-40) cc_final: 0.7957 (m110) REVERT: B 525 ASN cc_start: 0.9005 (OUTLIER) cc_final: 0.8597 (t0) REVERT: B 724 TYR cc_start: 0.8700 (m-10) cc_final: 0.8364 (t80) REVERT: B 785 TYR cc_start: 0.7910 (OUTLIER) cc_final: 0.4845 (m-80) REVERT: B 838 GLN cc_start: 0.7780 (tt0) cc_final: 0.7316 (tp40) REVERT: B 892 CYS cc_start: 0.7170 (OUTLIER) cc_final: 0.6859 (p) REVERT: C 41 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8118 (mt-10) REVERT: C 109 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7279 (mp0) REVERT: D 38 HIS cc_start: 0.9293 (p-80) cc_final: 0.8893 (p-80) REVERT: D 48 ASN cc_start: 0.9011 (t0) cc_final: 0.8790 (m-40) REVERT: D 68 THR cc_start: 0.9659 (p) cc_final: 0.9384 (t) REVERT: E 113 SER cc_start: 0.8964 (t) cc_final: 0.8610 (p) REVERT: F 62 ARG cc_start: 0.8683 (OUTLIER) cc_final: 0.7597 (ttp-170) REVERT: G 60 GLN cc_start: 0.8867 (mm110) cc_final: 0.8515 (mp10) REVERT: G 128 TYR cc_start: 0.7265 (m-80) cc_final: 0.7064 (m-80) REVERT: G 140 ASP cc_start: 0.8628 (p0) cc_final: 0.8338 (p0) REVERT: G 141 ASP cc_start: 0.6656 (m-30) cc_final: 0.5796 (m-30) REVERT: G 142 GLU cc_start: 0.8924 (mp0) cc_final: 0.7706 (pm20) REVERT: I 56 ASN cc_start: 0.7955 (t0) cc_final: 0.7061 (p0) REVERT: I 57 LYS cc_start: 0.7403 (mmtp) cc_final: 0.6903 (mtmt) REVERT: I 64 GLU cc_start: 0.7652 (tp30) cc_final: 0.7235 (tp30) REVERT: I 92 LYS cc_start: 0.8730 (mmmm) cc_final: 0.8466 (mmtp) REVERT: J 1 MET cc_start: 0.8731 (OUTLIER) cc_final: 0.7945 (mmt) REVERT: J 28 GLU cc_start: 0.8333 (mm-30) cc_final: 0.8076 (mm-30) REVERT: K 13 PHE cc_start: 0.8256 (p90) cc_final: 0.7893 (p90) REVERT: K 16 GLU cc_start: 0.7148 (mt-10) cc_final: 0.6533 (mt-10) REVERT: L 21 GLU cc_start: 0.8474 (tm-30) cc_final: 0.8067 (tm-30) REVERT: M 25 ARG cc_start: 0.8920 (ptp-110) cc_final: 0.8557 (ptp-110) REVERT: M 232 MET cc_start: 0.8946 (mmm) cc_final: 0.8614 (mmt) REVERT: M 237 MET cc_start: 0.8338 (OUTLIER) cc_final: 0.7510 (tpp) REVERT: M 299 MET cc_start: 0.6314 (pp-130) cc_final: 0.5682 (ppp) REVERT: M 315 GLN cc_start: 0.8685 (tp40) cc_final: 0.8437 (tp40) REVERT: M 323 MET cc_start: 0.7341 (ttm) cc_final: 0.6799 (ttm) REVERT: N 59 LEU cc_start: 0.9574 (tm) cc_final: 0.9318 (pp) REVERT: N 94 ARG cc_start: 0.8599 (ttt180) cc_final: 0.8347 (ttt180) REVERT: N 132 ARG cc_start: 0.8995 (tpt90) cc_final: 0.8461 (tpp-160) outliers start: 49 outliers final: 28 residues processed: 346 average time/residue: 0.7500 time to fit residues: 302.4300 Evaluate side-chains 348 residues out of total 3258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 307 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 660 MET Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 1287 CYS Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 214 LYS Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 309 PHE Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 525 ASN Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 648 TYR Chi-restraints excluded: chain B residue 674 MET Chi-restraints excluded: chain B residue 718 GLN Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain B residue 796 MET Chi-restraints excluded: chain B residue 892 CYS Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 86 ARG Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 98 ASN Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 62 ARG Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 158 PHE Chi-restraints excluded: chain H residue 7 GLU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain M residue 237 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 328 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 chunk 161 optimal weight: 1.9990 chunk 287 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 303 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 261 optimal weight: 1.9990 chunk 334 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 116 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 28 GLN H 76 ASN ** M 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 124 ASN N 138 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.110072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.074235 restraints weight = 57971.692| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 2.32 r_work: 0.3017 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 29892 Z= 0.190 Angle : 0.663 13.874 40376 Z= 0.336 Chirality : 0.047 0.282 4510 Planarity : 0.004 0.046 5224 Dihedral : 5.067 78.281 3995 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.45 % Allowed : 16.59 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.59 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.14), residues: 3601 helix: 1.17 (0.15), residues: 1275 sheet: 0.11 (0.20), residues: 591 loop : 0.35 (0.15), residues: 1735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 416 TYR 0.026 0.002 TYR M 231 PHE 0.036 0.002 PHE N 147 TRP 0.029 0.002 TRP N 157 HIS 0.007 0.001 HIS C 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.19 (29868) covalent geometry : angle 0.65570 / 0.34 (40340) hydrogen bonds : bond 0.04311 / 2.86 ( 1306) hydrogen bonds : angle 4.76424 / 3.37 ( 3672) metal coordination : bond 0.00573 / 0.38 ( 24) metal coordination : angle 3.38780 / 2.13 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7202 Ramachandran restraints generated. 3601 Oldfield, 0 Emsley, 3601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7202 Ramachandran restraints generated. 3601 Oldfield, 0 Emsley, 3601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 3258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 313 time to evaluate : 1.223 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: A 450 MET cc_start: 0.9313 (ttp) cc_final: 0.9105 (ttm) REVERT: A 458 PHE cc_start: 0.8629 (OUTLIER) cc_final: 0.8149 (t80) REVERT: A 467 MET cc_start: 0.2445 (mmt) cc_final: 0.1969 (pp-130) REVERT: A 501 MET cc_start: 0.6626 (OUTLIER) cc_final: 0.6398 (tpt) REVERT: A 660 MET cc_start: 0.9131 (OUTLIER) cc_final: 0.7622 (mmt) REVERT: A 899 GLU cc_start: 0.8506 (pt0) cc_final: 0.8234 (pm20) REVERT: A 940 LYS cc_start: 0.8706 (ttpp) cc_final: 0.8464 (tmmt) REVERT: A 1199 MET cc_start: 0.5659 (ppp) cc_final: 0.5117 (mpm) REVERT: A 1262 MET cc_start: 0.7365 (mmm) cc_final: 0.6951 (mmm) REVERT: A 1287 CYS cc_start: 0.7227 (OUTLIER) cc_final: 0.6993 (t) REVERT: A 1292 MET cc_start: 0.6789 (mtm) cc_final: 0.6471 (mmp) REVERT: B 200 MET cc_start: 0.8886 (OUTLIER) cc_final: 0.8598 (tpt) REVERT: B 381 GLU cc_start: 0.8469 (pt0) cc_final: 0.8240 (mp0) REVERT: B 410 ASN cc_start: 0.8351 (m-40) cc_final: 0.8042 (m110) REVERT: B 416 ARG cc_start: 0.7723 (ptm160) cc_final: 0.7443 (ptm160) REVERT: B 525 ASN cc_start: 0.8976 (OUTLIER) cc_final: 0.8582 (t0) REVERT: B 724 TYR cc_start: 0.8705 (m-10) cc_final: 0.8410 (t80) REVERT: B 785 TYR cc_start: 0.8008 (OUTLIER) cc_final: 0.4904 (m-80) REVERT: B 838 GLN cc_start: 0.7848 (tt0) cc_final: 0.7331 (tp40) REVERT: B 892 CYS cc_start: 0.7146 (OUTLIER) cc_final: 0.6675 (p) REVERT: C 41 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.8096 (mt-10) REVERT: C 109 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7312 (mp0) REVERT: D 38 HIS cc_start: 0.9255 (p-80) cc_final: 0.8913 (p-80) REVERT: D 48 ASN cc_start: 0.8926 (t0) cc_final: 0.8309 (m-40) REVERT: D 67 TYR cc_start: 0.9007 (t80) cc_final: 0.8716 (t80) REVERT: D 68 THR cc_start: 0.9634 (p) cc_final: 0.9361 (t) REVERT: E 113 SER cc_start: 0.8961 (t) cc_final: 0.8629 (p) REVERT: F 62 ARG cc_start: 0.8694 (OUTLIER) cc_final: 0.7613 (ttp-170) REVERT: G 41 LYS cc_start: 0.9222 (mppt) cc_final: 0.8176 (tptp) REVERT: G 60 GLN cc_start: 0.8847 (mm110) cc_final: 0.8630 (mm-40) REVERT: G 91 GLN cc_start: 0.8557 (tt0) cc_final: 0.8217 (tt0) REVERT: G 110 ARG cc_start: 0.8781 (tpm170) cc_final: 0.8058 (mmm160) REVERT: G 140 ASP cc_start: 0.8451 (p0) cc_final: 0.8122 (p0) REVERT: G 141 ASP cc_start: 0.6479 (m-30) cc_final: 0.5548 (m-30) REVERT: G 142 GLU cc_start: 0.8525 (mp0) cc_final: 0.7748 (pm20) REVERT: I 32 ASN cc_start: 0.8644 (m-40) cc_final: 0.8435 (m-40) REVERT: I 56 ASN cc_start: 0.8037 (t0) cc_final: 0.7239 (p0) REVERT: I 57 LYS cc_start: 0.7460 (mmtp) cc_final: 0.6973 (mtmt) REVERT: I 64 GLU cc_start: 0.7721 (tp30) cc_final: 0.7312 (tp30) REVERT: I 92 LYS cc_start: 0.8797 (mmmm) cc_final: 0.8534 (mmtp) REVERT: J 1 MET cc_start: 0.8797 (OUTLIER) cc_final: 0.7970 (mmt) REVERT: J 28 GLU cc_start: 0.8102 (mm-30) cc_final: 0.7890 (mm-30) REVERT: K 13 PHE cc_start: 0.8271 (p90) cc_final: 0.7906 (p90) REVERT: K 16 GLU cc_start: 0.7250 (mt-10) cc_final: 0.6630 (mt-10) REVERT: L 21 GLU cc_start: 0.8445 (tm-30) cc_final: 0.8096 (tm-30) REVERT: M 25 ARG cc_start: 0.8861 (ptp-110) cc_final: 0.8513 (ptp-110) REVERT: M 230 HIS cc_start: 0.7683 (t70) cc_final: 0.7467 (t70) REVERT: M 232 MET cc_start: 0.8957 (mmm) cc_final: 0.8481 (mmt) REVERT: M 237 MET cc_start: 0.8307 (OUTLIER) cc_final: 0.7490 (tpp) REVERT: M 315 GLN cc_start: 0.8677 (tp40) cc_final: 0.8421 (tp40) REVERT: N 59 LEU cc_start: 0.9543 (tm) cc_final: 0.9294 (pp) REVERT: N 94 ARG cc_start: 0.8555 (ttt180) cc_final: 0.7711 (ttt180) REVERT: N 132 ARG cc_start: 0.9014 (tpt90) cc_final: 0.8626 (tpp-160) outliers start: 47 outliers final: 32 residues processed: 339 average time/residue: 0.7423 time to fit residues: 294.2610 Evaluate side-chains 352 residues out of total 3258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 307 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 660 MET Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 1287 CYS Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 214 LYS Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 309 PHE Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 525 ASN Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 648 TYR Chi-restraints excluded: chain B residue 674 MET Chi-restraints excluded: chain B residue 718 GLN Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain B residue 796 MET Chi-restraints excluded: chain B residue 892 CYS Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 86 ARG Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain D residue 16 ASP Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 70 ARG Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 98 ASN Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 62 ARG Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 158 PHE Chi-restraints excluded: chain H residue 7 GLU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain M residue 237 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 251 optimal weight: 3.9990 chunk 171 optimal weight: 0.6980 chunk 47 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 219 optimal weight: 0.5980 chunk 285 optimal weight: 0.1980 chunk 33 optimal weight: 1.9990 chunk 26 optimal weight: 0.4980 chunk 6 optimal weight: 2.9990 chunk 120 optimal weight: 0.8980 chunk 287 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 28 GLN H 76 ASN M 298 HIS ** N 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 124 ASN N 138 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.110690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.074630 restraints weight = 58655.666| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.23 r_work: 0.3045 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.3513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 29892 Z= 0.143 Angle : 0.654 19.471 40376 Z= 0.333 Chirality : 0.046 0.283 4510 Planarity : 0.004 0.047 5224 Dihedral : 4.989 77.507 3995 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.48 % Allowed : 16.63 % Favored : 81.89 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.59 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.14), residues: 3601 helix: 1.25 (0.15), residues: 1277 sheet: 0.13 (0.20), residues: 592 loop : 0.38 (0.15), residues: 1732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 416 TYR 0.028 0.002 TYR E 125 PHE 0.043 0.002 PHE M 52 TRP 0.028 0.002 TRP N 157 HIS 0.005 0.001 HIS C 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.14 (29868) covalent geometry : angle 0.64688 / 0.33 (40340) hydrogen bonds : bond 0.04117 / 2.74 ( 1306) hydrogen bonds : angle 4.72557 / 3.33 ( 3672) metal coordination : bond 0.00503 / 0.35 ( 24) metal coordination : angle 3.35326 / 2.10 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14123.86 seconds wall clock time: 240 minutes 15.27 seconds (14415.27 seconds total)