Starting phenix.real_space_refine on Wed Aug 27 00:42:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jh4_36253/08_2025/8jh4_36253_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jh4_36253/08_2025/8jh4_36253.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8jh4_36253/08_2025/8jh4_36253_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jh4_36253/08_2025/8jh4_36253_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jh4_36253/08_2025/8jh4_36253.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jh4_36253/08_2025/8jh4_36253.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 353 5.49 5 Mg 1 5.21 5 S 200 5.16 5 C 26872 2.51 5 N 7902 2.21 5 O 9079 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 338 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 44415 Number of models: 1 Model: "" Number of chains: 29 Chain: "A" Number of atoms: 11038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1400, 11038 Classifications: {'peptide': 1400} Link IDs: {'PCIS': 3, 'PTRANS': 64, 'TRANS': 1332} 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: 1741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1741 Classifications: {'peptide': 213} Modifications used: {'COO': 1} 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: 1325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1325 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 160} Chain: "H" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1053 Classifications: {'peptide': 133} Modifications used: {'COO': 1} 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: "N" Number of atoms: 3415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 3415 Classifications: {'DNA': 166} Link IDs: {'rna3p': 165} Chain breaks: 1 Chain: "P" Number of atoms: 215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 215 Classifications: {'RNA': 10} Modifications used: {'rna3p_pur': 5, 'rna3p_pyr': 5} Link IDs: {'rna3p': 9} Chain: "T" Number of atoms: 3631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 3631 Classifications: {'DNA': 178} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 177} Chain: "a" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 786 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "b" Number of atoms: 614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 614 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 1, 'TRANS': 75} 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: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 720 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "e" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 815 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "f" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} 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: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 703 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} 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 74.462 61.192 141.615 1.00 48.57 S ATOM 549 SG CYS A 70 77.742 60.291 142.473 1.00 37.46 S ATOM 594 SG CYS A 77 76.614 63.418 143.902 1.00 28.74 S ATOM 829 SG CYS A 107 77.127 87.874 101.981 1.00 81.51 S ATOM 851 SG CYS A 110 78.091 84.475 100.784 1.00 88.03 S ATOM 1157 SG CYS A 148 79.964 87.550 99.577 1.00107.02 S ATOM 1163 SG CYS A 168 76.314 86.987 98.413 1.00 97.61 S ATOM 19831 SG CYS B1163 86.887 63.570 129.751 1.00 26.13 S ATOM 19849 SG CYS B1166 84.855 66.761 129.177 1.00 30.15 S ATOM 19972 SG CYS B1182 83.200 63.338 129.842 1.00 42.41 S ATOM 19995 SG CYS B1185 84.894 64.179 126.502 1.00 48.09 S ATOM 20940 SG CYS C 85 85.311 70.081 209.670 1.00 95.49 S ATOM 20953 SG CYS C 87 82.698 69.461 207.633 1.00 96.30 S ATOM 20988 SG CYS C 91 82.202 70.289 210.887 1.00 89.31 S ATOM 21011 SG CYS C 94 83.834 73.259 208.891 1.00 66.65 S ATOM 29100 SG CYS I 75 76.224 164.924 156.511 1.00110.74 S ATOM 29338 SG CYS I 103 73.628 162.036 158.268 1.00100.19 S ATOM 28738 SG CYS I 29 55.556 146.835 114.879 1.00120.13 S ATOM 28763 SG CYS I 32 53.696 148.697 114.131 1.00119.31 S ATOM 29479 SG CYS J 7 84.427 104.384 201.352 1.00 20.22 S ATOM 29502 SG CYS J 10 87.204 103.603 203.877 1.00 20.22 S ATOM 29778 SG CYS J 44 87.264 106.859 201.649 1.00 20.22 S ATOM 29784 SG CYS J 45 84.978 106.201 204.703 1.00 20.22 S ATOM 30946 SG CYS L 33 45.368 87.916 188.964 1.00 71.34 S ATOM 31071 SG CYS L 50 43.084 85.113 189.306 1.00 93.28 S ATOM 31095 SG CYS L 53 41.686 88.637 188.662 1.00110.38 S Time building chain proxies: 8.35, per 1000 atoms: 0.19 Number of scatterers: 44415 At special positions: 0 Unit cell: (170.66, 181.26, 239.56, 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 200 16.00 P 353 15.00 Mg 1 11.99 O 9079 8.00 N 7902 7.00 C 26872 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.97 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 715.3 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 67 " pdb="ZN ZN A1801 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 77 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 70 " pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 148 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 107 " 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 B1182 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1166 " pdb=" ZN C 401 " 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 ZN C 401 " - pdb=" SG CYS C 87 " 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 I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 29 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 32 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 50 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 33 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 53 " Number of angles added : 27 9214 Ramachandran restraints generated. 4607 Oldfield, 0 Emsley, 4607 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8754 Finding SS restraints... Secondary structure from input PDB file: 183 helices and 58 sheets defined 44.5% alpha, 16.4% beta 149 base pairs and 261 stacking pairs defined. Time for finding SS restraints: 5.70 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: 4.123A pdb=" N LEU A 141 " --> pdb=" O ALA A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 214 removed outlier: 3.803A pdb=" N HIS A 214 " --> pdb=" O ASN A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 224 removed outlier: 3.504A pdb=" N GLY A 224 " --> pdb=" O CYS A 220 " (cutoff:3.500A) 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: 3.606A 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: 3.988A 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 475 through 480 Processing helix chain 'A' and resid 495 through 506 Processing helix chain 'A' and resid 507 through 512 removed outlier: 3.660A pdb=" N ILE A 512 " --> pdb=" O PRO A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 536 removed outlier: 3.640A pdb=" N LEU A 529 " --> pdb=" O VAL A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 554 Processing helix chain 'A' and resid 575 through 583 removed outlier: 3.797A 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: 3.591A pdb=" N PHE A 647 " --> pdb=" O CYS A 643 " (cutoff:3.500A) removed outlier: 3.698A 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: 4.120A pdb=" N THR A 832 " --> pdb=" O THR A 828 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N ALA A 833 " --> pdb=" O ALA A 829 " (cutoff:3.500A) removed outlier: 4.373A 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: 3.589A pdb=" N ILE A 914 " --> pdb=" O PRO A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 921 removed outlier: 4.063A 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: 3.969A pdb=" N ARG A1102 " --> pdb=" O LEU A1098 " (cutoff:3.500A) Processing helix chain 'A' and resid 1123 through 1129 removed outlier: 3.815A pdb=" N ASP A1129 " --> pdb=" O GLU A1125 " (cutoff:3.500A) Processing helix chain 'A' and resid 1129 through 1141 removed outlier: 3.554A 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: 3.574A pdb=" N MET A1204 " --> pdb=" O ASP A1200 " (cutoff:3.500A) Processing helix chain 'A' and resid 1210 through 1222 removed outlier: 3.584A pdb=" N VAL A1214 " --> pdb=" O THR A1210 " (cutoff:3.500A) removed outlier: 3.738A 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: 3.518A pdb=" N ALA A1321 " --> pdb=" O ALA A1317 " (cutoff:3.500A) Processing helix chain 'A' and resid 1334 through 1343 Processing helix chain 'A' and resid 1343 through 1361 Processing helix chain 'A' and resid 1367 through 1379 removed outlier: 4.067A 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: 3.910A pdb=" N ASN A1430 " --> pdb=" O GLY A1426 " (cutoff:3.500A) Processing helix chain 'A' and resid 1439 through 1443 Processing helix chain 'A' and resid 1452 through 1456 Processing helix chain 'A' and resid 1457 through 1461 removed outlier: 3.944A 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 51 removed outlier: 5.592A pdb=" N ILE B 46 " --> pdb=" O MET B 42 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N GLN B 47 " --> pdb=" O GLU B 43 " (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 282 removed outlier: 3.657A 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: 3.589A 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: 3.631A pdb=" N ALA B 322 " --> pdb=" O ASP B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 351 removed outlier: 3.764A pdb=" N GLN B 343 " --> pdb=" O GLU B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 383 removed outlier: 4.042A 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: 3.707A pdb=" N ARG B 427 " --> pdb=" O ARG B 423 " (cutoff:3.500A) removed outlier: 3.643A 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: 3.665A pdb=" N THR B 447 " --> pdb=" O SER B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 465 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 Processing helix chain 'B' and resid 558 through 562 removed outlier: 3.746A pdb=" N TYR B 562 " --> pdb=" O LEU B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 599 removed outlier: 3.871A pdb=" N LEU B 589 " --> pdb=" O ASP B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 658 removed outlier: 3.502A 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: 3.556A 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: 3.618A 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: 3.679A 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 808 through 813 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: 3.933A pdb=" N LEU B1026 " --> pdb=" O THR B1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 1051 through 1062 removed outlier: 3.529A pdb=" N VAL B1055 " --> pdb=" O THR B1051 " (cutoff:3.500A) 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 91 through 95 removed outlier: 3.535A pdb=" N SER C 95 " --> pdb=" O ASP C 92 " (cutoff:3.500A) 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: 3.836A 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 111 Processing helix chain 'D' and resid 117 through 129 removed outlier: 3.566A pdb=" N CYS D 121 " --> pdb=" O ASP D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 148 removed outlier: 3.559A pdb=" N SER D 146 " --> pdb=" O ILE D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 160 removed outlier: 3.918A pdb=" N ALA D 156 " --> pdb=" O ASP D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 167 removed outlier: 3.922A pdb=" N ALA D 164 " --> pdb=" O PRO D 161 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA D 165 " --> pdb=" O SER D 162 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LYS D 166 " --> pdb=" O LEU D 163 " (cutoff:3.500A) removed outlier: 3.775A 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 removed outlier: 3.501A pdb=" N ASP E 35 " --> pdb=" O GLN E 31 " (cutoff:3.500A) 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: 3.691A 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: 3.568A 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: 3.563A 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: 4.149A pdb=" N GLY I 63 " --> pdb=" O ASP I 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 30 through 38 Processing helix chain 'J' and resid 42 through 51 removed outlier: 3.526A pdb=" N VAL J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 60 Processing helix chain 'K' and resid 39 through 51 removed outlier: 3.718A 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 77 removed outlier: 3.607A pdb=" N ASP a 77 " --> pdb=" O GLU a 73 " (cutoff:3.500A) 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: 3.500A pdb=" N GLU b 53 " --> pdb=" O LEU b 49 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP b 68 " --> pdb=" O ASN b 64 " (cutoff:3.500A) Processing helix chain 'b' and resid 82 through 93 Processing helix chain 'c' and resid 16 through 22 Processing helix chain 'c' and resid 26 through 37 Processing helix chain 'c' and resid 45 through 73 removed outlier: 4.357A pdb=" N VAL c 49 " --> pdb=" O ALA c 45 " (cutoff:3.500A) Processing helix chain 'c' and resid 79 through 89 Processing helix chain 'c' and resid 90 through 97 Processing helix chain 'c' and resid 112 through 116 Processing helix chain 'd' and resid 37 through 49 Processing helix chain 'd' and resid 55 through 84 Processing helix chain 'd' and resid 90 through 102 Processing helix chain 'd' and resid 103 through 123 Processing helix chain 'e' and resid 44 through 57 Processing helix chain 'e' and resid 63 through 77 Processing helix chain 'e' and resid 85 through 114 Processing helix chain 'e' and resid 120 through 131 Processing helix chain 'f' and resid 24 through 29 Processing helix chain 'f' and resid 30 through 41 Processing helix chain 'f' and resid 49 through 76 removed outlier: 3.501A pdb=" N ASP f 68 " --> pdb=" O ASN f 64 " (cutoff:3.500A) Processing helix chain 'f' and resid 82 through 93 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: 4.373A pdb=" N VAL g 49 " --> pdb=" O ALA g 45 " (cutoff:3.500A) Processing helix chain 'g' and resid 79 through 89 Processing helix chain 'g' and resid 90 through 97 Processing helix chain 'g' and resid 112 through 116 Processing helix chain 'h' and resid 37 through 49 Processing helix chain 'h' and resid 55 through 84 Processing helix chain 'h' and resid 90 through 102 Processing helix chain 'h' and resid 103 through 123 removed outlier: 3.503A pdb=" N ALA h 107 " --> pdb=" O PRO h 103 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1421 through 1422 removed outlier: 3.623A pdb=" N ARG B1215 " --> pdb=" O GLN A 18 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 82 through 91 removed outlier: 10.167A pdb=" N LEU A 86 " --> pdb=" O PRO A 241 " (cutoff:3.500A) removed outlier: 10.649A pdb=" N LYS A 88 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 7.037A 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: 4.434A pdb=" N LEU A 182 " --> pdb=" O LEU A 203 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS A 201 " --> pdb=" O GLY A 184 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 251 through 252 removed outlier: 3.884A pdb=" N ILE A 251 " --> pdb=" O GLY A 259 " (cutoff:3.500A) removed outlier: 3.838A 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: 4.042A 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: 3.647A pdb=" N THR A 352 " --> pdb=" O MET A 488 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N PHE A 469 " --> pdb=" O ARG A 351 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N VAL A 353 " --> pdb=" O PHE A 469 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N LEU A 471 " --> pdb=" O VAL A 353 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N SER A 355 " --> pdb=" O LEU A 471 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 376 through 380 removed outlier: 3.884A pdb=" N TYR A 405 " --> pdb=" O GLU A 434 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N HIS A 436 " --> pdb=" O ALA A 403 " (cutoff:3.500A) removed outlier: 7.279A 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: 6.048A pdb=" N VAL H 95 " --> pdb=" O LEU A 567 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR H 56 " --> pdb=" O ARG H 144 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE H 29 " --> pdb=" O THR H 11 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE H 27 " --> pdb=" O GLN H 13 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N LEU H 121 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS H 102 " --> pdb=" O TYR H 114 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N SER H 116 " --> pdb=" O VAL H 100 " (cutoff:3.500A) removed outlier: 5.791A 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: 6.916A 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: 6.784A pdb=" N THR A 857 " --> pdb=" O ILE A 865 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 879 through 883 Processing sheet with id=AB5, first strand: chain 'A' and resid 1284 through 1295 removed outlier: 3.953A pdb=" N LYS A1284 " --> pdb=" O ASP A1312 " (cutoff:3.500A) removed outlier: 4.042A 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: 6.895A pdb=" N THR A1143 " --> pdb=" O LEU A1276 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1227 through 1230 removed outlier: 3.503A pdb=" N LEU A1195 " --> pdb=" O CYS A1242 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA A1151 " --> pdb=" O GLU A1198 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ILE A1154 " --> pdb=" O VAL I 43 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 143 through 147 removed outlier: 5.298A pdb=" N VAL A1446 " --> pdb=" O ILE G 61 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLY G 59 " --> pdb=" O ILE A1448 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 55 through 60 removed outlier: 3.574A pdb=" N LEU B 56 " --> pdb=" O ILE B 77 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE B 77 " --> pdb=" O LEU B 56 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N ASP B 118 " --> pdb=" O GLY B 80 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ILE B 82 " --> pdb=" O TYR B 116 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N TYR B 116 " --> pdb=" O ILE B 82 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N LEU B 84 " --> pdb=" O PRO B 114 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N SER B 113 " --> pdb=" O LYS B 160 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LYS B 160 " --> pdb=" O SER B 113 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL B 115 " --> pdb=" O ILE B 158 " (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: 3.519A 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: 6.661A pdb=" N LEU B 249 " --> pdb=" O SER B 226 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N VAL B 228 " --> pdb=" O ILE B 247 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ILE B 247 " --> pdb=" O VAL B 228 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N GLU B 230 " --> pdb=" O MET B 245 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N MET B 245 " --> pdb=" O GLU B 230 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N ARG B 232 " --> pdb=" O SER B 243 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N SER B 243 " --> pdb=" O ARG B 232 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ALA B 234 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N LEU B 241 " --> pdb=" O ALA B 234 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 537 through 540 removed outlier: 4.797A pdb=" N ARG B 625 " --> pdb=" O SER B 539 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 537 through 540 removed outlier: 4.797A pdb=" N ARG B 625 " --> pdb=" O SER B 539 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 578 through 583 removed outlier: 5.526A pdb=" N TRP B 579 " --> pdb=" O VAL B 575 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL B 575 " --> pdb=" O TRP B 579 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY B 581 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ARG B 572 " --> pdb=" O PHE B 617 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N ILE B 619 " --> pdb=" O ARG B 572 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N PHE B 574 " --> pdb=" O ILE B 619 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 792 through 796 removed outlier: 5.821A pdb=" N ARG B 969 " --> pdb=" O VAL B 949 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N VAL B 949 " --> pdb=" O ARG B 969 " (cutoff:3.500A) removed outlier: 8.434A pdb=" N THR B 971 " --> pdb=" O GLY B 947 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N GLY B 947 " --> pdb=" O THR B 971 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 792 through 796 removed outlier: 5.821A pdb=" N ARG B 969 " --> pdb=" O VAL B 949 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N VAL B 949 " --> pdb=" O ARG B 969 " (cutoff:3.500A) removed outlier: 8.434A pdb=" N THR B 971 " --> pdb=" O GLY B 947 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N GLY B 947 " --> pdb=" O THR B 971 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N VAL B 952 " --> pdb=" O LYS L 60 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS L 60 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU B 954 " --> pdb=" O ILE L 58 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE L 58 " --> pdb=" O LEU B 954 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N VAL L 29 " --> pdb=" O LEU L 42 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU L 42 " --> pdb=" O VAL L 29 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE L 40 " --> pdb=" O TYR L 31 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 804 through 805 Processing sheet with id=AD2, first strand: chain 'B' and resid 1069 through 1070 removed outlier: 7.049A pdb=" N MET B 839 " --> pdb=" O GLY B 991 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N THR B 993 " --> pdb=" O MET B 839 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N MET B 841 " --> pdb=" O THR B 993 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N PHE B1086 " --> pdb=" O ILE B 827 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 873 through 874 removed outlier: 3.866A pdb=" N ASP B 936 " --> pdb=" O LEU B 883 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 910 through 912 Processing sheet with id=AD5, first strand: chain 'B' and resid 1001 through 1002 Processing sheet with id=AD6, first strand: chain 'B' and resid 1157 through 1163 Processing sheet with id=AD7, first strand: chain 'B' and resid 1171 through 1174 Processing sheet with id=AD8, first strand: chain 'C' and resid 6 through 12 removed outlier: 6.538A pdb=" N GLU C 18 " --> pdb=" O ILE C 10 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ALA C 12 " --> pdb=" O GLU C 16 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N GLU C 16 " --> pdb=" O ALA C 12 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 119 through 122 removed outlier: 6.902A pdb=" N VAL C 97 " --> pdb=" O VAL C 121 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N GLU C 152 " --> pdb=" O ASN C 53 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ASN C 53 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ASN C 154 " --> pdb=" O LYS C 51 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N LYS C 160 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ILE C 45 " --> pdb=" O LYS C 160 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N GLY C 162 " --> pdb=" O LEU C 43 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N LEU C 43 " --> pdb=" O GLY C 162 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE C 50 " --> pdb=" O ILE L 67 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N ILE L 67 " --> pdb=" O ILE C 50 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 71 through 73 removed outlier: 4.630A pdb=" N GLU C 131 " --> pdb=" O VAL C 72 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 111 through 114 removed outlier: 6.425A pdb=" N THR C 111 " --> pdb=" O LYS C 146 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N LYS C 146 " --> pdb=" O THR C 111 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL C 113 " --> pdb=" O LEU C 144 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 37 through 39 Processing sheet with id=AE4, first strand: chain 'E' and resid 27 through 28 removed outlier: 4.356A pdb=" N ASN E 62 " --> pdb=" O PHE E 28 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N TRP E 78 " --> pdb=" O ILE E 108 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N ILE E 110 " --> pdb=" O TRP E 78 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N GLU E 80 " --> pdb=" O ILE E 110 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 86 through 87 Processing sheet with id=AE6, first strand: chain 'E' and resid 151 through 154 removed outlier: 4.217A pdb=" N LYS E 151 " --> pdb=" O ILE E 198 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILE E 198 " --> pdb=" O LYS E 151 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 2 through 7 Processing sheet with id=AE8, first strand: chain 'G' and resid 169 through 170 removed outlier: 5.736A pdb=" N VAL G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N SER G 162 " --> pdb=" O VAL G 147 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY G 149 " --> pdb=" O ILE G 160 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TYR G 158 " --> pdb=" O ARG G 151 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ALA G 159 " --> pdb=" O ASN G 107 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE G 109 " --> pdb=" O ALA G 159 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N SER G 111 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE G 99 " --> pdb=" O VAL G 110 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N GLY G 98 " --> pdb=" O VAL G 94 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N VAL G 94 " --> pdb=" O GLY G 98 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N PHE G 100 " --> pdb=" O SER G 92 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE G 90 " --> pdb=" O ASP G 102 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 130 through 132 removed outlier: 3.956A pdb=" N TYR G 130 " --> pdb=" O ILE G 137 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 15 through 18 Processing sheet with id=AF2, first strand: chain 'I' and resid 70 through 71 Processing sheet with id=AF3, first strand: chain 'K' and resid 19 through 23 Processing sheet with id=AF4, first strand: chain 'a' and resid 83 through 84 removed outlier: 6.831A pdb=" N ARG a 83 " --> pdb=" O VAL b 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'a' and resid 118 through 119 Processing sheet with id=AF6, first strand: chain 'b' and resid 96 through 98 Processing sheet with id=AF7, first strand: chain 'c' and resid 42 through 43 removed outlier: 6.989A pdb=" N ARG c 42 " --> pdb=" O ILE d 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'c' and resid 77 through 78 Processing sheet with id=AF9, first strand: chain 'c' and resid 100 through 102 Processing sheet with id=AG1, first strand: chain 'e' and resid 83 through 84 removed outlier: 6.771A pdb=" N ARG e 83 " --> pdb=" O VAL f 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG1 Processing sheet with id=AG2, first strand: chain 'e' and resid 118 through 119 Processing sheet with id=AG3, first strand: chain 'g' and resid 42 through 43 removed outlier: 7.013A pdb=" N ARG g 42 " --> pdb=" O ILE h 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG3 Processing sheet with id=AG4, first strand: chain 'g' and resid 77 through 78 1741 hydrogen bonds defined for protein. 4863 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 380 hydrogen bonds 760 hydrogen bond angles 0 basepair planarities 149 basepair parallelities 261 stacking parallelities Total time for adding SS restraints: 12.66 Time building geometry restraints manager: 3.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 7160 1.32 - 1.45: 13287 1.45 - 1.57: 24471 1.57 - 1.70: 703 1.70 - 1.82: 326 Bond restraints: 45947 Sorted by residual: bond pdb=" CA GLY g 28 " pdb=" C GLY g 28 " ideal model delta sigma weight residual 1.516 1.468 0.048 1.12e-02 7.97e+03 1.87e+01 bond pdb=" CA MET B1210 " pdb=" C MET B1210 " ideal model delta sigma weight residual 1.526 1.480 0.046 1.23e-02 6.61e+03 1.39e+01 bond pdb=" C GLY G 104 " pdb=" N PRO G 105 " ideal model delta sigma weight residual 1.333 1.360 -0.027 7.80e-03 1.64e+04 1.22e+01 bond pdb=" N MET B1210 " pdb=" CA MET B1210 " ideal model delta sigma weight residual 1.459 1.419 0.040 1.19e-02 7.06e+03 1.11e+01 bond pdb=" CG MET B1210 " pdb=" SD MET B1210 " ideal model delta sigma weight residual 1.803 1.721 0.082 2.50e-02 1.60e+03 1.07e+01 ... (remaining 45942 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 61674 2.04 - 4.08: 1695 4.08 - 6.12: 175 6.12 - 8.17: 23 8.17 - 10.21: 2 Bond angle restraints: 63569 Sorted by residual: angle pdb=" N VAL a 117 " pdb=" CA VAL a 117 " pdb=" C VAL a 117 " ideal model delta sigma weight residual 113.47 106.29 7.18 1.01e+00 9.80e-01 5.06e+01 angle pdb=" N THR A1311 " pdb=" CA THR A1311 " pdb=" C THR A1311 " ideal model delta sigma weight residual 109.24 119.45 -10.21 1.51e+00 4.39e-01 4.57e+01 angle pdb=" N VAL e 117 " pdb=" CA VAL e 117 " pdb=" C VAL e 117 " ideal model delta sigma weight residual 113.47 107.58 5.89 1.01e+00 9.80e-01 3.40e+01 angle pdb=" N THR g 16 " pdb=" CA THR g 16 " pdb=" C THR g 16 " ideal model delta sigma weight residual 110.48 118.16 -7.68 1.48e+00 4.57e-01 2.70e+01 angle pdb=" C HIS h 49 " pdb=" N PRO h 50 " pdb=" CA PRO h 50 " ideal model delta sigma weight residual 119.47 125.31 -5.84 1.16e+00 7.43e-01 2.53e+01 ... (remaining 63564 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.57: 24617 28.57 - 57.13: 2258 57.13 - 85.70: 250 85.70 - 114.26: 12 114.26 - 142.83: 2 Dihedral angle restraints: 27139 sinusoidal: 13591 harmonic: 13548 Sorted by residual: dihedral pdb=" C CYS I 75 " pdb=" N CYS I 75 " pdb=" CA CYS I 75 " pdb=" CB CYS I 75 " ideal model delta harmonic sigma weight residual -122.60 -110.09 -12.51 0 2.50e+00 1.60e-01 2.50e+01 dihedral pdb=" C THR g 16 " pdb=" N THR g 16 " pdb=" CA THR g 16 " pdb=" CB THR g 16 " ideal model delta harmonic sigma weight residual -122.00 -132.01 10.01 0 2.50e+00 1.60e-01 1.60e+01 dihedral pdb=" N CYS I 75 " pdb=" C CYS I 75 " pdb=" CA CYS I 75 " pdb=" CB CYS I 75 " ideal model delta harmonic sigma weight residual 122.80 112.83 9.97 0 2.50e+00 1.60e-01 1.59e+01 ... (remaining 27136 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 6710 0.092 - 0.183: 404 0.183 - 0.275: 18 0.275 - 0.367: 6 0.367 - 0.458: 1 Chirality restraints: 7139 Sorted by residual: chirality pdb=" CA THR g 16 " pdb=" N THR g 16 " pdb=" C THR g 16 " pdb=" CB THR g 16 " both_signs ideal model delta sigma weight residual False 2.53 2.07 0.46 2.00e-01 2.50e+01 5.26e+00 chirality pdb=" CA CYS I 75 " pdb=" N CYS I 75 " pdb=" C CYS I 75 " pdb=" CB CYS I 75 " both_signs ideal model delta sigma weight residual False 2.51 2.87 -0.36 2.00e-01 2.50e+01 3.32e+00 chirality pdb=" C3' DG T 27 " pdb=" C4' DG T 27 " pdb=" O3' DG T 27 " pdb=" C2' DG T 27 " both_signs ideal model delta sigma weight residual False -2.66 -2.30 -0.36 2.00e-01 2.50e+01 3.22e+00 ... (remaining 7136 not shown) Planarity restraints: 6963 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS A 80 " 0.072 2.00e-02 2.50e+03 5.36e-02 4.31e+01 pdb=" CG HIS A 80 " -0.085 2.00e-02 2.50e+03 pdb=" ND1 HIS A 80 " -0.036 2.00e-02 2.50e+03 pdb=" CD2 HIS A 80 " -0.027 2.00e-02 2.50e+03 pdb=" CE1 HIS A 80 " 0.037 2.00e-02 2.50e+03 pdb=" NE2 HIS A 80 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 130 " -0.034 2.00e-02 2.50e+03 4.49e-02 4.04e+01 pdb=" CG TYR G 130 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 TYR G 130 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR G 130 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR G 130 " 0.036 2.00e-02 2.50e+03 pdb=" CE2 TYR G 130 " 0.050 2.00e-02 2.50e+03 pdb=" CZ TYR G 130 " 0.044 2.00e-02 2.50e+03 pdb=" OH TYR G 130 " -0.090 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 20 " 0.075 2.00e-02 2.50e+03 4.21e-02 3.55e+01 pdb=" CG TYR H 20 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR H 20 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 TYR H 20 " -0.041 2.00e-02 2.50e+03 pdb=" CE1 TYR H 20 " -0.031 2.00e-02 2.50e+03 pdb=" CE2 TYR H 20 " -0.018 2.00e-02 2.50e+03 pdb=" CZ TYR H 20 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR H 20 " 0.067 2.00e-02 2.50e+03 ... (remaining 6960 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 226 2.56 - 3.15: 34073 3.15 - 3.73: 71981 3.73 - 4.32: 102099 4.32 - 4.90: 159854 Nonbonded interactions: 368233 Sorted by model distance: nonbonded pdb=" O PRO A 5 " pdb=" NH1 ARG B1159 " model vdw 1.977 3.120 nonbonded pdb=" O3' G P 10 " pdb="MG MG A1803 " model vdw 2.022 2.170 nonbonded pdb=" OD1 ASP A 486 " pdb="MG MG A1803 " model vdw 2.039 2.170 nonbonded pdb=" NH2 ARG D 67 " pdb=" OE2 GLU G 35 " model vdw 2.086 3.120 nonbonded pdb=" O VAL A 830 " pdb=" NZ LYS B 500 " model vdw 2.097 3.120 ... (remaining 368228 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'a' selection = (chain 'e' and resid 38 through 133) } ncs_group { reference = chain 'b' selection = (chain 'f' and resid 25 through 101) } ncs_group { reference = chain 'c' selection = chain 'g' } ncs_group { reference = (chain 'd' and resid 34 through 123) 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 46.980 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.110 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:0.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6429 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.540 45974 Z= 0.319 Angle : 0.805 26.368 63596 Z= 0.494 Chirality : 0.046 0.458 7139 Planarity : 0.005 0.132 6963 Dihedral : 19.426 142.828 18385 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.02 % Favored : 96.87 % Rotamer: Outliers : 0.17 % Allowed : 1.03 % Favored : 98.80 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 2.46 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.84 (0.12), residues: 4607 helix: 0.12 (0.11), residues: 1838 sheet: -1.15 (0.20), residues: 636 loop : -0.86 (0.13), residues: 2133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG a 63 TYR 0.090 0.002 TYR G 130 PHE 0.034 0.002 PHE B 217 TRP 0.045 0.003 TRP A 234 HIS 0.016 0.001 HIS C 104 Details of bonding type rmsd covalent geometry : bond 0.00459 (45947) covalent geometry : angle 0.76295 (63569) hydrogen bonds : bond 0.16754 ( 2098) hydrogen bonds : angle 6.63544 ( 5623) metal coordination : bond 0.22406 ( 27) metal coordination : angle 12.46230 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9214 Ramachandran restraints generated. 4607 Oldfield, 0 Emsley, 4607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9214 Ramachandran restraints generated. 4607 Oldfield, 0 Emsley, 4607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 538 time to evaluate : 1.512 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 253 MET cc_start: 0.5348 (mpt) cc_final: 0.5115 (mtt) REVERT: B 349 LEU cc_start: 0.7853 (mm) cc_final: 0.7561 (tt) REVERT: B 730 MET cc_start: -0.0849 (ttp) cc_final: -0.1925 (ptm) REVERT: F 119 GLN cc_start: 0.6914 (mt0) cc_final: 0.6622 (mt0) outliers start: 7 outliers final: 0 residues processed: 544 average time/residue: 0.2889 time to fit residues: 241.6747 Evaluate side-chains 237 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 432 optimal weight: 20.0000 chunk 197 optimal weight: 8.9990 chunk 388 optimal weight: 1.9990 chunk 455 optimal weight: 5.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 0.4980 chunk 207 optimal weight: 6.9990 chunk 470 optimal weight: 20.0000 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 GLN A 446 ASN A 511 GLN A 974 HIS ** A1393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 376 ASN ** B 932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 264 ASN D 46 HIS D 170 ASN G 21 GLN G 118 ASN L 43 ASN c 104 GLN c 110 ASN d 84 ASN e 108 ASN ** h 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.093759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.066414 restraints weight = 203796.736| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 3.22 r_work: 0.3321 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 45974 Z= 0.219 Angle : 0.663 13.220 63596 Z= 0.355 Chirality : 0.043 0.233 7139 Planarity : 0.005 0.064 6963 Dihedral : 21.881 140.019 9051 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.23 % Favored : 96.72 % Rotamer: Outliers : 0.96 % Allowed : 7.58 % Favored : 91.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.46 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.12), residues: 4607 helix: 0.99 (0.12), residues: 1853 sheet: -0.66 (0.20), residues: 634 loop : -0.53 (0.13), residues: 2120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A1201 TYR 0.034 0.002 TYR b 51 PHE 0.021 0.002 PHE G 100 TRP 0.018 0.002 TRP C 201 HIS 0.008 0.001 HIS g 82 Details of bonding type rmsd covalent geometry : bond 0.00499 (45947) covalent geometry : angle 0.65818 (63569) hydrogen bonds : bond 0.04774 ( 2098) hydrogen bonds : angle 4.77733 ( 5623) metal coordination : bond 0.01119 ( 27) metal coordination : angle 3.79721 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9214 Ramachandran restraints generated. 4607 Oldfield, 0 Emsley, 4607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9214 Ramachandran restraints generated. 4607 Oldfield, 0 Emsley, 4607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 263 time to evaluate : 1.502 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: A 41 MET cc_start: 0.5216 (mmt) cc_final: 0.4824 (ptm) REVERT: A 253 MET cc_start: 0.5362 (mpt) cc_final: 0.4960 (mtt) REVERT: A 770 MET cc_start: 0.8799 (mmm) cc_final: 0.8554 (mmm) REVERT: B 374 MET cc_start: 0.8640 (ttm) cc_final: 0.8136 (mtp) REVERT: B 588 MET cc_start: 0.8577 (ttp) cc_final: 0.8307 (tmm) REVERT: B 730 MET cc_start: -0.1993 (ttp) cc_final: -0.2250 (tpt) REVERT: G 1 MET cc_start: 0.4012 (tmm) cc_final: 0.3506 (ptm) REVERT: G 33 ASP cc_start: 0.8090 (t0) cc_final: 0.7674 (m-30) REVERT: I 24 ARG cc_start: 0.7049 (ptt180) cc_final: 0.6770 (tmt-80) REVERT: I 92 ARG cc_start: 0.6857 (mmt90) cc_final: 0.6511 (mtt-85) REVERT: J 27 GLU cc_start: 0.8196 (pt0) cc_final: 0.7971 (pt0) REVERT: a 120 MET cc_start: 0.2789 (mmt) cc_final: 0.1788 (tpt) REVERT: b 58 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8379 (pp) REVERT: c 73 ASN cc_start: 0.7431 (t0) cc_final: 0.7087 (t0) REVERT: e 99 TYR cc_start: 0.7600 (t80) cc_final: 0.7168 (t80) REVERT: e 107 THR cc_start: 0.9136 (m) cc_final: 0.8769 (p) REVERT: h 65 PHE cc_start: 0.8291 (t80) cc_final: 0.8053 (t80) outliers start: 39 outliers final: 20 residues processed: 287 average time/residue: 0.2640 time to fit residues: 125.0131 Evaluate side-chains 228 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 207 time to evaluate : 1.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLN Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 1439 MET Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 736 HIS Chi-restraints excluded: chain B residue 1090 THR Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain E residue 48 SER Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain b residue 58 LEU Chi-restraints excluded: chain f residue 26 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 388 optimal weight: 2.9990 chunk 175 optimal weight: 20.0000 chunk 364 optimal weight: 10.0000 chunk 194 optimal weight: 4.9990 chunk 111 optimal weight: 20.0000 chunk 132 optimal weight: 6.9990 chunk 315 optimal weight: 3.9990 chunk 439 optimal weight: 30.0000 chunk 112 optimal weight: 0.7980 chunk 6 optimal weight: 0.0470 chunk 7 optimal weight: 7.9990 overall best weight: 2.5684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN ** A 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 974 HIS A1393 ASN B 376 ASN ** B 932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 996 HIS D 24 ASN E 112 GLN K 85 GLN L 43 ASN b 25 ASN ** h 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.092913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.065263 restraints weight = 202001.381| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 3.10 r_work: 0.3309 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 45974 Z= 0.177 Angle : 0.561 8.610 63596 Z= 0.306 Chirality : 0.041 0.221 7139 Planarity : 0.004 0.044 6963 Dihedral : 21.923 140.017 9051 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.84 % Favored : 97.13 % Rotamer: Outliers : 1.06 % Allowed : 8.91 % Favored : 90.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.46 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (0.12), residues: 4607 helix: 1.35 (0.12), residues: 1858 sheet: -0.46 (0.20), residues: 637 loop : -0.31 (0.13), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG A 127 TYR 0.020 0.001 TYR D 108 PHE 0.023 0.002 PHE B 38 TRP 0.013 0.001 TRP F 146 HIS 0.009 0.001 HIS A 452 Details of bonding type rmsd covalent geometry : bond 0.00404 (45947) covalent geometry : angle 0.55924 (63569) hydrogen bonds : bond 0.04218 ( 2098) hydrogen bonds : angle 4.44738 ( 5623) metal coordination : bond 0.00713 ( 27) metal coordination : angle 2.44700 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9214 Ramachandran restraints generated. 4607 Oldfield, 0 Emsley, 4607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9214 Ramachandran restraints generated. 4607 Oldfield, 0 Emsley, 4607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 229 time to evaluate : 1.239 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 41 MET cc_start: 0.5252 (mmt) cc_final: 0.4914 (ptm) REVERT: A 305 MET cc_start: 0.8915 (mtm) cc_final: 0.8564 (mtp) REVERT: A 770 MET cc_start: 0.8943 (mmm) cc_final: 0.8552 (mmm) REVERT: A 903 MET cc_start: 0.7940 (mpp) cc_final: 0.6948 (ppp) REVERT: A 1164 VAL cc_start: 0.4508 (OUTLIER) cc_final: 0.4235 (p) REVERT: A 1204 MET cc_start: 0.6800 (mtm) cc_final: 0.6579 (ppp) REVERT: B 374 MET cc_start: 0.8677 (ttm) cc_final: 0.8177 (mtp) REVERT: B 588 MET cc_start: 0.8653 (ttp) cc_final: 0.8369 (tmm) REVERT: B 860 MET cc_start: 0.8892 (tmm) cc_final: 0.8617 (tmm) REVERT: B 1217 TYR cc_start: 0.8715 (m-80) cc_final: 0.8416 (m-80) REVERT: C 20 MET cc_start: 0.7904 (tmm) cc_final: 0.7407 (ttp) REVERT: D 34 PHE cc_start: 0.2098 (m-80) cc_final: 0.1058 (m-10) REVERT: G 33 ASP cc_start: 0.7973 (t0) cc_final: 0.7621 (m-30) REVERT: I 24 ARG cc_start: 0.6778 (ptt180) cc_final: 0.6507 (tmt-80) REVERT: I 92 ARG cc_start: 0.6863 (mmt90) cc_final: 0.6449 (mtt-85) REVERT: I 113 GLU cc_start: 0.6163 (mt-10) cc_final: 0.5586 (mm-30) REVERT: a 106 ASP cc_start: 0.8227 (m-30) cc_final: 0.7756 (t0) REVERT: c 73 ASN cc_start: 0.7317 (t0) cc_final: 0.6996 (t0) REVERT: d 59 MET cc_start: 0.7353 (mtm) cc_final: 0.7147 (tmm) REVERT: e 99 TYR cc_start: 0.7916 (t80) cc_final: 0.7412 (t80) REVERT: e 107 THR cc_start: 0.9144 (m) cc_final: 0.8706 (p) REVERT: e 110 CYS cc_start: 0.7829 (m) cc_final: 0.7437 (t) REVERT: g 93 LEU cc_start: 0.7878 (mt) cc_final: 0.7437 (mt) REVERT: h 59 MET cc_start: 0.6751 (tmm) cc_final: 0.6275 (ptm) outliers start: 43 outliers final: 19 residues processed: 260 average time/residue: 0.2051 time to fit residues: 90.5221 Evaluate side-chains 227 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 207 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1439 MET Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 736 HIS Chi-restraints excluded: chain B residue 1090 THR Chi-restraints excluded: chain B residue 1094 ARG Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 24 ASN Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain E residue 48 SER Chi-restraints excluded: chain G residue 28 GLU Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain a residue 115 LYS Chi-restraints excluded: chain c residue 102 ILE Chi-restraints excluded: chain f residue 26 ILE Chi-restraints excluded: chain f residue 29 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 393 optimal weight: 20.0000 chunk 240 optimal weight: 5.9990 chunk 197 optimal weight: 9.9990 chunk 334 optimal weight: 20.0000 chunk 28 optimal weight: 1.9990 chunk 222 optimal weight: 20.0000 chunk 97 optimal weight: 1.9990 chunk 321 optimal weight: 7.9990 chunk 277 optimal weight: 0.0770 chunk 68 optimal weight: 10.0000 chunk 108 optimal weight: 2.9990 overall best weight: 2.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 974 HIS B 376 ASN B 932 HIS ** E 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 43 ASN L 55 HIS ** h 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.092079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.064657 restraints weight = 202057.422| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 3.09 r_work: 0.3291 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.3731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 45974 Z= 0.178 Angle : 0.552 10.361 63596 Z= 0.299 Chirality : 0.040 0.164 7139 Planarity : 0.004 0.049 6963 Dihedral : 21.949 140.963 9051 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.87 % Favored : 97.11 % Rotamer: Outliers : 1.15 % Allowed : 10.18 % Favored : 88.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.46 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.61 (0.12), residues: 4607 helix: 1.54 (0.12), residues: 1861 sheet: -0.47 (0.20), residues: 643 loop : -0.26 (0.13), residues: 2103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG b 55 TYR 0.029 0.002 TYR h 83 PHE 0.017 0.002 PHE b 61 TRP 0.012 0.001 TRP F 146 HIS 0.010 0.001 HIS A 452 Details of bonding type rmsd covalent geometry : bond 0.00409 (45947) covalent geometry : angle 0.54965 (63569) hydrogen bonds : bond 0.04000 ( 2098) hydrogen bonds : angle 4.27308 ( 5623) metal coordination : bond 0.00780 ( 27) metal coordination : angle 2.48024 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9214 Ramachandran restraints generated. 4607 Oldfield, 0 Emsley, 4607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9214 Ramachandran restraints generated. 4607 Oldfield, 0 Emsley, 4607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 223 time to evaluate : 1.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.5254 (mmt) cc_final: 0.5020 (ptm) REVERT: A 305 MET cc_start: 0.8947 (mtm) cc_final: 0.8707 (mtp) REVERT: A 770 MET cc_start: 0.8878 (mmm) cc_final: 0.8538 (mmm) REVERT: A 903 MET cc_start: 0.7777 (mpp) cc_final: 0.6828 (ppp) REVERT: A 1164 VAL cc_start: 0.4824 (OUTLIER) cc_final: 0.4566 (p) REVERT: B 374 MET cc_start: 0.8700 (ttm) cc_final: 0.8193 (mtp) REVERT: B 588 MET cc_start: 0.8772 (ttp) cc_final: 0.8470 (tmm) REVERT: B 860 MET cc_start: 0.8967 (tmm) cc_final: 0.8644 (tmm) REVERT: B 1094 ARG cc_start: 0.9236 (OUTLIER) cc_final: 0.7496 (tpt90) REVERT: C 20 MET cc_start: 0.7916 (tmm) cc_final: 0.7372 (ttm) REVERT: E 34 MET cc_start: 0.8839 (mmt) cc_final: 0.8626 (mmt) REVERT: G 22 MET cc_start: 0.8385 (mmm) cc_final: 0.8047 (mmm) REVERT: G 33 ASP cc_start: 0.7925 (t0) cc_final: 0.7592 (m-30) REVERT: G 71 GLU cc_start: 0.7329 (mt-10) cc_final: 0.6954 (mt-10) REVERT: a 106 ASP cc_start: 0.8168 (m-30) cc_final: 0.7713 (t0) REVERT: c 73 ASN cc_start: 0.7149 (t0) cc_final: 0.6827 (t0) REVERT: e 99 TYR cc_start: 0.7854 (t80) cc_final: 0.7439 (t80) REVERT: e 107 THR cc_start: 0.9096 (m) cc_final: 0.8686 (p) REVERT: e 110 CYS cc_start: 0.7947 (m) cc_final: 0.7532 (t) outliers start: 47 outliers final: 28 residues processed: 262 average time/residue: 0.2124 time to fit residues: 95.3606 Evaluate side-chains 234 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 204 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1119 THR Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1439 MET Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 366 ARG Chi-restraints excluded: chain B residue 736 HIS Chi-restraints excluded: chain B residue 1090 THR Chi-restraints excluded: chain B residue 1094 ARG Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain E residue 48 SER Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 122 MET Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain K residue 32 ILE Chi-restraints excluded: chain K residue 59 VAL Chi-restraints excluded: chain a residue 115 LYS Chi-restraints excluded: chain c residue 102 ILE Chi-restraints excluded: chain d residue 70 PHE Chi-restraints excluded: chain f residue 26 ILE Chi-restraints excluded: chain f residue 29 ILE Chi-restraints excluded: chain h residue 54 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 285 optimal weight: 0.7980 chunk 379 optimal weight: 10.0000 chunk 418 optimal weight: 20.0000 chunk 335 optimal weight: 30.0000 chunk 213 optimal weight: 0.6980 chunk 12 optimal weight: 10.0000 chunk 404 optimal weight: 10.0000 chunk 318 optimal weight: 4.9990 chunk 171 optimal weight: 8.9990 chunk 445 optimal weight: 0.5980 chunk 238 optimal weight: 0.9980 overall best weight: 1.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 511 GLN A 518 ASN A 974 HIS ** E 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 107 ASN L 43 ASN ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.092436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.064276 restraints weight = 201112.808| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.94 r_work: 0.3318 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.3955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 45974 Z= 0.132 Angle : 0.512 9.785 63596 Z= 0.279 Chirality : 0.039 0.155 7139 Planarity : 0.004 0.048 6963 Dihedral : 21.928 142.189 9051 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.76 % Favored : 97.22 % Rotamer: Outliers : 1.06 % Allowed : 11.09 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.46 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.83 (0.13), residues: 4607 helix: 1.75 (0.12), residues: 1859 sheet: -0.42 (0.20), residues: 651 loop : -0.14 (0.14), residues: 2097 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 6 TYR 0.014 0.001 TYR h 83 PHE 0.031 0.001 PHE b 61 TRP 0.008 0.001 TRP A 183 HIS 0.010 0.001 HIS g 82 Details of bonding type rmsd covalent geometry : bond 0.00299 (45947) covalent geometry : angle 0.50888 (63569) hydrogen bonds : bond 0.03560 ( 2098) hydrogen bonds : angle 4.09113 ( 5623) metal coordination : bond 0.00597 ( 27) metal coordination : angle 2.64287 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9214 Ramachandran restraints generated. 4607 Oldfield, 0 Emsley, 4607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9214 Ramachandran restraints generated. 4607 Oldfield, 0 Emsley, 4607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 212 time to evaluate : 1.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.5405 (mmt) cc_final: 0.5027 (ptp) REVERT: A 770 MET cc_start: 0.8860 (mmm) cc_final: 0.8544 (mmm) REVERT: A 903 MET cc_start: 0.7786 (mpp) cc_final: 0.6833 (ppp) REVERT: A 1164 VAL cc_start: 0.4744 (OUTLIER) cc_final: 0.4487 (p) REVERT: B 374 MET cc_start: 0.8701 (ttm) cc_final: 0.8180 (mtp) REVERT: B 588 MET cc_start: 0.8707 (ttp) cc_final: 0.8422 (tmm) REVERT: B 860 MET cc_start: 0.8965 (tmm) cc_final: 0.8644 (tmm) REVERT: B 1094 ARG cc_start: 0.9242 (OUTLIER) cc_final: 0.7311 (tpt90) REVERT: G 33 ASP cc_start: 0.7912 (t0) cc_final: 0.7524 (m-30) REVERT: G 71 GLU cc_start: 0.7347 (mt-10) cc_final: 0.6952 (mt-10) REVERT: a 106 ASP cc_start: 0.8155 (m-30) cc_final: 0.7739 (t0) REVERT: c 73 ASN cc_start: 0.7174 (t0) cc_final: 0.6875 (t0) REVERT: d 59 MET cc_start: 0.7439 (mtm) cc_final: 0.6977 (tmm) REVERT: e 99 TYR cc_start: 0.7962 (t80) cc_final: 0.7550 (t80) REVERT: e 110 CYS cc_start: 0.7943 (m) cc_final: 0.7508 (t) REVERT: h 59 MET cc_start: 0.7062 (tmm) cc_final: 0.6321 (ptm) outliers start: 43 outliers final: 27 residues processed: 250 average time/residue: 0.2380 time to fit residues: 101.7905 Evaluate side-chains 224 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 195 time to evaluate : 1.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 518 ASN Chi-restraints excluded: chain A residue 920 ILE Chi-restraints excluded: chain A residue 1119 THR Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 366 ARG Chi-restraints excluded: chain B residue 1090 THR Chi-restraints excluded: chain B residue 1094 ARG Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain E residue 48 SER Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 122 MET Chi-restraints excluded: chain G residue 107 ASN Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain K residue 32 ILE Chi-restraints excluded: chain K residue 59 VAL Chi-restraints excluded: chain a residue 115 LYS Chi-restraints excluded: chain c residue 102 ILE Chi-restraints excluded: chain d residue 70 PHE Chi-restraints excluded: chain f residue 29 ILE Chi-restraints excluded: chain h residue 54 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 318 optimal weight: 5.9990 chunk 75 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 chunk 210 optimal weight: 0.0070 chunk 276 optimal weight: 0.6980 chunk 314 optimal weight: 0.8980 chunk 492 optimal weight: 10.0000 chunk 37 optimal weight: 9.9990 chunk 159 optimal weight: 8.9990 chunk 150 optimal weight: 9.9990 chunk 325 optimal weight: 0.9990 overall best weight: 1.7202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 518 ASN A 974 HIS ** A1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 107 ASN H 51 GLN L 43 ASN ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.092203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.064150 restraints weight = 201207.389| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 3.07 r_work: 0.3308 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.4121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 45974 Z= 0.138 Angle : 0.508 8.061 63596 Z= 0.277 Chirality : 0.039 0.189 7139 Planarity : 0.003 0.044 6963 Dihedral : 21.917 142.470 9051 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.76 % Favored : 97.22 % Rotamer: Outliers : 1.06 % Allowed : 11.61 % Favored : 87.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.46 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.90 (0.13), residues: 4607 helix: 1.77 (0.12), residues: 1866 sheet: -0.34 (0.20), residues: 641 loop : -0.08 (0.14), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG f 95 TYR 0.022 0.001 TYR a 99 PHE 0.038 0.001 PHE b 61 TRP 0.007 0.001 TRP C 192 HIS 0.008 0.001 HIS g 82 Details of bonding type rmsd covalent geometry : bond 0.00315 (45947) covalent geometry : angle 0.50669 (63569) hydrogen bonds : bond 0.03556 ( 2098) hydrogen bonds : angle 4.03721 ( 5623) metal coordination : bond 0.00516 ( 27) metal coordination : angle 1.67807 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9214 Ramachandran restraints generated. 4607 Oldfield, 0 Emsley, 4607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9214 Ramachandran restraints generated. 4607 Oldfield, 0 Emsley, 4607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 209 time to evaluate : 1.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 770 MET cc_start: 0.8872 (mmm) cc_final: 0.8573 (mmm) REVERT: A 903 MET cc_start: 0.7791 (mpp) cc_final: 0.6807 (ppp) REVERT: A 1164 VAL cc_start: 0.4754 (OUTLIER) cc_final: 0.4542 (p) REVERT: A 1320 MET cc_start: 0.8752 (mtm) cc_final: 0.8279 (mtm) REVERT: B 374 MET cc_start: 0.8736 (ttm) cc_final: 0.8196 (mtp) REVERT: B 588 MET cc_start: 0.8750 (ttp) cc_final: 0.8478 (tmm) REVERT: B 730 MET cc_start: -0.2425 (tpt) cc_final: -0.3023 (tmm) REVERT: B 860 MET cc_start: 0.8959 (tmm) cc_final: 0.8624 (tmm) REVERT: B 1094 ARG cc_start: 0.9240 (OUTLIER) cc_final: 0.7387 (tpt90) REVERT: C 20 MET cc_start: 0.7990 (tmm) cc_final: 0.7509 (ttp) REVERT: D 142 ILE cc_start: 0.4265 (mt) cc_final: 0.3910 (tt) REVERT: G 1 MET cc_start: 0.3527 (OUTLIER) cc_final: 0.3045 (ptm) REVERT: G 22 MET cc_start: 0.8324 (mmm) cc_final: 0.8119 (mmm) REVERT: G 33 ASP cc_start: 0.8049 (t0) cc_final: 0.7677 (m-30) REVERT: G 71 GLU cc_start: 0.7375 (mt-10) cc_final: 0.6978 (mt-10) REVERT: a 106 ASP cc_start: 0.8163 (m-30) cc_final: 0.7752 (t0) REVERT: b 84 MET cc_start: 0.7780 (pmm) cc_final: 0.7159 (ppp) REVERT: c 73 ASN cc_start: 0.7235 (t0) cc_final: 0.6969 (t0) REVERT: d 59 MET cc_start: 0.7488 (mtm) cc_final: 0.7038 (tmm) REVERT: e 99 TYR cc_start: 0.7946 (t80) cc_final: 0.7567 (t80) REVERT: e 110 CYS cc_start: 0.7957 (m) cc_final: 0.7509 (t) REVERT: h 54 ILE cc_start: 0.4204 (OUTLIER) cc_final: 0.3818 (mt) outliers start: 43 outliers final: 31 residues processed: 243 average time/residue: 0.2560 time to fit residues: 107.2916 Evaluate side-chains 232 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 197 time to evaluate : 1.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 518 ASN Chi-restraints excluded: chain A residue 920 ILE Chi-restraints excluded: chain A residue 1119 THR Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1439 MET Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 366 ARG Chi-restraints excluded: chain B residue 1090 THR Chi-restraints excluded: chain B residue 1094 ARG Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain E residue 48 SER Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 122 MET Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 69 GLU Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain K residue 32 ILE Chi-restraints excluded: chain K residue 59 VAL Chi-restraints excluded: chain a residue 115 LYS Chi-restraints excluded: chain b residue 57 VAL Chi-restraints excluded: chain c residue 102 ILE Chi-restraints excluded: chain d residue 70 PHE Chi-restraints excluded: chain h residue 54 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 471 optimal weight: 9.9990 chunk 262 optimal weight: 0.3980 chunk 54 optimal weight: 3.9990 chunk 482 optimal weight: 9.9990 chunk 427 optimal weight: 9.9990 chunk 221 optimal weight: 8.9990 chunk 70 optimal weight: 3.9990 chunk 134 optimal weight: 8.9990 chunk 353 optimal weight: 1.9990 chunk 486 optimal weight: 0.5980 chunk 138 optimal weight: 0.0770 overall best weight: 1.4142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 516 GLN A 518 ASN A 974 HIS ** A1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 36 GLN L 43 ASN ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.092217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.064072 restraints weight = 200344.426| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 3.02 r_work: 0.3320 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.4263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 45974 Z= 0.126 Angle : 0.502 10.264 63596 Z= 0.273 Chirality : 0.039 0.153 7139 Planarity : 0.003 0.045 6963 Dihedral : 21.902 143.076 9051 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.78 % Favored : 97.20 % Rotamer: Outliers : 1.08 % Allowed : 12.02 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.46 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.00 (0.13), residues: 4607 helix: 1.84 (0.12), residues: 1869 sheet: -0.30 (0.20), residues: 644 loop : -0.01 (0.14), residues: 2094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG f 95 TYR 0.018 0.001 TYR a 99 PHE 0.033 0.001 PHE b 61 TRP 0.008 0.001 TRP A1307 HIS 0.006 0.001 HIS g 82 Details of bonding type rmsd covalent geometry : bond 0.00286 (45947) covalent geometry : angle 0.50101 (63569) hydrogen bonds : bond 0.03431 ( 2098) hydrogen bonds : angle 3.96627 ( 5623) metal coordination : bond 0.00399 ( 27) metal coordination : angle 1.63045 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9214 Ramachandran restraints generated. 4607 Oldfield, 0 Emsley, 4607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9214 Ramachandran restraints generated. 4607 Oldfield, 0 Emsley, 4607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 204 time to evaluate : 1.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 MET cc_start: 0.5614 (mtt) cc_final: 0.5344 (mpp) REVERT: A 770 MET cc_start: 0.8865 (mmm) cc_final: 0.8577 (mmm) REVERT: A 884 ILE cc_start: 0.8778 (OUTLIER) cc_final: 0.8572 (mt) REVERT: A 903 MET cc_start: 0.7772 (mpp) cc_final: 0.6794 (ppp) REVERT: A 1164 VAL cc_start: 0.4714 (OUTLIER) cc_final: 0.4493 (p) REVERT: B 374 MET cc_start: 0.8736 (ttm) cc_final: 0.8182 (mtp) REVERT: B 588 MET cc_start: 0.8707 (ttp) cc_final: 0.8461 (tmm) REVERT: B 730 MET cc_start: -0.2353 (tpt) cc_final: -0.2985 (tmm) REVERT: B 860 MET cc_start: 0.8954 (tmm) cc_final: 0.8628 (tmm) REVERT: C 20 MET cc_start: 0.7932 (tmm) cc_final: 0.7492 (ttp) REVERT: D 142 ILE cc_start: 0.4259 (mt) cc_final: 0.3915 (tt) REVERT: G 1 MET cc_start: 0.3306 (OUTLIER) cc_final: 0.3091 (ptm) REVERT: G 22 MET cc_start: 0.8318 (mmm) cc_final: 0.8087 (mmm) REVERT: G 33 ASP cc_start: 0.8044 (t0) cc_final: 0.7654 (m-30) REVERT: G 71 GLU cc_start: 0.7285 (mt-10) cc_final: 0.6876 (mt-10) REVERT: b 84 MET cc_start: 0.7726 (pmm) cc_final: 0.7357 (ptt) REVERT: c 73 ASN cc_start: 0.7123 (t0) cc_final: 0.6893 (t0) REVERT: c 96 LEU cc_start: 0.7448 (tt) cc_final: 0.7097 (mt) REVERT: d 59 MET cc_start: 0.7449 (mtm) cc_final: 0.7038 (tmm) REVERT: e 99 TYR cc_start: 0.7973 (t80) cc_final: 0.7597 (t80) REVERT: e 110 CYS cc_start: 0.8070 (m) cc_final: 0.7631 (t) REVERT: h 59 MET cc_start: 0.7059 (tmm) cc_final: 0.6059 (mmm) outliers start: 44 outliers final: 32 residues processed: 242 average time/residue: 0.2547 time to fit residues: 106.2054 Evaluate side-chains 233 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 198 time to evaluate : 1.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 518 ASN Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 920 ILE Chi-restraints excluded: chain A residue 1119 THR Chi-restraints excluded: chain A residue 1120 VAL Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1325 VAL Chi-restraints excluded: chain A residue 1439 MET Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 366 ARG Chi-restraints excluded: chain B residue 993 THR Chi-restraints excluded: chain B residue 1090 THR Chi-restraints excluded: chain B residue 1094 ARG Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 122 MET Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 69 GLU Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain K residue 32 ILE Chi-restraints excluded: chain K residue 59 VAL Chi-restraints excluded: chain a residue 115 LYS Chi-restraints excluded: chain c residue 102 ILE Chi-restraints excluded: chain d residue 70 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 67 optimal weight: 9.9990 chunk 78 optimal weight: 1.9990 chunk 353 optimal weight: 2.9990 chunk 330 optimal weight: 20.0000 chunk 272 optimal weight: 0.8980 chunk 137 optimal weight: 3.9990 chunk 419 optimal weight: 20.0000 chunk 356 optimal weight: 6.9990 chunk 377 optimal weight: 9.9990 chunk 180 optimal weight: 30.0000 chunk 40 optimal weight: 0.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 974 HIS ** A1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 43 ASN b 75 HIS ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 84 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.091826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.064259 restraints weight = 201377.514| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 3.03 r_work: 0.3301 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.4456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 45974 Z= 0.154 Angle : 0.520 11.436 63596 Z= 0.281 Chirality : 0.039 0.155 7139 Planarity : 0.004 0.043 6963 Dihedral : 21.938 142.567 9051 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.23 % Favored : 96.74 % Rotamer: Outliers : 1.06 % Allowed : 12.29 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.46 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.13), residues: 4607 helix: 1.83 (0.12), residues: 1862 sheet: -0.32 (0.20), residues: 653 loop : -0.03 (0.14), residues: 2092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG e 40 TYR 0.025 0.001 TYR a 99 PHE 0.022 0.001 PHE b 61 TRP 0.008 0.001 TRP F 146 HIS 0.007 0.001 HIS A 452 Details of bonding type rmsd covalent geometry : bond 0.00353 (45947) covalent geometry : angle 0.51851 (63569) hydrogen bonds : bond 0.03615 ( 2098) hydrogen bonds : angle 3.99384 ( 5623) metal coordination : bond 0.00649 ( 27) metal coordination : angle 1.81246 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9214 Ramachandran restraints generated. 4607 Oldfield, 0 Emsley, 4607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9214 Ramachandran restraints generated. 4607 Oldfield, 0 Emsley, 4607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 204 time to evaluate : 1.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 MET cc_start: 0.5622 (mtt) cc_final: 0.5385 (mpp) REVERT: A 770 MET cc_start: 0.8884 (mmm) cc_final: 0.8586 (mmm) REVERT: A 903 MET cc_start: 0.7788 (mpp) cc_final: 0.6806 (ppp) REVERT: A 1164 VAL cc_start: 0.4678 (OUTLIER) cc_final: 0.4468 (p) REVERT: A 1269 HIS cc_start: 0.7846 (OUTLIER) cc_final: 0.7282 (m170) REVERT: A 1274 ILE cc_start: 0.8370 (OUTLIER) cc_final: 0.8121 (mm) REVERT: A 1287 MET cc_start: 0.7740 (mmm) cc_final: 0.7189 (ppp) REVERT: B 374 MET cc_start: 0.8760 (ttm) cc_final: 0.8204 (mtp) REVERT: B 588 MET cc_start: 0.8743 (ttp) cc_final: 0.8479 (tmm) REVERT: B 730 MET cc_start: -0.2300 (tpt) cc_final: -0.2844 (tmm) REVERT: B 860 MET cc_start: 0.8975 (tmm) cc_final: 0.8650 (tmm) REVERT: C 20 MET cc_start: 0.7938 (tmm) cc_final: 0.7505 (ttp) REVERT: G 3 PHE cc_start: 0.4267 (OUTLIER) cc_final: 0.4041 (t80) REVERT: G 22 MET cc_start: 0.8281 (mmm) cc_final: 0.7945 (mmm) REVERT: G 33 ASP cc_start: 0.8054 (t0) cc_final: 0.7680 (m-30) REVERT: H 96 MET cc_start: 0.7975 (mtt) cc_final: 0.7577 (mtt) REVERT: b 84 MET cc_start: 0.7767 (pmm) cc_final: 0.7446 (ppp) REVERT: c 73 ASN cc_start: 0.7204 (t0) cc_final: 0.6990 (t0) REVERT: c 96 LEU cc_start: 0.7517 (tt) cc_final: 0.7225 (mt) REVERT: d 59 MET cc_start: 0.7461 (mtm) cc_final: 0.7045 (tmm) REVERT: d 120 LYS cc_start: 0.4410 (tttm) cc_final: 0.3902 (mtmt) REVERT: e 99 TYR cc_start: 0.8013 (t80) cc_final: 0.7636 (t80) REVERT: e 110 CYS cc_start: 0.8138 (m) cc_final: 0.7668 (t) outliers start: 43 outliers final: 32 residues processed: 241 average time/residue: 0.2565 time to fit residues: 106.3678 Evaluate side-chains 234 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 198 time to evaluate : 1.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 920 ILE Chi-restraints excluded: chain A residue 1119 THR Chi-restraints excluded: chain A residue 1120 VAL Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1269 HIS Chi-restraints excluded: chain A residue 1274 ILE Chi-restraints excluded: chain A residue 1325 VAL Chi-restraints excluded: chain A residue 1439 MET Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 366 ARG Chi-restraints excluded: chain B residue 993 THR Chi-restraints excluded: chain B residue 1090 THR Chi-restraints excluded: chain B residue 1094 ARG Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 3 PHE Chi-restraints excluded: chain G residue 69 GLU Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain K residue 32 ILE Chi-restraints excluded: chain K residue 59 VAL Chi-restraints excluded: chain a residue 115 LYS Chi-restraints excluded: chain b residue 57 VAL Chi-restraints excluded: chain c residue 102 ILE Chi-restraints excluded: chain d residue 70 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 53 optimal weight: 0.2980 chunk 243 optimal weight: 0.9980 chunk 286 optimal weight: 40.0000 chunk 329 optimal weight: 9.9990 chunk 240 optimal weight: 6.9990 chunk 297 optimal weight: 3.9990 chunk 463 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 394 optimal weight: 20.0000 chunk 366 optimal weight: 8.9990 chunk 482 optimal weight: 20.0000 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 518 ASN A 974 HIS ** A1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 43 ASN ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 108 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.091499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.063616 restraints weight = 199879.258| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 3.15 r_work: 0.3282 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.4837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 45974 Z= 0.156 Angle : 0.529 9.322 63596 Z= 0.286 Chirality : 0.039 0.159 7139 Planarity : 0.004 0.054 6963 Dihedral : 22.036 143.053 9051 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.23 % Favored : 96.74 % Rotamer: Outliers : 0.98 % Allowed : 12.32 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.46 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.13), residues: 4607 helix: 1.83 (0.12), residues: 1867 sheet: -0.29 (0.20), residues: 635 loop : -0.06 (0.14), residues: 2105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG b 78 TYR 0.028 0.001 TYR a 99 PHE 0.017 0.001 PHE C 260 TRP 0.009 0.001 TRP F 146 HIS 0.007 0.001 HIS A 452 Details of bonding type rmsd covalent geometry : bond 0.00359 (45947) covalent geometry : angle 0.52786 (63569) hydrogen bonds : bond 0.03671 ( 2098) hydrogen bonds : angle 3.99885 ( 5623) metal coordination : bond 0.00628 ( 27) metal coordination : angle 2.02773 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9214 Ramachandran restraints generated. 4607 Oldfield, 0 Emsley, 4607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9214 Ramachandran restraints generated. 4607 Oldfield, 0 Emsley, 4607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 214 time to evaluate : 1.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 709 MET cc_start: 0.6178 (ttt) cc_final: 0.5870 (ttt) REVERT: A 736 MET cc_start: 0.8367 (ptp) cc_final: 0.8154 (mtm) REVERT: A 770 MET cc_start: 0.8879 (mmm) cc_final: 0.8565 (mmm) REVERT: A 1164 VAL cc_start: 0.4909 (OUTLIER) cc_final: 0.4708 (p) REVERT: A 1229 MET cc_start: 0.7617 (ppp) cc_final: 0.6976 (tpt) REVERT: A 1274 ILE cc_start: 0.8436 (OUTLIER) cc_final: 0.8160 (mm) REVERT: A 1371 MET cc_start: 0.8293 (mtm) cc_final: 0.8049 (mtm) REVERT: B 374 MET cc_start: 0.8681 (ttm) cc_final: 0.8156 (mtp) REVERT: B 588 MET cc_start: 0.8785 (ttp) cc_final: 0.8443 (tmm) REVERT: B 730 MET cc_start: -0.2145 (tpt) cc_final: -0.2742 (tmm) REVERT: B 860 MET cc_start: 0.8944 (tmm) cc_final: 0.8610 (tmm) REVERT: C 20 MET cc_start: 0.7917 (tmm) cc_final: 0.7499 (ttp) REVERT: E 122 MET cc_start: 0.8244 (OUTLIER) cc_final: 0.7549 (mmm) REVERT: G 22 MET cc_start: 0.8323 (mmm) cc_final: 0.7996 (mmm) REVERT: G 33 ASP cc_start: 0.8024 (t0) cc_final: 0.7679 (m-30) REVERT: G 71 GLU cc_start: 0.7129 (mt-10) cc_final: 0.6673 (mt-10) REVERT: G 83 LYS cc_start: 0.3925 (tttm) cc_final: 0.3656 (tttp) REVERT: H 96 MET cc_start: 0.7997 (mtt) cc_final: 0.7630 (mtt) REVERT: a 120 MET cc_start: 0.2512 (mmt) cc_final: 0.1806 (tpt) REVERT: b 84 MET cc_start: 0.7494 (pmm) cc_final: 0.7237 (ppp) REVERT: c 73 ASN cc_start: 0.7301 (t0) cc_final: 0.7066 (t0) REVERT: c 96 LEU cc_start: 0.7495 (tt) cc_final: 0.7094 (mt) REVERT: d 59 MET cc_start: 0.7513 (mtm) cc_final: 0.7103 (tmm) REVERT: d 120 LYS cc_start: 0.4290 (tttm) cc_final: 0.3809 (mtmt) REVERT: e 99 TYR cc_start: 0.8072 (t80) cc_final: 0.7784 (t80) REVERT: e 110 CYS cc_start: 0.8308 (m) cc_final: 0.7898 (t) REVERT: e 115 LYS cc_start: 0.7061 (tppt) cc_final: 0.6844 (mmtm) REVERT: h 59 MET cc_start: 0.6852 (tmm) cc_final: 0.6140 (ptm) outliers start: 40 outliers final: 31 residues processed: 250 average time/residue: 0.2477 time to fit residues: 106.0399 Evaluate side-chains 232 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 198 time to evaluate : 1.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 518 ASN Chi-restraints excluded: chain A residue 920 ILE Chi-restraints excluded: chain A residue 1120 VAL Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1269 HIS Chi-restraints excluded: chain A residue 1274 ILE Chi-restraints excluded: chain A residue 1325 VAL Chi-restraints excluded: chain A residue 1439 MET Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 340 LYS Chi-restraints excluded: chain B residue 993 THR Chi-restraints excluded: chain B residue 1090 THR Chi-restraints excluded: chain B residue 1094 ARG Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 122 MET Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 84 VAL 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 a residue 115 LYS Chi-restraints excluded: chain c residue 102 ILE Chi-restraints excluded: chain d residue 70 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 290 optimal weight: 0.0370 chunk 420 optimal weight: 20.0000 chunk 32 optimal weight: 2.9990 chunk 337 optimal weight: 6.9990 chunk 163 optimal weight: 10.0000 chunk 286 optimal weight: 0.0030 chunk 54 optimal weight: 0.4980 chunk 122 optimal weight: 10.0000 chunk 336 optimal weight: 30.0000 chunk 230 optimal weight: 2.9990 chunk 160 optimal weight: 5.9990 overall best weight: 1.3072 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 974 HIS ** A1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 ASN L 43 ASN ** d 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.091853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.063849 restraints weight = 201350.023| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 2.96 r_work: 0.3304 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.4899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 45974 Z= 0.123 Angle : 0.514 13.012 63596 Z= 0.277 Chirality : 0.039 0.152 7139 Planarity : 0.003 0.044 6963 Dihedral : 22.003 144.085 9051 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.08 % Favored : 96.90 % Rotamer: Outliers : 0.86 % Allowed : 12.76 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.46 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.06 (0.13), residues: 4607 helix: 1.91 (0.12), residues: 1869 sheet: -0.24 (0.20), residues: 633 loop : -0.01 (0.14), residues: 2105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 180 TYR 0.031 0.001 TYR a 99 PHE 0.017 0.001 PHE C 260 TRP 0.009 0.001 TRP A1307 HIS 0.006 0.001 HIS g 82 Details of bonding type rmsd covalent geometry : bond 0.00277 (45947) covalent geometry : angle 0.51278 (63569) hydrogen bonds : bond 0.03432 ( 2098) hydrogen bonds : angle 3.91870 ( 5623) metal coordination : bond 0.00358 ( 27) metal coordination : angle 1.88508 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9214 Ramachandran restraints generated. 4607 Oldfield, 0 Emsley, 4607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9214 Ramachandran restraints generated. 4607 Oldfield, 0 Emsley, 4607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 206 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 709 MET cc_start: 0.6106 (ttt) cc_final: 0.5856 (ttt) REVERT: A 736 MET cc_start: 0.8405 (ptp) cc_final: 0.8191 (mtm) REVERT: A 770 MET cc_start: 0.8861 (mmm) cc_final: 0.8603 (mmm) REVERT: A 1164 VAL cc_start: 0.4938 (OUTLIER) cc_final: 0.4734 (p) REVERT: A 1274 ILE cc_start: 0.8394 (OUTLIER) cc_final: 0.8101 (mm) REVERT: A 1371 MET cc_start: 0.8270 (mtm) cc_final: 0.8039 (mtm) REVERT: B 374 MET cc_start: 0.8661 (ttm) cc_final: 0.8151 (mtp) REVERT: B 588 MET cc_start: 0.8777 (ttp) cc_final: 0.8397 (tmm) REVERT: B 730 MET cc_start: -0.2127 (tpt) cc_final: -0.2791 (tmm) REVERT: B 860 MET cc_start: 0.8908 (tmm) cc_final: 0.8590 (tmm) REVERT: B 1094 ARG cc_start: 0.9248 (OUTLIER) cc_final: 0.7395 (tpt90) REVERT: C 20 MET cc_start: 0.7913 (tmm) cc_final: 0.7516 (ttp) REVERT: E 122 MET cc_start: 0.8136 (OUTLIER) cc_final: 0.7730 (tpt) REVERT: G 22 MET cc_start: 0.8288 (mmm) cc_final: 0.7952 (mmm) REVERT: G 33 ASP cc_start: 0.8006 (t0) cc_final: 0.7669 (m-30) REVERT: G 83 LYS cc_start: 0.3849 (tttm) cc_final: 0.3588 (tttp) REVERT: H 96 MET cc_start: 0.7981 (mtt) cc_final: 0.7632 (mtt) REVERT: I 20 LYS cc_start: 0.3819 (tppt) cc_final: 0.3541 (tttt) REVERT: a 120 MET cc_start: 0.2436 (mmt) cc_final: 0.1760 (tpt) REVERT: b 84 MET cc_start: 0.7508 (pmm) cc_final: 0.7254 (ppp) REVERT: c 73 ASN cc_start: 0.7281 (t0) cc_final: 0.7037 (t0) REVERT: d 59 MET cc_start: 0.7567 (mtm) cc_final: 0.7160 (tmm) REVERT: d 120 LYS cc_start: 0.4271 (tttm) cc_final: 0.3806 (mtmt) REVERT: e 99 TYR cc_start: 0.7995 (t80) cc_final: 0.7638 (t80) REVERT: e 110 CYS cc_start: 0.8420 (m) cc_final: 0.8012 (t) REVERT: h 59 MET cc_start: 0.6941 (tmm) cc_final: 0.6164 (ptm) outliers start: 35 outliers final: 27 residues processed: 235 average time/residue: 0.1672 time to fit residues: 67.9183 Evaluate side-chains 229 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 198 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 920 ILE Chi-restraints excluded: chain A residue 1120 VAL Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1269 HIS Chi-restraints excluded: chain A residue 1274 ILE Chi-restraints excluded: chain A residue 1325 VAL Chi-restraints excluded: chain A residue 1439 MET Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 340 LYS Chi-restraints excluded: chain B residue 993 THR Chi-restraints excluded: chain B residue 1094 ARG Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 24 ASN Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 122 MET Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain K residue 32 ILE Chi-restraints excluded: chain K residue 59 VAL Chi-restraints excluded: chain a residue 115 LYS Chi-restraints excluded: chain c residue 102 ILE Chi-restraints excluded: chain d residue 70 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 266 optimal weight: 9.9990 chunk 278 optimal weight: 2.9990 chunk 317 optimal weight: 1.9990 chunk 132 optimal weight: 6.9990 chunk 490 optimal weight: 9.9990 chunk 408 optimal weight: 10.0000 chunk 106 optimal weight: 0.0970 chunk 227 optimal weight: 0.7980 chunk 232 optimal weight: 7.9990 chunk 5 optimal weight: 7.9990 chunk 388 optimal weight: 2.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 518 ASN A 974 HIS ** A1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 21 GLN L 43 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.091613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.063517 restraints weight = 200956.990| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 3.03 r_work: 0.3292 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.5000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 45974 Z= 0.139 Angle : 0.516 10.578 63596 Z= 0.279 Chirality : 0.039 0.167 7139 Planarity : 0.003 0.045 6963 Dihedral : 21.994 143.737 9051 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.28 % Favored : 96.70 % Rotamer: Outliers : 0.93 % Allowed : 12.81 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.46 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.13), residues: 4607 helix: 1.92 (0.12), residues: 1869 sheet: -0.23 (0.20), residues: 633 loop : -0.01 (0.14), residues: 2105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG e 53 TYR 0.033 0.001 TYR a 99 PHE 0.017 0.001 PHE C 260 TRP 0.009 0.001 TRP A1307 HIS 0.006 0.001 HIS A 787 Details of bonding type rmsd covalent geometry : bond 0.00318 (45947) covalent geometry : angle 0.51499 (63569) hydrogen bonds : bond 0.03513 ( 2098) hydrogen bonds : angle 3.91286 ( 5623) metal coordination : bond 0.00513 ( 27) metal coordination : angle 1.96470 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14081.45 seconds wall clock time: 240 minutes 42.13 seconds (14442.13 seconds total)