Starting phenix.real_space_refine on Mon Mar 25 05:55:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h0v_34415/03_2024/8h0v_34415.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h0v_34415/03_2024/8h0v_34415.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h0v_34415/03_2024/8h0v_34415.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h0v_34415/03_2024/8h0v_34415.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h0v_34415/03_2024/8h0v_34415.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h0v_34415/03_2024/8h0v_34415.pdb" } resolution = 3.8 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= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 8 6.06 5 P 425 5.49 5 Mg 1 5.21 5 S 204 5.16 5 C 27997 2.51 5 N 8299 2.21 5 O 9637 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 21": "OD1" <-> "OD2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 46571 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 11120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1412, 11120 Classifications: {'peptide': 1412} Link IDs: {'PCIS': 3, 'PTRANS': 65, 'TRANS': 1343} Chain breaks: 5 Chain: "B" Number of atoms: 9261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1161, 9261 Classifications: {'peptide': 1161} Link IDs: {'PTRANS': 52, 'TRANS': 1108} Chain breaks: 4 Chain: "C" Number of atoms: 2098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2098 Classifications: {'peptide': 263} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 249} Chain: "D" Number of atoms: 1314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1314 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 4, 'TRANS': 163} Chain breaks: 2 Chain: "E" Number of atoms: 1740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1740 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 202} Chain: "F" Number of atoms: 677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 677 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 5, 'TRANS': 78} Chain: "G" Number of atoms: 1324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1324 Classifications: {'peptide': 171} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 160} Chain: "H" Number of atoms: 1052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1052 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 4, 'TRANS': 128} Chain breaks: 1 Chain: "I" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 917 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 5, 'TRANS': 105} Chain: "J" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 545 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "K" Number of atoms: 932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 932 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 8, 'TRANS': 104} Chain: "L" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 359 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "P" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 302 Classifications: {'RNA': 14} Modifications used: {'rna3p_pur': 9, 'rna3p_pyr': 5} Link IDs: {'rna3p': 13} Chain: "T" Number of atoms: 4316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 4316 Classifications: {'DNA': 210} Link IDs: {'rna3p': 209} Chain: "N" Number of atoms: 4107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 4107 Classifications: {'DNA': 201} Link IDs: {'rna3p': 200} Chain breaks: 1 Chain: "a" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "b" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "c" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 810 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "d" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 746 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "e" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 800 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "f" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "g" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 810 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "h" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 725 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "u" Number of atoms: 525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 525 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 527 SG CYS A 67 73.951 62.155 164.485 1.00208.76 S ATOM 549 SG CYS A 70 77.434 61.191 163.574 1.00211.28 S ATOM 594 SG CYS A 77 76.767 64.722 164.847 1.00219.67 S ATOM 829 SG CYS A 107 59.451 86.667 125.458 1.00253.62 S ATOM 851 SG CYS A 110 59.923 83.135 124.013 1.00254.73 S ATOM 1157 SG CYS A 148 60.865 86.138 122.020 1.00281.57 S ATOM 1245 SG CYS A 168 57.117 85.619 122.811 1.00280.29 S ATOM 19913 SG CYS B1163 80.385 63.267 147.418 1.00240.13 S ATOM 19931 SG CYS B1166 78.423 66.477 147.688 1.00235.87 S ATOM 20054 SG CYS B1182 77.124 63.108 149.212 1.00231.12 S ATOM 20077 SG CYS B1185 77.264 63.679 145.409 1.00243.92 S ATOM 21022 SG CYS C 85 114.185 73.616 219.462 1.00264.38 S ATOM 21035 SG CYS C 87 110.443 73.549 218.830 1.00268.45 S ATOM 21070 SG CYS C 91 111.399 74.702 222.006 1.00249.73 S ATOM 21093 SG CYS C 94 112.039 76.941 219.110 1.00240.04 S ATOM 29179 SG CYS I 75 83.527 164.620 169.815 1.00521.29 S ATOM 29201 SG CYS I 78 81.596 166.797 172.887 1.00540.51 S ATOM 29417 SG CYS I 103 82.002 162.927 172.447 1.00484.85 S ATOM 29439 SG CYS I 106 79.730 165.380 169.846 1.00508.86 S ATOM 28631 SG CYS I 7 46.743 149.552 145.750 1.00361.24 S ATOM 28817 SG CYS I 29 47.141 146.045 142.859 1.00333.38 S ATOM 28842 SG CYS I 32 44.932 148.032 142.955 1.00355.69 S ATOM 29558 SG CYS J 7 109.637 107.721 210.027 1.00185.14 S ATOM 29581 SG CYS J 10 113.300 106.963 211.013 1.00186.17 S ATOM 29857 SG CYS J 44 112.464 110.071 208.824 1.00186.73 S ATOM 29863 SG CYS J 45 111.780 109.627 212.572 1.00192.08 S ATOM 31025 SG CYS L 33 69.076 92.110 216.377 1.00284.31 S ATOM 31040 SG CYS L 36 68.241 92.039 219.821 1.00290.88 S ATOM 31150 SG CYS L 50 67.310 89.180 216.631 1.00284.72 S ATOM 31174 SG CYS L 53 65.414 92.118 218.493 1.00291.42 S Time building chain proxies: 22.14, per 1000 atoms: 0.48 Number of scatterers: 46571 At special positions: 0 Unit cell: (175.82, 213.07, 247.34, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 8 29.99 S 204 16.00 P 425 15.00 Mg 1 11.99 O 9637 8.00 N 8299 7.00 C 27997 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 - 3.50 Amino acid : False - 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: 17.98 Conformation dependent library (CDL) restraints added in 7.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 70 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 67 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 77 " pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 107 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 148 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 168 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 110 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1163 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1185 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1166 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1182 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 87 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 91 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 94 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 85 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 103 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 75 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 78 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 106 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 29 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 32 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 7 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 33 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 53 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 50 " Number of angles added : 39 9400 Ramachandran restraints generated. 4700 Oldfield, 0 Emsley, 4700 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8928 Finding SS restraints... Secondary structure from input PDB file: 184 helices and 62 sheets defined 44.2% alpha, 16.2% beta 201 base pairs and 378 stacking pairs defined. Time for finding SS restraints: 18.87 Creating SS restraints... Processing helix chain 'A' and resid 23 through 31 Processing helix chain 'A' and resid 55 through 59 Processing helix chain 'A' and resid 95 through 106 Processing helix chain 'A' and resid 119 through 126 Processing helix chain 'A' and resid 130 through 143 removed outlier: 4.091A pdb=" N LEU A 141 " --> pdb=" O ALA A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 214 removed outlier: 3.771A pdb=" N HIS A 214 " --> pdb=" O ASN A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 224 Processing helix chain 'A' and resid 231 through 234 Processing helix chain 'A' and resid 244 through 248 Processing helix chain 'A' and resid 261 through 278 Processing helix chain 'A' and resid 289 through 306 removed outlier: 3.614A pdb=" N MET A 305 " --> pdb=" O VAL A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 331 Processing helix chain 'A' and resid 335 through 341 Processing helix chain 'A' and resid 369 through 375 Processing helix chain 'A' and resid 385 through 396 Processing helix chain 'A' and resid 421 through 425 removed outlier: 3.976A pdb=" N ILE A 425 " --> pdb=" O ALA A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 454 No H-bonds generated for 'chain 'A' and resid 452 through 454' Processing helix chain 'A' and resid 473 through 477 removed outlier: 3.634A pdb=" N THR A 476 " --> pdb=" O LEU A 473 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N SER A 477 " --> pdb=" O SER A 474 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 473 through 477' Processing helix chain 'A' and resid 495 through 506 Processing helix chain 'A' and resid 507 through 512 removed outlier: 3.706A pdb=" N ILE A 512 " --> pdb=" O PRO A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 536 Processing helix chain 'A' and resid 543 through 554 Processing helix chain 'A' and resid 575 through 583 removed outlier: 3.717A pdb=" N ALA A 582 " --> pdb=" O LEU A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 624 Processing helix chain 'A' and resid 629 through 639 Processing helix chain 'A' and resid 639 through 662 removed outlier: 3.602A pdb=" N PHE A 647 " --> pdb=" O CYS A 643 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY A 648 " --> pdb=" O ALA A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 671 Processing helix chain 'A' and resid 673 through 700 Processing helix chain 'A' and resid 710 through 738 Processing helix chain 'A' and resid 742 through 751 Processing helix chain 'A' and resid 755 through 764 Processing helix chain 'A' and resid 810 through 847 removed outlier: 3.964A pdb=" N THR A 832 " --> pdb=" O THR A 828 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N ALA A 833 " --> pdb=" O ALA A 829 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLU A 834 " --> pdb=" O VAL A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 872 Processing helix chain 'A' and resid 890 through 899 Processing helix chain 'A' and resid 910 through 914 removed outlier: 3.642A pdb=" N ILE A 914 " --> pdb=" O PRO A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 921 removed outlier: 4.119A pdb=" N LEU A 921 " --> pdb=" O ALA A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 947 Processing helix chain 'A' and resid 961 through 974 Processing helix chain 'A' and resid 984 through 997 Processing helix chain 'A' and resid 1006 through 1017 Processing helix chain 'A' and resid 1017 through 1028 Processing helix chain 'A' and resid 1029 through 1036 Processing helix chain 'A' and resid 1040 through 1058 Processing helix chain 'A' and resid 1065 through 1079 Proline residue: A1077 - end of helix Processing helix chain 'A' and resid 1098 through 1108 removed outlier: 3.924A pdb=" N ARG A1102 " --> pdb=" O LEU A1098 " (cutoff:3.500A) Processing helix chain 'A' and resid 1123 through 1129 removed outlier: 3.761A pdb=" N ASP A1129 " --> pdb=" O GLU A1125 " (cutoff:3.500A) Processing helix chain 'A' and resid 1129 through 1141 removed outlier: 3.516A pdb=" N ALA A1133 " --> pdb=" O ASP A1129 " (cutoff:3.500A) Processing helix chain 'A' and resid 1146 through 1149 Processing helix chain 'A' and resid 1168 through 1174 Processing helix chain 'A' and resid 1200 through 1207 removed outlier: 3.905A pdb=" N LYS A1207 " --> pdb=" O ARG A1203 " (cutoff:3.500A) Processing helix chain 'A' and resid 1210 through 1222 removed outlier: 3.799A pdb=" N VAL A1214 " --> pdb=" O THR A1210 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL A1221 " --> pdb=" O LYS A1217 " (cutoff:3.500A) Processing helix chain 'A' and resid 1261 through 1274 Processing helix chain 'A' and resid 1315 through 1322 removed outlier: 3.537A pdb=" N ALA A1321 " --> pdb=" O ALA A1317 " (cutoff:3.500A) Processing helix chain 'A' and resid 1334 through 1343 removed outlier: 3.519A pdb=" N GLY A1343 " --> pdb=" O LEU A1339 " (cutoff:3.500A) Processing helix chain 'A' and resid 1343 through 1361 Processing helix chain 'A' and resid 1367 through 1379 removed outlier: 4.056A pdb=" N MET A1371 " --> pdb=" O ASN A1367 " (cutoff:3.500A) Processing helix chain 'A' and resid 1388 through 1393 Processing helix chain 'A' and resid 1398 through 1406 Processing helix chain 'A' and resid 1407 through 1419 Processing helix chain 'A' and resid 1426 through 1433 removed outlier: 3.901A pdb=" N ASN A1430 " --> pdb=" O GLY A1426 " (cutoff:3.500A) Processing helix chain 'A' and resid 1439 through 1442 Processing helix chain 'A' and resid 1452 through 1456 Processing helix chain 'A' and resid 1457 through 1461 removed outlier: 3.999A pdb=" N ALA A1461 " --> pdb=" O ALA A1458 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 29 Processing helix chain 'B' and resid 31 through 53 removed outlier: 5.487A pdb=" N ILE B 46 " --> pdb=" O MET B 42 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N GLN B 47 " --> pdb=" O GLU B 43 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 107 Processing helix chain 'B' and resid 176 through 183 Processing helix chain 'B' and resid 273 through 281 removed outlier: 3.529A pdb=" N VAL B 277 " --> pdb=" O PRO B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 294 Processing helix chain 'B' and resid 300 through 313 removed outlier: 3.732A pdb=" N LYS B 307 " --> pdb=" O LEU B 303 " (cutoff:3.500A) Proline residue: B 308 - end of helix Processing helix chain 'B' and resid 318 through 328 removed outlier: 3.570A pdb=" N ALA B 322 " --> pdb=" O ASP B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 351 removed outlier: 3.737A pdb=" N GLN B 343 " --> pdb=" O GLU B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 383 removed outlier: 3.946A pdb=" N LYS B 367 " --> pdb=" O PHE B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 395 No H-bonds generated for 'chain 'B' and resid 393 through 395' Processing helix chain 'B' and resid 401 through 429 removed outlier: 4.343A pdb=" N ARG B 427 " --> pdb=" O ARG B 423 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE B 429 " --> pdb=" O MET B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 432 No H-bonds generated for 'chain 'B' and resid 430 through 432' Processing helix chain 'B' and resid 443 through 457 removed outlier: 3.729A pdb=" N THR B 447 " --> pdb=" O SER B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 465 removed outlier: 3.516A pdb=" N ALA B 465 " --> pdb=" O GLN B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 488 Processing helix chain 'B' and resid 508 through 512 Processing helix chain 'B' and resid 522 through 526 removed outlier: 4.312A pdb=" N ALA B 525 " --> pdb=" O GLU B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 555 removed outlier: 3.551A pdb=" N GLY B 555 " --> pdb=" O LEU B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 562 removed outlier: 3.738A pdb=" N TYR B 562 " --> pdb=" O LEU B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 599 removed outlier: 3.886A pdb=" N LEU B 589 " --> pdb=" O ASP B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 658 removed outlier: 3.593A pdb=" N ILE B 652 " --> pdb=" O THR B 648 " (cutoff:3.500A) Processing helix chain 'B' and resid 677 through 684 Processing helix chain 'B' and resid 692 through 696 removed outlier: 3.537A pdb=" N GLU B 696 " --> pdb=" O GLY B 692 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 692 through 696' Processing helix chain 'B' and resid 703 through 708 removed outlier: 3.578A pdb=" N LEU B 707 " --> pdb=" O PRO B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 744 through 749 Processing helix chain 'B' and resid 752 through 756 Processing helix chain 'B' and resid 758 through 762 Processing helix chain 'B' and resid 763 through 774 removed outlier: 3.553A pdb=" N ASN B 767 " --> pdb=" O GLN B 763 " (cutoff:3.500A) Processing helix chain 'B' and resid 775 through 777 No H-bonds generated for 'chain 'B' and resid 775 through 777' Processing helix chain 'B' and resid 806 through 811 Processing helix chain 'B' and resid 843 through 848 Processing helix chain 'B' and resid 1014 through 1017 Processing helix chain 'B' and resid 1022 through 1039 removed outlier: 3.921A pdb=" N LEU B1026 " --> pdb=" O THR B1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 1051 through 1062 Processing helix chain 'B' and resid 1098 through 1102 Processing helix chain 'B' and resid 1131 through 1142 Processing helix chain 'B' and resid 1143 through 1152 Processing helix chain 'B' and resid 1198 through 1210 Processing helix chain 'C' and resid 25 through 39 Processing helix chain 'C' and resid 58 through 68 Processing helix chain 'C' and resid 75 through 79 Processing helix chain 'C' and resid 116 through 118 No H-bonds generated for 'chain 'C' and resid 116 through 118' Processing helix chain 'C' and resid 167 through 171 Processing helix chain 'C' and resid 206 through 210 Processing helix chain 'C' and resid 239 through 264 Processing helix chain 'D' and resid 24 through 28 removed outlier: 3.905A pdb=" N LEU D 28 " --> pdb=" O ALA D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 72 Processing helix chain 'D' and resid 85 through 90 Processing helix chain 'D' and resid 91 through 93 No H-bonds generated for 'chain 'D' and resid 91 through 93' Processing helix chain 'D' and resid 95 through 112 Processing helix chain 'D' and resid 117 through 129 Processing helix chain 'D' and resid 138 through 148 removed outlier: 3.578A pdb=" N SER D 146 " --> pdb=" O ILE D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 160 removed outlier: 4.031A pdb=" N ALA D 156 " --> pdb=" O ASP D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 167 removed outlier: 4.014A pdb=" N ALA D 164 " --> pdb=" O PRO D 161 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA D 165 " --> pdb=" O SER D 162 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LYS D 166 " --> pdb=" O LEU D 163 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS D 167 " --> pdb=" O ALA D 164 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 161 through 167' Processing helix chain 'D' and resid 170 through 182 Processing helix chain 'E' and resid 3 through 26 Processing helix chain 'E' and resid 30 through 35 Processing helix chain 'E' and resid 37 through 46 Processing helix chain 'E' and resid 64 through 71 Processing helix chain 'E' and resid 88 through 102 Processing helix chain 'E' and resid 116 through 121 Processing helix chain 'E' and resid 137 through 140 removed outlier: 3.611A pdb=" N VAL E 140 " --> pdb=" O SER E 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 137 through 140' Processing helix chain 'E' and resid 142 through 146 Processing helix chain 'E' and resid 156 through 167 Processing helix chain 'E' and resid 170 through 174 removed outlier: 3.598A pdb=" N LEU E 174 " --> pdb=" O GLU E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 188 Processing helix chain 'F' and resid 86 through 103 Processing helix chain 'F' and resid 116 through 127 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 35 Processing helix chain 'G' and resid 50 through 54 removed outlier: 3.616A pdb=" N ILE G 54 " --> pdb=" O GLY G 51 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'H' and resid 87 through 92 Processing helix chain 'H' and resid 127 through 132 Processing helix chain 'H' and resid 133 through 135 No H-bonds generated for 'chain 'H' and resid 133 through 135' Processing helix chain 'I' and resid 59 through 65 removed outlier: 4.287A pdb=" N GLY I 63 " --> pdb=" O ASP I 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 27 removed outlier: 3.674A pdb=" N GLU J 27 " --> pdb=" O ARG J 23 " (cutoff:3.500A) Processing helix chain 'J' and resid 30 through 38 Processing helix chain 'J' and resid 42 through 51 Processing helix chain 'J' and resid 55 through 60 Processing helix chain 'K' and resid 39 through 51 removed outlier: 3.710A pdb=" N LEU K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 113 Processing helix chain 'a' and resid 44 through 57 Processing helix chain 'a' and resid 63 through 76 Processing helix chain 'a' and resid 85 through 114 Processing helix chain 'a' and resid 120 through 132 Processing helix chain 'b' and resid 25 through 29 Processing helix chain 'b' and resid 30 through 41 Processing helix chain 'b' and resid 49 through 76 removed outlier: 3.605A pdb=" N GLU b 53 " --> pdb=" O LEU b 49 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASP b 68 " --> pdb=" O ASN b 64 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA b 76 " --> pdb=" O TYR b 72 " (cutoff:3.500A) Processing helix chain 'b' and resid 82 through 93 Processing helix chain 'c' and resid 16 through 21 Processing helix chain 'c' and resid 26 through 36 Processing helix chain 'c' and resid 45 through 72 removed outlier: 4.403A pdb=" N VAL c 49 " --> pdb=" O ALA c 45 " (cutoff:3.500A) Processing helix chain 'c' and resid 79 through 90 Processing helix chain 'c' and resid 90 through 97 Processing helix chain 'd' and resid 34 through 46 Processing helix chain 'd' and resid 52 through 81 Processing helix chain 'd' and resid 87 through 99 Processing helix chain 'd' and resid 100 through 121 Processing helix chain 'e' and resid 44 through 57 Processing helix chain 'e' and resid 63 through 77 removed outlier: 3.876A pdb=" N ASP e 77 " --> pdb=" O GLU e 73 " (cutoff:3.500A) Processing helix chain 'e' and resid 85 through 114 Processing helix chain 'e' and resid 120 through 131 Processing helix chain 'f' and resid 25 through 29 Processing helix chain 'f' and resid 30 through 41 Processing helix chain 'f' and resid 49 through 76 removed outlier: 3.669A pdb=" N GLU f 53 " --> pdb=" O LEU f 49 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ASP f 68 " --> pdb=" O ASN f 64 " (cutoff:3.500A) Processing helix chain 'f' and resid 82 through 93 removed outlier: 3.849A pdb=" N GLN f 93 " --> pdb=" O ALA f 89 " (cutoff:3.500A) Processing helix chain 'g' and resid 16 through 22 Processing helix chain 'g' and resid 26 through 36 Processing helix chain 'g' and resid 45 through 73 removed outlier: 4.359A pdb=" N VAL g 49 " --> pdb=" O ALA g 45 " (cutoff:3.500A) Processing helix chain 'g' and resid 79 through 90 Processing helix chain 'g' and resid 90 through 97 Processing helix chain 'h' and resid 34 through 46 Processing helix chain 'h' and resid 52 through 81 Processing helix chain 'h' and resid 87 through 99 Processing helix chain 'h' and resid 100 through 121 Processing helix chain 'u' and resid 39 through 51 removed outlier: 3.531A pdb=" N LEU u 43 " --> pdb=" O PRO u 39 " (cutoff:3.500A) Processing helix chain 'u' and resid 59 through 69 Processing helix chain 'u' and resid 76 through 90 Processing helix chain 'u' and resid 99 through 102 removed outlier: 3.755A pdb=" N SER u 102 " --> pdb=" O THR u 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'u' and resid 99 through 102' Processing sheet with id=AA1, first strand: chain 'A' and resid 1421 through 1422 Processing sheet with id=AA2, first strand: chain 'A' and resid 82 through 91 removed outlier: 10.105A pdb=" N LEU A 86 " --> pdb=" O PRO A 241 " (cutoff:3.500A) removed outlier: 10.548A pdb=" N LYS A 88 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL A 239 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 174 through 178 removed outlier: 4.271A pdb=" N LEU A 182 " --> pdb=" O LEU A 203 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 251 through 252 removed outlier: 3.859A pdb=" N ILE A 251 " --> pdb=" O GLY A 259 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLY A 259 " --> pdb=" O ILE A 251 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 344 through 346 removed outlier: 3.626A pdb=" N LEU B1128 " --> pdb=" O VAL A 346 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1104 through 1106 removed outlier: 3.720A pdb=" N THR A 352 " --> pdb=" O MET A 488 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N VAL A 365 " --> pdb=" O LYS A 462 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N MET A 464 " --> pdb=" O VAL A 365 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N VAL A 367 " --> pdb=" O MET A 464 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 376 through 380 removed outlier: 3.621A pdb=" N TYR A 405 " --> pdb=" O GLU A 434 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N HIS A 436 " --> pdb=" O ALA A 403 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N ALA A 403 " --> pdb=" O HIS A 436 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 541 through 542 Processing sheet with id=AA9, first strand: chain 'A' and resid 566 through 568 removed outlier: 6.163A pdb=" N VAL H 95 " --> pdb=" O LEU A 567 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR H 56 " --> pdb=" O ARG H 144 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE H 29 " --> pdb=" O THR H 11 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ILE H 27 " --> pdb=" O GLN H 13 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N LEU H 121 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LYS H 102 " --> pdb=" O TYR H 114 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N SER H 116 " --> pdb=" O VAL H 100 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N VAL H 100 " --> pdb=" O SER H 116 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 589 through 591 removed outlier: 6.839A pdb=" N LEU A 607 " --> pdb=" O MET A 614 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 767 through 768 Processing sheet with id=AB3, first strand: chain 'A' and resid 850 through 851 removed outlier: 6.722A pdb=" N THR A 857 " --> pdb=" O ILE A 865 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 880 through 883 Processing sheet with id=AB5, first strand: chain 'A' and resid 1284 through 1295 removed outlier: 4.179A pdb=" N LYS A1284 " --> pdb=" O ASP A1312 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A1306 " --> pdb=" O HIS A1290 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU A1118 " --> pdb=" O THR A1311 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1143 through 1144 removed outlier: 6.859A pdb=" N THR A1143 " --> pdb=" O LEU A1276 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1151 through 1156 removed outlier: 3.856A pdb=" N ALA A1151 " --> pdb=" O GLU A1198 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1444 through 1448 Processing sheet with id=AB9, first strand: chain 'B' and resid 55 through 60 removed outlier: 4.198A pdb=" N LEU B 56 " --> pdb=" O ILE B 77 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ILE B 77 " --> pdb=" O LEU B 56 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN B 60 " --> pdb=" O LYS B 73 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS B 73 " --> pdb=" O GLN B 60 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N ASP B 118 " --> pdb=" O GLY B 80 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ILE B 82 " --> pdb=" O TYR B 116 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N TYR B 116 " --> pdb=" O ILE B 82 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N LEU B 84 " --> pdb=" O PRO B 114 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY B 159 " --> pdb=" O VAL B 115 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N LEU B 117 " --> pdb=" O HIS B 157 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N HIS B 157 " --> pdb=" O LEU B 117 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N MET B 119 " --> pdb=" O LYS B 155 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LYS B 155 " --> pdb=" O MET B 119 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 88 through 90 Processing sheet with id=AC2, first strand: chain 'B' and resid 194 through 196 Processing sheet with id=AC3, first strand: chain 'B' and resid 397 through 400 removed outlier: 3.572A pdb=" N ALA B 205 " --> pdb=" O ARG B 490 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 215 through 218 removed outlier: 6.647A pdb=" N LEU B 249 " --> pdb=" O SER B 226 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N VAL B 228 " --> pdb=" O ILE B 247 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ILE B 247 " --> pdb=" O VAL B 228 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLN B 246 " --> pdb=" O THR B 264 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 232 through 234 removed outlier: 3.849A pdb=" N SER B 243 " --> pdb=" O SER B 233 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 537 through 538 Processing sheet with id=AC7, first strand: chain 'B' and resid 537 through 538 Processing sheet with id=AC8, first strand: chain 'B' and resid 578 through 583 removed outlier: 5.358A pdb=" N TRP B 579 " --> pdb=" O VAL B 575 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N VAL B 575 " --> pdb=" O TRP B 579 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY B 581 " --> pdb=" O ILE B 573 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 792 through 796 removed outlier: 5.569A pdb=" N ARG B 969 " --> pdb=" O VAL B 949 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N VAL B 949 " --> pdb=" O ARG B 969 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N THR B 971 " --> pdb=" O GLY B 947 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N GLY B 947 " --> pdb=" O THR B 971 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 792 through 796 removed outlier: 5.569A pdb=" N ARG B 969 " --> pdb=" O VAL B 949 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N VAL B 949 " --> pdb=" O ARG B 969 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N THR B 971 " --> pdb=" O GLY B 947 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N GLY B 947 " --> pdb=" O THR B 971 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N VAL B 952 " --> pdb=" O LYS L 60 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL L 29 " --> pdb=" O LEU L 42 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU L 42 " --> pdb=" O VAL L 29 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 804 through 805 Processing sheet with id=AD3, first strand: chain 'B' and resid 1069 through 1070 removed outlier: 7.052A pdb=" N MET B 839 " --> pdb=" O GLY B 991 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N THR B 993 " --> pdb=" O MET B 839 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N MET B 841 " --> pdb=" O THR B 993 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N PHE B1086 " --> pdb=" O ILE B 827 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 873 through 874 removed outlier: 7.513A pdb=" N LEU B 883 " --> pdb=" O ASP B 936 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 910 through 912 removed outlier: 3.565A pdb=" N ILE B 912 " --> pdb=" O THR B 939 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1001 through 1002 Processing sheet with id=AD7, first strand: chain 'B' and resid 1157 through 1163 Processing sheet with id=AD8, first strand: chain 'B' and resid 1172 through 1174 Processing sheet with id=AD9, first strand: chain 'C' and resid 6 through 12 removed outlier: 5.514A pdb=" N VAL C 7 " --> pdb=" O SER C 22 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N SER C 22 " --> pdb=" O VAL C 7 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N ILE C 9 " --> pdb=" O MET C 20 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N MET C 20 " --> pdb=" O ILE C 9 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU C 233 " --> pdb=" O ALA C 175 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ALA C 175 " --> pdb=" O GLU C 233 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 119 through 122 removed outlier: 6.906A pdb=" N VAL C 97 " --> pdb=" O VAL C 121 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N GLU C 152 " --> pdb=" O ASN C 53 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ASN C 53 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ASN C 154 " --> pdb=" O LYS C 51 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N LYS C 160 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N ILE C 45 " --> pdb=" O LYS C 160 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N GLY C 162 " --> pdb=" O LEU C 43 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N LEU C 43 " --> pdb=" O GLY C 162 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ILE L 67 " --> pdb=" O ILE C 50 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 71 through 73 removed outlier: 4.576A pdb=" N GLU C 131 " --> pdb=" O VAL C 72 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 111 through 114 removed outlier: 6.438A pdb=" N THR C 111 " --> pdb=" O LYS C 146 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N LYS C 146 " --> pdb=" O THR C 111 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL C 113 " --> pdb=" O LEU C 144 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 5 through 6 removed outlier: 4.126A pdb=" N THR D 5 " --> pdb=" O SER G 8 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N VAL G 77 " --> pdb=" O VAL G 46 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL G 46 " --> pdb=" O VAL G 77 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 37 through 39 Processing sheet with id=AE6, first strand: chain 'E' and resid 27 through 28 removed outlier: 4.236A pdb=" N ASN E 62 " --> pdb=" O PHE E 28 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL E 79 " --> pdb=" O PHE E 59 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N TRP E 78 " --> pdb=" O ILE E 108 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N ILE E 110 " --> pdb=" O TRP E 78 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N GLU E 80 " --> pdb=" O ILE E 110 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 86 through 87 Processing sheet with id=AE8, first strand: chain 'E' and resid 151 through 154 removed outlier: 3.944A pdb=" N LYS E 151 " --> pdb=" O ILE E 198 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE E 198 " --> pdb=" O LYS E 151 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 10 through 13 removed outlier: 3.546A pdb=" N LEU G 11 " --> pdb=" O PHE G 70 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE G 70 " --> pdb=" O LEU G 11 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 106 through 111 removed outlier: 3.525A pdb=" N PHE G 99 " --> pdb=" O VAL G 110 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N GLY G 98 " --> pdb=" O VAL G 94 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N VAL G 94 " --> pdb=" O GLY G 98 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N PHE G 100 " --> pdb=" O SER G 92 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE G 90 " --> pdb=" O ASP G 102 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LYS G 146 " --> pdb=" O SER G 162 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ILE G 160 " --> pdb=" O VAL G 148 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N THR G 150 " --> pdb=" O TYR G 158 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N TYR G 158 " --> pdb=" O THR G 150 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'G' and resid 106 through 111 removed outlier: 3.525A pdb=" N PHE G 99 " --> pdb=" O VAL G 110 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N GLY G 98 " --> pdb=" O VAL G 94 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N VAL G 94 " --> pdb=" O GLY G 98 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N PHE G 100 " --> pdb=" O SER G 92 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE G 90 " --> pdb=" O ASP G 102 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG G 144 " --> pdb=" O GLY G 169 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'G' and resid 130 through 131 Processing sheet with id=AF4, first strand: chain 'I' and resid 15 through 18 removed outlier: 3.579A pdb=" N LYS I 17 " --> pdb=" O LEU I 26 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TYR I 27 " --> pdb=" O GLU I 36 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLU I 36 " --> pdb=" O TYR I 27 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'I' and resid 70 through 71 Processing sheet with id=AF6, first strand: chain 'K' and resid 19 through 23 Processing sheet with id=AF7, first strand: chain 'a' and resid 83 through 84 removed outlier: 6.829A pdb=" N ARG a 83 " --> pdb=" O VAL b 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'a' and resid 118 through 119 Processing sheet with id=AF9, first strand: chain 'b' and resid 97 through 98 Processing sheet with id=AG1, first strand: chain 'c' and resid 42 through 43 removed outlier: 7.247A pdb=" N ARG c 42 " --> pdb=" O ILE d 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG1 Processing sheet with id=AG2, first strand: chain 'c' and resid 77 through 78 Processing sheet with id=AG3, first strand: chain 'c' and resid 101 through 102 removed outlier: 7.008A pdb=" N THR c 101 " --> pdb=" O TYR f 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG3 Processing sheet with id=AG4, first strand: chain 'e' and resid 83 through 84 removed outlier: 6.760A pdb=" N ARG e 83 " --> pdb=" O VAL f 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG4 Processing sheet with id=AG5, first strand: chain 'e' and resid 118 through 119 Processing sheet with id=AG6, first strand: chain 'g' and resid 42 through 43 removed outlier: 7.351A pdb=" N ARG g 42 " --> pdb=" O ILE h 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG6 Processing sheet with id=AG7, first strand: chain 'g' and resid 77 through 78 Processing sheet with id=AG8, first strand: chain 'u' and resid 57 through 58 removed outlier: 6.369A pdb=" N SER u 104 " --> pdb=" O THR u 96 " (cutoff:3.500A) 1765 hydrogen bonds defined for protein. 4932 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 506 hydrogen bonds 1008 hydrogen bond angles 0 basepair planarities 201 basepair parallelities 378 stacking parallelities Total time for adding SS restraints: 37.31 Time building geometry restraints manager: 18.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 14021 1.34 - 1.47: 13325 1.47 - 1.60: 20134 1.60 - 1.73: 473 1.73 - 1.86: 331 Bond restraints: 48284 Sorted by residual: bond pdb=" C1' G P 5 " pdb=" N9 G P 5 " ideal model delta sigma weight residual 1.475 1.376 0.099 1.50e-02 4.44e+03 4.37e+01 bond pdb=" C1' A P 2 " pdb=" N9 A P 2 " ideal model delta sigma weight residual 1.475 1.392 0.083 1.50e-02 4.44e+03 3.04e+01 bond pdb=" C1' A P 4 " pdb=" N9 A P 4 " ideal model delta sigma weight residual 1.475 1.396 0.079 1.50e-02 4.44e+03 2.74e+01 bond pdb=" C1' U P 10 " pdb=" N1 U P 10 " ideal model delta sigma weight residual 1.480 1.557 -0.077 1.50e-02 4.44e+03 2.63e+01 bond pdb=" C1' DG T 94 " pdb=" N9 DG T 94 " ideal model delta sigma weight residual 1.460 1.379 0.081 2.00e-02 2.50e+03 1.63e+01 ... (remaining 48279 not shown) Histogram of bond angle deviations from ideal: 94.91 - 103.00: 1144 103.00 - 111.10: 20666 111.10 - 119.19: 20849 119.19 - 127.29: 23150 127.29 - 135.38: 1221 Bond angle restraints: 67030 Sorted by residual: angle pdb=" N CYS I 78 " pdb=" CA CYS I 78 " pdb=" CB CYS I 78 " ideal model delta sigma weight residual 111.20 101.11 10.09 1.65e+00 3.67e-01 3.74e+01 angle pdb=" O5' DA T 70 " pdb=" C5' DA T 70 " pdb=" C4' DA T 70 " ideal model delta sigma weight residual 110.80 119.64 -8.84 1.50e+00 4.44e-01 3.47e+01 angle pdb=" CA CYS I 103 " pdb=" CB CYS I 103 " pdb=" SG CYS I 103 " ideal model delta sigma weight residual 114.40 127.88 -13.48 2.30e+00 1.89e-01 3.43e+01 angle pdb=" CA CYS I 78 " pdb=" CB CYS I 78 " pdb=" SG CYS I 78 " ideal model delta sigma weight residual 114.40 127.16 -12.76 2.30e+00 1.89e-01 3.08e+01 angle pdb=" N CYS I 106 " pdb=" CA CYS I 106 " pdb=" CB CYS I 106 " ideal model delta sigma weight residual 110.53 102.36 8.17 1.49e+00 4.50e-01 3.01e+01 ... (remaining 67025 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.91: 25823 33.91 - 67.82: 2436 67.82 - 101.74: 101 101.74 - 135.65: 4 135.65 - 169.56: 3 Dihedral angle restraints: 28367 sinusoidal: 14550 harmonic: 13817 Sorted by residual: dihedral pdb=" CA VAL A 525 " pdb=" C VAL A 525 " pdb=" N GLN A 526 " pdb=" CA GLN A 526 " ideal model delta harmonic sigma weight residual 180.00 140.24 39.76 0 5.00e+00 4.00e-02 6.32e+01 dihedral pdb=" CA PRO A 959 " pdb=" C PRO A 959 " pdb=" N VAL A 960 " pdb=" CA VAL A 960 " ideal model delta harmonic sigma weight residual -180.00 -145.58 -34.42 0 5.00e+00 4.00e-02 4.74e+01 dihedral pdb=" CA ASP C 89 " pdb=" C ASP C 89 " pdb=" N TYR C 90 " pdb=" CA TYR C 90 " ideal model delta harmonic sigma weight residual 180.00 -147.18 -32.82 0 5.00e+00 4.00e-02 4.31e+01 ... (remaining 28364 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 6354 0.067 - 0.134: 1073 0.134 - 0.201: 96 0.201 - 0.268: 12 0.268 - 0.335: 5 Chirality restraints: 7540 Sorted by residual: chirality pdb=" C3' DA T 91 " pdb=" C4' DA T 91 " pdb=" O3' DA T 91 " pdb=" C2' DA T 91 " both_signs ideal model delta sigma weight residual False -2.66 -2.32 -0.34 2.00e-01 2.50e+01 2.81e+00 chirality pdb=" P DT T -94 " pdb=" OP1 DT T -94 " pdb=" OP2 DT T -94 " pdb=" O5' DT T -94 " both_signs ideal model delta sigma weight residual True 2.35 -2.68 -0.33 2.00e-01 2.50e+01 2.75e+00 chirality pdb=" CG LEU F 99 " pdb=" CB LEU F 99 " pdb=" CD1 LEU F 99 " pdb=" CD2 LEU F 99 " both_signs ideal model delta sigma weight residual False -2.59 -2.27 -0.32 2.00e-01 2.50e+01 2.57e+00 ... (remaining 7537 not shown) Planarity restraints: 7148 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT N -81 " 0.270 2.00e-02 2.50e+03 1.28e-01 4.10e+02 pdb=" N1 DT N -81 " -0.040 2.00e-02 2.50e+03 pdb=" C2 DT N -81 " -0.074 2.00e-02 2.50e+03 pdb=" O2 DT N -81 " -0.137 2.00e-02 2.50e+03 pdb=" N3 DT N -81 " -0.032 2.00e-02 2.50e+03 pdb=" C4 DT N -81 " 0.045 2.00e-02 2.50e+03 pdb=" O4 DT N -81 " 0.206 2.00e-02 2.50e+03 pdb=" C5 DT N -81 " -0.055 2.00e-02 2.50e+03 pdb=" C7 DT N -81 " -0.091 2.00e-02 2.50e+03 pdb=" C6 DT N -81 " -0.092 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT N -71 " 0.255 2.00e-02 2.50e+03 1.24e-01 3.84e+02 pdb=" N1 DT N -71 " -0.024 2.00e-02 2.50e+03 pdb=" C2 DT N -71 " -0.066 2.00e-02 2.50e+03 pdb=" O2 DT N -71 " -0.141 2.00e-02 2.50e+03 pdb=" N3 DT N -71 " -0.031 2.00e-02 2.50e+03 pdb=" C4 DT N -71 " 0.039 2.00e-02 2.50e+03 pdb=" O4 DT N -71 " 0.205 2.00e-02 2.50e+03 pdb=" C5 DT N -71 " -0.055 2.00e-02 2.50e+03 pdb=" C7 DT N -71 " -0.094 2.00e-02 2.50e+03 pdb=" C6 DT N -71 " -0.088 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA N 88 " 0.220 2.00e-02 2.50e+03 9.65e-02 2.56e+02 pdb=" N9 DA N 88 " -0.017 2.00e-02 2.50e+03 pdb=" C8 DA N 88 " -0.098 2.00e-02 2.50e+03 pdb=" N7 DA N 88 " -0.073 2.00e-02 2.50e+03 pdb=" C5 DA N 88 " -0.036 2.00e-02 2.50e+03 pdb=" C6 DA N 88 " 0.033 2.00e-02 2.50e+03 pdb=" N6 DA N 88 " 0.155 2.00e-02 2.50e+03 pdb=" N1 DA N 88 " 0.007 2.00e-02 2.50e+03 pdb=" C2 DA N 88 " -0.060 2.00e-02 2.50e+03 pdb=" N3 DA N 88 " -0.075 2.00e-02 2.50e+03 pdb=" C4 DA N 88 " -0.056 2.00e-02 2.50e+03 ... (remaining 7145 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 238 2.54 - 3.13: 34828 3.13 - 3.72: 75764 3.72 - 4.31: 108421 4.31 - 4.90: 169726 Nonbonded interactions: 388977 Sorted by model distance: nonbonded pdb=" OD1 ASP A 486 " pdb=" O2' U P 10 " model vdw 1.954 2.440 nonbonded pdb=" O ARG A1003 " pdb=" OG1 THR F 80 " model vdw 2.094 2.440 nonbonded pdb=" OE1 GLU A1064 " pdb=" OH TYR F 88 " model vdw 2.107 2.440 nonbonded pdb=" O LEU A1145 " pdb=" OG1 THR A1149 " model vdw 2.115 2.440 nonbonded pdb=" OD1 ASN H 17 " pdb=" OG SER H 24 " model vdw 2.115 2.440 ... (remaining 388972 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'a' and resid 39 through 134) selection = (chain 'e' and resid 39 through 134) } ncs_group { reference = (chain 'b' and resid 25 through 102) selection = chain 'f' } ncs_group { reference = chain 'c' selection = chain 'g' } ncs_group { reference = (chain 'd' and resid 29 through 121) selection = chain 'h' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.440 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: 0.000 Extract box with map and model: 4.980 Check model and map are aligned: 0.610 Set scattering table: 0.370 Process input model: 153.270 Find NCS groups from input model: 1.500 Set up NCS constraints: 0.240 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: 166.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6127 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.101 48284 Z= 0.352 Angle : 0.872 13.476 67030 Z= 0.509 Chirality : 0.050 0.335 7540 Planarity : 0.008 0.145 7148 Dihedral : 21.463 169.560 19439 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.79 % Favored : 96.13 % Rotamer: Outliers : 0.05 % Allowed : 0.60 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.45 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.59 (0.12), residues: 4700 helix: 0.59 (0.12), residues: 1848 sheet: -1.22 (0.19), residues: 654 loop : -0.91 (0.13), residues: 2198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.004 TRP A 139 HIS 0.012 0.002 HIS A 660 PHE 0.027 0.002 PHE C 260 TYR 0.041 0.002 TYR e 41 ARG 0.014 0.001 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9400 Ramachandran restraints generated. 4700 Oldfield, 0 Emsley, 4700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9400 Ramachandran restraints generated. 4700 Oldfield, 0 Emsley, 4700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 4149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 444 time to evaluate : 4.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 12 ARG cc_start: 0.5747 (mtm180) cc_final: 0.4784 (mpt180) REVERT: A 247 VAL cc_start: 0.8200 (t) cc_final: 0.7983 (t) REVERT: A 282 MET cc_start: 0.8990 (mtp) cc_final: 0.8423 (mpp) REVERT: A 305 MET cc_start: 0.5304 (mtt) cc_final: 0.4882 (mtt) REVERT: A 456 MET cc_start: 0.7186 (ttp) cc_final: 0.6344 (ttp) REVERT: A 457 MET cc_start: 0.5953 (mtm) cc_final: 0.5749 (ttp) REVERT: A 958 LEU cc_start: 0.8760 (mt) cc_final: 0.8350 (mt) REVERT: A 1037 PHE cc_start: 0.7591 (m-10) cc_final: 0.6956 (m-80) REVERT: A 1104 LYS cc_start: 0.9263 (ttmt) cc_final: 0.9053 (pttm) REVERT: A 1114 LYS cc_start: 0.8028 (mmtp) cc_final: 0.7793 (tttm) REVERT: A 1204 MET cc_start: 0.6100 (tpt) cc_final: 0.5180 (mmm) REVERT: A 1283 SER cc_start: 0.6287 (m) cc_final: 0.5835 (t) REVERT: A 1296 ASP cc_start: 0.8901 (t0) cc_final: 0.8454 (t70) REVERT: A 1378 MET cc_start: 0.7927 (mtp) cc_final: 0.7361 (mtp) REVERT: A 1424 CYS cc_start: 0.7392 (m) cc_final: 0.7175 (m) REVERT: B 35 LEU cc_start: 0.8616 (mt) cc_final: 0.8382 (tp) REVERT: B 106 LEU cc_start: 0.8285 (mt) cc_final: 0.7942 (mt) REVERT: B 482 SER cc_start: 0.9041 (m) cc_final: 0.8825 (p) REVERT: B 699 MET cc_start: 0.7872 (tpp) cc_final: 0.7003 (tpt) REVERT: B 702 MET cc_start: 0.4408 (tpp) cc_final: 0.4080 (ttt) REVERT: B 948 ILE cc_start: 0.7275 (mt) cc_final: 0.6865 (mt) REVERT: B 950 ASP cc_start: 0.7427 (t70) cc_final: 0.7219 (t0) REVERT: B 978 ASP cc_start: 0.6705 (m-30) cc_final: 0.6478 (m-30) REVERT: B 1204 PHE cc_start: 0.7203 (m-10) cc_final: 0.6935 (m-10) REVERT: G 73 LYS cc_start: 0.4491 (mmmt) cc_final: 0.3679 (mttt) REVERT: H 99 THR cc_start: 0.8419 (m) cc_final: 0.8002 (p) REVERT: I 19 ASP cc_start: 0.8346 (m-30) cc_final: 0.7644 (t70) REVERT: J 1 MET cc_start: 0.7171 (ttm) cc_final: 0.6758 (ttt) REVERT: K 108 GLU cc_start: 0.8758 (tp30) cc_final: 0.8293 (tt0) REVERT: L 66 MET cc_start: 0.5633 (ttp) cc_final: 0.5131 (tpt) REVERT: a 67 PHE cc_start: 0.7828 (t80) cc_final: 0.7146 (t80) REVERT: a 90 MET cc_start: 0.9459 (mmm) cc_final: 0.9248 (mmm) REVERT: a 92 LEU cc_start: 0.8692 (mt) cc_final: 0.8459 (tp) REVERT: d 59 MET cc_start: 0.8649 (mmm) cc_final: 0.8233 (mmm) outliers start: 2 outliers final: 0 residues processed: 446 average time/residue: 0.6243 time to fit residues: 447.7533 Evaluate side-chains 245 residues out of total 4149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 245 time to evaluate : 4.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 430 optimal weight: 20.0000 chunk 386 optimal weight: 30.0000 chunk 214 optimal weight: 6.9990 chunk 132 optimal weight: 6.9990 chunk 260 optimal weight: 9.9990 chunk 206 optimal weight: 0.0070 chunk 399 optimal weight: 10.0000 chunk 154 optimal weight: 1.9990 chunk 243 optimal weight: 6.9990 chunk 297 optimal weight: 0.4980 chunk 463 optimal weight: 10.0000 overall best weight: 3.3004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 170 ASN ** A 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 596 ASN A 649 ASN A 651 GLN ** A 787 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1021 GLN ** A1303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 ASN ** B 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 350 GLN ** B 932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 946 ASN ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 ASN G 155 ASN H 43 ASN I 11 ASN I 12 ASN a 68 GLN a 108 ASN ** d 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 60 ASN d 79 HIS ** h 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6269 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 48284 Z= 0.232 Angle : 0.644 12.859 67030 Z= 0.352 Chirality : 0.042 0.268 7540 Planarity : 0.005 0.076 7148 Dihedral : 24.366 178.757 9936 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.40 % Favored : 96.57 % Rotamer: Outliers : 0.82 % Allowed : 6.56 % Favored : 92.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.45 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.11 (0.12), residues: 4700 helix: 1.17 (0.12), residues: 1909 sheet: -0.64 (0.20), residues: 615 loop : -0.65 (0.13), residues: 2176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 201 HIS 0.011 0.001 HIS A 660 PHE 0.024 0.002 PHE G 18 TYR 0.025 0.002 TYR d 80 ARG 0.017 0.001 ARG E 206 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9400 Ramachandran restraints generated. 4700 Oldfield, 0 Emsley, 4700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9400 Ramachandran restraints generated. 4700 Oldfield, 0 Emsley, 4700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 4149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 266 time to evaluate : 4.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ARG cc_start: 0.5434 (mtm180) cc_final: 0.4732 (mmt180) REVERT: A 282 MET cc_start: 0.8973 (mtp) cc_final: 0.8386 (mpp) REVERT: A 305 MET cc_start: 0.6147 (mtt) cc_final: 0.5546 (mtt) REVERT: A 770 MET cc_start: 0.6426 (mmp) cc_final: 0.6146 (mmp) REVERT: A 847 GLU cc_start: 0.8689 (pt0) cc_final: 0.8030 (pt0) REVERT: A 1037 PHE cc_start: 0.7407 (m-10) cc_final: 0.6839 (m-80) REVERT: A 1065 MET cc_start: 0.7777 (tpp) cc_final: 0.7133 (tpp) REVERT: A 1114 LYS cc_start: 0.7809 (mmtp) cc_final: 0.7584 (tttm) REVERT: A 1371 MET cc_start: 0.6783 (mtm) cc_final: 0.6369 (mtm) REVERT: A 1385 MET cc_start: 0.6768 (mpp) cc_final: 0.6375 (ppp) REVERT: A 1439 MET cc_start: 0.6937 (ttp) cc_final: 0.6172 (tmm) REVERT: B 93 ASP cc_start: 0.8424 (OUTLIER) cc_final: 0.7811 (p0) REVERT: B 190 MET cc_start: 0.7126 (mmm) cc_final: 0.6784 (mmm) REVERT: B 482 SER cc_start: 0.9065 (m) cc_final: 0.8841 (p) REVERT: B 948 ILE cc_start: 0.6910 (mt) cc_final: 0.6431 (mm) REVERT: B 978 ASP cc_start: 0.7013 (m-30) cc_final: 0.5894 (m-30) REVERT: B 1082 MET cc_start: 0.7433 (mpp) cc_final: 0.7075 (mpp) REVERT: B 1096 ARG cc_start: 0.7851 (OUTLIER) cc_final: 0.7648 (ptm160) REVERT: C 52 MET cc_start: 0.8670 (ttt) cc_final: 0.7768 (tmm) REVERT: E 34 MET cc_start: 0.8811 (mtm) cc_final: 0.8541 (mtm) REVERT: E 92 MET cc_start: 0.8643 (tpp) cc_final: 0.7452 (tpp) REVERT: E 122 MET cc_start: 0.5560 (ttt) cc_final: 0.5256 (ttt) REVERT: G 73 LYS cc_start: 0.4120 (mmmt) cc_final: 0.3610 (mttt) REVERT: H 99 THR cc_start: 0.8687 (m) cc_final: 0.8366 (p) REVERT: I 19 ASP cc_start: 0.8362 (m-30) cc_final: 0.7923 (t0) REVERT: K 108 GLU cc_start: 0.8926 (tp30) cc_final: 0.8444 (tt0) REVERT: L 66 MET cc_start: 0.5831 (ttp) cc_final: 0.5218 (tpp) REVERT: a 67 PHE cc_start: 0.7997 (t80) cc_final: 0.7614 (t80) REVERT: a 90 MET cc_start: 0.9484 (mmm) cc_final: 0.9233 (mmm) REVERT: a 92 LEU cc_start: 0.9148 (mt) cc_final: 0.8944 (tp) REVERT: a 125 GLN cc_start: 0.9612 (OUTLIER) cc_final: 0.9314 (pp30) REVERT: d 59 MET cc_start: 0.8851 (mmm) cc_final: 0.8491 (mmm) REVERT: e 96 CYS cc_start: 0.8249 (m) cc_final: 0.7994 (p) outliers start: 34 outliers final: 20 residues processed: 293 average time/residue: 0.5859 time to fit residues: 287.8696 Evaluate side-chains 251 residues out of total 4149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 228 time to evaluate : 4.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 593 ASP Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 848 ASP Chi-restraints excluded: chain A residue 1028 LEU Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1336 VAL Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 408 ASN Chi-restraints excluded: chain B residue 971 THR Chi-restraints excluded: chain B residue 1096 ARG Chi-restraints excluded: chain B residue 1133 MET Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 138 TYR Chi-restraints excluded: chain C residue 260 PHE Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 114 ASN Chi-restraints excluded: chain E residue 200 ARG Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain H residue 43 ASN Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain a residue 125 GLN Chi-restraints excluded: chain b residue 37 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 257 optimal weight: 20.0000 chunk 143 optimal weight: 10.0000 chunk 385 optimal weight: 10.0000 chunk 315 optimal weight: 5.9990 chunk 127 optimal weight: 30.0000 chunk 463 optimal weight: 20.0000 chunk 501 optimal weight: 6.9990 chunk 413 optimal weight: 10.0000 chunk 460 optimal weight: 8.9990 chunk 158 optimal weight: 10.0000 chunk 372 optimal weight: 4.9990 overall best weight: 7.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 359 ASN A 480 ASN ** A 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 768 GLN A 787 HIS A 882 GLN ** A 970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 301 GLN ** B 932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 984 HIS ** B 986 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 996 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1015 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1025 HIS ** B1104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 11 ASN K 110 ASN a 108 ASN ** d 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 64 ASN ** e 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 75 HIS ** h 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 81 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6476 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.113 48284 Z= 0.368 Angle : 0.739 14.434 67030 Z= 0.398 Chirality : 0.044 0.307 7540 Planarity : 0.006 0.079 7148 Dihedral : 24.567 174.698 9936 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 18.35 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.47 % Favored : 95.49 % Rotamer: Outliers : 1.69 % Allowed : 9.50 % Favored : 88.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.45 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.29 (0.12), residues: 4700 helix: 0.79 (0.12), residues: 1909 sheet: -0.68 (0.20), residues: 638 loop : -0.86 (0.13), residues: 2153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP C 170 HIS 0.013 0.002 HIS B1015 PHE 0.039 0.003 PHE B1069 TYR 0.027 0.003 TYR B 769 ARG 0.008 0.001 ARG B 366 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9400 Ramachandran restraints generated. 4700 Oldfield, 0 Emsley, 4700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9400 Ramachandran restraints generated. 4700 Oldfield, 0 Emsley, 4700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 4149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 225 time to evaluate : 4.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ARG cc_start: 0.5154 (mtm180) cc_final: 0.3864 (mmt-90) REVERT: A 235 MET cc_start: 0.6557 (ptp) cc_final: 0.5904 (ptt) REVERT: A 282 MET cc_start: 0.8940 (mtp) cc_final: 0.8410 (mpp) REVERT: A 305 MET cc_start: 0.5991 (mtt) cc_final: 0.5569 (mtt) REVERT: A 464 MET cc_start: 0.7422 (mtt) cc_final: 0.7163 (mtp) REVERT: A 736 MET cc_start: 0.8506 (mmm) cc_final: 0.8283 (mmt) REVERT: A 747 MET cc_start: 0.8004 (mtm) cc_final: 0.7607 (mmm) REVERT: A 847 GLU cc_start: 0.8748 (pt0) cc_final: 0.8313 (pt0) REVERT: A 1114 LYS cc_start: 0.7820 (mmtp) cc_final: 0.7514 (ttpp) REVERT: A 1371 MET cc_start: 0.6897 (mtm) cc_final: 0.6508 (mtm) REVERT: A 1439 MET cc_start: 0.7209 (ttp) cc_final: 0.6709 (tmm) REVERT: B 89 MET cc_start: 0.3949 (tpt) cc_final: 0.3626 (tpp) REVERT: B 245 MET cc_start: 0.6846 (mtm) cc_final: 0.6550 (mpp) REVERT: B 482 SER cc_start: 0.9308 (m) cc_final: 0.9097 (p) REVERT: B 864 LYS cc_start: 0.9301 (mmmt) cc_final: 0.9090 (mmmt) REVERT: B 1082 MET cc_start: 0.8017 (mpp) cc_final: 0.7440 (mpp) REVERT: B 1152 MET cc_start: 0.6879 (OUTLIER) cc_final: 0.6668 (mtt) REVERT: C 21 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8560 (tp) REVERT: C 52 MET cc_start: 0.8563 (ttt) cc_final: 0.7779 (tmm) REVERT: E 34 MET cc_start: 0.8766 (mtm) cc_final: 0.8478 (mtm) REVERT: E 92 MET cc_start: 0.8479 (tpp) cc_final: 0.7437 (tpp) REVERT: G 18 PHE cc_start: 0.8747 (m-80) cc_final: 0.8197 (m-80) REVERT: G 73 LYS cc_start: 0.4016 (mmmt) cc_final: 0.3503 (mttt) REVERT: H 29 ILE cc_start: 0.8448 (OUTLIER) cc_final: 0.8190 (tt) REVERT: J 1 MET cc_start: 0.6670 (OUTLIER) cc_final: 0.5723 (ttm) REVERT: K 108 GLU cc_start: 0.9027 (tp30) cc_final: 0.8607 (tt0) REVERT: L 66 MET cc_start: 0.6096 (ttp) cc_final: 0.5263 (tpp) REVERT: a 67 PHE cc_start: 0.8349 (t80) cc_final: 0.7952 (t80) REVERT: a 92 LEU cc_start: 0.9250 (mt) cc_final: 0.9048 (tp) REVERT: e 77 ASP cc_start: 0.9317 (OUTLIER) cc_final: 0.8854 (p0) REVERT: h 68 GLU cc_start: 0.8745 (mm-30) cc_final: 0.8424 (mm-30) outliers start: 70 outliers final: 33 residues processed: 282 average time/residue: 0.5651 time to fit residues: 270.8021 Evaluate side-chains 242 residues out of total 4149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 204 time to evaluate : 4.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 593 ASP Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 848 ASP Chi-restraints excluded: chain A residue 1028 LEU Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1320 MET Chi-restraints excluded: chain A residue 1336 VAL Chi-restraints excluded: chain A residue 1412 LEU Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 408 ASN Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 971 THR Chi-restraints excluded: chain B residue 1152 MET Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 260 PHE Chi-restraints excluded: chain E residue 200 ARG Chi-restraints excluded: chain E residue 202 GLU Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 44 ASN Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 67 ILE Chi-restraints excluded: chain b residue 37 LEU Chi-restraints excluded: chain e residue 77 ASP Chi-restraints excluded: chain g residue 94 ASN Chi-restraints excluded: chain h residue 97 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 458 optimal weight: 5.9990 chunk 348 optimal weight: 7.9990 chunk 240 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 221 optimal weight: 10.0000 chunk 311 optimal weight: 0.0970 chunk 465 optimal weight: 7.9990 chunk 492 optimal weight: 20.0000 chunk 243 optimal weight: 4.9990 chunk 441 optimal weight: 20.0000 chunk 132 optimal weight: 3.9990 overall best weight: 3.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 GLN ** B 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 761 HIS ** B 932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 996 HIS ** B1015 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1093 GLN F 104 ASN H 43 ASN ** d 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6441 moved from start: 0.3603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 48284 Z= 0.220 Angle : 0.593 10.212 67030 Z= 0.324 Chirality : 0.040 0.254 7540 Planarity : 0.004 0.056 7148 Dihedral : 24.451 176.019 9936 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.66 % Favored : 96.32 % Rotamer: Outliers : 1.49 % Allowed : 11.40 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.45 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.09 (0.12), residues: 4700 helix: 1.17 (0.12), residues: 1926 sheet: -0.51 (0.20), residues: 641 loop : -0.74 (0.13), residues: 2133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP C 170 HIS 0.010 0.001 HIS A 288 PHE 0.015 0.001 PHE B1069 TYR 0.017 0.001 TYR E 27 ARG 0.008 0.000 ARG F 97 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9400 Ramachandran restraints generated. 4700 Oldfield, 0 Emsley, 4700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9400 Ramachandran restraints generated. 4700 Oldfield, 0 Emsley, 4700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 4149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 223 time to evaluate : 4.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ARG cc_start: 0.4849 (mtm180) cc_final: 0.3688 (mmt-90) REVERT: A 74 MET cc_start: 0.7403 (tpt) cc_final: 0.6971 (mmm) REVERT: A 180 MET cc_start: 0.4306 (tmm) cc_final: 0.3486 (tmm) REVERT: A 235 MET cc_start: 0.6456 (ptp) cc_final: 0.5781 (ptt) REVERT: A 282 MET cc_start: 0.8944 (mtp) cc_final: 0.8408 (mpp) REVERT: A 305 MET cc_start: 0.5412 (mtt) cc_final: 0.4968 (mmm) REVERT: A 457 MET cc_start: 0.5911 (ptt) cc_final: 0.5638 (ptt) REVERT: A 461 VAL cc_start: 0.6252 (OUTLIER) cc_final: 0.5990 (t) REVERT: A 464 MET cc_start: 0.7324 (mtt) cc_final: 0.6991 (mtp) REVERT: A 728 ASP cc_start: 0.9384 (OUTLIER) cc_final: 0.8897 (m-30) REVERT: A 736 MET cc_start: 0.8517 (mmm) cc_final: 0.8290 (mmt) REVERT: A 747 MET cc_start: 0.7966 (mtm) cc_final: 0.7441 (mmm) REVERT: A 843 VAL cc_start: 0.8248 (t) cc_final: 0.7743 (p) REVERT: A 847 GLU cc_start: 0.8784 (pt0) cc_final: 0.8224 (pt0) REVERT: A 1065 MET cc_start: 0.7800 (tpp) cc_final: 0.7292 (tpp) REVERT: A 1114 LYS cc_start: 0.7958 (mmtp) cc_final: 0.7757 (tttm) REVERT: A 1371 MET cc_start: 0.6827 (mtm) cc_final: 0.6379 (mtm) REVERT: A 1385 MET cc_start: 0.6916 (mpp) cc_final: 0.6431 (ppp) REVERT: A 1439 MET cc_start: 0.7081 (ttp) cc_final: 0.6733 (tmm) REVERT: A 1447 MET cc_start: 0.7994 (mtt) cc_final: 0.7744 (mmt) REVERT: B 89 MET cc_start: 0.3978 (tpt) cc_final: 0.3431 (tpp) REVERT: B 93 ASP cc_start: 0.8468 (OUTLIER) cc_final: 0.7560 (p0) REVERT: B 106 LEU cc_start: 0.8366 (mt) cc_final: 0.8054 (mt) REVERT: B 278 PHE cc_start: 0.9288 (OUTLIER) cc_final: 0.8963 (m-80) REVERT: B 283 VAL cc_start: 0.5248 (OUTLIER) cc_final: 0.5009 (p) REVERT: B 482 SER cc_start: 0.9214 (m) cc_final: 0.8994 (p) REVERT: B 773 MET cc_start: 0.7317 (mtm) cc_final: 0.6848 (mtm) REVERT: B 864 LYS cc_start: 0.9292 (mmmt) cc_final: 0.9079 (mmmt) REVERT: B 1082 MET cc_start: 0.7938 (mpp) cc_final: 0.7442 (mpp) REVERT: C 52 MET cc_start: 0.8673 (ttt) cc_final: 0.7769 (tmm) REVERT: C 190 ASP cc_start: 0.8872 (t0) cc_final: 0.8451 (m-30) REVERT: E 34 MET cc_start: 0.8719 (mtm) cc_final: 0.8265 (mtt) REVERT: E 92 MET cc_start: 0.8591 (tpp) cc_final: 0.7916 (tpp) REVERT: G 18 PHE cc_start: 0.8433 (m-10) cc_final: 0.7879 (m-80) REVERT: I 34 TYR cc_start: 0.7840 (t80) cc_final: 0.7526 (t80) REVERT: K 73 MET cc_start: 0.7915 (ttp) cc_final: 0.7487 (ttp) REVERT: K 108 GLU cc_start: 0.8998 (tp30) cc_final: 0.8569 (tt0) REVERT: L 66 MET cc_start: 0.6118 (ttp) cc_final: 0.5274 (tpp) REVERT: a 67 PHE cc_start: 0.8561 (t80) cc_final: 0.8248 (t80) REVERT: d 59 MET cc_start: 0.9118 (mmm) cc_final: 0.8820 (mmm) REVERT: e 120 MET cc_start: 0.6567 (mmm) cc_final: 0.6345 (mmm) REVERT: h 68 GLU cc_start: 0.8809 (mm-30) cc_final: 0.8439 (mm-30) outliers start: 62 outliers final: 30 residues processed: 279 average time/residue: 0.5650 time to fit residues: 269.9432 Evaluate side-chains 244 residues out of total 4149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 209 time to evaluate : 4.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 593 ASP Chi-restraints excluded: chain A residue 728 ASP Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 1028 LEU Chi-restraints excluded: chain A residue 1336 VAL Chi-restraints excluded: chain A residue 1427 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 408 ASN Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 971 THR Chi-restraints excluded: chain B residue 1034 VAL Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 260 PHE Chi-restraints excluded: chain E residue 200 ARG Chi-restraints excluded: chain E residue 202 GLU Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 55 ASP Chi-restraints excluded: chain H residue 17 ASN Chi-restraints excluded: chain H residue 43 ASN Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 32 ILE Chi-restraints excluded: chain K residue 59 VAL Chi-restraints excluded: chain K residue 72 VAL Chi-restraints excluded: chain b residue 37 LEU Chi-restraints excluded: chain g residue 94 ASN Chi-restraints excluded: chain h residue 97 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 410 optimal weight: 10.0000 chunk 279 optimal weight: 10.0000 chunk 7 optimal weight: 8.9990 chunk 367 optimal weight: 50.0000 chunk 203 optimal weight: 0.0370 chunk 420 optimal weight: 20.0000 chunk 340 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 251 optimal weight: 8.9990 chunk 442 optimal weight: 30.0000 chunk 124 optimal weight: 4.9990 overall best weight: 5.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1056 GLN ** A1303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 47 GLN B 72 ASN ** B 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1013 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1076 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 104 GLN ** d 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 25 ASN ** g 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6523 moved from start: 0.4362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 48284 Z= 0.294 Angle : 0.648 11.314 67030 Z= 0.352 Chirality : 0.041 0.193 7540 Planarity : 0.005 0.057 7148 Dihedral : 24.443 173.896 9936 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 17.93 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.00 % Favored : 94.98 % Rotamer: Outliers : 2.29 % Allowed : 12.41 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.45 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.03 (0.12), residues: 4700 helix: 1.10 (0.12), residues: 1920 sheet: -0.53 (0.20), residues: 649 loop : -0.74 (0.13), residues: 2131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 553 HIS 0.014 0.002 HIS A 288 PHE 0.022 0.002 PHE B1069 TYR 0.023 0.002 TYR B 859 ARG 0.007 0.001 ARG E 93 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9400 Ramachandran restraints generated. 4700 Oldfield, 0 Emsley, 4700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9400 Ramachandran restraints generated. 4700 Oldfield, 0 Emsley, 4700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 4149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 212 time to evaluate : 4.960 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ARG cc_start: 0.5213 (mtm180) cc_final: 0.3661 (mmt180) REVERT: A 74 MET cc_start: 0.7940 (tpt) cc_final: 0.7706 (mmm) REVERT: A 235 MET cc_start: 0.6704 (ptp) cc_final: 0.6148 (ptt) REVERT: A 282 MET cc_start: 0.8974 (mtp) cc_final: 0.8519 (mmt) REVERT: A 305 MET cc_start: 0.5708 (mtt) cc_final: 0.4870 (mmt) REVERT: A 461 VAL cc_start: 0.5760 (OUTLIER) cc_final: 0.5424 (t) REVERT: A 464 MET cc_start: 0.7326 (mtt) cc_final: 0.7010 (mtp) REVERT: A 728 ASP cc_start: 0.9386 (OUTLIER) cc_final: 0.8957 (m-30) REVERT: A 736 MET cc_start: 0.8467 (mmm) cc_final: 0.8219 (mmt) REVERT: A 747 MET cc_start: 0.8047 (mtm) cc_final: 0.7486 (mmm) REVERT: A 847 GLU cc_start: 0.8934 (pt0) cc_final: 0.8407 (pt0) REVERT: A 1065 MET cc_start: 0.7570 (tpp) cc_final: 0.7016 (tpp) REVERT: A 1114 LYS cc_start: 0.7996 (mmtp) cc_final: 0.7748 (tttm) REVERT: A 1262 MET cc_start: 0.8003 (tpt) cc_final: 0.7719 (mmm) REVERT: A 1335 PHE cc_start: 0.8129 (OUTLIER) cc_final: 0.7719 (p90) REVERT: A 1371 MET cc_start: 0.6832 (mtm) cc_final: 0.6377 (mtm) REVERT: A 1439 MET cc_start: 0.7137 (ttp) cc_final: 0.6903 (tmm) REVERT: B 34 GLN cc_start: 0.7030 (OUTLIER) cc_final: 0.6536 (mt0) REVERT: B 89 MET cc_start: 0.4547 (tpt) cc_final: 0.4089 (tpp) REVERT: B 93 ASP cc_start: 0.8482 (OUTLIER) cc_final: 0.7474 (p0) REVERT: B 278 PHE cc_start: 0.9282 (OUTLIER) cc_final: 0.9018 (m-80) REVERT: B 283 VAL cc_start: 0.5127 (OUTLIER) cc_final: 0.4881 (p) REVERT: B 482 SER cc_start: 0.9267 (m) cc_final: 0.9062 (p) REVERT: B 864 LYS cc_start: 0.9351 (mmmt) cc_final: 0.9110 (mmmt) REVERT: B 1082 MET cc_start: 0.8097 (mpp) cc_final: 0.7627 (mpp) REVERT: B 1152 MET cc_start: 0.6876 (OUTLIER) cc_final: 0.6606 (mtt) REVERT: C 52 MET cc_start: 0.8569 (ttt) cc_final: 0.7722 (tmm) REVERT: C 190 ASP cc_start: 0.8973 (t0) cc_final: 0.8569 (m-30) REVERT: E 34 MET cc_start: 0.8830 (mtm) cc_final: 0.8477 (mtt) REVERT: E 92 MET cc_start: 0.8646 (tpp) cc_final: 0.7943 (tpp) REVERT: G 18 PHE cc_start: 0.8469 (m-10) cc_final: 0.8226 (m-80) REVERT: I 34 TYR cc_start: 0.8034 (t80) cc_final: 0.7626 (t80) REVERT: K 108 GLU cc_start: 0.8893 (tp30) cc_final: 0.8390 (tt0) REVERT: L 66 MET cc_start: 0.6185 (ttp) cc_final: 0.5256 (tpt) REVERT: h 68 GLU cc_start: 0.8734 (OUTLIER) cc_final: 0.8394 (mm-30) outliers start: 95 outliers final: 59 residues processed: 290 average time/residue: 0.5497 time to fit residues: 274.4124 Evaluate side-chains 266 residues out of total 4149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 198 time to evaluate : 4.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 419 HIS Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 651 GLN Chi-restraints excluded: chain A residue 728 ASP Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 848 ASP Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 903 MET Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1028 LEU Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1119 THR Chi-restraints excluded: chain A residue 1320 MET Chi-restraints excluded: chain A residue 1335 PHE Chi-restraints excluded: chain A residue 1336 VAL Chi-restraints excluded: chain A residue 1347 THR Chi-restraints excluded: chain A residue 1427 VAL Chi-restraints excluded: chain A residue 1431 VAL Chi-restraints excluded: chain B residue 34 GLN Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 408 ASN Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 797 TYR Chi-restraints excluded: chain B residue 971 THR Chi-restraints excluded: chain B residue 1021 MET Chi-restraints excluded: chain B residue 1034 VAL Chi-restraints excluded: chain B residue 1090 THR Chi-restraints excluded: chain B residue 1103 ILE Chi-restraints excluded: chain B residue 1152 MET Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain C residue 260 PHE Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 200 ARG Chi-restraints excluded: chain E residue 202 GLU Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 55 ASP Chi-restraints excluded: chain H residue 17 ASN Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain I residue 19 ASP Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain J residue 35 LEU Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 32 ILE Chi-restraints excluded: chain K residue 59 VAL Chi-restraints excluded: chain K residue 72 VAL Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 67 ILE Chi-restraints excluded: chain a residue 125 GLN Chi-restraints excluded: chain b residue 37 LEU Chi-restraints excluded: chain e residue 77 ASP Chi-restraints excluded: chain g residue 94 ASN Chi-restraints excluded: chain h residue 68 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 165 optimal weight: 7.9990 chunk 443 optimal weight: 30.0000 chunk 97 optimal weight: 3.9990 chunk 289 optimal weight: 30.0000 chunk 121 optimal weight: 40.0000 chunk 493 optimal weight: 50.0000 chunk 409 optimal weight: 10.0000 chunk 228 optimal weight: 5.9990 chunk 41 optimal weight: 0.0270 chunk 163 optimal weight: 30.0000 chunk 259 optimal weight: 6.9990 overall best weight: 5.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1190 GLN A1303 ASN ** B 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 ASN B 531 ASN ** B 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 735 HIS ** B1013 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1076 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6521 moved from start: 0.4727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 48284 Z= 0.252 Angle : 0.606 12.259 67030 Z= 0.329 Chirality : 0.040 0.229 7540 Planarity : 0.004 0.056 7148 Dihedral : 24.465 174.808 9936 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 16.57 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.26 % Favored : 95.72 % Rotamer: Outliers : 2.07 % Allowed : 13.76 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.45 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.16 (0.12), residues: 4700 helix: 1.25 (0.12), residues: 1915 sheet: -0.52 (0.20), residues: 663 loop : -0.69 (0.13), residues: 2122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP C 170 HIS 0.012 0.001 HIS A 288 PHE 0.018 0.002 PHE B 25 TYR 0.017 0.002 TYR f 88 ARG 0.008 0.000 ARG B1183 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9400 Ramachandran restraints generated. 4700 Oldfield, 0 Emsley, 4700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9400 Ramachandran restraints generated. 4700 Oldfield, 0 Emsley, 4700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 4149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 206 time to evaluate : 4.502 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 12 ARG cc_start: 0.5123 (mtm180) cc_final: 0.3539 (mmt180) REVERT: A 122 MET cc_start: 0.4351 (ttt) cc_final: 0.4129 (mtt) REVERT: A 235 MET cc_start: 0.6775 (ptp) cc_final: 0.6268 (ptt) REVERT: A 282 MET cc_start: 0.8943 (mtp) cc_final: 0.8536 (mmt) REVERT: A 305 MET cc_start: 0.5800 (mtt) cc_final: 0.4992 (mmt) REVERT: A 324 LYS cc_start: 0.9088 (tppt) cc_final: 0.8783 (tppt) REVERT: A 461 VAL cc_start: 0.4957 (OUTLIER) cc_final: 0.4531 (t) REVERT: A 464 MET cc_start: 0.7382 (mtt) cc_final: 0.7092 (mtp) REVERT: A 728 ASP cc_start: 0.9420 (OUTLIER) cc_final: 0.9021 (m-30) REVERT: A 736 MET cc_start: 0.8192 (mmm) cc_final: 0.7977 (mmt) REVERT: A 747 MET cc_start: 0.8069 (mtm) cc_final: 0.7457 (mmm) REVERT: A 847 GLU cc_start: 0.8886 (pt0) cc_final: 0.8248 (pt0) REVERT: A 1065 MET cc_start: 0.7610 (tpp) cc_final: 0.6863 (tpp) REVERT: A 1114 LYS cc_start: 0.8009 (mmtp) cc_final: 0.7798 (tttm) REVERT: A 1335 PHE cc_start: 0.8277 (OUTLIER) cc_final: 0.7749 (p90) REVERT: A 1371 MET cc_start: 0.6850 (mtm) cc_final: 0.6375 (mtm) REVERT: A 1439 MET cc_start: 0.7154 (ttp) cc_final: 0.6746 (tmm) REVERT: B 34 GLN cc_start: 0.7113 (OUTLIER) cc_final: 0.6604 (mm-40) REVERT: B 93 ASP cc_start: 0.8467 (OUTLIER) cc_final: 0.7395 (p0) REVERT: B 106 LEU cc_start: 0.8412 (mt) cc_final: 0.8133 (mt) REVERT: B 190 MET cc_start: 0.6992 (mmm) cc_final: 0.6749 (mmm) REVERT: B 245 MET cc_start: 0.7273 (mtm) cc_final: 0.6550 (mpp) REVERT: B 278 PHE cc_start: 0.9286 (OUTLIER) cc_final: 0.9026 (m-80) REVERT: B 283 VAL cc_start: 0.5108 (OUTLIER) cc_final: 0.4863 (p) REVERT: B 482 SER cc_start: 0.9262 (m) cc_final: 0.9054 (p) REVERT: B 702 MET cc_start: 0.4961 (ttm) cc_final: 0.3467 (ttm) REVERT: B 860 MET cc_start: 0.7306 (mmp) cc_final: 0.6322 (mmp) REVERT: B 864 LYS cc_start: 0.9349 (mmmt) cc_final: 0.9107 (mmmt) REVERT: B 1082 MET cc_start: 0.8088 (mpp) cc_final: 0.7678 (mpp) REVERT: C 52 MET cc_start: 0.8648 (ttt) cc_final: 0.7741 (tmm) REVERT: C 190 ASP cc_start: 0.8965 (t0) cc_final: 0.8571 (m-30) REVERT: D 29 ARG cc_start: 0.4645 (mtt180) cc_final: 0.4273 (tpm170) REVERT: E 34 MET cc_start: 0.8761 (mtm) cc_final: 0.8442 (mtt) REVERT: G 18 PHE cc_start: 0.8756 (m-10) cc_final: 0.8306 (m-80) REVERT: G 22 MET cc_start: 0.4450 (tpt) cc_final: 0.4070 (mmm) REVERT: I 34 TYR cc_start: 0.7815 (t80) cc_final: 0.7242 (t80) REVERT: J 54 ASP cc_start: 0.6554 (OUTLIER) cc_final: 0.6213 (p0) REVERT: K 73 MET cc_start: 0.7917 (ttp) cc_final: 0.7467 (ttp) REVERT: K 108 GLU cc_start: 0.8921 (tp30) cc_final: 0.8416 (tt0) REVERT: L 66 MET cc_start: 0.6204 (ttp) cc_final: 0.5233 (tpt) REVERT: d 59 MET cc_start: 0.9231 (mmm) cc_final: 0.8997 (mmm) REVERT: e 120 MET cc_start: 0.6910 (mmm) cc_final: 0.6543 (mmm) REVERT: h 68 GLU cc_start: 0.8767 (mm-30) cc_final: 0.8429 (mm-30) outliers start: 86 outliers final: 50 residues processed: 281 average time/residue: 0.5892 time to fit residues: 283.5526 Evaluate side-chains 261 residues out of total 4149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 203 time to evaluate : 4.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 728 ASP Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 1028 LEU Chi-restraints excluded: chain A residue 1119 THR Chi-restraints excluded: chain A residue 1335 PHE Chi-restraints excluded: chain A residue 1336 VAL Chi-restraints excluded: chain A residue 1347 THR Chi-restraints excluded: chain A residue 1427 VAL Chi-restraints excluded: chain A residue 1431 VAL Chi-restraints excluded: chain B residue 34 GLN Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 408 ASN Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 797 TYR Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 971 THR Chi-restraints excluded: chain B residue 1034 VAL Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 260 PHE Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 200 ARG Chi-restraints excluded: chain E residue 202 GLU Chi-restraints excluded: chain E residue 212 ILE Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 55 ASP Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain H residue 17 ASN Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 32 ILE Chi-restraints excluded: chain K residue 59 VAL Chi-restraints excluded: chain K residue 72 VAL Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 50 CYS Chi-restraints excluded: chain L residue 67 ILE Chi-restraints excluded: chain a residue 67 PHE Chi-restraints excluded: chain a residue 125 GLN Chi-restraints excluded: chain b residue 37 LEU Chi-restraints excluded: chain g residue 94 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 475 optimal weight: 20.0000 chunk 55 optimal weight: 10.0000 chunk 281 optimal weight: 9.9990 chunk 360 optimal weight: 30.0000 chunk 279 optimal weight: 9.9990 chunk 415 optimal weight: 10.0000 chunk 275 optimal weight: 5.9990 chunk 491 optimal weight: 20.0000 chunk 307 optimal weight: 5.9990 chunk 299 optimal weight: 0.5980 chunk 226 optimal weight: 0.0070 overall best weight: 4.5204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 ASN ** B 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1013 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1076 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1112 GLN I 90 GLN ** c 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6540 moved from start: 0.5162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 48284 Z= 0.240 Angle : 0.601 12.617 67030 Z= 0.326 Chirality : 0.040 0.253 7540 Planarity : 0.004 0.060 7148 Dihedral : 24.420 175.087 9936 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 17.03 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.02 % Favored : 94.96 % Rotamer: Outliers : 2.34 % Allowed : 14.39 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.45 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.27 (0.12), residues: 4700 helix: 1.35 (0.12), residues: 1906 sheet: -0.45 (0.20), residues: 660 loop : -0.65 (0.14), residues: 2134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 170 HIS 0.011 0.001 HIS A 288 PHE 0.017 0.002 PHE J 8 TYR 0.016 0.001 TYR E 27 ARG 0.007 0.001 ARG F 135 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9400 Ramachandran restraints generated. 4700 Oldfield, 0 Emsley, 4700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9400 Ramachandran restraints generated. 4700 Oldfield, 0 Emsley, 4700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 4149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 210 time to evaluate : 4.688 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 12 ARG cc_start: 0.5154 (mtm180) cc_final: 0.3615 (mmt180) REVERT: A 74 MET cc_start: 0.8188 (mmm) cc_final: 0.7856 (mmm) REVERT: A 122 MET cc_start: 0.4092 (ttt) cc_final: 0.3862 (mtt) REVERT: A 235 MET cc_start: 0.6813 (ptp) cc_final: 0.6305 (ptt) REVERT: A 282 MET cc_start: 0.8907 (mtp) cc_final: 0.8519 (mmt) REVERT: A 305 MET cc_start: 0.5662 (mtt) cc_final: 0.4922 (mmt) REVERT: A 452 HIS cc_start: 0.7436 (OUTLIER) cc_final: 0.6934 (p90) REVERT: A 461 VAL cc_start: 0.4860 (OUTLIER) cc_final: 0.4418 (t) REVERT: A 464 MET cc_start: 0.7575 (mtt) cc_final: 0.7311 (mtp) REVERT: A 600 SER cc_start: 0.8163 (OUTLIER) cc_final: 0.7934 (p) REVERT: A 728 ASP cc_start: 0.9408 (OUTLIER) cc_final: 0.9057 (m-30) REVERT: A 736 MET cc_start: 0.8254 (mmm) cc_final: 0.7989 (mmt) REVERT: A 847 GLU cc_start: 0.8862 (pt0) cc_final: 0.8206 (pt0) REVERT: A 1065 MET cc_start: 0.7618 (tpp) cc_final: 0.6841 (tpp) REVERT: A 1335 PHE cc_start: 0.8214 (OUTLIER) cc_final: 0.7679 (p90) REVERT: A 1371 MET cc_start: 0.6735 (mtm) cc_final: 0.6242 (mtm) REVERT: A 1378 MET cc_start: 0.7817 (mtp) cc_final: 0.7609 (tpp) REVERT: A 1439 MET cc_start: 0.7130 (ttp) cc_final: 0.6781 (tmm) REVERT: B 34 GLN cc_start: 0.7149 (OUTLIER) cc_final: 0.6690 (mm-40) REVERT: B 93 ASP cc_start: 0.8437 (OUTLIER) cc_final: 0.7340 (p0) REVERT: B 106 LEU cc_start: 0.8413 (mt) cc_final: 0.8148 (mt) REVERT: B 190 MET cc_start: 0.7137 (mmm) cc_final: 0.6907 (mmm) REVERT: B 245 MET cc_start: 0.7245 (mtm) cc_final: 0.6585 (mpp) REVERT: B 278 PHE cc_start: 0.9318 (OUTLIER) cc_final: 0.9079 (m-80) REVERT: B 283 VAL cc_start: 0.5540 (OUTLIER) cc_final: 0.5327 (p) REVERT: B 482 SER cc_start: 0.9254 (m) cc_final: 0.9047 (p) REVERT: B 702 MET cc_start: 0.4888 (ttm) cc_final: 0.3504 (tpp) REVERT: B 864 LYS cc_start: 0.9320 (mmmt) cc_final: 0.9070 (mmmt) REVERT: B 964 VAL cc_start: 0.3490 (OUTLIER) cc_final: 0.3110 (p) REVERT: B 1082 MET cc_start: 0.8057 (mpp) cc_final: 0.7681 (mpp) REVERT: B 1092 TYR cc_start: 0.6933 (m-80) cc_final: 0.6466 (m-80) REVERT: B 1152 MET cc_start: 0.6753 (OUTLIER) cc_final: 0.6529 (mtt) REVERT: C 52 MET cc_start: 0.8660 (ttt) cc_final: 0.7890 (tmm) REVERT: C 190 ASP cc_start: 0.8799 (t0) cc_final: 0.8458 (m-30) REVERT: D 29 ARG cc_start: 0.4746 (mtt180) cc_final: 0.4370 (tpm170) REVERT: E 34 MET cc_start: 0.8702 (mtm) cc_final: 0.8401 (mtt) REVERT: E 92 MET cc_start: 0.8586 (tpp) cc_final: 0.8151 (tpp) REVERT: E 122 MET cc_start: 0.7352 (tmm) cc_final: 0.6988 (ppp) REVERT: G 2 PHE cc_start: 0.2274 (OUTLIER) cc_final: 0.1462 (p90) REVERT: G 18 PHE cc_start: 0.8783 (m-10) cc_final: 0.8372 (m-80) REVERT: G 22 MET cc_start: 0.4371 (tpt) cc_final: 0.3943 (mmm) REVERT: I 34 TYR cc_start: 0.7872 (t80) cc_final: 0.7265 (t80) REVERT: J 54 ASP cc_start: 0.6467 (OUTLIER) cc_final: 0.6181 (p0) REVERT: K 73 MET cc_start: 0.7942 (ttp) cc_final: 0.7520 (ttp) REVERT: K 108 GLU cc_start: 0.8883 (tp30) cc_final: 0.8311 (tt0) REVERT: L 66 MET cc_start: 0.6229 (ttp) cc_final: 0.5211 (tpt) REVERT: d 59 MET cc_start: 0.9328 (mmm) cc_final: 0.9003 (mmm) REVERT: e 120 MET cc_start: 0.7712 (mmm) cc_final: 0.7280 (mmm) REVERT: h 68 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.8476 (mm-30) outliers start: 97 outliers final: 63 residues processed: 295 average time/residue: 0.5618 time to fit residues: 285.0075 Evaluate side-chains 281 residues out of total 4149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 204 time to evaluate : 4.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 419 HIS Chi-restraints excluded: chain A residue 445 PHE Chi-restraints excluded: chain A residue 452 HIS Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 600 SER Chi-restraints excluded: chain A residue 728 ASP Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 848 ASP Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 1119 THR Chi-restraints excluded: chain A residue 1320 MET Chi-restraints excluded: chain A residue 1335 PHE Chi-restraints excluded: chain A residue 1336 VAL Chi-restraints excluded: chain A residue 1347 THR Chi-restraints excluded: chain A residue 1357 ASN Chi-restraints excluded: chain A residue 1427 VAL Chi-restraints excluded: chain A residue 1431 VAL Chi-restraints excluded: chain B residue 34 GLN Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 408 ASN Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 797 TYR Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 971 THR Chi-restraints excluded: chain B residue 1049 ASP Chi-restraints excluded: chain B residue 1090 THR Chi-restraints excluded: chain B residue 1103 ILE Chi-restraints excluded: chain B residue 1111 VAL Chi-restraints excluded: chain B residue 1152 MET Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 260 PHE Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 200 ARG Chi-restraints excluded: chain E residue 202 GLU Chi-restraints excluded: chain E residue 212 ILE Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain G residue 2 PHE Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 55 ASP Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain H residue 17 ASN Chi-restraints excluded: chain I residue 19 ASP Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 32 ILE Chi-restraints excluded: chain K residue 59 VAL Chi-restraints excluded: chain K residue 72 VAL Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 50 CYS Chi-restraints excluded: chain L residue 67 ILE Chi-restraints excluded: chain a residue 67 PHE Chi-restraints excluded: chain a residue 125 GLN Chi-restraints excluded: chain b residue 37 LEU Chi-restraints excluded: chain e residue 77 ASP Chi-restraints excluded: chain g residue 94 ASN Chi-restraints excluded: chain h residue 68 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 304 optimal weight: 8.9990 chunk 196 optimal weight: 5.9990 chunk 293 optimal weight: 5.9990 chunk 148 optimal weight: 6.9990 chunk 96 optimal weight: 30.0000 chunk 95 optimal weight: 10.0000 chunk 312 optimal weight: 5.9990 chunk 334 optimal weight: 30.0000 chunk 243 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 386 optimal weight: 20.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 364 GLN ** A 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1056 GLN ** B 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1013 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1076 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 142 ASN G 125 ASN ** c 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6539 moved from start: 0.5414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 48284 Z= 0.219 Angle : 0.590 13.624 67030 Z= 0.318 Chirality : 0.039 0.189 7540 Planarity : 0.004 0.056 7148 Dihedral : 24.425 176.159 9936 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 16.43 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.11 % Favored : 95.87 % Rotamer: Outliers : 2.22 % Allowed : 14.82 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.45 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.36 (0.12), residues: 4700 helix: 1.46 (0.12), residues: 1910 sheet: -0.43 (0.20), residues: 659 loop : -0.61 (0.14), residues: 2131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP C 170 HIS 0.010 0.001 HIS A 288 PHE 0.016 0.002 PHE C 178 TYR 0.014 0.001 TYR E 27 ARG 0.008 0.000 ARG B1183 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9400 Ramachandran restraints generated. 4700 Oldfield, 0 Emsley, 4700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9400 Ramachandran restraints generated. 4700 Oldfield, 0 Emsley, 4700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 4149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 212 time to evaluate : 4.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ARG cc_start: 0.5071 (mtm180) cc_final: 0.3585 (mmp-170) REVERT: A 74 MET cc_start: 0.8147 (mmm) cc_final: 0.7799 (mmm) REVERT: A 122 MET cc_start: 0.4045 (ttt) cc_final: 0.3798 (mtt) REVERT: A 180 MET cc_start: 0.4518 (tmm) cc_final: 0.4225 (tmm) REVERT: A 235 MET cc_start: 0.6812 (ptp) cc_final: 0.6349 (ptt) REVERT: A 282 MET cc_start: 0.8904 (mtp) cc_final: 0.8556 (mmt) REVERT: A 305 MET cc_start: 0.5701 (mtt) cc_final: 0.4971 (mmt) REVERT: A 452 HIS cc_start: 0.7484 (OUTLIER) cc_final: 0.6972 (p90) REVERT: A 461 VAL cc_start: 0.4841 (OUTLIER) cc_final: 0.4420 (t) REVERT: A 464 MET cc_start: 0.7586 (mtt) cc_final: 0.7323 (mtp) REVERT: A 728 ASP cc_start: 0.9308 (OUTLIER) cc_final: 0.9049 (m-30) REVERT: A 736 MET cc_start: 0.8249 (mmm) cc_final: 0.7964 (mmt) REVERT: A 847 GLU cc_start: 0.8874 (pt0) cc_final: 0.8291 (pt0) REVERT: A 1065 MET cc_start: 0.7623 (tpp) cc_final: 0.6819 (tpp) REVERT: A 1335 PHE cc_start: 0.8148 (OUTLIER) cc_final: 0.7617 (p90) REVERT: A 1371 MET cc_start: 0.6676 (mtm) cc_final: 0.6186 (mtm) REVERT: B 34 GLN cc_start: 0.7248 (OUTLIER) cc_final: 0.6878 (mm-40) REVERT: B 93 ASP cc_start: 0.8484 (OUTLIER) cc_final: 0.7395 (p0) REVERT: B 106 LEU cc_start: 0.8383 (mt) cc_final: 0.8145 (mt) REVERT: B 190 MET cc_start: 0.7140 (mmm) cc_final: 0.6904 (mmm) REVERT: B 245 MET cc_start: 0.7106 (mtm) cc_final: 0.6620 (mpp) REVERT: B 278 PHE cc_start: 0.9323 (OUTLIER) cc_final: 0.9049 (m-80) REVERT: B 283 VAL cc_start: 0.5179 (OUTLIER) cc_final: 0.4933 (p) REVERT: B 482 SER cc_start: 0.9244 (m) cc_final: 0.9033 (p) REVERT: B 593 MET cc_start: 0.5890 (mmp) cc_final: 0.5571 (mmp) REVERT: B 702 MET cc_start: 0.3986 (ttm) cc_final: 0.3286 (tpp) REVERT: B 730 MET cc_start: -0.0912 (ppp) cc_final: -0.1773 (ppp) REVERT: B 747 MET cc_start: 0.6980 (tmm) cc_final: 0.6745 (tmm) REVERT: B 860 MET cc_start: 0.7167 (mmp) cc_final: 0.6456 (mmp) REVERT: B 864 LYS cc_start: 0.9321 (mmmt) cc_final: 0.9034 (mmmt) REVERT: B 959 GLU cc_start: 0.8835 (OUTLIER) cc_final: 0.8582 (pm20) REVERT: B 964 VAL cc_start: 0.3658 (OUTLIER) cc_final: 0.3376 (p) REVERT: B 1082 MET cc_start: 0.8052 (mpp) cc_final: 0.7675 (mpp) REVERT: B 1092 TYR cc_start: 0.6978 (m-80) cc_final: 0.6535 (m-80) REVERT: B 1152 MET cc_start: 0.6729 (OUTLIER) cc_final: 0.6502 (mtt) REVERT: C 52 MET cc_start: 0.8671 (ttt) cc_final: 0.7890 (tmm) REVERT: C 190 ASP cc_start: 0.8807 (t0) cc_final: 0.8467 (m-30) REVERT: D 29 ARG cc_start: 0.4730 (mtt180) cc_final: 0.4388 (tpm170) REVERT: E 92 MET cc_start: 0.8552 (tpp) cc_final: 0.8076 (tpp) REVERT: E 122 MET cc_start: 0.7426 (tmm) cc_final: 0.7080 (ppp) REVERT: I 34 TYR cc_start: 0.7931 (t80) cc_final: 0.7340 (t80) REVERT: J 54 ASP cc_start: 0.6483 (OUTLIER) cc_final: 0.6160 (p0) REVERT: K 73 MET cc_start: 0.7928 (ttp) cc_final: 0.7542 (ttp) REVERT: K 108 GLU cc_start: 0.8860 (tp30) cc_final: 0.8286 (tt0) REVERT: L 66 MET cc_start: 0.5918 (ttp) cc_final: 0.5185 (tpt) REVERT: d 59 MET cc_start: 0.9347 (mmm) cc_final: 0.9024 (mmm) REVERT: e 120 MET cc_start: 0.8394 (mmm) cc_final: 0.8189 (mmm) REVERT: h 68 GLU cc_start: 0.8786 (mm-30) cc_final: 0.8485 (mm-30) outliers start: 92 outliers final: 66 residues processed: 293 average time/residue: 0.5723 time to fit residues: 287.4868 Evaluate side-chains 282 residues out of total 4149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 204 time to evaluate : 4.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 419 HIS Chi-restraints excluded: chain A residue 452 HIS Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 728 ASP Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 848 ASP Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 1028 LEU Chi-restraints excluded: chain A residue 1119 THR Chi-restraints excluded: chain A residue 1320 MET Chi-restraints excluded: chain A residue 1335 PHE Chi-restraints excluded: chain A residue 1336 VAL Chi-restraints excluded: chain A residue 1347 THR Chi-restraints excluded: chain A residue 1357 ASN Chi-restraints excluded: chain A residue 1427 VAL Chi-restraints excluded: chain A residue 1431 VAL Chi-restraints excluded: chain B residue 34 GLN Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 408 ASN Chi-restraints excluded: chain B residue 435 PHE Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 797 TYR Chi-restraints excluded: chain B residue 959 GLU Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 971 THR Chi-restraints excluded: chain B residue 978 ASP Chi-restraints excluded: chain B residue 1034 VAL Chi-restraints excluded: chain B residue 1090 THR Chi-restraints excluded: chain B residue 1103 ILE Chi-restraints excluded: chain B residue 1111 VAL Chi-restraints excluded: chain B residue 1152 MET Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 260 PHE Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 200 ARG Chi-restraints excluded: chain E residue 202 GLU Chi-restraints excluded: chain E residue 212 ILE Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 55 ASP Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain H residue 17 ASN Chi-restraints excluded: chain I residue 19 ASP Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 32 ILE Chi-restraints excluded: chain K residue 59 VAL Chi-restraints excluded: chain K residue 72 VAL Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 50 CYS Chi-restraints excluded: chain L residue 67 ILE Chi-restraints excluded: chain a residue 67 PHE Chi-restraints excluded: chain a residue 125 GLN Chi-restraints excluded: chain b residue 37 LEU Chi-restraints excluded: chain e residue 77 ASP Chi-restraints excluded: chain g residue 94 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 52.937 > 50: distance: 10 - 16: 5.562 distance: 16 - 17: 5.101 distance: 17 - 18: 6.804 distance: 17 - 20: 3.547 distance: 18 - 19: 10.816 distance: 18 - 25: 3.923 distance: 20 - 21: 7.872 distance: 21 - 22: 10.139 distance: 22 - 23: 9.693 distance: 23 - 24: 7.662 distance: 25 - 26: 9.820 distance: 26 - 27: 13.755 distance: 26 - 29: 15.009 distance: 27 - 28: 16.660 distance: 27 - 33: 16.718 distance: 28 - 48: 21.423 distance: 29 - 30: 14.820 distance: 30 - 31: 8.140 distance: 30 - 32: 19.839 distance: 33 - 34: 18.006 distance: 34 - 35: 24.921 distance: 34 - 37: 16.618 distance: 35 - 36: 49.662 distance: 35 - 41: 5.813 distance: 36 - 54: 36.340 distance: 37 - 38: 13.789 distance: 38 - 39: 13.673 distance: 38 - 40: 15.810 distance: 41 - 42: 6.514 distance: 42 - 43: 10.995 distance: 42 - 45: 35.712 distance: 43 - 44: 38.277 distance: 43 - 48: 23.561 distance: 45 - 46: 13.783 distance: 45 - 47: 21.471 distance: 48 - 49: 3.857 distance: 49 - 50: 14.347 distance: 49 - 52: 9.550 distance: 50 - 51: 11.201 distance: 50 - 54: 14.603 distance: 52 - 53: 28.832 distance: 54 - 55: 7.312 distance: 55 - 56: 17.322 distance: 55 - 58: 19.558 distance: 56 - 57: 14.210 distance: 56 - 62: 11.548 distance: 58 - 59: 8.911 distance: 59 - 60: 35.621 distance: 59 - 61: 40.590 distance: 62 - 63: 11.677 distance: 62 - 68: 14.123 distance: 63 - 64: 15.004 distance: 63 - 66: 8.178 distance: 64 - 65: 6.674 distance: 64 - 69: 12.364 distance: 65 - 82: 17.414 distance: 66 - 67: 3.898 distance: 67 - 68: 9.788 distance: 69 - 70: 9.051 distance: 70 - 71: 18.509 distance: 70 - 73: 17.400 distance: 71 - 72: 16.528 distance: 71 - 74: 24.643 distance: 74 - 75: 17.749 distance: 75 - 76: 4.632 distance: 75 - 78: 17.401 distance: 76 - 77: 13.443 distance: 76 - 82: 20.370 distance: 78 - 79: 14.331 distance: 79 - 80: 10.615 distance: 79 - 81: 4.967 distance: 82 - 83: 19.897 distance: 83 - 84: 4.565 distance: 83 - 86: 15.987 distance: 84 - 85: 16.711 distance: 84 - 94: 16.707 distance: 86 - 87: 10.751 distance: 87 - 88: 20.713 distance: 87 - 89: 11.044 distance: 88 - 90: 17.429 distance: 89 - 91: 14.702 distance: 90 - 92: 9.550 distance: 91 - 92: 25.888 distance: 92 - 93: 20.047