Starting phenix.real_space_refine on Mon Jul 6 15:22:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ei3_48075/07_2026/9ei3_48075.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ei3_48075/07_2026/9ei3_48075.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ei3_48075/07_2026/9ei3_48075.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ei3_48075/07_2026/9ei3_48075.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ei3_48075/07_2026/9ei3_48075.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ei3_48075/07_2026/9ei3_48075.map" } resolution = 3.2 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= 0.002 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 11 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 8 6.06 5 P 60 5.49 5 Mg 1 5.21 5 S 225 5.16 5 C 22919 2.51 5 N 6441 2.21 5 O 6967 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 36621 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 11426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1441, 11426 Classifications: {'peptide': 1441} Link IDs: {'PCIS': 1, 'PTRANS': 69, 'TRANS': 1370} Chain breaks: 3 Chain: "B" Number of atoms: 9062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1134, 9062 Classifications: {'peptide': 1134} Link IDs: {'PTRANS': 53, 'TRANS': 1080} Chain breaks: 2 Chain: "C" Number of atoms: 2060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2060 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 15, 'TRANS': 241} Chain breaks: 1 Chain: "D" Number of atoms: 1005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1005 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 3, 'TRANS': 124} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'GLU:plan': 5, 'GLN:plan1': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "E" Number of atoms: 1711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1711 Classifications: {'peptide': 209} Incomplete info: {'backbone_only': 2} Link IDs: {'PTRANS': 11, 'TRANS': 197} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 658 Classifications: {'peptide': 82} 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: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 927 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "J" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 533 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "K" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 920 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "L" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 372 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "N" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 455 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "P" Number of atoms: 239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 239 Classifications: {'RNA': 11} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 7, 'rna3p_pyr': 3} Link IDs: {'rna2p': 1, 'rna3p': 9} Chain: "T" Number of atoms: 486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 486 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "U" Number of atoms: 4207 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 538, 4201 Classifications: {'peptide': 538} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 515} Chain breaks: 5 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 39 Planarities with less than four sites: {'ARG:plan': 5, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 29 Conformer: "B" Number of residues, atoms: 538, 4201 Classifications: {'peptide': 538} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 515} Chain breaks: 5 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 39 Planarities with less than four sites: {'ARG:plan': 5, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 29 bond proxies already assigned to first conformer: 4269 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} 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: "U" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 464 SG CYS A 71 115.974 76.370 74.760 1.00 72.19 S ATOM 486 SG CYS A 74 115.287 72.707 74.314 1.00 78.26 S ATOM 533 SG CYS A 81 112.392 75.195 75.002 1.00 67.55 S ATOM 768 SG CYS A 111 103.531 66.383 120.422 1.00 68.99 S ATOM 796 SG CYS A 114 106.451 63.941 120.386 1.00 80.46 S ATOM 1109 SG CYS A 154 103.226 63.514 122.554 1.00100.26 S ATOM 1142 SG CYS A 184 105.941 66.373 123.215 1.00102.04 S ATOM 20058 SG CYS B1119 113.599 59.964 84.323 1.00 84.39 S ATOM 20080 SG CYS B1122 111.738 62.674 86.241 1.00 80.87 S ATOM 20195 SG CYS B1137 114.950 63.423 84.311 1.00 81.72 S ATOM 20216 SG CYS B1140 114.969 61.571 87.652 1.00 84.25 S ATOM 21183 SG CYS C 88 82.312 89.761 17.587 1.00 89.40 S ATOM 21196 SG CYS C 90 84.881 92.199 18.942 1.00 94.71 S ATOM 21231 SG CYS C 94 82.371 93.391 16.520 1.00 78.59 S ATOM 21253 SG CYS C 97 81.125 92.493 19.970 1.00 75.96 S ATOM 28489 SG CYS I 17 50.372 102.671 135.859 1.00 52.64 S ATOM 28513 SG CYS I 20 53.966 103.361 134.830 1.00 74.87 S ATOM 28674 SG CYS I 39 53.130 99.802 135.506 1.00 68.84 S ATOM 28699 SG CYS I 42 53.116 102.302 138.373 1.00 67.89 S ATOM 29051 SG CYS I 86 20.309 100.860 104.117 1.00 75.46 S ATOM 29075 SG CYS I 89 19.225 104.265 102.528 1.00 80.51 S ATOM 29279 SG CYS I 114 22.290 102.207 101.233 1.00 76.18 S ATOM 29314 SG CYS I 119 22.459 103.991 104.436 1.00 65.33 S ATOM 29424 SG CYS J 7 55.595 94.472 38.545 1.00 37.21 S ATOM 29448 SG CYS J 10 54.701 92.631 35.219 1.00 43.12 S ATOM 29712 SG CYS J 44 52.594 92.154 38.339 1.00 47.34 S ATOM 29718 SG CYS J 45 52.593 95.316 36.182 1.00 50.72 S ATOM 30864 SG CYS L 19 85.094 121.774 53.015 1.00 73.84 S ATOM 30883 SG CYS L 22 85.363 124.981 50.951 1.00 39.61 S ATOM 31000 SG CYS L 36 88.278 123.885 52.846 1.00 51.33 S ATOM 31026 SG CYS L 39 85.057 125.182 54.664 1.00 74.21 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ASER U 77 " occ=0.20 ... (10 atoms not shown) pdb=" OG BSER U 77 " occ=0.80 Time building chain proxies: 6.72, per 1000 atoms: 0.18 Number of scatterers: 36621 At special positions: 0 Unit cell: (176.064, 153.008, 197.024, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 8 29.99 S 225 16.00 P 60 15.00 Mg 1 11.99 O 6967 8.00 N 6441 7.00 C 22919 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS U 431 " - pdb=" SG CYS U 434 " distance=2.03 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: 3.14 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" NE2 HIS A 84 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 71 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 74 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 81 " pdb=" ZN A2002 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 111 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 114 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 184 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 154 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1122 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1137 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1140 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1119 " pdb=" ZN C 301 " 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 90 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 97 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 42 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 20 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 39 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 17 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 119 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 114 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 86 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 89 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " 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 7 " pdb=" ZN L 101 " 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 19 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 39 " Number of angles added : 45 8806 Ramachandran restraints generated. 4403 Oldfield, 0 Emsley, 4403 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8390 Finding SS restraints... Secondary structure from input PDB file: 154 helices and 51 sheets defined 40.0% alpha, 17.2% beta 17 base pairs and 39 stacking pairs defined. Time for finding SS restraints: 4.18 Creating SS restraints... Processing helix chain 'A' and resid 27 through 35 Processing helix chain 'A' and resid 99 through 110 Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'A' and resid 136 through 149 Processing helix chain 'A' and resid 217 through 227 removed outlier: 3.719A pdb=" N ARG A 227 " --> pdb=" O GLU A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 235 Processing helix chain 'A' and resid 244 through 247 Processing helix chain 'A' and resid 274 through 297 Processing helix chain 'A' and resid 301 through 319 removed outlier: 3.549A pdb=" N VAL A 318 " --> pdb=" O VAL A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 348 through 354 Processing helix chain 'A' and resid 382 through 388 Processing helix chain 'A' and resid 398 through 409 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 removed outlier: 3.719A pdb=" N TYR A 492 " --> pdb=" O VAL A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 519 Processing helix chain 'A' and resid 521 through 525 Processing helix chain 'A' and resid 539 through 550 removed outlier: 4.008A pdb=" N LYS A 550 " --> pdb=" O ARG A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 566 removed outlier: 3.919A pdb=" N PHE A 566 " --> pdb=" O ASN A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 596 removed outlier: 3.818A pdb=" N LEU A 594 " --> pdb=" O GLN A 590 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE A 595 " --> pdb=" O ILE A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 646 Processing helix chain 'A' and resid 651 through 660 Processing helix chain 'A' and resid 661 through 684 removed outlier: 3.860A pdb=" N ILE A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 693 removed outlier: 3.901A pdb=" N ILE A 693 " --> pdb=" O GLY A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 722 Processing helix chain 'A' and resid 732 through 759 Processing helix chain 'A' and resid 764 through 773 Processing helix chain 'A' and resid 777 through 786 Processing helix chain 'A' and resid 816 through 821 Processing helix chain 'A' and resid 832 through 869 removed outlier: 3.710A pdb=" N GLY A 846 " --> pdb=" O GLY A 842 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N THR A 854 " --> pdb=" O THR A 850 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N ALA A 855 " --> pdb=" O ALA A 851 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLU A 856 " --> pdb=" O VAL A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 894 Processing helix chain 'A' and resid 912 through 921 Processing helix chain 'A' and resid 928 through 934 Processing helix chain 'A' and resid 935 through 945 removed outlier: 4.016A pdb=" N LYS A 940 " --> pdb=" O GLU A 936 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASP A 941 " --> pdb=" O ASP A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 970 removed outlier: 3.773A pdb=" N GLN A 949 " --> pdb=" O ASN A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 974 removed outlier: 3.836A pdb=" N ASP A 974 " --> pdb=" O PRO A 971 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 971 through 974' Processing helix chain 'A' and resid 982 through 994 Processing helix chain 'A' and resid 1005 through 1020 removed outlier: 3.572A pdb=" N LYS A1018 " --> pdb=" O LYS A1014 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS A1019 " --> pdb=" O GLU A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1049 removed outlier: 5.025A pdb=" N LEU A1040 " --> pdb=" O ASN A1036 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N PHE A1041 " --> pdb=" O ALA A1037 " (cutoff:3.500A) Processing helix chain 'A' and resid 1050 through 1057 Processing helix chain 'A' and resid 1061 through 1080 Processing helix chain 'A' and resid 1086 through 1102 removed outlier: 3.542A pdb=" N LEU A1090 " --> pdb=" O MET A1086 " (cutoff:3.500A) Proline residue: A1098 - end of helix removed outlier: 3.971A pdb=" N GLN A1101 " --> pdb=" O GLU A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1119 through 1130 removed outlier: 3.716A pdb=" N ARG A1123 " --> pdb=" O LEU A1119 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1149 Processing helix chain 'A' and resid 1150 through 1162 Processing helix chain 'A' and resid 1165 through 1168 Processing helix chain 'A' and resid 1189 through 1197 Processing helix chain 'A' and resid 1217 through 1224 removed outlier: 3.695A pdb=" N ARG A1224 " --> pdb=" O HIS A1220 " (cutoff:3.500A) Processing helix chain 'A' and resid 1227 through 1240 Processing helix chain 'A' and resid 1280 through 1296 removed outlier: 3.627A pdb=" N MET A1296 " --> pdb=" O MET A1292 " (cutoff:3.500A) Processing helix chain 'A' and resid 1314 through 1318 Processing helix chain 'A' and resid 1342 through 1349 Processing helix chain 'A' and resid 1362 through 1369 Processing helix chain 'A' and resid 1370 through 1388 removed outlier: 3.525A pdb=" N VAL A1374 " --> pdb=" O GLY A1370 " (cutoff:3.500A) Processing helix chain 'A' and resid 1394 through 1406 removed outlier: 3.993A pdb=" N LEU A1398 " --> pdb=" O ASN A1394 " (cutoff:3.500A) Processing helix chain 'A' and resid 1415 through 1420 Processing helix chain 'A' and resid 1425 through 1431 removed outlier: 3.593A pdb=" N SER A1431 " --> pdb=" O LEU A1427 " (cutoff:3.500A) Processing helix chain 'A' and resid 1435 through 1446 Processing helix chain 'A' and resid 1453 through 1460 removed outlier: 3.750A pdb=" N ASN A1457 " --> pdb=" O GLY A1453 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU A1460 " --> pdb=" O GLU A1456 " (cutoff:3.500A) Processing helix chain 'A' and resid 1476 through 1481 removed outlier: 3.914A pdb=" N LYS A1481 " --> pdb=" O ALA A1477 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 37 removed outlier: 3.623A pdb=" N TRP B 27 " --> pdb=" O GLN B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 53 Processing helix chain 'B' and resid 53 through 62 Processing helix chain 'B' and resid 109 through 116 Processing helix chain 'B' and resid 167 through 174 Processing helix chain 'B' and resid 269 through 276 Processing helix chain 'B' and resid 280 through 289 Processing helix chain 'B' and resid 294 through 308 removed outlier: 3.939A pdb=" N MET B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) Proline residue: B 303 - end of helix removed outlier: 3.558A pdb=" N ALA B 308 " --> pdb=" O SER B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 323 Processing helix chain 'B' and resid 331 through 345 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: 3.612A pdb=" N GLY B 406 " --> pdb=" O PHE B 402 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASP B 424 " --> pdb=" O GLN B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 451 Processing helix chain 'B' and resid 474 through 483 Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 538 through 548 removed outlier: 3.561A pdb=" N LEU B 542 " --> pdb=" O PRO B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 561 removed outlier: 3.735A pdb=" N ILE B 561 " --> pdb=" O PRO B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 594 Processing helix chain 'B' and resid 636 through 645 removed outlier: 3.579A pdb=" N ILE B 640 " --> pdb=" O LYS B 636 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU B 645 " --> pdb=" O ASP B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 659 Processing helix chain 'B' and resid 667 through 671 Processing helix chain 'B' and resid 678 through 683 Processing helix chain 'B' and resid 699 through 704 Processing helix chain 'B' and resid 707 through 711 removed outlier: 3.657A pdb=" N ILE B 710 " --> pdb=" O CYS B 707 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE B 711 " --> pdb=" O ALA B 708 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 707 through 711' Processing helix chain 'B' and resid 713 through 717 Processing helix chain 'B' and resid 718 through 730 removed outlier: 4.084A pdb=" N LYS B 730 " --> pdb=" O SER B 726 " (cutoff:3.500A) Processing helix chain 'B' and resid 762 through 767 removed outlier: 4.338A pdb=" N TYR B 766 " --> pdb=" O ARG B 762 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 803 Processing helix chain 'B' and resid 970 through 976 removed outlier: 4.620A pdb=" N SER B 974 " --> pdb=" O HIS B 970 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG B 975 " --> pdb=" O ALA B 971 " (cutoff:3.500A) Processing helix chain 'B' and resid 977 through 994 removed outlier: 4.033A pdb=" N LEU B 981 " --> pdb=" O THR B 977 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASN B 992 " --> pdb=" O LYS B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1007 through 1017 Processing helix chain 'B' and resid 1054 through 1058 Processing helix chain 'B' and resid 1087 through 1098 Processing helix chain 'B' and resid 1099 through 1108 Processing helix chain 'B' and resid 1152 through 1165 Processing helix chain 'C' and resid 27 through 40 removed outlier: 3.771A pdb=" N ILE C 39 " --> pdb=" O ARG C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 70 Processing helix chain 'C' and resid 77 through 82 removed outlier: 4.575A 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 173 through 177 Processing helix chain 'C' and resid 199 through 203 Processing helix chain 'C' and resid 240 through 271 removed outlier: 3.539A pdb=" N VAL C 245 " --> pdb=" O PRO C 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 50 Processing helix chain 'D' and resid 58 through 71 removed outlier: 3.798A pdb=" N MET D 62 " --> pdb=" O SER D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 90 removed outlier: 3.620A pdb=" N LYS D 90 " --> pdb=" O LEU D 86 " (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 removed outlier: 3.609A pdb=" N GLU D 119 " --> pdb=" O PRO D 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 116 through 119' Processing helix chain 'D' and resid 123 through 138 Processing helix chain 'E' and resid 3 through 24 Processing helix chain 'E' and resid 29 through 34 removed outlier: 3.538A pdb=" N ASP E 34 " --> pdb=" O GLN E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 45 Processing helix chain 'E' and resid 83 through 97 Processing helix chain 'E' and resid 111 through 121 removed outlier: 4.392A pdb=" N MET E 121 " --> pdb=" O SER E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 137 removed outlier: 4.237A pdb=" N ILE E 137 " --> pdb=" O GLU E 134 " (cutoff:3.500A) 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 183 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 removed outlier: 3.626A pdb=" N GLU G 35 " --> pdb=" O PHE G 31 " (cutoff:3.500A) Processing helix chain 'H' and resid 129 through 133 Processing helix chain 'I' and resid 64 through 68 Processing helix chain 'I' and resid 69 through 75 removed outlier: 3.513A pdb=" N VAL I 72 " --> pdb=" O ILE I 69 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 28 Processing helix chain 'J' and resid 30 through 38 Processing helix chain 'J' and resid 42 through 51 removed outlier: 3.863A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 3.654A 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 39 through 53 removed outlier: 4.083A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU K 51 " --> pdb=" O LYS K 47 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS K 52 " --> pdb=" O SER K 48 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ASP K 53 " --> pdb=" O GLN K 49 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 113 Processing helix chain 'U' and resid 12 through 22 Processing helix chain 'U' and resid 31 through 41 removed outlier: 3.600A pdb=" N GLU U 35 " --> pdb=" O THR U 31 " (cutoff:3.500A) Processing helix chain 'U' and resid 79 through 93 removed outlier: 3.713A pdb=" N ILE U 83 " --> pdb=" O LEU U 79 " (cutoff:3.500A) Processing helix chain 'U' and resid 105 through 118 removed outlier: 3.614A pdb=" N ARG U 118 " --> pdb=" O ALA U 114 " (cutoff:3.500A) Processing helix chain 'U' and resid 129 through 134 removed outlier: 3.732A pdb=" N ALA U 134 " --> pdb=" O PRO U 130 " (cutoff:3.500A) Processing helix chain 'U' and resid 138 through 148 Processing helix chain 'U' and resid 196 through 208 Processing helix chain 'U' and resid 237 through 248 Processing helix chain 'U' and resid 270 through 283 Processing helix chain 'U' and resid 294 through 307 removed outlier: 3.509A pdb=" N TRP U 305 " --> pdb=" O VAL U 301 " (cutoff:3.500A) Processing helix chain 'U' and resid 339 through 348 Processing helix chain 'U' and resid 364 through 384 removed outlier: 3.506A pdb=" N GLU U 384 " --> pdb=" O ALA U 380 " (cutoff:3.500A) Processing helix chain 'U' and resid 390 through 407 removed outlier: 3.635A pdb=" N ILE U 396 " --> pdb=" O ASP U 392 " (cutoff:3.500A) Processing helix chain 'U' and resid 411 through 421 Processing helix chain 'U' and resid 431 through 436 Processing helix chain 'U' and resid 436 through 450 removed outlier: 3.688A pdb=" N VAL U 440 " --> pdb=" O ASN U 436 " (cutoff:3.500A) Processing helix chain 'U' and resid 499 through 514 removed outlier: 3.629A pdb=" N LEU U 514 " --> pdb=" O LYS U 510 " (cutoff:3.500A) Processing helix chain 'U' and resid 515 through 517 No H-bonds generated for 'chain 'U' and resid 515 through 517' Processing helix chain 'U' and resid 546 through 569 Processing helix chain 'U' and resid 573 through 591 removed outlier: 3.799A pdb=" N ALA U 578 " --> pdb=" O ALA U 574 " (cutoff:3.500A) Processing helix chain 'U' and resid 593 through 614 Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 16 removed outlier: 4.579A pdb=" N ARG B1150 " --> pdb=" O ARG A 16 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1448 through 1449 Processing sheet with id=AA3, first strand: chain 'A' and resid 86 through 95 removed outlier: 7.093A pdb=" N THR A 251 " --> pdb=" O LEU A 90 " (cutoff:3.500A) removed outlier: 10.281A pdb=" N LYS A 92 " --> pdb=" O ILE A 249 " (cutoff:3.500A) removed outlier: 10.250A pdb=" N ILE A 249 " --> pdb=" O LYS A 92 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 190 through 194 removed outlier: 4.484A pdb=" N LEU A 198 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ILE A 214 " --> pdb=" O ALA A 200 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 264 through 266 removed outlier: 3.722A pdb=" N VAL A 264 " --> pdb=" O ASN A 272 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASN A 272 " --> pdb=" O VAL A 264 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 357 through 358 Processing sheet with id=AA7, first strand: chain 'B' and resid 1060 through 1062 removed outlier: 3.564A pdb=" N THR A 365 " --> pdb=" O MET A 501 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N PHE A 482 " --> pdb=" O ARG A 364 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N VAL A 366 " --> pdb=" O PHE A 482 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N LEU A 484 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N THR A 368 " --> pdb=" O LEU A 484 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 389 through 393 removed outlier: 3.911A pdb=" N TYR A 418 " --> pdb=" O GLU A 447 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N HIS A 449 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ALA A 416 " --> pdb=" O HIS A 449 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 554 through 555 Processing sheet with id=AB1, first strand: chain 'A' and resid 579 through 581 removed outlier: 6.430A pdb=" N VAL H 91 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N PHE H 56 " --> pdb=" O ILE H 9 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N ILE H 9 " --> pdb=" O PHE H 56 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N LEU H 58 " --> pdb=" O GLU H 7 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N GLU H 7 " --> pdb=" O LEU H 58 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ILE H 60 " --> pdb=" O LEU H 5 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N HIS H 29 " --> pdb=" O LYS H 13 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG H 98 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 602 through 604 removed outlier: 7.005A pdb=" N VAL A 629 " --> pdb=" O ILE A 636 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 789 through 790 removed outlier: 3.501A pdb=" N GLY A 789 " --> pdb=" O VAL A 823 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 792 through 793 Processing sheet with id=AB5, first strand: chain 'A' and resid 872 through 873 removed outlier: 6.845A pdb=" N VAL A 879 " --> pdb=" O VAL A 887 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 902 through 905 Processing sheet with id=AB7, first strand: chain 'A' and resid 1306 through 1310 removed outlier: 3.814A pdb=" N LYS A1306 " --> pdb=" O ASP A1339 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU A1139 " --> pdb=" O THR A1338 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1245 through 1247 removed outlier: 4.188A pdb=" N LEU A1255 " --> pdb=" O LEU A1216 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N TYR I 54 " --> pdb=" O ILE A1175 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N TYR A1177 " --> pdb=" O CYS I 52 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N CYS I 52 " --> pdb=" O TYR A1177 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1319 through 1322 Processing sheet with id=AC1, first strand: chain 'F' and resid 115 through 119 removed outlier: 5.097A pdb=" N LEU A1473 " --> pdb=" O ILE G 59 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N GLY G 57 " --> pdb=" O LEU A1475 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N HIS G 9 " --> pdb=" O VAL G 70 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N TYR G 72 " --> pdb=" O LEU G 7 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 115 through 119 removed outlier: 5.097A pdb=" N LEU A1473 " --> pdb=" O ILE G 59 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N GLY G 57 " --> pdb=" O LEU A1475 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ASN G 53 " --> pdb=" O PRO G 69 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LYS G 71 " --> pdb=" O ILE G 51 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ILE G 51 " --> pdb=" O LYS G 71 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LYS G 73 " --> pdb=" O THR G 49 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N PHE G 77 " --> pdb=" O VAL G 45 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N VAL G 45 " --> pdb=" O PHE G 77 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 65 through 67 removed outlier: 6.228A pdb=" N ASP B 127 " --> pdb=" O GLU B 89 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ILE B 91 " --> pdb=" O TYR B 125 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N TYR B 125 " --> pdb=" O ILE B 91 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N LEU B 93 " --> pdb=" O PRO B 123 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ALA B 122 " --> pdb=" O GLY B 150 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N GLY B 150 " --> pdb=" O ALA B 122 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N LEU B 124 " --> pdb=" O PHE B 148 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N PHE B 148 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N VAL B 126 " --> pdb=" O LYS B 146 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS B 146 " --> pdb=" O VAL B 126 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 97 through 99 Processing sheet with id=AC5, first strand: chain 'B' and resid 185 through 187 Processing sheet with id=AC6, first strand: chain 'B' and resid 391 through 394 Processing sheet with id=AC7, first strand: chain 'B' and resid 206 through 208 removed outlier: 3.566A pdb=" N ILE B 235 " --> pdb=" O CYS B 221 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU B 225 " --> pdb=" O PRO B 231 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=AC9, first strand: chain 'B' and resid 632 through 633 Processing sheet with id=AD1, first strand: chain 'B' and resid 572 through 577 removed outlier: 5.292A pdb=" N TRP B 573 " --> pdb=" O VAL B 569 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL B 569 " --> pdb=" O TRP B 573 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLY B 575 " --> pdb=" O ILE B 567 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 748 through 751 removed outlier: 5.879A pdb=" N ARG B 924 " --> pdb=" O VAL B 904 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N VAL B 904 " --> pdb=" O ARG B 924 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 748 through 751 removed outlier: 5.879A pdb=" N ARG B 924 " --> pdb=" O VAL B 904 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N VAL B 904 " --> pdb=" O ARG B 924 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 759 through 760 Processing sheet with id=AD5, first strand: chain 'B' and resid 1025 through 1026 removed outlier: 7.061A pdb=" N VAL B 794 " --> pdb=" O GLY B 946 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N GLN B 948 " --> pdb=" O VAL B 794 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N MET B 796 " --> pdb=" O GLN B 948 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N PHE B1042 " --> pdb=" O ILE B 782 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 827 through 829 Processing sheet with id=AD7, first strand: chain 'B' and resid 865 through 867 removed outlier: 7.011A pdb=" N THR B 894 " --> pdb=" O ILE B 866 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1127 through 1129 Processing sheet with id=AD9, first strand: chain 'C' and resid 8 through 14 removed outlier: 5.838A pdb=" N VAL C 9 " --> pdb=" O GLU C 24 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N GLU C 24 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N ILE C 11 " --> pdb=" O ILE C 22 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N ILE C 22 " --> pdb=" O ILE C 11 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 121 through 122 removed outlier: 6.739A pdb=" N GLU C 158 " --> pdb=" O ASN C 55 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ASN C 55 " --> pdb=" O GLU C 158 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ARG C 160 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N LYS C 166 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N ILE C 47 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N GLY C 168 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N ILE C 45 " --> pdb=" O GLY C 168 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 113 through 116 removed outlier: 6.431A pdb=" N ARG C 113 " --> pdb=" O LYS C 152 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N LYS C 152 " --> pdb=" O ARG C 113 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N VAL C 115 " --> pdb=" O ILE C 150 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 26 through 27 removed outlier: 4.419A pdb=" N ALA E 63 " --> pdb=" O LEU E 27 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 81 through 82 removed outlier: 3.588A pdb=" N VAL E 82 " --> pdb=" O GLY E 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'E' and resid 101 through 106 removed outlier: 7.144A pdb=" N ALA E 102 " --> pdb=" O GLU E 128 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N PHE E 130 " --> pdb=" O ALA E 102 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N ILE E 104 " --> pdb=" O PHE E 130 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'E' and resid 147 through 150 Processing sheet with id=AE7, first strand: chain 'G' and resid 84 through 92 removed outlier: 7.138A pdb=" N PHE G 98 " --> pdb=" O THR G 90 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N VAL G 92 " --> pdb=" O GLY G 96 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N GLY G 96 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N SER G 105 " --> pdb=" O ALA G 159 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N GLY G 161 " --> pdb=" O SER G 105 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N PHE G 107 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLY G 149 " --> pdb=" O ILE G 160 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N SER G 162 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N ILE G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 118 through 120 removed outlier: 3.611A pdb=" N GLU G 118 " --> pdb=" O LYS G 129 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASP G 120 " --> pdb=" O CYS G 127 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N CYS G 127 " --> pdb=" O ASP G 120 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 25 through 29 removed outlier: 3.669A pdb=" N ILE I 34 " --> pdb=" O ASP I 29 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 80 through 81 Processing sheet with id=AF2, first strand: chain 'K' and resid 19 through 23 Processing sheet with id=AF3, first strand: chain 'U' and resid 190 through 191 removed outlier: 7.328A pdb=" N VAL U 48 " --> pdb=" O ALA U 190 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'U' and resid 97 through 100 Processing sheet with id=AF5, first strand: chain 'U' and resid 228 through 231 removed outlier: 6.949A pdb=" N ASP U 228 " --> pdb=" O LEU U 361 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N TYR U 363 " --> pdb=" O ASP U 228 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N GLN U 230 " --> pdb=" O TYR U 363 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'U' and resid 286 through 287 1543 hydrogen bonds defined for protein. 4323 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 42 hydrogen bonds 84 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 39 stacking parallelities Total time for adding SS restraints: 8.93 Time building geometry restraints manager: 4.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 7285 1.33 - 1.45: 8707 1.45 - 1.57: 20965 1.57 - 1.70: 118 1.70 - 1.82: 350 Bond restraints: 37425 Sorted by residual: bond pdb=" N3B ANP U1000 " pdb=" PG ANP U1000 " ideal model delta sigma weight residual 1.795 1.630 0.165 2.00e-02 2.50e+03 6.80e+01 bond pdb=" O3A ANP U1000 " pdb=" PB ANP U1000 " ideal model delta sigma weight residual 1.700 1.598 0.102 2.00e-02 2.50e+03 2.59e+01 bond pdb=" CA SER C 75 " pdb=" CB SER C 75 " ideal model delta sigma weight residual 1.528 1.466 0.062 1.39e-02 5.18e+03 2.01e+01 bond pdb=" C3' DT N 25 " pdb=" C2' DT N 25 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.20e+01 bond pdb=" C3' DA N 18 " pdb=" C2' DA N 18 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.09e+01 ... (remaining 37420 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.78: 50069 2.78 - 5.56: 634 5.56 - 8.33: 84 8.33 - 11.11: 15 11.11 - 13.89: 2 Bond angle restraints: 50804 Sorted by residual: angle pdb=" N PRO U 12 " pdb=" CA PRO U 12 " pdb=" C PRO U 12 " ideal model delta sigma weight residual 113.81 103.05 10.76 1.45e+00 4.76e-01 5.50e+01 angle pdb=" N GLU A1253 " pdb=" CA GLU A1253 " pdb=" C GLU A1253 " ideal model delta sigma weight residual 114.75 106.08 8.67 1.26e+00 6.30e-01 4.74e+01 angle pdb=" N ILE U 317 " pdb=" CA ILE U 317 " pdb=" C ILE U 317 " ideal model delta sigma weight residual 113.20 106.83 6.37 9.60e-01 1.09e+00 4.41e+01 angle pdb=" N ASP U 27 " pdb=" CA ASP U 27 " pdb=" C ASP U 27 " ideal model delta sigma weight residual 113.21 104.88 8.33 1.40e+00 5.10e-01 3.54e+01 angle pdb=" N PRO U 187 " pdb=" CA PRO U 187 " pdb=" CB PRO U 187 " ideal model delta sigma weight residual 103.25 97.51 5.74 1.05e+00 9.07e-01 2.99e+01 ... (remaining 50799 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.50: 21363 29.50 - 59.01: 1350 59.01 - 88.51: 135 88.51 - 118.01: 7 118.01 - 147.52: 3 Dihedral angle restraints: 22858 sinusoidal: 9901 harmonic: 12957 Sorted by residual: dihedral pdb=" CD ARG U 298 " pdb=" NE ARG U 298 " pdb=" CZ ARG U 298 " pdb=" NH1 ARG U 298 " ideal model delta sinusoidal sigma weight residual 0.00 -81.08 81.08 1 1.00e+01 1.00e-02 8.11e+01 dihedral pdb=" CD ARG U 267 " pdb=" NE ARG U 267 " pdb=" CZ ARG U 267 " pdb=" NH1 ARG U 267 " ideal model delta sinusoidal sigma weight residual 0.00 77.26 -77.26 1 1.00e+01 1.00e-02 7.48e+01 dihedral pdb=" CD ARG U 610 " pdb=" NE ARG U 610 " pdb=" CZ ARG U 610 " pdb=" NH1 ARG U 610 " ideal model delta sinusoidal sigma weight residual 0.00 -72.31 72.31 1 1.00e+01 1.00e-02 6.68e+01 ... (remaining 22855 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.121: 5570 0.121 - 0.243: 97 0.243 - 0.364: 4 0.364 - 0.485: 2 0.485 - 0.607: 12 Chirality restraints: 5685 Sorted by residual: chirality pdb=" P DC T 1 " pdb=" OP1 DC T 1 " pdb=" OP2 DC T 1 " pdb=" O5' DC T 1 " both_signs ideal model delta sigma weight residual True 2.34 -2.94 -0.61 2.00e-01 2.50e+01 9.21e+00 chirality pdb=" P DC N 35 " pdb=" OP1 DC N 35 " pdb=" OP2 DC N 35 " pdb=" O5' DC N 35 " both_signs ideal model delta sigma weight residual True 2.34 -2.94 -0.60 2.00e-01 2.50e+01 9.10e+00 chirality pdb=" P DC N 29 " pdb=" OP1 DC N 29 " pdb=" OP2 DC N 29 " pdb=" O5' DC N 29 " both_signs ideal model delta sigma weight residual True 2.34 -2.94 -0.60 2.00e-01 2.50e+01 9.03e+00 ... (remaining 5682 not shown) Planarity restraints: 6386 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG U 298 " 1.081 9.50e-02 1.11e+02 4.84e-01 1.41e+02 pdb=" NE ARG U 298 " -0.066 2.00e-02 2.50e+03 pdb=" CZ ARG U 298 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG U 298 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG U 298 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG U 267 " 1.073 9.50e-02 1.11e+02 4.81e-01 1.39e+02 pdb=" NE ARG U 267 " -0.064 2.00e-02 2.50e+03 pdb=" CZ ARG U 267 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG U 267 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG U 267 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG U 610 " -1.052 9.50e-02 1.11e+02 4.71e-01 1.34e+02 pdb=" NE ARG U 610 " 0.062 2.00e-02 2.50e+03 pdb=" CZ ARG U 610 " 0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG U 610 " -0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG U 610 " -0.022 2.00e-02 2.50e+03 ... (remaining 6383 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 300 2.50 - 3.10: 26763 3.10 - 3.70: 60100 3.70 - 4.30: 84610 4.30 - 4.90: 139765 Nonbonded interactions: 311538 Sorted by model distance: nonbonded pdb=" OE1 GLU U 278 " pdb=" NH1 ARG U 282 " model vdw 1.899 3.120 nonbonded pdb=" O ASP U 172 " pdb=" O ALA U 206 " model vdw 1.922 3.040 nonbonded pdb=" OD1 ASP A 495 " pdb="MG MG A2003 " model vdw 1.950 2.170 nonbonded pdb=" O3' C P 20 " pdb="MG MG A2003 " model vdw 1.954 2.170 nonbonded pdb=" N2 DG N 26 " pdb=" C5 DC T 3 " model vdw 2.033 3.420 ... (remaining 311533 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=0.20 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: 2.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.020 Extract box with map and model: 0.560 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 39.840 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 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 : 0.004 0.165 37458 Z= 0.240 Angle : 0.791 13.891 50851 Z= 0.471 Chirality : 0.054 0.607 5685 Planarity : 0.015 0.484 6386 Dihedral : 17.896 147.515 14465 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 0.57 % Allowed : 6.09 % Favored : 93.34 % Rotamer: Outliers : 1.28 % Allowed : 21.91 % Favored : 76.81 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.48 % 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: -0.02 (0.13), residues: 4403 helix: 1.14 (0.14), residues: 1564 sheet: -0.11 (0.22), residues: 596 loop : -0.79 (0.13), residues: 2243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A1286 TYR 0.020 0.001 TYR A 669 PHE 0.028 0.001 PHE E 75 TRP 0.023 0.002 TRP B 236 HIS 0.006 0.001 HIS K 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.24 (37425) covalent geometry : angle 0.78217 / 0.47 (50804) SS BOND : bond 0.00103 / 0.05 ( 1) SS BOND : angle 2.25821 / 1.20 ( 2) hydrogen bonds : bond 0.17491 / 11.44 ( 1557) hydrogen bonds : angle 7.35043 / 5.19 ( 4407) metal coordination : bond 0.00642 / 0.43 ( 32) metal coordination : angle 3.95010 / 2.62 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8806 Ramachandran restraints generated. 4403 Oldfield, 0 Emsley, 4403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8806 Ramachandran restraints generated. 4403 Oldfield, 0 Emsley, 4403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1089 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 1040 time to evaluate : 1.188 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 186 ARG cc_start: 0.7831 (mtp85) cc_final: 0.7548 (ttp-110) REVERT: A 188 GLN cc_start: 0.7759 (mm110) cc_final: 0.7421 (mm-40) REVERT: A 219 GLU cc_start: 0.7517 (tp30) cc_final: 0.7233 (tm-30) REVERT: A 223 GLU cc_start: 0.7669 (tp30) cc_final: 0.7350 (tp30) REVERT: A 232 GLU cc_start: 0.7331 (mt-10) cc_final: 0.7080 (mt-10) REVERT: A 234 PHE cc_start: 0.8007 (t80) cc_final: 0.7689 (t80) REVERT: A 296 ASN cc_start: 0.7798 (m-40) cc_final: 0.7593 (m-40) REVERT: A 360 ASP cc_start: 0.8183 (m-30) cc_final: 0.7904 (m-30) REVERT: A 387 ASN cc_start: 0.8407 (t0) cc_final: 0.8177 (t0) REVERT: A 412 GLN cc_start: 0.7999 (mp10) cc_final: 0.7723 (mp10) REVERT: A 418 TYR cc_start: 0.8103 (m-80) cc_final: 0.7720 (m-80) REVERT: A 428 ASP cc_start: 0.7141 (t0) cc_final: 0.6465 (t0) REVERT: A 467 MET cc_start: 0.8144 (mpp) cc_final: 0.7823 (mpp) REVERT: A 556 GLU cc_start: 0.7238 (mm-30) cc_final: 0.6910 (mm-30) REVERT: A 642 LYS cc_start: 0.8506 (tttt) cc_final: 0.8233 (ttpp) REVERT: A 662 HIS cc_start: 0.8383 (p-80) cc_final: 0.8155 (p-80) REVERT: A 691 ASP cc_start: 0.7468 (m-30) cc_final: 0.7140 (m-30) REVERT: A 699 TYR cc_start: 0.8186 (m-80) cc_final: 0.7983 (m-10) REVERT: A 711 GLN cc_start: 0.8186 (tp40) cc_final: 0.7776 (mm-40) REVERT: A 751 LYS cc_start: 0.8035 (tttp) cc_final: 0.7734 (ttpp) REVERT: A 868 MET cc_start: 0.7000 (mtp) cc_final: 0.6653 (mtt) REVERT: A 909 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7963 (tt) REVERT: A 914 LYS cc_start: 0.8003 (mmmm) cc_final: 0.7652 (mmmm) REVERT: A 921 ARG cc_start: 0.8131 (tpt-90) cc_final: 0.7878 (tpp80) REVERT: A 958 ARG cc_start: 0.7262 (ttp80) cc_final: 0.6848 (ttm110) REVERT: A 962 ASP cc_start: 0.7160 (m-30) cc_final: 0.6927 (m-30) REVERT: A 982 ASN cc_start: 0.7943 (t0) cc_final: 0.7632 (t0) REVERT: A 1031 ARG cc_start: 0.7798 (ttm-80) cc_final: 0.7485 (ttm-80) REVERT: A 1035 GLU cc_start: 0.7754 (tp30) cc_final: 0.7339 (tp30) REVERT: A 1102 MET cc_start: 0.7456 (mtp) cc_final: 0.7214 (mtp) REVERT: A 1155 LYS cc_start: 0.7476 (ttmm) cc_final: 0.7234 (ttmm) REVERT: A 1156 ASP cc_start: 0.7758 (t0) cc_final: 0.7376 (t0) REVERT: A 1176 TYR cc_start: 0.8118 (m-80) cc_final: 0.7685 (m-80) REVERT: A 1188 GLU cc_start: 0.7303 (pm20) cc_final: 0.6940 (pm20) REVERT: A 1225 LYS cc_start: 0.8316 (mttm) cc_final: 0.8111 (mttm) REVERT: A 1289 GLU cc_start: 0.8041 (tm-30) cc_final: 0.7650 (tt0) REVERT: A 1311 LEU cc_start: 0.8157 (mt) cc_final: 0.7630 (mt) REVERT: A 1344 MET cc_start: 0.7738 (tpt) cc_final: 0.7466 (tpt) REVERT: A 1349 GLU cc_start: 0.7169 (tp30) cc_final: 0.6846 (tp30) REVERT: A 1350 LYS cc_start: 0.7982 (mtpp) cc_final: 0.7242 (ttpp) REVERT: A 1372 GLU cc_start: 0.7208 (mm-30) cc_final: 0.6905 (mm-30) REVERT: A 1393 VAL cc_start: 0.8589 (t) cc_final: 0.8365 (p) REVERT: A 1441 GLU cc_start: 0.7295 (mm-30) cc_final: 0.6941 (mm-30) REVERT: A 1452 LYS cc_start: 0.8049 (mmtp) cc_final: 0.7785 (mmtp) REVERT: A 1479 LYS cc_start: 0.8008 (mtpp) cc_final: 0.7697 (mmtp) REVERT: B 35 ASP cc_start: 0.7476 (m-30) cc_final: 0.7199 (m-30) REVERT: B 97 THR cc_start: 0.8736 (p) cc_final: 0.8510 (p) REVERT: B 109 MET cc_start: 0.8132 (mmt) cc_final: 0.7743 (mmm) REVERT: B 126 VAL cc_start: 0.7547 (m) cc_final: 0.7209 (p) REVERT: B 144 HIS cc_start: 0.7640 (m170) cc_final: 0.7424 (m-70) REVERT: B 242 ARG cc_start: 0.5694 (tpt170) cc_final: 0.4037 (mmt180) REVERT: B 299 GLU cc_start: 0.6972 (mt-10) cc_final: 0.6741 (mt-10) REVERT: B 314 GLN cc_start: 0.8024 (tm-30) cc_final: 0.7773 (tm-30) REVERT: B 345 LYS cc_start: 0.8167 (mmtp) cc_final: 0.7756 (mtpp) REVERT: B 368 MET cc_start: 0.8162 (mtp) cc_final: 0.7953 (mtp) REVERT: B 380 ARG cc_start: 0.8010 (mtp85) cc_final: 0.7613 (mtt180) REVERT: B 407 MET cc_start: 0.8114 (ttm) cc_final: 0.7505 (mtp) REVERT: B 436 LYS cc_start: 0.7250 (mtpp) cc_final: 0.6924 (ptpp) REVERT: B 547 GLU cc_start: 0.7058 (tm-30) cc_final: 0.6626 (tm-30) REVERT: B 556 ILE cc_start: 0.8489 (tp) cc_final: 0.8217 (tt) REVERT: B 600 GLU cc_start: 0.7602 (tt0) cc_final: 0.7156 (tt0) REVERT: B 606 ASP cc_start: 0.7641 (t0) cc_final: 0.7127 (t0) REVERT: B 611 GLU cc_start: 0.7432 (mt-10) cc_final: 0.7226 (mt-10) REVERT: B 617 ASP cc_start: 0.7736 (t0) cc_final: 0.7342 (t0) REVERT: B 637 LYS cc_start: 0.8138 (tppt) cc_final: 0.7860 (tppt) REVERT: B 664 TYR cc_start: 0.8501 (m-80) cc_final: 0.7475 (m-80) REVERT: B 682 LEU cc_start: 0.7535 (mp) cc_final: 0.7203 (mp) REVERT: B 726 SER cc_start: 0.8311 (p) cc_final: 0.8032 (m) REVERT: B 767 LEU cc_start: 0.8273 (mt) cc_final: 0.8049 (mp) REVERT: B 792 ASP cc_start: 0.7142 (m-30) cc_final: 0.6879 (m-30) REVERT: B 796 MET cc_start: 0.8098 (mtp) cc_final: 0.7882 (mtp) REVERT: B 798 ARG cc_start: 0.8160 (tpt-90) cc_final: 0.7914 (tpt-90) REVERT: B 830 GLU cc_start: 0.7578 (pm20) cc_final: 0.6911 (pm20) REVERT: B 895 PHE cc_start: 0.8578 (m-10) cc_final: 0.8316 (m-80) REVERT: B 903 ILE cc_start: 0.7896 (mp) cc_final: 0.7631 (mp) REVERT: B 1012 SER cc_start: 0.8029 (t) cc_final: 0.7685 (m) REVERT: B 1018 TYR cc_start: 0.8386 (m-80) cc_final: 0.8124 (m-80) REVERT: B 1041 ILE cc_start: 0.7831 (mm) cc_final: 0.7592 (mm) REVERT: B 1053 HIS cc_start: 0.8159 (m90) cc_final: 0.7656 (m90) REVERT: B 1067 ILE cc_start: 0.8383 (pt) cc_final: 0.8180 (pt) REVERT: B 1070 LEU cc_start: 0.8265 (tp) cc_final: 0.8035 (tt) REVERT: B 1143 LYS cc_start: 0.7803 (mtmt) cc_final: 0.7578 (mtmm) REVERT: C 17 GLU cc_start: 0.7314 (pt0) cc_final: 0.7103 (pt0) REVERT: C 62 GLU cc_start: 0.7628 (pm20) cc_final: 0.7408 (pm20) REVERT: C 75 SER cc_start: 0.8545 (OUTLIER) cc_final: 0.8131 (p) REVERT: C 81 LYS cc_start: 0.8147 (ptpp) cc_final: 0.7937 (ptpp) REVERT: C 130 VAL cc_start: 0.7956 (t) cc_final: 0.7694 (t) REVERT: C 213 GLU cc_start: 0.7139 (tp30) cc_final: 0.6867 (tp30) REVERT: D 39 MET cc_start: 0.6120 (ptt) cc_final: 0.5859 (ptt) REVERT: E 6 GLU cc_start: 0.7855 (tp30) cc_final: 0.7583 (tp30) REVERT: E 12 LYS cc_start: 0.7745 (tptp) cc_final: 0.7320 (tppp) REVERT: E 26 TYR cc_start: 0.8072 (m-80) cc_final: 0.7861 (m-80) REVERT: E 27 LEU cc_start: 0.8333 (tp) cc_final: 0.7972 (tp) REVERT: E 91 CYS cc_start: 0.7046 (t) cc_final: 0.6771 (t) REVERT: E 97 GLU cc_start: 0.7758 (mm-30) cc_final: 0.7350 (tp30) REVERT: E 106 VAL cc_start: 0.8471 (t) cc_final: 0.8077 (m) REVERT: E 108 GLN cc_start: 0.6989 (mp10) cc_final: 0.6571 (mp10) REVERT: E 129 GLN cc_start: 0.7891 (tm-30) cc_final: 0.7667 (tm-30) REVERT: E 156 VAL cc_start: 0.8146 (t) cc_final: 0.7906 (t) REVERT: E 165 LEU cc_start: 0.8531 (mt) cc_final: 0.8227 (mt) REVERT: E 172 ARG cc_start: 0.8030 (mtt90) cc_final: 0.7820 (mtt90) REVERT: E 177 ASP cc_start: 0.7588 (t0) cc_final: 0.7178 (t0) REVERT: E 189 GLN cc_start: 0.8784 (mt0) cc_final: 0.8537 (mt0) REVERT: F 124 ILE cc_start: 0.7647 (pt) cc_final: 0.7440 (pt) REVERT: H 27 ARG cc_start: 0.8412 (ttm170) cc_final: 0.8199 (ttm-80) REVERT: H 36 LYS cc_start: 0.7902 (mmpt) cc_final: 0.7380 (mmpt) REVERT: H 37 MET cc_start: 0.8021 (mmm) cc_final: 0.7617 (mmm) REVERT: H 102 ASP cc_start: 0.8403 (p0) cc_final: 0.7712 (p0) REVERT: J 22 LEU cc_start: 0.8485 (mt) cc_final: 0.8116 (mt) REVERT: K 42 LEU cc_start: 0.7264 (mp) cc_final: 0.7041 (mt) REVERT: K 81 TYR cc_start: 0.7822 (t80) cc_final: 0.7382 (t80) REVERT: K 106 ARG cc_start: 0.8088 (ttm-80) cc_final: 0.7715 (mtt90) REVERT: U 13 GLU cc_start: 0.7770 (tm-30) cc_final: 0.7386 (tm-30) REVERT: U 185 HIS cc_start: 0.3787 (OUTLIER) cc_final: 0.2439 (p-80) REVERT: U 202 ASP cc_start: 0.6825 (m-30) cc_final: 0.6438 (m-30) REVERT: U 207 LEU cc_start: 0.7988 (mm) cc_final: 0.7686 (mm) REVERT: U 224 ASN cc_start: 0.6870 (p0) cc_final: 0.6498 (p0) REVERT: U 241 ASN cc_start: 0.7163 (t0) cc_final: 0.6872 (t0) REVERT: U 265 TYR cc_start: 0.6612 (m-80) cc_final: 0.5665 (m-80) REVERT: U 267 ARG cc_start: 0.7376 (OUTLIER) cc_final: 0.6909 (ttm-80) REVERT: U 293 LEU cc_start: 0.7176 (mt) cc_final: 0.6917 (mt) REVERT: U 318 SER cc_start: 0.6742 (p) cc_final: 0.6091 (m) REVERT: U 378 GLU cc_start: 0.7318 (tp30) cc_final: 0.6989 (tp30) REVERT: U 392 ASP cc_start: 0.7334 (m-30) cc_final: 0.7056 (m-30) REVERT: U 444 LEU cc_start: 0.7959 (tp) cc_final: 0.7742 (mt) REVERT: U 503 GLU cc_start: 0.6859 (mt-10) cc_final: 0.6458 (mt-10) REVERT: U 510 LYS cc_start: 0.7992 (ptmm) cc_final: 0.7786 (ptmm) REVERT: U 519 ASP cc_start: 0.6868 (t70) cc_final: 0.6517 (t70) REVERT: U 523 GLU cc_start: 0.6785 (mp0) cc_final: 0.6468 (mp0) REVERT: U 561 LEU cc_start: 0.8392 (mt) cc_final: 0.8101 (mt) REVERT: U 576 LEU cc_start: 0.7163 (mt) cc_final: 0.6919 (mp) REVERT: U 582 GLU cc_start: 0.7150 (tp30) cc_final: 0.6381 (tp30) outliers start: 49 outliers final: 18 residues processed: 1073 average time/residue: 0.2424 time to fit residues: 403.8908 Evaluate side-chains 970 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 948 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 1250 ASP Chi-restraints excluded: chain A residue 1251 ASN Chi-restraints excluded: chain A residue 1255 LEU Chi-restraints excluded: chain A residue 1259 ILE Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain U residue 158 GLU Chi-restraints excluded: chain U residue 161 CYS Chi-restraints excluded: chain U residue 165 TRP Chi-restraints excluded: chain U residue 170 ARG Chi-restraints excluded: chain U residue 179 LEU Chi-restraints excluded: chain U residue 183 LEU Chi-restraints excluded: chain U residue 185 HIS Chi-restraints excluded: chain U residue 187 PRO Chi-restraints excluded: chain U residue 191 LEU Chi-restraints excluded: chain U residue 267 ARG Chi-restraints excluded: chain U residue 294 LYS Chi-restraints excluded: chain U residue 297 GLU Chi-restraints excluded: chain U residue 300 LEU Chi-restraints excluded: chain U residue 604 LYS Chi-restraints excluded: chain U residue 620 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 432 optimal weight: 0.7980 chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 10.0000 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.4980 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 1.9990 chunk 401 optimal weight: 0.3980 chunk 424 optimal weight: 0.1980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 62 GLN A 72 GLN A 77 ASN ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 293 ASN A 403 GLN ** A 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 507 GLN A 531 ASN A 673 GLN A 678 ASN A 757 GLN ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 792 ASN A1032 GLN A1034 GLN A1082 HIS A1129 ASN A1163 HIS ** A1263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1267 ASN A1310 HIS A1384 HIS A1445 HIS ** A1457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1462 GLN B 56 GLN B 90 GLN B 111 ASN B 144 HIS B 344 GLN B 460 HIS B 500 GLN ** B 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 639 HIS B 699 HIS ** B 717 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 731 GLN ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 941 GLN ** B1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1025 ASN B1049 GLN ** B1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1120 ASN ** C 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS ** C 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 GLN D 89 GLN ** D 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 GLN E 107 GLN E 189 GLN G 21 ASN G 24 ASN G 53 ASN I 46 GLN I 91 HIS J 61 ASN U 164 GLN U 241 ASN U 345 GLN U 413 HIS U 433 HIS U 436 ASN U 566 GLN Total number of N/Q/H flips: 54 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.150098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.121509 restraints weight = 62631.372| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 1.99 r_work: 0.3398 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3250 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3252 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3252 r_free = 0.3252 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3252 r_free = 0.3252 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3252 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 37458 Z= 0.163 Angle : 0.685 12.218 50851 Z= 0.354 Chirality : 0.047 0.278 5685 Planarity : 0.006 0.160 6386 Dihedral : 12.783 144.905 5611 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.75 % Favored : 93.91 % Rotamer: Outliers : 3.39 % Allowed : 21.55 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.48 % 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: -0.11 (0.13), residues: 4403 helix: 0.99 (0.13), residues: 1604 sheet: -0.31 (0.20), residues: 646 loop : -0.76 (0.14), residues: 2153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG U 298 TYR 0.026 0.002 TYR U 265 PHE 0.026 0.002 PHE E 73 TRP 0.015 0.002 TRP U 358 HIS 0.011 0.001 HIS U 585 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 (37425) covalent geometry : angle 0.67312 / 0.35 (50804) SS BOND : bond 0.00188 / 0.10 ( 1) SS BOND : angle 1.74352 / 0.93 ( 2) hydrogen bonds : bond 0.04519 / 2.98 ( 1557) hydrogen bonds : angle 5.70658 / 4.02 ( 4407) metal coordination : bond 0.00707 / 0.48 ( 32) metal coordination : angle 4.37094 / 2.88 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8806 Ramachandran restraints generated. 4403 Oldfield, 0 Emsley, 4403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8806 Ramachandran restraints generated. 4403 Oldfield, 0 Emsley, 4403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1081 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 950 time to evaluate : 1.279 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 66 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.7116 (pm20) REVERT: A 186 ARG cc_start: 0.7927 (mtp85) cc_final: 0.7665 (ttp-110) REVERT: A 188 GLN cc_start: 0.7760 (mm110) cc_final: 0.7544 (mm-40) REVERT: A 232 GLU cc_start: 0.7407 (mt-10) cc_final: 0.7125 (mt-10) REVERT: A 289 GLN cc_start: 0.8447 (tt0) cc_final: 0.8209 (tt0) REVERT: A 387 ASN cc_start: 0.8567 (t0) cc_final: 0.8283 (t0) REVERT: A 388 MET cc_start: 0.8131 (mmm) cc_final: 0.7925 (mtp) REVERT: A 408 ARG cc_start: 0.7836 (mtp85) cc_final: 0.7529 (mtp180) REVERT: A 412 GLN cc_start: 0.8130 (mp10) cc_final: 0.7876 (mp10) REVERT: A 418 TYR cc_start: 0.8416 (m-80) cc_final: 0.8063 (m-80) REVERT: A 467 MET cc_start: 0.8180 (mpp) cc_final: 0.7834 (mpp) REVERT: A 473 ARG cc_start: 0.7849 (ttm-80) cc_final: 0.7592 (mtm110) REVERT: A 556 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7261 (mm-30) REVERT: A 583 ARG cc_start: 0.7472 (mtm110) cc_final: 0.7254 (mtm110) REVERT: A 642 LYS cc_start: 0.8630 (tttt) cc_final: 0.8357 (ttpp) REVERT: A 680 LEU cc_start: 0.8407 (tt) cc_final: 0.8186 (tp) REVERT: A 683 GLU cc_start: 0.7385 (OUTLIER) cc_final: 0.7171 (tp30) REVERT: A 691 ASP cc_start: 0.7509 (m-30) cc_final: 0.7181 (m-30) REVERT: A 735 GLN cc_start: 0.7988 (mt0) cc_final: 0.7729 (mt0) REVERT: A 751 LYS cc_start: 0.8249 (tttp) cc_final: 0.7994 (ttpp) REVERT: A 876 ASP cc_start: 0.8130 (p0) cc_final: 0.7743 (p0) REVERT: A 914 LYS cc_start: 0.8114 (mmmm) cc_final: 0.7881 (mmmm) REVERT: A 921 ARG cc_start: 0.8090 (tpt-90) cc_final: 0.7880 (tpp80) REVERT: A 948 ILE cc_start: 0.7952 (mm) cc_final: 0.7735 (mm) REVERT: A 951 GLU cc_start: 0.7514 (mm-30) cc_final: 0.7256 (mm-30) REVERT: A 958 ARG cc_start: 0.7461 (ttp80) cc_final: 0.7030 (ttm110) REVERT: A 1015 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7685 (mp0) REVERT: A 1035 GLU cc_start: 0.8170 (tp30) cc_final: 0.7818 (tp30) REVERT: A 1097 GLU cc_start: 0.7950 (tm-30) cc_final: 0.7714 (tm-30) REVERT: A 1102 MET cc_start: 0.7302 (OUTLIER) cc_final: 0.6992 (mtp) REVERT: A 1118 THR cc_start: 0.8151 (m) cc_final: 0.7793 (t) REVERT: A 1125 LYS cc_start: 0.8285 (ttpp) cc_final: 0.7891 (ttmm) REVERT: A 1156 ASP cc_start: 0.8158 (t0) cc_final: 0.7746 (t0) REVERT: A 1188 GLU cc_start: 0.7502 (pm20) cc_final: 0.7163 (pm20) REVERT: A 1225 LYS cc_start: 0.8608 (mttm) cc_final: 0.8405 (mttm) REVERT: A 1254 LYS cc_start: 0.8235 (OUTLIER) cc_final: 0.8027 (ttmt) REVERT: A 1344 MET cc_start: 0.7856 (tpt) cc_final: 0.7410 (tpt) REVERT: A 1349 GLU cc_start: 0.7432 (tp30) cc_final: 0.7113 (tp30) REVERT: A 1350 LYS cc_start: 0.8042 (mtpp) cc_final: 0.7417 (tttp) REVERT: A 1372 GLU cc_start: 0.7326 (mm-30) cc_final: 0.7073 (mm-30) REVERT: A 1393 VAL cc_start: 0.8712 (t) cc_final: 0.8452 (p) REVERT: A 1412 MET cc_start: 0.8225 (tmm) cc_final: 0.7875 (tmm) REVERT: A 1441 GLU cc_start: 0.7534 (mm-30) cc_final: 0.7147 (mm-30) REVERT: A 1452 LYS cc_start: 0.8199 (mmtp) cc_final: 0.7936 (mmtp) REVERT: B 35 ASP cc_start: 0.7503 (m-30) cc_final: 0.7207 (m-30) REVERT: B 97 THR cc_start: 0.8798 (p) cc_final: 0.8593 (p) REVERT: B 222 ARG cc_start: 0.8156 (ttm110) cc_final: 0.7799 (ttm170) REVERT: B 242 ARG cc_start: 0.6074 (tpt170) cc_final: 0.4367 (mmt180) REVERT: B 345 LYS cc_start: 0.8161 (mmtp) cc_final: 0.7891 (mttp) REVERT: B 407 MET cc_start: 0.8108 (ttm) cc_final: 0.7539 (mtp) REVERT: B 417 ILE cc_start: 0.7791 (mt) cc_final: 0.7549 (tt) REVERT: B 525 ASN cc_start: 0.7809 (m110) cc_final: 0.7606 (m110) REVERT: B 543 GLU cc_start: 0.8010 (mt-10) cc_final: 0.7756 (mt-10) REVERT: B 547 GLU cc_start: 0.7320 (tm-30) cc_final: 0.6988 (tm-30) REVERT: B 593 GLN cc_start: 0.7877 (pt0) cc_final: 0.7585 (pt0) REVERT: B 600 GLU cc_start: 0.7712 (tt0) cc_final: 0.7502 (tt0) REVERT: B 617 ASP cc_start: 0.8021 (t0) cc_final: 0.7709 (t0) REVERT: B 637 LYS cc_start: 0.8240 (tppt) cc_final: 0.7999 (tppt) REVERT: B 664 TYR cc_start: 0.8389 (m-80) cc_final: 0.7423 (m-80) REVERT: B 682 LEU cc_start: 0.7561 (mp) cc_final: 0.7359 (mt) REVERT: B 726 SER cc_start: 0.8325 (p) cc_final: 0.8021 (m) REVERT: B 758 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.8142 (mt) REVERT: B 784 SER cc_start: 0.8440 (m) cc_final: 0.8221 (p) REVERT: B 796 MET cc_start: 0.8200 (mtp) cc_final: 0.7956 (mtp) REVERT: B 798 ARG cc_start: 0.8379 (tpt-90) cc_final: 0.8173 (tpt-90) REVERT: B 817 GLN cc_start: 0.7058 (mm-40) cc_final: 0.6599 (mm-40) REVERT: B 830 GLU cc_start: 0.7653 (pm20) cc_final: 0.7231 (pm20) REVERT: B 869 LYS cc_start: 0.7768 (tttt) cc_final: 0.7430 (tttt) REVERT: B 870 THR cc_start: 0.8089 (m) cc_final: 0.7827 (p) REVERT: B 871 VAL cc_start: 0.8303 (t) cc_final: 0.8074 (p) REVERT: B 895 PHE cc_start: 0.8671 (m-10) cc_final: 0.8407 (m-80) REVERT: B 903 ILE cc_start: 0.8068 (mp) cc_final: 0.7822 (mp) REVERT: B 910 THR cc_start: 0.8380 (t) cc_final: 0.8152 (p) REVERT: B 993 LYS cc_start: 0.8146 (ttmm) cc_final: 0.7694 (ttpp) REVERT: B 1012 SER cc_start: 0.8005 (t) cc_final: 0.7647 (m) REVERT: B 1022 LEU cc_start: 0.8479 (pt) cc_final: 0.8260 (pt) REVERT: B 1070 LEU cc_start: 0.8371 (tp) cc_final: 0.8133 (tt) REVERT: B 1090 GLU cc_start: 0.7130 (mm-30) cc_final: 0.6751 (mp0) REVERT: C 17 GLU cc_start: 0.7677 (pt0) cc_final: 0.7363 (pt0) REVERT: C 75 SER cc_start: 0.8433 (OUTLIER) cc_final: 0.8202 (p) REVERT: C 130 VAL cc_start: 0.8015 (t) cc_final: 0.7705 (t) REVERT: C 240 ARG cc_start: 0.8131 (OUTLIER) cc_final: 0.7687 (ptm-80) REVERT: C 242 GLU cc_start: 0.7719 (pm20) cc_final: 0.7426 (pm20) REVERT: E 27 LEU cc_start: 0.8619 (tp) cc_final: 0.8380 (tp) REVERT: E 41 LYS cc_start: 0.8277 (ttmt) cc_final: 0.8050 (mtmt) REVERT: E 91 CYS cc_start: 0.7455 (t) cc_final: 0.7210 (t) REVERT: E 106 VAL cc_start: 0.8544 (t) cc_final: 0.8240 (m) REVERT: E 133 GLN cc_start: 0.7708 (mm-40) cc_final: 0.7063 (tm-30) REVERT: E 156 VAL cc_start: 0.8150 (t) cc_final: 0.7893 (t) REVERT: E 177 ASP cc_start: 0.7669 (t0) cc_final: 0.7346 (t0) REVERT: F 121 ASP cc_start: 0.8318 (p0) cc_final: 0.8101 (p0) REVERT: G 13 LEU cc_start: 0.8164 (mp) cc_final: 0.7944 (mt) REVERT: H 36 LYS cc_start: 0.8033 (mmpt) cc_final: 0.7364 (mmpt) REVERT: H 37 MET cc_start: 0.7964 (mmm) cc_final: 0.7578 (mmm) REVERT: H 102 ASP cc_start: 0.8365 (p0) cc_final: 0.7694 (p0) REVERT: J 22 LEU cc_start: 0.8331 (mt) cc_final: 0.7933 (mt) REVERT: J 24 LEU cc_start: 0.8476 (mp) cc_final: 0.8230 (mp) REVERT: K 81 TYR cc_start: 0.7927 (t80) cc_final: 0.7671 (t80) REVERT: K 106 ARG cc_start: 0.7995 (ttm-80) cc_final: 0.7652 (mtt90) REVERT: U 13 GLU cc_start: 0.8019 (tm-30) cc_final: 0.7123 (tm-30) REVERT: U 202 ASP cc_start: 0.7317 (m-30) cc_final: 0.7106 (m-30) REVERT: U 207 LEU cc_start: 0.7997 (mm) cc_final: 0.7691 (mm) REVERT: U 224 ASN cc_start: 0.6845 (p0) cc_final: 0.6392 (p0) REVERT: U 241 ASN cc_start: 0.7325 (t0) cc_final: 0.7033 (t0) REVERT: U 265 TYR cc_start: 0.5908 (m-80) cc_final: 0.5632 (m-80) REVERT: U 278 GLU cc_start: 0.7667 (mm-30) cc_final: 0.6731 (mm-30) REVERT: U 290 HIS cc_start: 0.5743 (OUTLIER) cc_final: 0.5443 (t-90) REVERT: U 318 SER cc_start: 0.7090 (p) cc_final: 0.6478 (m) REVERT: U 503 GLU cc_start: 0.7629 (mt-10) cc_final: 0.7212 (mt-10) REVERT: U 510 LYS cc_start: 0.8291 (ptmm) cc_final: 0.7938 (ptmm) REVERT: U 519 ASP cc_start: 0.7114 (t70) cc_final: 0.6670 (t70) REVERT: U 561 LEU cc_start: 0.8458 (mt) cc_final: 0.8158 (mt) REVERT: U 582 GLU cc_start: 0.7535 (tp30) cc_final: 0.6669 (tp30) REVERT: U 604 LYS cc_start: 0.8163 (OUTLIER) cc_final: 0.7867 (mtpt) REVERT: U 610 ARG cc_start: 0.6999 (ttm-80) cc_final: 0.6672 (ttm110) REVERT: U 620 MET cc_start: 0.5624 (mmp) cc_final: 0.4264 (mmp) outliers start: 131 outliers final: 55 residues processed: 1026 average time/residue: 0.2398 time to fit residues: 383.2233 Evaluate side-chains 991 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 926 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 337 LYS Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 683 GLU Chi-restraints excluded: chain A residue 883 ILE Chi-restraints excluded: chain A residue 912 SER Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1015 GLU Chi-restraints excluded: chain A residue 1026 ASP Chi-restraints excluded: chain A residue 1102 MET Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1128 ILE Chi-restraints excluded: chain A residue 1229 GLU Chi-restraints excluded: chain A residue 1251 ASN Chi-restraints excluded: chain A residue 1254 LYS Chi-restraints excluded: chain A residue 1327 GLU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 500 GLN Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 752 TYR Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain B residue 957 THR Chi-restraints excluded: chain B residue 995 GLU Chi-restraints excluded: chain B residue 1101 GLN Chi-restraints excluded: chain B residue 1173 SER Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 240 ARG Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 18 MET Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain F residue 57 MET Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain H residue 133 HIS Chi-restraints excluded: chain I residue 40 ARG Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain U residue 161 CYS Chi-restraints excluded: chain U residue 164 GLN Chi-restraints excluded: chain U residue 179 LEU Chi-restraints excluded: chain U residue 183 LEU Chi-restraints excluded: chain U residue 287 LYS Chi-restraints excluded: chain U residue 290 HIS Chi-restraints excluded: chain U residue 297 GLU Chi-restraints excluded: chain U residue 300 LEU Chi-restraints excluded: chain U residue 304 ASP Chi-restraints excluded: chain U residue 317 ILE Chi-restraints excluded: chain U residue 327 ASN Chi-restraints excluded: chain U residue 364 SER Chi-restraints excluded: chain U residue 604 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 297 optimal weight: 3.9990 chunk 316 optimal weight: 0.5980 chunk 12 optimal weight: 0.2980 chunk 162 optimal weight: 2.9990 chunk 257 optimal weight: 0.6980 chunk 136 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 418 optimal weight: 7.9990 chunk 317 optimal weight: 2.9990 chunk 53 optimal weight: 0.1980 chunk 92 optimal weight: 2.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 272 ASN A 439 HIS ** A 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 507 GLN A 671 ASN A 673 GLN A 757 GLN ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 982 ASN ** A1263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1384 HIS ** A1457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 GLN B 98 HIS B 312 GLN ** B 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 717 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 790 GLN B 930 GLN ** B1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 19 GLN I 98 GLN K 2 ASN ** U 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 413 HIS ** U 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.150094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.120917 restraints weight = 72324.789| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.40 r_work: 0.3367 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3204 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3204 r_free = 0.3204 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3204 r_free = 0.3204 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3204 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 37458 Z= 0.143 Angle : 0.638 11.830 50851 Z= 0.327 Chirality : 0.046 0.282 5685 Planarity : 0.005 0.059 6386 Dihedral : 12.510 144.534 5576 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.77 % Favored : 93.91 % Rotamer: Outliers : 4.24 % Allowed : 20.85 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.48 % 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: -0.07 (0.13), residues: 4403 helix: 1.00 (0.13), residues: 1614 sheet: -0.15 (0.21), residues: 609 loop : -0.78 (0.14), residues: 2180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG U 17 TYR 0.025 0.001 TYR U 597 PHE 0.034 0.001 PHE U 138 TRP 0.016 0.001 TRP C 49 HIS 0.008 0.001 HIS U 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (37425) covalent geometry : angle 0.62644 / 0.33 (50804) SS BOND : bond 0.00184 / 0.10 ( 1) SS BOND : angle 1.41584 / 0.76 ( 2) hydrogen bonds : bond 0.04025 / 2.67 ( 1557) hydrogen bonds : angle 5.37962 / 3.79 ( 4407) metal coordination : bond 0.00640 / 0.43 ( 32) metal coordination : angle 4.01997 / 2.59 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8806 Ramachandran restraints generated. 4403 Oldfield, 0 Emsley, 4403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8806 Ramachandran restraints generated. 4403 Oldfield, 0 Emsley, 4403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1120 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 956 time to evaluate : 1.368 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 66 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.7144 (pm20) REVERT: A 186 ARG cc_start: 0.7985 (mtp85) cc_final: 0.7691 (ttp-110) REVERT: A 188 GLN cc_start: 0.7725 (mm110) cc_final: 0.7452 (mm-40) REVERT: A 216 LEU cc_start: 0.8137 (tp) cc_final: 0.7914 (tp) REVERT: A 232 GLU cc_start: 0.7467 (mt-10) cc_final: 0.7166 (mt-10) REVERT: A 289 GLN cc_start: 0.8521 (tt0) cc_final: 0.8260 (tt0) REVERT: A 387 ASN cc_start: 0.8608 (t0) cc_final: 0.8320 (t0) REVERT: A 404 GLU cc_start: 0.8297 (tp30) cc_final: 0.8007 (tp30) REVERT: A 408 ARG cc_start: 0.7870 (mtp85) cc_final: 0.7634 (mtp180) REVERT: A 418 TYR cc_start: 0.8364 (m-80) cc_final: 0.8141 (m-80) REVERT: A 467 MET cc_start: 0.8152 (mpp) cc_final: 0.7416 (mpp) REVERT: A 477 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7619 (mt) REVERT: A 517 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7762 (mm-30) REVERT: A 540 ASP cc_start: 0.8340 (t0) cc_final: 0.7884 (t0) REVERT: A 556 GLU cc_start: 0.7774 (mm-30) cc_final: 0.7366 (mm-30) REVERT: A 642 LYS cc_start: 0.8673 (tttt) cc_final: 0.8410 (ttpp) REVERT: A 691 ASP cc_start: 0.7587 (m-30) cc_final: 0.7255 (m-30) REVERT: A 711 GLN cc_start: 0.8518 (tp40) cc_final: 0.8134 (mm-40) REVERT: A 735 GLN cc_start: 0.8118 (mt0) cc_final: 0.7876 (mt0) REVERT: A 750 ASP cc_start: 0.7717 (m-30) cc_final: 0.7489 (m-30) REVERT: A 751 LYS cc_start: 0.8333 (tttp) cc_final: 0.8098 (ttpt) REVERT: A 876 ASP cc_start: 0.8222 (p0) cc_final: 0.7833 (p0) REVERT: A 912 SER cc_start: 0.8655 (OUTLIER) cc_final: 0.8404 (p) REVERT: A 914 LYS cc_start: 0.8157 (mmmm) cc_final: 0.7955 (mmmm) REVERT: A 921 ARG cc_start: 0.8082 (tpt-90) cc_final: 0.7865 (tpp80) REVERT: A 945 ASN cc_start: 0.7993 (t0) cc_final: 0.7730 (t0) REVERT: A 951 GLU cc_start: 0.7603 (mm-30) cc_final: 0.7365 (mm-30) REVERT: A 955 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7295 (tt0) REVERT: A 958 ARG cc_start: 0.7353 (ttp80) cc_final: 0.7134 (ttm110) REVERT: A 960 ARG cc_start: 0.8128 (ttm110) cc_final: 0.7813 (ttm170) REVERT: A 1015 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7808 (mp0) REVERT: A 1035 GLU cc_start: 0.8262 (tp30) cc_final: 0.7907 (tp30) REVERT: A 1075 LYS cc_start: 0.8014 (mmtm) cc_final: 0.7802 (mmtp) REVERT: A 1102 MET cc_start: 0.7361 (OUTLIER) cc_final: 0.7062 (mtp) REVERT: A 1118 THR cc_start: 0.8158 (m) cc_final: 0.7810 (t) REVERT: A 1125 LYS cc_start: 0.8316 (ttpp) cc_final: 0.7926 (ttmm) REVERT: A 1156 ASP cc_start: 0.8298 (t0) cc_final: 0.7890 (t0) REVERT: A 1188 GLU cc_start: 0.7602 (pm20) cc_final: 0.7221 (pm20) REVERT: A 1257 LEU cc_start: 0.8230 (tt) cc_final: 0.7962 (tp) REVERT: A 1345 ARG cc_start: 0.7939 (OUTLIER) cc_final: 0.7372 (mtm180) REVERT: A 1349 GLU cc_start: 0.7513 (tp30) cc_final: 0.7141 (tp30) REVERT: A 1350 LYS cc_start: 0.8127 (mtpp) cc_final: 0.7510 (tttp) REVERT: A 1372 GLU cc_start: 0.7449 (mm-30) cc_final: 0.7179 (mm-30) REVERT: A 1412 MET cc_start: 0.8237 (tmm) cc_final: 0.7877 (tmm) REVERT: A 1428 MET cc_start: 0.7866 (tpp) cc_final: 0.7631 (tpp) REVERT: A 1441 GLU cc_start: 0.7588 (mm-30) cc_final: 0.7237 (mm-30) REVERT: A 1452 LYS cc_start: 0.8222 (mmtp) cc_final: 0.7950 (mmtp) REVERT: B 35 ASP cc_start: 0.7605 (m-30) cc_final: 0.7311 (m-30) REVERT: B 97 THR cc_start: 0.8817 (p) cc_final: 0.8600 (p) REVERT: B 98 HIS cc_start: 0.7986 (t70) cc_final: 0.7757 (t-90) REVERT: B 142 THR cc_start: 0.8053 (OUTLIER) cc_final: 0.7715 (p) REVERT: B 222 ARG cc_start: 0.8154 (ttm110) cc_final: 0.7596 (mtt90) REVERT: B 242 ARG cc_start: 0.6211 (tpt170) cc_final: 0.4329 (mtt180) REVERT: B 255 ARG cc_start: 0.8016 (tpt-90) cc_final: 0.7616 (tpp80) REVERT: B 300 MET cc_start: 0.7302 (OUTLIER) cc_final: 0.6988 (mtp) REVERT: B 407 MET cc_start: 0.8098 (ttm) cc_final: 0.7535 (mtp) REVERT: B 414 GLU cc_start: 0.7470 (tm-30) cc_final: 0.7170 (tm-30) REVERT: B 417 ILE cc_start: 0.7822 (mt) cc_final: 0.7609 (tt) REVERT: B 437 THR cc_start: 0.8383 (p) cc_final: 0.8100 (p) REVERT: B 543 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7816 (mt-10) REVERT: B 547 GLU cc_start: 0.7362 (tm-30) cc_final: 0.7052 (tm-30) REVERT: B 556 ILE cc_start: 0.8506 (tp) cc_final: 0.8263 (tt) REVERT: B 593 GLN cc_start: 0.7921 (pt0) cc_final: 0.7635 (pt0) REVERT: B 617 ASP cc_start: 0.8099 (t0) cc_final: 0.7827 (t0) REVERT: B 629 GLU cc_start: 0.7800 (mm-30) cc_final: 0.7541 (mm-30) REVERT: B 637 LYS cc_start: 0.8303 (tppt) cc_final: 0.8086 (tppt) REVERT: B 664 TYR cc_start: 0.8380 (m-80) cc_final: 0.7440 (m-80) REVERT: B 682 LEU cc_start: 0.7511 (mp) cc_final: 0.7298 (mt) REVERT: B 698 ILE cc_start: 0.8420 (OUTLIER) cc_final: 0.8122 (mt) REVERT: B 724 TYR cc_start: 0.8275 (m-80) cc_final: 0.7896 (m-80) REVERT: B 726 SER cc_start: 0.8286 (p) cc_final: 0.8024 (m) REVERT: B 758 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.8145 (mt) REVERT: B 796 MET cc_start: 0.8346 (mtp) cc_final: 0.8129 (mtp) REVERT: B 798 ARG cc_start: 0.8393 (tpt-90) cc_final: 0.8189 (tpt-90) REVERT: B 820 LYS cc_start: 0.7872 (mmtm) cc_final: 0.7189 (mmtm) REVERT: B 830 GLU cc_start: 0.7700 (pm20) cc_final: 0.7297 (pm20) REVERT: B 864 ASP cc_start: 0.7996 (m-30) cc_final: 0.7717 (m-30) REVERT: B 870 THR cc_start: 0.8202 (m) cc_final: 0.7853 (p) REVERT: B 871 VAL cc_start: 0.8409 (t) cc_final: 0.8060 (m) REVERT: B 895 PHE cc_start: 0.8694 (m-10) cc_final: 0.8409 (m-80) REVERT: B 910 THR cc_start: 0.8452 (t) cc_final: 0.8175 (p) REVERT: B 916 TYR cc_start: 0.8042 (m-10) cc_final: 0.7582 (m-80) REVERT: B 993 LYS cc_start: 0.8114 (ttmm) cc_final: 0.7861 (ttpp) REVERT: B 1012 SER cc_start: 0.8017 (t) cc_final: 0.7729 (m) REVERT: B 1070 LEU cc_start: 0.8375 (tp) cc_final: 0.8133 (tt) REVERT: B 1090 GLU cc_start: 0.7210 (mm-30) cc_final: 0.6861 (mp0) REVERT: B 1108 PHE cc_start: 0.8173 (t80) cc_final: 0.7854 (t80) REVERT: C 17 GLU cc_start: 0.7704 (pt0) cc_final: 0.7399 (pt0) REVERT: C 130 VAL cc_start: 0.8008 (t) cc_final: 0.7684 (t) REVERT: C 211 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8530 (pp) REVERT: D 45 LYS cc_start: 0.8219 (OUTLIER) cc_final: 0.7904 (mmmt) REVERT: E 27 LEU cc_start: 0.8661 (tp) cc_final: 0.8453 (tp) REVERT: E 38 GLU cc_start: 0.7439 (mp0) cc_final: 0.7170 (mp0) REVERT: E 91 CYS cc_start: 0.7472 (t) cc_final: 0.7229 (t) REVERT: E 106 VAL cc_start: 0.8680 (t) cc_final: 0.8423 (m) REVERT: E 134 GLU cc_start: 0.7721 (mt-10) cc_final: 0.7463 (mt-10) REVERT: E 156 VAL cc_start: 0.8197 (t) cc_final: 0.7933 (t) REVERT: E 177 ASP cc_start: 0.7727 (t0) cc_final: 0.7423 (t0) REVERT: G 117 MET cc_start: 0.7440 (OUTLIER) cc_final: 0.7116 (tpp) REVERT: H 102 ASP cc_start: 0.8383 (p0) cc_final: 0.7719 (p0) REVERT: J 22 LEU cc_start: 0.8379 (mt) cc_final: 0.7991 (mt) REVERT: J 24 LEU cc_start: 0.8518 (mp) cc_final: 0.8280 (mp) REVERT: J 50 LEU cc_start: 0.8535 (tt) cc_final: 0.8249 (tp) REVERT: K 81 TYR cc_start: 0.7948 (t80) cc_final: 0.7693 (t80) REVERT: K 106 ARG cc_start: 0.8080 (ttm-80) cc_final: 0.7575 (mtt90) REVERT: U 13 GLU cc_start: 0.8203 (tm-30) cc_final: 0.7326 (tm-30) REVERT: U 138 PHE cc_start: 0.8467 (t80) cc_final: 0.8267 (t80) REVERT: U 183 LEU cc_start: 0.7333 (OUTLIER) cc_final: 0.6832 (tp) REVERT: U 202 ASP cc_start: 0.7426 (m-30) cc_final: 0.7207 (m-30) REVERT: U 207 LEU cc_start: 0.7985 (mm) cc_final: 0.7719 (mm) REVERT: U 224 ASN cc_start: 0.6921 (p0) cc_final: 0.6450 (p0) REVERT: U 241 ASN cc_start: 0.7357 (t0) cc_final: 0.7021 (t0) REVERT: U 267 ARG cc_start: 0.7711 (OUTLIER) cc_final: 0.6862 (tmm-80) REVERT: U 278 GLU cc_start: 0.7757 (mm-30) cc_final: 0.6859 (mm-30) REVERT: U 290 HIS cc_start: 0.5843 (OUTLIER) cc_final: 0.5533 (t-90) REVERT: U 318 SER cc_start: 0.7099 (p) cc_final: 0.6480 (m) REVERT: U 346 GLU cc_start: 0.6373 (mm-30) cc_final: 0.6161 (mm-30) REVERT: U 441 ARG cc_start: 0.8080 (mtm110) cc_final: 0.7714 (mtm-85) REVERT: U 503 GLU cc_start: 0.7738 (mt-10) cc_final: 0.7365 (mt-10) REVERT: U 510 LYS cc_start: 0.8330 (ptmm) cc_final: 0.8062 (ptmm) REVERT: U 516 LYS cc_start: 0.8797 (tppt) cc_final: 0.8561 (mmtm) REVERT: U 519 ASP cc_start: 0.7211 (t70) cc_final: 0.6745 (t70) REVERT: U 523 GLU cc_start: 0.7136 (mp0) cc_final: 0.6364 (mp0) REVERT: U 561 LEU cc_start: 0.8479 (mt) cc_final: 0.8155 (mt) REVERT: U 565 ARG cc_start: 0.7451 (tpt170) cc_final: 0.7238 (tpt170) REVERT: U 582 GLU cc_start: 0.7672 (tp30) cc_final: 0.6790 (tp30) REVERT: U 602 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.7426 (tp) REVERT: U 604 LYS cc_start: 0.8208 (mtpp) cc_final: 0.7935 (mtpp) REVERT: U 610 ARG cc_start: 0.7014 (ttm-80) cc_final: 0.6681 (ttm110) REVERT: U 620 MET cc_start: 0.5564 (mmp) cc_final: 0.4217 (mmp) outliers start: 164 outliers final: 89 residues processed: 1052 average time/residue: 0.2360 time to fit residues: 386.5913 Evaluate side-chains 1029 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 922 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 62 GLN Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 301 HIS Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 673 GLN Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 803 LYS Chi-restraints excluded: chain A residue 865 ILE Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 883 ILE Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 912 SER Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 955 GLU Chi-restraints excluded: chain A residue 982 ASN Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1015 GLU Chi-restraints excluded: chain A residue 1102 MET Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1128 ILE Chi-restraints excluded: chain A residue 1229 GLU Chi-restraints excluded: chain A residue 1251 ASN Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1304 ILE Chi-restraints excluded: chain A residue 1345 ARG Chi-restraints excluded: chain A residue 1351 ASP Chi-restraints excluded: chain A residue 1411 LEU Chi-restraints excluded: chain A residue 1417 HIS Chi-restraints excluded: chain A residue 1480 CYS Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 298 MET Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain B residue 436 LYS Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 698 ILE Chi-restraints excluded: chain B residue 719 SER Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 752 TYR Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain B residue 894 THR Chi-restraints excluded: chain B residue 957 THR Chi-restraints excluded: chain B residue 1004 ASP Chi-restraints excluded: chain B residue 1071 ASN Chi-restraints excluded: chain B residue 1101 GLN Chi-restraints excluded: chain B residue 1173 SER Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 240 ARG Chi-restraints excluded: chain D residue 45 LYS Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 18 MET Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain G residue 117 MET Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain H residue 133 HIS Chi-restraints excluded: chain I residue 40 ARG Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain K residue 36 ASN Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain U residue 165 TRP Chi-restraints excluded: chain U residue 179 LEU Chi-restraints excluded: chain U residue 183 LEU Chi-restraints excluded: chain U residue 267 ARG Chi-restraints excluded: chain U residue 287 LYS Chi-restraints excluded: chain U residue 290 HIS Chi-restraints excluded: chain U residue 297 GLU Chi-restraints excluded: chain U residue 300 LEU Chi-restraints excluded: chain U residue 317 ILE Chi-restraints excluded: chain U residue 327 ASN Chi-restraints excluded: chain U residue 364 SER Chi-restraints excluded: chain U residue 431 CYS Chi-restraints excluded: chain U residue 570 THR Chi-restraints excluded: chain U residue 602 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 96 optimal weight: 1.9990 chunk 313 optimal weight: 2.9990 chunk 278 optimal weight: 1.9990 chunk 233 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 267 optimal weight: 3.9990 chunk 157 optimal weight: 3.9990 chunk 282 optimal weight: 2.9990 chunk 198 optimal weight: 2.9990 chunk 372 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 678 ASN ** A 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 904 GLN ** A1263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1384 HIS ** A1457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 GLN ** B 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 717 ASN ** B1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 43 HIS D 47 GLN ** D 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 98 GLN U 34 GLN ** U 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 413 HIS ** U 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.146959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.118178 restraints weight = 59961.563| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 1.98 r_work: 0.3344 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3180 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3180 r_free = 0.3180 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3180 r_free = 0.3180 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (5 function evaluations) r_final: 0.3180 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 37458 Z= 0.230 Angle : 0.681 13.661 50851 Z= 0.346 Chirality : 0.048 0.347 5685 Planarity : 0.005 0.064 6386 Dihedral : 12.510 143.924 5570 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.91 % Favored : 93.77 % Rotamer: Outliers : 4.78 % Allowed : 20.88 % Favored : 74.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.48 % 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: -0.23 (0.13), residues: 4403 helix: 0.85 (0.13), residues: 1622 sheet: -0.27 (0.21), residues: 627 loop : -0.85 (0.14), residues: 2154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 335 TYR 0.028 0.002 TYR U 265 PHE 0.029 0.002 PHE E 75 TRP 0.018 0.002 TRP A1192 HIS 0.009 0.001 HIS U 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00536 / 0.23 (37425) covalent geometry : angle 0.66547 / 0.35 (50804) SS BOND : bond 0.00188 / 0.10 ( 1) SS BOND : angle 1.35633 / 0.72 ( 2) hydrogen bonds : bond 0.04233 / 2.81 ( 1557) hydrogen bonds : angle 5.23088 / 3.69 ( 4407) metal coordination : bond 0.01054 / 0.68 ( 32) metal coordination : angle 4.90483 / 3.17 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8806 Ramachandran restraints generated. 4403 Oldfield, 0 Emsley, 4403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8806 Ramachandran restraints generated. 4403 Oldfield, 0 Emsley, 4403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1146 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 185 poor density : 961 time to evaluate : 1.007 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 33 ARG cc_start: 0.8052 (mtm-85) cc_final: 0.7756 (mtm110) REVERT: A 66 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.7113 (pm20) REVERT: A 186 ARG cc_start: 0.8014 (mtp85) cc_final: 0.7743 (ttp-110) REVERT: A 188 GLN cc_start: 0.7823 (mm110) cc_final: 0.7561 (mm-40) REVERT: A 216 LEU cc_start: 0.8119 (tp) cc_final: 0.7907 (tp) REVERT: A 232 GLU cc_start: 0.7373 (mt-10) cc_final: 0.7140 (mt-10) REVERT: A 289 GLN cc_start: 0.8506 (tt0) cc_final: 0.8274 (tt0) REVERT: A 325 LEU cc_start: 0.8273 (mm) cc_final: 0.7978 (mp) REVERT: A 327 ARG cc_start: 0.7783 (mmt180) cc_final: 0.7528 (mmt180) REVERT: A 387 ASN cc_start: 0.8621 (t0) cc_final: 0.8329 (t0) REVERT: A 408 ARG cc_start: 0.7839 (mtp85) cc_final: 0.7517 (mtp180) REVERT: A 418 TYR cc_start: 0.8424 (m-80) cc_final: 0.8158 (m-80) REVERT: A 467 MET cc_start: 0.8227 (mpp) cc_final: 0.7542 (mpp) REVERT: A 477 LEU cc_start: 0.7970 (OUTLIER) cc_final: 0.7664 (mt) REVERT: A 556 GLU cc_start: 0.7757 (mm-30) cc_final: 0.7314 (mm-30) REVERT: A 583 ARG cc_start: 0.7735 (mtm110) cc_final: 0.7449 (ptm-80) REVERT: A 642 LYS cc_start: 0.8682 (tttt) cc_final: 0.8451 (ttpp) REVERT: A 662 HIS cc_start: 0.8334 (p-80) cc_final: 0.8133 (p-80) REVERT: A 691 ASP cc_start: 0.7524 (m-30) cc_final: 0.7222 (m-30) REVERT: A 711 GLN cc_start: 0.8453 (tp40) cc_final: 0.8078 (mm-40) REVERT: A 735 GLN cc_start: 0.8056 (mt0) cc_final: 0.7821 (mt0) REVERT: A 750 ASP cc_start: 0.7658 (m-30) cc_final: 0.7444 (m-30) REVERT: A 751 LYS cc_start: 0.8316 (tttp) cc_final: 0.8075 (ttpt) REVERT: A 876 ASP cc_start: 0.8220 (p0) cc_final: 0.8001 (p0) REVERT: A 914 LYS cc_start: 0.8125 (mmmm) cc_final: 0.7876 (mmmm) REVERT: A 945 ASN cc_start: 0.8186 (t0) cc_final: 0.7905 (t0) REVERT: A 955 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.7157 (tt0) REVERT: A 1015 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7751 (mp0) REVERT: A 1082 HIS cc_start: 0.8325 (m90) cc_final: 0.8084 (m-70) REVERT: A 1102 MET cc_start: 0.7368 (OUTLIER) cc_final: 0.7098 (mtp) REVERT: A 1118 THR cc_start: 0.8215 (m) cc_final: 0.7859 (t) REVERT: A 1125 LYS cc_start: 0.8315 (ttpp) cc_final: 0.7833 (ttmm) REVERT: A 1156 ASP cc_start: 0.8256 (t0) cc_final: 0.7821 (t0) REVERT: A 1188 GLU cc_start: 0.7570 (pm20) cc_final: 0.7202 (pm20) REVERT: A 1221 MET cc_start: 0.7998 (mmm) cc_final: 0.7664 (tpt) REVERT: A 1257 LEU cc_start: 0.8303 (tt) cc_final: 0.8024 (tp) REVERT: A 1262 MET cc_start: 0.8070 (ptm) cc_final: 0.7797 (ptm) REVERT: A 1296 MET cc_start: 0.8303 (tpt) cc_final: 0.7294 (tpt) REVERT: A 1345 ARG cc_start: 0.7844 (OUTLIER) cc_final: 0.7225 (mtm180) REVERT: A 1349 GLU cc_start: 0.7490 (tp30) cc_final: 0.7164 (tp30) REVERT: A 1350 LYS cc_start: 0.8034 (mtpp) cc_final: 0.7285 (tttp) REVERT: A 1368 VAL cc_start: 0.8496 (t) cc_final: 0.8290 (p) REVERT: A 1372 GLU cc_start: 0.7384 (mm-30) cc_final: 0.7145 (mm-30) REVERT: A 1382 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.8050 (mt) REVERT: A 1428 MET cc_start: 0.7843 (tpp) cc_final: 0.7637 (tpp) REVERT: A 1441 GLU cc_start: 0.7490 (mm-30) cc_final: 0.7150 (mm-30) REVERT: A 1452 LYS cc_start: 0.8177 (mmtp) cc_final: 0.7887 (mmtp) REVERT: A 1484 MET cc_start: 0.5444 (ppp) cc_final: 0.4842 (ppp) REVERT: B 35 ASP cc_start: 0.7576 (m-30) cc_final: 0.7297 (m-30) REVERT: B 97 THR cc_start: 0.8788 (p) cc_final: 0.8570 (p) REVERT: B 222 ARG cc_start: 0.8208 (ttm110) cc_final: 0.7605 (mtt90) REVERT: B 242 ARG cc_start: 0.6311 (tpt170) cc_final: 0.4324 (mtt180) REVERT: B 255 ARG cc_start: 0.8174 (tpt-90) cc_final: 0.7806 (tpp80) REVERT: B 414 GLU cc_start: 0.7516 (tm-30) cc_final: 0.7185 (tm-30) REVERT: B 417 ILE cc_start: 0.7938 (mt) cc_final: 0.7730 (tt) REVERT: B 437 THR cc_start: 0.8395 (p) cc_final: 0.8145 (p) REVERT: B 543 GLU cc_start: 0.8064 (mt-10) cc_final: 0.7840 (mt-10) REVERT: B 547 GLU cc_start: 0.7395 (tm-30) cc_final: 0.7099 (tm-30) REVERT: B 556 ILE cc_start: 0.8619 (tp) cc_final: 0.8356 (tt) REVERT: B 572 CYS cc_start: 0.8375 (p) cc_final: 0.8141 (p) REVERT: B 593 GLN cc_start: 0.7924 (pt0) cc_final: 0.7669 (pt0) REVERT: B 599 SER cc_start: 0.8512 (p) cc_final: 0.8288 (t) REVERT: B 617 ASP cc_start: 0.8096 (t0) cc_final: 0.7824 (t0) REVERT: B 629 GLU cc_start: 0.7783 (mm-30) cc_final: 0.7530 (mm-30) REVERT: B 664 TYR cc_start: 0.8411 (m-80) cc_final: 0.7380 (m-80) REVERT: B 698 ILE cc_start: 0.8480 (OUTLIER) cc_final: 0.8153 (mt) REVERT: B 726 SER cc_start: 0.8311 (p) cc_final: 0.8018 (m) REVERT: B 751 LEU cc_start: 0.8484 (tp) cc_final: 0.8277 (tp) REVERT: B 796 MET cc_start: 0.8217 (mtp) cc_final: 0.7990 (mtp) REVERT: B 820 LYS cc_start: 0.7882 (mmtm) cc_final: 0.7210 (mmtm) REVERT: B 869 LYS cc_start: 0.7890 (tttt) cc_final: 0.7622 (tttp) REVERT: B 870 THR cc_start: 0.8253 (m) cc_final: 0.7796 (p) REVERT: B 871 VAL cc_start: 0.8281 (t) cc_final: 0.7960 (m) REVERT: B 895 PHE cc_start: 0.8715 (m-10) cc_final: 0.8382 (m-80) REVERT: B 910 THR cc_start: 0.8433 (t) cc_final: 0.8151 (p) REVERT: B 916 TYR cc_start: 0.8155 (m-10) cc_final: 0.7609 (m-80) REVERT: B 993 LYS cc_start: 0.8190 (ttmm) cc_final: 0.7935 (ttpp) REVERT: B 1012 SER cc_start: 0.7994 (t) cc_final: 0.7686 (m) REVERT: B 1090 GLU cc_start: 0.7127 (mm-30) cc_final: 0.6826 (mp0) REVERT: B 1091 ARG cc_start: 0.7784 (OUTLIER) cc_final: 0.7186 (ptt-90) REVERT: B 1108 PHE cc_start: 0.8198 (t80) cc_final: 0.7917 (t80) REVERT: C 17 GLU cc_start: 0.7683 (pt0) cc_final: 0.7392 (pt0) REVERT: C 62 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7610 (mp0) REVERT: C 75 SER cc_start: 0.8515 (OUTLIER) cc_final: 0.8266 (p) REVERT: C 211 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8547 (pp) REVERT: C 240 ARG cc_start: 0.8090 (OUTLIER) cc_final: 0.7659 (ptm-80) REVERT: C 258 ASP cc_start: 0.7745 (m-30) cc_final: 0.7450 (m-30) REVERT: D 45 LYS cc_start: 0.8231 (OUTLIER) cc_final: 0.7894 (mmmt) REVERT: E 23 ASP cc_start: 0.7754 (m-30) cc_final: 0.7330 (m-30) REVERT: E 38 GLU cc_start: 0.7451 (mp0) cc_final: 0.7123 (mp0) REVERT: E 106 VAL cc_start: 0.8723 (t) cc_final: 0.8497 (m) REVERT: E 151 MET cc_start: 0.8540 (mtp) cc_final: 0.8313 (mtm) REVERT: E 156 VAL cc_start: 0.8177 (t) cc_final: 0.7958 (t) REVERT: F 52 ILE cc_start: 0.8487 (OUTLIER) cc_final: 0.8269 (pp) REVERT: F 84 GLU cc_start: 0.8097 (mp0) cc_final: 0.7208 (mp0) REVERT: H 37 MET cc_start: 0.7966 (mmm) cc_final: 0.7554 (mmm) REVERT: H 102 ASP cc_start: 0.8465 (p0) cc_final: 0.7784 (p0) REVERT: J 50 LEU cc_start: 0.8509 (tt) cc_final: 0.8278 (tp) REVERT: U 13 GLU cc_start: 0.8048 (tm-30) cc_final: 0.7215 (tm-30) REVERT: U 138 PHE cc_start: 0.8407 (t80) cc_final: 0.8197 (t80) REVERT: U 183 LEU cc_start: 0.7377 (OUTLIER) cc_final: 0.6883 (tp) REVERT: U 202 ASP cc_start: 0.7421 (m-30) cc_final: 0.7211 (m-30) REVERT: U 207 LEU cc_start: 0.7977 (mm) cc_final: 0.7700 (mm) REVERT: U 224 ASN cc_start: 0.6921 (p0) cc_final: 0.6435 (p0) REVERT: U 241 ASN cc_start: 0.7379 (t0) cc_final: 0.6964 (t0) REVERT: U 267 ARG cc_start: 0.7822 (OUTLIER) cc_final: 0.6868 (tmm-80) REVERT: U 278 GLU cc_start: 0.7806 (mm-30) cc_final: 0.6864 (mm-30) REVERT: U 290 HIS cc_start: 0.6065 (OUTLIER) cc_final: 0.5640 (t-90) REVERT: U 321 MET cc_start: 0.7428 (mpp) cc_final: 0.7044 (mpp) REVERT: U 346 GLU cc_start: 0.6512 (mm-30) cc_final: 0.6164 (mm-30) REVERT: U 441 ARG cc_start: 0.8062 (mtm110) cc_final: 0.7712 (mtm-85) REVERT: U 500 HIS cc_start: 0.7410 (m-70) cc_final: 0.6914 (m-70) REVERT: U 503 GLU cc_start: 0.7724 (mt-10) cc_final: 0.7378 (mt-10) REVERT: U 510 LYS cc_start: 0.8386 (ptmm) cc_final: 0.8141 (ptmm) REVERT: U 512 MET cc_start: 0.7876 (OUTLIER) cc_final: 0.7618 (ttm) REVERT: U 516 LYS cc_start: 0.8831 (tppt) cc_final: 0.8623 (mmtm) REVERT: U 519 ASP cc_start: 0.7258 (t70) cc_final: 0.6782 (t70) REVERT: U 523 GLU cc_start: 0.7182 (mp0) cc_final: 0.6462 (mp0) REVERT: U 561 LEU cc_start: 0.8422 (mt) cc_final: 0.8103 (mt) REVERT: U 582 GLU cc_start: 0.7685 (tp30) cc_final: 0.6785 (tp30) REVERT: U 593 VAL cc_start: 0.7985 (m) cc_final: 0.7691 (p) REVERT: U 602 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.7378 (tp) REVERT: U 604 LYS cc_start: 0.8217 (mtpp) cc_final: 0.7904 (mtpp) REVERT: U 610 ARG cc_start: 0.7017 (ttm-80) cc_final: 0.6695 (ttm110) REVERT: U 620 MET cc_start: 0.5485 (mmp) cc_final: 0.4181 (mmp) outliers start: 185 outliers final: 98 residues processed: 1069 average time/residue: 0.2394 time to fit residues: 399.1839 Evaluate side-chains 1051 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 933 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 62 GLN Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 301 HIS Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 539 GLN Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 818 GLU Chi-restraints excluded: chain A residue 865 ILE Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 883 ILE Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 955 GLU Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1015 GLU Chi-restraints excluded: chain A residue 1047 SER Chi-restraints excluded: chain A residue 1102 MET Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1128 ILE Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1304 ILE Chi-restraints excluded: chain A residue 1309 MET Chi-restraints excluded: chain A residue 1345 ARG Chi-restraints excluded: chain A residue 1351 ASP Chi-restraints excluded: chain A residue 1382 LEU Chi-restraints excluded: chain A residue 1417 HIS Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 298 MET Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 436 LYS Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 698 ILE Chi-restraints excluded: chain B residue 719 SER Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 752 TYR Chi-restraints excluded: chain B residue 894 THR Chi-restraints excluded: chain B residue 928 ILE Chi-restraints excluded: chain B residue 957 THR Chi-restraints excluded: chain B residue 1004 ASP Chi-restraints excluded: chain B residue 1033 THR Chi-restraints excluded: chain B residue 1071 ASN Chi-restraints excluded: chain B residue 1091 ARG Chi-restraints excluded: chain B residue 1101 GLN Chi-restraints excluded: chain C residue 24 GLU Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 240 ARG Chi-restraints excluded: chain D residue 45 LYS Chi-restraints excluded: chain D residue 47 GLN Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 18 MET Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain H residue 133 HIS Chi-restraints excluded: chain I residue 25 TYR Chi-restraints excluded: chain I residue 27 LYS Chi-restraints excluded: chain I residue 40 ARG Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain K residue 36 ASN Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain U residue 183 LEU Chi-restraints excluded: chain U residue 267 ARG Chi-restraints excluded: chain U residue 287 LYS Chi-restraints excluded: chain U residue 290 HIS Chi-restraints excluded: chain U residue 297 GLU Chi-restraints excluded: chain U residue 300 LEU Chi-restraints excluded: chain U residue 317 ILE Chi-restraints excluded: chain U residue 327 ASN Chi-restraints excluded: chain U residue 364 SER Chi-restraints excluded: chain U residue 366 ASN Chi-restraints excluded: chain U residue 431 CYS Chi-restraints excluded: chain U residue 512 MET Chi-restraints excluded: chain U residue 559 GLU Chi-restraints excluded: chain U residue 602 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 39 optimal weight: 0.7980 chunk 3 optimal weight: 0.0070 chunk 72 optimal weight: 0.8980 chunk 321 optimal weight: 2.9990 chunk 208 optimal weight: 0.9980 chunk 296 optimal weight: 0.4980 chunk 388 optimal weight: 20.0000 chunk 30 optimal weight: 1.9990 chunk 393 optimal weight: 6.9990 chunk 37 optimal weight: 0.7980 chunk 406 optimal weight: 0.2980 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 472 HIS ** A 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 982 ASN ** A1263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 GLN ** B 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 139 GLN ** U 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 413 HIS ** U 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.149290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.119748 restraints weight = 73264.710| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.23 r_work: 0.3360 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3164 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3164 r_free = 0.3164 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3164 r_free = 0.3164 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.3164 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 37458 Z= 0.145 Angle : 0.639 12.529 50851 Z= 0.324 Chirality : 0.045 0.288 5685 Planarity : 0.005 0.064 6386 Dihedral : 12.434 144.199 5566 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.77 % Favored : 93.93 % Rotamer: Outliers : 4.19 % Allowed : 21.91 % Favored : 73.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.48 % 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: -0.20 (0.13), residues: 4403 helix: 0.91 (0.13), residues: 1618 sheet: -0.27 (0.20), residues: 626 loop : -0.87 (0.14), residues: 2159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG U 376 TYR 0.021 0.001 TYR A 669 PHE 0.026 0.001 PHE A1388 TRP 0.018 0.001 TRP C 49 HIS 0.008 0.001 HIS U 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 (37425) covalent geometry : angle 0.62597 / 0.32 (50804) SS BOND : bond 0.00129 / 0.07 ( 1) SS BOND : angle 1.58193 / 0.84 ( 2) hydrogen bonds : bond 0.03741 / 2.49 ( 1557) hydrogen bonds : angle 5.09592 / 3.59 ( 4407) metal coordination : bond 0.00659 / 0.44 ( 32) metal coordination : angle 4.26930 / 2.74 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8806 Ramachandran restraints generated. 4403 Oldfield, 0 Emsley, 4403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8806 Ramachandran restraints generated. 4403 Oldfield, 0 Emsley, 4403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1110 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 948 time to evaluate : 1.271 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 31 LEU cc_start: 0.8485 (mt) cc_final: 0.8230 (mt) REVERT: A 66 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.7091 (pm20) REVERT: A 186 ARG cc_start: 0.8007 (mtp85) cc_final: 0.7738 (ttp-110) REVERT: A 188 GLN cc_start: 0.7809 (mm110) cc_final: 0.7596 (mm-40) REVERT: A 192 ARG cc_start: 0.7117 (ttp80) cc_final: 0.6901 (ttm110) REVERT: A 216 LEU cc_start: 0.8102 (tp) cc_final: 0.7902 (tp) REVERT: A 223 GLU cc_start: 0.8149 (tp30) cc_final: 0.7871 (tp30) REVERT: A 232 GLU cc_start: 0.7500 (mt-10) cc_final: 0.7205 (mt-10) REVERT: A 289 GLN cc_start: 0.8464 (tt0) cc_final: 0.8200 (tt0) REVERT: A 327 ARG cc_start: 0.7792 (mmt180) cc_final: 0.7545 (mmt180) REVERT: A 375 ILE cc_start: 0.8054 (mm) cc_final: 0.7804 (tt) REVERT: A 387 ASN cc_start: 0.8607 (t0) cc_final: 0.8312 (t0) REVERT: A 408 ARG cc_start: 0.7793 (mtp85) cc_final: 0.7555 (mtp180) REVERT: A 418 TYR cc_start: 0.8452 (m-80) cc_final: 0.8146 (m-80) REVERT: A 467 MET cc_start: 0.8222 (mpp) cc_final: 0.7506 (mpp) REVERT: A 477 LEU cc_start: 0.8004 (OUTLIER) cc_final: 0.7677 (mt) REVERT: A 556 GLU cc_start: 0.7733 (mm-30) cc_final: 0.7305 (mm-30) REVERT: A 583 ARG cc_start: 0.7756 (mtm110) cc_final: 0.7463 (ptm-80) REVERT: A 631 GLU cc_start: 0.7574 (mt-10) cc_final: 0.7186 (mt-10) REVERT: A 642 LYS cc_start: 0.8687 (tttt) cc_final: 0.8439 (ttpp) REVERT: A 662 HIS cc_start: 0.8328 (p-80) cc_final: 0.8089 (p-80) REVERT: A 691 ASP cc_start: 0.7592 (m-30) cc_final: 0.7300 (m-30) REVERT: A 711 GLN cc_start: 0.8451 (tp40) cc_final: 0.8058 (mm-40) REVERT: A 735 GLN cc_start: 0.8060 (mt0) cc_final: 0.7827 (mt0) REVERT: A 750 ASP cc_start: 0.7670 (m-30) cc_final: 0.7452 (m-30) REVERT: A 751 LYS cc_start: 0.8301 (tttp) cc_final: 0.8074 (ttpt) REVERT: A 783 GLN cc_start: 0.8347 (mt0) cc_final: 0.8107 (mt0) REVERT: A 876 ASP cc_start: 0.8242 (p0) cc_final: 0.8004 (p0) REVERT: A 945 ASN cc_start: 0.8090 (t0) cc_final: 0.7799 (t0) REVERT: A 955 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.7171 (tt0) REVERT: A 1015 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7809 (mp0) REVERT: A 1082 HIS cc_start: 0.8298 (m90) cc_final: 0.8089 (m-70) REVERT: A 1118 THR cc_start: 0.8063 (m) cc_final: 0.7811 (t) REVERT: A 1125 LYS cc_start: 0.8300 (ttpp) cc_final: 0.7790 (ttmm) REVERT: A 1156 ASP cc_start: 0.8300 (t0) cc_final: 0.7866 (t0) REVERT: A 1221 MET cc_start: 0.8083 (mmm) cc_final: 0.7854 (tpp) REVERT: A 1257 LEU cc_start: 0.8254 (tt) cc_final: 0.7973 (tp) REVERT: A 1262 MET cc_start: 0.8076 (ptm) cc_final: 0.7848 (ptm) REVERT: A 1296 MET cc_start: 0.8260 (tpt) cc_final: 0.8058 (tpt) REVERT: A 1303 GLN cc_start: 0.7952 (pm20) cc_final: 0.7689 (pm20) REVERT: A 1344 MET cc_start: 0.7810 (tpt) cc_final: 0.7608 (tpt) REVERT: A 1349 GLU cc_start: 0.7490 (tp30) cc_final: 0.7127 (tp30) REVERT: A 1350 LYS cc_start: 0.8061 (OUTLIER) cc_final: 0.7307 (tttp) REVERT: A 1441 GLU cc_start: 0.7492 (mm-30) cc_final: 0.7117 (mm-30) REVERT: A 1452 LYS cc_start: 0.8175 (mmtp) cc_final: 0.7886 (mmtp) REVERT: A 1480 CYS cc_start: 0.8214 (m) cc_final: 0.7909 (m) REVERT: A 1484 MET cc_start: 0.5630 (ppp) cc_final: 0.4865 (ppp) REVERT: B 97 THR cc_start: 0.8836 (p) cc_final: 0.8625 (p) REVERT: B 142 THR cc_start: 0.8121 (OUTLIER) cc_final: 0.7840 (p) REVERT: B 222 ARG cc_start: 0.8223 (ttm110) cc_final: 0.7576 (mtt90) REVERT: B 242 ARG cc_start: 0.6258 (tpt170) cc_final: 0.4291 (mtt180) REVERT: B 255 ARG cc_start: 0.8012 (tpt-90) cc_final: 0.7694 (tpp80) REVERT: B 414 GLU cc_start: 0.7538 (tm-30) cc_final: 0.7207 (tm-30) REVERT: B 417 ILE cc_start: 0.7870 (mt) cc_final: 0.7666 (tt) REVERT: B 437 THR cc_start: 0.8328 (p) cc_final: 0.8108 (p) REVERT: B 543 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7875 (mt-10) REVERT: B 547 GLU cc_start: 0.7337 (tm-30) cc_final: 0.7039 (tm-30) REVERT: B 551 GLU cc_start: 0.7748 (mp0) cc_final: 0.7446 (mp0) REVERT: B 556 ILE cc_start: 0.8630 (tp) cc_final: 0.8372 (tt) REVERT: B 572 CYS cc_start: 0.8429 (p) cc_final: 0.8142 (p) REVERT: B 593 GLN cc_start: 0.7908 (pt0) cc_final: 0.7651 (pt0) REVERT: B 599 SER cc_start: 0.8561 (p) cc_final: 0.8330 (t) REVERT: B 617 ASP cc_start: 0.8126 (t0) cc_final: 0.7843 (t0) REVERT: B 629 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7584 (mm-30) REVERT: B 664 TYR cc_start: 0.8396 (m-80) cc_final: 0.7418 (m-80) REVERT: B 698 ILE cc_start: 0.8464 (OUTLIER) cc_final: 0.8127 (mt) REVERT: B 726 SER cc_start: 0.8297 (p) cc_final: 0.8035 (m) REVERT: B 751 LEU cc_start: 0.8495 (tp) cc_final: 0.8245 (tp) REVERT: B 796 MET cc_start: 0.8247 (mtp) cc_final: 0.8023 (mtp) REVERT: B 869 LYS cc_start: 0.7817 (tttt) cc_final: 0.7572 (tttp) REVERT: B 870 THR cc_start: 0.8226 (m) cc_final: 0.7897 (p) REVERT: B 871 VAL cc_start: 0.8308 (t) cc_final: 0.7947 (m) REVERT: B 895 PHE cc_start: 0.8722 (m-10) cc_final: 0.8404 (m-80) REVERT: B 910 THR cc_start: 0.8463 (t) cc_final: 0.8180 (p) REVERT: B 916 TYR cc_start: 0.8074 (m-10) cc_final: 0.7731 (m-80) REVERT: B 993 LYS cc_start: 0.8170 (ttmm) cc_final: 0.7901 (ttpp) REVERT: B 1012 SER cc_start: 0.8010 (t) cc_final: 0.7700 (m) REVERT: B 1090 GLU cc_start: 0.7144 (mm-30) cc_final: 0.6818 (mp0) REVERT: B 1091 ARG cc_start: 0.7697 (OUTLIER) cc_final: 0.7033 (ptt-90) REVERT: B 1104 ARG cc_start: 0.8118 (ttt90) cc_final: 0.7811 (ttt-90) REVERT: B 1108 PHE cc_start: 0.8164 (t80) cc_final: 0.7960 (t80) REVERT: C 17 GLU cc_start: 0.7744 (pt0) cc_final: 0.7452 (pt0) REVERT: C 62 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7630 (mp0) REVERT: C 75 SER cc_start: 0.8507 (OUTLIER) cc_final: 0.8250 (p) REVERT: C 211 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8515 (pp) REVERT: C 258 ASP cc_start: 0.7785 (m-30) cc_final: 0.7484 (m-30) REVERT: D 45 LYS cc_start: 0.8244 (OUTLIER) cc_final: 0.7910 (mmmt) REVERT: E 23 ASP cc_start: 0.7764 (m-30) cc_final: 0.7353 (m-30) REVERT: E 38 GLU cc_start: 0.7468 (mp0) cc_final: 0.7151 (mp0) REVERT: E 134 GLU cc_start: 0.7785 (mt-10) cc_final: 0.7444 (mt-10) REVERT: E 151 MET cc_start: 0.8521 (mtp) cc_final: 0.8291 (mtm) REVERT: E 156 VAL cc_start: 0.8205 (t) cc_final: 0.7994 (t) REVERT: E 177 ASP cc_start: 0.7760 (t0) cc_final: 0.7398 (t0) REVERT: F 52 ILE cc_start: 0.8473 (OUTLIER) cc_final: 0.8243 (pp) REVERT: F 84 GLU cc_start: 0.8108 (mp0) cc_final: 0.7252 (mp0) REVERT: H 37 MET cc_start: 0.8032 (mmm) cc_final: 0.7743 (mmm) REVERT: H 102 ASP cc_start: 0.8407 (p0) cc_final: 0.7771 (p0) REVERT: J 50 LEU cc_start: 0.8523 (tt) cc_final: 0.8277 (tp) REVERT: U 13 GLU cc_start: 0.7922 (tm-30) cc_final: 0.7301 (tm-30) REVERT: U 183 LEU cc_start: 0.7422 (OUTLIER) cc_final: 0.6908 (tp) REVERT: U 202 ASP cc_start: 0.7403 (m-30) cc_final: 0.7181 (m-30) REVERT: U 207 LEU cc_start: 0.7962 (mm) cc_final: 0.7685 (mm) REVERT: U 224 ASN cc_start: 0.6912 (p0) cc_final: 0.6433 (p0) REVERT: U 241 ASN cc_start: 0.7390 (t0) cc_final: 0.6959 (t0) REVERT: U 278 GLU cc_start: 0.7815 (mm-30) cc_final: 0.6880 (mm-30) REVERT: U 290 HIS cc_start: 0.6004 (OUTLIER) cc_final: 0.5677 (t-90) REVERT: U 310 VAL cc_start: 0.8518 (t) cc_final: 0.8267 (p) REVERT: U 321 MET cc_start: 0.7452 (mpp) cc_final: 0.7095 (mpp) REVERT: U 346 GLU cc_start: 0.6517 (mm-30) cc_final: 0.6127 (mm-30) REVERT: U 373 PHE cc_start: 0.7827 (OUTLIER) cc_final: 0.7523 (t80) REVERT: U 395 THR cc_start: 0.8078 (p) cc_final: 0.7021 (m) REVERT: U 396 ILE cc_start: 0.8334 (OUTLIER) cc_final: 0.7825 (tt) REVERT: U 441 ARG cc_start: 0.8054 (mtm110) cc_final: 0.7710 (mtm-85) REVERT: U 500 HIS cc_start: 0.7423 (m-70) cc_final: 0.6924 (m-70) REVERT: U 503 GLU cc_start: 0.7728 (mt-10) cc_final: 0.7304 (mt-10) REVERT: U 512 MET cc_start: 0.7916 (OUTLIER) cc_final: 0.7706 (ttm) REVERT: U 513 GLN cc_start: 0.7709 (tm-30) cc_final: 0.7430 (pt0) REVERT: U 516 LYS cc_start: 0.8817 (tppt) cc_final: 0.8608 (mmtm) REVERT: U 519 ASP cc_start: 0.7198 (t70) cc_final: 0.6762 (t70) REVERT: U 561 LEU cc_start: 0.8409 (mt) cc_final: 0.8091 (mt) REVERT: U 582 GLU cc_start: 0.7749 (tp30) cc_final: 0.6835 (tp30) REVERT: U 602 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7273 (tp) REVERT: U 604 LYS cc_start: 0.8176 (mtpp) cc_final: 0.7879 (mtpp) REVERT: U 610 ARG cc_start: 0.7062 (ttm-80) cc_final: 0.6732 (ttm110) REVERT: U 620 MET cc_start: 0.5459 (mmp) cc_final: 0.4180 (mmp) outliers start: 162 outliers final: 102 residues processed: 1045 average time/residue: 0.2321 time to fit residues: 379.1683 Evaluate side-chains 1048 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 927 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 62 GLN Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 301 HIS Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 818 GLU Chi-restraints excluded: chain A residue 865 ILE Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 883 ILE Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 955 GLU Chi-restraints excluded: chain A residue 982 ASN Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1015 GLU Chi-restraints excluded: chain A residue 1027 ASP Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1128 ILE Chi-restraints excluded: chain A residue 1133 LYS Chi-restraints excluded: chain A residue 1173 THR Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1309 MET Chi-restraints excluded: chain A residue 1350 LYS Chi-restraints excluded: chain A residue 1351 ASP Chi-restraints excluded: chain A residue 1417 HIS Chi-restraints excluded: chain A residue 1454 VAL Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 298 MET Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 436 LYS Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 698 ILE Chi-restraints excluded: chain B residue 719 SER Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 752 TYR Chi-restraints excluded: chain B residue 894 THR Chi-restraints excluded: chain B residue 928 ILE Chi-restraints excluded: chain B residue 957 THR Chi-restraints excluded: chain B residue 1004 ASP Chi-restraints excluded: chain B residue 1071 ASN Chi-restraints excluded: chain B residue 1091 ARG Chi-restraints excluded: chain B residue 1101 GLN Chi-restraints excluded: chain B residue 1124 ILE Chi-restraints excluded: chain C residue 24 GLU Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 240 ARG Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 45 LYS Chi-restraints excluded: chain D residue 47 GLN Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 18 MET Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain H residue 133 HIS Chi-restraints excluded: chain I residue 25 TYR Chi-restraints excluded: chain I residue 40 ARG Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain K residue 17 LYS Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain U residue 155 VAL Chi-restraints excluded: chain U residue 179 LEU Chi-restraints excluded: chain U residue 183 LEU Chi-restraints excluded: chain U residue 267 ARG Chi-restraints excluded: chain U residue 287 LYS Chi-restraints excluded: chain U residue 290 HIS Chi-restraints excluded: chain U residue 297 GLU Chi-restraints excluded: chain U residue 300 LEU Chi-restraints excluded: chain U residue 317 ILE Chi-restraints excluded: chain U residue 327 ASN Chi-restraints excluded: chain U residue 364 SER Chi-restraints excluded: chain U residue 366 ASN Chi-restraints excluded: chain U residue 373 PHE Chi-restraints excluded: chain U residue 396 ILE Chi-restraints excluded: chain U residue 431 CYS Chi-restraints excluded: chain U residue 512 MET Chi-restraints excluded: chain U residue 559 GLU Chi-restraints excluded: chain U residue 602 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 222 optimal weight: 2.9990 chunk 441 optimal weight: 0.9990 chunk 3 optimal weight: 0.0370 chunk 262 optimal weight: 2.9990 chunk 122 optimal weight: 8.9990 chunk 407 optimal weight: 10.0000 chunk 9 optimal weight: 1.9990 chunk 382 optimal weight: 0.0170 chunk 94 optimal weight: 0.9980 chunk 109 optimal weight: 0.9980 chunk 303 optimal weight: 0.0070 overall best weight: 0.4114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 678 ASN ** A 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 413 HIS ** U 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.150353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.120082 restraints weight = 76677.682| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 2.44 r_work: 0.3345 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3176 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3176 r_free = 0.3176 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3176 r_free = 0.3176 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3176 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 37458 Z= 0.134 Angle : 0.621 11.938 50851 Z= 0.316 Chirality : 0.045 0.285 5685 Planarity : 0.005 0.064 6386 Dihedral : 12.358 144.211 5566 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.77 % Favored : 93.95 % Rotamer: Outliers : 4.16 % Allowed : 22.42 % Favored : 73.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.48 % 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: -0.17 (0.13), residues: 4403 helix: 1.02 (0.13), residues: 1621 sheet: -0.32 (0.20), residues: 638 loop : -0.90 (0.14), residues: 2144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 430 TYR 0.021 0.001 TYR U 419 PHE 0.018 0.001 PHE A1388 TRP 0.024 0.001 TRP B 236 HIS 0.009 0.001 HIS U 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (37425) covalent geometry : angle 0.60995 / 0.31 (50804) SS BOND : bond 0.00133 / 0.07 ( 1) SS BOND : angle 1.55620 / 0.83 ( 2) hydrogen bonds : bond 0.03565 / 2.36 ( 1557) hydrogen bonds : angle 4.98550 / 3.51 ( 4407) metal coordination : bond 0.00610 / 0.41 ( 32) metal coordination : angle 4.01939 / 2.56 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8806 Ramachandran restraints generated. 4403 Oldfield, 0 Emsley, 4403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8806 Ramachandran restraints generated. 4403 Oldfield, 0 Emsley, 4403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1102 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 941 time to evaluate : 1.141 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 31 LEU cc_start: 0.8466 (mt) cc_final: 0.8234 (mt) REVERT: A 66 GLU cc_start: 0.7457 (OUTLIER) cc_final: 0.7119 (pm20) REVERT: A 186 ARG cc_start: 0.8072 (mtp85) cc_final: 0.7755 (ttp-110) REVERT: A 188 GLN cc_start: 0.7837 (mm110) cc_final: 0.7605 (mm-40) REVERT: A 192 ARG cc_start: 0.7144 (ttp80) cc_final: 0.6905 (ttm110) REVERT: A 232 GLU cc_start: 0.7586 (mt-10) cc_final: 0.7256 (mt-10) REVERT: A 289 GLN cc_start: 0.8452 (tt0) cc_final: 0.8158 (tt0) REVERT: A 321 GLU cc_start: 0.7669 (mm-30) cc_final: 0.7439 (mm-30) REVERT: A 325 LEU cc_start: 0.8295 (mm) cc_final: 0.7886 (mp) REVERT: A 375 ILE cc_start: 0.8065 (mm) cc_final: 0.7805 (tt) REVERT: A 387 ASN cc_start: 0.8621 (t0) cc_final: 0.8335 (t0) REVERT: A 408 ARG cc_start: 0.7826 (mtp85) cc_final: 0.7544 (mtp180) REVERT: A 418 TYR cc_start: 0.8447 (m-80) cc_final: 0.8077 (m-80) REVERT: A 467 MET cc_start: 0.8249 (mpp) cc_final: 0.7830 (mpp) REVERT: A 477 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7669 (mt) REVERT: A 514 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.7261 (pt0) REVERT: A 556 GLU cc_start: 0.7739 (mm-30) cc_final: 0.7514 (mm-30) REVERT: A 631 GLU cc_start: 0.7597 (mt-10) cc_final: 0.7187 (mt-10) REVERT: A 642 LYS cc_start: 0.8705 (tttt) cc_final: 0.8448 (ttpp) REVERT: A 691 ASP cc_start: 0.7669 (m-30) cc_final: 0.7354 (m-30) REVERT: A 711 GLN cc_start: 0.8466 (tp40) cc_final: 0.8077 (mm-40) REVERT: A 735 GLN cc_start: 0.8075 (mt0) cc_final: 0.7850 (mt0) REVERT: A 750 ASP cc_start: 0.7660 (m-30) cc_final: 0.7433 (m-30) REVERT: A 751 LYS cc_start: 0.8268 (tttp) cc_final: 0.8051 (ttpt) REVERT: A 783 GLN cc_start: 0.8344 (mt0) cc_final: 0.8110 (mt0) REVERT: A 945 ASN cc_start: 0.8103 (t0) cc_final: 0.7797 (t0) REVERT: A 955 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7195 (tt0) REVERT: A 1015 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7822 (mp0) REVERT: A 1082 HIS cc_start: 0.8296 (m90) cc_final: 0.8093 (m-70) REVERT: A 1118 THR cc_start: 0.8053 (m) cc_final: 0.7781 (t) REVERT: A 1125 LYS cc_start: 0.8281 (ttpp) cc_final: 0.7753 (ttmm) REVERT: A 1156 ASP cc_start: 0.8301 (t0) cc_final: 0.7865 (t0) REVERT: A 1257 LEU cc_start: 0.8240 (tt) cc_final: 0.7975 (tp) REVERT: A 1262 MET cc_start: 0.8085 (ptm) cc_final: 0.7798 (ptm) REVERT: A 1303 GLN cc_start: 0.7978 (pm20) cc_final: 0.7728 (pm20) REVERT: A 1308 TYR cc_start: 0.8386 (m-80) cc_final: 0.8186 (m-80) REVERT: A 1344 MET cc_start: 0.7850 (tpt) cc_final: 0.7600 (tpt) REVERT: A 1349 GLU cc_start: 0.7544 (tp30) cc_final: 0.7223 (tp30) REVERT: A 1350 LYS cc_start: 0.8021 (OUTLIER) cc_final: 0.7292 (tttp) REVERT: A 1361 ASP cc_start: 0.7545 (p0) cc_final: 0.7317 (p0) REVERT: A 1382 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.8030 (mt) REVERT: A 1441 GLU cc_start: 0.7564 (mm-30) cc_final: 0.7185 (mm-30) REVERT: A 1452 LYS cc_start: 0.8209 (mmtp) cc_final: 0.7919 (mmtp) REVERT: A 1480 CYS cc_start: 0.8146 (m) cc_final: 0.7841 (m) REVERT: A 1484 MET cc_start: 0.5661 (ppp) cc_final: 0.4997 (ppp) REVERT: B 97 THR cc_start: 0.8826 (p) cc_final: 0.8624 (p) REVERT: B 142 THR cc_start: 0.8112 (OUTLIER) cc_final: 0.7772 (p) REVERT: B 222 ARG cc_start: 0.8201 (ttm110) cc_final: 0.7599 (mtm-85) REVERT: B 242 ARG cc_start: 0.6266 (tpt170) cc_final: 0.4145 (mmt90) REVERT: B 255 ARG cc_start: 0.8031 (tpt-90) cc_final: 0.7725 (tpp80) REVERT: B 414 GLU cc_start: 0.7553 (tm-30) cc_final: 0.7201 (tm-30) REVERT: B 417 ILE cc_start: 0.7839 (mt) cc_final: 0.7636 (tt) REVERT: B 437 THR cc_start: 0.8268 (p) cc_final: 0.8066 (p) REVERT: B 510 CYS cc_start: 0.8382 (p) cc_final: 0.8182 (t) REVERT: B 543 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7887 (mt-10) REVERT: B 547 GLU cc_start: 0.7443 (tm-30) cc_final: 0.7110 (tm-30) REVERT: B 551 GLU cc_start: 0.7787 (mp0) cc_final: 0.7224 (mp0) REVERT: B 556 ILE cc_start: 0.8617 (tp) cc_final: 0.8357 (tt) REVERT: B 572 CYS cc_start: 0.8469 (p) cc_final: 0.8170 (p) REVERT: B 593 GLN cc_start: 0.7927 (pt0) cc_final: 0.7669 (pt0) REVERT: B 600 GLU cc_start: 0.7734 (tt0) cc_final: 0.7401 (tt0) REVERT: B 609 GLU cc_start: 0.7890 (mm-30) cc_final: 0.7614 (mm-30) REVERT: B 617 ASP cc_start: 0.8167 (t0) cc_final: 0.7853 (t0) REVERT: B 629 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7611 (mm-30) REVERT: B 646 ARG cc_start: 0.8204 (ttp-110) cc_final: 0.7957 (ttp-110) REVERT: B 664 TYR cc_start: 0.8417 (m-80) cc_final: 0.7378 (m-80) REVERT: B 698 ILE cc_start: 0.8445 (OUTLIER) cc_final: 0.8094 (mt) REVERT: B 726 SER cc_start: 0.8311 (p) cc_final: 0.8062 (m) REVERT: B 751 LEU cc_start: 0.8519 (tp) cc_final: 0.8265 (tp) REVERT: B 796 MET cc_start: 0.8276 (mtp) cc_final: 0.8068 (mtp) REVERT: B 828 VAL cc_start: 0.8395 (p) cc_final: 0.8185 (t) REVERT: B 869 LYS cc_start: 0.7757 (tttt) cc_final: 0.7515 (tttp) REVERT: B 870 THR cc_start: 0.8246 (m) cc_final: 0.7939 (p) REVERT: B 871 VAL cc_start: 0.8271 (t) cc_final: 0.7897 (m) REVERT: B 895 PHE cc_start: 0.8724 (m-10) cc_final: 0.8389 (m-80) REVERT: B 910 THR cc_start: 0.8508 (t) cc_final: 0.8218 (p) REVERT: B 993 LYS cc_start: 0.8202 (ttmm) cc_final: 0.7874 (ttpp) REVERT: B 1012 SER cc_start: 0.8040 (OUTLIER) cc_final: 0.7717 (m) REVERT: B 1090 GLU cc_start: 0.7203 (mm-30) cc_final: 0.6891 (mp0) REVERT: B 1091 ARG cc_start: 0.7694 (OUTLIER) cc_final: 0.7076 (ptt-90) REVERT: C 17 GLU cc_start: 0.7830 (pt0) cc_final: 0.7506 (pt0) REVERT: C 62 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7641 (mp0) REVERT: C 75 SER cc_start: 0.8506 (OUTLIER) cc_final: 0.8256 (p) REVERT: C 130 VAL cc_start: 0.7761 (t) cc_final: 0.7445 (t) REVERT: C 211 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8424 (pp) REVERT: C 258 ASP cc_start: 0.7831 (m-30) cc_final: 0.7516 (m-30) REVERT: D 45 LYS cc_start: 0.8184 (OUTLIER) cc_final: 0.7877 (mmmt) REVERT: D 132 ASP cc_start: 0.6558 (OUTLIER) cc_final: 0.6352 (p0) REVERT: E 23 ASP cc_start: 0.7781 (m-30) cc_final: 0.7380 (m-30) REVERT: E 38 GLU cc_start: 0.7548 (mp0) cc_final: 0.7211 (mp0) REVERT: E 134 GLU cc_start: 0.7805 (mt-10) cc_final: 0.7469 (mt-10) REVERT: E 151 MET cc_start: 0.8580 (mtp) cc_final: 0.8356 (mtm) REVERT: E 156 VAL cc_start: 0.8167 (t) cc_final: 0.7957 (t) REVERT: E 172 ARG cc_start: 0.8287 (tpp80) cc_final: 0.7890 (ttm-80) REVERT: E 177 ASP cc_start: 0.7789 (t0) cc_final: 0.7462 (t0) REVERT: F 52 ILE cc_start: 0.8480 (OUTLIER) cc_final: 0.8276 (pp) REVERT: F 84 GLU cc_start: 0.8131 (mp0) cc_final: 0.7263 (mp0) REVERT: H 37 MET cc_start: 0.8064 (mmm) cc_final: 0.7848 (mmm) REVERT: H 102 ASP cc_start: 0.8376 (p0) cc_final: 0.7741 (p0) REVERT: J 50 LEU cc_start: 0.8508 (tt) cc_final: 0.8271 (tp) REVERT: K 46 ILE cc_start: 0.7399 (OUTLIER) cc_final: 0.7157 (mp) REVERT: L 44 MET cc_start: 0.8528 (mmm) cc_final: 0.7279 (mmm) REVERT: U 202 ASP cc_start: 0.7501 (m-30) cc_final: 0.7271 (m-30) REVERT: U 207 LEU cc_start: 0.7960 (mm) cc_final: 0.7706 (mm) REVERT: U 224 ASN cc_start: 0.6882 (p0) cc_final: 0.6402 (p0) REVERT: U 241 ASN cc_start: 0.7406 (t0) cc_final: 0.6963 (t0) REVERT: U 278 GLU cc_start: 0.7776 (mm-30) cc_final: 0.6861 (mm-30) REVERT: U 290 HIS cc_start: 0.6043 (OUTLIER) cc_final: 0.5760 (t-90) REVERT: U 310 VAL cc_start: 0.8516 (t) cc_final: 0.8260 (p) REVERT: U 331 VAL cc_start: 0.8180 (t) cc_final: 0.7848 (m) REVERT: U 346 GLU cc_start: 0.6444 (mm-30) cc_final: 0.6062 (mm-30) REVERT: U 373 PHE cc_start: 0.7825 (OUTLIER) cc_final: 0.7452 (t80) REVERT: U 395 THR cc_start: 0.8090 (p) cc_final: 0.7076 (m) REVERT: U 396 ILE cc_start: 0.8178 (tt) cc_final: 0.7791 (tt) REVERT: U 441 ARG cc_start: 0.8067 (mtm110) cc_final: 0.7725 (mtm-85) REVERT: U 500 HIS cc_start: 0.7469 (m-70) cc_final: 0.6938 (m-70) REVERT: U 503 GLU cc_start: 0.7828 (mt-10) cc_final: 0.7358 (mt-10) REVERT: U 512 MET cc_start: 0.7966 (OUTLIER) cc_final: 0.7723 (ttm) REVERT: U 519 ASP cc_start: 0.7251 (t70) cc_final: 0.6777 (t70) REVERT: U 523 GLU cc_start: 0.7158 (mp0) cc_final: 0.6611 (pm20) REVERT: U 561 LEU cc_start: 0.8442 (mt) cc_final: 0.8164 (mt) REVERT: U 565 ARG cc_start: 0.7599 (tpt170) cc_final: 0.7344 (tpt170) REVERT: U 582 GLU cc_start: 0.7841 (tp30) cc_final: 0.6885 (tp30) REVERT: U 602 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7157 (tp) REVERT: U 604 LYS cc_start: 0.8205 (mtpp) cc_final: 0.7883 (mtpp) REVERT: U 610 ARG cc_start: 0.7130 (ttm-80) cc_final: 0.6832 (ttm110) REVERT: U 620 MET cc_start: 0.5451 (mmp) cc_final: 0.5162 (mmp) outliers start: 161 outliers final: 111 residues processed: 1028 average time/residue: 0.2289 time to fit residues: 366.7389 Evaluate side-chains 1064 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 931 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLN Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 301 HIS Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 818 GLU Chi-restraints excluded: chain A residue 865 ILE Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 883 ILE Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 955 GLU Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1015 GLU Chi-restraints excluded: chain A residue 1027 ASP Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1133 LYS Chi-restraints excluded: chain A residue 1173 THR Chi-restraints excluded: chain A residue 1219 LYS Chi-restraints excluded: chain A residue 1258 ARG Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1304 ILE Chi-restraints excluded: chain A residue 1350 LYS Chi-restraints excluded: chain A residue 1351 ASP Chi-restraints excluded: chain A residue 1382 LEU Chi-restraints excluded: chain A residue 1412 MET Chi-restraints excluded: chain A residue 1417 HIS Chi-restraints excluded: chain A residue 1478 GLU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 298 MET Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 436 LYS Chi-restraints excluded: chain B residue 595 ASP Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 698 ILE Chi-restraints excluded: chain B residue 719 SER Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 752 TYR Chi-restraints excluded: chain B residue 894 THR Chi-restraints excluded: chain B residue 928 ILE Chi-restraints excluded: chain B residue 957 THR Chi-restraints excluded: chain B residue 1004 ASP Chi-restraints excluded: chain B residue 1012 SER Chi-restraints excluded: chain B residue 1017 ASP Chi-restraints excluded: chain B residue 1071 ASN Chi-restraints excluded: chain B residue 1091 ARG Chi-restraints excluded: chain B residue 1101 GLN Chi-restraints excluded: chain B residue 1124 ILE Chi-restraints excluded: chain B residue 1173 SER Chi-restraints excluded: chain C residue 24 GLU Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 240 ARG Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 45 LYS Chi-restraints excluded: chain D residue 47 GLN Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 18 MET Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain H residue 133 HIS Chi-restraints excluded: chain I residue 25 TYR Chi-restraints excluded: chain I residue 40 ARG Chi-restraints excluded: chain I residue 69 ILE Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain K residue 17 LYS Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain K residue 46 ILE Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain U residue 23 VAL Chi-restraints excluded: chain U residue 155 VAL Chi-restraints excluded: chain U residue 179 LEU Chi-restraints excluded: chain U residue 183 LEU Chi-restraints excluded: chain U residue 267 ARG Chi-restraints excluded: chain U residue 287 LYS Chi-restraints excluded: chain U residue 290 HIS Chi-restraints excluded: chain U residue 300 LEU Chi-restraints excluded: chain U residue 317 ILE Chi-restraints excluded: chain U residue 327 ASN Chi-restraints excluded: chain U residue 364 SER Chi-restraints excluded: chain U residue 366 ASN Chi-restraints excluded: chain U residue 373 PHE Chi-restraints excluded: chain U residue 431 CYS Chi-restraints excluded: chain U residue 512 MET Chi-restraints excluded: chain U residue 602 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 114 optimal weight: 0.3980 chunk 9 optimal weight: 0.8980 chunk 420 optimal weight: 7.9990 chunk 260 optimal weight: 1.9990 chunk 210 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 323 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 113 optimal weight: 0.9990 chunk 436 optimal weight: 0.7980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 GLN B 486 ASN B 503 ASN ** B1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 GLN D 93 HIS U 164 GLN U 413 HIS ** U 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.149537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.119882 restraints weight = 65772.431| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.23 r_work: 0.3354 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3171 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3171 r_free = 0.3171 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3171 r_free = 0.3171 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3171 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 37458 Z= 0.156 Angle : 0.633 11.207 50851 Z= 0.319 Chirality : 0.046 0.285 5685 Planarity : 0.005 0.066 6386 Dihedral : 12.233 144.072 5563 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.93 % Favored : 93.80 % Rotamer: Outliers : 4.06 % Allowed : 22.91 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.48 % 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: -0.13 (0.13), residues: 4403 helix: 1.06 (0.13), residues: 1612 sheet: -0.26 (0.20), residues: 622 loop : -0.88 (0.14), residues: 2169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG U 17 TYR 0.019 0.001 TYR U 419 PHE 0.022 0.001 PHE E 75 TRP 0.019 0.002 TRP B 236 HIS 0.009 0.001 HIS U 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 (37425) covalent geometry : angle 0.62050 / 0.32 (50804) SS BOND : bond 0.00166 / 0.09 ( 1) SS BOND : angle 1.49292 / 0.79 ( 2) hydrogen bonds : bond 0.03613 / 2.39 ( 1557) hydrogen bonds : angle 4.92142 / 3.46 ( 4407) metal coordination : bond 0.00719 / 0.49 ( 32) metal coordination : angle 4.22410 / 2.71 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8806 Ramachandran restraints generated. 4403 Oldfield, 0 Emsley, 4403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8806 Ramachandran restraints generated. 4403 Oldfield, 0 Emsley, 4403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1100 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 943 time to evaluate : 1.357 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: A 31 LEU cc_start: 0.8462 (mt) cc_final: 0.8225 (mt) REVERT: A 33 ARG cc_start: 0.8043 (mtm-85) cc_final: 0.7494 (mtm-85) REVERT: A 66 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.7110 (pm20) REVERT: A 186 ARG cc_start: 0.8091 (mtp85) cc_final: 0.7765 (ttp-110) REVERT: A 188 GLN cc_start: 0.7831 (mm110) cc_final: 0.7617 (mm-40) REVERT: A 192 ARG cc_start: 0.7158 (ttp80) cc_final: 0.6909 (ttm110) REVERT: A 196 LEU cc_start: 0.8587 (mm) cc_final: 0.8376 (mt) REVERT: A 216 LEU cc_start: 0.7980 (tp) cc_final: 0.7732 (tp) REVERT: A 232 GLU cc_start: 0.7519 (mt-10) cc_final: 0.7205 (mt-10) REVERT: A 289 GLN cc_start: 0.8446 (tt0) cc_final: 0.8167 (tt0) REVERT: A 321 GLU cc_start: 0.7718 (mm-30) cc_final: 0.7444 (mm-30) REVERT: A 325 LEU cc_start: 0.8186 (mm) cc_final: 0.7934 (mp) REVERT: A 375 ILE cc_start: 0.8058 (mm) cc_final: 0.7818 (tt) REVERT: A 388 MET cc_start: 0.8263 (mmm) cc_final: 0.7758 (mtp) REVERT: A 408 ARG cc_start: 0.7812 (mtp85) cc_final: 0.7526 (mtp180) REVERT: A 418 TYR cc_start: 0.8436 (m-80) cc_final: 0.8221 (m-80) REVERT: A 467 MET cc_start: 0.8213 (mpp) cc_final: 0.7811 (mpp) REVERT: A 477 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7672 (mt) REVERT: A 514 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.7075 (pt0) REVERT: A 631 GLU cc_start: 0.7579 (mt-10) cc_final: 0.7139 (mt-10) REVERT: A 642 LYS cc_start: 0.8695 (tttt) cc_final: 0.8430 (tttp) REVERT: A 662 HIS cc_start: 0.8276 (p-80) cc_final: 0.7727 (p90) REVERT: A 691 ASP cc_start: 0.7637 (m-30) cc_final: 0.7312 (m-30) REVERT: A 711 GLN cc_start: 0.8425 (tp40) cc_final: 0.8038 (mm-40) REVERT: A 735 GLN cc_start: 0.8086 (mt0) cc_final: 0.7815 (mt0) REVERT: A 751 LYS cc_start: 0.8268 (tttp) cc_final: 0.8038 (ttpt) REVERT: A 783 GLN cc_start: 0.8328 (mt0) cc_final: 0.8085 (mt0) REVERT: A 914 LYS cc_start: 0.8140 (mmmm) cc_final: 0.7862 (mmmm) REVERT: A 936 GLU cc_start: 0.8143 (tp30) cc_final: 0.7697 (tp30) REVERT: A 945 ASN cc_start: 0.8173 (t0) cc_final: 0.7866 (t0) REVERT: A 955 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7163 (tt0) REVERT: A 967 ARG cc_start: 0.8395 (mtt90) cc_final: 0.8130 (mtt180) REVERT: A 1015 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7811 (mp0) REVERT: A 1082 HIS cc_start: 0.8296 (m90) cc_final: 0.8090 (m-70) REVERT: A 1118 THR cc_start: 0.8073 (m) cc_final: 0.7809 (t) REVERT: A 1125 LYS cc_start: 0.8270 (ttpp) cc_final: 0.7755 (ttmm) REVERT: A 1156 ASP cc_start: 0.8264 (t0) cc_final: 0.7827 (t0) REVERT: A 1162 GLU cc_start: 0.7442 (tt0) cc_final: 0.7199 (tt0) REVERT: A 1221 MET cc_start: 0.8358 (tpp) cc_final: 0.7842 (mmt) REVERT: A 1257 LEU cc_start: 0.8234 (tt) cc_final: 0.7984 (tp) REVERT: A 1258 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.8290 (ttm110) REVERT: A 1262 MET cc_start: 0.8076 (ptm) cc_final: 0.7827 (ptm) REVERT: A 1303 GLN cc_start: 0.7939 (pm20) cc_final: 0.7684 (pm20) REVERT: A 1344 MET cc_start: 0.7852 (tpt) cc_final: 0.7586 (tpt) REVERT: A 1349 GLU cc_start: 0.7506 (tp30) cc_final: 0.7221 (tp30) REVERT: A 1350 LYS cc_start: 0.8004 (OUTLIER) cc_final: 0.7287 (tttp) REVERT: A 1382 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.8040 (mt) REVERT: A 1441 GLU cc_start: 0.7521 (mm-30) cc_final: 0.7167 (mm-30) REVERT: A 1452 LYS cc_start: 0.8211 (mmtp) cc_final: 0.7918 (mmtp) REVERT: A 1480 CYS cc_start: 0.8163 (m) cc_final: 0.7859 (m) REVERT: A 1484 MET cc_start: 0.5664 (ppp) cc_final: 0.5006 (ppp) REVERT: B 35 ASP cc_start: 0.7642 (m-30) cc_final: 0.7359 (m-30) REVERT: B 142 THR cc_start: 0.8111 (OUTLIER) cc_final: 0.7795 (p) REVERT: B 222 ARG cc_start: 0.8176 (ttm110) cc_final: 0.7599 (mtm-85) REVERT: B 242 ARG cc_start: 0.6277 (tpt170) cc_final: 0.4372 (mtt180) REVERT: B 255 ARG cc_start: 0.8062 (tpt-90) cc_final: 0.7692 (tpp80) REVERT: B 414 GLU cc_start: 0.7537 (tm-30) cc_final: 0.7167 (tm-30) REVERT: B 417 ILE cc_start: 0.7886 (mt) cc_final: 0.7681 (tt) REVERT: B 543 GLU cc_start: 0.8083 (mt-10) cc_final: 0.7825 (mt-10) REVERT: B 547 GLU cc_start: 0.7416 (tm-30) cc_final: 0.7079 (tm-30) REVERT: B 551 GLU cc_start: 0.7770 (mp0) cc_final: 0.7222 (mp0) REVERT: B 556 ILE cc_start: 0.8620 (tp) cc_final: 0.8375 (tt) REVERT: B 572 CYS cc_start: 0.8399 (p) cc_final: 0.8141 (p) REVERT: B 593 GLN cc_start: 0.7889 (pt0) cc_final: 0.7267 (pt0) REVERT: B 595 ASP cc_start: 0.6372 (OUTLIER) cc_final: 0.5571 (m-30) REVERT: B 599 SER cc_start: 0.8543 (p) cc_final: 0.8269 (t) REVERT: B 600 GLU cc_start: 0.7703 (tt0) cc_final: 0.7386 (tt0) REVERT: B 609 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7488 (mm-30) REVERT: B 617 ASP cc_start: 0.8128 (t0) cc_final: 0.7829 (t0) REVERT: B 629 GLU cc_start: 0.7844 (mm-30) cc_final: 0.7619 (mm-30) REVERT: B 646 ARG cc_start: 0.8195 (ttp-110) cc_final: 0.7986 (ttp-110) REVERT: B 664 TYR cc_start: 0.8425 (m-80) cc_final: 0.7417 (m-80) REVERT: B 698 ILE cc_start: 0.8460 (OUTLIER) cc_final: 0.8117 (mt) REVERT: B 726 SER cc_start: 0.8296 (p) cc_final: 0.8054 (m) REVERT: B 751 LEU cc_start: 0.8506 (tp) cc_final: 0.8249 (tp) REVERT: B 796 MET cc_start: 0.8218 (mtp) cc_final: 0.7996 (mtp) REVERT: B 869 LYS cc_start: 0.7799 (tttt) cc_final: 0.7506 (tttp) REVERT: B 870 THR cc_start: 0.8263 (m) cc_final: 0.7938 (p) REVERT: B 871 VAL cc_start: 0.8250 (t) cc_final: 0.7873 (m) REVERT: B 895 PHE cc_start: 0.8724 (m-10) cc_final: 0.8470 (m-10) REVERT: B 910 THR cc_start: 0.8489 (t) cc_final: 0.8189 (p) REVERT: B 993 LYS cc_start: 0.8191 (ttmm) cc_final: 0.7909 (ttpp) REVERT: B 1012 SER cc_start: 0.8020 (OUTLIER) cc_final: 0.7702 (m) REVERT: B 1090 GLU cc_start: 0.7079 (mm-30) cc_final: 0.6777 (mp0) REVERT: B 1091 ARG cc_start: 0.7675 (OUTLIER) cc_final: 0.7037 (ptt-90) REVERT: B 1104 ARG cc_start: 0.8118 (ttt90) cc_final: 0.7805 (ttt-90) REVERT: C 17 GLU cc_start: 0.7787 (pt0) cc_final: 0.7486 (pt0) REVERT: C 62 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7633 (mp0) REVERT: C 75 SER cc_start: 0.8456 (OUTLIER) cc_final: 0.8203 (p) REVERT: C 130 VAL cc_start: 0.7706 (t) cc_final: 0.7393 (t) REVERT: C 211 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8434 (pp) REVERT: C 258 ASP cc_start: 0.7769 (m-30) cc_final: 0.7467 (m-30) REVERT: D 132 ASP cc_start: 0.6474 (OUTLIER) cc_final: 0.6271 (p0) REVERT: E 38 GLU cc_start: 0.7512 (mp0) cc_final: 0.7181 (mp0) REVERT: E 151 MET cc_start: 0.8605 (mtp) cc_final: 0.8384 (mtm) REVERT: E 156 VAL cc_start: 0.8163 (t) cc_final: 0.7952 (t) REVERT: E 172 ARG cc_start: 0.8285 (tpp80) cc_final: 0.7905 (ttm-80) REVERT: E 177 ASP cc_start: 0.7772 (t0) cc_final: 0.7446 (t0) REVERT: F 52 ILE cc_start: 0.8481 (OUTLIER) cc_final: 0.8276 (pp) REVERT: F 84 GLU cc_start: 0.8114 (mp0) cc_final: 0.7232 (mp0) REVERT: G 117 MET cc_start: 0.7122 (tpt) cc_final: 0.6783 (mpp) REVERT: H 37 MET cc_start: 0.8043 (mmm) cc_final: 0.7759 (mmm) REVERT: H 102 ASP cc_start: 0.8393 (p0) cc_final: 0.7770 (p0) REVERT: J 50 LEU cc_start: 0.8462 (tt) cc_final: 0.8258 (tp) REVERT: K 46 ILE cc_start: 0.7398 (OUTLIER) cc_final: 0.7159 (mp) REVERT: L 44 MET cc_start: 0.8467 (mmm) cc_final: 0.7110 (mmm) REVERT: U 202 ASP cc_start: 0.7516 (m-30) cc_final: 0.7287 (m-30) REVERT: U 207 LEU cc_start: 0.7951 (mm) cc_final: 0.7711 (mm) REVERT: U 224 ASN cc_start: 0.6899 (p0) cc_final: 0.6422 (p0) REVERT: U 241 ASN cc_start: 0.7454 (t0) cc_final: 0.7011 (t0) REVERT: U 278 GLU cc_start: 0.7799 (mm-30) cc_final: 0.6884 (mm-30) REVERT: U 290 HIS cc_start: 0.6118 (OUTLIER) cc_final: 0.5514 (t-90) REVERT: U 298 ARG cc_start: 0.7316 (mtt180) cc_final: 0.6713 (mpt-90) REVERT: U 310 VAL cc_start: 0.8466 (t) cc_final: 0.8237 (p) REVERT: U 321 MET cc_start: 0.7650 (mmm) cc_final: 0.7186 (mpp) REVERT: U 331 VAL cc_start: 0.8196 (t) cc_final: 0.7866 (m) REVERT: U 346 GLU cc_start: 0.6410 (mm-30) cc_final: 0.5988 (mm-30) REVERT: U 373 PHE cc_start: 0.7763 (OUTLIER) cc_final: 0.7461 (t80) REVERT: U 395 THR cc_start: 0.8129 (p) cc_final: 0.7149 (m) REVERT: U 500 HIS cc_start: 0.7424 (m-70) cc_final: 0.6926 (m-70) REVERT: U 503 GLU cc_start: 0.7790 (mt-10) cc_final: 0.7391 (mt-10) REVERT: U 508 TYR cc_start: 0.8376 (t80) cc_final: 0.7735 (t80) REVERT: U 511 GLN cc_start: 0.7766 (tp-100) cc_final: 0.7290 (mm-40) REVERT: U 519 ASP cc_start: 0.7274 (t70) cc_final: 0.6788 (t70) REVERT: U 523 GLU cc_start: 0.7172 (mp0) cc_final: 0.6661 (pm20) REVERT: U 561 LEU cc_start: 0.8425 (mt) cc_final: 0.8145 (mt) REVERT: U 582 GLU cc_start: 0.7807 (tp30) cc_final: 0.6846 (tp30) REVERT: U 602 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7159 (tp) REVERT: U 604 LYS cc_start: 0.8203 (mtpp) cc_final: 0.7878 (mtpp) REVERT: U 610 ARG cc_start: 0.7134 (ttm-80) cc_final: 0.6883 (ttm110) REVERT: U 620 MET cc_start: 0.5359 (mmp) cc_final: 0.5082 (mmp) outliers start: 157 outliers final: 108 residues processed: 1028 average time/residue: 0.2405 time to fit residues: 387.7893 Evaluate side-chains 1065 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 935 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 62 GLN Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 301 HIS Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 818 GLU Chi-restraints excluded: chain A residue 865 ILE Chi-restraints excluded: chain A residue 883 ILE Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 912 SER Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 955 GLU Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1015 GLU Chi-restraints excluded: chain A residue 1027 ASP Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1133 LYS Chi-restraints excluded: chain A residue 1258 ARG Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1304 ILE Chi-restraints excluded: chain A residue 1309 MET Chi-restraints excluded: chain A residue 1327 GLU Chi-restraints excluded: chain A residue 1350 LYS Chi-restraints excluded: chain A residue 1351 ASP Chi-restraints excluded: chain A residue 1382 LEU Chi-restraints excluded: chain A residue 1412 MET Chi-restraints excluded: chain A residue 1417 HIS Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 298 MET Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 436 LYS Chi-restraints excluded: chain B residue 595 ASP Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 698 ILE Chi-restraints excluded: chain B residue 719 SER Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 752 TYR Chi-restraints excluded: chain B residue 894 THR Chi-restraints excluded: chain B residue 928 ILE Chi-restraints excluded: chain B residue 957 THR Chi-restraints excluded: chain B residue 1004 ASP Chi-restraints excluded: chain B residue 1012 SER Chi-restraints excluded: chain B residue 1071 ASN Chi-restraints excluded: chain B residue 1091 ARG Chi-restraints excluded: chain B residue 1101 GLN Chi-restraints excluded: chain B residue 1124 ILE Chi-restraints excluded: chain B residue 1173 SER Chi-restraints excluded: chain C residue 24 GLU Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 81 LYS Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 240 ARG Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 47 GLN Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain H residue 133 HIS Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain I residue 40 ARG Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain K residue 17 LYS Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain K residue 46 ILE Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain U residue 23 VAL Chi-restraints excluded: chain U residue 155 VAL Chi-restraints excluded: chain U residue 164 GLN Chi-restraints excluded: chain U residue 179 LEU Chi-restraints excluded: chain U residue 183 LEU Chi-restraints excluded: chain U residue 267 ARG Chi-restraints excluded: chain U residue 287 LYS Chi-restraints excluded: chain U residue 290 HIS Chi-restraints excluded: chain U residue 317 ILE Chi-restraints excluded: chain U residue 327 ASN Chi-restraints excluded: chain U residue 364 SER Chi-restraints excluded: chain U residue 366 ASN Chi-restraints excluded: chain U residue 373 PHE Chi-restraints excluded: chain U residue 431 CYS Chi-restraints excluded: chain U residue 602 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 139 optimal weight: 3.9990 chunk 430 optimal weight: 2.9990 chunk 281 optimal weight: 1.9990 chunk 113 optimal weight: 0.6980 chunk 121 optimal weight: 0.0870 chunk 131 optimal weight: 0.7980 chunk 287 optimal weight: 5.9990 chunk 348 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 chunk 138 optimal weight: 0.9980 overall best weight: 0.9160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 441 GLN ** A 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 472 HIS ** A 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 452 ASN B 486 ASN ** B1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 413 HIS ** U 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.149093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.119456 restraints weight = 68167.764| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.22 r_work: 0.3345 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3171 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3171 r_free = 0.3171 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3171 r_free = 0.3171 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3171 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 37458 Z= 0.175 Angle : 0.645 11.566 50851 Z= 0.324 Chirality : 0.046 0.303 5685 Planarity : 0.005 0.063 6386 Dihedral : 12.209 144.047 5561 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.75 % Favored : 93.95 % Rotamer: Outliers : 4.06 % Allowed : 23.01 % Favored : 72.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.48 % 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: -0.14 (0.13), residues: 4403 helix: 1.05 (0.13), residues: 1608 sheet: -0.25 (0.20), residues: 622 loop : -0.90 (0.13), residues: 2173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 430 TYR 0.023 0.002 TYR U 419 PHE 0.025 0.001 PHE E 75 TRP 0.018 0.002 TRP B 236 HIS 0.010 0.001 HIS U 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.17 (37425) covalent geometry : angle 0.63199 / 0.32 (50804) SS BOND : bond 0.00170 / 0.09 ( 1) SS BOND : angle 1.47267 / 0.78 ( 2) hydrogen bonds : bond 0.03664 / 2.43 ( 1557) hydrogen bonds : angle 4.90798 / 3.46 ( 4407) metal coordination : bond 0.00781 / 0.52 ( 32) metal coordination : angle 4.31735 / 2.76 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8806 Ramachandran restraints generated. 4403 Oldfield, 0 Emsley, 4403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8806 Ramachandran restraints generated. 4403 Oldfield, 0 Emsley, 4403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1093 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 936 time to evaluate : 1.491 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 31 LEU cc_start: 0.8496 (mt) cc_final: 0.8280 (mt) REVERT: A 33 ARG cc_start: 0.8068 (mtm-85) cc_final: 0.7570 (mtm-85) REVERT: A 66 GLU cc_start: 0.7445 (OUTLIER) cc_final: 0.7124 (pm20) REVERT: A 186 ARG cc_start: 0.8087 (mtp85) cc_final: 0.7801 (ttp-110) REVERT: A 192 ARG cc_start: 0.7119 (ttp80) cc_final: 0.6889 (ttm110) REVERT: A 196 LEU cc_start: 0.8616 (mm) cc_final: 0.8407 (mt) REVERT: A 216 LEU cc_start: 0.7997 (tp) cc_final: 0.7759 (tp) REVERT: A 223 GLU cc_start: 0.8194 (tp30) cc_final: 0.7775 (tp30) REVERT: A 232 GLU cc_start: 0.7516 (mt-10) cc_final: 0.7199 (mt-10) REVERT: A 266 MET cc_start: 0.4299 (mmm) cc_final: 0.4052 (mmm) REVERT: A 289 GLN cc_start: 0.8489 (tt0) cc_final: 0.8228 (tt0) REVERT: A 321 GLU cc_start: 0.7704 (mm-30) cc_final: 0.7497 (mm-30) REVERT: A 325 LEU cc_start: 0.8189 (mm) cc_final: 0.7895 (mp) REVERT: A 375 ILE cc_start: 0.8073 (mm) cc_final: 0.7823 (tt) REVERT: A 388 MET cc_start: 0.8219 (mmm) cc_final: 0.7824 (mtp) REVERT: A 408 ARG cc_start: 0.7886 (mtp85) cc_final: 0.7596 (mtp180) REVERT: A 418 TYR cc_start: 0.8481 (m-80) cc_final: 0.8144 (m-80) REVERT: A 467 MET cc_start: 0.8214 (mpp) cc_final: 0.7842 (mpp) REVERT: A 477 LEU cc_start: 0.7996 (OUTLIER) cc_final: 0.7692 (mt) REVERT: A 514 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.7188 (pt0) REVERT: A 631 GLU cc_start: 0.7548 (mt-10) cc_final: 0.7143 (mt-10) REVERT: A 642 LYS cc_start: 0.8707 (tttt) cc_final: 0.8444 (tttp) REVERT: A 691 ASP cc_start: 0.7615 (m-30) cc_final: 0.7304 (m-30) REVERT: A 711 GLN cc_start: 0.8448 (tp40) cc_final: 0.8077 (mm-40) REVERT: A 728 THR cc_start: 0.8182 (m) cc_final: 0.7689 (p) REVERT: A 735 GLN cc_start: 0.8120 (mt0) cc_final: 0.7894 (mt0) REVERT: A 751 LYS cc_start: 0.8305 (tttp) cc_final: 0.8088 (ttpt) REVERT: A 777 SER cc_start: 0.8330 (p) cc_final: 0.8074 (m) REVERT: A 783 GLN cc_start: 0.8350 (mt0) cc_final: 0.8120 (mt0) REVERT: A 914 LYS cc_start: 0.8150 (mmmm) cc_final: 0.7881 (mmmm) REVERT: A 936 GLU cc_start: 0.8131 (tp30) cc_final: 0.7921 (tp30) REVERT: A 945 ASN cc_start: 0.8198 (t0) cc_final: 0.7926 (t0) REVERT: A 955 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.7186 (tt0) REVERT: A 1015 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7857 (mp0) REVERT: A 1035 GLU cc_start: 0.8353 (tp30) cc_final: 0.7839 (tp30) REVERT: A 1082 HIS cc_start: 0.8318 (m90) cc_final: 0.8106 (m-70) REVERT: A 1118 THR cc_start: 0.8085 (m) cc_final: 0.7817 (t) REVERT: A 1119 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7867 (mt) REVERT: A 1125 LYS cc_start: 0.8307 (ttpp) cc_final: 0.7804 (ttmm) REVERT: A 1156 ASP cc_start: 0.8302 (t0) cc_final: 0.7979 (t0) REVERT: A 1162 GLU cc_start: 0.7400 (tt0) cc_final: 0.7178 (tt0) REVERT: A 1221 MET cc_start: 0.8408 (tpp) cc_final: 0.7836 (mmt) REVERT: A 1257 LEU cc_start: 0.8264 (tt) cc_final: 0.7952 (tp) REVERT: A 1258 ARG cc_start: 0.8585 (OUTLIER) cc_final: 0.8320 (ttm110) REVERT: A 1303 GLN cc_start: 0.7925 (pm20) cc_final: 0.7707 (pm20) REVERT: A 1344 MET cc_start: 0.7833 (tpt) cc_final: 0.7574 (tpt) REVERT: A 1349 GLU cc_start: 0.7510 (tp30) cc_final: 0.6407 (tp30) REVERT: A 1350 LYS cc_start: 0.8048 (OUTLIER) cc_final: 0.7243 (tttp) REVERT: A 1441 GLU cc_start: 0.7501 (mm-30) cc_final: 0.7185 (mm-30) REVERT: A 1452 LYS cc_start: 0.8191 (mmtp) cc_final: 0.7911 (mmtp) REVERT: A 1480 CYS cc_start: 0.8191 (m) cc_final: 0.7907 (m) REVERT: A 1484 MET cc_start: 0.5650 (ppp) cc_final: 0.5068 (ppp) REVERT: B 142 THR cc_start: 0.8162 (OUTLIER) cc_final: 0.7805 (p) REVERT: B 222 ARG cc_start: 0.8187 (ttm110) cc_final: 0.7632 (mtm-85) REVERT: B 242 ARG cc_start: 0.6351 (tpt170) cc_final: 0.4402 (mtt180) REVERT: B 255 ARG cc_start: 0.8071 (tpt-90) cc_final: 0.7771 (tpp80) REVERT: B 407 MET cc_start: 0.8012 (OUTLIER) cc_final: 0.7656 (mtm) REVERT: B 414 GLU cc_start: 0.7587 (tm-30) cc_final: 0.7242 (tm-30) REVERT: B 417 ILE cc_start: 0.7984 (mt) cc_final: 0.7735 (tt) REVERT: B 543 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7861 (mt-10) REVERT: B 547 GLU cc_start: 0.7431 (tm-30) cc_final: 0.7091 (tm-30) REVERT: B 551 GLU cc_start: 0.7838 (mp0) cc_final: 0.7310 (mp0) REVERT: B 556 ILE cc_start: 0.8626 (tp) cc_final: 0.8389 (tt) REVERT: B 572 CYS cc_start: 0.8386 (p) cc_final: 0.8171 (p) REVERT: B 593 GLN cc_start: 0.7886 (pt0) cc_final: 0.7621 (pt0) REVERT: B 599 SER cc_start: 0.8551 (p) cc_final: 0.8291 (t) REVERT: B 600 GLU cc_start: 0.7715 (tt0) cc_final: 0.7395 (tt0) REVERT: B 609 GLU cc_start: 0.7787 (mm-30) cc_final: 0.7550 (mm-30) REVERT: B 617 ASP cc_start: 0.8095 (t0) cc_final: 0.7812 (t0) REVERT: B 629 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7634 (mm-30) REVERT: B 637 LYS cc_start: 0.8518 (ttmt) cc_final: 0.8306 (ttmm) REVERT: B 646 ARG cc_start: 0.8197 (ttp-110) cc_final: 0.7990 (ttp-110) REVERT: B 664 TYR cc_start: 0.8389 (m-80) cc_final: 0.7438 (m-80) REVERT: B 698 ILE cc_start: 0.8457 (OUTLIER) cc_final: 0.8121 (mt) REVERT: B 726 SER cc_start: 0.8299 (p) cc_final: 0.8037 (m) REVERT: B 751 LEU cc_start: 0.8492 (tp) cc_final: 0.8247 (tp) REVERT: B 796 MET cc_start: 0.8212 (mtp) cc_final: 0.8009 (mtp) REVERT: B 869 LYS cc_start: 0.7853 (tttt) cc_final: 0.7557 (tttp) REVERT: B 870 THR cc_start: 0.8240 (m) cc_final: 0.7972 (p) REVERT: B 871 VAL cc_start: 0.8318 (t) cc_final: 0.7984 (m) REVERT: B 895 PHE cc_start: 0.8757 (m-10) cc_final: 0.8555 (m-10) REVERT: B 910 THR cc_start: 0.8479 (t) cc_final: 0.8174 (p) REVERT: B 993 LYS cc_start: 0.8218 (ttmm) cc_final: 0.7955 (ttpp) REVERT: B 1012 SER cc_start: 0.8016 (OUTLIER) cc_final: 0.7626 (m) REVERT: B 1090 GLU cc_start: 0.7078 (mm-30) cc_final: 0.6800 (mp0) REVERT: B 1091 ARG cc_start: 0.7672 (OUTLIER) cc_final: 0.7130 (ptt-90) REVERT: C 17 GLU cc_start: 0.7824 (pt0) cc_final: 0.7532 (pt0) REVERT: C 62 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7645 (mp0) REVERT: C 75 SER cc_start: 0.8448 (OUTLIER) cc_final: 0.8174 (p) REVERT: C 201 GLU cc_start: 0.7768 (pm20) cc_final: 0.7512 (pm20) REVERT: C 211 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8449 (pp) REVERT: C 258 ASP cc_start: 0.7810 (m-30) cc_final: 0.7514 (m-30) REVERT: D 45 LYS cc_start: 0.8217 (OUTLIER) cc_final: 0.7900 (mmmt) REVERT: D 132 ASP cc_start: 0.6449 (OUTLIER) cc_final: 0.6241 (p0) REVERT: E 23 ASP cc_start: 0.7710 (m-30) cc_final: 0.7457 (m-30) REVERT: E 38 GLU cc_start: 0.7504 (mp0) cc_final: 0.7184 (mp0) REVERT: E 151 MET cc_start: 0.8553 (mtp) cc_final: 0.8319 (mtm) REVERT: E 156 VAL cc_start: 0.8221 (t) cc_final: 0.8005 (t) REVERT: E 172 ARG cc_start: 0.8228 (tpp80) cc_final: 0.7882 (ttm-80) REVERT: E 177 ASP cc_start: 0.7749 (t0) cc_final: 0.7449 (t0) REVERT: F 52 ILE cc_start: 0.8511 (OUTLIER) cc_final: 0.8304 (pp) REVERT: F 84 GLU cc_start: 0.8127 (mp0) cc_final: 0.7239 (mp0) REVERT: G 117 MET cc_start: 0.7052 (tpt) cc_final: 0.6729 (mpp) REVERT: H 37 MET cc_start: 0.8072 (mmm) cc_final: 0.7767 (mmm) REVERT: H 102 ASP cc_start: 0.8458 (p0) cc_final: 0.7814 (p0) REVERT: I 109 ARG cc_start: 0.8612 (ptp-110) cc_final: 0.8402 (ptp-110) REVERT: L 44 MET cc_start: 0.8443 (mmm) cc_final: 0.7194 (mmm) REVERT: U 202 ASP cc_start: 0.7510 (m-30) cc_final: 0.7279 (m-30) REVERT: U 207 LEU cc_start: 0.7919 (mm) cc_final: 0.7701 (mm) REVERT: U 224 ASN cc_start: 0.6941 (p0) cc_final: 0.6467 (p0) REVERT: U 241 ASN cc_start: 0.7456 (t0) cc_final: 0.7001 (t0) REVERT: U 265 TYR cc_start: 0.6320 (m-80) cc_final: 0.6038 (m-80) REVERT: U 278 GLU cc_start: 0.7847 (mm-30) cc_final: 0.6927 (mm-30) REVERT: U 290 HIS cc_start: 0.6162 (OUTLIER) cc_final: 0.5565 (t-90) REVERT: U 298 ARG cc_start: 0.7213 (mtt180) cc_final: 0.6660 (mpt-90) REVERT: U 310 VAL cc_start: 0.8441 (t) cc_final: 0.8222 (p) REVERT: U 321 MET cc_start: 0.7707 (mmm) cc_final: 0.7174 (mpp) REVERT: U 331 VAL cc_start: 0.8213 (t) cc_final: 0.7869 (m) REVERT: U 346 GLU cc_start: 0.6426 (mm-30) cc_final: 0.6067 (mm-30) REVERT: U 395 THR cc_start: 0.8160 (p) cc_final: 0.7231 (m) REVERT: U 503 GLU cc_start: 0.7811 (mt-10) cc_final: 0.7441 (mt-10) REVERT: U 509 GLN cc_start: 0.8230 (tp40) cc_final: 0.7689 (tp40) REVERT: U 511 GLN cc_start: 0.7864 (tp-100) cc_final: 0.7426 (mm-40) REVERT: U 519 ASP cc_start: 0.7297 (t70) cc_final: 0.6823 (t70) REVERT: U 525 PHE cc_start: 0.7330 (t80) cc_final: 0.6735 (t80) REVERT: U 561 LEU cc_start: 0.8425 (mt) cc_final: 0.8151 (mt) REVERT: U 582 GLU cc_start: 0.7764 (tp30) cc_final: 0.6849 (tp30) REVERT: U 602 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.7205 (tp) REVERT: U 604 LYS cc_start: 0.8171 (mtpp) cc_final: 0.7852 (mtpp) REVERT: U 610 ARG cc_start: 0.7151 (ttm-80) cc_final: 0.6911 (ttm110) REVERT: U 620 MET cc_start: 0.5281 (mmp) cc_final: 0.5017 (mmp) outliers start: 157 outliers final: 115 residues processed: 1029 average time/residue: 0.2436 time to fit residues: 391.5498 Evaluate side-chains 1060 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 924 time to evaluate : 1.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 62 GLN Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 301 HIS Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 818 GLU Chi-restraints excluded: chain A residue 865 ILE Chi-restraints excluded: chain A residue 883 ILE Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 912 SER Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 955 GLU Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1015 GLU Chi-restraints excluded: chain A residue 1027 ASP Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1128 ILE Chi-restraints excluded: chain A residue 1133 LYS Chi-restraints excluded: chain A residue 1173 THR Chi-restraints excluded: chain A residue 1258 ARG Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1304 ILE Chi-restraints excluded: chain A residue 1309 MET Chi-restraints excluded: chain A residue 1327 GLU Chi-restraints excluded: chain A residue 1350 LYS Chi-restraints excluded: chain A residue 1351 ASP Chi-restraints excluded: chain A residue 1412 MET Chi-restraints excluded: chain A residue 1417 HIS Chi-restraints excluded: chain A residue 1430 CYS Chi-restraints excluded: chain A residue 1478 GLU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 298 MET Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 436 LYS Chi-restraints excluded: chain B residue 550 MET Chi-restraints excluded: chain B residue 563 ASP Chi-restraints excluded: chain B residue 595 ASP Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 698 ILE Chi-restraints excluded: chain B residue 719 SER Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 752 TYR Chi-restraints excluded: chain B residue 894 THR Chi-restraints excluded: chain B residue 928 ILE Chi-restraints excluded: chain B residue 957 THR Chi-restraints excluded: chain B residue 1004 ASP Chi-restraints excluded: chain B residue 1012 SER Chi-restraints excluded: chain B residue 1033 THR Chi-restraints excluded: chain B residue 1071 ASN Chi-restraints excluded: chain B residue 1091 ARG Chi-restraints excluded: chain B residue 1101 GLN Chi-restraints excluded: chain B residue 1124 ILE Chi-restraints excluded: chain B residue 1173 SER Chi-restraints excluded: chain C residue 24 GLU Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 81 LYS Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 240 ARG Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 45 LYS Chi-restraints excluded: chain D residue 47 GLN Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain H residue 133 HIS Chi-restraints excluded: chain I residue 25 TYR Chi-restraints excluded: chain I residue 40 ARG Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain K residue 17 LYS Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain U residue 23 VAL Chi-restraints excluded: chain U residue 155 VAL Chi-restraints excluded: chain U residue 179 LEU Chi-restraints excluded: chain U residue 183 LEU Chi-restraints excluded: chain U residue 267 ARG Chi-restraints excluded: chain U residue 287 LYS Chi-restraints excluded: chain U residue 290 HIS Chi-restraints excluded: chain U residue 317 ILE Chi-restraints excluded: chain U residue 327 ASN Chi-restraints excluded: chain U residue 364 SER Chi-restraints excluded: chain U residue 366 ASN Chi-restraints excluded: chain U residue 431 CYS Chi-restraints excluded: chain U residue 513 GLN Chi-restraints excluded: chain U residue 602 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 416 optimal weight: 0.0000 chunk 154 optimal weight: 7.9990 chunk 199 optimal weight: 1.9990 chunk 245 optimal weight: 0.9980 chunk 307 optimal weight: 0.3980 chunk 406 optimal weight: 0.0170 chunk 259 optimal weight: 0.9990 chunk 126 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 201 optimal weight: 0.7980 chunk 234 optimal weight: 1.9990 overall best weight: 0.4422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 472 HIS A 662 HIS ** A 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 GLN B 452 ASN B 486 ASN ** B1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 GLN U 139 GLN U 164 GLN U 413 HIS ** U 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.150407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.121571 restraints weight = 58413.585| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.04 r_work: 0.3386 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3231 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3231 r_free = 0.3231 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3231 r_free = 0.3231 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3231 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 37458 Z= 0.134 Angle : 0.635 10.983 50851 Z= 0.320 Chirality : 0.045 0.286 5685 Planarity : 0.005 0.068 6386 Dihedral : 12.160 144.412 5561 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.57 % Favored : 94.14 % Rotamer: Outliers : 3.85 % Allowed : 23.42 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.48 % 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: -0.11 (0.13), residues: 4403 helix: 1.09 (0.13), residues: 1609 sheet: -0.25 (0.20), residues: 623 loop : -0.89 (0.14), residues: 2171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 160 TYR 0.024 0.001 TYR U 419 PHE 0.024 0.001 PHE E 75 TRP 0.019 0.001 TRP B 236 HIS 0.012 0.001 HIS A 662 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (37425) covalent geometry : angle 0.62406 / 0.32 (50804) SS BOND : bond 0.00136 / 0.07 ( 1) SS BOND : angle 1.57120 / 0.84 ( 2) hydrogen bonds : bond 0.03432 / 2.27 ( 1557) hydrogen bonds : angle 4.85489 / 3.42 ( 4407) metal coordination : bond 0.00589 / 0.40 ( 32) metal coordination : angle 3.97661 / 2.52 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8806 Ramachandran restraints generated. 4403 Oldfield, 0 Emsley, 4403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8806 Ramachandran restraints generated. 4403 Oldfield, 0 Emsley, 4403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1093 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 944 time to evaluate : 1.191 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 31 LEU cc_start: 0.8478 (mt) cc_final: 0.8267 (mt) REVERT: A 66 GLU cc_start: 0.7401 (OUTLIER) cc_final: 0.7098 (pm20) REVERT: A 186 ARG cc_start: 0.8020 (mtp85) cc_final: 0.7771 (ttp-110) REVERT: A 192 ARG cc_start: 0.7024 (ttp80) cc_final: 0.6798 (ttm110) REVERT: A 216 LEU cc_start: 0.7948 (tp) cc_final: 0.7744 (tp) REVERT: A 232 GLU cc_start: 0.7445 (mt-10) cc_final: 0.7147 (mt-10) REVERT: A 266 MET cc_start: 0.4203 (mmm) cc_final: 0.3915 (mmm) REVERT: A 289 GLN cc_start: 0.8459 (tt0) cc_final: 0.8180 (tt0) REVERT: A 321 GLU cc_start: 0.7698 (mm-30) cc_final: 0.7484 (mm-30) REVERT: A 325 LEU cc_start: 0.8162 (mm) cc_final: 0.7932 (mp) REVERT: A 375 ILE cc_start: 0.8051 (mm) cc_final: 0.7812 (tt) REVERT: A 388 MET cc_start: 0.8174 (mmm) cc_final: 0.7912 (mtp) REVERT: A 407 ARG cc_start: 0.8104 (ttp80) cc_final: 0.7751 (ttp80) REVERT: A 408 ARG cc_start: 0.7844 (mtp85) cc_final: 0.7547 (mtp180) REVERT: A 418 TYR cc_start: 0.8414 (m-80) cc_final: 0.8207 (m-80) REVERT: A 477 LEU cc_start: 0.7974 (OUTLIER) cc_final: 0.7655 (mt) REVERT: A 514 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.7107 (pt0) REVERT: A 565 MET cc_start: 0.7843 (ttp) cc_final: 0.7578 (ttt) REVERT: A 631 GLU cc_start: 0.7422 (mt-10) cc_final: 0.7012 (mt-10) REVERT: A 642 LYS cc_start: 0.8648 (tttt) cc_final: 0.8373 (tttp) REVERT: A 691 ASP cc_start: 0.7576 (m-30) cc_final: 0.7269 (m-30) REVERT: A 711 GLN cc_start: 0.8405 (tp40) cc_final: 0.8021 (mm-40) REVERT: A 728 THR cc_start: 0.8088 (m) cc_final: 0.7610 (p) REVERT: A 735 GLN cc_start: 0.8085 (mt0) cc_final: 0.7849 (mt0) REVERT: A 751 LYS cc_start: 0.8241 (tttp) cc_final: 0.8017 (ttpt) REVERT: A 783 GLN cc_start: 0.8294 (mt0) cc_final: 0.8049 (mt0) REVERT: A 914 LYS cc_start: 0.8122 (mmmm) cc_final: 0.7854 (mmmm) REVERT: A 936 GLU cc_start: 0.8131 (tp30) cc_final: 0.7912 (tp30) REVERT: A 945 ASN cc_start: 0.8101 (t0) cc_final: 0.7826 (t0) REVERT: A 955 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.7168 (tt0) REVERT: A 1015 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7798 (mp0) REVERT: A 1035 GLU cc_start: 0.8311 (tp30) cc_final: 0.7792 (tp30) REVERT: A 1071 GLU cc_start: 0.7193 (tt0) cc_final: 0.6971 (tt0) REVERT: A 1082 HIS cc_start: 0.8276 (m90) cc_final: 0.8063 (m-70) REVERT: A 1118 THR cc_start: 0.8092 (m) cc_final: 0.7837 (t) REVERT: A 1119 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7832 (mt) REVERT: A 1125 LYS cc_start: 0.8297 (ttpp) cc_final: 0.7713 (ttmm) REVERT: A 1156 ASP cc_start: 0.8247 (t0) cc_final: 0.7981 (t0) REVERT: A 1162 GLU cc_start: 0.7279 (tt0) cc_final: 0.7050 (tt0) REVERT: A 1221 MET cc_start: 0.8372 (tpp) cc_final: 0.7398 (mmm) REVERT: A 1258 ARG cc_start: 0.8525 (OUTLIER) cc_final: 0.8310 (ttm110) REVERT: A 1279 MET cc_start: 0.7669 (tpp) cc_final: 0.7456 (tpp) REVERT: A 1303 GLN cc_start: 0.7894 (pm20) cc_final: 0.7660 (pm20) REVERT: A 1441 GLU cc_start: 0.7436 (mm-30) cc_final: 0.7143 (mm-30) REVERT: A 1452 LYS cc_start: 0.8178 (mmtp) cc_final: 0.7901 (mmtp) REVERT: A 1480 CYS cc_start: 0.8179 (m) cc_final: 0.7899 (m) REVERT: A 1484 MET cc_start: 0.5602 (ppp) cc_final: 0.5047 (ppp) REVERT: B 109 MET cc_start: 0.7995 (mmt) cc_final: 0.7669 (mmt) REVERT: B 142 THR cc_start: 0.8135 (OUTLIER) cc_final: 0.7837 (p) REVERT: B 222 ARG cc_start: 0.8125 (ttm110) cc_final: 0.7525 (mtt90) REVERT: B 242 ARG cc_start: 0.6247 (tpt170) cc_final: 0.4388 (mtt180) REVERT: B 255 ARG cc_start: 0.7963 (tpt-90) cc_final: 0.7749 (tpp80) REVERT: B 381 GLU cc_start: 0.7754 (mp0) cc_final: 0.7391 (mp0) REVERT: B 414 GLU cc_start: 0.7537 (tm-30) cc_final: 0.7185 (tm-30) REVERT: B 417 ILE cc_start: 0.7969 (mt) cc_final: 0.7726 (tt) REVERT: B 543 GLU cc_start: 0.8016 (mt-10) cc_final: 0.7777 (mt-10) REVERT: B 547 GLU cc_start: 0.7344 (tm-30) cc_final: 0.7030 (tm-30) REVERT: B 551 GLU cc_start: 0.7707 (mp0) cc_final: 0.7183 (mp0) REVERT: B 556 ILE cc_start: 0.8616 (tp) cc_final: 0.8362 (tt) REVERT: B 572 CYS cc_start: 0.8357 (p) cc_final: 0.8143 (p) REVERT: B 593 GLN cc_start: 0.7839 (pt0) cc_final: 0.7206 (pt0) REVERT: B 595 ASP cc_start: 0.6274 (OUTLIER) cc_final: 0.5442 (m-30) REVERT: B 599 SER cc_start: 0.8509 (p) cc_final: 0.8252 (t) REVERT: B 600 GLU cc_start: 0.7708 (tt0) cc_final: 0.7379 (tt0) REVERT: B 629 GLU cc_start: 0.7840 (mm-30) cc_final: 0.7637 (mm-30) REVERT: B 645 GLU cc_start: 0.8231 (mt-10) cc_final: 0.7997 (mp0) REVERT: B 646 ARG cc_start: 0.8177 (ttp-110) cc_final: 0.7865 (ttp-110) REVERT: B 664 TYR cc_start: 0.8352 (m-80) cc_final: 0.7392 (m-80) REVERT: B 698 ILE cc_start: 0.8407 (OUTLIER) cc_final: 0.8079 (mt) REVERT: B 726 SER cc_start: 0.8277 (p) cc_final: 0.8010 (m) REVERT: B 751 LEU cc_start: 0.8498 (tp) cc_final: 0.8218 (tp) REVERT: B 796 MET cc_start: 0.8140 (mtp) cc_final: 0.7929 (mtp) REVERT: B 869 LYS cc_start: 0.7674 (tttt) cc_final: 0.7386 (tttp) REVERT: B 870 THR cc_start: 0.8217 (m) cc_final: 0.7945 (p) REVERT: B 871 VAL cc_start: 0.8278 (t) cc_final: 0.7947 (m) REVERT: B 910 THR cc_start: 0.8458 (t) cc_final: 0.8161 (p) REVERT: B 993 LYS cc_start: 0.8136 (ttmm) cc_final: 0.7931 (ttpp) REVERT: B 1006 VAL cc_start: 0.8889 (t) cc_final: 0.8679 (p) REVERT: B 1012 SER cc_start: 0.7927 (OUTLIER) cc_final: 0.7621 (m) REVERT: B 1090 GLU cc_start: 0.6977 (mm-30) cc_final: 0.6720 (mp0) REVERT: B 1091 ARG cc_start: 0.7562 (OUTLIER) cc_final: 0.7086 (ptt-90) REVERT: C 17 GLU cc_start: 0.7776 (pt0) cc_final: 0.7499 (pt0) REVERT: C 62 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7559 (mp0) REVERT: C 75 SER cc_start: 0.8422 (OUTLIER) cc_final: 0.8140 (p) REVERT: C 130 VAL cc_start: 0.7689 (t) cc_final: 0.7370 (t) REVERT: C 211 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8427 (pp) REVERT: C 258 ASP cc_start: 0.7776 (m-30) cc_final: 0.7463 (m-30) REVERT: D 45 LYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7860 (mmmt) REVERT: E 23 ASP cc_start: 0.7591 (m-30) cc_final: 0.7313 (m-30) REVERT: E 38 GLU cc_start: 0.7464 (mp0) cc_final: 0.7145 (mp0) REVERT: E 151 MET cc_start: 0.8458 (mtp) cc_final: 0.8232 (mtm) REVERT: E 156 VAL cc_start: 0.8190 (t) cc_final: 0.7988 (t) REVERT: E 172 ARG cc_start: 0.8159 (tpp80) cc_final: 0.7810 (ttm-80) REVERT: E 177 ASP cc_start: 0.7721 (t0) cc_final: 0.7415 (t0) REVERT: F 52 ILE cc_start: 0.8515 (OUTLIER) cc_final: 0.8302 (pp) REVERT: F 84 GLU cc_start: 0.8067 (mp0) cc_final: 0.7242 (mp0) REVERT: G 117 MET cc_start: 0.7030 (tpt) cc_final: 0.6688 (mpp) REVERT: H 37 MET cc_start: 0.8011 (mmm) cc_final: 0.7712 (mmm) REVERT: H 102 ASP cc_start: 0.8410 (p0) cc_final: 0.7812 (p0) REVERT: I 109 ARG cc_start: 0.8573 (ptp-110) cc_final: 0.8372 (ptp-110) REVERT: L 44 MET cc_start: 0.8385 (mmm) cc_final: 0.7210 (mmm) REVERT: U 182 ARG cc_start: 0.6985 (tpt90) cc_final: 0.6606 (tpt90) REVERT: U 202 ASP cc_start: 0.7558 (m-30) cc_final: 0.7325 (m-30) REVERT: U 224 ASN cc_start: 0.6942 (p0) cc_final: 0.6469 (p0) REVERT: U 241 ASN cc_start: 0.7428 (t0) cc_final: 0.6981 (t0) REVERT: U 267 ARG cc_start: 0.8041 (OUTLIER) cc_final: 0.7059 (tmm-80) REVERT: U 278 GLU cc_start: 0.7858 (mm-30) cc_final: 0.6921 (mm-30) REVERT: U 290 HIS cc_start: 0.6031 (OUTLIER) cc_final: 0.5661 (t-90) REVERT: U 310 VAL cc_start: 0.8419 (t) cc_final: 0.8205 (p) REVERT: U 321 MET cc_start: 0.7695 (mmm) cc_final: 0.7233 (mpp) REVERT: U 331 VAL cc_start: 0.8153 (t) cc_final: 0.7832 (m) REVERT: U 346 GLU cc_start: 0.6358 (mm-30) cc_final: 0.5921 (mm-30) REVERT: U 395 THR cc_start: 0.8121 (p) cc_final: 0.7205 (m) REVERT: U 500 HIS cc_start: 0.7342 (m-70) cc_final: 0.6832 (m-70) REVERT: U 503 GLU cc_start: 0.7757 (mt-10) cc_final: 0.7388 (mt-10) REVERT: U 509 GLN cc_start: 0.8058 (tp40) cc_final: 0.7562 (tp40) REVERT: U 511 GLN cc_start: 0.7787 (tp-100) cc_final: 0.7371 (mm-40) REVERT: U 519 ASP cc_start: 0.7244 (t70) cc_final: 0.6762 (t70) REVERT: U 523 GLU cc_start: 0.7138 (mp0) cc_final: 0.6688 (pm20) REVERT: U 561 LEU cc_start: 0.8398 (mt) cc_final: 0.8125 (mt) REVERT: U 565 ARG cc_start: 0.7700 (tpt170) cc_final: 0.7465 (tpt170) REVERT: U 582 GLU cc_start: 0.7733 (tp30) cc_final: 0.6818 (tp30) REVERT: U 602 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7155 (tp) REVERT: U 604 LYS cc_start: 0.8131 (mtpp) cc_final: 0.7796 (mtpp) REVERT: U 610 ARG cc_start: 0.7148 (ttm-80) cc_final: 0.6905 (ttm110) REVERT: U 620 MET cc_start: 0.5202 (mmp) cc_final: 0.4940 (mmp) outliers start: 149 outliers final: 117 residues processed: 1030 average time/residue: 0.2309 time to fit residues: 371.6862 Evaluate side-chains 1053 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 916 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 62 GLN Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 301 HIS Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 818 GLU Chi-restraints excluded: chain A residue 865 ILE Chi-restraints excluded: chain A residue 883 ILE Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 912 SER Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 955 GLU Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1015 GLU Chi-restraints excluded: chain A residue 1027 ASP Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1128 ILE Chi-restraints excluded: chain A residue 1133 LYS Chi-restraints excluded: chain A residue 1173 THR Chi-restraints excluded: chain A residue 1258 ARG Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1304 ILE Chi-restraints excluded: chain A residue 1351 ASP Chi-restraints excluded: chain A residue 1412 MET Chi-restraints excluded: chain A residue 1417 HIS Chi-restraints excluded: chain A residue 1430 CYS Chi-restraints excluded: chain A residue 1478 GLU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 298 MET Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 436 LYS Chi-restraints excluded: chain B residue 550 MET Chi-restraints excluded: chain B residue 595 ASP Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 698 ILE Chi-restraints excluded: chain B residue 719 SER Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 752 TYR Chi-restraints excluded: chain B residue 765 GLU Chi-restraints excluded: chain B residue 894 THR Chi-restraints excluded: chain B residue 928 ILE Chi-restraints excluded: chain B residue 957 THR Chi-restraints excluded: chain B residue 1004 ASP Chi-restraints excluded: chain B residue 1012 SER Chi-restraints excluded: chain B residue 1033 THR Chi-restraints excluded: chain B residue 1043 ILE Chi-restraints excluded: chain B residue 1071 ASN Chi-restraints excluded: chain B residue 1091 ARG Chi-restraints excluded: chain B residue 1101 GLN Chi-restraints excluded: chain B residue 1124 ILE Chi-restraints excluded: chain B residue 1173 SER Chi-restraints excluded: chain C residue 24 GLU Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 81 LYS Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 240 ARG Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 45 LYS Chi-restraints excluded: chain D residue 47 GLN Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain H residue 133 HIS Chi-restraints excluded: chain I residue 25 TYR Chi-restraints excluded: chain I residue 40 ARG Chi-restraints excluded: chain I residue 69 ILE Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain K residue 17 LYS Chi-restraints excluded: chain K residue 36 ASN Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain U residue 23 VAL Chi-restraints excluded: chain U residue 155 VAL Chi-restraints excluded: chain U residue 164 GLN Chi-restraints excluded: chain U residue 179 LEU Chi-restraints excluded: chain U residue 183 LEU Chi-restraints excluded: chain U residue 267 ARG Chi-restraints excluded: chain U residue 287 LYS Chi-restraints excluded: chain U residue 290 HIS Chi-restraints excluded: chain U residue 317 ILE Chi-restraints excluded: chain U residue 327 ASN Chi-restraints excluded: chain U residue 366 ASN Chi-restraints excluded: chain U residue 431 CYS Chi-restraints excluded: chain U residue 513 GLN Chi-restraints excluded: chain U residue 602 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 317 optimal weight: 0.7980 chunk 168 optimal weight: 0.6980 chunk 115 optimal weight: 3.9990 chunk 230 optimal weight: 0.8980 chunk 247 optimal weight: 0.9980 chunk 400 optimal weight: 3.9990 chunk 232 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 384 optimal weight: 0.1980 chunk 55 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 472 HIS ** A 662 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 861 GLN ** A1457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 GLN B 452 ASN B 486 ASN ** B 817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 139 GLN U 413 HIS ** U 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.150382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.120760 restraints weight = 64415.785| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.24 r_work: 0.3366 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3193 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3193 r_free = 0.3193 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3193 r_free = 0.3193 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (18 function evaluations) r_final: 0.3193 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.227 37458 Z= 0.176 Angle : 0.725 59.118 50851 Z= 0.384 Chirality : 0.045 0.292 5685 Planarity : 0.005 0.073 6386 Dihedral : 12.159 144.419 5561 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.61 % Favored : 94.11 % Rotamer: Outliers : 3.65 % Allowed : 23.83 % Favored : 72.52 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.48 % 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: -0.11 (0.13), residues: 4403 helix: 1.09 (0.13), residues: 1609 sheet: -0.25 (0.20), residues: 623 loop : -0.89 (0.14), residues: 2171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.001 ARG U 540 TYR 0.023 0.001 TYR U 419 PHE 0.039 0.001 PHE U 525 TRP 0.018 0.001 TRP C 49 HIS 0.022 0.001 HIS A 662 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.18 (37425) covalent geometry : angle 0.71578 / 0.38 (50804) SS BOND : bond 0.00135 / 0.07 ( 1) SS BOND : angle 1.56773 / 0.83 ( 2) hydrogen bonds : bond 0.03436 / 2.27 ( 1557) hydrogen bonds : angle 4.85474 / 3.42 ( 4407) metal coordination : bond 0.00636 / 0.43 ( 32) metal coordination : angle 3.96832 / 2.52 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8806 Ramachandran restraints generated. 4403 Oldfield, 0 Emsley, 4403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8806 Ramachandran restraints generated. 4403 Oldfield, 0 Emsley, 4403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1058 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 917 time to evaluate : 1.082 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 31 LEU cc_start: 0.8442 (mt) cc_final: 0.8228 (mt) REVERT: A 66 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.7108 (pm20) REVERT: A 186 ARG cc_start: 0.8064 (mtp85) cc_final: 0.7779 (ttp-110) REVERT: A 192 ARG cc_start: 0.7111 (ttp80) cc_final: 0.6862 (ttm110) REVERT: A 216 LEU cc_start: 0.7955 (tp) cc_final: 0.7745 (tp) REVERT: A 232 GLU cc_start: 0.7550 (mt-10) cc_final: 0.7215 (mt-10) REVERT: A 266 MET cc_start: 0.4135 (mmm) cc_final: 0.3808 (mmm) REVERT: A 289 GLN cc_start: 0.8434 (tt0) cc_final: 0.8139 (tt0) REVERT: A 325 LEU cc_start: 0.8166 (mm) cc_final: 0.7949 (mp) REVERT: A 375 ILE cc_start: 0.8060 (mm) cc_final: 0.7813 (tt) REVERT: A 388 MET cc_start: 0.8168 (mmm) cc_final: 0.7814 (mtp) REVERT: A 407 ARG cc_start: 0.8117 (ttp80) cc_final: 0.7751 (ttp80) REVERT: A 408 ARG cc_start: 0.7817 (mtp85) cc_final: 0.7514 (mtp180) REVERT: A 418 TYR cc_start: 0.8476 (m-80) cc_final: 0.8217 (m-80) REVERT: A 477 LEU cc_start: 0.7935 (OUTLIER) cc_final: 0.7628 (mt) REVERT: A 514 GLU cc_start: 0.7490 (OUTLIER) cc_final: 0.7179 (pt0) REVERT: A 565 MET cc_start: 0.7891 (ttp) cc_final: 0.7622 (ttt) REVERT: A 631 GLU cc_start: 0.7462 (mt-10) cc_final: 0.7042 (mt-10) REVERT: A 642 LYS cc_start: 0.8652 (tttt) cc_final: 0.8386 (tttp) REVERT: A 691 ASP cc_start: 0.7620 (m-30) cc_final: 0.7311 (m-30) REVERT: A 711 GLN cc_start: 0.8410 (tp40) cc_final: 0.8021 (mm-40) REVERT: A 728 THR cc_start: 0.8076 (m) cc_final: 0.7587 (p) REVERT: A 735 GLN cc_start: 0.8099 (mt0) cc_final: 0.7852 (mt0) REVERT: A 751 LYS cc_start: 0.8182 (tttp) cc_final: 0.7957 (ttpt) REVERT: A 783 GLN cc_start: 0.8289 (mt0) cc_final: 0.8034 (mt0) REVERT: A 914 LYS cc_start: 0.8134 (mmmm) cc_final: 0.7852 (mmmm) REVERT: A 936 GLU cc_start: 0.8142 (tp30) cc_final: 0.7916 (tp30) REVERT: A 945 ASN cc_start: 0.8128 (t0) cc_final: 0.7795 (t0) REVERT: A 955 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.7168 (tt0) REVERT: A 1015 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7795 (mp0) REVERT: A 1035 GLU cc_start: 0.8301 (tp30) cc_final: 0.7769 (tp30) REVERT: A 1082 HIS cc_start: 0.8292 (m90) cc_final: 0.8080 (m-70) REVERT: A 1118 THR cc_start: 0.8070 (m) cc_final: 0.7806 (t) REVERT: A 1119 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7841 (mt) REVERT: A 1125 LYS cc_start: 0.8212 (ttpp) cc_final: 0.7670 (ttmm) REVERT: A 1156 ASP cc_start: 0.8246 (t0) cc_final: 0.7962 (t0) REVERT: A 1162 GLU cc_start: 0.7341 (tt0) cc_final: 0.7096 (tt0) REVERT: A 1221 MET cc_start: 0.8359 (tpp) cc_final: 0.7374 (mmm) REVERT: A 1257 LEU cc_start: 0.8172 (tt) cc_final: 0.7929 (tp) REVERT: A 1258 ARG cc_start: 0.8550 (OUTLIER) cc_final: 0.8305 (ttm110) REVERT: A 1303 GLN cc_start: 0.7946 (pm20) cc_final: 0.7717 (pm20) REVERT: A 1441 GLU cc_start: 0.7512 (mm-30) cc_final: 0.7161 (mm-30) REVERT: A 1452 LYS cc_start: 0.8198 (mmtp) cc_final: 0.7902 (mmtp) REVERT: A 1480 CYS cc_start: 0.8162 (m) cc_final: 0.7867 (m) REVERT: A 1484 MET cc_start: 0.5627 (ppp) cc_final: 0.5089 (ppp) REVERT: B 109 MET cc_start: 0.8019 (mmt) cc_final: 0.7671 (mmt) REVERT: B 142 THR cc_start: 0.8106 (OUTLIER) cc_final: 0.7791 (p) REVERT: B 222 ARG cc_start: 0.8180 (ttm110) cc_final: 0.7531 (mtt90) REVERT: B 242 ARG cc_start: 0.6242 (tpt170) cc_final: 0.4349 (mtt180) REVERT: B 255 ARG cc_start: 0.8001 (tpt-90) cc_final: 0.7740 (tpp80) REVERT: B 381 GLU cc_start: 0.7807 (mp0) cc_final: 0.7423 (mp0) REVERT: B 414 GLU cc_start: 0.7527 (tm-30) cc_final: 0.7160 (tm-30) REVERT: B 417 ILE cc_start: 0.7919 (mt) cc_final: 0.7674 (tt) REVERT: B 543 GLU cc_start: 0.8059 (mt-10) cc_final: 0.7805 (mt-10) REVERT: B 547 GLU cc_start: 0.7393 (tm-30) cc_final: 0.7057 (tm-30) REVERT: B 551 GLU cc_start: 0.7772 (mp0) cc_final: 0.7199 (mp0) REVERT: B 556 ILE cc_start: 0.8573 (tp) cc_final: 0.8325 (tt) REVERT: B 572 CYS cc_start: 0.8403 (p) cc_final: 0.8157 (p) REVERT: B 593 GLN cc_start: 0.7878 (pt0) cc_final: 0.7233 (pt0) REVERT: B 595 ASP cc_start: 0.6353 (OUTLIER) cc_final: 0.5490 (m-30) REVERT: B 599 SER cc_start: 0.8540 (p) cc_final: 0.8270 (t) REVERT: B 600 GLU cc_start: 0.7748 (tt0) cc_final: 0.7389 (tt0) REVERT: B 609 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7522 (mm-30) REVERT: B 617 ASP cc_start: 0.7858 (t0) cc_final: 0.7483 (t0) REVERT: B 629 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7651 (mm-30) REVERT: B 645 GLU cc_start: 0.8268 (mt-10) cc_final: 0.8015 (mp0) REVERT: B 646 ARG cc_start: 0.8191 (ttp-110) cc_final: 0.7860 (ttp-110) REVERT: B 664 TYR cc_start: 0.8399 (m-80) cc_final: 0.7415 (m-80) REVERT: B 698 ILE cc_start: 0.8412 (OUTLIER) cc_final: 0.8080 (mt) REVERT: B 726 SER cc_start: 0.8300 (p) cc_final: 0.8042 (m) REVERT: B 751 LEU cc_start: 0.8510 (tp) cc_final: 0.8231 (tp) REVERT: B 796 MET cc_start: 0.8185 (mtp) cc_final: 0.7984 (mtp) REVERT: B 869 LYS cc_start: 0.7625 (tttt) cc_final: 0.7361 (tttp) REVERT: B 870 THR cc_start: 0.8235 (m) cc_final: 0.7940 (p) REVERT: B 871 VAL cc_start: 0.8232 (t) cc_final: 0.7890 (m) REVERT: B 910 THR cc_start: 0.8497 (t) cc_final: 0.8192 (p) REVERT: B 993 LYS cc_start: 0.8147 (ttmm) cc_final: 0.7907 (ttpp) REVERT: B 1006 VAL cc_start: 0.8875 (t) cc_final: 0.8657 (p) REVERT: B 1012 SER cc_start: 0.7971 (OUTLIER) cc_final: 0.7647 (m) REVERT: B 1090 GLU cc_start: 0.7029 (mm-30) cc_final: 0.6778 (mp0) REVERT: B 1091 ARG cc_start: 0.7560 (OUTLIER) cc_final: 0.7066 (ptt-90) REVERT: C 17 GLU cc_start: 0.7801 (pt0) cc_final: 0.7497 (pt0) REVERT: C 62 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7571 (mp0) REVERT: C 75 SER cc_start: 0.8431 (OUTLIER) cc_final: 0.8169 (p) REVERT: C 130 VAL cc_start: 0.7646 (t) cc_final: 0.7338 (t) REVERT: C 211 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8396 (pp) REVERT: C 258 ASP cc_start: 0.7804 (m-30) cc_final: 0.7479 (m-30) REVERT: E 23 ASP cc_start: 0.7627 (m-30) cc_final: 0.7356 (m-30) REVERT: E 38 GLU cc_start: 0.7536 (mp0) cc_final: 0.7192 (mp0) REVERT: E 151 MET cc_start: 0.8523 (mtp) cc_final: 0.8316 (mtm) REVERT: E 156 VAL cc_start: 0.8132 (t) cc_final: 0.7916 (t) REVERT: E 172 ARG cc_start: 0.8192 (tpp80) cc_final: 0.7821 (ttm-80) REVERT: E 177 ASP cc_start: 0.7804 (t0) cc_final: 0.7480 (t0) REVERT: F 52 ILE cc_start: 0.8506 (OUTLIER) cc_final: 0.8302 (pp) REVERT: F 84 GLU cc_start: 0.8105 (mp0) cc_final: 0.7246 (mp0) REVERT: G 117 MET cc_start: 0.7207 (tpt) cc_final: 0.6853 (mpp) REVERT: H 37 MET cc_start: 0.8034 (mmm) cc_final: 0.7734 (mmm) REVERT: H 102 ASP cc_start: 0.8395 (p0) cc_final: 0.7785 (p0) REVERT: I 109 ARG cc_start: 0.8608 (ptp-110) cc_final: 0.8377 (ptp-110) REVERT: L 44 MET cc_start: 0.8419 (mmm) cc_final: 0.7225 (mmm) REVERT: U 202 ASP cc_start: 0.7592 (m-30) cc_final: 0.7353 (m-30) REVERT: U 224 ASN cc_start: 0.6927 (p0) cc_final: 0.6445 (p0) REVERT: U 241 ASN cc_start: 0.7453 (t0) cc_final: 0.6998 (t0) REVERT: U 267 ARG cc_start: 0.8023 (OUTLIER) cc_final: 0.7050 (tmm-80) REVERT: U 278 GLU cc_start: 0.7787 (mm-30) cc_final: 0.6850 (mm-30) REVERT: U 290 HIS cc_start: 0.6041 (OUTLIER) cc_final: 0.5692 (t-90) REVERT: U 310 VAL cc_start: 0.8462 (t) cc_final: 0.8230 (p) REVERT: U 321 MET cc_start: 0.7650 (mmm) cc_final: 0.7170 (mpp) REVERT: U 331 VAL cc_start: 0.8148 (t) cc_final: 0.7828 (m) REVERT: U 346 GLU cc_start: 0.6347 (mm-30) cc_final: 0.5908 (mm-30) REVERT: U 395 THR cc_start: 0.8146 (p) cc_final: 0.7263 (m) REVERT: U 500 HIS cc_start: 0.7411 (m-70) cc_final: 0.6890 (m-70) REVERT: U 503 GLU cc_start: 0.7789 (mt-10) cc_final: 0.7384 (mt-10) REVERT: U 509 GLN cc_start: 0.8107 (tp40) cc_final: 0.7576 (tp40) REVERT: U 511 GLN cc_start: 0.7829 (tp-100) cc_final: 0.7419 (mm-40) REVERT: U 519 ASP cc_start: 0.7300 (t70) cc_final: 0.6802 (t70) REVERT: U 523 GLU cc_start: 0.7141 (mp0) cc_final: 0.6652 (pm20) REVERT: U 561 LEU cc_start: 0.8426 (mt) cc_final: 0.8150 (mt) REVERT: U 565 ARG cc_start: 0.7701 (tpt170) cc_final: 0.7442 (tpt170) REVERT: U 582 GLU cc_start: 0.7833 (tp30) cc_final: 0.6896 (tp30) REVERT: U 589 ARG cc_start: 0.7541 (ptp90) cc_final: 0.7149 (ptp-110) REVERT: U 602 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7130 (tp) REVERT: U 604 LYS cc_start: 0.8180 (mtpp) cc_final: 0.7852 (mtpp) REVERT: U 610 ARG cc_start: 0.7180 (ttm-80) cc_final: 0.6902 (ttm110) REVERT: U 620 MET cc_start: 0.5281 (mmp) cc_final: 0.5020 (mmp) outliers start: 141 outliers final: 119 residues processed: 999 average time/residue: 0.2332 time to fit residues: 364.0850 Evaluate side-chains 1049 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 911 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 62 GLN Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 301 HIS Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 818 GLU Chi-restraints excluded: chain A residue 865 ILE Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 883 ILE Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 912 SER Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 955 GLU Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1015 GLU Chi-restraints excluded: chain A residue 1027 ASP Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1128 ILE Chi-restraints excluded: chain A residue 1133 LYS Chi-restraints excluded: chain A residue 1173 THR Chi-restraints excluded: chain A residue 1258 ARG Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1304 ILE Chi-restraints excluded: chain A residue 1351 ASP Chi-restraints excluded: chain A residue 1352 VAL Chi-restraints excluded: chain A residue 1412 MET Chi-restraints excluded: chain A residue 1417 HIS Chi-restraints excluded: chain A residue 1430 CYS Chi-restraints excluded: chain A residue 1478 GLU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 298 MET Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 436 LYS Chi-restraints excluded: chain B residue 550 MET Chi-restraints excluded: chain B residue 595 ASP Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 698 ILE Chi-restraints excluded: chain B residue 719 SER Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 752 TYR Chi-restraints excluded: chain B residue 765 GLU Chi-restraints excluded: chain B residue 894 THR Chi-restraints excluded: chain B residue 928 ILE Chi-restraints excluded: chain B residue 957 THR Chi-restraints excluded: chain B residue 1004 ASP Chi-restraints excluded: chain B residue 1012 SER Chi-restraints excluded: chain B residue 1033 THR Chi-restraints excluded: chain B residue 1043 ILE Chi-restraints excluded: chain B residue 1071 ASN Chi-restraints excluded: chain B residue 1091 ARG Chi-restraints excluded: chain B residue 1101 GLN Chi-restraints excluded: chain B residue 1124 ILE Chi-restraints excluded: chain B residue 1173 SER Chi-restraints excluded: chain C residue 24 GLU Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 81 LYS Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 240 ARG Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 47 GLN Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain H residue 133 HIS Chi-restraints excluded: chain I residue 25 TYR Chi-restraints excluded: chain I residue 40 ARG Chi-restraints excluded: chain I residue 69 ILE Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain K residue 17 LYS Chi-restraints excluded: chain K residue 36 ASN Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain U residue 23 VAL Chi-restraints excluded: chain U residue 155 VAL Chi-restraints excluded: chain U residue 179 LEU Chi-restraints excluded: chain U residue 183 LEU Chi-restraints excluded: chain U residue 267 ARG Chi-restraints excluded: chain U residue 287 LYS Chi-restraints excluded: chain U residue 290 HIS Chi-restraints excluded: chain U residue 302 GLN Chi-restraints excluded: chain U residue 317 ILE Chi-restraints excluded: chain U residue 327 ASN Chi-restraints excluded: chain U residue 366 ASN Chi-restraints excluded: chain U residue 431 CYS Chi-restraints excluded: chain U residue 513 GLN Chi-restraints excluded: chain U residue 602 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 280 optimal weight: 0.8980 chunk 274 optimal weight: 0.0040 chunk 247 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 140 optimal weight: 3.9990 chunk 246 optimal weight: 2.9990 chunk 425 optimal weight: 4.9990 chunk 190 optimal weight: 1.9990 chunk 303 optimal weight: 3.9990 chunk 271 optimal weight: 1.9990 overall best weight: 1.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 472 HIS ** A 662 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 GLN B 452 ASN B 486 ASN ** B 817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 413 HIS ** U 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.150316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.120643 restraints weight = 69514.717| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 2.26 r_work: 0.3363 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3196 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3196 r_free = 0.3196 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3196 r_free = 0.3196 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (12 function evaluations) r_final: 0.3196 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.227 37458 Z= 0.176 Angle : 0.725 59.118 50851 Z= 0.384 Chirality : 0.045 0.292 5685 Planarity : 0.005 0.073 6386 Dihedral : 12.159 144.419 5561 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.61 % Favored : 94.11 % Rotamer: Outliers : 3.57 % Allowed : 23.88 % Favored : 72.55 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.48 % 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: -0.11 (0.13), residues: 4403 helix: 1.09 (0.13), residues: 1609 sheet: -0.25 (0.20), residues: 623 loop : -0.89 (0.14), residues: 2171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.001 ARG U 540 TYR 0.023 0.001 TYR U 419 PHE 0.039 0.001 PHE U 525 TRP 0.018 0.001 TRP C 49 HIS 0.022 0.001 HIS A 662 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.18 (37425) covalent geometry : angle 0.71578 / 0.38 (50804) SS BOND : bond 0.00135 / 0.07 ( 1) SS BOND : angle 1.56773 / 0.83 ( 2) hydrogen bonds : bond 0.03436 / 2.27 ( 1557) hydrogen bonds : angle 4.85474 / 3.42 ( 4407) metal coordination : bond 0.00636 / 0.43 ( 32) metal coordination : angle 3.96832 / 2.52 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12443.43 seconds wall clock time: 212 minutes 41.14 seconds (12761.14 seconds total)