Starting phenix.real_space_refine on Fri Jun 27 07:29:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mu8_48623/06_2025/9mu8_48623.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mu8_48623/06_2025/9mu8_48623.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mu8_48623/06_2025/9mu8_48623.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mu8_48623/06_2025/9mu8_48623.map" model { file = "/net/cci-nas-00/data/ceres_data/9mu8_48623/06_2025/9mu8_48623.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mu8_48623/06_2025/9mu8_48623.cif" } resolution = 3.37 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.043 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 217 5.16 5 C 19549 2.51 5 N 5509 2.21 5 O 6103 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 31485 Number of models: 1 Model: "" Number of chains: 19 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, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 3} 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: "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: "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 67 113.323 90.812 80.769 1.00112.73 S ATOM 491 SG CYS A 70 113.358 87.263 79.383 1.00113.49 S ATOM 538 SG CYS A 77 110.050 88.988 80.078 1.00107.39 S ATOM 774 SG CYS A 107 100.534 82.321 126.185 1.00149.09 S ATOM 803 SG CYS A 110 103.570 80.229 126.476 1.00156.40 S ATOM 1123 SG CYS A 150 100.420 79.255 128.416 1.00171.43 S ATOM 1315 SG CYS A 176 102.393 82.381 129.453 1.00163.60 S ATOM 20460 SG CYS B1121 114.786 75.713 90.675 1.00123.37 S ATOM 20485 SG CYS B1124 111.817 77.637 92.017 1.00124.43 S ATOM 20599 SG CYS B1139 114.832 79.539 90.972 1.00132.95 S ATOM 20618 SG CYS B1142 114.991 77.430 94.119 1.00130.55 S ATOM 21583 SG CYS C 88 78.126 90.269 20.342 1.00156.13 S ATOM 21597 SG CYS C 90 80.567 93.107 21.534 1.00148.84 S ATOM 21630 SG CYS C 94 78.309 93.918 19.099 1.00139.18 S ATOM 21652 SG CYS C 97 77.013 92.664 22.848 1.00140.73 S ATOM 24973 SG CYS I 21 40.022 109.187 137.382 1.00116.11 S ATOM 24997 SG CYS I 24 43.421 110.257 136.536 1.00123.55 S ATOM 25156 SG CYS I 43 42.874 106.816 137.850 1.00134.37 S ATOM 25181 SG CYS I 46 42.370 110.158 140.189 1.00123.19 S ATOM 25534 SG CYS I 90 12.505 95.507 104.728 1.00112.85 S ATOM 25556 SG CYS I 93 10.615 98.659 103.545 1.00119.34 S ATOM 25774 SG CYS I 118 14.176 98.087 102.480 1.00111.65 S ATOM 25812 SG CYS I 123 13.191 98.977 106.137 1.00116.73 S ATOM 25926 SG CYS J 7 51.386 91.304 40.158 1.00109.29 S ATOM 25950 SG CYS J 10 50.333 89.453 36.659 1.00119.99 S ATOM 26215 SG CYS J 44 48.410 89.103 39.990 1.00124.41 S ATOM 26221 SG CYS J 45 48.401 92.249 38.021 1.00115.28 S ATOM 27388 SG CYS L 18 74.225 128.013 52.775 1.00117.90 S ATOM 27407 SG CYS L 21 72.925 131.401 51.206 1.00120.72 S ATOM 27530 SG CYS L 35 76.549 130.908 52.541 1.00119.47 S ATOM 27556 SG CYS L 38 73.389 131.291 54.672 1.00132.30 S Time building chain proxies: 17.39, per 1000 atoms: 0.55 Number of scatterers: 31485 At special positions: 0 Unit cell: (130.379, 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 217 16.00 P 99 15.00 O 6103 8.00 N 5509 7.00 C 19549 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: 7.55 Conformation dependent library (CDL) restraints added in 3.9 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 150 " pdb="ZN ZN A1502 " - pdb=" SG CYS A 176 " pdb=" ZN B2001 " pdb="ZN ZN B2001 " - pdb=" SG CYS B1124 " pdb="ZN ZN B2001 " - pdb=" SG CYS B1139 " pdb="ZN ZN B2001 " - pdb=" SG CYS B1142 " pdb="ZN ZN B2001 " - pdb=" SG CYS B1121 " 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 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6930 Finding SS restraints... Secondary structure from input PDB file: 131 helices and 43 sheets defined 38.2% alpha, 17.8% beta 46 base pairs and 91 stacking pairs defined. Time for finding SS restraints: 11.92 Creating SS restraints... Processing helix chain 'A' and resid 23 through 31 Processing helix chain 'A' and resid 95 through 104 removed outlier: 4.190A 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: 3.802A 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: 3.563A 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: 3.952A 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: 4.000A pdb=" N GLN A 665 " --> pdb=" O TYR A 661 " (cutoff:3.500A) removed outlier: 3.517A 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: 3.649A pdb=" N LEU A 673 " --> pdb=" O ASN A 669 " (cutoff:3.500A) removed outlier: 3.941A 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: 3.737A 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: 4.586A 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: 3.558A 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: 5.897A 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: 3.661A 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: 3.870A 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: 3.997A pdb=" N THR A1176 " --> pdb=" O PRO A1173 " (cutoff:3.500A) Processing helix chain 'A' and resid 1178 through 1189 removed outlier: 3.929A 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: 4.872A 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: 4.031A 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: 3.820A 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: 3.533A 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: 3.602A 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: 3.930A 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: 3.597A pdb=" N LEU B 306 " --> pdb=" O VAL B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 324 Processing helix chain 'B' and resid 333 through 347 removed outlier: 3.670A pdb=" N LYS B 346 " --> pdb=" O GLU B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 378 Processing helix chain 'B' and resid 388 through 390 No H-bonds generated for 'chain 'B' and resid 388 through 390' Processing helix chain 'B' and resid 396 through 423 removed outlier: 3.503A pdb=" N LEU B 400 " --> pdb=" O LEU B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 436 Processing helix chain 'B' and resid 438 through 451 removed outlier: 4.032A pdb=" N THR B 442 " --> pdb=" O THR B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 463 removed outlier: 3.573A pdb=" N GLN B 462 " --> pdb=" O LYS B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 483 Processing helix chain 'B' and resid 497 through 501 removed outlier: 3.523A pdb=" N GLN B 501 " --> pdb=" O LYS B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 507 removed outlier: 3.579A pdb=" N LEU B 506 " --> pdb=" O HIS B 503 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TRP B 507 " --> pdb=" O ASN B 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 503 through 507' Processing helix chain 'B' and resid 539 through 550 removed outlier: 3.758A pdb=" N SER B 550 " --> pdb=" O LEU B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 562 removed outlier: 4.057A pdb=" N ILE B 562 " --> pdb=" O PRO B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 595 Processing helix chain 'B' and resid 637 through 648 removed outlier: 3.540A pdb=" N VAL B 641 " --> pdb=" O LYS B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 660 Processing helix chain 'B' and resid 669 through 673 removed outlier: 3.759A pdb=" N GLU B 672 " --> pdb=" O LEU B 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 683 Processing helix chain 'B' and resid 701 through 706 removed outlier: 3.576A pdb=" N LEU B 706 " --> pdb=" O ALA B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 715 through 719 removed outlier: 3.627A pdb=" N ASN B 719 " --> pdb=" O PRO B 716 " (cutoff:3.500A) Processing helix chain 'B' and resid 720 through 731 Processing helix chain 'B' and resid 763 through 768 Processing helix chain 'B' and resid 800 through 806 Processing helix chain 'B' and resid 846 through 850 removed outlier: 4.258A pdb=" N LYS B 849 " --> pdb=" O HIS B 846 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU B 850 " --> pdb=" O TYR B 847 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 846 through 850' Processing helix chain 'B' and resid 883 through 887 removed outlier: 3.727A pdb=" N THR B 886 " --> pdb=" O ASP B 883 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LYS B 887 " --> pdb=" O SER B 884 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 883 through 887' Processing helix chain 'B' and resid 952 through 956 Processing helix chain 'B' and resid 971 through 974 Processing helix chain 'B' and resid 979 through 996 removed outlier: 3.897A pdb=" N LEU B 983 " --> pdb=" O THR B 979 " (cutoff:3.500A) Processing helix chain 'B' and resid 1009 through 1019 removed outlier: 3.847A pdb=" N GLU B1019 " --> pdb=" O THR B1015 " (cutoff:3.500A) Processing helix chain 'B' and resid 1089 through 1100 Processing helix chain 'B' and resid 1101 through 1110 removed outlier: 3.587A pdb=" N LEU B1105 " --> pdb=" O ALA B1101 " (cutoff:3.500A) Processing helix chain 'B' and resid 1155 through 1166 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: 3.542A 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: 3.585A 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 'F' and resid 50 through 54 removed outlier: 3.680A pdb=" N ARG F 54 " --> pdb=" O LYS F 51 " (cutoff:3.500A) Processing helix chain 'F' and resid 61 through 78 removed outlier: 3.577A 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: 3.925A pdb=" N GLN F 102 " --> pdb=" O LYS F 98 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 88 removed outlier: 3.782A 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: 4.101A 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: 3.947A 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: 4.089A 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: 4.066A 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: 3.746A 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 B1174 " (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: 6.849A pdb=" N THR A 243 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 10.219A 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 1062 through 1064 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: 3.946A pdb=" N TYR A 410 " --> pdb=" O GLU A 439 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N HIS A 441 " --> pdb=" O ALA A 408 " (cutoff:3.500A) removed outlier: 7.052A 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: 6.173A 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: 4.554A 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: 3.684A 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: 6.483A pdb=" N GLU A 623 " --> pdb=" O LEU A 627 " (cutoff:3.500A) removed outlier: 5.247A 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: 3.703A 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: 4.098A pdb=" N LEU A1247 " --> pdb=" O LEU A1208 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ILE A1253 " --> pdb=" O TRP A1202 " (cutoff:3.500A) removed outlier: 6.596A 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: 6.892A 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 'A' and resid 1463 through 1467 Processing sheet with id=AB9, 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: 6.701A 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: 5.610A pdb=" N PHE B 89 " --> pdb=" O THR B 130 " (cutoff:3.500A) removed outlier: 7.123A 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: 7.365A 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: 3.584A pdb=" N LYS B 147 " --> pdb=" O VAL B 127 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 98 through 100 Processing sheet with id=AC2, first strand: chain 'B' and resid 186 through 188 Processing sheet with id=AC3, first strand: chain 'B' and resid 392 through 395 removed outlier: 6.308A pdb=" N ALA B 197 " --> pdb=" O ASN B 487 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 207 through 210 removed outlier: 3.918A pdb=" N PHE B 218 " --> pdb=" O MET B 240 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 532 through 533 Processing sheet with id=AC6, first strand: chain 'B' and resid 633 through 634 Processing sheet with id=AC7, first strand: chain 'B' and resid 552 through 553 removed outlier: 7.066A pdb=" N ILE B 568 " --> pdb=" O VAL B 575 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ILE B 577 " --> pdb=" O THR B 566 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N THR B 566 " --> pdb=" O ILE B 577 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 749 through 753 removed outlier: 6.032A pdb=" N ARG B 926 " --> pdb=" O VAL B 906 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N VAL B 906 " --> pdb=" O ARG B 926 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N VAL B 928 " --> pdb=" O GLY B 904 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N GLY B 904 " --> pdb=" O VAL B 928 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 749 through 753 removed outlier: 6.032A pdb=" N ARG B 926 " --> pdb=" O VAL B 906 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N VAL B 906 " --> pdb=" O ARG B 926 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N VAL B 928 " --> pdb=" O GLY B 904 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N GLY B 904 " --> pdb=" O VAL B 928 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N VAL B 909 " --> pdb=" O LYS L 45 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 761 through 762 Processing sheet with id=AD2, first strand: chain 'B' and resid 1027 through 1028 removed outlier: 7.715A pdb=" N LEU B 798 " --> pdb=" O GLY B 948 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLN B 950 " --> pdb=" O LEU B 798 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N PHE B1044 " --> pdb=" O ILE B 784 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 829 through 831 Processing sheet with id=AD4, first strand: chain 'B' and resid 867 through 869 Processing sheet with id=AD5, first strand: chain 'B' and resid 958 through 959 Processing sheet with id=AD6, first strand: chain 'B' and resid 1115 through 1121 Processing sheet with id=AD7, first strand: chain 'B' and resid 1129 through 1131 Processing sheet with id=AD8, 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: 8.229A 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: 4.125A 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: 4.356A 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=AD9, 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: 6.053A 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: 6.835A pdb=" N ARG C 163 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N VAL C 50 " --> pdb=" O ARG C 163 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N TYR C 165 " --> pdb=" O ASP C 48 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 113 through 116 Processing sheet with id=AE2, first strand: chain 'I' and resid 28 through 33 Processing sheet with id=AE3, first strand: chain 'I' and resid 84 through 85 Processing sheet with id=AE4, first strand: chain 'K' and resid 19 through 23 removed outlier: 6.500A pdb=" N VAL K 72 " --> pdb=" O TYR K 61 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N TYR K 61 " --> pdb=" O VAL K 72 " (cutoff:3.500A) removed outlier: 6.587A 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: 6.452A pdb=" N GLN K 76 " --> pdb=" O LEU K 57 " (cutoff:3.500A) Processing sheet with id=AE5, 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: 8.042A pdb=" N ILE E 103 " --> pdb=" O GLN E 71 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N PHE E 73 " --> pdb=" O ILE E 103 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N VAL E 105 " --> pdb=" O PHE E 73 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N PHE E 75 " --> pdb=" O VAL E 105 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 81 through 82 Processing sheet with id=AE7, 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) 1222 hydrogen bonds defined for protein. 3384 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: 19.05 Time building geometry restraints manager: 8.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 5273 1.32 - 1.45: 8557 1.45 - 1.57: 17911 1.57 - 1.70: 194 1.70 - 1.82: 355 Bond restraints: 32290 Sorted by residual: bond pdb=" C PRO A 470 " pdb=" O PRO A 470 " ideal model delta sigma weight residual 1.238 1.195 0.043 1.36e-02 5.41e+03 9.90e+00 bond pdb=" CA SER A 472 " pdb=" CB SER A 472 " ideal model delta sigma weight residual 1.526 1.473 0.052 1.68e-02 3.54e+03 9.71e+00 bond pdb=" N TRP A 471 " pdb=" CA TRP A 471 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.29e-02 6.01e+03 8.10e+00 bond pdb=" N HIS A 424 " pdb=" CA HIS A 424 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.41e-02 5.03e+03 6.45e+00 bond pdb=" N ILE A 61 " pdb=" CA ILE A 61 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.25e-02 6.40e+03 6.08e+00 ... (remaining 32285 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.40: 43750 3.40 - 6.79: 241 6.79 - 10.19: 23 10.19 - 13.58: 4 13.58 - 16.98: 1 Bond angle restraints: 44019 Sorted by residual: angle pdb=" N LEU A 421 " pdb=" CA LEU A 421 " pdb=" C LEU A 421 " ideal model delta sigma weight residual 113.61 102.60 11.01 1.50e+00 4.44e-01 5.38e+01 angle pdb=" N PRO A 470 " pdb=" CA PRO A 470 " pdb=" C PRO A 470 " ideal model delta sigma weight residual 113.47 122.59 -9.12 1.43e+00 4.89e-01 4.07e+01 angle pdb=" C PRO A 470 " pdb=" CA PRO A 470 " pdb=" CB PRO A 470 " ideal model delta sigma weight residual 113.06 103.09 9.97 1.59e+00 3.96e-01 3.93e+01 angle pdb=" N SER A 472 " pdb=" CA SER A 472 " pdb=" C SER A 472 " ideal model delta sigma weight residual 110.44 116.29 -5.85 1.20e+00 6.94e-01 2.38e+01 angle pdb=" CA SER A 472 " pdb=" C SER A 472 " pdb=" O SER A 472 " ideal model delta sigma weight residual 121.89 116.24 5.65 1.29e+00 6.01e-01 1.92e+01 ... (remaining 44014 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 17414 17.88 - 35.76: 1529 35.76 - 53.64: 501 53.64 - 71.52: 115 71.52 - 89.40: 19 Dihedral angle restraints: 19578 sinusoidal: 8853 harmonic: 10725 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 -86.17 86.17 1 1.00e+01 1.00e-02 8.96e+01 dihedral pdb=" CA ASN B 650 " pdb=" C ASN B 650 " pdb=" N ASN B 651 " pdb=" CA ASN B 651 " 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 A 425 " pdb=" C PRO A 425 " pdb=" N LYS A 426 " pdb=" CA LYS A 426 " ideal model delta harmonic sigma weight residual -180.00 -154.89 -25.11 0 5.00e+00 4.00e-02 2.52e+01 ... (remaining 19575 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 4152 0.067 - 0.133: 647 0.133 - 0.200: 67 0.200 - 0.266: 8 0.266 - 0.333: 2 Chirality restraints: 4876 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 2.77e+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 1.78e+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 4873 not shown) Planarity restraints: 5375 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 " 0.012 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 " -0.026 2.00e-02 2.50e+03 5.21e-02 2.72e+01 pdb=" C ASP A 420 " 0.090 2.00e-02 2.50e+03 pdb=" O ASP A 420 " -0.034 2.00e-02 2.50e+03 pdb=" N LEU A 421 " -0.030 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 3.50e-02 1.23e+01 pdb=" C ILE B 52 " 0.061 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 5372 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 5631 2.77 - 3.31: 27347 3.31 - 3.84: 54021 3.84 - 4.37: 63364 4.37 - 4.90: 107096 Nonbonded interactions: 257459 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 B1042 " pdb=" OG1 THR C 196 " model vdw 2.275 3.040 nonbonded pdb=" OG SER A1200 " pdb=" OD2 ASP A1273 " model vdw 2.278 3.040 nonbonded pdb=" OD1 ASP A 491 " pdb=" O2' A R 46 " model vdw 2.303 3.040 nonbonded pdb=" OG1 THR I 85 " pdb=" OD1 ASP I 87 " model vdw 2.305 3.040 ... (remaining 257454 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: 3.460 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: 0.030 Extract box with map and model: 1.290 Check model and map are aligned: 0.240 Set scattering table: 0.290 Process input model: 88.010 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.150 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:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 32322 Z= 0.198 Angle : 0.753 16.981 44064 Z= 0.401 Chirality : 0.050 0.333 4876 Planarity : 0.009 0.492 5375 Dihedral : 15.600 89.397 12648 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.71 % Favored : 96.24 % Rotamer: Outliers : 0.09 % Allowed : 1.20 % Favored : 98.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.12), residues: 3669 helix: -1.25 (0.12), residues: 1222 sheet: -0.12 (0.22), residues: 557 loop : -0.86 (0.13), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 49 HIS 0.011 0.001 HIS B 288 PHE 0.038 0.002 PHE A 450 TYR 0.028 0.002 TYR B 754 ARG 0.006 0.000 ARG A 726 Details of bonding type rmsd hydrogen bonds : bond 0.14880 ( 1294) hydrogen bonds : angle 6.57638 ( 3568) metal coordination : bond 0.00809 ( 32) metal coordination : angle 5.46231 ( 45) covalent geometry : bond 0.00421 (32290) covalent geometry : angle 0.73315 (44019) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 398 time to evaluate : 3.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 421 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8858 (mm) REVERT: A 898 MET cc_start: 0.8741 (tpp) cc_final: 0.8395 (tpt) REVERT: A 1078 MET cc_start: 0.8929 (mmm) cc_final: 0.8034 (mmm) REVERT: B 643 MET cc_start: 0.8748 (mmp) cc_final: 0.8546 (mmp) REVERT: F 98 LYS cc_start: 0.9330 (tttp) cc_final: 0.9026 (tttt) REVERT: I 28 LEU cc_start: 0.8572 (mt) cc_final: 0.8321 (mp) REVERT: K 107 ASP cc_start: 0.8807 (m-30) cc_final: 0.7531 (m-30) outliers start: 3 outliers final: 2 residues processed: 401 average time/residue: 0.4958 time to fit residues: 302.4463 Evaluate side-chains 240 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 237 time to evaluate : 3.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 423 PHE Chi-restraints excluded: chain A residue 424 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 314 optimal weight: 4.9990 chunk 282 optimal weight: 6.9990 chunk 156 optimal weight: 7.9990 chunk 96 optimal weight: 0.0040 chunk 190 optimal weight: 2.9990 chunk 151 optimal weight: 5.9990 chunk 292 optimal weight: 9.9990 chunk 113 optimal weight: 8.9990 chunk 177 optimal weight: 4.9990 chunk 217 optimal weight: 5.9990 chunk 338 optimal weight: 0.9980 overall best weight: 2.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN A 118 HIS A 516 GLN A 598 HIS ** A 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 731 ASN B1018 GLN B1042 GLN ** C 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 269 GLN F 94 GLN I 36 ASN I 71 HIS ** I 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 89 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.059356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.043110 restraints weight = 138481.015| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 3.90 r_work: 0.2799 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 32322 Z= 0.257 Angle : 0.657 16.099 44064 Z= 0.336 Chirality : 0.043 0.180 4876 Planarity : 0.004 0.042 5375 Dihedral : 14.939 89.077 5188 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.05 % Allowed : 6.92 % Favored : 92.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.14), residues: 3669 helix: 0.46 (0.15), residues: 1246 sheet: -0.00 (0.21), residues: 567 loop : -0.46 (0.14), residues: 1856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 28 HIS 0.005 0.001 HIS B 288 PHE 0.015 0.002 PHE K 87 TYR 0.019 0.002 TYR B 813 ARG 0.014 0.001 ARG L 30 Details of bonding type rmsd hydrogen bonds : bond 0.04332 ( 1294) hydrogen bonds : angle 4.97119 ( 3568) metal coordination : bond 0.01101 ( 32) metal coordination : angle 5.34226 ( 45) covalent geometry : bond 0.00568 (32290) covalent geometry : angle 0.63464 (44019) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 241 time to evaluate : 3.960 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 493 MET cc_start: 0.8415 (OUTLIER) cc_final: 0.8076 (tpp) REVERT: A 629 MET cc_start: 0.8118 (mtp) cc_final: 0.7868 (mtm) REVERT: A 853 GLN cc_start: 0.9252 (mt0) cc_final: 0.9022 (mt0) REVERT: A 898 MET cc_start: 0.8634 (tpp) cc_final: 0.8324 (tpt) REVERT: A 1078 MET cc_start: 0.9291 (mmm) cc_final: 0.8977 (mmt) REVERT: A 1094 MET cc_start: 0.8994 (mtp) cc_final: 0.8364 (mtp) REVERT: A 1280 ILE cc_start: 0.8797 (mm) cc_final: 0.8580 (tt) REVERT: A 1359 GLN cc_start: 0.8750 (OUTLIER) cc_final: 0.8545 (pm20) REVERT: A 1392 LEU cc_start: 0.9041 (tp) cc_final: 0.8758 (tt) REVERT: B 211 MET cc_start: 0.8706 (mmm) cc_final: 0.7323 (tpp) REVERT: B 213 ASP cc_start: 0.8900 (p0) cc_final: 0.8497 (p0) REVERT: B 978 MET cc_start: 0.9270 (mtm) cc_final: 0.9009 (mtt) REVERT: B 1077 MET cc_start: 0.8682 (mmm) cc_final: 0.8039 (mmm) REVERT: F 89 GLU cc_start: 0.8511 (mp0) cc_final: 0.7855 (pm20) REVERT: F 97 MET cc_start: 0.9352 (mtm) cc_final: 0.8890 (mtm) REVERT: H 37 MET cc_start: 0.9013 (OUTLIER) cc_final: 0.8314 (mpp) REVERT: H 144 MET cc_start: 0.8218 (ttt) cc_final: 0.7940 (tmm) REVERT: I 116 TYR cc_start: 0.8119 (m-10) cc_final: 0.7869 (m-10) REVERT: J 57 GLU cc_start: 0.9414 (mm-30) cc_final: 0.8811 (tm-30) REVERT: K 22 GLU cc_start: 0.8791 (pt0) cc_final: 0.8461 (pp20) REVERT: K 93 ASP cc_start: 0.8984 (m-30) cc_final: 0.8751 (m-30) REVERT: K 103 GLU cc_start: 0.8507 (tm-30) cc_final: 0.7976 (tm-30) REVERT: K 107 ASP cc_start: 0.8805 (m-30) cc_final: 0.8191 (m-30) outliers start: 34 outliers final: 15 residues processed: 258 average time/residue: 0.4486 time to fit residues: 189.2915 Evaluate side-chains 245 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 227 time to evaluate : 3.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 423 PHE Chi-restraints excluded: chain A residue 493 MET Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 739 ASP Chi-restraints excluded: chain A residue 827 GLU Chi-restraints excluded: chain A residue 1116 LEU Chi-restraints excluded: chain A residue 1359 GLN Chi-restraints excluded: chain A residue 1415 ASP Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 1043 VAL Chi-restraints excluded: chain B residue 1061 ILE Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain H residue 35 PHE Chi-restraints excluded: chain H residue 37 MET Chi-restraints excluded: chain I residue 18 ILE Chi-restraints excluded: chain I residue 57 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 343 optimal weight: 6.9990 chunk 113 optimal weight: 8.9990 chunk 195 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 233 optimal weight: 9.9990 chunk 367 optimal weight: 1.9990 chunk 275 optimal weight: 7.9990 chunk 34 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 HIS A 279 ASN ** A 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1409 HIS ** H 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 36 ASN ** I 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.058022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.041721 restraints weight = 139160.832| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 3.85 r_work: 0.2762 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 32322 Z= 0.252 Angle : 0.636 17.545 44064 Z= 0.322 Chirality : 0.043 0.163 4876 Planarity : 0.004 0.045 5375 Dihedral : 14.871 86.278 5184 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.27 % Allowed : 8.62 % Favored : 90.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.14), residues: 3669 helix: 0.96 (0.15), residues: 1249 sheet: -0.07 (0.21), residues: 563 loop : -0.27 (0.14), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 28 HIS 0.006 0.001 HIS I 125 PHE 0.017 0.002 PHE K 87 TYR 0.016 0.002 TYR B 813 ARG 0.007 0.000 ARG I 106 Details of bonding type rmsd hydrogen bonds : bond 0.04078 ( 1294) hydrogen bonds : angle 4.78290 ( 3568) metal coordination : bond 0.01160 ( 32) metal coordination : angle 5.93380 ( 45) covalent geometry : bond 0.00559 (32290) covalent geometry : angle 0.60753 (44019) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 225 time to evaluate : 3.821 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: A 336 LYS cc_start: 0.9424 (tttt) cc_final: 0.8780 (ttmt) REVERT: A 493 MET cc_start: 0.8607 (OUTLIER) cc_final: 0.8166 (tpp) REVERT: A 853 GLN cc_start: 0.9346 (mt0) cc_final: 0.9145 (mt0) REVERT: A 898 MET cc_start: 0.8691 (tpp) cc_final: 0.8218 (tpt) REVERT: A 1058 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.8556 (pt0) REVERT: A 1078 MET cc_start: 0.9281 (mmm) cc_final: 0.8738 (mmm) REVERT: A 1275 MET cc_start: 0.9428 (mmm) cc_final: 0.9138 (mmm) REVERT: A 1443 MET cc_start: 0.8920 (mtp) cc_final: 0.8674 (mtp) REVERT: B 54 MET cc_start: 0.8932 (mpp) cc_final: 0.8694 (mpp) REVERT: B 211 MET cc_start: 0.8697 (mmm) cc_final: 0.7359 (tpp) REVERT: B 213 ASP cc_start: 0.8864 (p0) cc_final: 0.8416 (p0) REVERT: B 240 MET cc_start: 0.8651 (ttp) cc_final: 0.8272 (ttp) REVERT: B 322 ILE cc_start: 0.9470 (mm) cc_final: 0.9267 (mt) REVERT: B 544 GLU cc_start: 0.9129 (OUTLIER) cc_final: 0.8848 (mt-10) REVERT: B 551 MET cc_start: 0.7577 (ttt) cc_final: 0.6948 (ttt) REVERT: B 754 TYR cc_start: 0.9526 (OUTLIER) cc_final: 0.9073 (m-10) REVERT: B 766 MET cc_start: 0.9060 (mtp) cc_final: 0.8696 (mtm) REVERT: B 978 MET cc_start: 0.9336 (mtm) cc_final: 0.9070 (mtt) REVERT: B 1077 MET cc_start: 0.8634 (mmm) cc_final: 0.8309 (mmm) REVERT: B 1167 MET cc_start: 0.8067 (mmm) cc_final: 0.7672 (mtt) REVERT: F 78 MET cc_start: 0.8638 (mmm) cc_final: 0.8339 (mmm) REVERT: F 89 GLU cc_start: 0.8577 (mp0) cc_final: 0.7936 (mp0) REVERT: F 94 GLN cc_start: 0.9423 (mm110) cc_final: 0.9182 (mm110) REVERT: F 97 MET cc_start: 0.9367 (mtm) cc_final: 0.8739 (mtm) REVERT: H 15 MET cc_start: 0.9056 (ttt) cc_final: 0.8832 (tpp) REVERT: H 37 MET cc_start: 0.9041 (mmm) cc_final: 0.8259 (mpp) REVERT: I 96 ARG cc_start: 0.8739 (mmm160) cc_final: 0.8525 (mmm160) REVERT: I 116 TYR cc_start: 0.8124 (m-10) cc_final: 0.7861 (m-10) REVERT: J 57 GLU cc_start: 0.9366 (mm-30) cc_final: 0.8862 (tm-30) REVERT: K 93 ASP cc_start: 0.8927 (m-30) cc_final: 0.8691 (m-30) REVERT: K 103 GLU cc_start: 0.8622 (tm-30) cc_final: 0.7985 (tm-30) REVERT: K 107 ASP cc_start: 0.8792 (m-30) cc_final: 0.8072 (m-30) REVERT: L 27 MET cc_start: 0.7174 (pmm) cc_final: 0.6943 (pmm) REVERT: E 99 ILE cc_start: 0.7905 (OUTLIER) cc_final: 0.7655 (tt) outliers start: 41 outliers final: 17 residues processed: 251 average time/residue: 0.4466 time to fit residues: 184.5166 Evaluate side-chains 237 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 215 time to evaluate : 3.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain A residue 423 PHE Chi-restraints excluded: chain A residue 424 HIS Chi-restraints excluded: chain A residue 493 MET Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 739 ASP Chi-restraints excluded: chain A residue 827 GLU Chi-restraints excluded: chain A residue 1058 GLU Chi-restraints excluded: chain A residue 1116 LEU Chi-restraints excluded: chain A residue 1415 ASP Chi-restraints excluded: chain A residue 1432 MET Chi-restraints excluded: chain B residue 544 GLU Chi-restraints excluded: chain B residue 754 TYR Chi-restraints excluded: chain B residue 1043 VAL Chi-restraints excluded: chain B residue 1061 ILE Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain H residue 35 PHE Chi-restraints excluded: chain I residue 57 ILE Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain E residue 99 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 302 optimal weight: 0.0070 chunk 225 optimal weight: 0.8980 chunk 334 optimal weight: 0.7980 chunk 367 optimal weight: 0.7980 chunk 242 optimal weight: 0.8980 chunk 188 optimal weight: 8.9990 chunk 246 optimal weight: 5.9990 chunk 241 optimal weight: 3.9990 chunk 207 optimal weight: 3.9990 chunk 310 optimal weight: 0.9990 chunk 269 optimal weight: 1.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 HIS ** A 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 942 GLN ** H 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 36 ASN ** I 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 25 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.059371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.042947 restraints weight = 138352.314| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 3.93 r_work: 0.2803 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 32322 Z= 0.111 Angle : 0.543 14.822 44064 Z= 0.275 Chirality : 0.041 0.156 4876 Planarity : 0.003 0.040 5375 Dihedral : 14.837 86.773 5184 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.02 % Allowed : 9.60 % Favored : 89.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.14), residues: 3669 helix: 1.33 (0.15), residues: 1245 sheet: 0.01 (0.21), residues: 566 loop : -0.14 (0.15), residues: 1858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 28 HIS 0.003 0.001 HIS A 801 PHE 0.012 0.001 PHE K 87 TYR 0.017 0.001 TYR H 48 ARG 0.005 0.000 ARG L 28 Details of bonding type rmsd hydrogen bonds : bond 0.03322 ( 1294) hydrogen bonds : angle 4.49821 ( 3568) metal coordination : bond 0.00604 ( 32) metal coordination : angle 5.16847 ( 45) covalent geometry : bond 0.00246 (32290) covalent geometry : angle 0.51746 (44019) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 229 time to evaluate : 3.716 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 347 MET cc_start: 0.9088 (mmt) cc_final: 0.8786 (mmp) REVERT: A 493 MET cc_start: 0.8315 (OUTLIER) cc_final: 0.7984 (tpp) REVERT: A 853 GLN cc_start: 0.9282 (mt0) cc_final: 0.9054 (mt0) REVERT: A 1094 MET cc_start: 0.8927 (mtp) cc_final: 0.8499 (mtp) REVERT: A 1275 MET cc_start: 0.9398 (mmm) cc_final: 0.9138 (mmm) REVERT: A 1392 LEU cc_start: 0.9071 (tp) cc_final: 0.8786 (tt) REVERT: A 1443 MET cc_start: 0.8904 (mtp) cc_final: 0.8597 (mtp) REVERT: B 211 MET cc_start: 0.8753 (mmm) cc_final: 0.8186 (tpp) REVERT: B 544 GLU cc_start: 0.9145 (OUTLIER) cc_final: 0.8804 (mt-10) REVERT: B 704 MET cc_start: 0.8840 (mmm) cc_final: 0.8344 (mmm) REVERT: B 754 TYR cc_start: 0.9523 (OUTLIER) cc_final: 0.8986 (m-10) REVERT: B 766 MET cc_start: 0.8915 (mtp) cc_final: 0.8539 (mtm) REVERT: B 978 MET cc_start: 0.9277 (mtm) cc_final: 0.9005 (mtt) REVERT: B 1077 MET cc_start: 0.8668 (mmm) cc_final: 0.8054 (mmm) REVERT: B 1167 MET cc_start: 0.8004 (mmm) cc_final: 0.7756 (mtt) REVERT: B 1174 MET cc_start: 0.9185 (mmm) cc_final: 0.8953 (mmm) REVERT: C 248 MET cc_start: 0.9183 (mtt) cc_final: 0.8625 (mtt) REVERT: F 78 MET cc_start: 0.8620 (mmm) cc_final: 0.8268 (mmm) REVERT: F 89 GLU cc_start: 0.8502 (mp0) cc_final: 0.7941 (pm20) REVERT: F 94 GLN cc_start: 0.9411 (mm110) cc_final: 0.9185 (mm110) REVERT: F 97 MET cc_start: 0.9455 (mtm) cc_final: 0.8705 (mtm) REVERT: H 144 MET cc_start: 0.7885 (tmm) cc_final: 0.7243 (tmm) REVERT: I 63 MET cc_start: 0.8912 (ppp) cc_final: 0.8600 (ptt) REVERT: J 57 GLU cc_start: 0.9353 (mm-30) cc_final: 0.8830 (tm-30) REVERT: K 45 MET cc_start: 0.8915 (mmm) cc_final: 0.8635 (mmm) REVERT: K 88 MET cc_start: 0.9288 (mmm) cc_final: 0.9045 (mmm) REVERT: K 93 ASP cc_start: 0.8947 (m-30) cc_final: 0.8717 (m-30) REVERT: K 103 GLU cc_start: 0.8463 (tm-30) cc_final: 0.7694 (tm-30) REVERT: K 107 ASP cc_start: 0.8794 (m-30) cc_final: 0.7992 (m-30) REVERT: L 27 MET cc_start: 0.7023 (pmm) cc_final: 0.6807 (pmm) REVERT: E 43 MET cc_start: 0.9214 (ttt) cc_final: 0.8897 (tmm) REVERT: E 44 PHE cc_start: 0.8229 (m-80) cc_final: 0.7300 (m-80) outliers start: 33 outliers final: 16 residues processed: 250 average time/residue: 0.4252 time to fit residues: 176.4108 Evaluate side-chains 237 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 218 time to evaluate : 3.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain A residue 423 PHE Chi-restraints excluded: chain A residue 424 HIS Chi-restraints excluded: chain A residue 493 MET Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 739 ASP Chi-restraints excluded: chain A residue 827 GLU Chi-restraints excluded: chain A residue 942 GLN Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain A residue 1116 LEU Chi-restraints excluded: chain A residue 1370 VAL Chi-restraints excluded: chain B residue 544 GLU Chi-restraints excluded: chain B residue 754 TYR Chi-restraints excluded: chain B residue 1043 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain H residue 35 PHE Chi-restraints excluded: chain I residue 57 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 241 optimal weight: 3.9990 chunk 178 optimal weight: 0.9990 chunk 305 optimal weight: 0.8980 chunk 302 optimal weight: 0.8980 chunk 72 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 147 optimal weight: 9.9990 chunk 223 optimal weight: 2.9990 chunk 166 optimal weight: 2.9990 chunk 179 optimal weight: 0.7980 chunk 195 optimal weight: 0.5980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 36 ASN ** I 104 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 = 0.3486 r_free = 0.3486 target = 0.059480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.043120 restraints weight = 137727.129| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 3.86 r_work: 0.2811 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 32322 Z= 0.116 Angle : 0.534 14.349 44064 Z= 0.269 Chirality : 0.041 0.164 4876 Planarity : 0.003 0.038 5375 Dihedral : 14.817 87.052 5184 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.96 % Allowed : 10.13 % Favored : 88.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.14), residues: 3669 helix: 1.51 (0.15), residues: 1247 sheet: -0.01 (0.21), residues: 575 loop : -0.06 (0.15), residues: 1847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 49 HIS 0.004 0.001 HIS I 125 PHE 0.010 0.001 PHE C 21 TYR 0.016 0.001 TYR K 13 ARG 0.007 0.000 ARG C 81 Details of bonding type rmsd hydrogen bonds : bond 0.03188 ( 1294) hydrogen bonds : angle 4.37686 ( 3568) metal coordination : bond 0.00577 ( 32) metal coordination : angle 4.92204 ( 45) covalent geometry : bond 0.00259 (32290) covalent geometry : angle 0.51015 (44019) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 227 time to evaluate : 3.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 336 LYS cc_start: 0.9386 (tttt) cc_final: 0.9109 (ptmm) REVERT: A 347 MET cc_start: 0.9071 (mmt) cc_final: 0.8767 (mmp) REVERT: A 493 MET cc_start: 0.8256 (OUTLIER) cc_final: 0.7915 (tpp) REVERT: A 629 MET cc_start: 0.7971 (mtp) cc_final: 0.7679 (mtm) REVERT: A 1094 MET cc_start: 0.8889 (mtp) cc_final: 0.8480 (mtp) REVERT: A 1275 MET cc_start: 0.9416 (mmm) cc_final: 0.9122 (mmm) REVERT: A 1392 LEU cc_start: 0.9063 (tp) cc_final: 0.8786 (tt) REVERT: B 211 MET cc_start: 0.8741 (mmm) cc_final: 0.8173 (tpp) REVERT: B 298 MET cc_start: 0.8991 (mmt) cc_final: 0.8209 (mmt) REVERT: B 544 GLU cc_start: 0.9140 (OUTLIER) cc_final: 0.8784 (mt-10) REVERT: B 568 ILE cc_start: 0.8511 (OUTLIER) cc_final: 0.8039 (mp) REVERT: B 704 MET cc_start: 0.8816 (mmm) cc_final: 0.8337 (mmm) REVERT: B 754 TYR cc_start: 0.9514 (OUTLIER) cc_final: 0.9067 (m-10) REVERT: B 766 MET cc_start: 0.8896 (mtp) cc_final: 0.8518 (mtm) REVERT: B 978 MET cc_start: 0.9294 (mtm) cc_final: 0.9019 (mtt) REVERT: B 1077 MET cc_start: 0.8685 (mmm) cc_final: 0.8054 (mmm) REVERT: B 1167 MET cc_start: 0.7965 (mmm) cc_final: 0.7688 (mtt) REVERT: C 248 MET cc_start: 0.9206 (mtt) cc_final: 0.8633 (mtt) REVERT: F 78 MET cc_start: 0.8637 (mmm) cc_final: 0.8250 (mmm) REVERT: F 89 GLU cc_start: 0.8468 (mp0) cc_final: 0.7864 (pm20) REVERT: F 97 MET cc_start: 0.9481 (mtm) cc_final: 0.8727 (mtm) REVERT: H 144 MET cc_start: 0.8027 (tmm) cc_final: 0.7350 (tmm) REVERT: I 63 MET cc_start: 0.8939 (ppp) cc_final: 0.8682 (ptt) REVERT: I 116 TYR cc_start: 0.8005 (m-10) cc_final: 0.7796 (m-10) REVERT: J 57 GLU cc_start: 0.9342 (mm-30) cc_final: 0.8867 (tm-30) REVERT: K 93 ASP cc_start: 0.8930 (m-30) cc_final: 0.8701 (m-30) REVERT: K 103 GLU cc_start: 0.8575 (tm-30) cc_final: 0.7899 (tm-30) REVERT: K 107 ASP cc_start: 0.8812 (m-30) cc_final: 0.8040 (m-30) REVERT: L 27 MET cc_start: 0.7105 (pmm) cc_final: 0.6895 (pmm) REVERT: E 44 PHE cc_start: 0.8262 (m-80) cc_final: 0.7652 (m-80) REVERT: E 94 MET cc_start: 0.9043 (mtp) cc_final: 0.8817 (ttt) outliers start: 31 outliers final: 20 residues processed: 244 average time/residue: 0.4302 time to fit residues: 172.8653 Evaluate side-chains 237 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 213 time to evaluate : 3.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 423 PHE Chi-restraints excluded: chain A residue 424 HIS Chi-restraints excluded: chain A residue 493 MET Chi-restraints excluded: chain A residue 583 ILE Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 739 ASP Chi-restraints excluded: chain A residue 827 GLU Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain A residue 1116 LEU Chi-restraints excluded: chain B residue 544 GLU Chi-restraints excluded: chain B residue 568 ILE Chi-restraints excluded: chain B residue 754 TYR Chi-restraints excluded: chain B residue 1043 VAL Chi-restraints excluded: chain B residue 1061 ILE Chi-restraints excluded: chain B residue 1094 ASP Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain H residue 35 PHE Chi-restraints excluded: chain I residue 57 ILE Chi-restraints excluded: chain L residue 14 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 277 optimal weight: 10.0000 chunk 245 optimal weight: 7.9990 chunk 216 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 24 optimal weight: 0.0050 chunk 229 optimal weight: 0.0970 chunk 54 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 chunk 32 optimal weight: 4.9990 chunk 289 optimal weight: 10.0000 chunk 212 optimal weight: 0.9990 overall best weight: 1.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 104 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 = 0.3479 r_free = 0.3479 target = 0.059186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.042841 restraints weight = 138752.391| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 3.85 r_work: 0.2801 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 32322 Z= 0.133 Angle : 0.539 14.737 44064 Z= 0.272 Chirality : 0.041 0.154 4876 Planarity : 0.003 0.039 5375 Dihedral : 14.799 86.801 5184 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.96 % Allowed : 10.56 % Favored : 88.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.14), residues: 3669 helix: 1.64 (0.15), residues: 1248 sheet: 0.04 (0.21), residues: 564 loop : -0.05 (0.15), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 49 HIS 0.004 0.001 HIS I 125 PHE 0.010 0.001 PHE K 87 TYR 0.016 0.001 TYR K 13 ARG 0.013 0.000 ARG A 399 Details of bonding type rmsd hydrogen bonds : bond 0.03226 ( 1294) hydrogen bonds : angle 4.32854 ( 3568) metal coordination : bond 0.00626 ( 32) metal coordination : angle 4.96946 ( 45) covalent geometry : bond 0.00298 (32290) covalent geometry : angle 0.51484 (44019) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 223 time to evaluate : 3.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 336 LYS cc_start: 0.9382 (tttt) cc_final: 0.8702 (ttmt) REVERT: A 493 MET cc_start: 0.8296 (OUTLIER) cc_final: 0.7944 (tpp) REVERT: A 629 MET cc_start: 0.7980 (mtp) cc_final: 0.7716 (mtm) REVERT: A 1094 MET cc_start: 0.8838 (mtp) cc_final: 0.8498 (mtp) REVERT: A 1275 MET cc_start: 0.9403 (mmm) cc_final: 0.9094 (mmm) REVERT: A 1392 LEU cc_start: 0.9068 (tp) cc_final: 0.8784 (tt) REVERT: B 211 MET cc_start: 0.8741 (mmm) cc_final: 0.8250 (tpp) REVERT: B 240 MET cc_start: 0.8481 (ttp) cc_final: 0.8103 (ttp) REVERT: B 568 ILE cc_start: 0.8608 (OUTLIER) cc_final: 0.8155 (mp) REVERT: B 704 MET cc_start: 0.8802 (mmm) cc_final: 0.8339 (mmm) REVERT: B 754 TYR cc_start: 0.9518 (OUTLIER) cc_final: 0.9066 (m-10) REVERT: B 978 MET cc_start: 0.9294 (mtm) cc_final: 0.9019 (mtt) REVERT: B 1077 MET cc_start: 0.8746 (mmm) cc_final: 0.8300 (mmm) REVERT: B 1167 MET cc_start: 0.7956 (mmm) cc_final: 0.7740 (mtt) REVERT: B 1174 MET cc_start: 0.9214 (mmm) cc_final: 0.8984 (mmm) REVERT: C 248 MET cc_start: 0.9192 (mtt) cc_final: 0.8633 (mtt) REVERT: F 89 GLU cc_start: 0.8482 (mp0) cc_final: 0.7868 (mp0) REVERT: F 97 MET cc_start: 0.9514 (mtm) cc_final: 0.8849 (mtm) REVERT: F 101 LYS cc_start: 0.9390 (mmtm) cc_final: 0.9180 (mmtm) REVERT: J 57 GLU cc_start: 0.9330 (mm-30) cc_final: 0.8903 (tm-30) REVERT: K 45 MET cc_start: 0.8758 (mmm) cc_final: 0.8500 (mmm) REVERT: K 93 ASP cc_start: 0.8886 (m-30) cc_final: 0.8646 (m-30) REVERT: K 103 GLU cc_start: 0.8593 (tm-30) cc_final: 0.7949 (tm-30) REVERT: K 107 ASP cc_start: 0.8811 (m-30) cc_final: 0.8031 (m-30) REVERT: E 44 PHE cc_start: 0.8231 (m-80) cc_final: 0.7552 (m-80) REVERT: E 94 MET cc_start: 0.9031 (mtp) cc_final: 0.8753 (ttt) outliers start: 31 outliers final: 19 residues processed: 240 average time/residue: 0.4160 time to fit residues: 164.9776 Evaluate side-chains 237 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 215 time to evaluate : 3.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 423 PHE Chi-restraints excluded: chain A residue 424 HIS Chi-restraints excluded: chain A residue 493 MET Chi-restraints excluded: chain A residue 583 ILE Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 739 ASP Chi-restraints excluded: chain A residue 827 GLU Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain A residue 1116 LEU Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 568 ILE Chi-restraints excluded: chain B residue 754 TYR Chi-restraints excluded: chain B residue 1061 ILE Chi-restraints excluded: chain B residue 1094 ASP Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain H residue 35 PHE Chi-restraints excluded: chain I residue 57 ILE Chi-restraints excluded: chain K residue 25 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 137 optimal weight: 6.9990 chunk 156 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 11 optimal weight: 0.0060 chunk 365 optimal weight: 0.7980 chunk 107 optimal weight: 0.7980 chunk 322 optimal weight: 0.7980 chunk 265 optimal weight: 0.9990 chunk 178 optimal weight: 0.7980 chunk 110 optimal weight: 2.9990 chunk 264 optimal weight: 2.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 853 GLN A1454 GLN ** H 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.059564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.043425 restraints weight = 138751.017| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 3.91 r_work: 0.2823 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 32322 Z= 0.106 Angle : 0.537 13.872 44064 Z= 0.269 Chirality : 0.040 0.160 4876 Planarity : 0.003 0.040 5375 Dihedral : 14.776 86.938 5184 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.93 % Allowed : 10.59 % Favored : 88.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.14), residues: 3669 helix: 1.67 (0.15), residues: 1258 sheet: 0.02 (0.21), residues: 580 loop : 0.00 (0.15), residues: 1831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 49 HIS 0.003 0.000 HIS I 64 PHE 0.023 0.001 PHE E 44 TYR 0.017 0.001 TYR K 13 ARG 0.006 0.000 ARG A 399 Details of bonding type rmsd hydrogen bonds : bond 0.03024 ( 1294) hydrogen bonds : angle 4.26263 ( 3568) metal coordination : bond 0.00549 ( 32) metal coordination : angle 4.71920 ( 45) covalent geometry : bond 0.00236 (32290) covalent geometry : angle 0.51527 (44019) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 223 time to evaluate : 4.695 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: A 336 LYS cc_start: 0.9389 (tttt) cc_final: 0.8708 (ttmt) REVERT: A 493 MET cc_start: 0.8250 (OUTLIER) cc_final: 0.7937 (tpp) REVERT: A 629 MET cc_start: 0.7918 (mtp) cc_final: 0.7650 (mtm) REVERT: A 1094 MET cc_start: 0.8792 (mtp) cc_final: 0.8528 (mtp) REVERT: A 1275 MET cc_start: 0.9354 (mmm) cc_final: 0.9041 (mmm) REVERT: A 1392 LEU cc_start: 0.9063 (tp) cc_final: 0.8778 (tt) REVERT: B 211 MET cc_start: 0.8821 (mmm) cc_final: 0.8274 (tpp) REVERT: B 568 ILE cc_start: 0.8480 (OUTLIER) cc_final: 0.8004 (mp) REVERT: B 704 MET cc_start: 0.8772 (mmm) cc_final: 0.8314 (mmm) REVERT: B 754 TYR cc_start: 0.9503 (OUTLIER) cc_final: 0.9043 (m-10) REVERT: B 766 MET cc_start: 0.8747 (mtp) cc_final: 0.8349 (mtm) REVERT: B 818 ASP cc_start: 0.7979 (t0) cc_final: 0.7247 (m-30) REVERT: B 978 MET cc_start: 0.9295 (mtm) cc_final: 0.9014 (mtt) REVERT: B 1077 MET cc_start: 0.8726 (mmm) cc_final: 0.8286 (mmm) REVERT: B 1174 MET cc_start: 0.9213 (mmm) cc_final: 0.8979 (mmm) REVERT: C 248 MET cc_start: 0.9182 (mtt) cc_final: 0.8636 (mtt) REVERT: F 89 GLU cc_start: 0.8522 (mp0) cc_final: 0.7888 (pm20) REVERT: F 97 MET cc_start: 0.9450 (mtm) cc_final: 0.8686 (mtm) REVERT: H 144 MET cc_start: 0.8125 (tmm) cc_final: 0.7327 (tmm) REVERT: I 116 TYR cc_start: 0.7989 (m-10) cc_final: 0.7777 (m-10) REVERT: J 57 GLU cc_start: 0.9314 (mm-30) cc_final: 0.8888 (tm-30) REVERT: K 45 MET cc_start: 0.8788 (mmm) cc_final: 0.8543 (mmm) REVERT: K 93 ASP cc_start: 0.8894 (m-30) cc_final: 0.8665 (m-30) REVERT: K 103 GLU cc_start: 0.8560 (tm-30) cc_final: 0.7906 (tm-30) REVERT: K 107 ASP cc_start: 0.8796 (m-30) cc_final: 0.7990 (m-30) REVERT: E 44 PHE cc_start: 0.8193 (m-80) cc_final: 0.7845 (m-80) REVERT: E 94 MET cc_start: 0.9012 (mtp) cc_final: 0.8698 (ttt) outliers start: 30 outliers final: 19 residues processed: 240 average time/residue: 0.4775 time to fit residues: 188.9636 Evaluate side-chains 239 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 217 time to evaluate : 3.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 423 PHE Chi-restraints excluded: chain A residue 424 HIS Chi-restraints excluded: chain A residue 493 MET Chi-restraints excluded: chain A residue 583 ILE Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 739 ASP Chi-restraints excluded: chain A residue 827 GLU Chi-restraints excluded: chain A residue 853 GLN Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain A residue 1111 LEU Chi-restraints excluded: chain A residue 1116 LEU Chi-restraints excluded: chain B residue 568 ILE Chi-restraints excluded: chain B residue 754 TYR Chi-restraints excluded: chain B residue 1094 ASP Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain H residue 35 PHE Chi-restraints excluded: chain I residue 57 ILE Chi-restraints excluded: chain K residue 25 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 78 optimal weight: 4.9990 chunk 43 optimal weight: 6.9990 chunk 113 optimal weight: 9.9990 chunk 314 optimal weight: 0.7980 chunk 84 optimal weight: 6.9990 chunk 170 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 16 optimal weight: 0.3980 chunk 267 optimal weight: 4.9990 chunk 228 optimal weight: 7.9990 chunk 123 optimal weight: 10.0000 overall best weight: 3.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 HIS ** A 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 853 GLN A1305 GLN ** H 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.056766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.040275 restraints weight = 142539.043| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 3.86 r_work: 0.2722 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.3438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.086 32322 Z= 0.320 Angle : 0.716 18.697 44064 Z= 0.356 Chirality : 0.044 0.170 4876 Planarity : 0.005 0.090 5375 Dihedral : 14.947 85.017 5184 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.02 % Allowed : 10.99 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.14), residues: 3669 helix: 1.35 (0.15), residues: 1248 sheet: -0.16 (0.21), residues: 564 loop : -0.17 (0.14), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 28 HIS 0.008 0.001 HIS B 145 PHE 0.020 0.002 PHE K 87 TYR 0.022 0.002 TYR A 851 ARG 0.020 0.001 ARG A 399 Details of bonding type rmsd hydrogen bonds : bond 0.04470 ( 1294) hydrogen bonds : angle 4.71800 ( 3568) metal coordination : bond 0.01492 ( 32) metal coordination : angle 6.31040 ( 45) covalent geometry : bond 0.00708 (32290) covalent geometry : angle 0.68723 (44019) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 210 time to evaluate : 3.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 MET cc_start: 0.0316 (OUTLIER) cc_final: -0.1573 (mtt) REVERT: A 336 LYS cc_start: 0.9393 (tttt) cc_final: 0.8726 (ttmt) REVERT: A 493 MET cc_start: 0.8647 (OUTLIER) cc_final: 0.8186 (tpp) REVERT: A 1336 MET cc_start: 0.9149 (mmm) cc_final: 0.8707 (mmm) REVERT: B 211 MET cc_start: 0.8837 (mmm) cc_final: 0.7637 (tpp) REVERT: B 213 ASP cc_start: 0.9147 (p0) cc_final: 0.8816 (p0) REVERT: B 568 ILE cc_start: 0.8710 (OUTLIER) cc_final: 0.8276 (mp) REVERT: B 754 TYR cc_start: 0.9530 (OUTLIER) cc_final: 0.9154 (m-10) REVERT: B 766 MET cc_start: 0.8854 (mtp) cc_final: 0.8486 (mtm) REVERT: B 1077 MET cc_start: 0.8809 (mmm) cc_final: 0.8174 (mmm) REVERT: C 248 MET cc_start: 0.9265 (mtt) cc_final: 0.8757 (mtt) REVERT: F 78 MET cc_start: 0.8687 (mmm) cc_final: 0.8067 (tmm) REVERT: F 89 GLU cc_start: 0.8476 (mp0) cc_final: 0.7464 (mp0) REVERT: F 97 MET cc_start: 0.9481 (mtm) cc_final: 0.8642 (mtm) REVERT: I 116 TYR cc_start: 0.8059 (m-10) cc_final: 0.7823 (m-10) REVERT: J 57 GLU cc_start: 0.9341 (mm-30) cc_final: 0.8948 (tm-30) REVERT: K 45 MET cc_start: 0.8902 (mmm) cc_final: 0.8604 (mmm) REVERT: K 93 ASP cc_start: 0.8916 (m-30) cc_final: 0.8682 (m-30) REVERT: K 103 GLU cc_start: 0.8615 (tm-30) cc_final: 0.7947 (tm-30) REVERT: K 107 ASP cc_start: 0.8791 (m-30) cc_final: 0.8059 (m-30) REVERT: L 26 GLU cc_start: 0.9027 (pm20) cc_final: 0.8614 (tp30) REVERT: E 44 PHE cc_start: 0.8223 (m-80) cc_final: 0.7857 (m-80) outliers start: 33 outliers final: 19 residues processed: 231 average time/residue: 0.6424 time to fit residues: 249.4929 Evaluate side-chains 229 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 206 time to evaluate : 7.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 258 MET Chi-restraints excluded: chain A residue 423 PHE Chi-restraints excluded: chain A residue 424 HIS Chi-restraints excluded: chain A residue 493 MET Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 739 ASP Chi-restraints excluded: chain A residue 827 GLU Chi-restraints excluded: chain A residue 1032 LEU Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain A residue 1111 LEU Chi-restraints excluded: chain A residue 1116 LEU Chi-restraints excluded: chain B residue 568 ILE Chi-restraints excluded: chain B residue 754 TYR Chi-restraints excluded: chain B residue 1061 ILE Chi-restraints excluded: chain B residue 1094 ASP Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain H residue 35 PHE Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain L residue 43 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 81 optimal weight: 0.0570 chunk 223 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 266 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 133 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 370 optimal weight: 0.9990 chunk 109 optimal weight: 0.9990 overall best weight: 0.7902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 665 GLN A 942 GLN B 655 GLN ** H 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.058670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.042181 restraints weight = 139901.547| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 3.85 r_work: 0.2794 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.3335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 32322 Z= 0.118 Angle : 0.580 15.499 44064 Z= 0.288 Chirality : 0.041 0.155 4876 Planarity : 0.003 0.055 5375 Dihedral : 14.894 84.932 5184 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.83 % Allowed : 11.43 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.14), residues: 3669 helix: 1.68 (0.15), residues: 1249 sheet: -0.14 (0.21), residues: 575 loop : -0.03 (0.15), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 49 HIS 0.004 0.001 HIS I 64 PHE 0.017 0.001 PHE E 44 TYR 0.019 0.001 TYR C 217 ARG 0.015 0.000 ARG A 399 Details of bonding type rmsd hydrogen bonds : bond 0.03267 ( 1294) hydrogen bonds : angle 4.40375 ( 3568) metal coordination : bond 0.00581 ( 32) metal coordination : angle 5.19384 ( 45) covalent geometry : bond 0.00264 (32290) covalent geometry : angle 0.55579 (44019) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 217 time to evaluate : 3.386 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: A 336 LYS cc_start: 0.9395 (tttt) cc_final: 0.9106 (ptmm) REVERT: A 493 MET cc_start: 0.8233 (OUTLIER) cc_final: 0.7976 (tpp) REVERT: A 1094 MET cc_start: 0.8735 (OUTLIER) cc_final: 0.8501 (mtp) REVERT: A 1336 MET cc_start: 0.9121 (mmm) cc_final: 0.8719 (mmm) REVERT: A 1359 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.8159 (pm20) REVERT: A 1392 LEU cc_start: 0.9035 (tp) cc_final: 0.8756 (tt) REVERT: B 211 MET cc_start: 0.8899 (mmm) cc_final: 0.7821 (tpp) REVERT: B 213 ASP cc_start: 0.9138 (p0) cc_final: 0.8789 (p0) REVERT: B 568 ILE cc_start: 0.8572 (OUTLIER) cc_final: 0.8124 (mp) REVERT: B 704 MET cc_start: 0.8731 (mmm) cc_final: 0.8309 (mmm) REVERT: B 754 TYR cc_start: 0.9506 (OUTLIER) cc_final: 0.9061 (m-10) REVERT: B 766 MET cc_start: 0.8756 (mtp) cc_final: 0.8386 (mtm) REVERT: B 978 MET cc_start: 0.9219 (mtm) cc_final: 0.8994 (mtt) REVERT: B 1077 MET cc_start: 0.8653 (mmm) cc_final: 0.8011 (mmm) REVERT: C 248 MET cc_start: 0.9229 (mtt) cc_final: 0.8698 (mtt) REVERT: F 78 MET cc_start: 0.8581 (mmm) cc_final: 0.8018 (tmm) REVERT: F 89 GLU cc_start: 0.8472 (mp0) cc_final: 0.7861 (mp0) REVERT: F 97 MET cc_start: 0.9457 (mtm) cc_final: 0.8654 (mtm) REVERT: H 144 MET cc_start: 0.8296 (tmm) cc_final: 0.7517 (tmm) REVERT: I 112 MET cc_start: 0.8510 (mmm) cc_final: 0.8309 (mmm) REVERT: I 116 TYR cc_start: 0.7930 (m-10) cc_final: 0.7706 (m-10) REVERT: J 57 GLU cc_start: 0.9316 (mm-30) cc_final: 0.8926 (tm-30) REVERT: K 45 MET cc_start: 0.8934 (mmm) cc_final: 0.8715 (mmm) REVERT: K 76 GLN cc_start: 0.9285 (OUTLIER) cc_final: 0.8729 (tp40) REVERT: K 93 ASP cc_start: 0.8850 (m-30) cc_final: 0.8612 (m-30) REVERT: K 103 GLU cc_start: 0.8455 (tm-30) cc_final: 0.7707 (tm-30) REVERT: K 107 ASP cc_start: 0.8776 (m-30) cc_final: 0.7951 (m-30) REVERT: L 26 GLU cc_start: 0.8979 (pm20) cc_final: 0.8580 (tp30) outliers start: 27 outliers final: 19 residues processed: 234 average time/residue: 0.4326 time to fit residues: 166.5107 Evaluate side-chains 237 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 212 time to evaluate : 3.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 423 PHE Chi-restraints excluded: chain A residue 424 HIS Chi-restraints excluded: chain A residue 493 MET Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 739 ASP Chi-restraints excluded: chain A residue 827 GLU Chi-restraints excluded: chain A residue 942 GLN Chi-restraints excluded: chain A residue 1032 LEU Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain A residue 1094 MET Chi-restraints excluded: chain A residue 1111 LEU Chi-restraints excluded: chain A residue 1116 LEU Chi-restraints excluded: chain A residue 1359 GLN Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 568 ILE Chi-restraints excluded: chain B residue 754 TYR Chi-restraints excluded: chain B residue 1094 ASP Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain H residue 35 PHE Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain K residue 76 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 308 optimal weight: 6.9990 chunk 232 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 350 optimal weight: 10.0000 chunk 312 optimal weight: 4.9990 chunk 137 optimal weight: 6.9990 chunk 67 optimal weight: 7.9990 chunk 81 optimal weight: 0.9990 chunk 159 optimal weight: 2.9990 chunk 255 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 104 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 = 0.3461 r_free = 0.3461 target = 0.058388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.041929 restraints weight = 140967.251| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 3.94 r_work: 0.2785 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.3413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 32322 Z= 0.145 Angle : 0.588 15.823 44064 Z= 0.292 Chirality : 0.041 0.155 4876 Planarity : 0.003 0.062 5375 Dihedral : 14.879 85.113 5184 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 0.83 % Allowed : 11.37 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.14), residues: 3669 helix: 1.71 (0.15), residues: 1250 sheet: -0.09 (0.21), residues: 566 loop : -0.04 (0.15), residues: 1853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 49 HIS 0.004 0.001 HIS I 64 PHE 0.017 0.001 PHE K 87 TYR 0.016 0.001 TYR K 13 ARG 0.015 0.000 ARG A 399 Details of bonding type rmsd hydrogen bonds : bond 0.03373 ( 1294) hydrogen bonds : angle 4.36843 ( 3568) metal coordination : bond 0.00670 ( 32) metal coordination : angle 5.23530 ( 45) covalent geometry : bond 0.00326 (32290) covalent geometry : angle 0.56371 (44019) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 214 time to evaluate : 3.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 301 MET cc_start: 0.9075 (mmp) cc_final: 0.8519 (tmm) REVERT: A 317 MET cc_start: 0.7798 (ttm) cc_final: 0.7479 (mtm) REVERT: A 336 LYS cc_start: 0.9386 (tttt) cc_final: 0.8969 (ttmm) REVERT: A 347 MET cc_start: 0.9117 (mmt) cc_final: 0.8747 (mmp) REVERT: A 493 MET cc_start: 0.8357 (OUTLIER) cc_final: 0.8037 (tpp) REVERT: A 1094 MET cc_start: 0.8781 (OUTLIER) cc_final: 0.8525 (mtp) REVERT: A 1336 MET cc_start: 0.9136 (mmm) cc_final: 0.8720 (mmm) REVERT: A 1359 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.8146 (pm20) REVERT: A 1392 LEU cc_start: 0.9107 (tp) cc_final: 0.8816 (tt) REVERT: B 211 MET cc_start: 0.8914 (mmm) cc_final: 0.7845 (tpp) REVERT: B 213 ASP cc_start: 0.9146 (p0) cc_final: 0.8831 (p0) REVERT: B 241 MET cc_start: 0.8621 (mmm) cc_final: 0.8333 (mmm) REVERT: B 568 ILE cc_start: 0.8636 (OUTLIER) cc_final: 0.8185 (mp) REVERT: B 704 MET cc_start: 0.8644 (mmm) cc_final: 0.8277 (mmm) REVERT: B 754 TYR cc_start: 0.9511 (OUTLIER) cc_final: 0.9062 (m-10) REVERT: B 766 MET cc_start: 0.8792 (mtp) cc_final: 0.8416 (mtm) REVERT: B 978 MET cc_start: 0.9254 (mtm) cc_final: 0.9015 (mtt) REVERT: B 1077 MET cc_start: 0.8727 (mmm) cc_final: 0.8105 (mmm) REVERT: C 248 MET cc_start: 0.9232 (mtt) cc_final: 0.8701 (mtt) REVERT: F 78 MET cc_start: 0.8602 (mmm) cc_final: 0.8025 (tmm) REVERT: F 89 GLU cc_start: 0.8532 (mp0) cc_final: 0.7914 (mp0) REVERT: F 97 MET cc_start: 0.9474 (mtm) cc_final: 0.8671 (mtm) REVERT: H 144 MET cc_start: 0.8401 (tmm) cc_final: 0.7614 (tmm) REVERT: I 96 ARG cc_start: 0.8723 (mmm160) cc_final: 0.8423 (mmm160) REVERT: I 116 TYR cc_start: 0.7933 (m-10) cc_final: 0.7701 (m-10) REVERT: J 57 GLU cc_start: 0.9327 (mm-30) cc_final: 0.8944 (tm-30) REVERT: K 45 MET cc_start: 0.8900 (mmm) cc_final: 0.8664 (mmm) REVERT: K 76 GLN cc_start: 0.9335 (OUTLIER) cc_final: 0.8761 (tp40) REVERT: K 93 ASP cc_start: 0.8862 (m-30) cc_final: 0.8620 (m-30) REVERT: K 103 GLU cc_start: 0.8556 (tm-30) cc_final: 0.7898 (tm-30) REVERT: K 107 ASP cc_start: 0.8775 (m-30) cc_final: 0.7966 (m-30) REVERT: L 26 GLU cc_start: 0.9034 (pm20) cc_final: 0.8592 (tp30) outliers start: 27 outliers final: 21 residues processed: 231 average time/residue: 0.4541 time to fit residues: 172.3540 Evaluate side-chains 237 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 210 time to evaluate : 3.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 423 PHE Chi-restraints excluded: chain A residue 424 HIS Chi-restraints excluded: chain A residue 493 MET Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 739 ASP Chi-restraints excluded: chain A residue 827 GLU Chi-restraints excluded: chain A residue 1032 LEU Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain A residue 1094 MET Chi-restraints excluded: chain A residue 1111 LEU Chi-restraints excluded: chain A residue 1116 LEU Chi-restraints excluded: chain A residue 1359 GLN Chi-restraints excluded: chain A residue 1450 ILE Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 568 ILE Chi-restraints excluded: chain B residue 754 TYR Chi-restraints excluded: chain B residue 1061 ILE Chi-restraints excluded: chain B residue 1094 ASP Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain H residue 35 PHE Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain K residue 76 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 7 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 165 optimal weight: 4.9990 chunk 154 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 chunk 206 optimal weight: 3.9990 chunk 148 optimal weight: 1.9990 chunk 235 optimal weight: 3.9990 chunk 275 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 942 GLN ** H 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 29 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.057625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.041135 restraints weight = 141169.406| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 3.94 r_work: 0.2760 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.3588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 32322 Z= 0.202 Angle : 0.624 17.010 44064 Z= 0.310 Chirality : 0.042 0.159 4876 Planarity : 0.004 0.060 5375 Dihedral : 14.926 87.193 5184 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.99 % Allowed : 11.18 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.14), residues: 3669 helix: 1.61 (0.15), residues: 1256 sheet: -0.14 (0.21), residues: 570 loop : -0.04 (0.15), residues: 1843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 916 HIS 0.005 0.001 HIS I 64 PHE 0.018 0.001 PHE K 87 TYR 0.024 0.001 TYR C 217 ARG 0.015 0.000 ARG A 399 Details of bonding type rmsd hydrogen bonds : bond 0.03683 ( 1294) hydrogen bonds : angle 4.48553 ( 3568) metal coordination : bond 0.00900 ( 32) metal coordination : angle 5.64911 ( 45) covalent geometry : bond 0.00452 (32290) covalent geometry : angle 0.59713 (44019) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16019.93 seconds wall clock time: 279 minutes 51.87 seconds (16791.87 seconds total)