Starting phenix.real_space_refine on Mon Sep 14 20:26:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/5flm_3218/09_2026/5flm_3218.cif Found real_map, /net/cci-nas-00/data/ceres_data/5flm_3218/09_2026/5flm_3218.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/5flm_3218/09_2026/5flm_3218.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/5flm_3218/09_2026/5flm_3218.cif" model { file = "/net/cci-nas-00/data/ceres_data/5flm_3218/09_2026/5flm_3218.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5flm_3218/09_2026/5flm_3218.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5flm_3218/09_2026/5flm_3218.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5flm_3218/09_2026/5flm_3218.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 8 6.06 5 P 77 5.49 5 Mg 1 5.21 5 S 197 5.16 5 C 20401 2.51 5 N 5746 2.21 5 O 6282 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.23s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32712 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 11291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1427, 11291 Classifications: {'peptide': 1427} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 2, 'PTRANS': 68, 'TRANS': 1356} Chain breaks: 4 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 1, 'PHE:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 14 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: 2059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2059 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} Link IDs: {'PTRANS': 11, 'TRANS': 197} 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: 552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 552 Inner-chain residues flagged as termini: ['pdbres=" DA N 26 "'] Classifications: {'DNA': 27} Modifications used: {'5*END': 2} Link IDs: {'rna3p': 26} Chain: "P" Number of atoms: 301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 301 Classifications: {'RNAv2': 14} Modifications used: {'rna3p_pur': 9, 'rna3p_pyr': 5} Link IDs: {'rna3p': 13} Chain: "T" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 792 Classifications: {'DNA': 39} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 38} 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 464 SG CYS A 71 40.497 79.632 104.965 1.00141.57 S ATOM 486 SG CYS A 74 41.563 82.656 106.029 1.00137.29 S ATOM 533 SG CYS A 81 42.957 81.009 102.896 1.00138.71 S ATOM 768 SG CYS A 111 87.760 73.539 119.494 1.00164.45 S ATOM 796 SG CYS A 114 86.283 75.814 123.074 1.00163.67 S ATOM 1142 SG CYS A 184 88.465 71.879 122.453 1.00171.81 S ATOM 19923 SG CYS B1119 52.935 91.627 113.327 1.00141.59 S ATOM 19945 SG CYS B1122 55.330 88.850 112.486 1.00142.57 S ATOM 20060 SG CYS B1137 52.108 88.033 113.226 1.00148.67 S ATOM 20081 SG CYS B1140 55.498 88.754 115.930 1.00152.98 S ATOM 21047 SG CYS C 88 10.267 92.706 46.170 1.00138.12 S ATOM 21060 SG CYS C 90 8.040 90.403 47.680 1.00147.15 S ATOM 21095 SG CYS C 94 8.573 90.395 44.256 1.00132.97 S ATOM 21117 SG CYS C 97 11.926 89.780 44.938 1.00132.45 S ATOM 28353 SG CYS I 17 120.070 40.420 72.491 1.00161.53 S ATOM 28377 SG CYS I 20 116.343 39.810 74.838 1.00163.91 S ATOM 28538 SG CYS I 39 118.190 42.758 75.819 1.00169.29 S ATOM 28563 SG CYS I 42 120.159 39.727 76.138 1.00167.79 S ATOM 28915 SG CYS I 86 111.911 58.941 32.990 1.00150.39 S ATOM 28939 SG CYS I 89 110.757 56.215 30.363 1.00155.57 S ATOM 29143 SG CYS I 114 108.240 58.211 32.722 1.00146.35 S ATOM 29178 SG CYS I 119 111.008 55.637 33.868 1.00152.45 S ATOM 29288 SG CYS J 7 40.861 84.127 32.213 1.00 98.61 S ATOM 29312 SG CYS J 10 39.589 87.410 30.255 1.00 95.35 S ATOM 29576 SG CYS J 44 43.316 87.698 29.823 1.00107.46 S ATOM 29582 SG CYS J 45 40.359 85.046 27.921 1.00108.23 S ATOM 30728 SG CYS L 19 28.576 49.198 55.525 1.00146.64 S ATOM 30747 SG CYS L 22 26.451 46.723 52.945 1.00145.85 S ATOM 30864 SG CYS L 36 25.573 47.537 57.007 1.00153.01 S ATOM 30890 SG CYS L 39 28.303 45.733 55.677 1.00150.68 S Time building chain proxies: 5.70, per 1000 atoms: 0.17 Number of scatterers: 32712 At special positions: 0 Unit cell: (155.25, 168.75, 168.75, 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 197 16.00 P 77 15.00 Mg 1 11.99 O 6282 8.00 N 5746 7.00 C 20401 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.41 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2488 " pdb="ZN ZN A2488 " - pdb=" NE2 HIS A 84 " pdb="ZN ZN A2488 " - pdb=" SG CYS A 74 " pdb="ZN ZN A2488 " - pdb=" SG CYS A 81 " pdb="ZN ZN A2488 " - pdb=" SG CYS A 71 " pdb=" ZN A2489 " pdb="ZN ZN A2489 " - pdb=" SG CYS A 111 " pdb="ZN ZN A2489 " - pdb=" SG CYS A 114 " pdb="ZN ZN A2489 " - pdb=" SG CYS A 184 " pdb=" ZN B2175 " pdb="ZN ZN B2175 " - pdb=" SG CYS B1137 " pdb="ZN ZN B2175 " - pdb=" SG CYS B1140 " pdb="ZN ZN B2175 " - pdb=" SG CYS B1122 " pdb="ZN ZN B2175 " - pdb=" SG CYS B1119 " pdb=" ZN C1272 " pdb="ZN ZN C1272 " - pdb=" SG CYS C 94 " pdb="ZN ZN C1272 " - pdb=" SG CYS C 90 " pdb="ZN ZN C1272 " - pdb=" SG CYS C 88 " pdb="ZN ZN C1272 " - pdb=" SG CYS C 97 " pdb=" ZN I1126 " pdb="ZN ZN I1126 " - pdb=" SG CYS I 42 " pdb="ZN ZN I1126 " - pdb=" SG CYS I 20 " pdb="ZN ZN I1126 " - pdb=" SG CYS I 17 " pdb="ZN ZN I1126 " - pdb=" SG CYS I 39 " pdb=" ZN I1127 " pdb="ZN ZN I1127 " - pdb=" SG CYS I 86 " pdb="ZN ZN I1127 " - pdb=" SG CYS I 89 " pdb="ZN ZN I1127 " - pdb=" SG CYS I 114 " pdb="ZN ZN I1127 " - pdb=" SG CYS I 119 " pdb=" ZN J1068 " pdb="ZN ZN J1068 " - pdb=" SG CYS J 10 " pdb="ZN ZN J1068 " - pdb=" SG CYS J 45 " pdb="ZN ZN J1068 " - pdb=" SG CYS J 44 " pdb="ZN ZN J1068 " - pdb=" SG CYS J 7 " pdb=" ZN L1059 " pdb="ZN ZN L1059 " - pdb=" SG CYS L 19 " pdb="ZN ZN L1059 " - pdb=" SG CYS L 39 " pdb="ZN ZN L1059 " - pdb=" SG CYS L 22 " pdb="ZN ZN L1059 " - pdb=" SG CYS L 36 " Number of angles added : 39 7716 Ramachandran restraints generated. 3858 Oldfield, 0 Emsley, 3858 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7330 Finding SS restraints... Secondary structure from input PDB file: 131 helices and 50 sheets defined 37.8% alpha, 18.9% beta 32 base pairs and 64 stacking pairs defined. Time for finding SS restraints: 4.31 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 removed outlier: 3.527A pdb=" N LEU A 141 " --> pdb=" O PRO A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 227 removed outlier: 4.044A pdb=" N ARG A 227 " --> pdb=" O GLU A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 236 Processing helix chain 'A' and resid 244 through 247 Processing helix chain 'A' and resid 274 through 297 Processing helix chain 'A' and resid 300 through 319 removed outlier: 3.839A pdb=" N ALA A 304 " --> pdb=" O ALA A 300 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VAL A 318 " --> pdb=" O VAL A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 344 Processing helix chain 'A' and resid 348 through 354 Processing helix chain 'A' and resid 383 through 388 Processing helix chain 'A' and resid 398 through 409 Processing helix chain 'A' and resid 435 through 439 removed outlier: 3.734A pdb=" N LEU A 438 " --> pdb=" O PRO A 435 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N HIS A 439 " --> pdb=" O SER A 436 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 435 through 439' 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 485 through 487 No H-bonds generated for 'chain 'A' and resid 485 through 487' Processing helix chain 'A' and resid 488 through 493 removed outlier: 3.974A pdb=" N TYR A 492 " --> pdb=" O VAL A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 518 Processing helix chain 'A' and resid 521 through 525 removed outlier: 3.929A pdb=" N ILE A 525 " --> pdb=" O PRO A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 550 removed outlier: 3.602A pdb=" N THR A 543 " --> pdb=" O GLN A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 566 Processing helix chain 'A' and resid 588 through 596 removed outlier: 3.907A pdb=" N LEU A 594 " --> pdb=" O GLN A 590 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE A 595 " --> pdb=" O ILE A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 660 Processing helix chain 'A' and resid 661 through 684 removed outlier: 3.682A pdb=" N LEU A 667 " --> pdb=" O ASP A 663 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ILE A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLU A 683 " --> pdb=" O TRP A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 693 removed outlier: 3.634A pdb=" N SER A 692 " --> pdb=" O GLY A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 722 removed outlier: 3.984A pdb=" N GLN A 700 " --> pdb=" O SER A 696 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASN A 722 " --> pdb=" O GLU A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 759 Processing helix chain 'A' and resid 764 through 772 removed outlier: 4.003A pdb=" N SER A 772 " --> pdb=" O SER A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 777 through 786 Processing helix chain 'A' and resid 832 through 869 removed outlier: 3.643A pdb=" N GLU A 845 " --> pdb=" O MET A 841 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLY A 846 " --> pdb=" O GLY A 842 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N THR A 854 " --> pdb=" O THR A 850 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N ALA A 855 " --> pdb=" O ALA A 851 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLU A 856 " --> pdb=" O VAL A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 921 Processing helix chain 'A' and resid 927 through 934 Processing helix chain 'A' and resid 935 through 945 removed outlier: 4.288A pdb=" N LYS A 940 " --> pdb=" O GLU A 936 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ASP A 941 " --> pdb=" O ASP A 937 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN A 945 " --> pdb=" O ASP A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 970 removed outlier: 3.837A pdb=" N GLN A 949 " --> pdb=" O ASN A 945 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N PHE A 956 " --> pdb=" O LEU A 952 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 974 removed outlier: 4.186A 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 removed outlier: 3.796A pdb=" N LYS A 992 " --> pdb=" O TRP A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1018 removed outlier: 3.582A pdb=" N VAL A1009 " --> pdb=" O HIS A1005 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL A1010 " --> pdb=" O PRO A1006 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS A1018 " --> pdb=" O LYS A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1049 removed outlier: 5.480A pdb=" N LEU A1040 " --> pdb=" O ASN A1036 " (cutoff:3.500A) removed outlier: 5.715A 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 removed outlier: 3.523A pdb=" N ILE A1080 " --> pdb=" O PHE A1076 " (cutoff:3.500A) Processing helix chain 'A' and resid 1086 through 1097 removed outlier: 3.704A pdb=" N LEU A1090 " --> pdb=" O MET A1086 " (cutoff:3.500A) Processing helix chain 'A' and resid 1098 through 1102 Processing helix chain 'A' and resid 1120 through 1130 Processing helix chain 'A' and resid 1145 through 1150 removed outlier: 4.141A pdb=" N ARG A1149 " --> pdb=" O GLY A1145 " (cutoff:3.500A) Processing helix chain 'A' and resid 1150 through 1161 removed outlier: 3.537A pdb=" N ALA A1154 " --> pdb=" O ASP A1150 " (cutoff:3.500A) Processing helix chain 'A' and resid 1189 through 1199 removed outlier: 4.445A pdb=" N MET A1199 " --> pdb=" O VAL A1195 " (cutoff:3.500A) Processing helix chain 'A' and resid 1217 through 1224 removed outlier: 3.657A 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 1262 through 1267 removed outlier: 3.838A pdb=" N GLU A1266 " --> pdb=" O MET A1262 " (cutoff:3.500A) Processing helix chain 'A' and resid 1281 through 1296 removed outlier: 4.143A pdb=" N THR A1294 " --> pdb=" O SER A1290 " (cutoff:3.500A) Processing helix chain 'A' and resid 1342 through 1349 removed outlier: 3.756A pdb=" N VAL A1346 " --> pdb=" O SER A1342 " (cutoff:3.500A) Processing helix chain 'A' and resid 1362 through 1370 removed outlier: 3.960A pdb=" N VAL A1368 " --> pdb=" O GLU A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1370 through 1389 removed outlier: 3.527A pdb=" N VAL A1374 " --> pdb=" O GLY A1370 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ASP A1389 " --> pdb=" O VAL A1385 " (cutoff:3.500A) Processing helix chain 'A' and resid 1394 through 1407 removed outlier: 4.051A pdb=" N LEU A1398 " --> pdb=" O ASN A1394 " (cutoff:3.500A) Processing helix chain 'A' and resid 1415 through 1422 removed outlier: 4.089A pdb=" N GLN A1422 " --> pdb=" O GLY A1418 " (cutoff:3.500A) Processing helix chain 'A' and resid 1425 through 1431 removed outlier: 3.641A pdb=" N LYS A1429 " --> pdb=" O GLY A1425 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N SER A1431 " --> pdb=" O LEU A1427 " (cutoff:3.500A) Processing helix chain 'A' and resid 1435 through 1445 removed outlier: 3.734A pdb=" N LEU A1439 " --> pdb=" O THR A1435 " (cutoff:3.500A) Processing helix chain 'A' and resid 1453 through 1460 removed outlier: 3.587A pdb=" N LEU A1460 " --> pdb=" O GLU A1456 " (cutoff:3.500A) Processing helix chain 'A' and resid 1478 through 1482 removed outlier: 3.718A pdb=" N LYS A1481 " --> pdb=" O GLU A1478 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 37 removed outlier: 3.639A pdb=" N ALA B 25 " --> pdb=" O LEU B 21 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N TRP B 27 " --> pdb=" O GLN B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 53 removed outlier: 3.505A pdb=" N LEU B 44 " --> pdb=" O VAL B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 61 Processing helix chain 'B' and resid 109 through 116 Processing helix chain 'B' and resid 167 through 174 Processing helix chain 'B' and resid 246 through 253 removed outlier: 3.526A pdb=" N ALA B 251 " --> pdb=" O ALA B 247 " (cutoff:3.500A) 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: 3.838A pdb=" N MET B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) Proline residue: B 303 - end of helix removed outlier: 3.575A pdb=" N ASP B 306 " --> pdb=" O LYS B 302 " (cutoff:3.500A) removed outlier: 3.503A 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 removed outlier: 3.600A pdb=" N ARG B 335 " --> pdb=" O THR B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 377 removed outlier: 4.128A pdb=" N LYS B 360 " --> pdb=" O PHE B 356 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TYR B 363 " --> pdb=" O THR B 359 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU B 365 " --> pdb=" O LYS B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 424 removed outlier: 4.167A pdb=" N GLY B 406 " --> pdb=" O PHE B 402 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N MET B 407 " --> pdb=" O LEU B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 450 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: 3.676A pdb=" N LEU B 542 " --> pdb=" O PRO B 538 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU B 543 " --> pdb=" O SER B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 593 removed outlier: 3.593A pdb=" N LEU B 583 " --> pdb=" O ASP B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 645 removed outlier: 3.528A pdb=" N ILE B 640 " --> pdb=" O LYS B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 658 Processing helix chain 'B' and resid 667 through 671 removed outlier: 3.724A pdb=" N GLU B 671 " --> pdb=" O THR B 667 " (cutoff:3.500A) No H-bonds generated for '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 706 through 711 removed outlier: 3.862A pdb=" N ILE B 710 " --> pdb=" O CYS B 707 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE B 711 " --> pdb=" O ALA B 708 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 716 Processing helix chain 'B' and resid 718 through 729 Processing helix chain 'B' and resid 761 through 768 removed outlier: 3.837A pdb=" N GLU B 765 " --> pdb=" O ARG B 762 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG B 768 " --> pdb=" O GLU B 765 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 802 Processing helix chain 'B' and resid 970 through 976 removed outlier: 4.797A pdb=" N SER B 974 " --> pdb=" O HIS B 970 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARG B 975 " --> pdb=" O ALA B 971 " (cutoff:3.500A) Processing helix chain 'B' and resid 978 through 994 removed outlier: 3.524A pdb=" N LYS B 988 " --> pdb=" O CYS B 984 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ASN B 992 " --> pdb=" O LYS B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1007 through 1016 Processing helix chain 'B' and resid 1017 through 1019 No H-bonds generated for 'chain 'B' and resid 1017 through 1019' Processing helix chain 'B' and resid 1054 through 1059 removed outlier: 3.557A pdb=" N LYS B1058 " --> pdb=" O MET B1054 " (cutoff:3.500A) Processing helix chain 'B' and resid 1087 through 1098 removed outlier: 3.569A pdb=" N GLY B1098 " --> pdb=" O GLN B1094 " (cutoff:3.500A) Processing helix chain 'B' and resid 1099 through 1108 removed outlier: 3.799A pdb=" N LEU B1103 " --> pdb=" O ALA B1099 " (cutoff:3.500A) Processing helix chain 'B' and resid 1152 through 1164 Processing helix chain 'C' and resid 27 through 38 removed outlier: 3.534A pdb=" N ALA C 31 " --> pdb=" O ASP C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 70 removed outlier: 3.718A pdb=" N GLY C 69 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU C 70 " --> pdb=" O HIS C 66 " (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 removed outlier: 3.544A pdb=" N GLU C 202 " --> pdb=" O LYS C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 271 removed outlier: 4.078A pdb=" N VAL C 245 " --> pdb=" O PRO C 241 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU C 246 " --> pdb=" O GLU C 242 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL C 271 " --> pdb=" O ILE C 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 50 Processing helix chain 'D' and resid 58 through 71 Processing helix chain 'D' and resid 76 through 90 Processing helix chain 'D' and resid 93 through 104 Processing helix chain 'D' and resid 107 through 115 Processing helix chain 'D' and resid 116 through 119 Processing helix chain 'D' and resid 123 through 138 Processing helix chain 'E' and resid 2 through 24 Processing helix chain 'E' and resid 29 through 34 Processing helix chain 'E' and resid 36 through 45 Processing helix chain 'E' and resid 83 through 98 Processing helix chain 'E' and resid 111 through 121 removed outlier: 4.396A pdb=" N MET E 121 " --> pdb=" O SER E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 136 Processing helix chain 'E' and resid 138 through 142 removed outlier: 3.545A pdb=" N GLU E 141 " --> pdb=" O ASN E 138 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 163 Processing helix chain 'E' and resid 166 through 170 removed outlier: 3.579A pdb=" N LEU E 170 " --> pdb=" O GLU E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 184 Processing helix chain 'F' and resid 58 through 75 Processing helix chain 'F' and resid 88 through 100 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 35 Processing helix chain 'H' and resid 129 through 133 removed outlier: 3.735A pdb=" N HIS H 133 " --> pdb=" O ALA H 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 129 through 133' Processing helix chain 'I' and resid 63 through 67 Processing helix chain 'I' and resid 69 through 75 Processing helix chain 'J' and resid 17 through 28 Processing helix chain 'J' and resid 30 through 38 removed outlier: 3.548A pdb=" N ASP J 36 " --> pdb=" O GLY J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 42 through 51 removed outlier: 3.617A pdb=" N ARG J 46 " --> pdb=" O ARG J 42 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 3.833A 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 51 removed outlier: 3.530A pdb=" N GLY K 43 " --> pdb=" O ASP K 39 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 113 removed outlier: 3.815A pdb=" N LEU K 100 " --> pdb=" O SER K 96 " (cutoff:3.500A) Processing sheet with id=AA, first strand: chain 'A' and resid 1448 through 1449 Processing sheet with id=AB, first strand: chain 'A' and resid 86 through 95 removed outlier: 10.180A pdb=" N LEU A 90 " --> pdb=" O PRO A 254 " (cutoff:3.500A) removed outlier: 11.164A pdb=" N LYS A 92 " --> pdb=" O VAL A 252 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N VAL A 252 " --> pdb=" O LYS A 92 " (cutoff:3.500A) Processing sheet with id=AC, first strand: chain 'A' and resid 190 through 194 removed outlier: 4.511A pdb=" N LEU A 198 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA A 200 " --> pdb=" O ILE A 214 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE A 214 " --> pdb=" O ALA A 200 " (cutoff:3.500A) Processing sheet with id=AD, first strand: chain 'A' and resid 264 through 266 removed outlier: 3.581A pdb=" N ALA A 270 " --> pdb=" O MET A 266 " (cutoff:3.500A) Processing sheet with id=AE, first strand: chain 'A' and resid 329 through 331 removed outlier: 6.936A pdb=" N ARG A 334 " --> pdb=" O GLN A 330 " (cutoff:3.500A) Processing sheet with id=AF, first strand: chain 'A' and resid 357 through 358 Processing sheet with id=AG, first strand: chain 'A' and resid 362 through 369 removed outlier: 3.676A pdb=" N THR A 365 " --> pdb=" O MET A 501 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU A 484 " --> pdb=" O THR A 368 " (cutoff:3.500A) Processing sheet with id=AH, first strand: chain 'A' and resid 389 through 393 removed outlier: 6.570A pdb=" N LYS A 445 " --> pdb=" O ILE A 419 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ILE A 419 " --> pdb=" O LYS A 445 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N GLU A 447 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing sheet with id=AI, first strand: chain 'A' and resid 554 through 555 Processing sheet with id=AJ, first strand: chain 'A' and resid 579 through 581 removed outlier: 6.685A pdb=" N VAL H 91 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N HIS H 29 " --> pdb=" O LYS H 13 " (cutoff:3.500A) Processing sheet with id=AK, first strand: chain 'A' and resid 628 through 631 removed outlier: 6.615A pdb=" N VAL A 629 " --> pdb=" O ILE A 636 " (cutoff:3.500A) Processing sheet with id=AL, first strand: chain 'A' and resid 789 through 790 Processing sheet with id=AM, first strand: chain 'A' and resid 792 through 793 Processing sheet with id=AN, first strand: chain 'A' and resid 872 through 873 removed outlier: 6.733A pdb=" N VAL A 879 " --> pdb=" O VAL A 887 " (cutoff:3.500A) Processing sheet with id=AO, first strand: chain 'A' and resid 902 through 905 Processing sheet with id=AP, first strand: chain 'A' and resid 1306 through 1310 removed outlier: 3.748A pdb=" N LYS A1306 " --> pdb=" O ASP A1339 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR A1358 " --> pdb=" O THR A1140 " (cutoff:3.500A) Processing sheet with id=AQ, first strand: chain 'A' and resid 1243 through 1247 removed outlier: 4.328A pdb=" N LEU A1255 " --> pdb=" O LEU A1216 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ILE A1261 " --> pdb=" O TRP A1210 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N TRP A1210 " --> pdb=" O ILE A1261 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LEU A1211 " --> pdb=" O ILE A1175 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ILE A1175 " --> pdb=" O LEU A1211 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ARG A1213 " --> pdb=" O THR A1173 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N THR A1173 " --> pdb=" O ARG A1213 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N GLU A1215 " --> pdb=" O ALA A1171 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N ALA A1171 " --> pdb=" O LYS I 57 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N LYS I 57 " --> pdb=" O ALA A1171 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N THR A1173 " --> pdb=" O VAL I 55 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N VAL I 55 " --> pdb=" O THR A1173 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ILE A1175 " --> pdb=" O ILE I 53 " (cutoff:3.500A) Processing sheet with id=AR, first strand: chain 'A' and resid 1319 through 1322 removed outlier: 3.551A pdb=" N LYS A1319 " --> pdb=" O LEU A1331 " (cutoff:3.500A) Processing sheet with id=DA, first strand: chain 'D' and resid 30 through 31 removed outlier: 3.567A pdb=" N GLU D 30 " --> pdb=" O HIS G 4 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL G 66 " --> pdb=" O LEU G 13 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N GLY G 57 " --> pdb=" O LEU A1475 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N LEU A1473 " --> pdb=" O ILE G 59 " (cutoff:3.500A) Processing sheet with id=DB, first strand: chain 'D' and resid 30 through 31 removed outlier: 3.567A pdb=" N GLU D 30 " --> pdb=" O HIS G 4 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL G 66 " --> pdb=" O LEU G 13 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N PHE G 44 " --> pdb=" O ILE G 75 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N ILE G 46 " --> pdb=" O PHE G 77 " (cutoff:3.500A) Processing sheet with id=BA, first strand: chain 'B' and resid 65 through 67 removed outlier: 5.941A pdb=" N TYR B 84 " --> pdb=" O ILE B 133 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ILE B 133 " --> pdb=" O TYR B 84 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N LEU B 86 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N THR B 131 " --> pdb=" O LEU B 86 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N PHE B 88 " --> pdb=" O THR B 129 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N THR B 129 " --> pdb=" O PHE B 88 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLN B 90 " --> pdb=" O ASP B 127 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ALA B 122 " --> pdb=" O GLY B 150 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N GLY B 150 " --> pdb=" O ALA B 122 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N LEU B 124 " --> pdb=" O PHE B 148 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N PHE B 148 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N VAL B 126 " --> pdb=" O LYS B 146 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LYS B 146 " --> pdb=" O VAL B 126 " (cutoff:3.500A) Processing sheet with id=BB, first strand: chain 'B' and resid 97 through 99 Processing sheet with id=BC, first strand: chain 'B' and resid 185 through 187 removed outlier: 3.643A pdb=" N GLN B 468 " --> pdb=" O VAL B 193 " (cutoff:3.500A) Processing sheet with id=BD, first strand: chain 'B' and resid 391 through 394 removed outlier: 3.838A pdb=" N ALA B 196 " --> pdb=" O ARG B 484 " (cutoff:3.500A) Processing sheet with id=BE, first strand: chain 'B' and resid 205 through 208 removed outlier: 4.576A pdb=" N TYR B 215 " --> pdb=" O MET B 239 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N MET B 239 " --> pdb=" O TYR B 215 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N TYR B 217 " --> pdb=" O VAL B 237 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N VAL B 237 " --> pdb=" O TYR B 217 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N GLY B 219 " --> pdb=" O ILE B 235 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N ILE B 235 " --> pdb=" O GLY B 219 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N CYS B 221 " --> pdb=" O SER B 233 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N SER B 233 " --> pdb=" O CYS B 221 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N SER B 223 " --> pdb=" O PRO B 231 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N LEU B 225 " --> pdb=" O SER B 229 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N SER B 229 " --> pdb=" O LEU B 225 " (cutoff:3.500A) Processing sheet with id=BF, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=BG, first strand: chain 'B' and resid 632 through 633 Processing sheet with id=BH, first strand: chain 'B' and resid 662 through 666 Processing sheet with id=BI, first strand: chain 'B' and resid 675 through 676 Processing sheet with id=BJ, first strand: chain 'B' and resid 675 through 676 Processing sheet with id=BK, first strand: chain 'B' and resid 572 through 577 removed outlier: 5.111A pdb=" N TRP B 573 " --> pdb=" O VAL B 569 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL B 569 " --> pdb=" O TRP B 573 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY B 575 " --> pdb=" O ILE B 567 " (cutoff:3.500A) Processing sheet with id=BL, first strand: chain 'B' and resid 748 through 751 removed outlier: 6.405A pdb=" N PHE B 918 " --> pdb=" O VAL B 909 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N VAL B 909 " --> pdb=" O PHE B 918 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N LYS B 920 " --> pdb=" O VAL B 907 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N VAL B 907 " --> pdb=" O LYS B 920 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ARG B 922 " --> pdb=" O ASP B 905 " (cutoff:3.500A) Processing sheet with id=BM, first strand: chain 'B' and resid 748 through 751 removed outlier: 6.405A pdb=" N PHE B 918 " --> pdb=" O VAL B 909 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N VAL B 909 " --> pdb=" O PHE B 918 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N LYS B 920 " --> pdb=" O VAL B 907 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N VAL B 907 " --> pdb=" O LYS B 920 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ARG B 922 " --> pdb=" O ASP B 905 " (cutoff:3.500A) Processing sheet with id=BN, first strand: chain 'B' and resid 759 through 760 Processing sheet with id=BO, first strand: chain 'B' and resid 776 through 782 removed outlier: 4.116A pdb=" N PHE B1042 " --> pdb=" O ILE B 782 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 1025 through 1026 current: chain 'B' and resid 942 through 949 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 934 through 937 current: chain 'B' and resid 965 through 967 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 965 through 967 current: chain 'B' and resid 776 through 782 Processing sheet with id=BP, first strand: chain 'B' and resid 827 through 829 Processing sheet with id=BQ, first strand: chain 'B' and resid 865 through 867 removed outlier: 7.148A pdb=" N THR B 894 " --> pdb=" O ILE B 866 " (cutoff:3.500A) Processing sheet with id=BR, first strand: chain 'B' and resid 1115 through 1119 Processing sheet with id=BS, first strand: chain 'B' and resid 1127 through 1128 Processing sheet with id=CA, first strand: chain 'C' and resid 8 through 14 removed outlier: 6.651A pdb=" N LYS C 20 " --> pdb=" O THR C 12 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N LEU C 14 " --> pdb=" O ASN C 18 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ASN C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE C 21 " --> pdb=" O TYR C 231 " (cutoff:3.500A) Processing sheet with id=CB, first strand: chain 'C' and resid 121 through 122 removed outlier: 5.826A pdb=" N GLU C 158 " --> pdb=" O ALA C 54 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ALA C 54 " --> pdb=" O GLU C 158 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N ARG C 160 " --> pdb=" O ILE C 52 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N ILE C 52 " --> pdb=" O ARG C 160 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N ARG C 162 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N VAL C 50 " --> pdb=" O ARG C 162 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N TYR C 164 " --> pdb=" O ASP C 48 " (cutoff:3.500A) Processing sheet with id=CC, first strand: chain 'C' and resid 113 through 116 removed outlier: 6.686A pdb=" N ARG C 113 " --> pdb=" O LYS C 152 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N LYS C 152 " --> pdb=" O ARG C 113 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N VAL C 115 " --> pdb=" O ILE C 150 " (cutoff:3.500A) Processing sheet with id=EA, first strand: chain 'E' and resid 60 through 61 removed outlier: 3.842A pdb=" N GLU E 128 " --> pdb=" O ALA E 102 " (cutoff:3.500A) Processing sheet with id=EB, first strand: chain 'E' and resid 81 through 82 removed outlier: 3.671A pdb=" N VAL E 82 " --> pdb=" O GLY E 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=EB Processing sheet with id=EC, first strand: chain 'E' and resid 147 through 150 removed outlier: 3.524A pdb=" N GLU E 147 " --> pdb=" O ILE E 194 " (cutoff:3.500A) Processing sheet with id=GA, first strand: chain 'G' and resid 84 through 92 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 142 through 153 current: chain 'G' and resid 142 through 153 Processing sheet with id=GB, first strand: chain 'G' and resid 118 through 120 Processing sheet with id=IA, first strand: chain 'I' and resid 25 through 28 removed outlier: 3.523A pdb=" N TYR I 25 " --> pdb=" O ALA I 38 " (cutoff:3.500A) Processing sheet with id=IB, first strand: chain 'I' and resid 80 through 81 removed outlier: 3.591A pdb=" N TYR I 112 " --> pdb=" O TRP I 123 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TRP I 123 " --> pdb=" O TYR I 112 " (cutoff:3.500A) Processing sheet with id=KA, first strand: chain 'K' and resid 19 through 23 removed outlier: 6.425A pdb=" N ILE K 72 " --> pdb=" O TYR K 61 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N TYR K 61 " --> pdb=" O ILE K 72 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ARG K 74 " --> pdb=" O ALA K 59 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ALA K 59 " --> pdb=" O ARG K 74 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N GLN K 76 " --> pdb=" O LEU K 57 " (cutoff:3.500A) 1248 hydrogen bonds defined for protein. 3504 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 78 hydrogen bonds 156 hydrogen bond angles 0 basepair planarities 32 basepair parallelities 64 stacking parallelities Total time for adding SS restraints: 10.40 Time building geometry restraints manager: 3.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8173 1.33 - 1.45: 6392 1.45 - 1.57: 18463 1.57 - 1.69: 152 1.69 - 1.82: 312 Bond restraints: 33492 Sorted by residual: bond pdb=" O3' DT T 26 " pdb=" P DT T 27 " ideal model delta sigma weight residual 1.607 1.416 0.191 1.20e-02 6.94e+03 2.54e+02 bond pdb=" C ILE F 102 " pdb=" N PRO F 103 " ideal model delta sigma weight residual 1.334 1.564 -0.230 2.34e-02 1.83e+03 9.64e+01 bond pdb=" C1' DC N 8 " pdb=" N1 DC N 8 " ideal model delta sigma weight residual 1.468 1.556 -0.088 1.40e-02 5.10e+03 3.95e+01 bond pdb=" C1' DT N 6 " pdb=" N1 DT N 6 " ideal model delta sigma weight residual 1.468 1.556 -0.088 1.40e-02 5.10e+03 3.95e+01 bond pdb=" C1' DT N 9 " pdb=" N1 DT N 9 " ideal model delta sigma weight residual 1.468 1.556 -0.088 1.40e-02 5.10e+03 3.94e+01 ... (remaining 33487 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.10: 45222 3.10 - 6.20: 329 6.20 - 9.31: 35 9.31 - 12.41: 1 12.41 - 15.51: 4 Bond angle restraints: 45591 Sorted by residual: angle pdb=" C3' DT T 26 " pdb=" O3' DT T 26 " pdb=" P DT T 27 " ideal model delta sigma weight residual 119.70 133.35 -13.65 1.20e+00 6.94e-01 1.29e+02 angle pdb=" O3' DT T 26 " pdb=" P DT T 27 " pdb=" O5' DT T 27 " ideal model delta sigma weight residual 104.00 119.51 -15.51 1.90e+00 2.77e-01 6.66e+01 angle pdb=" N3 DT N 32 " pdb=" C4 DT N 32 " pdb=" O4 DT N 32 " ideal model delta sigma weight residual 119.90 122.76 -2.86 6.00e-01 2.78e+00 2.27e+01 angle pdb=" N3 DT T 5 " pdb=" C4 DT T 5 " pdb=" O4 DT T 5 " ideal model delta sigma weight residual 119.90 122.73 -2.83 6.00e-01 2.78e+00 2.22e+01 angle pdb=" O4' DC T 19 " pdb=" C4' DC T 19 " pdb=" C3' DC T 19 " ideal model delta sigma weight residual 106.00 103.18 2.82 6.00e-01 2.78e+00 2.22e+01 ... (remaining 45586 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.81: 19975 33.81 - 67.63: 327 67.63 - 101.44: 13 101.44 - 135.25: 2 135.25 - 169.06: 2 Dihedral angle restraints: 20319 sinusoidal: 8985 harmonic: 11334 Sorted by residual: dihedral pdb=" CA LYS B 497 " pdb=" C LYS B 497 " pdb=" N PRO B 498 " pdb=" CA PRO B 498 " ideal model delta harmonic sigma weight residual 180.00 118.91 61.09 0 5.00e+00 4.00e-02 1.49e+02 dihedral pdb=" CA LYS A 910 " pdb=" C LYS A 910 " pdb=" N PRO A 911 " pdb=" CA PRO A 911 " ideal model delta harmonic sigma weight residual 180.00 137.77 42.23 0 5.00e+00 4.00e-02 7.13e+01 dihedral pdb=" CA PHE K 7 " pdb=" C PHE K 7 " pdb=" N GLU K 8 " pdb=" CA GLU K 8 " ideal model delta harmonic sigma weight residual 180.00 138.92 41.08 0 5.00e+00 4.00e-02 6.75e+01 ... (remaining 20316 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 3840 0.050 - 0.101: 928 0.101 - 0.151: 304 0.151 - 0.201: 14 0.201 - 0.252: 18 Chirality restraints: 5104 Sorted by residual: chirality pdb=" P G P 13 " pdb=" OP1 G P 13 " pdb=" OP2 G P 13 " pdb=" O5' G P 13 " both_signs ideal model delta sigma weight residual True 2.17 -2.42 -0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" P A P 12 " pdb=" OP1 A P 12 " pdb=" OP2 A P 12 " pdb=" O5' A P 12 " both_signs ideal model delta sigma weight residual True 2.17 -2.42 -0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" P U P 9 " pdb=" OP1 U P 9 " pdb=" OP2 U P 9 " pdb=" O5' U P 9 " both_signs ideal model delta sigma weight residual True 2.17 -2.42 -0.24 2.00e-01 2.50e+01 1.48e+00 ... (remaining 5101 not shown) Planarity restraints: 5635 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 497 " -0.048 5.00e-02 4.00e+02 7.29e-02 8.50e+00 pdb=" N PRO B 498 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO B 498 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 498 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 988 " 0.017 2.00e-02 2.50e+03 1.76e-02 7.71e+00 pdb=" CG TRP A 988 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP A 988 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP A 988 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP A 988 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP A 988 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 988 " 0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 988 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 988 " -0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP A 988 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 573 " 0.011 2.00e-02 2.50e+03 1.51e-02 5.68e+00 pdb=" CG TRP B 573 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP B 573 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP B 573 " 0.013 2.00e-02 2.50e+03 pdb=" NE1 TRP B 573 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP B 573 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 573 " 0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 573 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 573 " -0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP B 573 " 0.006 2.00e-02 2.50e+03 ... (remaining 5632 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 359 2.61 - 3.18: 28840 3.18 - 3.75: 48857 3.75 - 4.33: 71287 4.33 - 4.90: 115074 Nonbonded interactions: 264417 Sorted by model distance: nonbonded pdb=" N1 DA N 13 " pdb=" O2 DT T 27 " model vdw 2.034 3.120 nonbonded pdb=" O PHE A 312 " pdb=" OG1 THR A 316 " model vdw 2.101 3.040 nonbonded pdb=" O ASN D 34 " pdb=" OG1 THR D 68 " model vdw 2.114 3.040 nonbonded pdb=" O3' C P 20 " pdb="MG MG A2490 " model vdw 2.127 2.170 nonbonded pdb=" OD2 ASP B 851 " pdb=" OH TYR L 17 " model vdw 2.161 3.040 ... (remaining 264412 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.630 Check model and map are aligned: 0.120 Set scattering table: 0.120 Process input model: 38.900 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.080 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6639 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 : 0.007 0.488 33523 Z= 0.344 Angle : 0.918 52.727 45630 Z= 0.483 Chirality : 0.050 0.252 5104 Planarity : 0.004 0.073 5635 Dihedral : 11.481 169.063 12989 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.61 (0.11), residues: 3858 helix: -2.50 (0.11), residues: 1230 sheet: -1.29 (0.17), residues: 577 loop : -1.27 (0.12), residues: 2051 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 807 TYR 0.033 0.002 TYR B 752 PHE 0.024 0.002 PHE H 88 TRP 0.045 0.003 TRP A 988 HIS 0.015 0.002 HIS B 939 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.27 (33492) covalent geometry : angle 0.75838 / 0.47 (45591) hydrogen bonds : bond 0.15958 / 10.38 ( 1288) hydrogen bonds : angle 9.31485 / 6.52 ( 3660) metal coordination : bond 0.19867 / 12.00 ( 31) metal coordination : angle 17.68534 / 11.52 ( 39) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7716 Ramachandran restraints generated. 3858 Oldfield, 0 Emsley, 3858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7716 Ramachandran restraints generated. 3858 Oldfield, 0 Emsley, 3858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 949 residues out of total 3448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 949 time to evaluate : 1.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LYS cc_start: 0.7732 (mttp) cc_final: 0.7429 (mttp) REVERT: A 58 MET cc_start: 0.7496 (ttp) cc_final: 0.7010 (ttp) REVERT: A 116 LYS cc_start: 0.6761 (mttt) cc_final: 0.6461 (mtmm) REVERT: A 119 VAL cc_start: 0.8255 (t) cc_final: 0.8052 (m) REVERT: A 138 LYS cc_start: 0.6846 (tttm) cc_final: 0.6626 (ttmm) REVERT: A 152 ASN cc_start: 0.7672 (m-40) cc_final: 0.7015 (t0) REVERT: A 186 ARG cc_start: 0.7738 (mtt180) cc_final: 0.7514 (mtp85) REVERT: A 214 ILE cc_start: 0.7850 (pt) cc_final: 0.7552 (pt) REVERT: A 223 GLU cc_start: 0.6500 (mt-10) cc_final: 0.5909 (tm-30) REVERT: A 235 VAL cc_start: 0.8125 (t) cc_final: 0.7893 (t) REVERT: A 238 MET cc_start: 0.7688 (mtm) cc_final: 0.7247 (mtt) REVERT: A 266 MET cc_start: 0.1429 (mmm) cc_final: 0.0554 (tpt) REVERT: A 321 GLU cc_start: 0.6639 (mt-10) cc_final: 0.6224 (tm-30) REVERT: A 355 MET cc_start: 0.8890 (mmm) cc_final: 0.8689 (mmm) REVERT: A 397 PHE cc_start: 0.7485 (m-80) cc_final: 0.7246 (m-80) REVERT: A 438 LEU cc_start: 0.7230 (mt) cc_final: 0.6936 (mp) REVERT: A 441 GLN cc_start: 0.6965 (pt0) cc_final: 0.6722 (mt0) REVERT: A 461 GLN cc_start: 0.8232 (mp10) cc_final: 0.7682 (mp10) REVERT: A 571 ASP cc_start: 0.8538 (m-30) cc_final: 0.7754 (t0) REVERT: A 642 LYS cc_start: 0.7620 (tttt) cc_final: 0.7048 (ttmm) REVERT: A 643 LYS cc_start: 0.7595 (mttp) cc_final: 0.6989 (mttt) REVERT: A 678 ASN cc_start: 0.7879 (m-40) cc_final: 0.7529 (m-40) REVERT: A 723 ASN cc_start: 0.7257 (t0) cc_final: 0.6690 (m-40) REVERT: A 758 LYS cc_start: 0.7082 (mttt) cc_final: 0.6512 (mmtt) REVERT: A 778 LYS cc_start: 0.7489 (mttt) cc_final: 0.7074 (mttm) REVERT: A 803 LYS cc_start: 0.7128 (mttt) cc_final: 0.6835 (mmmt) REVERT: A 845 GLU cc_start: 0.6241 (tt0) cc_final: 0.5978 (tt0) REVERT: A 849 ASP cc_start: 0.6925 (m-30) cc_final: 0.6723 (m-30) REVERT: A 899 GLU cc_start: 0.7657 (pt0) cc_final: 0.6874 (mp0) REVERT: A 917 GLU cc_start: 0.6952 (tt0) cc_final: 0.6394 (pt0) REVERT: A 918 LYS cc_start: 0.7265 (ttpp) cc_final: 0.7057 (tppt) REVERT: A 926 ASN cc_start: 0.7194 (m-40) cc_final: 0.6939 (m110) REVERT: A 928 ARG cc_start: 0.8348 (mtp-110) cc_final: 0.7990 (ttp-170) REVERT: A 932 ARG cc_start: 0.6886 (tpt170) cc_final: 0.6208 (tpt90) REVERT: A 1034 GLN cc_start: 0.7162 (tt0) cc_final: 0.6801 (tt0) REVERT: A 1097 GLU cc_start: 0.7001 (tm-30) cc_final: 0.6577 (tm-30) REVERT: A 1167 ARG cc_start: 0.7184 (ttp-110) cc_final: 0.6854 (ttt90) REVERT: A 1225 LYS cc_start: 0.7715 (mttt) cc_final: 0.7424 (mmtt) REVERT: A 1279 MET cc_start: 0.6465 (mmm) cc_final: 0.6065 (ttt) REVERT: A 1284 PHE cc_start: 0.6694 (t80) cc_final: 0.6231 (t80) REVERT: A 1303 GLN cc_start: 0.8507 (mt0) cc_final: 0.8136 (mp10) REVERT: A 1306 LYS cc_start: 0.6587 (mttt) cc_final: 0.5880 (mmmt) REVERT: A 1333 GLU cc_start: 0.7933 (pt0) cc_final: 0.7520 (mt-10) REVERT: A 1334 TRP cc_start: 0.8932 (m100) cc_final: 0.8565 (m100) REVERT: A 1350 LYS cc_start: 0.6810 (tttm) cc_final: 0.6535 (ttpp) REVERT: A 1351 ASP cc_start: 0.7138 (m-30) cc_final: 0.6709 (m-30) REVERT: A 1376 LYS cc_start: 0.6558 (ttmm) cc_final: 0.5796 (tptt) REVERT: A 1476 ASP cc_start: 0.4691 (t0) cc_final: 0.4430 (t0) REVERT: B 21 LEU cc_start: 0.6517 (tp) cc_final: 0.6245 (tp) REVERT: B 24 GLU cc_start: 0.7307 (tp30) cc_final: 0.7089 (tt0) REVERT: B 53 MET cc_start: 0.6991 (mmm) cc_final: 0.6496 (mmm) REVERT: B 155 MET cc_start: 0.7758 (ttm) cc_final: 0.7071 (ttm) REVERT: B 170 ASP cc_start: 0.7835 (m-30) cc_final: 0.7393 (m-30) REVERT: B 174 LEU cc_start: 0.7201 (mt) cc_final: 0.6917 (mp) REVERT: B 198 GLU cc_start: 0.7095 (tt0) cc_final: 0.6573 (tt0) REVERT: B 200 MET cc_start: 0.8017 (ttm) cc_final: 0.7591 (tpp) REVERT: B 229 SER cc_start: 0.8138 (t) cc_final: 0.7933 (p) REVERT: B 345 LYS cc_start: 0.7580 (mptt) cc_final: 0.7201 (mmtm) REVERT: B 420 GLN cc_start: 0.5661 (tt0) cc_final: 0.5358 (tp-100) REVERT: B 436 LYS cc_start: 0.6318 (mttp) cc_final: 0.5440 (ttpp) REVERT: B 488 PRO cc_start: 0.7938 (Cg_endo) cc_final: 0.7736 (Cg_exo) REVERT: B 543 GLU cc_start: 0.7203 (mt-10) cc_final: 0.6776 (tm-30) REVERT: B 547 GLU cc_start: 0.7689 (mm-30) cc_final: 0.7036 (mm-30) REVERT: B 551 GLU cc_start: 0.7585 (mt-10) cc_final: 0.7142 (mp0) REVERT: B 627 ILE cc_start: 0.8863 (mt) cc_final: 0.8578 (mt) REVERT: B 665 ILE cc_start: 0.7808 (mt) cc_final: 0.7537 (mm) REVERT: B 671 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7496 (mt-10) REVERT: B 724 TYR cc_start: 0.7060 (m-80) cc_final: 0.6625 (m-10) REVERT: B 739 ASN cc_start: 0.7091 (p0) cc_final: 0.6796 (p0) REVERT: B 765 GLU cc_start: 0.7435 (tt0) cc_final: 0.7106 (mm-30) REVERT: B 796 MET cc_start: 0.8472 (mtm) cc_final: 0.8093 (mtp) REVERT: B 827 GLU cc_start: 0.7583 (mt-10) cc_final: 0.6794 (mp0) REVERT: B 830 GLU cc_start: 0.7688 (pt0) cc_final: 0.7332 (pt0) REVERT: B 846 ASP cc_start: 0.7694 (m-30) cc_final: 0.7487 (p0) REVERT: B 900 GLU cc_start: 0.6859 (tt0) cc_final: 0.6246 (mt-10) REVERT: B 975 ARG cc_start: 0.7019 (mtt90) cc_final: 0.6655 (mtt180) REVERT: B 976 MET cc_start: 0.8151 (mtm) cc_final: 0.7941 (mtm) REVERT: B 1004 ASP cc_start: 0.7489 (m-30) cc_final: 0.6916 (t70) REVERT: B 1026 GLU cc_start: 0.8125 (tt0) cc_final: 0.7323 (tp30) REVERT: B 1071 ASN cc_start: 0.8221 (m-40) cc_final: 0.8007 (m-40) REVERT: B 1092 ASP cc_start: 0.6659 (m-30) cc_final: 0.6355 (m-30) REVERT: B 1124 ILE cc_start: 0.7867 (mt) cc_final: 0.7661 (mt) REVERT: B 1141 ARG cc_start: 0.7242 (mmt-90) cc_final: 0.6567 (mtm-85) REVERT: C 17 GLU cc_start: 0.7504 (mt-10) cc_final: 0.7256 (pm20) REVERT: C 39 ILE cc_start: 0.7257 (mt) cc_final: 0.6977 (mt) REVERT: C 81 LYS cc_start: 0.7592 (mtpt) cc_final: 0.7144 (mmtm) REVERT: C 113 ARG cc_start: 0.7003 (ttt180) cc_final: 0.6727 (ttm-80) REVERT: C 121 ILE cc_start: 0.7527 (mt) cc_final: 0.7286 (mm) REVERT: C 240 ARG cc_start: 0.7322 (mtp180) cc_final: 0.6850 (mtp-110) REVERT: D 106 GLU cc_start: 0.4117 (mt-10) cc_final: 0.3259 (pm20) REVERT: E 5 GLU cc_start: 0.5535 (mt-10) cc_final: 0.5299 (tp30) REVERT: E 38 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7501 (mm-30) REVERT: E 88 LYS cc_start: 0.8209 (tptm) cc_final: 0.7965 (mtmt) REVERT: E 94 MET cc_start: 0.7168 (mmm) cc_final: 0.6884 (mmm) REVERT: E 106 VAL cc_start: 0.6656 (t) cc_final: 0.6233 (t) REVERT: E 108 GLN cc_start: 0.7722 (mt0) cc_final: 0.7311 (mm-40) REVERT: E 117 SER cc_start: 0.7306 (m) cc_final: 0.6851 (m) REVERT: E 164 LYS cc_start: 0.7626 (mttt) cc_final: 0.7388 (mtmm) REVERT: E 166 ARG cc_start: 0.7322 (mtt180) cc_final: 0.6859 (mtm110) REVERT: E 172 ARG cc_start: 0.6950 (mtt180) cc_final: 0.6713 (mtm180) REVERT: E 186 LYS cc_start: 0.7377 (mtpt) cc_final: 0.6931 (mmmt) REVERT: E 192 LYS cc_start: 0.7356 (tttt) cc_final: 0.6955 (tttm) REVERT: F 53 THR cc_start: 0.8782 (p) cc_final: 0.8549 (p) REVERT: G 15 PRO cc_start: 0.7921 (Cg_exo) cc_final: 0.7673 (Cg_endo) REVERT: G 45 VAL cc_start: 0.5063 (t) cc_final: 0.4861 (m) REVERT: G 66 VAL cc_start: 0.6686 (p) cc_final: 0.6206 (m) REVERT: H 4 ILE cc_start: 0.8494 (mt) cc_final: 0.7977 (mm) REVERT: H 20 LYS cc_start: 0.8464 (tttt) cc_final: 0.8250 (ttpp) REVERT: H 37 MET cc_start: 0.7158 (mtp) cc_final: 0.6944 (mtp) REVERT: H 55 LYS cc_start: 0.7168 (mttt) cc_final: 0.6699 (mtpp) REVERT: H 62 SER cc_start: 0.8371 (m) cc_final: 0.7998 (p) REVERT: H 146 LYS cc_start: 0.7244 (tttt) cc_final: 0.6673 (ttpt) REVERT: I 22 ASN cc_start: 0.7674 (m-40) cc_final: 0.7398 (t0) REVERT: I 27 LYS cc_start: 0.6644 (tttt) cc_final: 0.6412 (pttt) REVERT: I 37 TYR cc_start: 0.6955 (m-80) cc_final: 0.6579 (m-80) REVERT: I 41 ASN cc_start: 0.7123 (m-40) cc_final: 0.6067 (p0) REVERT: I 93 GLU cc_start: 0.7356 (mt-10) cc_final: 0.7094 (tt0) REVERT: I 109 ARG cc_start: 0.8197 (mtt180) cc_final: 0.7913 (ptp-110) REVERT: J 31 GLU cc_start: 0.6591 (mp0) cc_final: 0.6296 (mp0) REVERT: K 2 ASN cc_start: 0.6937 (m-40) cc_final: 0.5990 (m-40) REVERT: K 23 LYS cc_start: 0.8357 (mttt) cc_final: 0.7920 (tptt) REVERT: K 69 HIS cc_start: 0.7303 (m-70) cc_final: 0.6746 (m90) REVERT: K 74 ARG cc_start: 0.7895 (ttt-90) cc_final: 0.7532 (ttt-90) REVERT: L 21 GLU cc_start: 0.6429 (tp30) cc_final: 0.6202 (tp30) outliers start: 0 outliers final: 0 residues processed: 949 average time/residue: 0.2514 time to fit residues: 362.5187 Evaluate side-chains 565 residues out of total 3448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 565 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 197 optimal weight: 10.0000 chunk 388 optimal weight: 9.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 62 GLN A 278 HIS A 330 GLN A 449 HIS ** A 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 472 HIS A 671 ASN A 673 GLN A 721 HIS A 757 GLN A 791 GLN ** A 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 839 HIS A1024 ASN A1082 HIS A1093 GLN A1163 HIS A1220 HIS A1248 ASN A1310 HIS A1462 GLN B 117 ASN B 245 GLN B 312 GLN B 370 HIS B 582 GLN B 639 HIS B 699 HIS ** B 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 749 HIS B 825 GLN B 912 ASN ** B 992 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1021 HIS B1117 HIS B1120 ASN ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 48 ASN G 4 HIS G 14 HIS H 46 GLN I 41 ASN I 118 HIS L 26 ASN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.182460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.141427 restraints weight = 38446.715| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 2.15 r_work: 0.3266 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 33523 Z= 0.262 Angle : 0.774 14.909 45630 Z= 0.398 Chirality : 0.051 0.385 5104 Planarity : 0.006 0.101 5635 Dihedral : 14.192 179.416 5145 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.94 % Favored : 96.03 % Rotamer: Outliers : 1.93 % Allowed : 6.39 % Favored : 91.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.12), residues: 3858 helix: -0.76 (0.13), residues: 1283 sheet: -1.02 (0.18), residues: 613 loop : -1.07 (0.13), residues: 1962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 841 TYR 0.031 0.003 TYR B 811 PHE 0.024 0.002 PHE C 184 TRP 0.028 0.003 TRP A 988 HIS 0.012 0.002 HIS K 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00631 / 0.26 (33492) covalent geometry : angle 0.75428 / 0.40 (45591) hydrogen bonds : bond 0.05429 / 3.68 ( 1288) hydrogen bonds : angle 5.92115 / 4.14 ( 3660) metal coordination : bond 0.01325 / 0.78 ( 31) metal coordination : angle 5.93276 / 4.58 ( 39) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7716 Ramachandran restraints generated. 3858 Oldfield, 0 Emsley, 3858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7716 Ramachandran restraints generated. 3858 Oldfield, 0 Emsley, 3858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 656 residues out of total 3448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 590 time to evaluate : 1.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 MET cc_start: 0.8278 (ttp) cc_final: 0.7987 (ttp) REVERT: A 127 LYS cc_start: 0.7544 (mttt) cc_final: 0.7258 (mttp) REVERT: A 152 ASN cc_start: 0.7620 (m-40) cc_final: 0.7378 (t0) REVERT: A 241 ARG cc_start: 0.8252 (ptm-80) cc_final: 0.7616 (ptp90) REVERT: A 266 MET cc_start: 0.1975 (mmm) cc_final: 0.0877 (tpt) REVERT: A 411 SER cc_start: 0.7896 (m) cc_final: 0.7542 (t) REVERT: A 418 TYR cc_start: 0.8215 (m-80) cc_final: 0.7966 (m-10) REVERT: A 441 GLN cc_start: 0.7884 (pt0) cc_final: 0.7559 (mt0) REVERT: A 687 ILE cc_start: 0.9067 (OUTLIER) cc_final: 0.8836 (mm) REVERT: A 758 LYS cc_start: 0.8199 (mttt) cc_final: 0.7688 (mmtt) REVERT: A 845 GLU cc_start: 0.7895 (tt0) cc_final: 0.7621 (tt0) REVERT: A 849 ASP cc_start: 0.7848 (m-30) cc_final: 0.7527 (m-30) REVERT: A 928 ARG cc_start: 0.8305 (mtp-110) cc_final: 0.7943 (mtp85) REVERT: A 932 ARG cc_start: 0.7054 (tpt170) cc_final: 0.6759 (tpt90) REVERT: A 1008 LYS cc_start: 0.8192 (mttt) cc_final: 0.7707 (ttpp) REVERT: A 1085 GLU cc_start: 0.8368 (tt0) cc_final: 0.8163 (tt0) REVERT: A 1097 GLU cc_start: 0.8038 (tm-30) cc_final: 0.7807 (tm-30) REVERT: A 1135 LYS cc_start: 0.8513 (mttt) cc_final: 0.8073 (mmpt) REVERT: A 1170 THR cc_start: 0.8605 (m) cc_final: 0.8392 (m) REVERT: A 1230 GLN cc_start: 0.8241 (mt0) cc_final: 0.7945 (mt0) REVERT: A 1279 MET cc_start: 0.6696 (mmm) cc_final: 0.6440 (ttt) REVERT: A 1284 PHE cc_start: 0.7650 (t80) cc_final: 0.6970 (t80) REVERT: A 1306 LYS cc_start: 0.8277 (mttt) cc_final: 0.7749 (mmmt) REVERT: A 1376 LYS cc_start: 0.8563 (ttmm) cc_final: 0.8358 (tptt) REVERT: A 1405 MET cc_start: 0.9020 (mtp) cc_final: 0.8653 (mtp) REVERT: A 1476 ASP cc_start: 0.6315 (t0) cc_final: 0.6094 (t0) REVERT: B 200 MET cc_start: 0.8661 (ttm) cc_final: 0.8443 (tpp) REVERT: B 254 GLN cc_start: 0.8211 (mp10) cc_final: 0.7902 (mm-40) REVERT: B 345 LYS cc_start: 0.8600 (mptt) cc_final: 0.8292 (mmtp) REVERT: B 420 GLN cc_start: 0.6706 (tt0) cc_final: 0.6212 (tp-100) REVERT: B 436 LYS cc_start: 0.7525 (mttp) cc_final: 0.6871 (tttt) REVERT: B 488 PRO cc_start: 0.8535 (Cg_endo) cc_final: 0.8131 (Cg_exo) REVERT: B 547 GLU cc_start: 0.8028 (mm-30) cc_final: 0.7513 (mm-30) REVERT: B 847 LYS cc_start: 0.8442 (OUTLIER) cc_final: 0.7976 (mtpp) REVERT: B 900 GLU cc_start: 0.6849 (tt0) cc_final: 0.6538 (mt-10) REVERT: B 1004 ASP cc_start: 0.7567 (m-30) cc_final: 0.7286 (t70) REVERT: B 1092 ASP cc_start: 0.7579 (m-30) cc_final: 0.7288 (m-30) REVERT: B 1118 VAL cc_start: 0.9299 (t) cc_final: 0.8990 (m) REVERT: B 1135 TYR cc_start: 0.8677 (m-80) cc_final: 0.8400 (m-10) REVERT: C 79 VAL cc_start: 0.8901 (t) cc_final: 0.8654 (p) REVERT: C 189 ASP cc_start: 0.6652 (p0) cc_final: 0.6376 (p0) REVERT: C 207 GLU cc_start: 0.7358 (pt0) cc_final: 0.7156 (pt0) REVERT: C 210 GLU cc_start: 0.7682 (mt-10) cc_final: 0.7165 (pt0) REVERT: D 106 GLU cc_start: 0.5935 (mt-10) cc_final: 0.3926 (pm20) REVERT: D 110 GLU cc_start: 0.1772 (tt0) cc_final: 0.1394 (tt0) REVERT: D 119 GLU cc_start: 0.1064 (mm-30) cc_final: 0.0268 (mp0) REVERT: D 125 GLU cc_start: 0.4678 (pt0) cc_final: 0.4406 (pp20) REVERT: E 5 GLU cc_start: 0.6641 (mt-10) cc_final: 0.6368 (tp30) REVERT: E 62 VAL cc_start: 0.9138 (m) cc_final: 0.8849 (p) REVERT: E 172 ARG cc_start: 0.8581 (mtt180) cc_final: 0.8344 (mtm180) REVERT: H 48 TYR cc_start: 0.8281 (t80) cc_final: 0.7879 (t80) REVERT: H 62 SER cc_start: 0.8888 (m) cc_final: 0.8608 (p) REVERT: K 2 ASN cc_start: 0.7686 (m-40) cc_final: 0.6937 (m-40) REVERT: K 29 ASN cc_start: 0.7973 (t0) cc_final: 0.7721 (t0) REVERT: K 74 ARG cc_start: 0.9001 (ttt-90) cc_final: 0.8764 (ttt-90) outliers start: 66 outliers final: 44 residues processed: 635 average time/residue: 0.2263 time to fit residues: 226.4558 Evaluate side-chains 528 residues out of total 3448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 482 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 647 THR Chi-restraints excluded: chain A residue 687 ILE Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 819 SER Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 870 SER Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 937 ASP Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1156 ASP Chi-restraints excluded: chain A residue 1255 LEU Chi-restraints excluded: chain A residue 1389 ASP Chi-restraints excluded: chain A residue 1421 ARG Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 833 THR Chi-restraints excluded: chain B residue 847 LYS Chi-restraints excluded: chain B residue 903 ILE Chi-restraints excluded: chain B residue 914 GLU Chi-restraints excluded: chain B residue 1067 ILE Chi-restraints excluded: chain B residue 1115 GLN Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 99 SER Chi-restraints excluded: chain I residue 108 MET Chi-restraints excluded: chain K residue 48 SER Chi-restraints excluded: chain K residue 107 VAL Chi-restraints excluded: chain L residue 16 ILE Chi-restraints excluded: chain L residue 37 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 177 optimal weight: 0.7980 chunk 320 optimal weight: 6.9990 chunk 8 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 27 optimal weight: 8.9990 chunk 379 optimal weight: 7.9990 chunk 138 optimal weight: 6.9990 chunk 217 optimal weight: 3.9990 chunk 210 optimal weight: 0.0570 chunk 347 optimal weight: 0.0030 overall best weight: 1.7712 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 278 HIS A 353 ASN ** A 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 757 GLN A 804 HIS ** A 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1163 HIS A1417 HIS B 410 ASN ** B 992 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 GLN I 74 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.184139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.143212 restraints weight = 38257.742| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 2.16 r_work: 0.3275 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 33523 Z= 0.158 Angle : 0.646 12.800 45630 Z= 0.333 Chirality : 0.047 0.310 5104 Planarity : 0.005 0.088 5635 Dihedral : 14.001 177.846 5145 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.93 % Allowed : 8.93 % Favored : 89.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 1.08 % 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: -0.88 (0.13), residues: 3858 helix: 0.03 (0.14), residues: 1290 sheet: -0.80 (0.19), residues: 590 loop : -0.85 (0.14), residues: 1978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 841 TYR 0.023 0.002 TYR B 766 PHE 0.027 0.002 PHE B 422 TRP 0.021 0.002 TRP A 988 HIS 0.007 0.001 HIS K 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 (33492) covalent geometry : angle 0.62934 / 0.33 (45591) hydrogen bonds : bond 0.04585 / 3.12 ( 1288) hydrogen bonds : angle 5.31261 / 3.71 ( 3660) metal coordination : bond 0.00951 / 0.57 ( 31) metal coordination : angle 4.95895 / 3.79 ( 39) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7716 Ramachandran restraints generated. 3858 Oldfield, 0 Emsley, 3858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7716 Ramachandran restraints generated. 3858 Oldfield, 0 Emsley, 3858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 3448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 515 time to evaluate : 1.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 LYS cc_start: 0.8801 (OUTLIER) cc_final: 0.8566 (mtmm) REVERT: A 127 LYS cc_start: 0.7550 (mttt) cc_final: 0.7330 (mttp) REVERT: A 241 ARG cc_start: 0.8099 (ptm-80) cc_final: 0.7610 (ptp90) REVERT: A 250 VAL cc_start: 0.9201 (t) cc_final: 0.8849 (p) REVERT: A 266 MET cc_start: 0.1806 (mmm) cc_final: 0.0715 (tpt) REVERT: A 441 GLN cc_start: 0.7805 (pt0) cc_final: 0.7488 (mt0) REVERT: A 540 ASP cc_start: 0.7807 (m-30) cc_final: 0.7496 (m-30) REVERT: A 687 ILE cc_start: 0.9075 (OUTLIER) cc_final: 0.8824 (mm) REVERT: A 758 LYS cc_start: 0.8298 (mttt) cc_final: 0.7748 (mmtt) REVERT: A 845 GLU cc_start: 0.7659 (tt0) cc_final: 0.7341 (tt0) REVERT: A 849 ASP cc_start: 0.7681 (m-30) cc_final: 0.7337 (m-30) REVERT: A 928 ARG cc_start: 0.8248 (mtp-110) cc_final: 0.7884 (mtp85) REVERT: A 932 ARG cc_start: 0.6859 (tpt170) cc_final: 0.6494 (tpt90) REVERT: A 1008 LYS cc_start: 0.8026 (mttt) cc_final: 0.7596 (ttpp) REVERT: A 1097 GLU cc_start: 0.7984 (tm-30) cc_final: 0.7738 (tm-30) REVERT: A 1135 LYS cc_start: 0.8538 (mttt) cc_final: 0.8306 (mttt) REVERT: A 1170 THR cc_start: 0.8573 (m) cc_final: 0.8351 (m) REVERT: A 1306 LYS cc_start: 0.8331 (mttt) cc_final: 0.7816 (mmmt) REVERT: A 1349 GLU cc_start: 0.7505 (tm-30) cc_final: 0.7230 (tp30) REVERT: A 1405 MET cc_start: 0.8937 (mtp) cc_final: 0.8680 (mtp) REVERT: B 53 MET cc_start: 0.7672 (mmm) cc_final: 0.6845 (mtm) REVERT: B 187 ILE cc_start: 0.8863 (OUTLIER) cc_final: 0.8607 (mt) REVERT: B 254 GLN cc_start: 0.8038 (mp10) cc_final: 0.7730 (mm-40) REVERT: B 420 GLN cc_start: 0.6577 (tt0) cc_final: 0.6188 (tp-100) REVERT: B 436 LYS cc_start: 0.7351 (mttp) cc_final: 0.6800 (tttt) REVERT: B 488 PRO cc_start: 0.8491 (Cg_endo) cc_final: 0.8076 (Cg_exo) REVERT: B 847 LYS cc_start: 0.8375 (OUTLIER) cc_final: 0.8012 (mtpp) REVERT: B 900 GLU cc_start: 0.6991 (tt0) cc_final: 0.6770 (mt-10) REVERT: B 1075 MET cc_start: 0.8728 (mmt) cc_final: 0.8495 (mmt) REVERT: B 1089 MET cc_start: 0.8218 (OUTLIER) cc_final: 0.7604 (mtp) REVERT: B 1092 ASP cc_start: 0.7640 (m-30) cc_final: 0.7362 (m-30) REVERT: B 1118 VAL cc_start: 0.9237 (t) cc_final: 0.8976 (m) REVERT: B 1135 TYR cc_start: 0.8583 (m-80) cc_final: 0.8335 (m-10) REVERT: C 189 ASP cc_start: 0.6379 (p0) cc_final: 0.6013 (p0) REVERT: C 207 GLU cc_start: 0.7234 (pt0) cc_final: 0.6995 (pt0) REVERT: C 210 GLU cc_start: 0.7599 (mt-10) cc_final: 0.7148 (pt0) REVERT: C 268 GLN cc_start: 0.6802 (mt0) cc_final: 0.6180 (pt0) REVERT: D 106 GLU cc_start: 0.5866 (mt-10) cc_final: 0.3919 (pm20) REVERT: D 110 GLU cc_start: 0.1635 (tt0) cc_final: 0.1264 (tt0) REVERT: G 10 GLU cc_start: 0.6870 (mt-10) cc_final: 0.6354 (mt-10) REVERT: H 40 ILE cc_start: 0.8551 (mt) cc_final: 0.8214 (tt) REVERT: H 48 TYR cc_start: 0.8256 (t80) cc_final: 0.7955 (t80) REVERT: H 62 SER cc_start: 0.8919 (m) cc_final: 0.8644 (p) REVERT: I 19 GLU cc_start: 0.7756 (tm-30) cc_final: 0.7522 (tm-30) REVERT: I 23 MET cc_start: 0.8516 (ttp) cc_final: 0.8192 (ttp) REVERT: I 41 ASN cc_start: 0.7300 (m110) cc_final: 0.6441 (p0) REVERT: K 2 ASN cc_start: 0.7610 (m-40) cc_final: 0.6625 (m110) REVERT: K 29 ASN cc_start: 0.7858 (t0) cc_final: 0.7609 (t0) REVERT: K 74 ARG cc_start: 0.8930 (ttt-90) cc_final: 0.8668 (ttt-90) REVERT: L 28 ILE cc_start: 0.8477 (tt) cc_final: 0.8238 (tt) outliers start: 66 outliers final: 40 residues processed: 559 average time/residue: 0.2271 time to fit residues: 201.7812 Evaluate side-chains 522 residues out of total 3448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 477 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 647 THR Chi-restraints excluded: chain A residue 687 ILE Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 870 SER Chi-restraints excluded: chain A residue 937 ASP Chi-restraints excluded: chain A residue 1156 ASP Chi-restraints excluded: chain A residue 1421 ARG Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 319 ASN Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 537 GLN Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 760 THR Chi-restraints excluded: chain B residue 833 THR Chi-restraints excluded: chain B residue 847 LYS Chi-restraints excluded: chain B residue 903 ILE Chi-restraints excluded: chain B residue 914 GLU Chi-restraints excluded: chain B residue 958 CYS Chi-restraints excluded: chain B residue 1033 THR Chi-restraints excluded: chain B residue 1067 ILE Chi-restraints excluded: chain B residue 1089 MET Chi-restraints excluded: chain B residue 1115 GLN Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain H residue 87 GLN Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 108 MET Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain L residue 16 ILE Chi-restraints excluded: chain L residue 37 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 3 optimal weight: 0.7980 chunk 109 optimal weight: 9.9990 chunk 342 optimal weight: 0.6980 chunk 225 optimal weight: 6.9990 chunk 76 optimal weight: 0.9980 chunk 133 optimal weight: 6.9990 chunk 87 optimal weight: 6.9990 chunk 140 optimal weight: 0.0170 chunk 103 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 209 optimal weight: 1.9990 overall best weight: 0.9020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 278 HIS A 320 ASN ** A 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 757 GLN A 809 HIS ** A 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 683 GLN B 817 GLN C 51 GLN D 38 HIS E 98 ASN H 46 GLN I 22 ASN I 41 ASN I 74 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.183959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.142415 restraints weight = 38174.289| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.18 r_work: 0.3200 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 33523 Z= 0.124 Angle : 0.598 11.058 45630 Z= 0.311 Chirality : 0.045 0.291 5104 Planarity : 0.004 0.087 5635 Dihedral : 13.849 175.503 5145 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.33 % Favored : 95.65 % Rotamer: Outliers : 1.96 % Allowed : 10.34 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.13), residues: 3858 helix: 0.53 (0.14), residues: 1297 sheet: -0.55 (0.19), residues: 585 loop : -0.70 (0.14), residues: 1976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 35 TYR 0.030 0.002 TYR B 215 PHE 0.018 0.001 PHE B 320 TRP 0.024 0.002 TRP A1210 HIS 0.005 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (33492) covalent geometry : angle 0.58750 / 0.31 (45591) hydrogen bonds : bond 0.04043 / 2.77 ( 1288) hydrogen bonds : angle 4.89921 / 3.41 ( 3660) metal coordination : bond 0.00939 / 0.57 ( 31) metal coordination : angle 3.87351 / 3.01 ( 39) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7716 Ramachandran restraints generated. 3858 Oldfield, 0 Emsley, 3858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7716 Ramachandran restraints generated. 3858 Oldfield, 0 Emsley, 3858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 3448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 500 time to evaluate : 1.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 LYS cc_start: 0.8486 (ttmm) cc_final: 0.8271 (ttmm) REVERT: A 192 ARG cc_start: 0.7039 (mtm110) cc_final: 0.6731 (mtt90) REVERT: A 241 ARG cc_start: 0.8066 (ptm-80) cc_final: 0.7560 (ptp90) REVERT: A 250 VAL cc_start: 0.9203 (t) cc_final: 0.8874 (p) REVERT: A 266 MET cc_start: 0.1732 (mmm) cc_final: 0.0681 (tpt) REVERT: A 329 MET cc_start: 0.7602 (mtt) cc_final: 0.7215 (mtp) REVERT: A 423 ASN cc_start: 0.7091 (m-40) cc_final: 0.6739 (t0) REVERT: A 441 GLN cc_start: 0.7840 (pt0) cc_final: 0.7437 (mt0) REVERT: A 540 ASP cc_start: 0.7756 (m-30) cc_final: 0.7491 (m-30) REVERT: A 687 ILE cc_start: 0.9067 (OUTLIER) cc_final: 0.8860 (mm) REVERT: A 701 ASP cc_start: 0.7325 (m-30) cc_final: 0.7039 (m-30) REVERT: A 758 LYS cc_start: 0.8359 (mttt) cc_final: 0.7876 (mmtt) REVERT: A 845 GLU cc_start: 0.7597 (tt0) cc_final: 0.7242 (tt0) REVERT: A 849 ASP cc_start: 0.7622 (m-30) cc_final: 0.7256 (m-30) REVERT: A 928 ARG cc_start: 0.8239 (mtp-110) cc_final: 0.7882 (mtp85) REVERT: A 932 ARG cc_start: 0.6681 (tpt170) cc_final: 0.6457 (tpt90) REVERT: A 942 VAL cc_start: 0.8054 (t) cc_final: 0.7660 (t) REVERT: A 1008 LYS cc_start: 0.7935 (mttt) cc_final: 0.7572 (ttpp) REVERT: A 1086 MET cc_start: 0.8576 (mmm) cc_final: 0.8370 (mmp) REVERT: A 1097 GLU cc_start: 0.8001 (tm-30) cc_final: 0.7603 (tm-30) REVERT: A 1135 LYS cc_start: 0.8602 (mttt) cc_final: 0.8299 (mttt) REVERT: A 1170 THR cc_start: 0.8502 (m) cc_final: 0.8296 (m) REVERT: A 1279 MET cc_start: 0.6975 (mmm) cc_final: 0.6734 (ttt) REVERT: A 1284 PHE cc_start: 0.7662 (t80) cc_final: 0.6889 (t80) REVERT: A 1306 LYS cc_start: 0.8269 (mttt) cc_final: 0.7777 (mmmt) REVERT: A 1349 GLU cc_start: 0.7595 (tm-30) cc_final: 0.7321 (tp30) REVERT: B 53 MET cc_start: 0.7659 (mmm) cc_final: 0.6774 (mtm) REVERT: B 187 ILE cc_start: 0.8828 (OUTLIER) cc_final: 0.8558 (mt) REVERT: B 215 TYR cc_start: 0.8313 (m-10) cc_final: 0.8019 (m-80) REVERT: B 254 GLN cc_start: 0.7892 (mp10) cc_final: 0.7566 (mm-40) REVERT: B 360 LYS cc_start: 0.8538 (mttt) cc_final: 0.8059 (mtmt) REVERT: B 407 MET cc_start: 0.8300 (OUTLIER) cc_final: 0.7920 (mtt) REVERT: B 414 GLU cc_start: 0.6803 (mt-10) cc_final: 0.6365 (mm-30) REVERT: B 420 GLN cc_start: 0.6441 (tt0) cc_final: 0.6167 (tp-100) REVERT: B 436 LYS cc_start: 0.7357 (mttp) cc_final: 0.6779 (tttt) REVERT: B 529 MET cc_start: 0.9013 (mmm) cc_final: 0.8526 (mmm) REVERT: B 617 ASP cc_start: 0.7868 (t0) cc_final: 0.7615 (t0) REVERT: B 847 LYS cc_start: 0.8327 (OUTLIER) cc_final: 0.7921 (mtpp) REVERT: B 900 GLU cc_start: 0.7110 (tt0) cc_final: 0.6892 (mt-10) REVERT: B 1075 MET cc_start: 0.8711 (mmt) cc_final: 0.8407 (mmt) REVERT: B 1092 ASP cc_start: 0.7624 (m-30) cc_final: 0.7423 (m-30) REVERT: B 1118 VAL cc_start: 0.9154 (t) cc_final: 0.8898 (m) REVERT: B 1150 ARG cc_start: 0.7889 (mtp85) cc_final: 0.7611 (mtp180) REVERT: C 17 GLU cc_start: 0.7907 (pm20) cc_final: 0.7591 (pt0) REVERT: C 189 ASP cc_start: 0.6384 (p0) cc_final: 0.5807 (p0) REVERT: C 207 GLU cc_start: 0.7232 (pt0) cc_final: 0.6996 (pt0) REVERT: C 210 GLU cc_start: 0.7588 (mt-10) cc_final: 0.7246 (pt0) REVERT: C 268 GLN cc_start: 0.6839 (mt0) cc_final: 0.6271 (pt0) REVERT: D 106 GLU cc_start: 0.5739 (mt-10) cc_final: 0.3926 (pm20) REVERT: D 110 GLU cc_start: 0.1502 (tt0) cc_final: 0.1060 (tt0) REVERT: G 10 GLU cc_start: 0.6861 (mt-10) cc_final: 0.6314 (mt-10) REVERT: G 45 VAL cc_start: 0.6211 (t) cc_final: 0.6009 (m) REVERT: H 48 TYR cc_start: 0.8225 (t80) cc_final: 0.7894 (t80) REVERT: H 62 SER cc_start: 0.8867 (m) cc_final: 0.8617 (p) REVERT: I 23 MET cc_start: 0.8549 (ttp) cc_final: 0.8291 (ttp) REVERT: I 41 ASN cc_start: 0.7235 (m-40) cc_final: 0.6179 (p0) REVERT: I 98 GLN cc_start: 0.8634 (mt0) cc_final: 0.8224 (mt0) REVERT: K 2 ASN cc_start: 0.7563 (m-40) cc_final: 0.6479 (m110) REVERT: K 74 ARG cc_start: 0.8901 (ttt-90) cc_final: 0.8626 (ttt-90) REVERT: L 28 ILE cc_start: 0.8248 (tt) cc_final: 0.8043 (tt) outliers start: 67 outliers final: 46 residues processed: 543 average time/residue: 0.2214 time to fit residues: 191.1772 Evaluate side-chains 511 residues out of total 3448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 461 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 687 ILE Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 870 SER Chi-restraints excluded: chain A residue 937 ASP Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1389 ASP Chi-restraints excluded: chain A residue 1421 ARG Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 319 ASN Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 468 GLN Chi-restraints excluded: chain B residue 537 GLN Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 572 CYS Chi-restraints excluded: chain B residue 683 GLN Chi-restraints excluded: chain B residue 760 THR Chi-restraints excluded: chain B residue 796 MET Chi-restraints excluded: chain B residue 833 THR Chi-restraints excluded: chain B residue 847 LYS Chi-restraints excluded: chain B residue 903 ILE Chi-restraints excluded: chain B residue 914 GLU Chi-restraints excluded: chain B residue 1067 ILE Chi-restraints excluded: chain B residue 1115 GLN Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain E residue 98 ASN Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 132 GLN Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 108 MET Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain L residue 16 ILE Chi-restraints excluded: chain L residue 37 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 30 optimal weight: 0.0040 chunk 309 optimal weight: 7.9990 chunk 16 optimal weight: 10.0000 chunk 262 optimal weight: 7.9990 chunk 142 optimal weight: 9.9990 chunk 68 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 181 optimal weight: 10.0000 chunk 32 optimal weight: 0.7980 chunk 145 optimal weight: 4.9990 chunk 136 optimal weight: 10.0000 overall best weight: 2.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 278 HIS A 531 ASN A 757 GLN ** B 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 817 GLN C 111 GLN ** E 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 GLN I 74 GLN K 29 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.183913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.142485 restraints weight = 38207.976| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 2.50 r_work: 0.3160 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.3297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 33523 Z= 0.193 Angle : 0.631 11.149 45630 Z= 0.325 Chirality : 0.046 0.297 5104 Planarity : 0.005 0.090 5635 Dihedral : 13.809 174.667 5145 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.67 % Favored : 95.31 % Rotamer: Outliers : 2.66 % Allowed : 10.72 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 1.08 % 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: -0.42 (0.13), residues: 3858 helix: 0.63 (0.14), residues: 1298 sheet: -0.66 (0.19), residues: 593 loop : -0.71 (0.14), residues: 1967 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 797 TYR 0.025 0.002 TYR B 811 PHE 0.019 0.002 PHE A 458 TRP 0.020 0.002 TRP B 573 HIS 0.011 0.001 HIS K 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.19 (33492) covalent geometry : angle 0.61964 / 0.32 (45591) hydrogen bonds : bond 0.04270 / 2.91 ( 1288) hydrogen bonds : angle 4.82680 / 3.36 ( 3660) metal coordination : bond 0.00835 / 0.49 ( 31) metal coordination : angle 4.16952 / 3.23 ( 39) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7716 Ramachandran restraints generated. 3858 Oldfield, 0 Emsley, 3858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7716 Ramachandran restraints generated. 3858 Oldfield, 0 Emsley, 3858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 3448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 471 time to evaluate : 1.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 LYS cc_start: 0.8606 (ttmm) cc_final: 0.8370 (ttmm) REVERT: A 241 ARG cc_start: 0.8241 (ptm-80) cc_final: 0.7553 (ptp90) REVERT: A 250 VAL cc_start: 0.9236 (t) cc_final: 0.8888 (p) REVERT: A 266 MET cc_start: 0.1611 (mmm) cc_final: 0.0466 (tpt) REVERT: A 278 HIS cc_start: 0.6812 (m170) cc_final: 0.6510 (t-90) REVERT: A 329 MET cc_start: 0.7746 (mtt) cc_final: 0.7288 (mtp) REVERT: A 423 ASN cc_start: 0.7303 (m-40) cc_final: 0.6728 (t0) REVERT: A 441 GLN cc_start: 0.7853 (pt0) cc_final: 0.7502 (mt0) REVERT: A 540 ASP cc_start: 0.8278 (m-30) cc_final: 0.8009 (m-30) REVERT: A 621 ILE cc_start: 0.8419 (OUTLIER) cc_final: 0.8057 (mm) REVERT: A 758 LYS cc_start: 0.8451 (mttt) cc_final: 0.7820 (mmtt) REVERT: A 845 GLU cc_start: 0.7951 (tt0) cc_final: 0.7694 (tt0) REVERT: A 849 ASP cc_start: 0.7839 (m-30) cc_final: 0.7535 (m-30) REVERT: A 928 ARG cc_start: 0.8328 (mtp-110) cc_final: 0.7933 (mtp85) REVERT: A 932 ARG cc_start: 0.6807 (tpt170) cc_final: 0.6519 (tpt90) REVERT: A 1008 LYS cc_start: 0.8143 (mttt) cc_final: 0.7692 (ttpp) REVERT: A 1086 MET cc_start: 0.8881 (mmm) cc_final: 0.8680 (mmp) REVERT: A 1097 GLU cc_start: 0.8162 (tm-30) cc_final: 0.7627 (tm-30) REVERT: A 1135 LYS cc_start: 0.8665 (mttt) cc_final: 0.8207 (mmpt) REVERT: A 1170 THR cc_start: 0.8553 (m) cc_final: 0.8322 (m) REVERT: A 1199 MET cc_start: 0.5798 (OUTLIER) cc_final: 0.4764 (tmm) REVERT: A 1279 MET cc_start: 0.7018 (mmm) cc_final: 0.6758 (ttt) REVERT: A 1284 PHE cc_start: 0.7916 (t80) cc_final: 0.7211 (t80) REVERT: A 1306 LYS cc_start: 0.8421 (mttt) cc_final: 0.7938 (mmmt) REVERT: A 1405 MET cc_start: 0.9018 (mtp) cc_final: 0.8804 (mtp) REVERT: A 1456 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7725 (mt-10) REVERT: B 53 MET cc_start: 0.7938 (mmm) cc_final: 0.6995 (mtm) REVERT: B 187 ILE cc_start: 0.8878 (OUTLIER) cc_final: 0.8635 (mt) REVERT: B 200 MET cc_start: 0.8425 (tpp) cc_final: 0.8069 (mmm) REVERT: B 215 TYR cc_start: 0.8451 (m-10) cc_final: 0.8162 (m-80) REVERT: B 254 GLN cc_start: 0.8009 (mp10) cc_final: 0.7535 (mm-40) REVERT: B 402 PHE cc_start: 0.7994 (t80) cc_final: 0.7725 (t80) REVERT: B 414 GLU cc_start: 0.6918 (mt-10) cc_final: 0.6487 (mm-30) REVERT: B 420 GLN cc_start: 0.6552 (tt0) cc_final: 0.6250 (tp-100) REVERT: B 436 LYS cc_start: 0.7401 (mttp) cc_final: 0.6609 (tttt) REVERT: B 617 ASP cc_start: 0.8163 (t0) cc_final: 0.7902 (t0) REVERT: B 765 GLU cc_start: 0.8408 (tp30) cc_final: 0.8119 (mm-30) REVERT: B 847 LYS cc_start: 0.8337 (OUTLIER) cc_final: 0.7853 (mtpp) REVERT: B 900 GLU cc_start: 0.7416 (tt0) cc_final: 0.7017 (mt-10) REVERT: B 1075 MET cc_start: 0.8929 (mmt) cc_final: 0.8633 (mmt) REVERT: B 1092 ASP cc_start: 0.8020 (m-30) cc_final: 0.7817 (m-30) REVERT: B 1118 VAL cc_start: 0.9222 (t) cc_final: 0.8976 (m) REVERT: B 1150 ARG cc_start: 0.8086 (mtp85) cc_final: 0.7798 (mtp180) REVERT: C 17 GLU cc_start: 0.8378 (pm20) cc_final: 0.7883 (pt0) REVERT: C 189 ASP cc_start: 0.6673 (p0) cc_final: 0.6331 (p0) REVERT: C 207 GLU cc_start: 0.7423 (pt0) cc_final: 0.7211 (pt0) REVERT: C 210 GLU cc_start: 0.7892 (mt-10) cc_final: 0.7435 (pt0) REVERT: C 268 GLN cc_start: 0.6695 (mt0) cc_final: 0.6085 (pt0) REVERT: D 106 GLU cc_start: 0.5834 (mt-10) cc_final: 0.3909 (pm20) REVERT: D 110 GLU cc_start: 0.1529 (tt0) cc_final: 0.1077 (tt0) REVERT: E 191 VAL cc_start: 0.9049 (OUTLIER) cc_final: 0.8833 (p) REVERT: F 100 ARG cc_start: 0.7676 (mtp85) cc_final: 0.7341 (ttm-80) REVERT: G 10 GLU cc_start: 0.7032 (mt-10) cc_final: 0.6501 (mt-10) REVERT: G 45 VAL cc_start: 0.6286 (t) cc_final: 0.6061 (m) REVERT: H 48 TYR cc_start: 0.8334 (t80) cc_final: 0.8092 (t80) REVERT: H 62 SER cc_start: 0.8965 (m) cc_final: 0.8693 (p) REVERT: H 87 GLN cc_start: 0.8402 (OUTLIER) cc_final: 0.8181 (mp10) REVERT: I 23 MET cc_start: 0.8806 (ttp) cc_final: 0.8579 (ttp) REVERT: I 41 ASN cc_start: 0.7700 (m-40) cc_final: 0.6485 (p0) REVERT: I 98 GLN cc_start: 0.8826 (mt0) cc_final: 0.8388 (mt0) REVERT: K 2 ASN cc_start: 0.7582 (m-40) cc_final: 0.6283 (m110) REVERT: K 74 ARG cc_start: 0.9016 (ttt-90) cc_final: 0.8717 (ttt-90) REVERT: L 28 ILE cc_start: 0.8250 (tt) cc_final: 0.8046 (tt) outliers start: 91 outliers final: 66 residues processed: 536 average time/residue: 0.2258 time to fit residues: 193.7325 Evaluate side-chains 513 residues out of total 3448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 441 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 647 THR Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 870 SER Chi-restraints excluded: chain A residue 937 ASP Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 947 HIS Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1156 ASP Chi-restraints excluded: chain A residue 1199 MET Chi-restraints excluded: chain A residue 1261 ILE Chi-restraints excluded: chain A residue 1363 VAL Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1389 ASP Chi-restraints excluded: chain A residue 1404 THR Chi-restraints excluded: chain A residue 1421 ARG Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 319 ASN Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 468 GLN Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain B residue 537 GLN Chi-restraints excluded: chain B residue 572 CYS Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 760 THR Chi-restraints excluded: chain B residue 796 MET Chi-restraints excluded: chain B residue 833 THR Chi-restraints excluded: chain B residue 847 LYS Chi-restraints excluded: chain B residue 903 ILE Chi-restraints excluded: chain B residue 914 GLU Chi-restraints excluded: chain B residue 958 CYS Chi-restraints excluded: chain B residue 1033 THR Chi-restraints excluded: chain B residue 1067 ILE Chi-restraints excluded: chain B residue 1115 GLN Chi-restraints excluded: chain B residue 1125 MET Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain E residue 98 ASN Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain E residue 132 GLN Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain H residue 87 GLN Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 108 MET Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain K residue 48 SER Chi-restraints excluded: chain L residue 16 ILE Chi-restraints excluded: chain L residue 37 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 342 optimal weight: 5.9990 chunk 388 optimal weight: 20.0000 chunk 382 optimal weight: 0.9990 chunk 90 optimal weight: 9.9990 chunk 169 optimal weight: 3.9990 chunk 365 optimal weight: 0.9990 chunk 56 optimal weight: 10.0000 chunk 119 optimal weight: 20.0000 chunk 250 optimal weight: 10.0000 chunk 12 optimal weight: 0.3980 chunk 20 optimal weight: 0.0010 overall best weight: 1.2792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 507 GLN A 757 GLN ** A 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1024 ASN ** B 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 650 ASN B 817 GLN C 111 GLN E 98 ASN H 46 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.185721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.144748 restraints weight = 37965.237| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.13 r_work: 0.3110 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 33523 Z= 0.129 Angle : 0.585 12.718 45630 Z= 0.301 Chirality : 0.045 0.292 5104 Planarity : 0.004 0.085 5635 Dihedral : 13.746 173.212 5145 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.43 % Favored : 95.54 % Rotamer: Outliers : 2.57 % Allowed : 11.36 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 1.08 % 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: -0.24 (0.13), residues: 3858 helix: 0.82 (0.14), residues: 1313 sheet: -0.46 (0.20), residues: 570 loop : -0.69 (0.14), residues: 1975 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 192 TYR 0.027 0.001 TYR I 37 PHE 0.016 0.001 PHE B 320 TRP 0.013 0.001 TRP B 573 HIS 0.006 0.001 HIS K 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (33492) covalent geometry : angle 0.57125 / 0.30 (45591) hydrogen bonds : bond 0.03815 / 2.61 ( 1288) hydrogen bonds : angle 4.63070 / 3.22 ( 3660) metal coordination : bond 0.00799 / 0.48 ( 31) metal coordination : angle 4.33755 / 3.43 ( 39) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7716 Ramachandran restraints generated. 3858 Oldfield, 0 Emsley, 3858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7716 Ramachandran restraints generated. 3858 Oldfield, 0 Emsley, 3858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 3448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 467 time to evaluate : 1.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 ARG cc_start: 0.7205 (mtm110) cc_final: 0.6669 (mtt90) REVERT: A 241 ARG cc_start: 0.8148 (ptm-80) cc_final: 0.7583 (ptp90) REVERT: A 250 VAL cc_start: 0.9231 (t) cc_final: 0.8894 (p) REVERT: A 266 MET cc_start: 0.1629 (mmm) cc_final: 0.0483 (tpt) REVERT: A 278 HIS cc_start: 0.6787 (m170) cc_final: 0.6500 (t-90) REVERT: A 329 MET cc_start: 0.7667 (mtt) cc_final: 0.7226 (mtp) REVERT: A 441 GLN cc_start: 0.7816 (pt0) cc_final: 0.7494 (mt0) REVERT: A 540 ASP cc_start: 0.8106 (m-30) cc_final: 0.7805 (m-30) REVERT: A 621 ILE cc_start: 0.8256 (OUTLIER) cc_final: 0.7869 (mm) REVERT: A 758 LYS cc_start: 0.8450 (mttt) cc_final: 0.7836 (mmtt) REVERT: A 845 GLU cc_start: 0.7940 (tt0) cc_final: 0.7616 (tt0) REVERT: A 849 ASP cc_start: 0.7797 (m-30) cc_final: 0.7442 (m-30) REVERT: A 928 ARG cc_start: 0.8376 (mtp-110) cc_final: 0.7930 (mtp85) REVERT: A 932 ARG cc_start: 0.6784 (tpt170) cc_final: 0.6496 (tpt90) REVERT: A 942 VAL cc_start: 0.7957 (t) cc_final: 0.7526 (t) REVERT: A 1008 LYS cc_start: 0.8096 (mttt) cc_final: 0.7707 (ttpp) REVERT: A 1086 MET cc_start: 0.8901 (mmm) cc_final: 0.8683 (mmp) REVERT: A 1097 GLU cc_start: 0.8176 (tm-30) cc_final: 0.7760 (tm-30) REVERT: A 1126 GLU cc_start: 0.8391 (mt-10) cc_final: 0.8121 (mt-10) REVERT: A 1199 MET cc_start: 0.5832 (OUTLIER) cc_final: 0.4805 (tmm) REVERT: A 1279 MET cc_start: 0.6928 (mmm) cc_final: 0.6713 (ttt) REVERT: A 1306 LYS cc_start: 0.8462 (mttt) cc_final: 0.7957 (mmmt) REVERT: A 1456 GLU cc_start: 0.8009 (mt-10) cc_final: 0.7690 (mt-10) REVERT: B 19 PRO cc_start: 0.7987 (Cg_endo) cc_final: 0.7778 (Cg_exo) REVERT: B 53 MET cc_start: 0.7898 (mmm) cc_final: 0.7007 (mtm) REVERT: B 187 ILE cc_start: 0.8836 (OUTLIER) cc_final: 0.8574 (mt) REVERT: B 200 MET cc_start: 0.8401 (tpp) cc_final: 0.8035 (mmm) REVERT: B 215 TYR cc_start: 0.8441 (m-10) cc_final: 0.8170 (m-80) REVERT: B 254 GLN cc_start: 0.7936 (mp10) cc_final: 0.7484 (mm-40) REVERT: B 360 LYS cc_start: 0.8699 (mttt) cc_final: 0.8188 (mtmt) REVERT: B 402 PHE cc_start: 0.7928 (t80) cc_final: 0.7632 (t80) REVERT: B 414 GLU cc_start: 0.6994 (mt-10) cc_final: 0.6582 (mm-30) REVERT: B 420 GLN cc_start: 0.6542 (tt0) cc_final: 0.6302 (tp-100) REVERT: B 436 LYS cc_start: 0.7386 (mttp) cc_final: 0.6725 (ttpp) REVERT: B 547 GLU cc_start: 0.8269 (tm-30) cc_final: 0.7663 (mm-30) REVERT: B 582 GLN cc_start: 0.8391 (mm-40) cc_final: 0.8046 (tt0) REVERT: B 847 LYS cc_start: 0.8327 (OUTLIER) cc_final: 0.7822 (mtpp) REVERT: B 900 GLU cc_start: 0.7471 (tt0) cc_final: 0.7165 (mt-10) REVERT: B 1075 MET cc_start: 0.8906 (mmt) cc_final: 0.8610 (mmt) REVERT: B 1118 VAL cc_start: 0.9180 (t) cc_final: 0.8938 (m) REVERT: B 1150 ARG cc_start: 0.8145 (mtp85) cc_final: 0.7870 (mtp180) REVERT: C 189 ASP cc_start: 0.6600 (p0) cc_final: 0.6284 (p0) REVERT: C 210 GLU cc_start: 0.7888 (mt-10) cc_final: 0.7461 (pt0) REVERT: C 268 GLN cc_start: 0.6738 (mt0) cc_final: 0.6118 (pt0) REVERT: D 106 GLU cc_start: 0.5893 (mt-10) cc_final: 0.3893 (pm20) REVERT: D 110 GLU cc_start: 0.1445 (tt0) cc_final: 0.1020 (tt0) REVERT: E 61 LEU cc_start: 0.8486 (tp) cc_final: 0.8240 (tp) REVERT: E 62 VAL cc_start: 0.9210 (OUTLIER) cc_final: 0.8872 (p) REVERT: E 91 CYS cc_start: 0.7814 (t) cc_final: 0.7272 (m) REVERT: E 191 VAL cc_start: 0.9004 (OUTLIER) cc_final: 0.8798 (p) REVERT: F 80 MET cc_start: 0.7579 (ptp) cc_final: 0.7333 (ptp) REVERT: F 100 ARG cc_start: 0.7626 (mtp85) cc_final: 0.7255 (ttm-80) REVERT: G 10 GLU cc_start: 0.6960 (mt-10) cc_final: 0.6340 (mt-10) REVERT: H 48 TYR cc_start: 0.8315 (t80) cc_final: 0.7957 (t80) REVERT: H 62 SER cc_start: 0.8815 (m) cc_final: 0.8551 (p) REVERT: I 23 MET cc_start: 0.8761 (ttp) cc_final: 0.8529 (ttp) REVERT: I 41 ASN cc_start: 0.7675 (m-40) cc_final: 0.6382 (p0) REVERT: I 98 GLN cc_start: 0.8778 (mt0) cc_final: 0.8490 (mt0) REVERT: K 2 ASN cc_start: 0.7685 (m-40) cc_final: 0.7413 (m110) REVERT: K 74 ARG cc_start: 0.9017 (ttt-90) cc_final: 0.8406 (ttt-90) outliers start: 88 outliers final: 63 residues processed: 530 average time/residue: 0.2202 time to fit residues: 188.1291 Evaluate side-chains 508 residues out of total 3448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 439 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 647 THR Chi-restraints excluded: chain A residue 687 ILE Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 937 ASP Chi-restraints excluded: chain A residue 947 HIS Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1199 MET Chi-restraints excluded: chain A residue 1261 ILE Chi-restraints excluded: chain A residue 1363 VAL Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1421 ARG Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 319 ASN Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 468 GLN Chi-restraints excluded: chain B residue 537 GLN Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 760 THR Chi-restraints excluded: chain B residue 796 MET Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 833 THR Chi-restraints excluded: chain B residue 847 LYS Chi-restraints excluded: chain B residue 903 ILE Chi-restraints excluded: chain B residue 909 VAL Chi-restraints excluded: chain B residue 914 GLU Chi-restraints excluded: chain B residue 958 CYS Chi-restraints excluded: chain B residue 1067 ILE Chi-restraints excluded: chain B residue 1115 GLN Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 113 ARG Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 98 ASN Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 132 GLN Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 108 MET Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain K residue 48 SER Chi-restraints excluded: chain L residue 16 ILE Chi-restraints excluded: chain L residue 37 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 237 optimal weight: 10.0000 chunk 120 optimal weight: 4.9990 chunk 378 optimal weight: 7.9990 chunk 11 optimal weight: 20.0000 chunk 279 optimal weight: 5.9990 chunk 230 optimal weight: 0.6980 chunk 273 optimal weight: 0.7980 chunk 251 optimal weight: 8.9990 chunk 242 optimal weight: 4.9990 chunk 125 optimal weight: 0.0570 chunk 346 optimal weight: 0.3980 overall best weight: 1.3900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 320 ASN ** A 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 757 GLN A1024 ASN ** B 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 650 ASN B 717 ASN C 111 GLN G 9 HIS H 46 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.182748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.141811 restraints weight = 38191.907| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 2.26 r_work: 0.3152 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.3579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 33523 Z= 0.130 Angle : 0.576 11.238 45630 Z= 0.297 Chirality : 0.044 0.296 5104 Planarity : 0.004 0.082 5635 Dihedral : 13.700 172.367 5145 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.59 % Favored : 95.39 % Rotamer: Outliers : 2.83 % Allowed : 11.45 % Favored : 85.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 1.08 % 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: 3858 helix: 0.98 (0.15), residues: 1316 sheet: -0.46 (0.20), residues: 579 loop : -0.66 (0.14), residues: 1963 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 27 TYR 0.020 0.001 TYR I 37 PHE 0.015 0.001 PHE B 320 TRP 0.016 0.001 TRP B 573 HIS 0.006 0.001 HIS K 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (33492) covalent geometry : angle 0.56484 / 0.30 (45591) hydrogen bonds : bond 0.03727 / 2.55 ( 1288) hydrogen bonds : angle 4.52822 / 3.15 ( 3660) metal coordination : bond 0.00714 / 0.43 ( 31) metal coordination : angle 3.95655 / 3.16 ( 39) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7716 Ramachandran restraints generated. 3858 Oldfield, 0 Emsley, 3858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7716 Ramachandran restraints generated. 3858 Oldfield, 0 Emsley, 3858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 3448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 460 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 ARG cc_start: 0.7202 (mtm110) cc_final: 0.6710 (mtt90) REVERT: A 241 ARG cc_start: 0.8166 (ptm-80) cc_final: 0.7519 (ptp90) REVERT: A 250 VAL cc_start: 0.9237 (t) cc_final: 0.8889 (p) REVERT: A 266 MET cc_start: 0.1646 (mmm) cc_final: 0.0578 (tpt) REVERT: A 278 HIS cc_start: 0.6965 (m170) cc_final: 0.6504 (t-90) REVERT: A 329 MET cc_start: 0.7622 (mtt) cc_final: 0.7176 (mtp) REVERT: A 441 GLN cc_start: 0.7742 (pt0) cc_final: 0.7410 (mt0) REVERT: A 540 ASP cc_start: 0.8080 (m-30) cc_final: 0.7793 (m-30) REVERT: A 701 ASP cc_start: 0.7642 (m-30) cc_final: 0.7265 (m-30) REVERT: A 758 LYS cc_start: 0.8412 (mttt) cc_final: 0.7759 (mmtt) REVERT: A 804 HIS cc_start: 0.8264 (m90) cc_final: 0.8024 (m90) REVERT: A 845 GLU cc_start: 0.7858 (tt0) cc_final: 0.7511 (tt0) REVERT: A 849 ASP cc_start: 0.7768 (m-30) cc_final: 0.7417 (m-30) REVERT: A 928 ARG cc_start: 0.8401 (mtp-110) cc_final: 0.7951 (mtp85) REVERT: A 932 ARG cc_start: 0.6757 (tpt170) cc_final: 0.6468 (tpt90) REVERT: A 942 VAL cc_start: 0.7860 (t) cc_final: 0.7437 (t) REVERT: A 1008 LYS cc_start: 0.8082 (mttt) cc_final: 0.7629 (ttpp) REVERT: A 1086 MET cc_start: 0.8984 (mmm) cc_final: 0.8784 (mmp) REVERT: A 1097 GLU cc_start: 0.8169 (tm-30) cc_final: 0.7821 (tm-30) REVERT: A 1126 GLU cc_start: 0.8367 (mt-10) cc_final: 0.8104 (mt-10) REVERT: A 1199 MET cc_start: 0.5776 (OUTLIER) cc_final: 0.4788 (tmm) REVERT: A 1279 MET cc_start: 0.6974 (mmm) cc_final: 0.6708 (ttt) REVERT: A 1306 LYS cc_start: 0.8414 (mttt) cc_final: 0.7849 (mmmt) REVERT: A 1451 MET cc_start: 0.8096 (mmm) cc_final: 0.7820 (mmm) REVERT: A 1456 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7596 (mt-10) REVERT: B 19 PRO cc_start: 0.7973 (Cg_endo) cc_final: 0.7765 (Cg_exo) REVERT: B 53 MET cc_start: 0.7777 (mmm) cc_final: 0.6784 (mtm) REVERT: B 173 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.8124 (pt0) REVERT: B 187 ILE cc_start: 0.8791 (OUTLIER) cc_final: 0.8543 (mt) REVERT: B 215 TYR cc_start: 0.8395 (m-10) cc_final: 0.8146 (m-80) REVERT: B 254 GLN cc_start: 0.7943 (mp10) cc_final: 0.7452 (mm-40) REVERT: B 360 LYS cc_start: 0.8605 (mttt) cc_final: 0.8072 (mtmt) REVERT: B 402 PHE cc_start: 0.7953 (t80) cc_final: 0.7701 (t80) REVERT: B 414 GLU cc_start: 0.6882 (mt-10) cc_final: 0.6454 (mm-30) REVERT: B 420 GLN cc_start: 0.6404 (tt0) cc_final: 0.6115 (tp-100) REVERT: B 436 LYS cc_start: 0.7358 (mttp) cc_final: 0.6613 (ttpp) REVERT: B 473 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8723 (mt) REVERT: B 547 GLU cc_start: 0.8293 (tm-30) cc_final: 0.7629 (mm-30) REVERT: B 582 GLN cc_start: 0.8438 (mm-40) cc_final: 0.7780 (tp40) REVERT: B 847 LYS cc_start: 0.8313 (OUTLIER) cc_final: 0.8017 (mtpp) REVERT: B 900 GLU cc_start: 0.7452 (tt0) cc_final: 0.7160 (mt-10) REVERT: B 1075 MET cc_start: 0.8854 (mmt) cc_final: 0.8540 (mmt) REVERT: B 1118 VAL cc_start: 0.9149 (t) cc_final: 0.8901 (m) REVERT: B 1150 ARG cc_start: 0.8219 (mtp85) cc_final: 0.7924 (mtp180) REVERT: C 189 ASP cc_start: 0.6605 (p0) cc_final: 0.6292 (p0) REVERT: C 210 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7415 (pt0) REVERT: C 268 GLN cc_start: 0.6614 (mt0) cc_final: 0.6020 (pt0) REVERT: D 106 GLU cc_start: 0.5912 (mt-10) cc_final: 0.4159 (pm20) REVERT: D 110 GLU cc_start: 0.1401 (tt0) cc_final: 0.0752 (tt0) REVERT: E 61 LEU cc_start: 0.8485 (tp) cc_final: 0.8228 (tp) REVERT: E 91 CYS cc_start: 0.7819 (t) cc_final: 0.7249 (m) REVERT: E 191 VAL cc_start: 0.9017 (OUTLIER) cc_final: 0.8794 (p) REVERT: F 80 MET cc_start: 0.7410 (ptp) cc_final: 0.7154 (ptp) REVERT: F 100 ARG cc_start: 0.7624 (mtp85) cc_final: 0.7318 (ttm-80) REVERT: G 10 GLU cc_start: 0.6931 (mt-10) cc_final: 0.6220 (mt-10) REVERT: H 48 TYR cc_start: 0.8293 (t80) cc_final: 0.7996 (t80) REVERT: H 62 SER cc_start: 0.8825 (m) cc_final: 0.8549 (p) REVERT: I 23 MET cc_start: 0.8819 (ttp) cc_final: 0.8573 (ttp) REVERT: I 41 ASN cc_start: 0.7641 (m-40) cc_final: 0.6348 (p0) REVERT: K 2 ASN cc_start: 0.7635 (m-40) cc_final: 0.7399 (m110) REVERT: K 74 ARG cc_start: 0.9052 (ttt-90) cc_final: 0.8809 (ttt-90) outliers start: 97 outliers final: 70 residues processed: 530 average time/residue: 0.2121 time to fit residues: 181.9098 Evaluate side-chains 515 residues out of total 3448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 439 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 320 ASN Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 647 THR Chi-restraints excluded: chain A residue 687 ILE Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 937 ASP Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 947 HIS Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1156 ASP Chi-restraints excluded: chain A residue 1199 MET Chi-restraints excluded: chain A residue 1261 ILE Chi-restraints excluded: chain A residue 1363 VAL Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1421 ARG Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 319 ASN Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 468 GLN Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain B residue 537 GLN Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 572 CYS Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 760 THR Chi-restraints excluded: chain B residue 796 MET Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 833 THR Chi-restraints excluded: chain B residue 847 LYS Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 903 ILE Chi-restraints excluded: chain B residue 914 GLU Chi-restraints excluded: chain B residue 958 CYS Chi-restraints excluded: chain B residue 1067 ILE Chi-restraints excluded: chain B residue 1115 GLN Chi-restraints excluded: chain B residue 1125 MET Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 98 ASN Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain E residue 132 GLN Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain H residue 71 ASP Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 108 MET Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain K residue 48 SER Chi-restraints excluded: chain L residue 16 ILE Chi-restraints excluded: chain L residue 37 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 24 optimal weight: 10.0000 chunk 266 optimal weight: 9.9990 chunk 97 optimal weight: 0.0470 chunk 69 optimal weight: 6.9990 chunk 120 optimal weight: 9.9990 chunk 75 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 270 optimal weight: 7.9990 chunk 228 optimal weight: 0.9990 chunk 218 optimal weight: 5.9990 overall best weight: 2.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 678 ASN A 757 GLN A 926 ASN A1024 ASN B 460 HIS ** B 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 GLN E 107 GLN H 46 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.181380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.140641 restraints weight = 38299.818| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.28 r_work: 0.3113 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.3683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 33523 Z= 0.161 Angle : 0.595 11.347 45630 Z= 0.307 Chirality : 0.045 0.295 5104 Planarity : 0.004 0.082 5635 Dihedral : 13.698 171.924 5145 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.98 % Favored : 95.00 % Rotamer: Outliers : 2.63 % Allowed : 12.06 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 1.08 % 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: -0.15 (0.13), residues: 3858 helix: 0.99 (0.15), residues: 1317 sheet: -0.52 (0.20), residues: 586 loop : -0.67 (0.14), residues: 1955 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 768 TYR 0.021 0.002 TYR I 37 PHE 0.015 0.001 PHE A 458 TRP 0.024 0.001 TRP B 573 HIS 0.006 0.001 HIS K 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 (33492) covalent geometry : angle 0.58386 / 0.31 (45591) hydrogen bonds : bond 0.03846 / 2.61 ( 1288) hydrogen bonds : angle 4.52854 / 3.15 ( 3660) metal coordination : bond 0.00760 / 0.45 ( 31) metal coordination : angle 4.00890 / 3.21 ( 39) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7716 Ramachandran restraints generated. 3858 Oldfield, 0 Emsley, 3858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7716 Ramachandran restraints generated. 3858 Oldfield, 0 Emsley, 3858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 3448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 449 time to evaluate : 1.241 Fit side-chains revert: symmetry clash REVERT: A 67 ARG cc_start: 0.7391 (ttp80) cc_final: 0.7022 (ttp-170) REVERT: A 241 ARG cc_start: 0.8222 (ptm-80) cc_final: 0.7573 (ptp90) REVERT: A 250 VAL cc_start: 0.9240 (t) cc_final: 0.8874 (p) REVERT: A 266 MET cc_start: 0.1567 (mmm) cc_final: 0.0506 (tpt) REVERT: A 278 HIS cc_start: 0.6990 (m170) cc_final: 0.6514 (t-90) REVERT: A 441 GLN cc_start: 0.7775 (pt0) cc_final: 0.7449 (mt0) REVERT: A 447 GLU cc_start: 0.8712 (mp0) cc_final: 0.8292 (mp0) REVERT: A 540 ASP cc_start: 0.8198 (m-30) cc_final: 0.7895 (m-30) REVERT: A 701 ASP cc_start: 0.7702 (m-30) cc_final: 0.7321 (m-30) REVERT: A 758 LYS cc_start: 0.8477 (mttt) cc_final: 0.7794 (mmtt) REVERT: A 804 HIS cc_start: 0.8321 (m90) cc_final: 0.8095 (m90) REVERT: A 845 GLU cc_start: 0.7883 (tt0) cc_final: 0.7520 (tt0) REVERT: A 849 ASP cc_start: 0.7829 (m-30) cc_final: 0.7462 (m-30) REVERT: A 928 ARG cc_start: 0.8458 (mtp-110) cc_final: 0.7972 (mtp85) REVERT: A 932 ARG cc_start: 0.6757 (tpt170) cc_final: 0.6467 (tpt90) REVERT: A 942 VAL cc_start: 0.7859 (t) cc_final: 0.7438 (t) REVERT: A 1008 LYS cc_start: 0.8080 (mttt) cc_final: 0.7644 (ttpp) REVERT: A 1097 GLU cc_start: 0.8217 (tm-30) cc_final: 0.7854 (tm-30) REVERT: A 1126 GLU cc_start: 0.8372 (mt-10) cc_final: 0.8117 (mt-10) REVERT: A 1199 MET cc_start: 0.5910 (OUTLIER) cc_final: 0.4924 (tmm) REVERT: A 1279 MET cc_start: 0.6936 (mmm) cc_final: 0.6690 (ttt) REVERT: A 1284 PHE cc_start: 0.7697 (t80) cc_final: 0.7045 (t80) REVERT: A 1306 LYS cc_start: 0.8410 (mttt) cc_final: 0.7831 (mmmt) REVERT: A 1344 MET cc_start: 0.7929 (tpt) cc_final: 0.7054 (mtm) REVERT: A 1451 MET cc_start: 0.8118 (mmm) cc_final: 0.7860 (mmm) REVERT: A 1456 GLU cc_start: 0.7859 (mt-10) cc_final: 0.7444 (mt-10) REVERT: B 17 ILE cc_start: 0.8680 (OUTLIER) cc_final: 0.8107 (mm) REVERT: B 19 PRO cc_start: 0.7899 (Cg_endo) cc_final: 0.7680 (Cg_exo) REVERT: B 53 MET cc_start: 0.7800 (mmm) cc_final: 0.7471 (mmt) REVERT: B 173 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8253 (pt0) REVERT: B 187 ILE cc_start: 0.8758 (OUTLIER) cc_final: 0.8504 (mt) REVERT: B 215 TYR cc_start: 0.8448 (m-10) cc_final: 0.8189 (m-80) REVERT: B 254 GLN cc_start: 0.7954 (mp10) cc_final: 0.7432 (mm-40) REVERT: B 360 LYS cc_start: 0.8620 (mttt) cc_final: 0.8081 (mtmt) REVERT: B 402 PHE cc_start: 0.8015 (t80) cc_final: 0.7799 (t80) REVERT: B 414 GLU cc_start: 0.6885 (mt-10) cc_final: 0.6464 (mm-30) REVERT: B 420 GLN cc_start: 0.6514 (tt0) cc_final: 0.6237 (tp-100) REVERT: B 436 LYS cc_start: 0.7392 (mttp) cc_final: 0.6623 (ttpp) REVERT: B 473 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8744 (mt) REVERT: B 582 GLN cc_start: 0.8445 (mm-40) cc_final: 0.7793 (tp40) REVERT: B 847 LYS cc_start: 0.8346 (OUTLIER) cc_final: 0.8025 (mtpp) REVERT: B 1075 MET cc_start: 0.8852 (mmt) cc_final: 0.8542 (mmt) REVERT: B 1118 VAL cc_start: 0.9167 (t) cc_final: 0.8923 (m) REVERT: B 1150 ARG cc_start: 0.8230 (mtp85) cc_final: 0.7933 (mtp180) REVERT: B 1165 MET cc_start: 0.9133 (mtm) cc_final: 0.8929 (mtp) REVERT: C 189 ASP cc_start: 0.6818 (p0) cc_final: 0.6537 (p0) REVERT: C 210 GLU cc_start: 0.7820 (mt-10) cc_final: 0.7388 (pt0) REVERT: C 268 GLN cc_start: 0.6636 (mt0) cc_final: 0.6015 (pt0) REVERT: D 106 GLU cc_start: 0.5942 (mt-10) cc_final: 0.4169 (pm20) REVERT: D 110 GLU cc_start: 0.1395 (tt0) cc_final: 0.0795 (tt0) REVERT: E 61 LEU cc_start: 0.8510 (tp) cc_final: 0.8234 (tp) REVERT: E 91 CYS cc_start: 0.7776 (t) cc_final: 0.7202 (m) REVERT: E 191 VAL cc_start: 0.9054 (OUTLIER) cc_final: 0.8801 (p) REVERT: F 80 MET cc_start: 0.7530 (ptp) cc_final: 0.7259 (ptp) REVERT: F 86 GLU cc_start: 0.7111 (mm-30) cc_final: 0.6853 (mm-30) REVERT: F 100 ARG cc_start: 0.7770 (mtp85) cc_final: 0.7453 (ttm-80) REVERT: G 10 GLU cc_start: 0.6922 (mt-10) cc_final: 0.6198 (mt-10) REVERT: G 104 MET cc_start: -0.0168 (ttp) cc_final: -0.0713 (ttp) REVERT: H 48 TYR cc_start: 0.8319 (t80) cc_final: 0.8018 (t80) REVERT: H 62 SER cc_start: 0.8842 (m) cc_final: 0.8568 (p) REVERT: I 23 MET cc_start: 0.8842 (ttp) cc_final: 0.8586 (ttp) REVERT: I 41 ASN cc_start: 0.7269 (m-40) cc_final: 0.6263 (p0) REVERT: K 2 ASN cc_start: 0.7835 (m-40) cc_final: 0.7600 (m110) REVERT: K 74 ARG cc_start: 0.9076 (ttt-90) cc_final: 0.8755 (ttt-90) outliers start: 90 outliers final: 71 residues processed: 512 average time/residue: 0.2230 time to fit residues: 183.8512 Evaluate side-chains 512 residues out of total 3448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 434 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 647 THR Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 937 ASP Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 947 HIS Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1156 ASP Chi-restraints excluded: chain A residue 1199 MET Chi-restraints excluded: chain A residue 1261 ILE Chi-restraints excluded: chain A residue 1363 VAL Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1421 ARG Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 319 ASN Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 468 GLN Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain B residue 537 GLN Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 760 THR Chi-restraints excluded: chain B residue 796 MET Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 833 THR Chi-restraints excluded: chain B residue 847 LYS Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 903 ILE Chi-restraints excluded: chain B residue 909 VAL Chi-restraints excluded: chain B residue 914 GLU Chi-restraints excluded: chain B residue 958 CYS Chi-restraints excluded: chain B residue 1067 ILE Chi-restraints excluded: chain B residue 1115 GLN Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain E residue 132 GLN Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain H residue 71 ASP Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 108 MET Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain K residue 48 SER Chi-restraints excluded: chain L residue 16 ILE Chi-restraints excluded: chain L residue 25 GLU Chi-restraints excluded: chain L residue 37 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 332 optimal weight: 0.0020 chunk 276 optimal weight: 0.8980 chunk 22 optimal weight: 10.0000 chunk 148 optimal weight: 0.1980 chunk 190 optimal weight: 0.1980 chunk 181 optimal weight: 8.9990 chunk 222 optimal weight: 10.0000 chunk 385 optimal weight: 9.9990 chunk 124 optimal weight: 1.9990 chunk 159 optimal weight: 0.6980 chunk 26 optimal weight: 10.0000 overall best weight: 0.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 757 GLN ** A 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1024 ASN A1163 HIS A1248 ASN ** B 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1071 ASN C 111 GLN D 66 ASN H 46 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.187843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.147375 restraints weight = 37703.608| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.02 r_work: 0.3211 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.3816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 33523 Z= 0.104 Angle : 0.560 10.669 45630 Z= 0.289 Chirality : 0.043 0.297 5104 Planarity : 0.004 0.078 5635 Dihedral : 13.657 170.858 5145 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.67 % Favored : 95.31 % Rotamer: Outliers : 2.01 % Allowed : 12.96 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 1.08 % 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: 0.08 (0.14), residues: 3858 helix: 1.25 (0.15), residues: 1319 sheet: -0.37 (0.21), residues: 567 loop : -0.60 (0.14), residues: 1972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG A 192 TYR 0.021 0.001 TYR B 84 PHE 0.018 0.001 PHE H 35 TRP 0.014 0.001 TRP B 573 HIS 0.008 0.001 HIS K 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 (33492) covalent geometry : angle 0.55028 / 0.29 (45591) hydrogen bonds : bond 0.03381 / 2.32 ( 1288) hydrogen bonds : angle 4.37982 / 3.04 ( 3660) metal coordination : bond 0.00585 / 0.33 ( 31) metal coordination : angle 3.53449 / 2.87 ( 39) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7716 Ramachandran restraints generated. 3858 Oldfield, 0 Emsley, 3858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7716 Ramachandran restraints generated. 3858 Oldfield, 0 Emsley, 3858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 3448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 468 time to evaluate : 1.500 Fit side-chains revert: symmetry clash REVERT: A 67 ARG cc_start: 0.7482 (ttp80) cc_final: 0.7106 (ttp-170) REVERT: A 192 ARG cc_start: 0.7188 (mtm110) cc_final: 0.6730 (mtt90) REVERT: A 241 ARG cc_start: 0.8192 (ptm-80) cc_final: 0.7485 (ptp90) REVERT: A 250 VAL cc_start: 0.9209 (t) cc_final: 0.8929 (m) REVERT: A 266 MET cc_start: 0.1606 (mmm) cc_final: 0.0554 (tpt) REVERT: A 278 HIS cc_start: 0.6885 (m170) cc_final: 0.6455 (t-90) REVERT: A 441 GLN cc_start: 0.7657 (pt0) cc_final: 0.7410 (mt0) REVERT: A 447 GLU cc_start: 0.8685 (mp0) cc_final: 0.8199 (mp0) REVERT: A 540 ASP cc_start: 0.7979 (m-30) cc_final: 0.7687 (m-30) REVERT: A 758 LYS cc_start: 0.8382 (mttt) cc_final: 0.7752 (mmtt) REVERT: A 845 GLU cc_start: 0.7759 (tt0) cc_final: 0.7345 (tt0) REVERT: A 849 ASP cc_start: 0.7752 (m-30) cc_final: 0.7380 (m-30) REVERT: A 928 ARG cc_start: 0.8497 (mtp-110) cc_final: 0.8037 (mtp85) REVERT: A 932 ARG cc_start: 0.6731 (tpt170) cc_final: 0.6453 (tpt90) REVERT: A 942 VAL cc_start: 0.7745 (t) cc_final: 0.7324 (t) REVERT: A 1008 LYS cc_start: 0.7989 (mttt) cc_final: 0.7574 (ttpp) REVERT: A 1097 GLU cc_start: 0.8078 (tm-30) cc_final: 0.7766 (tm-30) REVERT: A 1199 MET cc_start: 0.5999 (OUTLIER) cc_final: 0.4966 (tmm) REVERT: A 1279 MET cc_start: 0.6831 (mmm) cc_final: 0.6618 (ttt) REVERT: A 1306 LYS cc_start: 0.8367 (mttt) cc_final: 0.7805 (mmmt) REVERT: A 1344 MET cc_start: 0.7728 (tpt) cc_final: 0.7085 (mtm) REVERT: A 1376 LYS cc_start: 0.8706 (tptt) cc_final: 0.8320 (mmmt) REVERT: A 1456 GLU cc_start: 0.7813 (mt-10) cc_final: 0.7343 (mt-10) REVERT: B 17 ILE cc_start: 0.8589 (OUTLIER) cc_final: 0.8037 (mm) REVERT: B 19 PRO cc_start: 0.7784 (Cg_endo) cc_final: 0.7160 (Cg_exo) REVERT: B 53 MET cc_start: 0.7714 (mmm) cc_final: 0.6708 (mtm) REVERT: B 173 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.8168 (pt0) REVERT: B 187 ILE cc_start: 0.8769 (OUTLIER) cc_final: 0.8502 (mt) REVERT: B 215 TYR cc_start: 0.8426 (m-10) cc_final: 0.8161 (m-80) REVERT: B 254 GLN cc_start: 0.7867 (mp10) cc_final: 0.7398 (mm-40) REVERT: B 297 MET cc_start: 0.8376 (mtm) cc_final: 0.8106 (mmm) REVERT: B 360 LYS cc_start: 0.8567 (mttt) cc_final: 0.8016 (mtmt) REVERT: B 402 PHE cc_start: 0.7987 (t80) cc_final: 0.7740 (t80) REVERT: B 414 GLU cc_start: 0.6675 (mt-10) cc_final: 0.6244 (mm-30) REVERT: B 436 LYS cc_start: 0.7349 (mttp) cc_final: 0.6600 (ttpp) REVERT: B 582 GLN cc_start: 0.8367 (mm-40) cc_final: 0.7753 (tp40) REVERT: B 847 LYS cc_start: 0.8267 (OUTLIER) cc_final: 0.7825 (mtpp) REVERT: B 1075 MET cc_start: 0.8766 (mmt) cc_final: 0.8480 (mmt) REVERT: B 1118 VAL cc_start: 0.9011 (t) cc_final: 0.8749 (m) REVERT: B 1150 ARG cc_start: 0.8070 (mtp85) cc_final: 0.7803 (mtp180) REVERT: C 189 ASP cc_start: 0.6661 (p0) cc_final: 0.6381 (p0) REVERT: C 210 GLU cc_start: 0.7744 (mt-10) cc_final: 0.7351 (pt0) REVERT: C 268 GLN cc_start: 0.6607 (mt0) cc_final: 0.6003 (pt0) REVERT: D 106 GLU cc_start: 0.5832 (mt-10) cc_final: 0.4182 (pm20) REVERT: D 110 GLU cc_start: 0.1308 (tt0) cc_final: 0.0736 (tt0) REVERT: E 61 LEU cc_start: 0.8388 (tp) cc_final: 0.8141 (tp) REVERT: E 91 CYS cc_start: 0.7740 (t) cc_final: 0.7147 (m) REVERT: E 128 GLU cc_start: 0.8342 (mt-10) cc_final: 0.7833 (mp0) REVERT: F 80 MET cc_start: 0.7576 (ptp) cc_final: 0.7337 (ptp) REVERT: F 86 GLU cc_start: 0.7129 (mm-30) cc_final: 0.6857 (mm-30) REVERT: F 100 ARG cc_start: 0.7665 (mtp85) cc_final: 0.7418 (ttm-80) REVERT: G 10 GLU cc_start: 0.6880 (mt-10) cc_final: 0.5935 (mt-10) REVERT: H 48 TYR cc_start: 0.8259 (t80) cc_final: 0.7995 (t80) REVERT: H 62 SER cc_start: 0.8801 (m) cc_final: 0.8534 (p) REVERT: I 23 MET cc_start: 0.8734 (ttp) cc_final: 0.8487 (ttp) REVERT: I 41 ASN cc_start: 0.7420 (m-40) cc_final: 0.6269 (p0) REVERT: K 2 ASN cc_start: 0.7644 (m-40) cc_final: 0.7443 (m110) REVERT: K 74 ARG cc_start: 0.8973 (ttt-90) cc_final: 0.8734 (ttt-90) outliers start: 69 outliers final: 55 residues processed: 516 average time/residue: 0.2252 time to fit residues: 188.4620 Evaluate side-chains 498 residues out of total 3448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 438 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 647 THR Chi-restraints excluded: chain A residue 687 ILE Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 947 HIS Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1156 ASP Chi-restraints excluded: chain A residue 1199 MET Chi-restraints excluded: chain A residue 1261 ILE Chi-restraints excluded: chain A residue 1363 VAL Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1421 ARG Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 319 ASN Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 468 GLN Chi-restraints excluded: chain B residue 537 GLN Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 760 THR Chi-restraints excluded: chain B residue 796 MET Chi-restraints excluded: chain B residue 833 THR Chi-restraints excluded: chain B residue 847 LYS Chi-restraints excluded: chain B residue 909 VAL Chi-restraints excluded: chain B residue 914 GLU Chi-restraints excluded: chain B residue 1067 ILE Chi-restraints excluded: chain B residue 1115 GLN Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain E residue 132 GLN Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain I residue 108 MET Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain L residue 16 ILE Chi-restraints excluded: chain L residue 37 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 339 optimal weight: 3.9990 chunk 208 optimal weight: 0.0070 chunk 320 optimal weight: 5.9990 chunk 86 optimal weight: 0.9990 chunk 333 optimal weight: 9.9990 chunk 147 optimal weight: 8.9990 chunk 203 optimal weight: 0.9990 chunk 31 optimal weight: 8.9990 chunk 119 optimal weight: 8.9990 chunk 315 optimal weight: 8.9990 chunk 343 optimal weight: 7.9990 overall best weight: 2.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 273 GLN ** A 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 757 GLN A1024 ASN A1163 HIS ** B 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 717 ASN C 111 GLN H 46 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.180996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.140293 restraints weight = 38253.769| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 2.25 r_work: 0.3246 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.3895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 33523 Z= 0.172 Angle : 0.606 11.233 45630 Z= 0.312 Chirality : 0.045 0.294 5104 Planarity : 0.005 0.119 5635 Dihedral : 13.652 170.694 5145 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.95 % Favored : 95.02 % Rotamer: Outliers : 2.13 % Allowed : 13.20 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 1.08 % 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: -0.03 (0.14), residues: 3858 helix: 1.14 (0.15), residues: 1318 sheet: -0.46 (0.20), residues: 589 loop : -0.64 (0.14), residues: 1951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 192 TYR 0.023 0.002 TYR B 811 PHE 0.017 0.002 PHE H 35 TRP 0.037 0.002 TRP B 573 HIS 0.005 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.17 (33492) covalent geometry : angle 0.59536 / 0.31 (45591) hydrogen bonds : bond 0.03864 / 2.62 ( 1288) hydrogen bonds : angle 4.46485 / 3.10 ( 3660) metal coordination : bond 0.00774 / 0.47 ( 31) metal coordination : angle 3.85772 / 3.09 ( 39) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7716 Ramachandran restraints generated. 3858 Oldfield, 0 Emsley, 3858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7716 Ramachandran restraints generated. 3858 Oldfield, 0 Emsley, 3858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 3448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 448 time to evaluate : 1.259 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 ARG cc_start: 0.7525 (ttp80) cc_final: 0.7262 (ttp-170) REVERT: A 138 LYS cc_start: 0.8481 (ttmm) cc_final: 0.8180 (mtpp) REVERT: A 192 ARG cc_start: 0.7404 (mtm110) cc_final: 0.6973 (mtt90) REVERT: A 241 ARG cc_start: 0.8175 (ptm-80) cc_final: 0.7697 (ptp90) REVERT: A 250 VAL cc_start: 0.9222 (t) cc_final: 0.8913 (p) REVERT: A 266 MET cc_start: 0.1611 (mmm) cc_final: 0.0557 (tpt) REVERT: A 278 HIS cc_start: 0.6893 (m170) cc_final: 0.6679 (t-90) REVERT: A 441 GLN cc_start: 0.7747 (pt0) cc_final: 0.7518 (mt0) REVERT: A 447 GLU cc_start: 0.8593 (mp0) cc_final: 0.8246 (mp0) REVERT: A 540 ASP cc_start: 0.7781 (m-30) cc_final: 0.7454 (m-30) REVERT: A 758 LYS cc_start: 0.8488 (mttt) cc_final: 0.7981 (mmtt) REVERT: A 845 GLU cc_start: 0.7630 (tt0) cc_final: 0.7239 (tt0) REVERT: A 849 ASP cc_start: 0.7833 (m-30) cc_final: 0.7439 (m-30) REVERT: A 928 ARG cc_start: 0.8490 (mtp-110) cc_final: 0.8150 (mtp85) REVERT: A 932 ARG cc_start: 0.6714 (tpt170) cc_final: 0.6476 (tpt90) REVERT: A 942 VAL cc_start: 0.7970 (t) cc_final: 0.7524 (t) REVERT: A 1008 LYS cc_start: 0.8069 (mttt) cc_final: 0.7761 (ttpp) REVERT: A 1199 MET cc_start: 0.6131 (OUTLIER) cc_final: 0.5059 (tmm) REVERT: A 1230 GLN cc_start: 0.8189 (mt0) cc_final: 0.7736 (mp10) REVERT: A 1306 LYS cc_start: 0.8416 (mttt) cc_final: 0.7961 (mmmt) REVERT: A 1344 MET cc_start: 0.7966 (tpt) cc_final: 0.7242 (mtm) REVERT: A 1456 GLU cc_start: 0.7643 (mt-10) cc_final: 0.7219 (mt-10) REVERT: B 17 ILE cc_start: 0.8559 (OUTLIER) cc_final: 0.8092 (mm) REVERT: B 173 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8258 (pt0) REVERT: B 187 ILE cc_start: 0.8825 (OUTLIER) cc_final: 0.8576 (mt) REVERT: B 215 TYR cc_start: 0.8319 (m-10) cc_final: 0.8018 (m-80) REVERT: B 254 GLN cc_start: 0.7881 (mp10) cc_final: 0.7514 (mm-40) REVERT: B 297 MET cc_start: 0.8418 (mtm) cc_final: 0.8103 (mmm) REVERT: B 360 LYS cc_start: 0.8693 (mttt) cc_final: 0.8195 (mtmt) REVERT: B 402 PHE cc_start: 0.8085 (t80) cc_final: 0.7867 (t80) REVERT: B 414 GLU cc_start: 0.6861 (mt-10) cc_final: 0.6426 (mm-30) REVERT: B 436 LYS cc_start: 0.7329 (mttp) cc_final: 0.6779 (ttpp) REVERT: B 582 GLN cc_start: 0.8180 (mm-40) cc_final: 0.7733 (tp40) REVERT: B 617 ASP cc_start: 0.7840 (t0) cc_final: 0.7613 (t0) REVERT: B 649 ASN cc_start: 0.8133 (t0) cc_final: 0.7852 (t0) REVERT: B 847 LYS cc_start: 0.8360 (OUTLIER) cc_final: 0.7998 (mtpp) REVERT: B 1075 MET cc_start: 0.8673 (mmt) cc_final: 0.8399 (mmt) REVERT: B 1118 VAL cc_start: 0.9189 (t) cc_final: 0.8973 (m) REVERT: B 1150 ARG cc_start: 0.7764 (mtp85) cc_final: 0.7543 (mtp180) REVERT: C 210 GLU cc_start: 0.7594 (mt-10) cc_final: 0.7303 (pt0) REVERT: C 268 GLN cc_start: 0.6749 (mt0) cc_final: 0.6205 (pt0) REVERT: D 106 GLU cc_start: 0.6035 (mt-10) cc_final: 0.4239 (pm20) REVERT: D 110 GLU cc_start: 0.1339 (tt0) cc_final: 0.1102 (tt0) REVERT: E 91 CYS cc_start: 0.7733 (t) cc_final: 0.7184 (m) REVERT: E 128 GLU cc_start: 0.8262 (mt-10) cc_final: 0.7908 (mp0) REVERT: F 80 MET cc_start: 0.7630 (ptp) cc_final: 0.7414 (ptp) REVERT: F 86 GLU cc_start: 0.7359 (mm-30) cc_final: 0.7126 (mm-30) REVERT: F 100 ARG cc_start: 0.7739 (mtp85) cc_final: 0.7463 (ttm-80) REVERT: G 10 GLU cc_start: 0.6574 (mt-10) cc_final: 0.5725 (mt-10) REVERT: G 104 MET cc_start: 0.0204 (ttp) cc_final: -0.0351 (ttp) REVERT: H 48 TYR cc_start: 0.8234 (t80) cc_final: 0.7988 (t80) REVERT: H 62 SER cc_start: 0.8785 (m) cc_final: 0.8525 (p) REVERT: I 23 MET cc_start: 0.8661 (ttp) cc_final: 0.8402 (ttp) REVERT: I 41 ASN cc_start: 0.7228 (m-40) cc_final: 0.6314 (p0) REVERT: K 2 ASN cc_start: 0.7726 (m-40) cc_final: 0.7521 (m110) REVERT: K 74 ARG cc_start: 0.9010 (ttt-90) cc_final: 0.8712 (ttt-90) REVERT: L 58 ARG cc_start: 0.7756 (mtt180) cc_final: 0.7523 (mtt180) outliers start: 73 outliers final: 60 residues processed: 498 average time/residue: 0.2265 time to fit residues: 181.1738 Evaluate side-chains 496 residues out of total 3448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 431 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 647 THR Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 718 GLU Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1156 ASP Chi-restraints excluded: chain A residue 1199 MET Chi-restraints excluded: chain A residue 1261 ILE Chi-restraints excluded: chain A residue 1363 VAL Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1421 ARG Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 319 ASN Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 468 GLN Chi-restraints excluded: chain B residue 537 GLN Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 760 THR Chi-restraints excluded: chain B residue 796 MET Chi-restraints excluded: chain B residue 833 THR Chi-restraints excluded: chain B residue 847 LYS Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 888 THR Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 909 VAL Chi-restraints excluded: chain B residue 914 GLU Chi-restraints excluded: chain B residue 958 CYS Chi-restraints excluded: chain B residue 1067 ILE Chi-restraints excluded: chain B residue 1115 GLN Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain E residue 132 GLN Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain H residue 71 ASP Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain I residue 108 MET Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain L residue 16 ILE Chi-restraints excluded: chain L residue 37 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 296 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 chunk 242 optimal weight: 0.9980 chunk 284 optimal weight: 10.0000 chunk 361 optimal weight: 10.0000 chunk 223 optimal weight: 0.5980 chunk 243 optimal weight: 5.9990 chunk 251 optimal weight: 10.0000 chunk 331 optimal weight: 9.9990 chunk 191 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 757 GLN ** A 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 947 HIS A1024 ASN A1163 HIS ** B 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 GLN H 46 GLN I 74 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.184267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.143010 restraints weight = 38205.898| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 2.38 r_work: 0.3155 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.3978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 33523 Z= 0.125 Angle : 0.575 11.444 45630 Z= 0.296 Chirality : 0.044 0.294 5104 Planarity : 0.004 0.117 5635 Dihedral : 13.637 170.121 5145 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.74 % Favored : 95.23 % Rotamer: Outliers : 2.13 % Allowed : 13.37 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 1.08 % 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: 0.08 (0.14), residues: 3858 helix: 1.27 (0.15), residues: 1313 sheet: -0.40 (0.20), residues: 589 loop : -0.60 (0.14), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 192 TYR 0.020 0.001 TYR B 217 PHE 0.018 0.001 PHE H 35 TRP 0.028 0.001 TRP B 573 HIS 0.004 0.001 HIS B 749 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 (33492) covalent geometry : angle 0.56528 / 0.30 (45591) hydrogen bonds : bond 0.03530 / 2.41 ( 1288) hydrogen bonds : angle 4.39278 / 3.05 ( 3660) metal coordination : bond 0.00644 / 0.38 ( 31) metal coordination : angle 3.67582 / 2.99 ( 39) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8827.36 seconds wall clock time: 151 minutes 49.06 seconds (9109.06 seconds total)