Starting phenix.real_space_refine on Mon Jul 6 11:05:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mu7_48622/07_2026/9mu7_48622.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mu7_48622/07_2026/9mu7_48622.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9mu7_48622/07_2026/9mu7_48622.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mu7_48622/07_2026/9mu7_48622.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mu7_48622/07_2026/9mu7_48622.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mu7_48622/07_2026/9mu7_48622.map" } resolution = 3.44 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= 0.007 sd= 0.045 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 8 6.06 5 P 99 5.49 5 S 230 5.16 5 C 21088 2.51 5 N 5901 2.21 5 O 6561 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 33887 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 11634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1470, 11634 Classifications: {'peptide': 1470} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 68, 'TRANS': 1398} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 9257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1164, 9257 Classifications: {'peptide': 1164} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 51, 'TRANS': 1112} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 3, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "C" Number of atoms: 2156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2156 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 13, 'TRANS': 255} Chain: "D" Number of atoms: 1058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1058 Classifications: {'peptide': 130} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 125} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 678 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 5, 'TRANS': 78} Chain: "G" Number of atoms: 1344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1344 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 162} Chain: "H" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1186 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 4, 'TRANS': 142} Chain: "I" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 959 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain: "J" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 530 Classifications: {'peptide': 67} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 64} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "K" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 935 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 6, 'TRANS': 109} Chain: "L" Number of atoms: 390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 390 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "R" Number of atoms: 220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 220 Classifications: {'RNA': 10} Modifications used: {'rna3p_pur': 10} Link IDs: {'rna3p': 9} Chain: "T" Number of atoms: 998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 998 Classifications: {'DNA': 50} Link IDs: {'rna3p': 49} Chain: "N" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 819 Classifications: {'DNA': 39} Link IDs: {'rna3p': 38} Chain breaks: 1 Chain: "E" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1715 Classifications: {'peptide': 210} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 200} Chain: "A" 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: "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 469 SG CYS A 67 113.350 90.828 80.696 1.00112.73 S ATOM 491 SG CYS A 70 113.385 87.280 79.309 1.00113.49 S ATOM 538 SG CYS A 77 110.077 89.002 80.009 1.00107.39 S ATOM 774 SG CYS A 107 100.625 82.316 126.126 1.00149.09 S ATOM 803 SG CYS A 110 103.663 80.226 126.413 1.00156.40 S ATOM 1123 SG CYS A 150 100.516 79.249 128.357 1.00171.43 S ATOM 1315 SG CYS A 176 102.488 82.377 129.392 1.00163.60 S ATOM 20460 SG CYS B1221 114.835 75.727 90.596 1.00123.37 S ATOM 20485 SG CYS B1224 111.866 77.649 91.943 1.00124.43 S ATOM 20599 SG CYS B1239 114.879 79.553 90.894 1.00132.95 S ATOM 20618 SG CYS B1242 115.044 77.443 94.040 1.00130.55 S ATOM 21583 SG CYS C 88 78.075 90.278 20.315 1.00156.13 S ATOM 21597 SG CYS C 90 80.516 93.118 21.504 1.00148.84 S ATOM 21630 SG CYS C 94 78.254 93.928 19.073 1.00139.18 S ATOM 21652 SG CYS C 97 76.963 92.673 22.823 1.00140.73 S ATOM 27375 SG CYS I 21 40.110 109.140 137.409 1.00116.11 S ATOM 27399 SG CYS I 24 43.507 110.213 136.559 1.00123.55 S ATOM 27558 SG CYS I 43 42.965 106.771 137.873 1.00134.37 S ATOM 27583 SG CYS I 46 42.461 110.112 140.213 1.00123.19 S ATOM 27936 SG CYS I 90 12.559 95.451 104.787 1.00112.85 S ATOM 27958 SG CYS I 93 10.666 98.603 103.607 1.00119.34 S ATOM 28176 SG CYS I 118 14.226 98.034 102.537 1.00111.65 S ATOM 28214 SG CYS I 123 13.245 98.922 106.196 1.00116.73 S ATOM 28328 SG CYS J 7 51.360 91.291 40.165 1.00109.29 S ATOM 28352 SG CYS J 10 50.303 89.441 36.667 1.00119.99 S ATOM 28617 SG CYS J 44 48.385 89.089 40.001 1.00124.41 S ATOM 28623 SG CYS J 45 48.371 92.235 38.033 1.00115.28 S ATOM 29790 SG CYS L 18 74.191 128.011 52.763 1.00117.90 S ATOM 29809 SG CYS L 21 72.887 131.399 51.196 1.00120.72 S ATOM 29932 SG CYS L 35 76.513 130.908 52.526 1.00119.47 S ATOM 29958 SG CYS L 38 73.356 131.289 54.662 1.00132.30 S Time building chain proxies: 6.65, per 1000 atoms: 0.20 Number of scatterers: 33887 At special positions: 0 Unit cell: (178.839, 166.147, 178.839, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 8 29.99 S 230 16.00 P 99 15.00 O 6561 8.00 N 5901 7.00 C 21088 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: 2.62 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1501 " pdb="ZN ZN A1501 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A1501 " - pdb=" SG CYS A 77 " pdb="ZN ZN A1501 " - pdb=" SG CYS A 70 " pdb="ZN ZN A1501 " - pdb=" SG CYS A 67 " pdb=" ZN A1502 " pdb="ZN ZN A1502 " - pdb=" SG CYS A 107 " pdb="ZN ZN A1502 " - pdb=" SG CYS A 110 " pdb="ZN ZN A1502 " - pdb=" SG CYS A 176 " pdb="ZN ZN A1502 " - pdb=" SG CYS A 150 " pdb=" ZN B2001 " pdb="ZN ZN B2001 " - pdb=" SG CYS B1224 " pdb="ZN ZN B2001 " - pdb=" SG CYS B1239 " pdb="ZN ZN B2001 " - pdb=" SG CYS B1242 " pdb="ZN ZN B2001 " - pdb=" SG CYS B1221 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 90 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 94 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 97 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 21 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 24 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 43 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 46 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 93 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 123 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 118 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 90 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb=" ZN L 201 " pdb="ZN ZN L 201 " - pdb=" SG CYS L 38 " pdb="ZN ZN L 201 " - pdb=" SG CYS L 21 " pdb="ZN ZN L 201 " - pdb=" SG CYS L 35 " pdb="ZN ZN L 201 " - pdb=" SG CYS L 18 " Number of angles added : 45 7932 Ramachandran restraints generated. 3966 Oldfield, 0 Emsley, 3966 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7496 Finding SS restraints... Secondary structure from input PDB file: 141 helices and 46 sheets defined 38.1% alpha, 19.4% beta 46 base pairs and 91 stacking pairs defined. Time for finding SS restraints: 4.26 Creating SS restraints... Processing helix chain 'A' and resid 23 through 31 Processing helix chain 'A' and resid 95 through 104 removed outlier: 4.191A pdb=" N LYS A 101 " --> pdb=" O THR A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 129 Processing helix chain 'A' and resid 132 through 144 Processing helix chain 'A' and resid 209 through 219 removed outlier: 3.803A pdb=" N HIS A 219 " --> pdb=" O GLU A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 228 Processing helix chain 'A' and resid 236 through 239 Processing helix chain 'A' and resid 266 through 288 removed outlier: 3.562A pdb=" N HIS A 270 " --> pdb=" O ASP A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 311 Processing helix chain 'A' and resid 330 through 336 Processing helix chain 'A' and resid 373 through 380 Processing helix chain 'A' and resid 390 through 401 Processing helix chain 'A' and resid 426 through 430 Processing helix chain 'A' and resid 457 through 459 No H-bonds generated for 'chain 'A' and resid 457 through 459' Processing helix chain 'A' and resid 480 through 485 Processing helix chain 'A' and resid 500 through 510 Processing helix chain 'A' and resid 512 through 517 removed outlier: 3.953A pdb=" N ILE A 517 " --> pdb=" O PRO A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 541 removed outlier: 3.521A pdb=" N LEU A 534 " --> pdb=" O VAL A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 556 Processing helix chain 'A' and resid 557 through 559 No H-bonds generated for 'chain 'A' and resid 557 through 559' Processing helix chain 'A' and resid 580 through 588 removed outlier: 4.064A pdb=" N LEU A 586 " --> pdb=" O GLN A 582 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE A 587 " --> pdb=" O ILE A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 653 Processing helix chain 'A' and resid 653 through 676 removed outlier: 3.633A pdb=" N GLY A 662 " --> pdb=" O GLY A 658 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLN A 665 " --> pdb=" O TYR A 661 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR A 666 " --> pdb=" O GLY A 662 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL A 667 " --> pdb=" O ASN A 663 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU A 673 " --> pdb=" O ASN A 669 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N PHE A 674 " --> pdb=" O ASN A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 685 removed outlier: 3.590A pdb=" N THR A 684 " --> pdb=" O ILE A 681 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE A 685 " --> pdb=" O GLY A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 714 Processing helix chain 'A' and resid 724 through 752 Processing helix chain 'A' and resid 756 through 764 Processing helix chain 'A' and resid 769 through 778 Processing helix chain 'A' and resid 808 through 813 Processing helix chain 'A' and resid 824 through 860 removed outlier: 3.736A pdb=" N GLU A 837 " --> pdb=" O MET A 833 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLY A 838 " --> pdb=" O GLY A 834 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU A 839 " --> pdb=" O GLY A 835 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS A 845 " --> pdb=" O ASP A 841 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N THR A 846 " --> pdb=" O THR A 842 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ALA A 847 " --> pdb=" O ALA A 843 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N GLU A 848 " --> pdb=" O VAL A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 882 through 886 Processing helix chain 'A' and resid 904 through 913 Processing helix chain 'A' and resid 918 through 926 Processing helix chain 'A' and resid 927 through 937 Processing helix chain 'A' and resid 939 through 962 Processing helix chain 'A' and resid 974 through 986 removed outlier: 3.557A pdb=" N PHE A 986 " --> pdb=" O VAL A 982 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1012 Processing helix chain 'A' and resid 1019 through 1041 removed outlier: 5.898A pdb=" N LEU A1032 " --> pdb=" O ASN A1028 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N PHE A1033 " --> pdb=" O ALA A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1044 through 1049 Processing helix chain 'A' and resid 1053 through 1071 Processing helix chain 'A' and resid 1078 through 1089 removed outlier: 3.703A pdb=" N LEU A1082 " --> pdb=" O MET A1078 " (cutoff:3.500A) Processing helix chain 'A' and resid 1090 through 1094 removed outlier: 3.660A pdb=" N MET A1094 " --> pdb=" O ALA A1091 " (cutoff:3.500A) Processing helix chain 'A' and resid 1112 through 1121 Processing helix chain 'A' and resid 1137 through 1142 removed outlier: 3.869A pdb=" N ARG A1141 " --> pdb=" O GLY A1137 " (cutoff:3.500A) Processing helix chain 'A' and resid 1142 through 1154 Processing helix chain 'A' and resid 1172 through 1176 removed outlier: 3.998A pdb=" N THR A1176 " --> pdb=" O PRO A1173 " (cutoff:3.500A) Processing helix chain 'A' and resid 1178 through 1189 removed outlier: 3.928A pdb=" N GLU A1183 " --> pdb=" O SER A1179 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N PHE A1184 " --> pdb=" O GLU A1180 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ASN A1186 " --> pdb=" O GLN A1182 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N VAL A1187 " --> pdb=" O GLU A1183 " (cutoff:3.500A) Processing helix chain 'A' and resid 1209 through 1216 Processing helix chain 'A' and resid 1219 through 1232 Processing helix chain 'A' and resid 1272 through 1287 Processing helix chain 'A' and resid 1335 through 1340 removed outlier: 3.858A pdb=" N SER A1340 " --> pdb=" O MET A1336 " (cutoff:3.500A) Processing helix chain 'A' and resid 1353 through 1361 Processing helix chain 'A' and resid 1362 through 1381 removed outlier: 4.032A pdb=" N TYR A1381 " --> pdb=" O VAL A1377 " (cutoff:3.500A) Processing helix chain 'A' and resid 1386 through 1398 removed outlier: 3.780A pdb=" N LEU A1390 " --> pdb=" O ASN A1386 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU A1393 " --> pdb=" O HIS A1389 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR A1398 " --> pdb=" O CYS A1394 " (cutoff:3.500A) Processing helix chain 'A' and resid 1417 through 1423 Processing helix chain 'A' and resid 1426 through 1438 Processing helix chain 'A' and resid 1445 through 1453 removed outlier: 3.819A pdb=" N ASN A1449 " --> pdb=" O GLY A1445 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 38 Processing helix chain 'B' and resid 41 through 63 removed outlier: 3.532A pdb=" N LEU B 45 " --> pdb=" O VAL B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 117 Processing helix chain 'B' and resid 168 through 175 Processing helix chain 'B' and resid 247 through 254 removed outlier: 4.072A pdb=" N ALA B 252 " --> pdb=" O ILE B 248 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE B 253 " --> pdb=" O LYS B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 277 Processing helix chain 'B' and resid 281 through 290 removed outlier: 3.931A pdb=" N ILE B 285 " --> pdb=" O ALA B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 302 removed outlier: 3.808A pdb=" N MET B 299 " --> pdb=" O ASP B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 309 removed outlier: 3.596A pdb=" N LEU B 306 " --> pdb=" O VAL B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 424 Processing helix chain 'B' and resid 433 through 447 removed outlier: 3.671A pdb=" N LYS B 446 " --> pdb=" O GLU B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 478 Processing helix chain 'B' and resid 488 through 490 No H-bonds generated for 'chain 'B' and resid 488 through 490' Processing helix chain 'B' and resid 496 through 523 removed outlier: 3.502A pdb=" N LEU B 500 " --> pdb=" O LEU B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 536 Processing helix chain 'B' and resid 538 through 551 removed outlier: 4.032A pdb=" N THR B 542 " --> pdb=" O THR B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 563 removed outlier: 3.572A pdb=" N GLN B 562 " --> pdb=" O LYS B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 575 through 583 Processing helix chain 'B' and resid 597 through 601 removed outlier: 3.523A pdb=" N GLN B 601 " --> pdb=" O LYS B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 603 through 607 removed outlier: 3.578A pdb=" N LEU B 606 " --> pdb=" O HIS B 603 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TRP B 607 " --> pdb=" O ASN B 604 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 603 through 607' Processing helix chain 'B' and resid 639 through 650 removed outlier: 3.758A pdb=" N SER B 650 " --> pdb=" O LEU B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 658 through 662 removed outlier: 4.057A pdb=" N ILE B 662 " --> pdb=" O PRO B 659 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 695 Processing helix chain 'B' and resid 737 through 748 removed outlier: 3.541A pdb=" N VAL B 741 " --> pdb=" O LYS B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 753 through 760 Processing helix chain 'B' and resid 769 through 773 removed outlier: 3.758A pdb=" N GLU B 772 " --> pdb=" O LEU B 769 " (cutoff:3.500A) Processing helix chain 'B' and resid 779 through 783 Processing helix chain 'B' and resid 801 through 806 removed outlier: 3.576A pdb=" N LEU B 806 " --> pdb=" O ALA B 803 " (cutoff:3.500A) Processing helix chain 'B' and resid 815 through 819 removed outlier: 3.628A pdb=" N ASN B 819 " --> pdb=" O PRO B 816 " (cutoff:3.500A) Processing helix chain 'B' and resid 820 through 831 Processing helix chain 'B' and resid 863 through 868 Processing helix chain 'B' and resid 900 through 906 Processing helix chain 'B' and resid 946 through 950 removed outlier: 4.257A pdb=" N LYS B 949 " --> pdb=" O HIS B 946 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU B 950 " --> pdb=" O TYR B 947 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 946 through 950' Processing helix chain 'B' and resid 983 through 987 removed outlier: 3.727A pdb=" N THR B 986 " --> pdb=" O ASP B 983 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LYS B 987 " --> pdb=" O SER B 984 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 983 through 987' Processing helix chain 'B' and resid 1052 through 1056 Processing helix chain 'B' and resid 1071 through 1074 Processing helix chain 'B' and resid 1079 through 1096 removed outlier: 3.896A pdb=" N LEU B1083 " --> pdb=" O THR B1079 " (cutoff:3.500A) Processing helix chain 'B' and resid 1109 through 1119 removed outlier: 3.847A pdb=" N GLU B1119 " --> pdb=" O THR B1115 " (cutoff:3.500A) Processing helix chain 'B' and resid 1189 through 1200 Processing helix chain 'B' and resid 1201 through 1210 removed outlier: 3.586A pdb=" N LEU B1205 " --> pdb=" O ALA B1201 " (cutoff:3.500A) Processing helix chain 'B' and resid 1255 through 1266 Processing helix chain 'C' and resid 27 through 40 Processing helix chain 'C' and resid 60 through 70 Processing helix chain 'C' and resid 84 through 88 removed outlier: 3.541A pdb=" N CYS C 88 " --> pdb=" O THR C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 120 No H-bonds generated for 'chain 'C' and resid 118 through 120' Processing helix chain 'C' and resid 129 through 133 Processing helix chain 'C' and resid 174 through 178 Processing helix chain 'C' and resid 200 through 204 removed outlier: 3.586A pdb=" N TRP C 204 " --> pdb=" O PRO C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 268 Processing helix chain 'D' and resid 4 through 8 removed outlier: 3.578A pdb=" N ASP D 7 " --> pdb=" O ASP D 4 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 15 removed outlier: 3.543A pdb=" N GLU D 15 " --> pdb=" O LYS D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 39 removed outlier: 3.534A pdb=" N ALA D 39 " --> pdb=" O GLN D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 58 Processing helix chain 'D' and resid 64 through 76 removed outlier: 3.759A pdb=" N ILE D 68 " --> pdb=" O ASN D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 91 Processing helix chain 'D' and resid 95 through 103 Processing helix chain 'D' and resid 111 through 127 Processing helix chain 'F' and resid 50 through 54 removed outlier: 3.679A pdb=" N ARG F 54 " --> pdb=" O LYS F 51 " (cutoff:3.500A) Processing helix chain 'F' and resid 61 through 78 removed outlier: 3.578A pdb=" N ARG F 67 " --> pdb=" O TYR F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 102 removed outlier: 3.518A pdb=" N ILE F 95 " --> pdb=" O ASP F 91 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLN F 102 " --> pdb=" O LYS F 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 18 removed outlier: 3.724A pdb=" N TYR G 17 " --> pdb=" O HIS G 14 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N PHE G 18 " --> pdb=" O PRO G 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 14 through 18' Processing helix chain 'G' and resid 21 through 34 removed outlier: 3.756A pdb=" N VAL G 34 " --> pdb=" O LEU G 30 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 88 removed outlier: 3.781A pdb=" N SER H 87 " --> pdb=" O ARG H 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 129 through 131 No H-bonds generated for 'chain 'H' and resid 129 through 131' Processing helix chain 'I' and resid 67 through 72 Processing helix chain 'I' and resid 73 through 79 removed outlier: 3.518A pdb=" N VAL I 76 " --> pdb=" O VAL I 73 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ILE I 77 " --> pdb=" O PRO I 74 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP I 79 " --> pdb=" O VAL I 76 " (cutoff:3.500A) Processing helix chain 'I' and resid 107 through 111 removed outlier: 3.624A pdb=" N GLU I 110 " --> pdb=" O ARG I 107 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLU I 111 " --> pdb=" O ALA I 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 107 through 111' Processing helix chain 'J' and resid 18 through 28 removed outlier: 3.930A pdb=" N GLU J 28 " --> pdb=" O LEU J 24 " (cutoff:3.500A) Processing helix chain 'J' and resid 30 through 39 Processing helix chain 'J' and resid 42 through 51 removed outlier: 3.948A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 60 Processing helix chain 'K' and resid 5 through 10 removed outlier: 4.090A pdb=" N SER K 9 " --> pdb=" O THR K 6 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE K 10 " --> pdb=" O PHE K 7 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 51 removed outlier: 3.653A pdb=" N GLY K 43 " --> pdb=" O ASP K 39 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 116 removed outlier: 3.563A pdb=" N GLY K 116 " --> pdb=" O LYS K 112 " (cutoff:3.500A) 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 removed outlier: 3.613A pdb=" N ILE E 87 " --> pdb=" O GLY E 83 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 122 Processing helix chain 'E' and resid 133 through 137 removed outlier: 3.666A pdb=" N LEU E 136 " --> pdb=" O SER E 133 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ILE E 137 " --> pdb=" O GLU E 134 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 133 through 137' Processing helix chain 'E' and resid 138 through 142 Processing helix chain 'E' and resid 152 through 163 Processing helix chain 'E' and resid 166 through 170 removed outlier: 3.745A pdb=" N LEU E 170 " --> pdb=" O GLU E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 184 Processing sheet with id=AA1, first strand: chain 'A' and resid 1440 through 1441 removed outlier: 3.703A pdb=" N ARG A 16 " --> pdb=" O MET B1274 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AA3, first strand: chain 'A' and resid 82 through 91 removed outlier: 6.850A pdb=" N THR A 243 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 10.220A pdb=" N LYS A 88 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 10.190A pdb=" N ILE A 241 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 182 through 185 removed outlier: 4.452A pdb=" N LEU A 190 " --> pdb=" O VAL A 208 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 1162 through 1164 removed outlier: 5.913A pdb=" N VAL A 370 " --> pdb=" O LYS A 467 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N PHE A 474 " --> pdb=" O ARG A 356 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL A 358 " --> pdb=" O PHE A 474 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N MET A 476 " --> pdb=" O VAL A 358 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N THR A 360 " --> pdb=" O MET A 476 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 381 through 385 removed outlier: 3.945A pdb=" N TYR A 410 " --> pdb=" O GLU A 439 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N HIS A 441 " --> pdb=" O ALA A 408 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N ALA A 408 " --> pdb=" O HIS A 441 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 546 through 547 Processing sheet with id=AA8, first strand: chain 'A' and resid 571 through 573 removed outlier: 6.174A pdb=" N VAL H 91 " --> pdb=" O LEU A 572 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N HIS H 29 " --> pdb=" O LYS H 13 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N MET H 15 " --> pdb=" O ARG H 27 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ARG H 27 " --> pdb=" O MET H 15 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N LEU H 121 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER H 112 " --> pdb=" O GLU H 100 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG H 98 " --> pdb=" O TYR H 114 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N SER H 116 " --> pdb=" O ILE H 96 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N ILE H 96 " --> pdb=" O SER H 116 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 594 through 597 removed outlier: 6.484A pdb=" N GLU A 623 " --> pdb=" O LEU A 627 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N LEU A 627 " --> pdb=" O GLU A 623 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 781 through 782 Processing sheet with id=AB2, first strand: chain 'A' and resid 864 through 865 Processing sheet with id=AB3, first strand: chain 'A' and resid 894 through 897 Processing sheet with id=AB4, first strand: chain 'A' and resid 1299 through 1302 removed outlier: 3.602A pdb=" N THR A1132 " --> pdb=" O SER A1350 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER A1350 " --> pdb=" O THR A1132 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1156 through 1157 removed outlier: 3.514A pdb=" N GLN A1291 " --> pdb=" O THR A1156 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1235 through 1239 removed outlier: 4.099A pdb=" N LEU A1247 " --> pdb=" O LEU A1208 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ILE A1253 " --> pdb=" O TRP A1202 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N TRP A1202 " --> pdb=" O ILE A1253 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N TYR I 58 " --> pdb=" O ILE A1167 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N TYR A1169 " --> pdb=" O CYS I 56 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N CYS I 56 " --> pdb=" O TYR A1169 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1311 through 1314 Processing sheet with id=AB8, first strand: chain 'F' and resid 118 through 122 removed outlier: 5.008A pdb=" N LEU A1465 " --> pdb=" O ILE G 59 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N GLY G 57 " --> pdb=" O LEU A1467 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL G 66 " --> pdb=" O LEU G 13 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 118 through 122 removed outlier: 5.008A pdb=" N LEU A1465 " --> pdb=" O ILE G 59 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N GLY G 57 " --> pdb=" O LEU A1467 " (cutoff:3.500A) removed outlier: 11.956A pdb=" N VAL G 67 " --> pdb=" O ILE G 54 " (cutoff:3.500A) removed outlier: 10.974A pdb=" N ILE G 54 " --> pdb=" O VAL G 67 " (cutoff:3.500A) removed outlier: 9.122A pdb=" N ASP G 52 " --> pdb=" O PRO G 69 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N LYS G 71 " --> pdb=" O THR G 50 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N THR G 50 " --> pdb=" O LYS G 71 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N LYS G 73 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N VAL G 48 " --> pdb=" O LYS G 73 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ILE G 75 " --> pdb=" O ILE G 46 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR G 39 " --> pdb=" O GLY G 43 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 66 through 67 removed outlier: 5.127A pdb=" N PHE B 85 " --> pdb=" O ASN B 134 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ASN B 134 " --> pdb=" O PHE B 85 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N LEU B 87 " --> pdb=" O THR B 132 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N THR B 132 " --> pdb=" O LEU B 87 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N PHE B 89 " --> pdb=" O THR B 130 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N THR B 130 " --> pdb=" O PHE B 89 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N GLN B 91 " --> pdb=" O ASP B 128 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ALA B 123 " --> pdb=" O GLY B 151 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N GLY B 151 " --> pdb=" O ALA B 123 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N LEU B 125 " --> pdb=" O PHE B 149 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N PHE B 149 " --> pdb=" O LEU B 125 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N VAL B 127 " --> pdb=" O LYS B 147 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS B 147 " --> pdb=" O VAL B 127 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 98 through 100 Processing sheet with id=AC3, first strand: chain 'B' and resid 186 through 188 Processing sheet with id=AC4, first strand: chain 'B' and resid 492 through 495 removed outlier: 6.309A pdb=" N ALA B 197 " --> pdb=" O ASN B 587 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 207 through 210 removed outlier: 3.919A pdb=" N PHE B 218 " --> pdb=" O MET B 240 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 632 through 633 Processing sheet with id=AC7, first strand: chain 'B' and resid 733 through 734 Processing sheet with id=AC8, first strand: chain 'B' and resid 652 through 653 removed outlier: 7.065A pdb=" N ILE B 668 " --> pdb=" O VAL B 675 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ILE B 677 " --> pdb=" O THR B 666 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N THR B 666 " --> pdb=" O ILE B 677 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 849 through 853 removed outlier: 6.032A pdb=" N ARG B1026 " --> pdb=" O VAL B1006 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N VAL B1006 " --> pdb=" O ARG B1026 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N VAL B1028 " --> pdb=" O GLY B1004 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N GLY B1004 " --> pdb=" O VAL B1028 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 849 through 853 removed outlier: 6.032A pdb=" N ARG B1026 " --> pdb=" O VAL B1006 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N VAL B1006 " --> pdb=" O ARG B1026 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N VAL B1028 " --> pdb=" O GLY B1004 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N GLY B1004 " --> pdb=" O VAL B1028 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N VAL B1009 " --> pdb=" O LYS L 45 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 861 through 862 Processing sheet with id=AD3, first strand: chain 'B' and resid 1127 through 1128 removed outlier: 7.716A pdb=" N LEU B 898 " --> pdb=" O GLY B1048 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N GLN B1050 " --> pdb=" O LEU B 898 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N PHE B1144 " --> pdb=" O ILE B 884 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 929 through 931 Processing sheet with id=AD5, first strand: chain 'B' and resid 967 through 969 Processing sheet with id=AD6, first strand: chain 'B' and resid 1058 through 1059 Processing sheet with id=AD7, first strand: chain 'B' and resid 1215 through 1221 Processing sheet with id=AD8, first strand: chain 'B' and resid 1229 through 1231 Processing sheet with id=AD9, first strand: chain 'C' and resid 8 through 14 removed outlier: 6.494A pdb=" N LYS C 20 " --> pdb=" O THR C 12 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N LEU C 14 " --> pdb=" O ASN C 18 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ASN C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N LYS C 229 " --> pdb=" O TYR C 187 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N TYR C 187 " --> pdb=" O LYS C 229 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N PHE C 231 " --> pdb=" O PHE C 185 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N PHE C 185 " --> pdb=" O PHE C 231 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ASN C 233 " --> pdb=" O VAL C 183 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N VAL C 183 " --> pdb=" O ASN C 233 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N GLU C 235 " --> pdb=" O ALA C 181 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 121 through 122 removed outlier: 6.068A pdb=" N GLU C 159 " --> pdb=" O ALA C 54 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N ALA C 54 " --> pdb=" O GLU C 159 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N LYS C 161 " --> pdb=" O LEU C 52 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N LEU C 52 " --> pdb=" O LYS C 161 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ARG C 163 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N VAL C 50 " --> pdb=" O ARG C 163 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N TYR C 165 " --> pdb=" O ASP C 48 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 113 through 116 Processing sheet with id=AE3, first strand: chain 'G' and resid 169 through 170 removed outlier: 3.526A pdb=" N GLY G 169 " --> pdb=" O ARG G 144 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N ILE G 147 " --> pdb=" O THR G 162 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N THR G 162 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N SER G 105 " --> pdb=" O ALA G 159 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N GLY G 161 " --> pdb=" O SER G 105 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N PHE G 107 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N GLY G 96 " --> pdb=" O ILE G 92 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N ILE G 92 " --> pdb=" O GLY G 96 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N PHE G 98 " --> pdb=" O LYS G 90 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 117 through 120 removed outlier: 3.731A pdb=" N TYR G 128 " --> pdb=" O ILE G 137 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 28 through 33 Processing sheet with id=AE6, first strand: chain 'I' and resid 84 through 85 Processing sheet with id=AE7, first strand: chain 'K' and resid 19 through 23 removed outlier: 6.499A pdb=" N VAL K 72 " --> pdb=" O TYR K 61 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N TYR K 61 " --> pdb=" O VAL K 72 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ARG K 74 " --> pdb=" O ALA K 59 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA K 59 " --> pdb=" O ARG K 74 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N GLN K 76 " --> pdb=" O LEU K 57 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 60 through 63 removed outlier: 6.231A pdb=" N GLN E 71 " --> pdb=" O ARG E 101 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N ILE E 103 " --> pdb=" O GLN E 71 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N PHE E 73 " --> pdb=" O ILE E 103 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N VAL E 105 " --> pdb=" O PHE E 73 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N PHE E 75 " --> pdb=" O VAL E 105 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 81 through 82 Processing sheet with id=AF1, first strand: chain 'E' and resid 147 through 150 removed outlier: 6.773A pdb=" N MET E 171 " --> pdb=" O LEU E 208 " (cutoff:3.500A) 1345 hydrogen bonds defined for protein. 3735 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 92 hydrogen bonds 184 hydrogen bond angles 0 basepair planarities 46 basepair parallelities 91 stacking parallelities Total time for adding SS restraints: 10.57 Time building geometry restraints manager: 3.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.38: 13336 1.38 - 1.57: 20833 1.57 - 1.76: 195 1.76 - 1.95: 375 1.95 - 2.14: 1 Bond restraints: 34740 Sorted by residual: bond pdb=" C PRO A 425 " pdb=" N LYS A 426 " ideal model delta sigma weight residual 1.330 2.142 -0.812 1.32e-02 5.74e+03 3.78e+03 bond pdb=" C3' DT T 16 " pdb=" C2' DT T 16 " ideal model delta sigma weight residual 1.516 1.547 -0.031 8.00e-03 1.56e+04 1.49e+01 bond pdb=" C1' DT T 30 " pdb=" N1 DT T 30 " ideal model delta sigma weight residual 1.468 1.515 -0.047 1.40e-02 5.10e+03 1.15e+01 bond pdb=" C3' DT T 12 " pdb=" C2' DT T 12 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.04e+01 bond pdb=" C ASP A 420 " pdb=" N LEU A 421 " ideal model delta sigma weight residual 1.333 1.286 0.046 1.47e-02 4.63e+03 9.99e+00 ... (remaining 34735 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.67: 47081 3.67 - 7.34: 210 7.34 - 11.00: 25 11.00 - 14.67: 3 14.67 - 18.34: 4 Bond angle restraints: 47323 Sorted by residual: angle pdb=" O PRO A 425 " pdb=" C PRO A 425 " pdb=" N LYS A 426 " ideal model delta sigma weight residual 123.00 140.66 -17.66 1.22e+00 6.72e-01 2.10e+02 angle pdb=" CA PRO A 425 " pdb=" C PRO A 425 " pdb=" N LYS A 426 " ideal model delta sigma weight residual 114.82 96.71 18.11 1.35e+00 5.49e-01 1.80e+02 angle pdb=" O ASP A 420 " pdb=" C ASP A 420 " pdb=" N LEU A 421 " ideal model delta sigma weight residual 122.96 113.69 9.27 1.13e+00 7.83e-01 6.73e+01 angle pdb=" C ASP A 420 " pdb=" N LEU A 421 " pdb=" CA LEU A 421 " ideal model delta sigma weight residual 122.26 136.18 -13.92 1.73e+00 3.34e-01 6.47e+01 angle pdb=" C PRO A 425 " pdb=" N LYS A 426 " pdb=" CA LYS A 426 " ideal model delta sigma weight residual 120.87 111.37 9.50 1.42e+00 4.96e-01 4.48e+01 ... (remaining 47318 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 18776 17.88 - 35.76: 1636 35.76 - 53.65: 518 53.65 - 71.53: 118 71.53 - 89.41: 20 Dihedral angle restraints: 21068 sinusoidal: 9465 harmonic: 11603 Sorted by residual: dihedral pdb=" CD ARG A 475 " pdb=" NE ARG A 475 " pdb=" CZ ARG A 475 " pdb=" NH1 ARG A 475 " ideal model delta sinusoidal sigma weight residual 0.00 -86.21 86.21 1 1.00e+01 1.00e-02 8.96e+01 dihedral pdb=" CA ASN B 750 " pdb=" C ASN B 750 " pdb=" N ASN B 751 " pdb=" CA ASN B 751 " ideal model delta harmonic sigma weight residual -180.00 -153.27 -26.73 0 5.00e+00 4.00e-02 2.86e+01 dihedral pdb=" CA PRO E 123 " pdb=" C PRO E 123 " pdb=" N LYS E 124 " pdb=" CA LYS E 124 " ideal model delta harmonic sigma weight residual 180.00 156.14 23.86 0 5.00e+00 4.00e-02 2.28e+01 ... (remaining 21065 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 4385 0.066 - 0.133: 773 0.133 - 0.199: 77 0.199 - 0.266: 5 0.266 - 0.332: 2 Chirality restraints: 5242 Sorted by residual: chirality pdb=" CB ILE A 613 " pdb=" CA ILE A 613 " pdb=" CG1 ILE A 613 " pdb=" CG2 ILE A 613 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.75e+00 chirality pdb=" CA VAL A 60 " pdb=" N VAL A 60 " pdb=" C VAL A 60 " pdb=" CB VAL A 60 " both_signs ideal model delta sigma weight residual False 2.44 2.71 -0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CG LEU A1285 " pdb=" CB LEU A1285 " pdb=" CD1 LEU A1285 " pdb=" CD2 LEU A1285 " both_signs ideal model delta sigma weight residual False -2.59 -2.83 0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 5239 not shown) Planarity restraints: 5804 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 475 " -1.098 9.50e-02 1.11e+02 4.92e-01 1.46e+02 pdb=" NE ARG A 475 " 0.066 2.00e-02 2.50e+03 pdb=" CZ ARG A 475 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG A 475 " -0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG A 475 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 420 " -0.019 2.00e-02 2.50e+03 3.50e-02 1.23e+01 pdb=" C ASP A 420 " 0.061 2.00e-02 2.50e+03 pdb=" O ASP A 420 " -0.021 2.00e-02 2.50e+03 pdb=" N LEU A 421 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 52 " -0.017 2.00e-02 2.50e+03 3.48e-02 1.21e+01 pdb=" C ILE B 52 " 0.060 2.00e-02 2.50e+03 pdb=" O ILE B 52 " -0.023 2.00e-02 2.50e+03 pdb=" N GLN B 53 " -0.020 2.00e-02 2.50e+03 ... (remaining 5801 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 5981 2.77 - 3.31: 29383 3.31 - 3.84: 57917 3.84 - 4.37: 67812 4.37 - 4.90: 114699 Nonbonded interactions: 275792 Sorted by model distance: nonbonded pdb=" OG1 THR F 61 " pdb=" OE1 GLU F 64 " model vdw 2.242 3.040 nonbonded pdb=" OE1 GLN B1142 " pdb=" OG1 THR C 196 " model vdw 2.275 3.040 nonbonded pdb=" OG SER A1200 " pdb=" OD2 ASP A1273 " model vdw 2.279 3.040 nonbonded pdb=" OD1 ASP A 491 " pdb=" O2' A R 46 " model vdw 2.304 3.040 nonbonded pdb=" OG1 THR I 85 " pdb=" OD1 ASP I 87 " model vdw 2.305 3.040 ... (remaining 275787 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: 3.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.580 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 40.750 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 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 : 0.006 0.812 34772 Z= 0.422 Angle : 0.794 18.340 47368 Z= 0.481 Chirality : 0.051 0.332 5242 Planarity : 0.009 0.492 5804 Dihedral : 15.445 89.410 13572 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.12), residues: 3966 helix: -1.29 (0.12), residues: 1314 sheet: -0.06 (0.21), residues: 603 loop : -0.80 (0.13), residues: 2049 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 726 TYR 0.028 0.002 TYR B 854 PHE 0.038 0.002 PHE A 450 TRP 0.017 0.002 TRP C 49 HIS 0.011 0.001 HIS B 288 Details of bonding type rmsd/Z covalent geometry : bond 0.00622 / 0.42 (34740) covalent geometry : angle 0.77665 / 0.48 (47323) hydrogen bonds : bond 0.14660 / 9.73 ( 1405) hydrogen bonds : angle 6.58787 / 4.66 ( 3919) metal coordination : bond 0.00812 / 0.58 ( 32) metal coordination : angle 5.45725 / 3.55 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7932 Ramachandran restraints generated. 3966 Oldfield, 0 Emsley, 3966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7932 Ramachandran restraints generated. 3966 Oldfield, 0 Emsley, 3966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 3517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 304 time to evaluate : 1.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 MET cc_start: 0.8863 (ttt) cc_final: 0.8584 (tmm) REVERT: A 860 MET cc_start: 0.8410 (mtp) cc_final: 0.8201 (mtp) REVERT: A 1420 MET cc_start: 0.8743 (ttt) cc_final: 0.8086 (tmm) REVERT: B 609 MET cc_start: 0.8883 (mmt) cc_final: 0.8574 (mmp) REVERT: B 1078 MET cc_start: 0.9068 (mtt) cc_final: 0.8810 (mtt) REVERT: D 105 SER cc_start: 0.5904 (p) cc_final: 0.5696 (m) REVERT: F 98 LYS cc_start: 0.9273 (tttp) cc_final: 0.8791 (ttpt) REVERT: G 97 MET cc_start: 0.4248 (tpt) cc_final: 0.4004 (mmm) outliers start: 0 outliers final: 0 residues processed: 304 average time/residue: 0.2549 time to fit residues: 121.2324 Evaluate side-chains 194 residues out of total 3517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 3.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 3.9990 chunk 401 optimal weight: 5.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 18 GLN A 118 HIS A 598 HIS ** A 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 731 ASN B 921 ASN B1043 GLN B1142 GLN C 158 GLN C 269 GLN D 36 ASN G 60 GLN H 80 HIS ** I 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 89 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.054226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.036855 restraints weight = 180997.165| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 3.84 r_work: 0.2757 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 34772 Z= 0.292 Angle : 0.688 16.567 47368 Z= 0.353 Chirality : 0.045 0.178 5242 Planarity : 0.005 0.045 5804 Dihedral : 14.797 86.297 5504 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.51 % Allowed : 6.03 % Favored : 93.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.29 (0.13), residues: 3968 helix: 0.27 (0.14), residues: 1341 sheet: -0.08 (0.21), residues: 608 loop : -0.45 (0.13), residues: 2019 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 81 TYR 0.017 0.002 TYR B 913 PHE 0.023 0.002 PHE A 450 TRP 0.018 0.002 TRP B 23 HIS 0.009 0.001 HIS D 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00646 / 0.29 (34740) covalent geometry : angle 0.66652 / 0.35 (47323) hydrogen bonds : bond 0.04706 / 3.09 ( 1405) hydrogen bonds : angle 5.13889 / 3.59 ( 3919) metal coordination : bond 0.01210 / 0.78 ( 32) metal coordination : angle 5.53537 / 3.68 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 3517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 189 time to evaluate : 1.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 MET cc_start: 0.9209 (ttm) cc_final: 0.8907 (ttm) REVERT: A 127 MET cc_start: 0.8962 (ttt) cc_final: 0.8685 (tmm) REVERT: A 156 MET cc_start: 0.1624 (ptt) cc_final: 0.1053 (ptt) REVERT: A 301 MET cc_start: 0.9217 (mmm) cc_final: 0.8853 (mmm) REVERT: A 347 MET cc_start: 0.9427 (mmt) cc_final: 0.9205 (mmp) REVERT: A 860 MET cc_start: 0.8951 (mtp) cc_final: 0.8655 (mtp) REVERT: A 1420 MET cc_start: 0.8823 (ttt) cc_final: 0.7846 (tmm) REVERT: A 1458 MET cc_start: 0.8079 (ppp) cc_final: 0.7661 (ppp) REVERT: B 299 MET cc_start: 0.9108 (mmt) cc_final: 0.8901 (mmt) REVERT: B 448 MET cc_start: 0.8889 (OUTLIER) cc_final: 0.8619 (ttp) REVERT: B 609 MET cc_start: 0.9194 (mmt) cc_final: 0.8986 (mmm) REVERT: B 1078 MET cc_start: 0.9268 (mtt) cc_final: 0.8967 (mtt) REVERT: D 4 ASP cc_start: 0.7843 (t0) cc_final: 0.7170 (p0) REVERT: D 76 MET cc_start: 0.8770 (ptt) cc_final: 0.8480 (ptp) REVERT: D 83 PHE cc_start: 0.7569 (t80) cc_final: 0.7282 (t80) REVERT: D 105 SER cc_start: 0.7201 (p) cc_final: 0.6759 (m) REVERT: F 59 TYR cc_start: 0.8706 (m-80) cc_final: 0.8490 (m-10) REVERT: F 89 GLU cc_start: 0.7702 (tp30) cc_final: 0.6950 (tp30) REVERT: F 94 GLN cc_start: 0.9275 (mm-40) cc_final: 0.8810 (mp10) REVERT: G 1 MET cc_start: 0.8382 (tmm) cc_final: 0.8172 (pmm) REVERT: J 48 MET cc_start: 0.8843 (tpp) cc_final: 0.8631 (mpp) REVERT: E 151 MET cc_start: 0.9098 (mtm) cc_final: 0.8894 (ttm) outliers start: 18 outliers final: 7 residues processed: 200 average time/residue: 0.2204 time to fit residues: 73.3720 Evaluate side-chains 191 residues out of total 3517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 183 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain B residue 448 MET Chi-restraints excluded: chain B residue 1248 ILE Chi-restraints excluded: chain D residue 55 TYR Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain J residue 14 ILE Chi-restraints excluded: chain J residue 66 GLU Chi-restraints excluded: chain K residue 91 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 25 optimal weight: 20.0000 chunk 42 optimal weight: 7.9990 chunk 107 optimal weight: 0.7980 chunk 304 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 264 optimal weight: 5.9990 chunk 236 optimal weight: 1.9990 chunk 184 optimal weight: 2.9990 chunk 344 optimal weight: 8.9990 chunk 307 optimal weight: 9.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 118 HIS ** A 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.054514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.037074 restraints weight = 180352.842| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 3.91 r_work: 0.2768 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 34772 Z= 0.171 Angle : 0.567 15.064 47368 Z= 0.293 Chirality : 0.043 0.176 5242 Planarity : 0.004 0.043 5804 Dihedral : 14.707 87.867 5504 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.60 % Allowed : 7.37 % Favored : 92.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.13), residues: 3968 helix: 0.92 (0.14), residues: 1337 sheet: -0.10 (0.21), residues: 609 loop : -0.25 (0.14), residues: 2022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 81 TYR 0.013 0.001 TYR B1131 PHE 0.022 0.001 PHE A 450 TRP 0.016 0.001 TRP B 23 HIS 0.013 0.001 HIS A1100 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.17 (34740) covalent geometry : angle 0.54406 / 0.29 (47323) hydrogen bonds : bond 0.03847 / 2.52 ( 1405) hydrogen bonds : angle 4.80825 / 3.33 ( 3919) metal coordination : bond 0.00724 / 0.50 ( 32) metal coordination : angle 5.21086 / 3.42 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 3517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 186 time to evaluate : 1.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 MET cc_start: 0.9169 (ttm) cc_final: 0.8764 (ttm) REVERT: A 127 MET cc_start: 0.8966 (ttt) cc_final: 0.8620 (tmm) REVERT: A 156 MET cc_start: 0.2003 (ptt) cc_final: 0.1356 (ptt) REVERT: A 301 MET cc_start: 0.9265 (mmm) cc_final: 0.8878 (mmm) REVERT: A 347 MET cc_start: 0.9375 (mmt) cc_final: 0.9172 (mmp) REVERT: A 501 MET cc_start: 0.8643 (OUTLIER) cc_final: 0.8207 (mtt) REVERT: A 860 MET cc_start: 0.8825 (mtp) cc_final: 0.8533 (mtp) REVERT: A 898 MET cc_start: 0.9106 (tpp) cc_final: 0.8678 (tpt) REVERT: A 1094 MET cc_start: 0.8877 (mtp) cc_final: 0.8257 (mtt) REVERT: A 1420 MET cc_start: 0.8808 (ttt) cc_final: 0.7877 (tmm) REVERT: B 448 MET cc_start: 0.8869 (ttp) cc_final: 0.8654 (ttp) REVERT: B 609 MET cc_start: 0.9220 (mmt) cc_final: 0.8970 (mmm) REVERT: B 630 MET cc_start: 0.9097 (mmt) cc_final: 0.8850 (mmm) REVERT: B 942 MET cc_start: 0.6583 (ptp) cc_final: 0.6345 (ptp) REVERT: B 1078 MET cc_start: 0.9216 (mtt) cc_final: 0.8898 (mtt) REVERT: D 28 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8934 (mt) REVERT: F 59 TYR cc_start: 0.8707 (m-80) cc_final: 0.8459 (m-10) REVERT: F 89 GLU cc_start: 0.7774 (tp30) cc_final: 0.7102 (tp30) REVERT: F 94 GLN cc_start: 0.9210 (mm-40) cc_final: 0.8742 (mp10) REVERT: H 37 MET cc_start: 0.8894 (mmm) cc_final: 0.8244 (mmm) REVERT: J 48 MET cc_start: 0.8800 (tpp) cc_final: 0.8507 (tpp) outliers start: 21 outliers final: 10 residues processed: 202 average time/residue: 0.2080 time to fit residues: 70.4548 Evaluate side-chains 191 residues out of total 3517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 179 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain B residue 523 PHE Chi-restraints excluded: chain B residue 898 LEU Chi-restraints excluded: chain B residue 1248 ILE Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain I residue 56 CYS Chi-restraints excluded: chain J residue 14 ILE Chi-restraints excluded: chain K residue 91 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 102 optimal weight: 0.7980 chunk 208 optimal weight: 5.9990 chunk 381 optimal weight: 30.0000 chunk 314 optimal weight: 20.0000 chunk 171 optimal weight: 8.9990 chunk 295 optimal weight: 2.9990 chunk 221 optimal weight: 0.9980 chunk 111 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 170 optimal weight: 9.9990 chunk 374 optimal weight: 40.0000 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 71 HIS ** K 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.053536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.036207 restraints weight = 180360.376| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 3.79 r_work: 0.2733 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 34772 Z= 0.226 Angle : 0.609 15.732 47368 Z= 0.311 Chirality : 0.043 0.171 5242 Planarity : 0.004 0.046 5804 Dihedral : 14.738 87.671 5504 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.86 % Allowed : 8.60 % Favored : 90.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.41 (0.13), residues: 3968 helix: 1.28 (0.15), residues: 1336 sheet: -0.21 (0.20), residues: 626 loop : -0.16 (0.14), residues: 2006 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 81 TYR 0.016 0.001 TYR A 867 PHE 0.037 0.002 PHE E 44 TRP 0.018 0.001 TRP B 23 HIS 0.006 0.001 HIS B 288 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.23 (34740) covalent geometry : angle 0.58541 / 0.31 (47323) hydrogen bonds : bond 0.03988 / 2.60 ( 1405) hydrogen bonds : angle 4.69480 / 3.25 ( 3919) metal coordination : bond 0.00977 / 0.65 ( 32) metal coordination : angle 5.48198 / 3.58 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 3517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 183 time to evaluate : 1.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 MET cc_start: 0.8996 (mmm) cc_final: 0.8792 (mmm) REVERT: A 54 MET cc_start: 0.9230 (ttm) cc_final: 0.8835 (ttm) REVERT: A 127 MET cc_start: 0.9026 (ttt) cc_final: 0.8690 (tmm) REVERT: A 156 MET cc_start: 0.1651 (ptt) cc_final: 0.1080 (ptt) REVERT: A 301 MET cc_start: 0.9275 (mmm) cc_final: 0.8898 (mmm) REVERT: A 347 MET cc_start: 0.9358 (mmt) cc_final: 0.9141 (mmp) REVERT: A 501 MET cc_start: 0.8699 (OUTLIER) cc_final: 0.8400 (mtt) REVERT: A 860 MET cc_start: 0.8880 (mtp) cc_final: 0.8604 (mtp) REVERT: A 1094 MET cc_start: 0.8819 (mtp) cc_final: 0.8135 (mtt) REVERT: A 1420 MET cc_start: 0.8817 (ttt) cc_final: 0.7907 (tmm) REVERT: A 1458 MET cc_start: 0.8150 (ppp) cc_final: 0.7522 (ppp) REVERT: B 609 MET cc_start: 0.9313 (mmt) cc_final: 0.8994 (mmm) REVERT: B 630 MET cc_start: 0.9187 (mmt) cc_final: 0.8911 (mmm) REVERT: B 743 MET cc_start: 0.9015 (mmp) cc_final: 0.8063 (mmm) REVERT: B 854 TYR cc_start: 0.9110 (OUTLIER) cc_final: 0.8564 (m-10) REVERT: B 1078 MET cc_start: 0.9264 (mtt) cc_final: 0.8987 (mtt) REVERT: D 28 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.8963 (mt) REVERT: D 83 PHE cc_start: 0.7377 (t80) cc_final: 0.6048 (t80) REVERT: F 89 GLU cc_start: 0.7841 (tp30) cc_final: 0.7090 (tp30) REVERT: F 94 GLN cc_start: 0.9290 (mm-40) cc_final: 0.8702 (mp10) REVERT: H 37 MET cc_start: 0.8842 (mmm) cc_final: 0.8351 (mmm) REVERT: J 48 MET cc_start: 0.8861 (tpp) cc_final: 0.8475 (tpp) REVERT: E 94 MET cc_start: 0.9268 (ttt) cc_final: 0.8936 (tpt) REVERT: E 151 MET cc_start: 0.9049 (ttm) cc_final: 0.8800 (ttt) outliers start: 30 outliers final: 12 residues processed: 203 average time/residue: 0.2050 time to fit residues: 70.6740 Evaluate side-chains 192 residues out of total 3517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 177 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 MET Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain B residue 212 LYS Chi-restraints excluded: chain B residue 523 PHE Chi-restraints excluded: chain B residue 854 TYR Chi-restraints excluded: chain B residue 1248 ILE Chi-restraints excluded: chain B residue 1259 LEU Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain I residue 56 CYS Chi-restraints excluded: chain J residue 14 ILE Chi-restraints excluded: chain K residue 91 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 79 optimal weight: 0.1980 chunk 238 optimal weight: 0.9980 chunk 128 optimal weight: 5.9990 chunk 355 optimal weight: 0.9980 chunk 86 optimal weight: 0.7980 chunk 248 optimal weight: 4.9990 chunk 101 optimal weight: 7.9990 chunk 122 optimal weight: 9.9990 chunk 241 optimal weight: 0.7980 chunk 290 optimal weight: 6.9990 chunk 106 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 173 HIS ** A 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 942 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.054436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.037112 restraints weight = 178793.077| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 3.78 r_work: 0.2769 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 34772 Z= 0.107 Angle : 0.527 14.078 47368 Z= 0.270 Chirality : 0.042 0.162 5242 Planarity : 0.003 0.042 5804 Dihedral : 14.688 87.971 5504 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.57 % Allowed : 9.54 % Favored : 89.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.14), residues: 3968 helix: 1.44 (0.15), residues: 1340 sheet: -0.06 (0.20), residues: 614 loop : -0.04 (0.14), residues: 2014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 81 TYR 0.010 0.001 TYR F 59 PHE 0.022 0.001 PHE E 44 TRP 0.016 0.001 TRP B 23 HIS 0.003 0.001 HIS B 288 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.11 (34740) covalent geometry : angle 0.50346 / 0.27 (47323) hydrogen bonds : bond 0.03365 / 2.21 ( 1405) hydrogen bonds : angle 4.51788 / 3.12 ( 3919) metal coordination : bond 0.00691 / 0.46 ( 32) metal coordination : angle 5.05462 / 3.31 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 3517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 187 time to evaluate : 1.309 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 54 MET cc_start: 0.9145 (ttm) cc_final: 0.8749 (ttm) REVERT: A 127 MET cc_start: 0.8980 (ttt) cc_final: 0.8643 (tmm) REVERT: A 156 MET cc_start: 0.1366 (ptt) cc_final: 0.0800 (ptt) REVERT: A 501 MET cc_start: 0.8595 (OUTLIER) cc_final: 0.8291 (mtt) REVERT: A 860 MET cc_start: 0.8775 (mtp) cc_final: 0.8456 (mtp) REVERT: A 1420 MET cc_start: 0.8786 (ttt) cc_final: 0.7903 (tmm) REVERT: A 1458 MET cc_start: 0.8146 (ppp) cc_final: 0.7557 (ppp) REVERT: B 609 MET cc_start: 0.9264 (mmt) cc_final: 0.8979 (mmm) REVERT: B 630 MET cc_start: 0.9153 (mmt) cc_final: 0.8853 (mmm) REVERT: B 854 TYR cc_start: 0.9113 (OUTLIER) cc_final: 0.8604 (m-10) REVERT: B 1078 MET cc_start: 0.9211 (mtt) cc_final: 0.8916 (mtt) REVERT: D 28 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8883 (mt) REVERT: F 83 MET cc_start: 0.8788 (mmp) cc_final: 0.8320 (mmm) REVERT: F 89 GLU cc_start: 0.7870 (tp30) cc_final: 0.7210 (tp30) REVERT: F 94 GLN cc_start: 0.9241 (mm-40) cc_final: 0.8794 (mp10) REVERT: G 10 GLU cc_start: 0.8607 (mp0) cc_final: 0.8214 (mm-30) REVERT: H 37 MET cc_start: 0.8836 (mmm) cc_final: 0.8433 (mmm) REVERT: J 48 MET cc_start: 0.8772 (tpp) cc_final: 0.8391 (tpp) REVERT: E 151 MET cc_start: 0.8972 (ttm) cc_final: 0.8714 (ttt) outliers start: 20 outliers final: 10 residues processed: 200 average time/residue: 0.2040 time to fit residues: 69.7457 Evaluate side-chains 193 residues out of total 3517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 180 time to evaluate : 1.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 MET Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain B residue 212 LYS Chi-restraints excluded: chain B residue 523 PHE Chi-restraints excluded: chain B residue 854 TYR Chi-restraints excluded: chain B residue 1259 LEU Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain I residue 56 CYS Chi-restraints excluded: chain J residue 14 ILE Chi-restraints excluded: chain K residue 91 ILE Chi-restraints excluded: chain E residue 191 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 269 optimal weight: 0.9990 chunk 212 optimal weight: 5.9990 chunk 11 optimal weight: 8.9990 chunk 340 optimal weight: 9.9990 chunk 402 optimal weight: 4.9990 chunk 299 optimal weight: 40.0000 chunk 157 optimal weight: 0.8980 chunk 242 optimal weight: 0.6980 chunk 241 optimal weight: 0.4980 chunk 185 optimal weight: 0.9990 chunk 168 optimal weight: 6.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.054487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.037184 restraints weight = 178579.048| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 3.84 r_work: 0.2775 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 34772 Z= 0.108 Angle : 0.534 16.270 47368 Z= 0.270 Chirality : 0.041 0.192 5242 Planarity : 0.003 0.040 5804 Dihedral : 14.673 87.565 5504 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.83 % Allowed : 9.62 % Favored : 89.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.14), residues: 3968 helix: 1.56 (0.15), residues: 1340 sheet: 0.01 (0.20), residues: 616 loop : 0.02 (0.14), residues: 2012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 30 TYR 0.010 0.001 TYR G 128 PHE 0.028 0.001 PHE G 2 TRP 0.015 0.001 TRP B 23 HIS 0.005 0.001 HIS A 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 (34740) covalent geometry : angle 0.51280 / 0.27 (47323) hydrogen bonds : bond 0.03259 / 2.14 ( 1405) hydrogen bonds : angle 4.40895 / 3.04 ( 3919) metal coordination : bond 0.00611 / 0.43 ( 32) metal coordination : angle 4.85230 / 3.18 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 3517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 183 time to evaluate : 1.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 MET cc_start: 0.9127 (ttm) cc_final: 0.8700 (ttm) REVERT: A 127 MET cc_start: 0.8955 (ttt) cc_final: 0.8601 (tmm) REVERT: A 156 MET cc_start: 0.1470 (ptt) cc_final: 0.0900 (ptt) REVERT: A 301 MET cc_start: 0.9206 (mmm) cc_final: 0.8918 (mmm) REVERT: A 501 MET cc_start: 0.8589 (OUTLIER) cc_final: 0.8299 (mtt) REVERT: A 860 MET cc_start: 0.8726 (mtp) cc_final: 0.8420 (mtp) REVERT: A 1094 MET cc_start: 0.8872 (mtp) cc_final: 0.8247 (mtt) REVERT: A 1420 MET cc_start: 0.8777 (ttt) cc_final: 0.7924 (tmm) REVERT: A 1458 MET cc_start: 0.8118 (ppp) cc_final: 0.7541 (ppp) REVERT: B 609 MET cc_start: 0.9266 (mmt) cc_final: 0.8967 (mmm) REVERT: B 630 MET cc_start: 0.9170 (mmt) cc_final: 0.8872 (mmm) REVERT: B 854 TYR cc_start: 0.9148 (OUTLIER) cc_final: 0.8608 (m-10) REVERT: B 1078 MET cc_start: 0.9208 (mtt) cc_final: 0.8921 (mtt) REVERT: D 28 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8912 (mt) REVERT: F 59 TYR cc_start: 0.8770 (m-80) cc_final: 0.8523 (m-10) REVERT: F 89 GLU cc_start: 0.7941 (tp30) cc_final: 0.7317 (tp30) REVERT: F 94 GLN cc_start: 0.9304 (mm-40) cc_final: 0.8750 (mp10) REVERT: J 48 MET cc_start: 0.8755 (tpp) cc_final: 0.8336 (tpp) REVERT: E 94 MET cc_start: 0.9356 (ttt) cc_final: 0.9042 (tpt) REVERT: E 151 MET cc_start: 0.8964 (ttm) cc_final: 0.8696 (ttt) outliers start: 29 outliers final: 11 residues processed: 203 average time/residue: 0.2075 time to fit residues: 72.1986 Evaluate side-chains 192 residues out of total 3517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 178 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 MET Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 975 LEU Chi-restraints excluded: chain B residue 212 LYS Chi-restraints excluded: chain B residue 523 PHE Chi-restraints excluded: chain B residue 854 TYR Chi-restraints excluded: chain B residue 1259 LEU Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain G residue 97 MET Chi-restraints excluded: chain I residue 56 CYS Chi-restraints excluded: chain E residue 191 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 191 optimal weight: 9.9990 chunk 344 optimal weight: 0.5980 chunk 199 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 136 optimal weight: 0.9990 chunk 91 optimal weight: 7.9990 chunk 96 optimal weight: 7.9990 chunk 171 optimal weight: 10.0000 chunk 238 optimal weight: 5.9990 chunk 359 optimal weight: 7.9990 chunk 123 optimal weight: 10.0000 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.053472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.036237 restraints weight = 180091.684| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 3.76 r_work: 0.2738 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 34772 Z= 0.200 Angle : 0.591 15.026 47368 Z= 0.297 Chirality : 0.042 0.163 5242 Planarity : 0.004 0.045 5804 Dihedral : 14.721 87.413 5504 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.83 % Allowed : 9.85 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.14), residues: 3968 helix: 1.59 (0.15), residues: 1341 sheet: -0.10 (0.20), residues: 619 loop : 0.02 (0.14), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 81 TYR 0.014 0.001 TYR A 867 PHE 0.027 0.001 PHE A 450 TRP 0.018 0.001 TRP B 23 HIS 0.005 0.001 HIS K 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.20 (34740) covalent geometry : angle 0.56720 / 0.30 (47323) hydrogen bonds : bond 0.03693 / 2.40 ( 1405) hydrogen bonds : angle 4.45613 / 3.07 ( 3919) metal coordination : bond 0.00883 / 0.58 ( 32) metal coordination : angle 5.36321 / 3.53 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 3517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 176 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 MET cc_start: 0.9212 (ttm) cc_final: 0.8827 (ttm) REVERT: A 127 MET cc_start: 0.9019 (ttt) cc_final: 0.8656 (tmm) REVERT: A 156 MET cc_start: 0.1625 (ptt) cc_final: 0.1066 (ptt) REVERT: A 301 MET cc_start: 0.9293 (mmm) cc_final: 0.8983 (mmm) REVERT: A 501 MET cc_start: 0.8690 (OUTLIER) cc_final: 0.8409 (mtt) REVERT: A 860 MET cc_start: 0.8861 (mtp) cc_final: 0.8584 (mtp) REVERT: A 1094 MET cc_start: 0.8877 (mtp) cc_final: 0.8540 (mtt) REVERT: A 1336 MET cc_start: 0.9234 (mmm) cc_final: 0.8891 (mmm) REVERT: A 1420 MET cc_start: 0.8830 (ttt) cc_final: 0.7927 (tmm) REVERT: A 1458 MET cc_start: 0.8143 (ppp) cc_final: 0.7522 (ppp) REVERT: B 609 MET cc_start: 0.9337 (mmt) cc_final: 0.9023 (mmm) REVERT: B 630 MET cc_start: 0.9221 (mmt) cc_final: 0.8964 (mmm) REVERT: B 854 TYR cc_start: 0.9128 (OUTLIER) cc_final: 0.8549 (m-10) REVERT: B 866 MET cc_start: 0.9124 (mtp) cc_final: 0.8830 (mtm) REVERT: B 1078 MET cc_start: 0.9293 (mtt) cc_final: 0.8989 (mtt) REVERT: D 28 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8902 (mt) REVERT: F 59 TYR cc_start: 0.8748 (m-80) cc_final: 0.8532 (m-10) REVERT: F 83 MET cc_start: 0.8807 (mmp) cc_final: 0.8440 (mmm) REVERT: F 94 GLN cc_start: 0.9315 (mm-40) cc_final: 0.8708 (mp10) REVERT: J 48 MET cc_start: 0.8817 (tpp) cc_final: 0.8394 (tpp) REVERT: E 94 MET cc_start: 0.9413 (ttt) cc_final: 0.8727 (tpt) REVERT: E 151 MET cc_start: 0.9043 (ttm) cc_final: 0.8767 (ttt) outliers start: 29 outliers final: 17 residues processed: 195 average time/residue: 0.2090 time to fit residues: 69.9908 Evaluate side-chains 196 residues out of total 3517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 176 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 258 MET Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 975 LEU Chi-restraints excluded: chain B residue 212 LYS Chi-restraints excluded: chain B residue 523 PHE Chi-restraints excluded: chain B residue 854 TYR Chi-restraints excluded: chain B residue 898 LEU Chi-restraints excluded: chain B residue 1130 MET Chi-restraints excluded: chain B residue 1259 LEU Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 97 MET Chi-restraints excluded: chain I residue 56 CYS Chi-restraints excluded: chain K residue 91 ILE Chi-restraints excluded: chain E residue 191 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 291 optimal weight: 10.0000 chunk 149 optimal weight: 3.9990 chunk 395 optimal weight: 0.6980 chunk 193 optimal weight: 4.9990 chunk 332 optimal weight: 1.9990 chunk 88 optimal weight: 7.9990 chunk 367 optimal weight: 0.9980 chunk 365 optimal weight: 3.9990 chunk 256 optimal weight: 1.9990 chunk 117 optimal weight: 0.8980 chunk 362 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.054032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.036733 restraints weight = 177761.425| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 3.85 r_work: 0.2757 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 34772 Z= 0.120 Angle : 0.548 14.028 47368 Z= 0.276 Chirality : 0.042 0.155 5242 Planarity : 0.003 0.041 5804 Dihedral : 14.696 87.584 5504 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.77 % Allowed : 10.42 % Favored : 88.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.14), residues: 3968 helix: 1.64 (0.15), residues: 1348 sheet: -0.02 (0.20), residues: 617 loop : 0.07 (0.14), residues: 2003 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 30 TYR 0.010 0.001 TYR H 97 PHE 0.028 0.001 PHE A 450 TRP 0.017 0.001 TRP B 23 HIS 0.003 0.001 HIS K 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (34740) covalent geometry : angle 0.52543 / 0.28 (47323) hydrogen bonds : bond 0.03292 / 2.15 ( 1405) hydrogen bonds : angle 4.36697 / 3.01 ( 3919) metal coordination : bond 0.00626 / 0.44 ( 32) metal coordination : angle 5.05715 / 3.30 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 3517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 181 time to evaluate : 1.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 MET cc_start: 0.9164 (ttm) cc_final: 0.8795 (ttm) REVERT: A 127 MET cc_start: 0.8980 (ttt) cc_final: 0.8610 (tmm) REVERT: A 156 MET cc_start: 0.1738 (ptt) cc_final: 0.1155 (ptt) REVERT: A 301 MET cc_start: 0.9251 (mmm) cc_final: 0.8959 (mmm) REVERT: A 501 MET cc_start: 0.8608 (OUTLIER) cc_final: 0.8322 (mtt) REVERT: A 860 MET cc_start: 0.8754 (mtp) cc_final: 0.8448 (mtp) REVERT: A 1094 MET cc_start: 0.8856 (mtp) cc_final: 0.8237 (mtt) REVERT: A 1336 MET cc_start: 0.9181 (mmm) cc_final: 0.8813 (mmm) REVERT: A 1420 MET cc_start: 0.8811 (ttt) cc_final: 0.7916 (tmm) REVERT: A 1458 MET cc_start: 0.8130 (ppp) cc_final: 0.7543 (ppp) REVERT: B 211 MET cc_start: 0.8616 (mmp) cc_final: 0.8245 (mmt) REVERT: B 609 MET cc_start: 0.9314 (mmt) cc_final: 0.9003 (mmm) REVERT: B 630 MET cc_start: 0.9174 (mmt) cc_final: 0.8923 (mmm) REVERT: B 854 TYR cc_start: 0.9135 (OUTLIER) cc_final: 0.8603 (m-10) REVERT: B 1078 MET cc_start: 0.9230 (mtt) cc_final: 0.8946 (mtt) REVERT: F 59 TYR cc_start: 0.8768 (m-80) cc_final: 0.8563 (m-80) REVERT: F 83 MET cc_start: 0.8852 (mmp) cc_final: 0.8426 (mmm) REVERT: F 94 GLN cc_start: 0.9362 (mm-40) cc_final: 0.8733 (mp10) REVERT: I 63 MET cc_start: 0.8861 (tmm) cc_final: 0.7798 (pmm) REVERT: J 48 MET cc_start: 0.8782 (tpp) cc_final: 0.8384 (tpp) REVERT: E 94 MET cc_start: 0.9390 (ttt) cc_final: 0.9086 (tpt) REVERT: E 151 MET cc_start: 0.9019 (ttm) cc_final: 0.8757 (ttt) outliers start: 27 outliers final: 15 residues processed: 200 average time/residue: 0.2039 time to fit residues: 70.4175 Evaluate side-chains 196 residues out of total 3517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 179 time to evaluate : 1.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 258 MET Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 975 LEU Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain B residue 212 LYS Chi-restraints excluded: chain B residue 523 PHE Chi-restraints excluded: chain B residue 854 TYR Chi-restraints excluded: chain B residue 898 LEU Chi-restraints excluded: chain B residue 1259 LEU Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 97 MET Chi-restraints excluded: chain I residue 56 CYS Chi-restraints excluded: chain E residue 191 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 173 optimal weight: 6.9990 chunk 224 optimal weight: 0.7980 chunk 311 optimal weight: 1.9990 chunk 383 optimal weight: 6.9990 chunk 266 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 159 optimal weight: 6.9990 chunk 118 optimal weight: 6.9990 chunk 149 optimal weight: 2.9990 chunk 394 optimal weight: 10.0000 chunk 24 optimal weight: 0.8980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 43 GLN ** L 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.053712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.036512 restraints weight = 178550.008| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 3.71 r_work: 0.2751 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 34772 Z= 0.154 Angle : 0.569 14.251 47368 Z= 0.285 Chirality : 0.042 0.164 5242 Planarity : 0.003 0.042 5804 Dihedral : 14.708 87.378 5504 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.63 % Allowed : 10.65 % Favored : 88.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.14), residues: 3968 helix: 1.65 (0.15), residues: 1348 sheet: -0.09 (0.20), residues: 618 loop : 0.07 (0.15), residues: 2002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 67 TYR 0.019 0.001 TYR B 207 PHE 0.017 0.001 PHE A 450 TRP 0.022 0.001 TRP A 916 HIS 0.004 0.001 HIS K 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (34740) covalent geometry : angle 0.54671 / 0.28 (47323) hydrogen bonds : bond 0.03412 / 2.22 ( 1405) hydrogen bonds : angle 4.36041 / 3.01 ( 3919) metal coordination : bond 0.00702 / 0.48 ( 32) metal coordination : angle 5.13980 / 3.35 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 3517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 176 time to evaluate : 1.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 MET cc_start: 0.8807 (tpp) cc_final: 0.8201 (mmm) REVERT: A 54 MET cc_start: 0.9214 (ttm) cc_final: 0.8865 (ttm) REVERT: A 127 MET cc_start: 0.9005 (ttt) cc_final: 0.8635 (tmm) REVERT: A 156 MET cc_start: 0.1672 (ptt) cc_final: 0.1116 (ptt) REVERT: A 301 MET cc_start: 0.9235 (mmm) cc_final: 0.8948 (mmm) REVERT: A 501 MET cc_start: 0.8651 (OUTLIER) cc_final: 0.8382 (mtt) REVERT: A 860 MET cc_start: 0.8771 (mtp) cc_final: 0.8462 (mtp) REVERT: A 1094 MET cc_start: 0.8877 (mtp) cc_final: 0.8539 (mtt) REVERT: A 1213 MET cc_start: 0.9109 (mmm) cc_final: 0.8675 (mmm) REVERT: A 1336 MET cc_start: 0.9240 (mmm) cc_final: 0.8900 (mmm) REVERT: A 1420 MET cc_start: 0.8817 (ttt) cc_final: 0.7920 (tmm) REVERT: A 1458 MET cc_start: 0.8126 (ppp) cc_final: 0.7536 (ppp) REVERT: B 211 MET cc_start: 0.8731 (mmp) cc_final: 0.8376 (mmt) REVERT: B 609 MET cc_start: 0.9328 (mmt) cc_final: 0.9005 (mmm) REVERT: B 630 MET cc_start: 0.9198 (mmt) cc_final: 0.8942 (mmm) REVERT: B 743 MET cc_start: 0.9000 (mmp) cc_final: 0.8074 (mmm) REVERT: B 854 TYR cc_start: 0.9120 (OUTLIER) cc_final: 0.8549 (m-10) REVERT: B 1078 MET cc_start: 0.9253 (mtt) cc_final: 0.8965 (mtt) REVERT: D 43 GLN cc_start: 0.3259 (OUTLIER) cc_final: 0.3003 (pp30) REVERT: F 83 MET cc_start: 0.8837 (mmp) cc_final: 0.8462 (mmm) REVERT: F 94 GLN cc_start: 0.9385 (mm-40) cc_final: 0.8753 (mp10) REVERT: I 63 MET cc_start: 0.8923 (tmm) cc_final: 0.8000 (pmm) REVERT: J 48 MET cc_start: 0.8812 (tpp) cc_final: 0.8391 (tpp) REVERT: K 80 ASP cc_start: 0.8750 (p0) cc_final: 0.8537 (p0) REVERT: E 94 MET cc_start: 0.9424 (ttt) cc_final: 0.9099 (tpt) REVERT: E 151 MET cc_start: 0.9021 (ttm) cc_final: 0.8763 (ttt) outliers start: 22 outliers final: 15 residues processed: 192 average time/residue: 0.2059 time to fit residues: 67.3827 Evaluate side-chains 192 residues out of total 3517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 174 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 258 MET Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain B residue 212 LYS Chi-restraints excluded: chain B residue 523 PHE Chi-restraints excluded: chain B residue 854 TYR Chi-restraints excluded: chain B residue 898 LEU Chi-restraints excluded: chain B residue 1130 MET Chi-restraints excluded: chain B residue 1259 LEU Chi-restraints excluded: chain D residue 43 GLN Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 97 MET Chi-restraints excluded: chain I residue 56 CYS Chi-restraints excluded: chain E residue 191 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 235 optimal weight: 5.9990 chunk 331 optimal weight: 1.9990 chunk 224 optimal weight: 0.1980 chunk 282 optimal weight: 0.0870 chunk 260 optimal weight: 8.9990 chunk 120 optimal weight: 6.9990 chunk 314 optimal weight: 3.9990 chunk 2 optimal weight: 7.9990 chunk 258 optimal weight: 3.9990 chunk 226 optimal weight: 0.7980 chunk 107 optimal weight: 10.0000 overall best weight: 1.4162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.053824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.036628 restraints weight = 180415.613| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 3.75 r_work: 0.2757 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 34772 Z= 0.137 Angle : 0.570 14.233 47368 Z= 0.285 Chirality : 0.042 0.158 5242 Planarity : 0.003 0.041 5804 Dihedral : 14.708 87.472 5504 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.63 % Allowed : 10.74 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.14), residues: 3968 helix: 1.64 (0.15), residues: 1350 sheet: -0.06 (0.20), residues: 625 loop : 0.10 (0.15), residues: 1993 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 30 TYR 0.011 0.001 TYR B 207 PHE 0.022 0.001 PHE A 450 TRP 0.017 0.001 TRP B 23 HIS 0.004 0.001 HIS K 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (34740) covalent geometry : angle 0.54887 / 0.28 (47323) hydrogen bonds : bond 0.03333 / 2.19 ( 1405) hydrogen bonds : angle 4.37360 / 3.01 ( 3919) metal coordination : bond 0.00645 / 0.45 ( 32) metal coordination : angle 5.06837 / 3.31 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 3517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 175 time to evaluate : 1.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 MET cc_start: 0.8830 (tpp) cc_final: 0.8233 (mmm) REVERT: A 54 MET cc_start: 0.9195 (ttm) cc_final: 0.8842 (ttm) REVERT: A 127 MET cc_start: 0.9007 (ttt) cc_final: 0.8631 (tmm) REVERT: A 156 MET cc_start: 0.1734 (ptt) cc_final: 0.1172 (ptt) REVERT: A 301 MET cc_start: 0.9233 (mmm) cc_final: 0.8976 (mmm) REVERT: A 501 MET cc_start: 0.8634 (OUTLIER) cc_final: 0.8368 (mtt) REVERT: A 860 MET cc_start: 0.8760 (mtp) cc_final: 0.8455 (mtp) REVERT: A 1094 MET cc_start: 0.8845 (mtp) cc_final: 0.8512 (mtt) REVERT: A 1336 MET cc_start: 0.9228 (mmm) cc_final: 0.8957 (mmm) REVERT: A 1420 MET cc_start: 0.8812 (ttt) cc_final: 0.7929 (tmm) REVERT: A 1458 MET cc_start: 0.8118 (ppp) cc_final: 0.7532 (ppp) REVERT: B 211 MET cc_start: 0.8735 (mmp) cc_final: 0.8399 (mmt) REVERT: B 609 MET cc_start: 0.9332 (mmt) cc_final: 0.9012 (mmm) REVERT: B 630 MET cc_start: 0.9184 (mmt) cc_final: 0.8934 (mmm) REVERT: B 743 MET cc_start: 0.9000 (mmp) cc_final: 0.8107 (mmm) REVERT: B 854 TYR cc_start: 0.9120 (OUTLIER) cc_final: 0.8564 (m-10) REVERT: B 1078 MET cc_start: 0.9232 (mtt) cc_final: 0.8922 (mtt) REVERT: F 83 MET cc_start: 0.8823 (mmp) cc_final: 0.8469 (mmm) REVERT: F 94 GLN cc_start: 0.9394 (mm-40) cc_final: 0.8739 (mp10) REVERT: I 27 MET cc_start: 0.9444 (tpt) cc_final: 0.8384 (tmm) REVERT: I 63 MET cc_start: 0.8937 (tmm) cc_final: 0.7968 (pmm) REVERT: J 48 MET cc_start: 0.8773 (tpp) cc_final: 0.8343 (tpp) REVERT: K 80 ASP cc_start: 0.8761 (p0) cc_final: 0.8548 (p0) REVERT: E 94 MET cc_start: 0.9499 (ttt) cc_final: 0.8985 (tpt) REVERT: E 151 MET cc_start: 0.8990 (ttm) cc_final: 0.8739 (ttt) outliers start: 22 outliers final: 16 residues processed: 189 average time/residue: 0.1915 time to fit residues: 62.5037 Evaluate side-chains 192 residues out of total 3517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 174 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 258 MET Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 212 LYS Chi-restraints excluded: chain B residue 523 PHE Chi-restraints excluded: chain B residue 854 TYR Chi-restraints excluded: chain B residue 898 LEU Chi-restraints excluded: chain B residue 1130 MET Chi-restraints excluded: chain B residue 1259 LEU Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 97 MET Chi-restraints excluded: chain I residue 56 CYS Chi-restraints excluded: chain E residue 191 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 1 optimal weight: 6.9990 chunk 7 optimal weight: 20.0000 chunk 26 optimal weight: 8.9990 chunk 70 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 230 optimal weight: 10.0000 chunk 104 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 293 optimal weight: 10.0000 chunk 117 optimal weight: 0.6980 chunk 211 optimal weight: 2.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 43 GLN ** L 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.053801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.036655 restraints weight = 179857.397| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 3.74 r_work: 0.2754 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8828 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 34772 Z= 0.139 Angle : 0.573 14.822 47368 Z= 0.286 Chirality : 0.042 0.155 5242 Planarity : 0.003 0.042 5804 Dihedral : 14.711 87.501 5504 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.60 % Allowed : 10.77 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.14), residues: 3968 helix: 1.63 (0.15), residues: 1350 sheet: -0.09 (0.20), residues: 614 loop : 0.12 (0.15), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 436 TYR 0.013 0.001 TYR H 48 PHE 0.015 0.001 PHE A 450 TRP 0.018 0.001 TRP B 23 HIS 0.004 0.001 HIS K 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (34740) covalent geometry : angle 0.55148 / 0.28 (47323) hydrogen bonds : bond 0.03325 / 2.18 ( 1405) hydrogen bonds : angle 4.36692 / 3.01 ( 3919) metal coordination : bond 0.00652 / 0.45 ( 32) metal coordination : angle 5.04925 / 3.29 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8032.60 seconds wall clock time: 138 minutes 41.83 seconds (8321.83 seconds total)