Starting phenix.real_space_refine on Mon Mar 18 20:03:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l54_0837/03_2024/6l54_0837_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l54_0837/03_2024/6l54_0837.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l54_0837/03_2024/6l54_0837.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l54_0837/03_2024/6l54_0837.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l54_0837/03_2024/6l54_0837_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l54_0837/03_2024/6l54_0837_updated.pdb" } resolution = 3.43 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1617 atoms to isotropic. 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 P 3 5.49 5 Mg 1 5.21 5 S 109 5.16 5 C 12379 2.51 5 N 3340 2.21 5 O 3698 1.98 5 H 857 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 291": "OE1" <-> "OE2" Residue "A ASP 320": "OD1" <-> "OD2" Residue "A PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 597": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 812": "NH1" <-> "NH2" Residue "A ARG 814": "NH1" <-> "NH2" Residue "A GLU 840": "OE1" <-> "OE2" Residue "A GLU 919": "OE1" <-> "OE2" Residue "A TYR 995": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1308": "OE1" <-> "OE2" Residue "A TYR 1355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1599": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1727": "OE1" <-> "OE2" Residue "A TYR 2152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2374": "NH1" <-> "NH2" Residue "A PHE 2417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 433": "NH1" <-> "NH2" Residue "B ARG 533": "NH1" <-> "NH2" Residue "B PHE 544": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 248": "NH1" <-> "NH2" Residue "C ARG 264": "NH1" <-> "NH2" Residue "C PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 482": "NH1" <-> "NH2" Residue "C ARG 501": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 20387 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 13859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1911, 13859 Classifications: {'peptide': 1911} Incomplete info: {'truncation_to_alanine': 288} Link IDs: {'CIS': 41, 'PCIS': 4, 'PTRANS': 62, 'TRANS': 1803} Chain breaks: 28 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 1401 Unresolved non-hydrogen angles: 1775 Unresolved non-hydrogen dihedrals: 1261 Unresolved non-hydrogen chiralities: 57 Planarities with less than four sites: {'GLN:plan1': 22, 'ASP:plan': 9, 'TYR:plan': 20, 'ASN:plan1': 11, 'TRP:plan': 17, 'HIS:plan': 10, 'PHE:plan': 15, 'GLU:plan': 26, 'ARG:plan': 49} Unresolved non-hydrogen planarities: 929 Chain: "B" Number of atoms: 3551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 3551 Classifications: {'peptide': 389} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 369} Chain breaks: 7 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 2977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2977 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'peptide': 308, 'undetermined': 2} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 289, None: 2} Not linked: pdbres="LEU C 519 " pdbres="GTP C 601 " Not linked: pdbres="GTP C 601 " pdbres=" MG C 602 " Chain breaks: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Time building chain proxies: 10.70, per 1000 atoms: 0.52 Number of scatterers: 20387 At special positions: 0 Unit cell: (128.96, 178.88, 142.48, 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) S 109 16.00 P 3 15.00 Mg 1 11.99 O 3698 8.00 N 3340 7.00 C 12379 6.00 H 857 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 9.74 Conformation dependent library (CDL) restraints added in 4.0 seconds 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4992 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 130 helices and 3 sheets defined 53.8% alpha, 1.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.08 Creating SS restraints... Processing helix chain 'A' and resid 37 through 42 Processing helix chain 'A' and resid 62 through 73 removed outlier: 3.634A pdb=" N ARG A 70 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N HIS A 71 " --> pdb=" O SER A 67 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ASP A 72 " --> pdb=" O ARG A 68 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ASP A 73 " --> pdb=" O GLN A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 88 removed outlier: 4.108A pdb=" N LYS A 85 " --> pdb=" O GLN A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 105 removed outlier: 3.737A pdb=" N SER A 103 " --> pdb=" O TYR A 99 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N LEU A 104 " --> pdb=" O GLY A 100 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N GLY A 105 " --> pdb=" O ARG A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 117 removed outlier: 3.809A pdb=" N GLU A 117 " --> pdb=" O VAL A 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 113 through 117' Processing helix chain 'A' and resid 124 through 141 removed outlier: 3.722A pdb=" N THR A 130 " --> pdb=" O ARG A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 162 Processing helix chain 'A' and resid 169 through 174 removed outlier: 4.245A pdb=" N LYS A 173 " --> pdb=" O LYS A 170 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLU A 174 " --> pdb=" O GLN A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 181 No H-bonds generated for 'chain 'A' and resid 178 through 181' Processing helix chain 'A' and resid 189 through 198 removed outlier: 4.288A pdb=" N HIS A 197 " --> pdb=" O LEU A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 204 No H-bonds generated for 'chain 'A' and resid 202 through 204' Processing helix chain 'A' and resid 211 through 222 removed outlier: 3.768A pdb=" N CYS A 217 " --> pdb=" O GLU A 213 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N LEU A 218 " --> pdb=" O GLY A 214 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLY A 219 " --> pdb=" O ALA A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 245 removed outlier: 3.835A pdb=" N SER A 238 " --> pdb=" O TRP A 235 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LYS A 239 " --> pdb=" O ILE A 236 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N SER A 241 " --> pdb=" O SER A 238 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYS A 245 " --> pdb=" O SER A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 268 Processing helix chain 'A' and resid 279 through 292 Proline residue: A 290 - end of helix Processing helix chain 'A' and resid 301 through 314 Proline residue: A 308 - end of helix removed outlier: 4.258A pdb=" N ASN A 314 " --> pdb=" O ILE A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 324 No H-bonds generated for 'chain 'A' and resid 322 through 324' Processing helix chain 'A' and resid 326 through 330 Processing helix chain 'A' and resid 339 through 355 removed outlier: 3.865A pdb=" N LEU A 343 " --> pdb=" O VAL A 339 " (cutoff:3.500A) Proline residue: A 348 - end of helix Processing helix chain 'A' and resid 363 through 368 removed outlier: 4.105A pdb=" N MET A 368 " --> pdb=" O PHE A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 394 Proline residue: A 389 - end of helix Processing helix chain 'A' and resid 399 through 424 removed outlier: 4.099A pdb=" N VAL A 404 " --> pdb=" O ALA A 400 " (cutoff:3.500A) Proline residue: A 418 - end of helix removed outlier: 4.037A pdb=" N GLY A 421 " --> pdb=" O SER A 417 " (cutoff:3.500A) Proline residue: A 422 - end of helix Processing helix chain 'A' and resid 444 through 459 removed outlier: 3.952A pdb=" N ALA A 455 " --> pdb=" O VAL A 452 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ALA A 456 " --> pdb=" O LEU A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 479 removed outlier: 4.324A pdb=" N VAL A 478 " --> pdb=" O HIS A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 484 No H-bonds generated for 'chain 'A' and resid 481 through 484' Processing helix chain 'A' and resid 488 through 491 No H-bonds generated for 'chain 'A' and resid 488 through 491' Processing helix chain 'A' and resid 494 through 508 removed outlier: 3.761A pdb=" N VAL A 508 " --> pdb=" O LEU A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 557 removed outlier: 4.284A pdb=" N GLN A 550 " --> pdb=" O HIS A 546 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU A 555 " --> pdb=" O ALA A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 580 removed outlier: 4.542A pdb=" N ILE A 568 " --> pdb=" O ALA A 564 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU A 571 " --> pdb=" O LEU A 567 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU A 579 " --> pdb=" O ALA A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 600 No H-bonds generated for 'chain 'A' and resid 598 through 600' Processing helix chain 'A' and resid 606 through 616 removed outlier: 4.064A pdb=" N VAL A 611 " --> pdb=" O ALA A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 630 Processing helix chain 'A' and resid 632 through 635 No H-bonds generated for 'chain 'A' and resid 632 through 635' Processing helix chain 'A' and resid 642 through 654 removed outlier: 3.715A pdb=" N SER A 651 " --> pdb=" O MET A 647 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N ALA A 654 " --> pdb=" O HIS A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 659 through 667 Processing helix chain 'A' and resid 715 through 727 removed outlier: 3.613A pdb=" N THR A 727 " --> pdb=" O LEU A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 735 through 745 removed outlier: 3.902A pdb=" N ALA A 739 " --> pdb=" O ALA A 735 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N VAL A 740 " --> pdb=" O LEU A 736 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU A 741 " --> pdb=" O GLU A 737 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS A 744 " --> pdb=" O VAL A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 767 No H-bonds generated for 'chain 'A' and resid 764 through 767' Processing helix chain 'A' and resid 809 through 824 removed outlier: 3.954A pdb=" N ALA A 816 " --> pdb=" O ARG A 812 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 849 removed outlier: 3.674A pdb=" N HIS A 848 " --> pdb=" O ALA A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 892 removed outlier: 4.010A pdb=" N ASN A 873 " --> pdb=" O ILE A 869 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER A 874 " --> pdb=" O LEU A 870 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN A 891 " --> pdb=" O PHE A 887 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N ARG A 892 " --> pdb=" O TYR A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 905 through 912 removed outlier: 4.112A pdb=" N THR A 908 " --> pdb=" O LEU A 905 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ALA A 910 " --> pdb=" O LYS A 907 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU A 912 " --> pdb=" O ASP A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 921 Processing helix chain 'A' and resid 923 through 932 removed outlier: 3.597A pdb=" N ARG A 930 " --> pdb=" O SER A 927 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N THR A 931 " --> pdb=" O LYS A 928 " (cutoff:3.500A) Proline residue: A 932 - end of helix Processing helix chain 'A' and resid 934 through 947 removed outlier: 3.770A pdb=" N ASP A 938 " --> pdb=" O ARG A 935 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N THR A 939 " --> pdb=" O ALA A 936 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N THR A 942 " --> pdb=" O THR A 939 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU A 944 " --> pdb=" O GLN A 941 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N GLY A 945 " --> pdb=" O THR A 942 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ILE A 947 " --> pdb=" O GLU A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 973 through 984 removed outlier: 3.865A pdb=" N GLN A 977 " --> pdb=" O HIS A 973 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N LEU A 978 " --> pdb=" O GLY A 974 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 998 removed outlier: 3.537A pdb=" N TYR A 995 " --> pdb=" O GLU A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1010 through 1015 Processing helix chain 'A' and resid 1017 through 1020 No H-bonds generated for 'chain 'A' and resid 1017 through 1020' Processing helix chain 'A' and resid 1027 through 1034 Processing helix chain 'A' and resid 1074 through 1084 removed outlier: 4.360A pdb=" N ALA A1079 " --> pdb=" O MET A1075 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N LEU A1080 " --> pdb=" O VAL A1076 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N CYS A1081 " --> pdb=" O VAL A1077 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N GLU A1082 " --> pdb=" O GLU A1078 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU A1083 " --> pdb=" O ALA A1079 " (cutoff:3.500A) Processing helix chain 'A' and resid 1093 through 1105 removed outlier: 4.143A pdb=" N LEU A1105 " --> pdb=" O GLY A1101 " (cutoff:3.500A) Processing helix chain 'A' and resid 1114 through 1121 removed outlier: 3.917A pdb=" N GLU A1119 " --> pdb=" O GLU A1115 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N LYS A1120 " --> pdb=" O GLY A1116 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N ALA A1121 " --> pdb=" O ARG A1117 " (cutoff:3.500A) Processing helix chain 'A' and resid 1124 through 1133 removed outlier: 4.683A pdb=" N THR A1133 " --> pdb=" O LEU A1129 " (cutoff:3.500A) Processing helix chain 'A' and resid 1195 through 1204 removed outlier: 3.702A pdb=" N TRP A1200 " --> pdb=" O ILE A1197 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA A1202 " --> pdb=" O ASP A1199 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N VAL A1203 " --> pdb=" O TRP A1200 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLN A1204 " --> pdb=" O ALA A1201 " (cutoff:3.500A) Processing helix chain 'A' and resid 1206 through 1214 removed outlier: 4.608A pdb=" N HIS A1211 " --> pdb=" O GLN A1207 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASP A1212 " --> pdb=" O ASN A1208 " (cutoff:3.500A) Processing helix chain 'A' and resid 1282 through 1304 removed outlier: 4.326A pdb=" N GLN A1286 " --> pdb=" O ARG A1283 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N LYS A1287 " --> pdb=" O GLU A1284 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N GLU A1290 " --> pdb=" O LYS A1287 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N VAL A1291 " --> pdb=" O SER A1288 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU A1294 " --> pdb=" O VAL A1291 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N SER A1297 " --> pdb=" O LEU A1294 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N CYS A1299 " --> pdb=" O SER A1296 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR A1302 " --> pdb=" O CYS A1299 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU A1304 " --> pdb=" O ALA A1301 " (cutoff:3.500A) Processing helix chain 'A' and resid 1316 through 1330 Processing helix chain 'A' and resid 1351 through 1354 No H-bonds generated for 'chain 'A' and resid 1351 through 1354' Processing helix chain 'A' and resid 1356 through 1367 removed outlier: 3.897A pdb=" N GLU A1361 " --> pdb=" O SER A1357 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL A1364 " --> pdb=" O LEU A1360 " (cutoff:3.500A) Processing helix chain 'A' and resid 1400 through 1410 Processing helix chain 'A' and resid 1417 through 1427 Processing helix chain 'A' and resid 1452 through 1465 removed outlier: 4.329A pdb=" N THR A1457 " --> pdb=" O GLY A1454 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N THR A1458 " --> pdb=" O LYS A1455 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP A1461 " --> pdb=" O THR A1458 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU A1462 " --> pdb=" O ALA A1459 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN A1464 " --> pdb=" O ASP A1461 " (cutoff:3.500A) Processing helix chain 'A' and resid 1467 through 1480 removed outlier: 3.564A pdb=" N GLY A1480 " --> pdb=" O ASP A1476 " (cutoff:3.500A) Processing helix chain 'A' and resid 1486 through 1501 removed outlier: 4.104A pdb=" N LEU A1491 " --> pdb=" O LYS A1487 " (cutoff:3.500A) Processing helix chain 'A' and resid 1512 through 1516 Processing helix chain 'A' and resid 1524 through 1538 removed outlier: 3.508A pdb=" N GLU A1535 " --> pdb=" O TRP A1531 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N TRP A1536 " --> pdb=" O ILE A1532 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N LYS A1537 " --> pdb=" O GLN A1533 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N GLU A1538 " --> pdb=" O ALA A1534 " (cutoff:3.500A) Processing helix chain 'A' and resid 1599 through 1609 removed outlier: 3.963A pdb=" N SER A1609 " --> pdb=" O TYR A1605 " (cutoff:3.500A) Processing helix chain 'A' and resid 1618 through 1639 removed outlier: 3.763A pdb=" N LEU A1622 " --> pdb=" O SER A1618 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TRP A1625 " --> pdb=" O ALA A1621 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS A1632 " --> pdb=" O ARG A1628 " (cutoff:3.500A) Processing helix chain 'A' and resid 1645 through 1654 Processing helix chain 'A' and resid 1661 through 1676 removed outlier: 3.646A pdb=" N GLU A1665 " --> pdb=" O ILE A1661 " (cutoff:3.500A) Processing helix chain 'A' and resid 1701 through 1712 removed outlier: 3.875A pdb=" N ASP A1705 " --> pdb=" O ASP A1701 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL A1706 " --> pdb=" O ASP A1702 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU A1711 " --> pdb=" O ILE A1707 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ILE A1712 " --> pdb=" O TRP A1708 " (cutoff:3.500A) Processing helix chain 'A' and resid 1728 through 1738 removed outlier: 3.730A pdb=" N VAL A1732 " --> pdb=" O GLY A1728 " (cutoff:3.500A) Processing helix chain 'A' and resid 1740 through 1759 removed outlier: 4.383A pdb=" N LYS A1745 " --> pdb=" O PHE A1741 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N LEU A1746 " --> pdb=" O SER A1742 " (cutoff:3.500A) Processing helix chain 'A' and resid 1785 through 1798 Processing helix chain 'A' and resid 1804 through 1810 removed outlier: 3.989A pdb=" N HIS A1809 " --> pdb=" O GLN A1805 " (cutoff:3.500A) Processing helix chain 'A' and resid 1824 through 1826 No H-bonds generated for 'chain 'A' and resid 1824 through 1826' Processing helix chain 'A' and resid 1838 through 1850 removed outlier: 3.566A pdb=" N ASN A1843 " --> pdb=" O GLN A1839 " (cutoff:3.500A) Processing helix chain 'A' and resid 1853 through 1855 No H-bonds generated for 'chain 'A' and resid 1853 through 1855' Processing helix chain 'A' and resid 1861 through 1865 removed outlier: 3.572A pdb=" N ILE A1865 " --> pdb=" O ILE A1861 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1861 through 1865' Processing helix chain 'A' and resid 1927 through 1938 removed outlier: 4.056A pdb=" N LYS A1932 " --> pdb=" O ASP A1928 " (cutoff:3.500A) Processing helix chain 'A' and resid 1942 through 1958 removed outlier: 3.506A pdb=" N VAL A1948 " --> pdb=" O MET A1944 " (cutoff:3.500A) Processing helix chain 'A' and resid 1965 through 1972 removed outlier: 4.276A pdb=" N GLN A1972 " --> pdb=" O GLY A1968 " (cutoff:3.500A) Processing helix chain 'A' and resid 1976 through 1990 Processing helix chain 'A' and resid 2011 through 2027 removed outlier: 4.305A pdb=" N MET A2014 " --> pdb=" O THR A2011 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LYS A2015 " --> pdb=" O ALA A2012 " (cutoff:3.500A) Proline residue: A2016 - end of helix removed outlier: 3.883A pdb=" N VAL A2024 " --> pdb=" O LEU A2021 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE A2027 " --> pdb=" O VAL A2024 " (cutoff:3.500A) Processing helix chain 'A' and resid 2040 through 2043 No H-bonds generated for 'chain 'A' and resid 2040 through 2043' Processing helix chain 'A' and resid 2049 through 2052 No H-bonds generated for 'chain 'A' and resid 2049 through 2052' Processing helix chain 'A' and resid 2054 through 2058 Proline residue: A2058 - end of helix No H-bonds generated for 'chain 'A' and resid 2054 through 2058' Processing helix chain 'A' and resid 2072 through 2083 removed outlier: 3.553A pdb=" N LEU A2078 " --> pdb=" O ILE A2074 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ARG A2081 " --> pdb=" O SER A2077 " (cutoff:3.500A) Processing helix chain 'A' and resid 2098 through 2101 No H-bonds generated for 'chain 'A' and resid 2098 through 2101' Processing helix chain 'A' and resid 2162 through 2178 Processing helix chain 'A' and resid 2214 through 2230 Processing helix chain 'A' and resid 2251 through 2256 removed outlier: 3.719A pdb=" N LYS A2256 " --> pdb=" O LEU A2252 " (cutoff:3.500A) Processing helix chain 'A' and resid 2280 through 2288 removed outlier: 3.563A pdb=" N GLU A2285 " --> pdb=" O LYS A2281 " (cutoff:3.500A) Processing helix chain 'A' and resid 2295 through 2302 Processing helix chain 'A' and resid 2307 through 2330 removed outlier: 3.752A pdb=" N TRP A2311 " --> pdb=" O PRO A2307 " (cutoff:3.500A) Processing helix chain 'A' and resid 2361 through 2363 No H-bonds generated for 'chain 'A' and resid 2361 through 2363' Processing helix chain 'A' and resid 2378 through 2381 No H-bonds generated for 'chain 'A' and resid 2378 through 2381' Processing helix chain 'A' and resid 2392 through 2405 removed outlier: 3.675A pdb=" N GLN A2398 " --> pdb=" O LEU A2394 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N VAL A2399 " --> pdb=" O SER A2395 " (cutoff:3.500A) Processing helix chain 'A' and resid 2408 through 2418 removed outlier: 3.777A pdb=" N LEU A2414 " --> pdb=" O LEU A2410 " (cutoff:3.500A) Processing helix chain 'A' and resid 3609 through 3620 Processing helix chain 'A' and resid 3633 through 3643 Processing helix chain 'A' and resid 3647 through 3651 Processing helix chain 'A' and resid 3655 through 3657 No H-bonds generated for 'chain 'A' and resid 3655 through 3657' Processing helix chain 'B' and resid 7 through 10 No H-bonds generated for 'chain 'B' and resid 7 through 10' Processing helix chain 'B' and resid 63 through 71 Processing helix chain 'B' and resid 161 through 170 Processing helix chain 'B' and resid 182 through 205 removed outlier: 3.617A pdb=" N LEU B 203 " --> pdb=" O SER B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 236 removed outlier: 3.802A pdb=" N ARG B 225 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP B 231 " --> pdb=" O PHE B 227 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N GLY B 232 " --> pdb=" O ARG B 228 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU B 233 " --> pdb=" O ALA B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 244 removed outlier: 4.176A pdb=" N ALA B 244 " --> pdb=" O LEU B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 257 Processing helix chain 'B' and resid 296 through 314 removed outlier: 3.523A pdb=" N LEU B 300 " --> pdb=" O PRO B 296 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N HIS B 302 " --> pdb=" O ARG B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 360 removed outlier: 3.752A pdb=" N ARG B 356 " --> pdb=" O LEU B 352 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N SER B 357 " --> pdb=" O ASP B 353 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N THR B 360 " --> pdb=" O ARG B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 422 removed outlier: 4.464A pdb=" N HIS B 417 " --> pdb=" O PHE B 413 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N LEU B 420 " --> pdb=" O GLN B 416 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL B 421 " --> pdb=" O HIS B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 459 removed outlier: 3.773A pdb=" N LYS B 454 " --> pdb=" O SER B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 481 No H-bonds generated for 'chain 'B' and resid 479 through 481' Processing helix chain 'B' and resid 483 through 485 No H-bonds generated for 'chain 'B' and resid 483 through 485' Processing helix chain 'B' and resid 491 through 513 Proline residue: B 505 - end of helix removed outlier: 3.786A pdb=" N SER B 509 " --> pdb=" O PRO B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 538 removed outlier: 4.683A pdb=" N GLN B 530 " --> pdb=" O ASN B 526 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ARG B 533 " --> pdb=" O ALA B 529 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLN B 537 " --> pdb=" O ARG B 533 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N HIS B 538 " --> pdb=" O VAL B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 556 removed outlier: 3.568A pdb=" N MET B 549 " --> pdb=" O HIS B 545 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N HIS B 552 " --> pdb=" O ALA B 548 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N GLU B 553 " --> pdb=" O MET B 549 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP B 554 " --> pdb=" O GLN B 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 219 through 225 Processing helix chain 'C' and resid 276 through 284 Processing helix chain 'C' and resid 297 through 310 removed outlier: 3.747A pdb=" N GLU C 301 " --> pdb=" O HIS C 297 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N MET C 302 " --> pdb=" O THR C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 340 removed outlier: 3.549A pdb=" N GLN C 335 " --> pdb=" O TYR C 331 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THR C 336 " --> pdb=" O ARG C 332 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N MET C 339 " --> pdb=" O GLN C 335 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL C 340 " --> pdb=" O THR C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 379 No H-bonds generated for 'chain 'C' and resid 377 through 379' Processing helix chain 'C' and resid 381 through 394 Processing helix chain 'C' and resid 466 through 479 Processing helix chain 'C' and resid 492 through 507 removed outlier: 3.556A pdb=" N PHE C 496 " --> pdb=" O GLU C 492 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ARG C 501 " --> pdb=" O HIS C 497 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 517 removed outlier: 3.905A pdb=" N ARG C 517 " --> pdb=" O ALA C 513 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 209 through 211 removed outlier: 3.526A pdb=" N ILE B 209 " --> pdb=" O VAL B 49 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 267 through 270 Processing sheet with id= C, first strand: chain 'C' and resid 266 through 269 removed outlier: 6.185A pdb=" N VAL C 317 " --> pdb=" O GLY C 208 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N LEU C 210 " --> pdb=" O VAL C 317 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N ILE C 319 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N VAL C 368 " --> pdb=" O VAL C 320 " (cutoff:3.500A) 737 hydrogen bonds defined for protein. 1983 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.11 Time building geometry restraints manager: 10.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 857 1.03 - 1.23: 0 1.23 - 1.42: 8033 1.42 - 1.62: 11661 1.62 - 1.81: 161 Bond restraints: 20712 Sorted by residual: bond pdb=" CA ASP A2420 " pdb=" C ASP A2420 " ideal model delta sigma weight residual 1.532 1.525 0.007 6.50e-03 2.37e+04 1.33e+00 bond pdb=" N VAL B 348 " pdb=" CA VAL B 348 " ideal model delta sigma weight residual 1.474 1.458 0.017 1.57e-02 4.06e+03 1.11e+00 bond pdb=" C ASP A2420 " pdb=" O ASP A2420 " ideal model delta sigma weight residual 1.233 1.238 -0.005 4.80e-03 4.34e+04 9.52e-01 bond pdb=" CA VAL A3637 " pdb=" CB VAL A3637 " ideal model delta sigma weight residual 1.540 1.528 0.012 1.25e-02 6.40e+03 9.32e-01 bond pdb=" C HIS A 675 " pdb=" N ASP A 676 " ideal model delta sigma weight residual 1.329 1.342 -0.013 1.40e-02 5.10e+03 9.21e-01 ... (remaining 20707 not shown) Histogram of bond angle deviations from ideal: 61.60 - 76.29: 6 76.29 - 90.97: 0 90.97 - 105.66: 394 105.66 - 120.35: 20594 120.35 - 135.04: 8119 Bond angle restraints: 29113 Sorted by residual: angle pdb=" C LEU B 137 " pdb=" N LEU B 138 " pdb=" H LEU B 138 " ideal model delta sigma weight residual 124.53 71.73 52.80 3.00e+00 1.11e-01 3.10e+02 angle pdb=" CA LEU B 138 " pdb=" N LEU B 138 " pdb=" H LEU B 138 " ideal model delta sigma weight residual 114.23 61.60 52.63 3.00e+00 1.11e-01 3.08e+02 angle pdb=" C HIS C 399 " pdb=" N LEU C 400 " pdb=" H LEU C 400 " ideal model delta sigma weight residual 124.11 72.13 51.98 3.00e+00 1.11e-01 3.00e+02 angle pdb=" CA LEU C 400 " pdb=" N LEU C 400 " pdb=" H LEU C 400 " ideal model delta sigma weight residual 113.81 62.54 51.27 3.00e+00 1.11e-01 2.92e+02 angle pdb=" C PHE C 325 " pdb=" N THR C 326 " pdb=" H THR C 326 " ideal model delta sigma weight residual 123.83 72.65 51.19 3.00e+00 1.11e-01 2.91e+02 ... (remaining 29108 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.30: 12165 20.30 - 40.60: 173 40.60 - 60.90: 21 60.90 - 81.20: 8 81.20 - 101.50: 3 Dihedral angle restraints: 12370 sinusoidal: 4717 harmonic: 7653 Sorted by residual: dihedral pdb=" O5' GTP C 601 " pdb=" O3A GTP C 601 " pdb=" PA GTP C 601 " pdb=" PB GTP C 601 " ideal model delta sinusoidal sigma weight residual 274.12 172.62 101.50 1 2.00e+01 2.50e-03 2.88e+01 dihedral pdb=" CA ALA A1088 " pdb=" C ALA A1088 " pdb=" N ILE A1089 " pdb=" CA ILE A1089 " ideal model delta harmonic sigma weight residual 180.00 -154.21 -25.79 0 5.00e+00 4.00e-02 2.66e+01 dihedral pdb=" CA LEU A1657 " pdb=" C LEU A1657 " pdb=" N PRO A1658 " pdb=" CA PRO A1658 " ideal model delta harmonic sigma weight residual -180.00 -155.34 -24.66 0 5.00e+00 4.00e-02 2.43e+01 ... (remaining 12367 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 2828 0.051 - 0.102: 399 0.102 - 0.153: 39 0.153 - 0.204: 0 0.204 - 0.255: 1 Chirality restraints: 3267 Sorted by residual: chirality pdb=" CA PRO A3627 " pdb=" N PRO A3627 " pdb=" C PRO A3627 " pdb=" CB PRO A3627 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CA PRO A1658 " pdb=" N PRO A1658 " pdb=" C PRO A1658 " pdb=" CB PRO A1658 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 5.01e-01 chirality pdb=" CA VAL A2367 " pdb=" N VAL A2367 " pdb=" C VAL A2367 " pdb=" CB VAL A2367 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.13 2.00e-01 2.50e+01 4.51e-01 ... (remaining 3264 not shown) Planarity restraints: 3786 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A1346 " 0.040 5.00e-02 4.00e+02 6.06e-02 5.87e+00 pdb=" N PRO A1347 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO A1347 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A1347 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP A2275 " 0.030 5.00e-02 4.00e+02 4.57e-02 3.34e+00 pdb=" N PRO A2276 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO A2276 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A2276 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A2246 " 0.027 5.00e-02 4.00e+02 4.16e-02 2.76e+00 pdb=" N PRO A2247 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO A2247 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A2247 " 0.021 5.00e-02 4.00e+02 ... (remaining 3783 not shown) Histogram of nonbonded interaction distances: 1.47 - 2.10: 60 2.10 - 2.72: 4561 2.72 - 3.35: 32033 3.35 - 3.97: 42689 3.97 - 4.60: 64695 Nonbonded interactions: 144038 Sorted by model distance: nonbonded pdb=" H LEU C 400 " pdb=" HA LEU C 400 " model vdw 1.469 1.816 nonbonded pdb=" H LEU B 138 " pdb=" HA LEU B 138 " model vdw 1.552 1.816 nonbonded pdb=" O LEU C 212 " pdb=" HZ2 LYS C 217 " model vdw 1.646 1.850 nonbonded pdb=" O THR C 491 " pdb=" H TRP C 495 " model vdw 1.649 1.850 nonbonded pdb=" O GLU B 44 " pdb=" H TYR B 445 " model vdw 1.686 1.850 ... (remaining 144033 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.120 Construct map_model_manager: 0.500 Extract box with map and model: 7.780 Check model and map are aligned: 0.350 Set scattering table: 0.210 Process input model: 57.140 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.090 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: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 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 : 0.002 0.044 19855 Z= 0.103 Angle : 0.492 12.576 27014 Z= 0.294 Chirality : 0.035 0.255 3267 Planarity : 0.003 0.061 3422 Dihedral : 7.603 101.504 6981 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 61.71 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.79 % Favored : 91.17 % Rotamer: Outliers : 0.79 % Allowed : 4.34 % Favored : 94.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 1.66 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.87 (0.15), residues: 2526 helix: -1.52 (0.13), residues: 1356 sheet: -4.08 (0.37), residues: 109 loop : -3.85 (0.18), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1819 HIS 0.002 0.000 HIS A 309 PHE 0.007 0.000 PHE A 240 TYR 0.005 0.000 TYR A 143 ARG 0.002 0.000 ARG C 474 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 5 is missing expected H atoms. Skipping. Residue SER 6 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue VAL 49 is missing expected H atoms. Skipping. Residue VAL 50 is missing expected H atoms. Skipping. Residue ILE 52 is missing expected H atoms. Skipping. Residue LYS 55 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue ALA 57 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue LEU 137 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue ALA 140 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 142 is missing expected H atoms. Skipping. Residue SER 143 is missing expected H atoms. Skipping. Residue SER 146 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue VAL 148 is missing expected H atoms. Skipping. Residue LEU 149 is missing expected H atoms. Skipping. Residue TYR 150 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LEU 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue ALA 165 is missing expected H atoms. Skipping. Residue ALA 185 is missing expected H atoms. Skipping. Residue LYS 194 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue LEU 198 is missing expected H atoms. Skipping. Residue LEU 200 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue TYR 202 is missing expected H atoms. Skipping. Residue LEU 203 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue ILE 209 is missing expected H atoms. Skipping. Residue LEU 210 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue LEU 212 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue THR 216 is missing expected H atoms. Skipping. Residue SER 218 is missing expected H atoms. Skipping. Residue ILE 221 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue TYR 223 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue LEU 233 is missing expected H atoms. Skipping. Residue LYS 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue LEU 238 is missing expected H atoms. Skipping. Residue LEU 240 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue THR 243 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue LEU 300 is missing expected H atoms. Skipping. Residue ALA 303 is missing expected H atoms. Skipping. Residue LEU 304 is missing expected H atoms. Skipping. Residue ILE 308 is missing expected H atoms. Skipping. Residue TYR 309 is missing expected H atoms. Skipping. Residue ILE 311 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue SER 315 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue ALA 334 is missing expected H atoms. Skipping. Residue VAL 336 is missing expected H atoms. Skipping. Residue TYR 337 is missing expected H atoms. Skipping. Residue ILE 338 is missing expected H atoms. Skipping. Residue VAL 339 is missing expected H atoms. Skipping. Residue THR 409 is missing expected H atoms. Skipping. Residue VAL 418 is missing expected H atoms. Skipping. Residue LEU 420 is missing expected H atoms. Skipping. Residue THR 444 is missing expected H atoms. Skipping. Residue TYR 445 is missing expected H atoms. Skipping. Residue LYS 447 is missing expected H atoms. Skipping. Residue ILE 449 is missing expected H atoms. Skipping. Residue SER 450 is missing expected H atoms. Skipping. Residue ALA 451 is missing expected H atoms. Skipping. Residue SER 453 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LEU 455 is missing expected H atoms. Skipping. Residue TYR 456 is missing expected H atoms. Skipping. Residue VAL 458 is missing expected H atoms. Skipping. Residue ALA 459 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 493 is missing expected H atoms. Skipping. Residue LYS 494 is missing expected H atoms. Skipping. Residue SER 496 is missing expected H atoms. Skipping. Residue LEU 528 is missing expected H atoms. Skipping. Residue ALA 529 is missing expected H atoms. Skipping. Residue ALA 531 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue VAL 534 is missing expected H atoms. Skipping. Residue TYR 535 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue ALA 539 is missing expected H atoms. Skipping. Residue ALA 543 is missing expected H atoms. Skipping. Residue LYS 546 is missing expected H atoms. Skipping. Residue TYR 547 is missing expected H atoms. Skipping. Residue ALA 548 is missing expected H atoms. Skipping. Residue MET 549 is missing expected H atoms. Skipping. Residue LEU 551 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 181 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue LEU 183 is missing expected H atoms. Skipping. Residue VAL 184 is missing expected H atoms. Skipping. Residue MET 188 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue ALA 194 is missing expected H atoms. Skipping. Residue ILE 195 is missing expected H atoms. Skipping. Residue TYR 197 is missing expected H atoms. Skipping. Residue LEU 198 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue THR 202 is missing expected H atoms. Skipping. Residue VAL 204 is missing expected H atoms. Skipping. Residue LEU 205 is missing expected H atoms. Skipping. Residue VAL 207 is missing expected H atoms. Skipping. Residue VAL 209 is missing expected H atoms. Skipping. Residue LEU 210 is missing expected H atoms. Skipping. Residue LEU 212 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue VAL 220 is missing expected H atoms. Skipping. Residue MET 221 is missing expected H atoms. Skipping. Residue SER 225 is missing expected H atoms. Skipping. Residue ALA 226 is missing expected H atoms. Skipping. Residue THR 228 is missing expected H atoms. Skipping. Residue THR 235 is missing expected H atoms. Skipping. Residue ILE 256 is missing expected H atoms. Skipping. Residue ILE 265 is missing expected H atoms. Skipping. Residue VAL 266 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue TYR 299 is missing expected H atoms. Skipping. Residue VAL 300 is missing expected H atoms. Skipping. Residue MET 302 is missing expected H atoms. Skipping. Residue SER 304 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue ILE 307 is missing expected H atoms. Skipping. Residue ALA 308 is missing expected H atoms. Skipping. Residue ALA 309 is missing expected H atoms. Skipping. Residue LEU 311 is missing expected H atoms. Skipping. Residue THR 313 is missing expected H atoms. Skipping. Residue VAL 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue VAL 318 is missing expected H atoms. Skipping. Residue ILE 319 is missing expected H atoms. Skipping. Residue VAL 320 is missing expected H atoms. Skipping. Residue VAL 321 is missing expected H atoms. Skipping. Residue THR 326 is missing expected H atoms. Skipping. Residue LEU 328 is missing expected H atoms. Skipping. Residue SER 329 is missing expected H atoms. Skipping. Residue LEU 330 is missing expected H atoms. Skipping. Residue TYR 331 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 336 is missing expected H atoms. Skipping. Residue ALA 337 is missing expected H atoms. Skipping. Residue MET 339 is missing expected H atoms. Skipping. Residue VAL 340 is missing expected H atoms. Skipping. Residue LYS 341 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue VAL 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue LYS 373 is missing expected H atoms. Skipping. Residue ALA 374 is missing expected H atoms. Skipping. Residue LYS 383 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue MET 387 is missing expected H atoms. Skipping. Residue LEU 389 is missing expected H atoms. Skipping. Residue MET 390 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue LEU 394 is missing expected H atoms. Skipping. Residue MET 395 is missing expected H atoms. Skipping. Residue ALA 396 is missing expected H atoms. Skipping. Residue SER 398 is missing expected H atoms. Skipping. Residue LEU 400 is missing expected H atoms. Skipping. Residue SER 424 is missing expected H atoms. Skipping. Residue VAL 426 is missing expected H atoms. Skipping. Residue SER 465 is missing expected H atoms. Skipping. Residue SER 468 is missing expected H atoms. Skipping. Residue LEU 469 is missing expected H atoms. Skipping. Residue VAL 470 is missing expected H atoms. Skipping. Residue SER 471 is missing expected H atoms. Skipping. Residue LYS 472 is missing expected H atoms. Skipping. Residue SER 475 is missing expected H atoms. Skipping. Residue VAL 477 is missing expected H atoms. Skipping. Residue MET 478 is missing expected H atoms. Skipping. Residue THR 491 is missing expected H atoms. Skipping. Residue LYS 493 is missing expected H atoms. Skipping. Residue ALA 499 is missing expected H atoms. Skipping. Residue ALA 500 is missing expected H atoms. Skipping. Residue ILE 502 is missing expected H atoms. Skipping. Residue SER 510 is missing expected H atoms. Skipping. Residue ALA 511 is missing expected H atoms. Skipping. Residue ALA 513 is missing expected H atoms. Skipping. Residue SER 516 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Evaluate side-chains 635 residues out of total 2320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 619 time to evaluate : 2.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 PHE cc_start: 0.7733 (m-80) cc_final: 0.4593 (m-80) REVERT: A 252 TYR cc_start: 0.6642 (m-80) cc_final: 0.6282 (m-10) REVERT: A 257 TYR cc_start: 0.5499 (t80) cc_final: 0.4543 (t80) REVERT: A 267 LYS cc_start: 0.7054 (tptt) cc_final: 0.6745 (tttp) REVERT: A 331 GLN cc_start: 0.8162 (tt0) cc_final: 0.7944 (tm-30) REVERT: A 368 MET cc_start: 0.5817 (mmt) cc_final: 0.5217 (ttp) REVERT: A 500 VAL cc_start: 0.8009 (t) cc_final: 0.6822 (m) REVERT: A 565 TYR cc_start: 0.5132 (m-80) cc_final: 0.4088 (m-80) REVERT: A 666 TYR cc_start: 0.6537 (t80) cc_final: 0.6082 (t80) REVERT: A 721 ASP cc_start: 0.6941 (t70) cc_final: 0.6638 (t0) REVERT: A 903 ARG cc_start: 0.4549 (mpt90) cc_final: 0.2139 (mmp80) REVERT: A 905 LEU cc_start: 0.5752 (pp) cc_final: 0.5502 (pp) REVERT: A 1090 GLN cc_start: 0.4430 (tp-100) cc_final: 0.4104 (tp40) REVERT: A 1129 LEU cc_start: 0.8523 (mt) cc_final: 0.8034 (mm) REVERT: A 1293 LEU cc_start: 0.8516 (mm) cc_final: 0.8264 (mm) REVERT: A 1496 GLN cc_start: 0.8153 (tm-30) cc_final: 0.7899 (tm-30) REVERT: A 1666 LYS cc_start: 0.8182 (mmtt) cc_final: 0.7021 (mmtt) REVERT: A 1703 MET cc_start: 0.6397 (mmm) cc_final: 0.6058 (mmm) REVERT: A 2128 ILE cc_start: 0.7706 (pt) cc_final: 0.7470 (mp) REVERT: A 2176 MET cc_start: 0.7838 (mtp) cc_final: 0.7602 (ttm) REVERT: A 2276 PRO cc_start: 0.7861 (Cg_exo) cc_final: 0.7460 (Cg_endo) REVERT: A 2299 GLU cc_start: 0.7480 (tp30) cc_final: 0.7043 (tp30) REVERT: A 2315 GLN cc_start: 0.7991 (mm-40) cc_final: 0.7768 (mm-40) REVERT: A 2374 ARG cc_start: 0.7890 (pmt170) cc_final: 0.7177 (pmt170) REVERT: A 2393 ARG cc_start: 0.7199 (ptm-80) cc_final: 0.6879 (mtt90) REVERT: B 268 LEU cc_start: 0.8578 (mt) cc_final: 0.8329 (mt) REVERT: B 445 TYR cc_start: 0.8756 (t80) cc_final: 0.8460 (t80) REVERT: C 269 ASP cc_start: 0.7231 (p0) cc_final: 0.6745 (p0) outliers start: 16 outliers final: 8 residues processed: 631 average time/residue: 0.3694 time to fit residues: 341.0277 Evaluate side-chains 406 residues out of total 2320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 398 time to evaluate : 2.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 613 PHE Chi-restraints excluded: chain A residue 1368 LEU Chi-restraints excluded: chain A residue 1464 GLN Chi-restraints excluded: chain A residue 1521 VAL Chi-restraints excluded: chain A residue 1816 THR Chi-restraints excluded: chain A residue 1964 GLU Chi-restraints excluded: chain A residue 2279 VAL Chi-restraints excluded: chain B residue 408 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 219 optimal weight: 9.9990 chunk 197 optimal weight: 0.9990 chunk 109 optimal weight: 0.0040 chunk 67 optimal weight: 1.9990 chunk 132 optimal weight: 0.0010 chunk 105 optimal weight: 1.9990 chunk 203 optimal weight: 4.9990 chunk 78 optimal weight: 0.0020 chunk 123 optimal weight: 0.6980 chunk 151 optimal weight: 20.0000 chunk 236 optimal weight: 2.9990 overall best weight: 0.3408 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 HIS A 171 GLN ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 ASN A 326 HIS A 338 GLN ** A 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 557 ASN ** A 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 600 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 603 ASN ** A 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 839 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 858 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 881 ASN A 904 ASN ** A 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 989 ASN ** A1090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1103 ASN ** A1184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1305 ASN ** A1405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1452 GLN A1591 HIS ** A1654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1832 HIS ** A2023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2050 ASN ** A2189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2206 GLN A2229 GLN A2315 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 192 GLN ** B 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 GLN ** B 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 508 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 538 HIS ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 371 GLN C 393 GLN ** C 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 463 HIS C 484 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 19855 Z= 0.129 Angle : 0.501 12.658 27014 Z= 0.263 Chirality : 0.036 0.149 3267 Planarity : 0.004 0.058 3422 Dihedral : 5.391 100.299 2750 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 64.92 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.83 % Favored : 91.13 % Rotamer: Outliers : 2.37 % Allowed : 13.51 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 1.66 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.82 (0.17), residues: 2526 helix: -0.54 (0.14), residues: 1366 sheet: -3.67 (0.40), residues: 113 loop : -3.55 (0.19), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 495 HIS 0.005 0.001 HIS A 329 PHE 0.019 0.001 PHE A 356 TYR 0.015 0.001 TYR A1017 ARG 0.006 0.000 ARG A 420 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 5 is missing expected H atoms. Skipping. Residue SER 6 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue VAL 49 is missing expected H atoms. Skipping. Residue VAL 50 is missing expected H atoms. Skipping. Residue ILE 52 is missing expected H atoms. Skipping. Residue LYS 55 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue ALA 57 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue LEU 137 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue ALA 140 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 142 is missing expected H atoms. Skipping. Residue SER 143 is missing expected H atoms. Skipping. Residue SER 146 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue VAL 148 is missing expected H atoms. Skipping. Residue LEU 149 is missing expected H atoms. Skipping. Residue TYR 150 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LEU 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue ALA 165 is missing expected H atoms. Skipping. Residue ALA 185 is missing expected H atoms. Skipping. Residue LYS 194 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue LEU 198 is missing expected H atoms. Skipping. Residue LEU 200 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue TYR 202 is missing expected H atoms. Skipping. Residue LEU 203 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue ILE 209 is missing expected H atoms. Skipping. Residue LEU 210 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue LEU 212 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue THR 216 is missing expected H atoms. Skipping. Residue SER 218 is missing expected H atoms. Skipping. Residue ILE 221 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue TYR 223 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue LEU 233 is missing expected H atoms. Skipping. Residue LYS 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue LEU 238 is missing expected H atoms. Skipping. Residue LEU 240 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue THR 243 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue LEU 300 is missing expected H atoms. Skipping. Residue ALA 303 is missing expected H atoms. Skipping. Residue LEU 304 is missing expected H atoms. Skipping. Residue ILE 308 is missing expected H atoms. Skipping. Residue TYR 309 is missing expected H atoms. Skipping. Residue ILE 311 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue SER 315 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue ALA 334 is missing expected H atoms. Skipping. Residue VAL 336 is missing expected H atoms. Skipping. Residue TYR 337 is missing expected H atoms. Skipping. Residue ILE 338 is missing expected H atoms. Skipping. Residue VAL 339 is missing expected H atoms. Skipping. Residue THR 409 is missing expected H atoms. Skipping. Residue VAL 418 is missing expected H atoms. Skipping. Residue LEU 420 is missing expected H atoms. Skipping. Residue THR 444 is missing expected H atoms. Skipping. Residue TYR 445 is missing expected H atoms. Skipping. Residue LYS 447 is missing expected H atoms. Skipping. Residue ILE 449 is missing expected H atoms. Skipping. Residue SER 450 is missing expected H atoms. Skipping. Residue ALA 451 is missing expected H atoms. Skipping. Residue SER 453 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LEU 455 is missing expected H atoms. Skipping. Residue TYR 456 is missing expected H atoms. Skipping. Residue VAL 458 is missing expected H atoms. Skipping. Residue ALA 459 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 493 is missing expected H atoms. Skipping. Residue LYS 494 is missing expected H atoms. Skipping. Residue SER 496 is missing expected H atoms. Skipping. Residue LEU 528 is missing expected H atoms. Skipping. Residue ALA 529 is missing expected H atoms. Skipping. Residue ALA 531 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue VAL 534 is missing expected H atoms. Skipping. Residue TYR 535 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue ALA 539 is missing expected H atoms. Skipping. Residue ALA 543 is missing expected H atoms. Skipping. Residue LYS 546 is missing expected H atoms. Skipping. Residue TYR 547 is missing expected H atoms. Skipping. Residue ALA 548 is missing expected H atoms. Skipping. Residue MET 549 is missing expected H atoms. Skipping. Residue LEU 551 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 181 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue LEU 183 is missing expected H atoms. Skipping. Residue VAL 184 is missing expected H atoms. Skipping. Residue MET 188 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue ALA 194 is missing expected H atoms. Skipping. Residue ILE 195 is missing expected H atoms. Skipping. Residue TYR 197 is missing expected H atoms. Skipping. Residue LEU 198 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue THR 202 is missing expected H atoms. Skipping. Residue VAL 204 is missing expected H atoms. Skipping. Residue LEU 205 is missing expected H atoms. Skipping. Residue VAL 207 is missing expected H atoms. Skipping. Residue VAL 209 is missing expected H atoms. Skipping. Residue LEU 210 is missing expected H atoms. Skipping. Residue LEU 212 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue VAL 220 is missing expected H atoms. Skipping. Residue MET 221 is missing expected H atoms. Skipping. Residue SER 225 is missing expected H atoms. Skipping. Residue ALA 226 is missing expected H atoms. Skipping. Residue THR 228 is missing expected H atoms. Skipping. Residue THR 235 is missing expected H atoms. Skipping. Residue ILE 256 is missing expected H atoms. Skipping. Residue ILE 265 is missing expected H atoms. Skipping. Residue VAL 266 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue TYR 299 is missing expected H atoms. Skipping. Residue VAL 300 is missing expected H atoms. Skipping. Residue MET 302 is missing expected H atoms. Skipping. Residue SER 304 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue ILE 307 is missing expected H atoms. Skipping. Residue ALA 308 is missing expected H atoms. Skipping. Residue ALA 309 is missing expected H atoms. Skipping. Residue LEU 311 is missing expected H atoms. Skipping. Residue THR 313 is missing expected H atoms. Skipping. Residue VAL 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue VAL 318 is missing expected H atoms. Skipping. Residue ILE 319 is missing expected H atoms. Skipping. Residue VAL 320 is missing expected H atoms. Skipping. Residue VAL 321 is missing expected H atoms. Skipping. Residue THR 326 is missing expected H atoms. Skipping. Residue LEU 328 is missing expected H atoms. Skipping. Residue SER 329 is missing expected H atoms. Skipping. Residue LEU 330 is missing expected H atoms. Skipping. Residue TYR 331 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 336 is missing expected H atoms. Skipping. Residue ALA 337 is missing expected H atoms. Skipping. Residue MET 339 is missing expected H atoms. Skipping. Residue VAL 340 is missing expected H atoms. Skipping. Residue LYS 341 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue VAL 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue LYS 373 is missing expected H atoms. Skipping. Residue ALA 374 is missing expected H atoms. Skipping. Residue LYS 383 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue MET 387 is missing expected H atoms. Skipping. Residue LEU 389 is missing expected H atoms. Skipping. Residue MET 390 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue LEU 394 is missing expected H atoms. Skipping. Residue MET 395 is missing expected H atoms. Skipping. Residue ALA 396 is missing expected H atoms. Skipping. Residue SER 398 is missing expected H atoms. Skipping. Residue LEU 400 is missing expected H atoms. Skipping. Residue SER 424 is missing expected H atoms. Skipping. Residue VAL 426 is missing expected H atoms. Skipping. Residue SER 465 is missing expected H atoms. Skipping. Residue SER 468 is missing expected H atoms. Skipping. Residue LEU 469 is missing expected H atoms. Skipping. Residue VAL 470 is missing expected H atoms. Skipping. Residue SER 471 is missing expected H atoms. Skipping. Residue LYS 472 is missing expected H atoms. Skipping. Residue SER 475 is missing expected H atoms. Skipping. Residue VAL 477 is missing expected H atoms. Skipping. Residue MET 478 is missing expected H atoms. Skipping. Residue THR 491 is missing expected H atoms. Skipping. Residue LYS 493 is missing expected H atoms. Skipping. Residue ALA 499 is missing expected H atoms. Skipping. Residue ALA 500 is missing expected H atoms. Skipping. Residue ILE 502 is missing expected H atoms. Skipping. Residue SER 510 is missing expected H atoms. Skipping. Residue ALA 511 is missing expected H atoms. Skipping. Residue ALA 513 is missing expected H atoms. Skipping. Residue SER 516 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Evaluate side-chains 466 residues out of total 2320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 418 time to evaluate : 2.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 PHE cc_start: 0.7634 (m-80) cc_final: 0.5567 (m-10) REVERT: A 252 TYR cc_start: 0.6488 (m-80) cc_final: 0.6232 (m-10) REVERT: A 267 LYS cc_start: 0.7095 (tptt) cc_final: 0.6849 (tttp) REVERT: A 342 TRP cc_start: 0.5566 (m100) cc_final: 0.5271 (m100) REVERT: A 368 MET cc_start: 0.6069 (mmt) cc_final: 0.5185 (ttp) REVERT: A 500 VAL cc_start: 0.8102 (t) cc_final: 0.6766 (m) REVERT: A 565 TYR cc_start: 0.5430 (m-80) cc_final: 0.4050 (m-80) REVERT: A 721 ASP cc_start: 0.7004 (t70) cc_final: 0.6665 (t0) REVERT: A 903 ARG cc_start: 0.4728 (mpt90) cc_final: 0.2297 (mmp80) REVERT: A 1666 LYS cc_start: 0.7731 (mmtt) cc_final: 0.7274 (mmtt) REVERT: A 1708 TRP cc_start: 0.6959 (m100) cc_final: 0.6565 (m100) REVERT: A 2128 ILE cc_start: 0.7739 (pt) cc_final: 0.7531 (mp) REVERT: A 2276 PRO cc_start: 0.7973 (Cg_exo) cc_final: 0.7642 (Cg_endo) REVERT: A 2326 MET cc_start: 0.7871 (mmp) cc_final: 0.7563 (mmp) REVERT: A 2373 PHE cc_start: 0.5910 (m-80) cc_final: 0.5333 (m-80) REVERT: A 2374 ARG cc_start: 0.7914 (pmt170) cc_final: 0.7024 (pmt170) REVERT: A 2393 ARG cc_start: 0.7387 (ptm-80) cc_final: 0.6974 (mtt90) REVERT: B 190 LYS cc_start: 0.8573 (OUTLIER) cc_final: 0.8193 (mtpt) REVERT: B 550 GLN cc_start: 0.7509 (mt0) cc_final: 0.7243 (mt0) REVERT: C 197 TYR cc_start: 0.8269 (m-80) cc_final: 0.7985 (m-80) REVERT: C 409 LEU cc_start: 0.7341 (mp) cc_final: 0.6954 (mp) outliers start: 48 outliers final: 37 residues processed: 453 average time/residue: 0.3472 time to fit residues: 238.4980 Evaluate side-chains 399 residues out of total 2320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 361 time to evaluate : 2.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 613 PHE Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 650 HIS Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 809 SER Chi-restraints excluded: chain A residue 989 ASN Chi-restraints excluded: chain A residue 1099 ILE Chi-restraints excluded: chain A residue 1316 ILE Chi-restraints excluded: chain A residue 1368 LEU Chi-restraints excluded: chain A residue 1464 GLN Chi-restraints excluded: chain A residue 1521 VAL Chi-restraints excluded: chain A residue 1598 ASP Chi-restraints excluded: chain A residue 1599 PHE Chi-restraints excluded: chain A residue 1729 VAL Chi-restraints excluded: chain A residue 1964 GLU Chi-restraints excluded: chain A residue 2204 LEU Chi-restraints excluded: chain A residue 2279 VAL Chi-restraints excluded: chain A residue 2320 SER Chi-restraints excluded: chain A residue 2327 VAL Chi-restraints excluded: chain A residue 2337 HIS Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 190 LYS Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 408 PHE Chi-restraints excluded: chain B residue 545 HIS Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 281 HIS Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 411 CYS Chi-restraints excluded: chain C residue 417 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 131 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 chunk 196 optimal weight: 3.9990 chunk 160 optimal weight: 6.9990 chunk 65 optimal weight: 0.8980 chunk 236 optimal weight: 0.5980 chunk 255 optimal weight: 0.8980 chunk 210 optimal weight: 0.6980 chunk 234 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 chunk 189 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 578 ASN ** A 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 839 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 858 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 904 ASN A 989 ASN ** A1021 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2023 HIS A2080 GLN ** A2192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 307 GLN ** B 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 508 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19855 Z= 0.166 Angle : 0.517 12.577 27014 Z= 0.270 Chirality : 0.036 0.212 3267 Planarity : 0.003 0.054 3422 Dihedral : 5.527 100.693 2749 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 66.36 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.74 % Favored : 90.22 % Rotamer: Outliers : 2.96 % Allowed : 14.35 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 1.66 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.17), residues: 2526 helix: -0.10 (0.15), residues: 1373 sheet: -3.39 (0.42), residues: 113 loop : -3.45 (0.19), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 350 HIS 0.010 0.001 HIS A 329 PHE 0.014 0.001 PHE A 609 TYR 0.016 0.001 TYR A1670 ARG 0.007 0.000 ARG A 420 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 5 is missing expected H atoms. Skipping. Residue SER 6 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue VAL 49 is missing expected H atoms. Skipping. Residue VAL 50 is missing expected H atoms. Skipping. Residue ILE 52 is missing expected H atoms. Skipping. Residue LYS 55 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue ALA 57 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue LEU 137 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue ALA 140 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 142 is missing expected H atoms. Skipping. Residue SER 143 is missing expected H atoms. Skipping. Residue SER 146 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue VAL 148 is missing expected H atoms. Skipping. Residue LEU 149 is missing expected H atoms. Skipping. Residue TYR 150 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LEU 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue ALA 165 is missing expected H atoms. Skipping. Residue ALA 185 is missing expected H atoms. Skipping. Residue LYS 194 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue LEU 198 is missing expected H atoms. Skipping. Residue LEU 200 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue TYR 202 is missing expected H atoms. Skipping. Residue LEU 203 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue ILE 209 is missing expected H atoms. Skipping. Residue LEU 210 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue LEU 212 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue THR 216 is missing expected H atoms. Skipping. Residue SER 218 is missing expected H atoms. Skipping. Residue ILE 221 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue TYR 223 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue LEU 233 is missing expected H atoms. Skipping. Residue LYS 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue LEU 238 is missing expected H atoms. Skipping. Residue LEU 240 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue THR 243 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue LEU 300 is missing expected H atoms. Skipping. Residue ALA 303 is missing expected H atoms. Skipping. Residue LEU 304 is missing expected H atoms. Skipping. Residue ILE 308 is missing expected H atoms. Skipping. Residue TYR 309 is missing expected H atoms. Skipping. Residue ILE 311 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue SER 315 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue ALA 334 is missing expected H atoms. Skipping. Residue VAL 336 is missing expected H atoms. Skipping. Residue TYR 337 is missing expected H atoms. Skipping. Residue ILE 338 is missing expected H atoms. Skipping. Residue VAL 339 is missing expected H atoms. Skipping. Residue THR 409 is missing expected H atoms. Skipping. Residue VAL 418 is missing expected H atoms. Skipping. Residue LEU 420 is missing expected H atoms. Skipping. Residue THR 444 is missing expected H atoms. Skipping. Residue TYR 445 is missing expected H atoms. Skipping. Residue LYS 447 is missing expected H atoms. Skipping. Residue ILE 449 is missing expected H atoms. Skipping. Residue SER 450 is missing expected H atoms. Skipping. Residue ALA 451 is missing expected H atoms. Skipping. Residue SER 453 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LEU 455 is missing expected H atoms. Skipping. Residue TYR 456 is missing expected H atoms. Skipping. Residue VAL 458 is missing expected H atoms. Skipping. Residue ALA 459 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 493 is missing expected H atoms. Skipping. Residue LYS 494 is missing expected H atoms. Skipping. Residue SER 496 is missing expected H atoms. Skipping. Residue LEU 528 is missing expected H atoms. Skipping. Residue ALA 529 is missing expected H atoms. Skipping. Residue ALA 531 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue VAL 534 is missing expected H atoms. Skipping. Residue TYR 535 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue ALA 539 is missing expected H atoms. Skipping. Residue ALA 543 is missing expected H atoms. Skipping. Residue LYS 546 is missing expected H atoms. Skipping. Residue TYR 547 is missing expected H atoms. Skipping. Residue ALA 548 is missing expected H atoms. Skipping. Residue MET 549 is missing expected H atoms. Skipping. Residue LEU 551 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 181 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue LEU 183 is missing expected H atoms. Skipping. Residue VAL 184 is missing expected H atoms. Skipping. Residue MET 188 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue ALA 194 is missing expected H atoms. Skipping. Residue ILE 195 is missing expected H atoms. Skipping. Residue TYR 197 is missing expected H atoms. Skipping. Residue LEU 198 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue THR 202 is missing expected H atoms. Skipping. Residue VAL 204 is missing expected H atoms. Skipping. Residue LEU 205 is missing expected H atoms. Skipping. Residue VAL 207 is missing expected H atoms. Skipping. Residue VAL 209 is missing expected H atoms. Skipping. Residue LEU 210 is missing expected H atoms. Skipping. Residue LEU 212 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue VAL 220 is missing expected H atoms. Skipping. Residue MET 221 is missing expected H atoms. Skipping. Residue SER 225 is missing expected H atoms. Skipping. Residue ALA 226 is missing expected H atoms. Skipping. Residue THR 228 is missing expected H atoms. Skipping. Residue THR 235 is missing expected H atoms. Skipping. Residue ILE 256 is missing expected H atoms. Skipping. Residue ILE 265 is missing expected H atoms. Skipping. Residue VAL 266 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue TYR 299 is missing expected H atoms. Skipping. Residue VAL 300 is missing expected H atoms. Skipping. Residue MET 302 is missing expected H atoms. Skipping. Residue SER 304 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue ILE 307 is missing expected H atoms. Skipping. Residue ALA 308 is missing expected H atoms. Skipping. Residue ALA 309 is missing expected H atoms. Skipping. Residue LEU 311 is missing expected H atoms. Skipping. Residue THR 313 is missing expected H atoms. Skipping. Residue VAL 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue VAL 318 is missing expected H atoms. Skipping. Residue ILE 319 is missing expected H atoms. Skipping. Residue VAL 320 is missing expected H atoms. Skipping. Residue VAL 321 is missing expected H atoms. Skipping. Residue THR 326 is missing expected H atoms. Skipping. Residue LEU 328 is missing expected H atoms. Skipping. Residue SER 329 is missing expected H atoms. Skipping. Residue LEU 330 is missing expected H atoms. Skipping. Residue TYR 331 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 336 is missing expected H atoms. Skipping. Residue ALA 337 is missing expected H atoms. Skipping. Residue MET 339 is missing expected H atoms. Skipping. Residue VAL 340 is missing expected H atoms. Skipping. Residue LYS 341 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue VAL 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue LYS 373 is missing expected H atoms. Skipping. Residue ALA 374 is missing expected H atoms. Skipping. Residue LYS 383 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue MET 387 is missing expected H atoms. Skipping. Residue LEU 389 is missing expected H atoms. Skipping. Residue MET 390 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue LEU 394 is missing expected H atoms. Skipping. Residue MET 395 is missing expected H atoms. Skipping. Residue ALA 396 is missing expected H atoms. Skipping. Residue SER 398 is missing expected H atoms. Skipping. Residue LEU 400 is missing expected H atoms. Skipping. Residue SER 424 is missing expected H atoms. Skipping. Residue VAL 426 is missing expected H atoms. Skipping. Residue SER 465 is missing expected H atoms. Skipping. Residue SER 468 is missing expected H atoms. Skipping. Residue LEU 469 is missing expected H atoms. Skipping. Residue VAL 470 is missing expected H atoms. Skipping. Residue SER 471 is missing expected H atoms. Skipping. Residue LYS 472 is missing expected H atoms. Skipping. Residue SER 475 is missing expected H atoms. Skipping. Residue VAL 477 is missing expected H atoms. Skipping. Residue MET 478 is missing expected H atoms. Skipping. Residue THR 491 is missing expected H atoms. Skipping. Residue LYS 493 is missing expected H atoms. Skipping. Residue ALA 499 is missing expected H atoms. Skipping. Residue ALA 500 is missing expected H atoms. Skipping. Residue ILE 502 is missing expected H atoms. Skipping. Residue SER 510 is missing expected H atoms. Skipping. Residue ALA 511 is missing expected H atoms. Skipping. Residue ALA 513 is missing expected H atoms. Skipping. Residue SER 516 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Evaluate side-chains 441 residues out of total 2320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 381 time to evaluate : 2.157 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 149 LEU cc_start: 0.2932 (OUTLIER) cc_final: 0.2466 (pt) REVERT: A 342 TRP cc_start: 0.5715 (m100) cc_final: 0.5498 (m100) REVERT: A 368 MET cc_start: 0.6304 (mmt) cc_final: 0.5331 (ttp) REVERT: A 500 VAL cc_start: 0.8082 (t) cc_final: 0.6778 (m) REVERT: A 721 ASP cc_start: 0.7064 (t70) cc_final: 0.6719 (t0) REVERT: A 903 ARG cc_start: 0.5344 (mpt90) cc_final: 0.2048 (mpt90) REVERT: A 1666 LYS cc_start: 0.7906 (mmtt) cc_final: 0.7616 (mmtt) REVERT: A 1708 TRP cc_start: 0.6990 (m100) cc_final: 0.6609 (m100) REVERT: A 2326 MET cc_start: 0.8078 (mmp) cc_final: 0.7740 (mmp) REVERT: A 2393 ARG cc_start: 0.7560 (ptm-80) cc_final: 0.6912 (mtt180) REVERT: B 190 LYS cc_start: 0.8719 (OUTLIER) cc_final: 0.8252 (mtpt) REVERT: C 197 TYR cc_start: 0.8325 (m-80) cc_final: 0.8022 (m-80) REVERT: C 473 LEU cc_start: 0.9305 (tp) cc_final: 0.9058 (tp) outliers start: 60 outliers final: 47 residues processed: 416 average time/residue: 0.3550 time to fit residues: 224.3663 Evaluate side-chains 412 residues out of total 2320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 363 time to evaluate : 2.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 325 TRP Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 563 THR Chi-restraints excluded: chain A residue 613 PHE Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 809 SER Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 1099 ILE Chi-restraints excluded: chain A residue 1316 ILE Chi-restraints excluded: chain A residue 1368 LEU Chi-restraints excluded: chain A residue 1397 LEU Chi-restraints excluded: chain A residue 1521 VAL Chi-restraints excluded: chain A residue 1598 ASP Chi-restraints excluded: chain A residue 1599 PHE Chi-restraints excluded: chain A residue 1753 THR Chi-restraints excluded: chain A residue 1858 TYR Chi-restraints excluded: chain A residue 2279 VAL Chi-restraints excluded: chain A residue 2327 VAL Chi-restraints excluded: chain A residue 2337 HIS Chi-restraints excluded: chain A residue 2386 THR Chi-restraints excluded: chain A residue 2403 MET Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 190 LYS Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 408 PHE Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 538 HIS Chi-restraints excluded: chain B residue 545 HIS Chi-restraints excluded: chain B residue 547 TYR Chi-restraints excluded: chain C residue 281 HIS Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 411 CYS Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 487 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 233 optimal weight: 0.8980 chunk 177 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 26 optimal weight: 9.9990 chunk 112 optimal weight: 0.0670 chunk 158 optimal weight: 6.9990 chunk 237 optimal weight: 5.9990 chunk 251 optimal weight: 0.0870 chunk 124 optimal weight: 0.8980 chunk 224 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 overall best weight: 0.5696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 326 HIS ** A 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 600 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 839 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 858 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 904 ASN ** A 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 508 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 19855 Z= 0.145 Angle : 0.499 12.560 27014 Z= 0.262 Chirality : 0.036 0.203 3267 Planarity : 0.003 0.051 3422 Dihedral : 5.275 102.349 2743 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 65.66 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.33 % Favored : 89.63 % Rotamer: Outliers : 3.01 % Allowed : 14.69 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 1.66 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.18), residues: 2526 helix: 0.17 (0.15), residues: 1394 sheet: -3.06 (0.45), residues: 113 loop : -3.42 (0.19), residues: 1019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 350 HIS 0.006 0.001 HIS A 329 PHE 0.012 0.001 PHE A 609 TYR 0.039 0.001 TYR A1670 ARG 0.005 0.000 ARG A 420 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 5 is missing expected H atoms. Skipping. Residue SER 6 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue VAL 49 is missing expected H atoms. Skipping. Residue VAL 50 is missing expected H atoms. Skipping. Residue ILE 52 is missing expected H atoms. Skipping. Residue LYS 55 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue ALA 57 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue LEU 137 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue ALA 140 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 142 is missing expected H atoms. Skipping. Residue SER 143 is missing expected H atoms. Skipping. Residue SER 146 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue VAL 148 is missing expected H atoms. Skipping. Residue LEU 149 is missing expected H atoms. Skipping. Residue TYR 150 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LEU 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue ALA 165 is missing expected H atoms. Skipping. Residue ALA 185 is missing expected H atoms. Skipping. Residue LYS 194 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue LEU 198 is missing expected H atoms. Skipping. Residue LEU 200 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue TYR 202 is missing expected H atoms. Skipping. Residue LEU 203 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue ILE 209 is missing expected H atoms. Skipping. Residue LEU 210 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue LEU 212 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue THR 216 is missing expected H atoms. Skipping. Residue SER 218 is missing expected H atoms. Skipping. Residue ILE 221 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue TYR 223 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue LEU 233 is missing expected H atoms. Skipping. Residue LYS 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue LEU 238 is missing expected H atoms. Skipping. Residue LEU 240 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue THR 243 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue LEU 300 is missing expected H atoms. Skipping. Residue ALA 303 is missing expected H atoms. Skipping. Residue LEU 304 is missing expected H atoms. Skipping. Residue ILE 308 is missing expected H atoms. Skipping. Residue TYR 309 is missing expected H atoms. Skipping. Residue ILE 311 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue SER 315 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue ALA 334 is missing expected H atoms. Skipping. Residue VAL 336 is missing expected H atoms. Skipping. Residue TYR 337 is missing expected H atoms. Skipping. Residue ILE 338 is missing expected H atoms. Skipping. Residue VAL 339 is missing expected H atoms. Skipping. Residue THR 409 is missing expected H atoms. Skipping. Residue VAL 418 is missing expected H atoms. Skipping. Residue LEU 420 is missing expected H atoms. Skipping. Residue THR 444 is missing expected H atoms. Skipping. Residue TYR 445 is missing expected H atoms. Skipping. Residue LYS 447 is missing expected H atoms. Skipping. Residue ILE 449 is missing expected H atoms. Skipping. Residue SER 450 is missing expected H atoms. Skipping. Residue ALA 451 is missing expected H atoms. Skipping. Residue SER 453 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LEU 455 is missing expected H atoms. Skipping. Residue TYR 456 is missing expected H atoms. Skipping. Residue VAL 458 is missing expected H atoms. Skipping. Residue ALA 459 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 493 is missing expected H atoms. Skipping. Residue LYS 494 is missing expected H atoms. Skipping. Residue SER 496 is missing expected H atoms. Skipping. Residue LEU 528 is missing expected H atoms. Skipping. Residue ALA 529 is missing expected H atoms. Skipping. Residue ALA 531 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue VAL 534 is missing expected H atoms. Skipping. Residue TYR 535 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue ALA 539 is missing expected H atoms. Skipping. Residue ALA 543 is missing expected H atoms. Skipping. Residue LYS 546 is missing expected H atoms. Skipping. Residue TYR 547 is missing expected H atoms. Skipping. Residue ALA 548 is missing expected H atoms. Skipping. Residue MET 549 is missing expected H atoms. Skipping. Residue LEU 551 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 181 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue LEU 183 is missing expected H atoms. Skipping. Residue VAL 184 is missing expected H atoms. Skipping. Residue MET 188 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue ALA 194 is missing expected H atoms. Skipping. Residue ILE 195 is missing expected H atoms. Skipping. Residue TYR 197 is missing expected H atoms. Skipping. Residue LEU 198 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue THR 202 is missing expected H atoms. Skipping. Residue VAL 204 is missing expected H atoms. Skipping. Residue LEU 205 is missing expected H atoms. Skipping. Residue VAL 207 is missing expected H atoms. Skipping. Residue VAL 209 is missing expected H atoms. Skipping. Residue LEU 210 is missing expected H atoms. Skipping. Residue LEU 212 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue VAL 220 is missing expected H atoms. Skipping. Residue MET 221 is missing expected H atoms. Skipping. Residue SER 225 is missing expected H atoms. Skipping. Residue ALA 226 is missing expected H atoms. Skipping. Residue THR 228 is missing expected H atoms. Skipping. Residue THR 235 is missing expected H atoms. Skipping. Residue ILE 256 is missing expected H atoms. Skipping. Residue ILE 265 is missing expected H atoms. Skipping. Residue VAL 266 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue TYR 299 is missing expected H atoms. Skipping. Residue VAL 300 is missing expected H atoms. Skipping. Residue MET 302 is missing expected H atoms. Skipping. Residue SER 304 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue ILE 307 is missing expected H atoms. Skipping. Residue ALA 308 is missing expected H atoms. Skipping. Residue ALA 309 is missing expected H atoms. Skipping. Residue LEU 311 is missing expected H atoms. Skipping. Residue THR 313 is missing expected H atoms. Skipping. Residue VAL 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue VAL 318 is missing expected H atoms. Skipping. Residue ILE 319 is missing expected H atoms. Skipping. Residue VAL 320 is missing expected H atoms. Skipping. Residue VAL 321 is missing expected H atoms. Skipping. Residue THR 326 is missing expected H atoms. Skipping. Residue LEU 328 is missing expected H atoms. Skipping. Residue SER 329 is missing expected H atoms. Skipping. Residue LEU 330 is missing expected H atoms. Skipping. Residue TYR 331 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 336 is missing expected H atoms. Skipping. Residue ALA 337 is missing expected H atoms. Skipping. Residue MET 339 is missing expected H atoms. Skipping. Residue VAL 340 is missing expected H atoms. Skipping. Residue LYS 341 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue VAL 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue LYS 373 is missing expected H atoms. Skipping. Residue ALA 374 is missing expected H atoms. Skipping. Residue LYS 383 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue MET 387 is missing expected H atoms. Skipping. Residue LEU 389 is missing expected H atoms. Skipping. Residue MET 390 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue LEU 394 is missing expected H atoms. Skipping. Residue MET 395 is missing expected H atoms. Skipping. Residue ALA 396 is missing expected H atoms. Skipping. Residue SER 398 is missing expected H atoms. Skipping. Residue LEU 400 is missing expected H atoms. Skipping. Residue SER 424 is missing expected H atoms. Skipping. Residue VAL 426 is missing expected H atoms. Skipping. Residue SER 465 is missing expected H atoms. Skipping. Residue SER 468 is missing expected H atoms. Skipping. Residue LEU 469 is missing expected H atoms. Skipping. Residue VAL 470 is missing expected H atoms. Skipping. Residue SER 471 is missing expected H atoms. Skipping. Residue LYS 472 is missing expected H atoms. Skipping. Residue SER 475 is missing expected H atoms. Skipping. Residue VAL 477 is missing expected H atoms. Skipping. Residue MET 478 is missing expected H atoms. Skipping. Residue THR 491 is missing expected H atoms. Skipping. Residue LYS 493 is missing expected H atoms. Skipping. Residue ALA 499 is missing expected H atoms. Skipping. Residue ALA 500 is missing expected H atoms. Skipping. Residue ILE 502 is missing expected H atoms. Skipping. Residue SER 510 is missing expected H atoms. Skipping. Residue ALA 511 is missing expected H atoms. Skipping. Residue ALA 513 is missing expected H atoms. Skipping. Residue SER 516 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Evaluate side-chains 437 residues out of total 2320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 376 time to evaluate : 2.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 GLU cc_start: 0.3876 (tp30) cc_final: 0.2127 (tm-30) REVERT: A 149 LEU cc_start: 0.2496 (OUTLIER) cc_final: 0.1992 (pt) REVERT: A 342 TRP cc_start: 0.5684 (m100) cc_final: 0.5480 (m100) REVERT: A 368 MET cc_start: 0.6466 (mmt) cc_final: 0.5363 (ttp) REVERT: A 434 TYR cc_start: 0.7323 (p90) cc_final: 0.7119 (p90) REVERT: A 500 VAL cc_start: 0.8071 (t) cc_final: 0.6762 (m) REVERT: A 625 LYS cc_start: 0.7300 (tptp) cc_final: 0.6740 (tptt) REVERT: A 721 ASP cc_start: 0.7063 (t70) cc_final: 0.6750 (t0) REVERT: A 903 ARG cc_start: 0.5573 (mpt90) cc_final: 0.2314 (mpt90) REVERT: A 1322 LYS cc_start: 0.7443 (ttmm) cc_final: 0.7192 (ttmm) REVERT: A 1708 TRP cc_start: 0.7099 (m100) cc_final: 0.6569 (m100) REVERT: A 2326 MET cc_start: 0.8048 (mmp) cc_final: 0.7487 (mmp) REVERT: A 2393 ARG cc_start: 0.7574 (ptm-80) cc_final: 0.6777 (mtt90) REVERT: B 190 LYS cc_start: 0.8729 (OUTLIER) cc_final: 0.8265 (mtpt) REVERT: B 550 GLN cc_start: 0.7574 (mt0) cc_final: 0.7200 (mt0) REVERT: C 197 TYR cc_start: 0.8351 (m-80) cc_final: 0.8040 (m-80) REVERT: C 473 LEU cc_start: 0.9291 (tp) cc_final: 0.9048 (tp) outliers start: 61 outliers final: 48 residues processed: 414 average time/residue: 0.3503 time to fit residues: 220.3249 Evaluate side-chains 407 residues out of total 2320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 357 time to evaluate : 2.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 325 TRP Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 613 PHE Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 833 ASN Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1099 ILE Chi-restraints excluded: chain A residue 1316 ILE Chi-restraints excluded: chain A residue 1358 SER Chi-restraints excluded: chain A residue 1368 LEU Chi-restraints excluded: chain A residue 1407 LEU Chi-restraints excluded: chain A residue 1521 VAL Chi-restraints excluded: chain A residue 1598 ASP Chi-restraints excluded: chain A residue 1599 PHE Chi-restraints excluded: chain A residue 1729 VAL Chi-restraints excluded: chain A residue 1816 THR Chi-restraints excluded: chain A residue 1858 TYR Chi-restraints excluded: chain A residue 2279 VAL Chi-restraints excluded: chain A residue 2337 HIS Chi-restraints excluded: chain A residue 2367 VAL Chi-restraints excluded: chain A residue 2391 VAL Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 190 LYS Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 258 CYS Chi-restraints excluded: chain B residue 408 PHE Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 538 HIS Chi-restraints excluded: chain B residue 545 HIS Chi-restraints excluded: chain B residue 547 TYR Chi-restraints excluded: chain C residue 281 HIS Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 380 CYS Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 411 CYS Chi-restraints excluded: chain C residue 417 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 209 optimal weight: 2.9990 chunk 142 optimal weight: 0.0670 chunk 3 optimal weight: 0.0470 chunk 187 optimal weight: 10.0000 chunk 103 optimal weight: 7.9990 chunk 214 optimal weight: 3.9990 chunk 173 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 128 optimal weight: 0.9980 chunk 225 optimal weight: 5.9990 chunk 63 optimal weight: 0.0170 overall best weight: 0.3654 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 ASN ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 600 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 858 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 975 ASN ** A 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1021 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 508 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 19855 Z= 0.122 Angle : 0.489 12.529 27014 Z= 0.255 Chirality : 0.035 0.188 3267 Planarity : 0.003 0.055 3422 Dihedral : 5.243 103.037 2743 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 64.64 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.86 % Favored : 90.10 % Rotamer: Outliers : 3.21 % Allowed : 14.99 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 1.66 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.18), residues: 2526 helix: 0.43 (0.15), residues: 1392 sheet: -2.87 (0.46), residues: 113 loop : -3.28 (0.19), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 350 HIS 0.004 0.000 HIS A 329 PHE 0.010 0.001 PHE A 609 TYR 0.041 0.001 TYR A1670 ARG 0.003 0.000 ARG A 420 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 5 is missing expected H atoms. Skipping. Residue SER 6 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue VAL 49 is missing expected H atoms. Skipping. Residue VAL 50 is missing expected H atoms. Skipping. Residue ILE 52 is missing expected H atoms. Skipping. Residue LYS 55 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue ALA 57 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue LEU 137 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue ALA 140 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 142 is missing expected H atoms. Skipping. Residue SER 143 is missing expected H atoms. Skipping. Residue SER 146 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue VAL 148 is missing expected H atoms. Skipping. Residue LEU 149 is missing expected H atoms. Skipping. Residue TYR 150 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LEU 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue ALA 165 is missing expected H atoms. Skipping. Residue ALA 185 is missing expected H atoms. Skipping. Residue LYS 194 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue LEU 198 is missing expected H atoms. Skipping. Residue LEU 200 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue TYR 202 is missing expected H atoms. Skipping. Residue LEU 203 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue ILE 209 is missing expected H atoms. Skipping. Residue LEU 210 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue LEU 212 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue THR 216 is missing expected H atoms. Skipping. Residue SER 218 is missing expected H atoms. Skipping. Residue ILE 221 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue TYR 223 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue LEU 233 is missing expected H atoms. Skipping. Residue LYS 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue LEU 238 is missing expected H atoms. Skipping. Residue LEU 240 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue THR 243 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue LEU 300 is missing expected H atoms. Skipping. Residue ALA 303 is missing expected H atoms. Skipping. Residue LEU 304 is missing expected H atoms. Skipping. Residue ILE 308 is missing expected H atoms. Skipping. Residue TYR 309 is missing expected H atoms. Skipping. Residue ILE 311 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue SER 315 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue ALA 334 is missing expected H atoms. Skipping. Residue VAL 336 is missing expected H atoms. Skipping. Residue TYR 337 is missing expected H atoms. Skipping. Residue ILE 338 is missing expected H atoms. Skipping. Residue VAL 339 is missing expected H atoms. Skipping. Residue THR 409 is missing expected H atoms. Skipping. Residue VAL 418 is missing expected H atoms. Skipping. Residue LEU 420 is missing expected H atoms. Skipping. Residue THR 444 is missing expected H atoms. Skipping. Residue TYR 445 is missing expected H atoms. Skipping. Residue LYS 447 is missing expected H atoms. Skipping. Residue ILE 449 is missing expected H atoms. Skipping. Residue SER 450 is missing expected H atoms. Skipping. Residue ALA 451 is missing expected H atoms. Skipping. Residue SER 453 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LEU 455 is missing expected H atoms. Skipping. Residue TYR 456 is missing expected H atoms. Skipping. Residue VAL 458 is missing expected H atoms. Skipping. Residue ALA 459 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 493 is missing expected H atoms. Skipping. Residue LYS 494 is missing expected H atoms. Skipping. Residue SER 496 is missing expected H atoms. Skipping. Residue LEU 528 is missing expected H atoms. Skipping. Residue ALA 529 is missing expected H atoms. Skipping. Residue ALA 531 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue VAL 534 is missing expected H atoms. Skipping. Residue TYR 535 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue ALA 539 is missing expected H atoms. Skipping. Residue ALA 543 is missing expected H atoms. Skipping. Residue LYS 546 is missing expected H atoms. Skipping. Residue TYR 547 is missing expected H atoms. Skipping. Residue ALA 548 is missing expected H atoms. Skipping. Residue MET 549 is missing expected H atoms. Skipping. Residue LEU 551 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 181 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue LEU 183 is missing expected H atoms. Skipping. Residue VAL 184 is missing expected H atoms. Skipping. Residue MET 188 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue ALA 194 is missing expected H atoms. Skipping. Residue ILE 195 is missing expected H atoms. Skipping. Residue TYR 197 is missing expected H atoms. Skipping. Residue LEU 198 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue THR 202 is missing expected H atoms. Skipping. Residue VAL 204 is missing expected H atoms. Skipping. Residue LEU 205 is missing expected H atoms. Skipping. Residue VAL 207 is missing expected H atoms. Skipping. Residue VAL 209 is missing expected H atoms. Skipping. Residue LEU 210 is missing expected H atoms. Skipping. Residue LEU 212 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue VAL 220 is missing expected H atoms. Skipping. Residue MET 221 is missing expected H atoms. Skipping. Residue SER 225 is missing expected H atoms. Skipping. Residue ALA 226 is missing expected H atoms. Skipping. Residue THR 228 is missing expected H atoms. Skipping. Residue THR 235 is missing expected H atoms. Skipping. Residue ILE 256 is missing expected H atoms. Skipping. Residue ILE 265 is missing expected H atoms. Skipping. Residue VAL 266 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue TYR 299 is missing expected H atoms. Skipping. Residue VAL 300 is missing expected H atoms. Skipping. Residue MET 302 is missing expected H atoms. Skipping. Residue SER 304 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue ILE 307 is missing expected H atoms. Skipping. Residue ALA 308 is missing expected H atoms. Skipping. Residue ALA 309 is missing expected H atoms. Skipping. Residue LEU 311 is missing expected H atoms. Skipping. Residue THR 313 is missing expected H atoms. Skipping. Residue VAL 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue VAL 318 is missing expected H atoms. Skipping. Residue ILE 319 is missing expected H atoms. Skipping. Residue VAL 320 is missing expected H atoms. Skipping. Residue VAL 321 is missing expected H atoms. Skipping. Residue THR 326 is missing expected H atoms. Skipping. Residue LEU 328 is missing expected H atoms. Skipping. Residue SER 329 is missing expected H atoms. Skipping. Residue LEU 330 is missing expected H atoms. Skipping. Residue TYR 331 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 336 is missing expected H atoms. Skipping. Residue ALA 337 is missing expected H atoms. Skipping. Residue MET 339 is missing expected H atoms. Skipping. Residue VAL 340 is missing expected H atoms. Skipping. Residue LYS 341 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue VAL 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue LYS 373 is missing expected H atoms. Skipping. Residue ALA 374 is missing expected H atoms. Skipping. Residue LYS 383 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue MET 387 is missing expected H atoms. Skipping. Residue LEU 389 is missing expected H atoms. Skipping. Residue MET 390 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue LEU 394 is missing expected H atoms. Skipping. Residue MET 395 is missing expected H atoms. Skipping. Residue ALA 396 is missing expected H atoms. Skipping. Residue SER 398 is missing expected H atoms. Skipping. Residue LEU 400 is missing expected H atoms. Skipping. Residue SER 424 is missing expected H atoms. Skipping. Residue VAL 426 is missing expected H atoms. Skipping. Residue SER 465 is missing expected H atoms. Skipping. Residue SER 468 is missing expected H atoms. Skipping. Residue LEU 469 is missing expected H atoms. Skipping. Residue VAL 470 is missing expected H atoms. Skipping. Residue SER 471 is missing expected H atoms. Skipping. Residue LYS 472 is missing expected H atoms. Skipping. Residue SER 475 is missing expected H atoms. Skipping. Residue VAL 477 is missing expected H atoms. Skipping. Residue MET 478 is missing expected H atoms. Skipping. Residue THR 491 is missing expected H atoms. Skipping. Residue LYS 493 is missing expected H atoms. Skipping. Residue ALA 499 is missing expected H atoms. Skipping. Residue ALA 500 is missing expected H atoms. Skipping. Residue ILE 502 is missing expected H atoms. Skipping. Residue SER 510 is missing expected H atoms. Skipping. Residue ALA 511 is missing expected H atoms. Skipping. Residue ALA 513 is missing expected H atoms. Skipping. Residue SER 516 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Evaluate side-chains 428 residues out of total 2320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 363 time to evaluate : 2.220 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 146 GLU cc_start: 0.3666 (tp30) cc_final: 0.2207 (tm-30) REVERT: A 149 LEU cc_start: 0.2326 (OUTLIER) cc_final: 0.1800 (pt) REVERT: A 368 MET cc_start: 0.6426 (mmt) cc_final: 0.5286 (ttp) REVERT: A 625 LYS cc_start: 0.7313 (tptp) cc_final: 0.6591 (tptt) REVERT: A 629 ILE cc_start: 0.8592 (mm) cc_final: 0.8334 (mm) REVERT: A 666 TYR cc_start: 0.6671 (t80) cc_final: 0.6177 (t80) REVERT: A 721 ASP cc_start: 0.7008 (t70) cc_final: 0.6679 (t0) REVERT: A 903 ARG cc_start: 0.5531 (mpt90) cc_final: 0.2073 (mpt90) REVERT: A 1326 GLN cc_start: 0.8117 (tt0) cc_final: 0.7779 (tt0) REVERT: A 1648 ARG cc_start: 0.8469 (ptm160) cc_final: 0.8234 (ptm160) REVERT: A 1795 LEU cc_start: 0.8639 (tp) cc_final: 0.8368 (tp) REVERT: A 2326 MET cc_start: 0.8037 (mmp) cc_final: 0.7537 (mmp) REVERT: A 2393 ARG cc_start: 0.7574 (ptm-80) cc_final: 0.6774 (mtt90) REVERT: B 190 LYS cc_start: 0.8704 (OUTLIER) cc_final: 0.8274 (mtpt) REVERT: C 197 TYR cc_start: 0.8355 (m-80) cc_final: 0.8089 (m-80) outliers start: 65 outliers final: 54 residues processed: 398 average time/residue: 0.3365 time to fit residues: 203.2413 Evaluate side-chains 403 residues out of total 2320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 347 time to evaluate : 2.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 444 ASN Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 613 PHE Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 650 HIS Chi-restraints excluded: chain A residue 674 ARG Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 809 SER Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 1099 ILE Chi-restraints excluded: chain A residue 1316 ILE Chi-restraints excluded: chain A residue 1358 SER Chi-restraints excluded: chain A residue 1368 LEU Chi-restraints excluded: chain A residue 1423 GLU Chi-restraints excluded: chain A residue 1521 VAL Chi-restraints excluded: chain A residue 1598 ASP Chi-restraints excluded: chain A residue 1599 PHE Chi-restraints excluded: chain A residue 1729 VAL Chi-restraints excluded: chain A residue 1816 THR Chi-restraints excluded: chain A residue 1858 TYR Chi-restraints excluded: chain A residue 2279 VAL Chi-restraints excluded: chain A residue 2327 VAL Chi-restraints excluded: chain A residue 2337 HIS Chi-restraints excluded: chain A residue 2367 VAL Chi-restraints excluded: chain A residue 2403 MET Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 190 LYS Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 408 PHE Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 538 HIS Chi-restraints excluded: chain B residue 545 HIS Chi-restraints excluded: chain B residue 547 TYR Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 281 HIS Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 411 CYS Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 487 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 84 optimal weight: 3.9990 chunk 226 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 147 optimal weight: 10.0000 chunk 62 optimal weight: 0.9990 chunk 251 optimal weight: 0.0770 chunk 208 optimal weight: 0.9980 chunk 116 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 chunk 83 optimal weight: 4.9990 chunk 132 optimal weight: 3.9990 overall best weight: 0.9542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 326 HIS A 331 GLN ** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 600 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 858 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 922 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1128 HIS ** A1184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1413 GLN ** A1452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2080 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 508 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19855 Z= 0.194 Angle : 0.547 12.734 27014 Z= 0.287 Chirality : 0.037 0.246 3267 Planarity : 0.004 0.053 3422 Dihedral : 5.567 104.946 2743 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 67.46 Ramachandran Plot: Outliers : 0.08 % Allowed : 12.15 % Favored : 87.77 % Rotamer: Outliers : 4.04 % Allowed : 15.29 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 1.66 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.18), residues: 2526 helix: 0.36 (0.15), residues: 1415 sheet: -2.73 (0.47), residues: 113 loop : -3.43 (0.19), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 342 HIS 0.005 0.001 HIS A1084 PHE 0.016 0.001 PHE A 609 TYR 0.038 0.001 TYR A1670 ARG 0.004 0.000 ARG A2224 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 5 is missing expected H atoms. Skipping. Residue SER 6 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue VAL 49 is missing expected H atoms. Skipping. Residue VAL 50 is missing expected H atoms. Skipping. Residue ILE 52 is missing expected H atoms. Skipping. Residue LYS 55 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue ALA 57 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue LEU 137 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue ALA 140 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 142 is missing expected H atoms. Skipping. Residue SER 143 is missing expected H atoms. Skipping. Residue SER 146 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue VAL 148 is missing expected H atoms. Skipping. Residue LEU 149 is missing expected H atoms. Skipping. Residue TYR 150 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LEU 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue ALA 165 is missing expected H atoms. Skipping. Residue ALA 185 is missing expected H atoms. Skipping. Residue LYS 194 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue LEU 198 is missing expected H atoms. Skipping. Residue LEU 200 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue TYR 202 is missing expected H atoms. Skipping. Residue LEU 203 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue ILE 209 is missing expected H atoms. Skipping. Residue LEU 210 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue LEU 212 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue THR 216 is missing expected H atoms. Skipping. Residue SER 218 is missing expected H atoms. Skipping. Residue ILE 221 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue TYR 223 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue LEU 233 is missing expected H atoms. Skipping. Residue LYS 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue LEU 238 is missing expected H atoms. Skipping. Residue LEU 240 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue THR 243 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue LEU 300 is missing expected H atoms. Skipping. Residue ALA 303 is missing expected H atoms. Skipping. Residue LEU 304 is missing expected H atoms. Skipping. Residue ILE 308 is missing expected H atoms. Skipping. Residue TYR 309 is missing expected H atoms. Skipping. Residue ILE 311 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue SER 315 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue ALA 334 is missing expected H atoms. Skipping. Residue VAL 336 is missing expected H atoms. Skipping. Residue TYR 337 is missing expected H atoms. Skipping. Residue ILE 338 is missing expected H atoms. Skipping. Residue VAL 339 is missing expected H atoms. Skipping. Residue THR 409 is missing expected H atoms. Skipping. Residue VAL 418 is missing expected H atoms. Skipping. Residue LEU 420 is missing expected H atoms. Skipping. Residue THR 444 is missing expected H atoms. Skipping. Residue TYR 445 is missing expected H atoms. Skipping. Residue LYS 447 is missing expected H atoms. Skipping. Residue ILE 449 is missing expected H atoms. Skipping. Residue SER 450 is missing expected H atoms. Skipping. Residue ALA 451 is missing expected H atoms. Skipping. Residue SER 453 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LEU 455 is missing expected H atoms. Skipping. Residue TYR 456 is missing expected H atoms. Skipping. Residue VAL 458 is missing expected H atoms. Skipping. Residue ALA 459 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 493 is missing expected H atoms. Skipping. Residue LYS 494 is missing expected H atoms. Skipping. Residue SER 496 is missing expected H atoms. Skipping. Residue LEU 528 is missing expected H atoms. Skipping. Residue ALA 529 is missing expected H atoms. Skipping. Residue ALA 531 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue VAL 534 is missing expected H atoms. Skipping. Residue TYR 535 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue ALA 539 is missing expected H atoms. Skipping. Residue ALA 543 is missing expected H atoms. Skipping. Residue LYS 546 is missing expected H atoms. Skipping. Residue TYR 547 is missing expected H atoms. Skipping. Residue ALA 548 is missing expected H atoms. Skipping. Residue MET 549 is missing expected H atoms. Skipping. Residue LEU 551 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 181 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue LEU 183 is missing expected H atoms. Skipping. Residue VAL 184 is missing expected H atoms. Skipping. Residue MET 188 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue ALA 194 is missing expected H atoms. Skipping. Residue ILE 195 is missing expected H atoms. Skipping. Residue TYR 197 is missing expected H atoms. Skipping. Residue LEU 198 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue THR 202 is missing expected H atoms. Skipping. Residue VAL 204 is missing expected H atoms. Skipping. Residue LEU 205 is missing expected H atoms. Skipping. Residue VAL 207 is missing expected H atoms. Skipping. Residue VAL 209 is missing expected H atoms. Skipping. Residue LEU 210 is missing expected H atoms. Skipping. Residue LEU 212 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue VAL 220 is missing expected H atoms. Skipping. Residue MET 221 is missing expected H atoms. Skipping. Residue SER 225 is missing expected H atoms. Skipping. Residue ALA 226 is missing expected H atoms. Skipping. Residue THR 228 is missing expected H atoms. Skipping. Residue THR 235 is missing expected H atoms. Skipping. Residue ILE 256 is missing expected H atoms. Skipping. Residue ILE 265 is missing expected H atoms. Skipping. Residue VAL 266 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue TYR 299 is missing expected H atoms. Skipping. Residue VAL 300 is missing expected H atoms. Skipping. Residue MET 302 is missing expected H atoms. Skipping. Residue SER 304 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue ILE 307 is missing expected H atoms. Skipping. Residue ALA 308 is missing expected H atoms. Skipping. Residue ALA 309 is missing expected H atoms. Skipping. Residue LEU 311 is missing expected H atoms. Skipping. Residue THR 313 is missing expected H atoms. Skipping. Residue VAL 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue VAL 318 is missing expected H atoms. Skipping. Residue ILE 319 is missing expected H atoms. Skipping. Residue VAL 320 is missing expected H atoms. Skipping. Residue VAL 321 is missing expected H atoms. Skipping. Residue THR 326 is missing expected H atoms. Skipping. Residue LEU 328 is missing expected H atoms. Skipping. Residue SER 329 is missing expected H atoms. Skipping. Residue LEU 330 is missing expected H atoms. Skipping. Residue TYR 331 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 336 is missing expected H atoms. Skipping. Residue ALA 337 is missing expected H atoms. Skipping. Residue MET 339 is missing expected H atoms. Skipping. Residue VAL 340 is missing expected H atoms. Skipping. Residue LYS 341 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue VAL 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue LYS 373 is missing expected H atoms. Skipping. Residue ALA 374 is missing expected H atoms. Skipping. Residue LYS 383 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue MET 387 is missing expected H atoms. Skipping. Residue LEU 389 is missing expected H atoms. Skipping. Residue MET 390 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue LEU 394 is missing expected H atoms. Skipping. Residue MET 395 is missing expected H atoms. Skipping. Residue ALA 396 is missing expected H atoms. Skipping. Residue SER 398 is missing expected H atoms. Skipping. Residue LEU 400 is missing expected H atoms. Skipping. Residue SER 424 is missing expected H atoms. Skipping. Residue VAL 426 is missing expected H atoms. Skipping. Residue SER 465 is missing expected H atoms. Skipping. Residue SER 468 is missing expected H atoms. Skipping. Residue LEU 469 is missing expected H atoms. Skipping. Residue VAL 470 is missing expected H atoms. Skipping. Residue SER 471 is missing expected H atoms. Skipping. Residue LYS 472 is missing expected H atoms. Skipping. Residue SER 475 is missing expected H atoms. Skipping. Residue VAL 477 is missing expected H atoms. Skipping. Residue MET 478 is missing expected H atoms. Skipping. Residue THR 491 is missing expected H atoms. Skipping. Residue LYS 493 is missing expected H atoms. Skipping. Residue ALA 499 is missing expected H atoms. Skipping. Residue ALA 500 is missing expected H atoms. Skipping. Residue ILE 502 is missing expected H atoms. Skipping. Residue SER 510 is missing expected H atoms. Skipping. Residue ALA 511 is missing expected H atoms. Skipping. Residue ALA 513 is missing expected H atoms. Skipping. Residue SER 516 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Evaluate side-chains 451 residues out of total 2320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 369 time to evaluate : 2.313 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 146 GLU cc_start: 0.3700 (tp30) cc_final: 0.2686 (tm-30) REVERT: A 368 MET cc_start: 0.6659 (mmt) cc_final: 0.5474 (ttp) REVERT: A 625 LYS cc_start: 0.7373 (tptp) cc_final: 0.7037 (tptt) REVERT: A 629 ILE cc_start: 0.8806 (mm) cc_final: 0.8549 (mm) REVERT: A 721 ASP cc_start: 0.7001 (t70) cc_final: 0.6710 (t0) REVERT: A 903 ARG cc_start: 0.6360 (mpt90) cc_final: 0.3474 (mpt90) REVERT: A 922 GLN cc_start: 0.8326 (OUTLIER) cc_final: 0.8056 (pp30) REVERT: A 1117 ARG cc_start: 0.8282 (ptt180) cc_final: 0.7982 (ptt180) REVERT: A 1326 GLN cc_start: 0.8129 (tt0) cc_final: 0.7805 (tt0) REVERT: A 1635 ASP cc_start: 0.8203 (m-30) cc_final: 0.7887 (m-30) REVERT: A 1842 CYS cc_start: 0.7688 (p) cc_final: 0.7375 (m) REVERT: A 1929 CYS cc_start: 0.7413 (m) cc_final: 0.7017 (t) REVERT: A 2326 MET cc_start: 0.8055 (mmp) cc_final: 0.7687 (mmp) REVERT: A 2393 ARG cc_start: 0.7670 (ptm-80) cc_final: 0.6667 (mtt180) REVERT: B 190 LYS cc_start: 0.8750 (OUTLIER) cc_final: 0.8355 (mtpt) REVERT: C 197 TYR cc_start: 0.8432 (m-80) cc_final: 0.8095 (m-80) outliers start: 82 outliers final: 65 residues processed: 418 average time/residue: 0.3327 time to fit residues: 212.7779 Evaluate side-chains 412 residues out of total 2320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 345 time to evaluate : 2.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 325 TRP Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 444 ASN Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 613 PHE Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 809 SER Chi-restraints excluded: chain A residue 833 ASN Chi-restraints excluded: chain A residue 922 GLN Chi-restraints excluded: chain A residue 942 THR Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1099 ILE Chi-restraints excluded: chain A residue 1194 TYR Chi-restraints excluded: chain A residue 1309 GLN Chi-restraints excluded: chain A residue 1316 ILE Chi-restraints excluded: chain A residue 1358 SER Chi-restraints excluded: chain A residue 1368 LEU Chi-restraints excluded: chain A residue 1397 LEU Chi-restraints excluded: chain A residue 1407 LEU Chi-restraints excluded: chain A residue 1423 GLU Chi-restraints excluded: chain A residue 1521 VAL Chi-restraints excluded: chain A residue 1599 PHE Chi-restraints excluded: chain A residue 1711 LEU Chi-restraints excluded: chain A residue 1729 VAL Chi-restraints excluded: chain A residue 1753 THR Chi-restraints excluded: chain A residue 1816 THR Chi-restraints excluded: chain A residue 1858 TYR Chi-restraints excluded: chain A residue 2193 TYR Chi-restraints excluded: chain A residue 2279 VAL Chi-restraints excluded: chain A residue 2327 VAL Chi-restraints excluded: chain A residue 2337 HIS Chi-restraints excluded: chain A residue 2367 VAL Chi-restraints excluded: chain A residue 2403 MET Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 190 LYS Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 258 CYS Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 408 PHE Chi-restraints excluded: chain B residue 538 HIS Chi-restraints excluded: chain B residue 545 HIS Chi-restraints excluded: chain B residue 547 TYR Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 222 SER Chi-restraints excluded: chain C residue 281 HIS Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 380 CYS Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 411 CYS Chi-restraints excluded: chain C residue 417 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 242 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 chunk 183 optimal weight: 3.9990 chunk 142 optimal weight: 0.9980 chunk 211 optimal weight: 0.6980 chunk 140 optimal weight: 0.0570 chunk 250 optimal weight: 3.9990 chunk 156 optimal weight: 4.9990 chunk 152 optimal weight: 1.9990 chunk 115 optimal weight: 0.0870 overall best weight: 0.7678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 600 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 858 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 922 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 61 ASN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 508 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 322 GLN ** C 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19855 Z= 0.164 Angle : 0.519 12.592 27014 Z= 0.274 Chirality : 0.037 0.194 3267 Planarity : 0.004 0.053 3422 Dihedral : 5.600 105.630 2743 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 67.62 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.32 % Favored : 88.64 % Rotamer: Outliers : 3.75 % Allowed : 16.67 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 1.66 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.18), residues: 2526 helix: 0.47 (0.15), residues: 1415 sheet: -2.74 (0.49), residues: 103 loop : -3.34 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A1106 HIS 0.004 0.001 HIS A 329 PHE 0.015 0.001 PHE A1015 TYR 0.041 0.001 TYR A1670 ARG 0.006 0.000 ARG A2404 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 5 is missing expected H atoms. Skipping. Residue SER 6 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue VAL 49 is missing expected H atoms. Skipping. Residue VAL 50 is missing expected H atoms. Skipping. Residue ILE 52 is missing expected H atoms. Skipping. Residue LYS 55 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue ALA 57 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue LEU 137 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue ALA 140 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 142 is missing expected H atoms. Skipping. Residue SER 143 is missing expected H atoms. Skipping. Residue SER 146 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue VAL 148 is missing expected H atoms. Skipping. Residue LEU 149 is missing expected H atoms. Skipping. Residue TYR 150 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LEU 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue ALA 165 is missing expected H atoms. Skipping. Residue ALA 185 is missing expected H atoms. Skipping. Residue LYS 194 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue LEU 198 is missing expected H atoms. Skipping. Residue LEU 200 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue TYR 202 is missing expected H atoms. Skipping. Residue LEU 203 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue ILE 209 is missing expected H atoms. Skipping. Residue LEU 210 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue LEU 212 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue THR 216 is missing expected H atoms. Skipping. Residue SER 218 is missing expected H atoms. Skipping. Residue ILE 221 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue TYR 223 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue LEU 233 is missing expected H atoms. Skipping. Residue LYS 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue LEU 238 is missing expected H atoms. Skipping. Residue LEU 240 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue THR 243 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue LEU 300 is missing expected H atoms. Skipping. Residue ALA 303 is missing expected H atoms. Skipping. Residue LEU 304 is missing expected H atoms. Skipping. Residue ILE 308 is missing expected H atoms. Skipping. Residue TYR 309 is missing expected H atoms. Skipping. Residue ILE 311 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue SER 315 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue ALA 334 is missing expected H atoms. Skipping. Residue VAL 336 is missing expected H atoms. Skipping. Residue TYR 337 is missing expected H atoms. Skipping. Residue ILE 338 is missing expected H atoms. Skipping. Residue VAL 339 is missing expected H atoms. Skipping. Residue THR 409 is missing expected H atoms. Skipping. Residue VAL 418 is missing expected H atoms. Skipping. Residue LEU 420 is missing expected H atoms. Skipping. Residue THR 444 is missing expected H atoms. Skipping. Residue TYR 445 is missing expected H atoms. Skipping. Residue LYS 447 is missing expected H atoms. Skipping. Residue ILE 449 is missing expected H atoms. Skipping. Residue SER 450 is missing expected H atoms. Skipping. Residue ALA 451 is missing expected H atoms. Skipping. Residue SER 453 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LEU 455 is missing expected H atoms. Skipping. Residue TYR 456 is missing expected H atoms. Skipping. Residue VAL 458 is missing expected H atoms. Skipping. Residue ALA 459 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 493 is missing expected H atoms. Skipping. Residue LYS 494 is missing expected H atoms. Skipping. Residue SER 496 is missing expected H atoms. Skipping. Residue LEU 528 is missing expected H atoms. Skipping. Residue ALA 529 is missing expected H atoms. Skipping. Residue ALA 531 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue VAL 534 is missing expected H atoms. Skipping. Residue TYR 535 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue ALA 539 is missing expected H atoms. Skipping. Residue ALA 543 is missing expected H atoms. Skipping. Residue LYS 546 is missing expected H atoms. Skipping. Residue TYR 547 is missing expected H atoms. Skipping. Residue ALA 548 is missing expected H atoms. Skipping. Residue MET 549 is missing expected H atoms. Skipping. Residue LEU 551 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 181 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue LEU 183 is missing expected H atoms. Skipping. Residue VAL 184 is missing expected H atoms. Skipping. Residue MET 188 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue ALA 194 is missing expected H atoms. Skipping. Residue ILE 195 is missing expected H atoms. Skipping. Residue TYR 197 is missing expected H atoms. Skipping. Residue LEU 198 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue THR 202 is missing expected H atoms. Skipping. Residue VAL 204 is missing expected H atoms. Skipping. Residue LEU 205 is missing expected H atoms. Skipping. Residue VAL 207 is missing expected H atoms. Skipping. Residue VAL 209 is missing expected H atoms. Skipping. Residue LEU 210 is missing expected H atoms. Skipping. Residue LEU 212 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue VAL 220 is missing expected H atoms. Skipping. Residue MET 221 is missing expected H atoms. Skipping. Residue SER 225 is missing expected H atoms. Skipping. Residue ALA 226 is missing expected H atoms. Skipping. Residue THR 228 is missing expected H atoms. Skipping. Residue THR 235 is missing expected H atoms. Skipping. Residue ILE 256 is missing expected H atoms. Skipping. Residue ILE 265 is missing expected H atoms. Skipping. Residue VAL 266 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue TYR 299 is missing expected H atoms. Skipping. Residue VAL 300 is missing expected H atoms. Skipping. Residue MET 302 is missing expected H atoms. Skipping. Residue SER 304 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue ILE 307 is missing expected H atoms. Skipping. Residue ALA 308 is missing expected H atoms. Skipping. Residue ALA 309 is missing expected H atoms. Skipping. Residue LEU 311 is missing expected H atoms. Skipping. Residue THR 313 is missing expected H atoms. Skipping. Residue VAL 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue VAL 318 is missing expected H atoms. Skipping. Residue ILE 319 is missing expected H atoms. Skipping. Residue VAL 320 is missing expected H atoms. Skipping. Residue VAL 321 is missing expected H atoms. Skipping. Residue THR 326 is missing expected H atoms. Skipping. Residue LEU 328 is missing expected H atoms. Skipping. Residue SER 329 is missing expected H atoms. Skipping. Residue LEU 330 is missing expected H atoms. Skipping. Residue TYR 331 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 336 is missing expected H atoms. Skipping. Residue ALA 337 is missing expected H atoms. Skipping. Residue MET 339 is missing expected H atoms. Skipping. Residue VAL 340 is missing expected H atoms. Skipping. Residue LYS 341 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue VAL 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue LYS 373 is missing expected H atoms. Skipping. Residue ALA 374 is missing expected H atoms. Skipping. Residue LYS 383 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue MET 387 is missing expected H atoms. Skipping. Residue LEU 389 is missing expected H atoms. Skipping. Residue MET 390 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue LEU 394 is missing expected H atoms. Skipping. Residue MET 395 is missing expected H atoms. Skipping. Residue ALA 396 is missing expected H atoms. Skipping. Residue SER 398 is missing expected H atoms. Skipping. Residue LEU 400 is missing expected H atoms. Skipping. Residue SER 424 is missing expected H atoms. Skipping. Residue VAL 426 is missing expected H atoms. Skipping. Residue SER 465 is missing expected H atoms. Skipping. Residue SER 468 is missing expected H atoms. Skipping. Residue LEU 469 is missing expected H atoms. Skipping. Residue VAL 470 is missing expected H atoms. Skipping. Residue SER 471 is missing expected H atoms. Skipping. Residue LYS 472 is missing expected H atoms. Skipping. Residue SER 475 is missing expected H atoms. Skipping. Residue VAL 477 is missing expected H atoms. Skipping. Residue MET 478 is missing expected H atoms. Skipping. Residue THR 491 is missing expected H atoms. Skipping. Residue LYS 493 is missing expected H atoms. Skipping. Residue ALA 499 is missing expected H atoms. Skipping. Residue ALA 500 is missing expected H atoms. Skipping. Residue ILE 502 is missing expected H atoms. Skipping. Residue SER 510 is missing expected H atoms. Skipping. Residue ALA 511 is missing expected H atoms. Skipping. Residue ALA 513 is missing expected H atoms. Skipping. Residue SER 516 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Evaluate side-chains 427 residues out of total 2320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 351 time to evaluate : 2.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 GLU cc_start: 0.3456 (tp30) cc_final: 0.3212 (tm-30) REVERT: A 368 MET cc_start: 0.6711 (mmt) cc_final: 0.5480 (ttp) REVERT: A 721 ASP cc_start: 0.6997 (t70) cc_final: 0.6691 (t0) REVERT: A 903 ARG cc_start: 0.6305 (mpt90) cc_final: 0.3448 (mpt90) REVERT: A 1117 ARG cc_start: 0.8244 (ptt180) cc_final: 0.7916 (ptt180) REVERT: A 1326 GLN cc_start: 0.8131 (tt0) cc_final: 0.7799 (tt0) REVERT: A 1708 TRP cc_start: 0.6750 (m100) cc_final: 0.6512 (m100) REVERT: A 1842 CYS cc_start: 0.7690 (p) cc_final: 0.7363 (m) REVERT: A 1929 CYS cc_start: 0.7430 (m) cc_final: 0.7013 (t) REVERT: A 2326 MET cc_start: 0.7990 (mmp) cc_final: 0.7576 (mmp) REVERT: A 2393 ARG cc_start: 0.7649 (ptm-80) cc_final: 0.6486 (mtt180) REVERT: B 190 LYS cc_start: 0.8732 (OUTLIER) cc_final: 0.8316 (mtpt) REVERT: C 197 TYR cc_start: 0.8454 (m-80) cc_final: 0.8149 (m-80) outliers start: 76 outliers final: 62 residues processed: 394 average time/residue: 0.3298 time to fit residues: 199.2343 Evaluate side-chains 405 residues out of total 2320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 342 time to evaluate : 2.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 325 TRP Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 444 ASN Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 613 PHE Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 809 SER Chi-restraints excluded: chain A residue 833 ASN Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 989 ASN Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 1099 ILE Chi-restraints excluded: chain A residue 1316 ILE Chi-restraints excluded: chain A residue 1358 SER Chi-restraints excluded: chain A residue 1368 LEU Chi-restraints excluded: chain A residue 1423 GLU Chi-restraints excluded: chain A residue 1521 VAL Chi-restraints excluded: chain A residue 1599 PHE Chi-restraints excluded: chain A residue 1729 VAL Chi-restraints excluded: chain A residue 1753 THR Chi-restraints excluded: chain A residue 1816 THR Chi-restraints excluded: chain A residue 1858 TYR Chi-restraints excluded: chain A residue 2279 VAL Chi-restraints excluded: chain A residue 2327 VAL Chi-restraints excluded: chain A residue 2337 HIS Chi-restraints excluded: chain A residue 2367 VAL Chi-restraints excluded: chain A residue 2381 THR Chi-restraints excluded: chain A residue 2400 LEU Chi-restraints excluded: chain A residue 2403 MET Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 190 LYS Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 258 CYS Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 408 PHE Chi-restraints excluded: chain B residue 538 HIS Chi-restraints excluded: chain B residue 545 HIS Chi-restraints excluded: chain B residue 547 TYR Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 222 SER Chi-restraints excluded: chain C residue 281 HIS Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 380 CYS Chi-restraints excluded: chain C residue 405 THR Chi-restraints excluded: chain C residue 411 CYS Chi-restraints excluded: chain C residue 487 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 155 optimal weight: 5.9990 chunk 100 optimal weight: 0.5980 chunk 149 optimal weight: 4.9990 chunk 75 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 159 optimal weight: 10.0000 chunk 170 optimal weight: 0.0030 chunk 123 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 196 optimal weight: 4.9990 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 326 HIS ** A 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 600 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 858 HIS ** A 922 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 508 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 19855 Z= 0.155 Angle : 0.515 12.580 27014 Z= 0.272 Chirality : 0.036 0.191 3267 Planarity : 0.004 0.055 3422 Dihedral : 5.611 105.943 2743 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 67.83 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.88 % Favored : 88.08 % Rotamer: Outliers : 3.30 % Allowed : 17.21 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 1.66 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.18), residues: 2526 helix: 0.56 (0.15), residues: 1419 sheet: -2.62 (0.50), residues: 103 loop : -3.33 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1106 HIS 0.003 0.001 HIS A 329 PHE 0.013 0.001 PHE A 237 TYR 0.042 0.001 TYR A1670 ARG 0.005 0.000 ARG B 59 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 5 is missing expected H atoms. Skipping. Residue SER 6 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue VAL 49 is missing expected H atoms. Skipping. Residue VAL 50 is missing expected H atoms. Skipping. Residue ILE 52 is missing expected H atoms. Skipping. Residue LYS 55 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue ALA 57 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue LEU 137 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue ALA 140 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 142 is missing expected H atoms. Skipping. Residue SER 143 is missing expected H atoms. Skipping. Residue SER 146 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue VAL 148 is missing expected H atoms. Skipping. Residue LEU 149 is missing expected H atoms. Skipping. Residue TYR 150 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LEU 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue ALA 165 is missing expected H atoms. Skipping. Residue ALA 185 is missing expected H atoms. Skipping. Residue LYS 194 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue LEU 198 is missing expected H atoms. Skipping. Residue LEU 200 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue TYR 202 is missing expected H atoms. Skipping. Residue LEU 203 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue ILE 209 is missing expected H atoms. Skipping. Residue LEU 210 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue LEU 212 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue THR 216 is missing expected H atoms. Skipping. Residue SER 218 is missing expected H atoms. Skipping. Residue ILE 221 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue TYR 223 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue LEU 233 is missing expected H atoms. Skipping. Residue LYS 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue LEU 238 is missing expected H atoms. Skipping. Residue LEU 240 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue THR 243 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue LEU 300 is missing expected H atoms. Skipping. Residue ALA 303 is missing expected H atoms. Skipping. Residue LEU 304 is missing expected H atoms. Skipping. Residue ILE 308 is missing expected H atoms. Skipping. Residue TYR 309 is missing expected H atoms. Skipping. Residue ILE 311 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue SER 315 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue ALA 334 is missing expected H atoms. Skipping. Residue VAL 336 is missing expected H atoms. Skipping. Residue TYR 337 is missing expected H atoms. Skipping. Residue ILE 338 is missing expected H atoms. Skipping. Residue VAL 339 is missing expected H atoms. Skipping. Residue THR 409 is missing expected H atoms. Skipping. Residue VAL 418 is missing expected H atoms. Skipping. Residue LEU 420 is missing expected H atoms. Skipping. Residue THR 444 is missing expected H atoms. Skipping. Residue TYR 445 is missing expected H atoms. Skipping. Residue LYS 447 is missing expected H atoms. Skipping. Residue ILE 449 is missing expected H atoms. Skipping. Residue SER 450 is missing expected H atoms. Skipping. Residue ALA 451 is missing expected H atoms. Skipping. Residue SER 453 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LEU 455 is missing expected H atoms. Skipping. Residue TYR 456 is missing expected H atoms. Skipping. Residue VAL 458 is missing expected H atoms. Skipping. Residue ALA 459 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 493 is missing expected H atoms. Skipping. Residue LYS 494 is missing expected H atoms. Skipping. Residue SER 496 is missing expected H atoms. Skipping. Residue LEU 528 is missing expected H atoms. Skipping. Residue ALA 529 is missing expected H atoms. Skipping. Residue ALA 531 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue VAL 534 is missing expected H atoms. Skipping. Residue TYR 535 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue ALA 539 is missing expected H atoms. Skipping. Residue ALA 543 is missing expected H atoms. Skipping. Residue LYS 546 is missing expected H atoms. Skipping. Residue TYR 547 is missing expected H atoms. Skipping. Residue ALA 548 is missing expected H atoms. Skipping. Residue MET 549 is missing expected H atoms. Skipping. Residue LEU 551 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 181 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue LEU 183 is missing expected H atoms. Skipping. Residue VAL 184 is missing expected H atoms. Skipping. Residue MET 188 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue ALA 194 is missing expected H atoms. Skipping. Residue ILE 195 is missing expected H atoms. Skipping. Residue TYR 197 is missing expected H atoms. Skipping. Residue LEU 198 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue THR 202 is missing expected H atoms. Skipping. Residue VAL 204 is missing expected H atoms. Skipping. Residue LEU 205 is missing expected H atoms. Skipping. Residue VAL 207 is missing expected H atoms. Skipping. Residue VAL 209 is missing expected H atoms. Skipping. Residue LEU 210 is missing expected H atoms. Skipping. Residue LEU 212 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue VAL 220 is missing expected H atoms. Skipping. Residue MET 221 is missing expected H atoms. Skipping. Residue SER 225 is missing expected H atoms. Skipping. Residue ALA 226 is missing expected H atoms. Skipping. Residue THR 228 is missing expected H atoms. Skipping. Residue THR 235 is missing expected H atoms. Skipping. Residue ILE 256 is missing expected H atoms. Skipping. Residue ILE 265 is missing expected H atoms. Skipping. Residue VAL 266 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue TYR 299 is missing expected H atoms. Skipping. Residue VAL 300 is missing expected H atoms. Skipping. Residue MET 302 is missing expected H atoms. Skipping. Residue SER 304 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue ILE 307 is missing expected H atoms. Skipping. Residue ALA 308 is missing expected H atoms. Skipping. Residue ALA 309 is missing expected H atoms. Skipping. Residue LEU 311 is missing expected H atoms. Skipping. Residue THR 313 is missing expected H atoms. Skipping. Residue VAL 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue VAL 318 is missing expected H atoms. Skipping. Residue ILE 319 is missing expected H atoms. Skipping. Residue VAL 320 is missing expected H atoms. Skipping. Residue VAL 321 is missing expected H atoms. Skipping. Residue THR 326 is missing expected H atoms. Skipping. Residue LEU 328 is missing expected H atoms. Skipping. Residue SER 329 is missing expected H atoms. Skipping. Residue LEU 330 is missing expected H atoms. Skipping. Residue TYR 331 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 336 is missing expected H atoms. Skipping. Residue ALA 337 is missing expected H atoms. Skipping. Residue MET 339 is missing expected H atoms. Skipping. Residue VAL 340 is missing expected H atoms. Skipping. Residue LYS 341 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue VAL 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue LYS 373 is missing expected H atoms. Skipping. Residue ALA 374 is missing expected H atoms. Skipping. Residue LYS 383 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue MET 387 is missing expected H atoms. Skipping. Residue LEU 389 is missing expected H atoms. Skipping. Residue MET 390 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue LEU 394 is missing expected H atoms. Skipping. Residue MET 395 is missing expected H atoms. Skipping. Residue ALA 396 is missing expected H atoms. Skipping. Residue SER 398 is missing expected H atoms. Skipping. Residue LEU 400 is missing expected H atoms. Skipping. Residue SER 424 is missing expected H atoms. Skipping. Residue VAL 426 is missing expected H atoms. Skipping. Residue SER 465 is missing expected H atoms. Skipping. Residue SER 468 is missing expected H atoms. Skipping. Residue LEU 469 is missing expected H atoms. Skipping. Residue VAL 470 is missing expected H atoms. Skipping. Residue SER 471 is missing expected H atoms. Skipping. Residue LYS 472 is missing expected H atoms. Skipping. Residue SER 475 is missing expected H atoms. Skipping. Residue VAL 477 is missing expected H atoms. Skipping. Residue MET 478 is missing expected H atoms. Skipping. Residue THR 491 is missing expected H atoms. Skipping. Residue LYS 493 is missing expected H atoms. Skipping. Residue ALA 499 is missing expected H atoms. Skipping. Residue ALA 500 is missing expected H atoms. Skipping. Residue ILE 502 is missing expected H atoms. Skipping. Residue SER 510 is missing expected H atoms. Skipping. Residue ALA 511 is missing expected H atoms. Skipping. Residue ALA 513 is missing expected H atoms. Skipping. Residue SER 516 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Evaluate side-chains 421 residues out of total 2320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 354 time to evaluate : 2.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 368 MET cc_start: 0.6713 (mmt) cc_final: 0.5499 (ttp) REVERT: A 721 ASP cc_start: 0.6994 (t70) cc_final: 0.6694 (t0) REVERT: A 903 ARG cc_start: 0.6303 (mpt90) cc_final: 0.3416 (tpp-160) REVERT: A 1326 GLN cc_start: 0.8131 (tt0) cc_final: 0.7723 (tt0) REVERT: A 1635 ASP cc_start: 0.8187 (m-30) cc_final: 0.7853 (m-30) REVERT: A 1708 TRP cc_start: 0.6803 (m100) cc_final: 0.6534 (m100) REVERT: A 1842 CYS cc_start: 0.7626 (p) cc_final: 0.7090 (m) REVERT: A 1929 CYS cc_start: 0.7424 (m) cc_final: 0.6962 (t) REVERT: A 2207 TRP cc_start: 0.7898 (t-100) cc_final: 0.7367 (t60) REVERT: A 2326 MET cc_start: 0.7917 (mmp) cc_final: 0.7500 (mmp) REVERT: A 2393 ARG cc_start: 0.7668 (ptm-80) cc_final: 0.6518 (mtt180) REVERT: B 190 LYS cc_start: 0.8732 (OUTLIER) cc_final: 0.8318 (mtpt) REVERT: C 197 TYR cc_start: 0.8479 (m-80) cc_final: 0.8153 (m-80) outliers start: 67 outliers final: 61 residues processed: 390 average time/residue: 0.3365 time to fit residues: 200.1350 Evaluate side-chains 406 residues out of total 2320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 344 time to evaluate : 2.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 325 TRP Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 444 ASN Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 613 PHE Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 809 SER Chi-restraints excluded: chain A residue 833 ASN Chi-restraints excluded: chain A residue 981 VAL Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 989 ASN Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 1099 ILE Chi-restraints excluded: chain A residue 1118 PHE Chi-restraints excluded: chain A residue 1194 TYR Chi-restraints excluded: chain A residue 1309 GLN Chi-restraints excluded: chain A residue 1316 ILE Chi-restraints excluded: chain A residue 1358 SER Chi-restraints excluded: chain A residue 1368 LEU Chi-restraints excluded: chain A residue 1423 GLU Chi-restraints excluded: chain A residue 1521 VAL Chi-restraints excluded: chain A residue 1599 PHE Chi-restraints excluded: chain A residue 1729 VAL Chi-restraints excluded: chain A residue 1753 THR Chi-restraints excluded: chain A residue 1816 THR Chi-restraints excluded: chain A residue 1858 TYR Chi-restraints excluded: chain A residue 2193 TYR Chi-restraints excluded: chain A residue 2279 VAL Chi-restraints excluded: chain A residue 2337 HIS Chi-restraints excluded: chain A residue 2367 VAL Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 190 LYS Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 258 CYS Chi-restraints excluded: chain B residue 408 PHE Chi-restraints excluded: chain B residue 538 HIS Chi-restraints excluded: chain B residue 545 HIS Chi-restraints excluded: chain B residue 547 TYR Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 222 SER Chi-restraints excluded: chain C residue 281 HIS Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 380 CYS Chi-restraints excluded: chain C residue 405 THR Chi-restraints excluded: chain C residue 411 CYS Chi-restraints excluded: chain C residue 417 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 227 optimal weight: 0.7980 chunk 240 optimal weight: 1.9990 chunk 219 optimal weight: 4.9990 chunk 233 optimal weight: 0.3980 chunk 140 optimal weight: 0.5980 chunk 101 optimal weight: 2.9990 chunk 183 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 211 optimal weight: 0.9990 chunk 220 optimal weight: 3.9990 chunk 232 optimal weight: 0.5980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 600 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 922 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 61 ASN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 508 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.3678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 19855 Z= 0.160 Angle : 0.525 12.578 27014 Z= 0.276 Chirality : 0.036 0.187 3267 Planarity : 0.004 0.057 3422 Dihedral : 5.652 106.350 2743 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 68.56 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.36 % Favored : 88.56 % Rotamer: Outliers : 3.35 % Allowed : 17.75 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 1.66 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.18), residues: 2526 helix: 0.57 (0.15), residues: 1423 sheet: -2.51 (0.48), residues: 113 loop : -3.33 (0.19), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1106 HIS 0.003 0.001 HIS A 329 PHE 0.019 0.001 PHE A 240 TYR 0.044 0.001 TYR A1670 ARG 0.003 0.000 ARG A 316 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 5 is missing expected H atoms. Skipping. Residue SER 6 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue VAL 49 is missing expected H atoms. Skipping. Residue VAL 50 is missing expected H atoms. Skipping. Residue ILE 52 is missing expected H atoms. Skipping. Residue LYS 55 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue ALA 57 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue LEU 137 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue ALA 140 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 142 is missing expected H atoms. Skipping. Residue SER 143 is missing expected H atoms. Skipping. Residue SER 146 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue VAL 148 is missing expected H atoms. Skipping. Residue LEU 149 is missing expected H atoms. Skipping. Residue TYR 150 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LEU 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue ALA 165 is missing expected H atoms. Skipping. Residue ALA 185 is missing expected H atoms. Skipping. Residue LYS 194 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue LEU 198 is missing expected H atoms. Skipping. Residue LEU 200 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue TYR 202 is missing expected H atoms. Skipping. Residue LEU 203 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue ILE 209 is missing expected H atoms. Skipping. Residue LEU 210 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue LEU 212 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue THR 216 is missing expected H atoms. Skipping. Residue SER 218 is missing expected H atoms. Skipping. Residue ILE 221 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue TYR 223 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue LEU 233 is missing expected H atoms. Skipping. Residue LYS 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue LEU 238 is missing expected H atoms. Skipping. Residue LEU 240 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue THR 243 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue LEU 300 is missing expected H atoms. Skipping. Residue ALA 303 is missing expected H atoms. Skipping. Residue LEU 304 is missing expected H atoms. Skipping. Residue ILE 308 is missing expected H atoms. Skipping. Residue TYR 309 is missing expected H atoms. Skipping. Residue ILE 311 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue SER 315 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue ALA 334 is missing expected H atoms. Skipping. Residue VAL 336 is missing expected H atoms. Skipping. Residue TYR 337 is missing expected H atoms. Skipping. Residue ILE 338 is missing expected H atoms. Skipping. Residue VAL 339 is missing expected H atoms. Skipping. Residue THR 409 is missing expected H atoms. Skipping. Residue VAL 418 is missing expected H atoms. Skipping. Residue LEU 420 is missing expected H atoms. Skipping. Residue THR 444 is missing expected H atoms. Skipping. Residue TYR 445 is missing expected H atoms. Skipping. Residue LYS 447 is missing expected H atoms. Skipping. Residue ILE 449 is missing expected H atoms. Skipping. Residue SER 450 is missing expected H atoms. Skipping. Residue ALA 451 is missing expected H atoms. Skipping. Residue SER 453 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LEU 455 is missing expected H atoms. Skipping. Residue TYR 456 is missing expected H atoms. Skipping. Residue VAL 458 is missing expected H atoms. Skipping. Residue ALA 459 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 493 is missing expected H atoms. Skipping. Residue LYS 494 is missing expected H atoms. Skipping. Residue SER 496 is missing expected H atoms. Skipping. Residue LEU 528 is missing expected H atoms. Skipping. Residue ALA 529 is missing expected H atoms. Skipping. Residue ALA 531 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue VAL 534 is missing expected H atoms. Skipping. Residue TYR 535 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue ALA 539 is missing expected H atoms. Skipping. Residue ALA 543 is missing expected H atoms. Skipping. Residue LYS 546 is missing expected H atoms. Skipping. Residue TYR 547 is missing expected H atoms. Skipping. Residue ALA 548 is missing expected H atoms. Skipping. Residue MET 549 is missing expected H atoms. Skipping. Residue LEU 551 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 181 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue LEU 183 is missing expected H atoms. Skipping. Residue VAL 184 is missing expected H atoms. Skipping. Residue MET 188 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue ALA 194 is missing expected H atoms. Skipping. Residue ILE 195 is missing expected H atoms. Skipping. Residue TYR 197 is missing expected H atoms. Skipping. Residue LEU 198 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue THR 202 is missing expected H atoms. Skipping. Residue VAL 204 is missing expected H atoms. Skipping. Residue LEU 205 is missing expected H atoms. Skipping. Residue VAL 207 is missing expected H atoms. Skipping. Residue VAL 209 is missing expected H atoms. Skipping. Residue LEU 210 is missing expected H atoms. Skipping. Residue LEU 212 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue VAL 220 is missing expected H atoms. Skipping. Residue MET 221 is missing expected H atoms. Skipping. Residue SER 225 is missing expected H atoms. Skipping. Residue ALA 226 is missing expected H atoms. Skipping. Residue THR 228 is missing expected H atoms. Skipping. Residue THR 235 is missing expected H atoms. Skipping. Residue ILE 256 is missing expected H atoms. Skipping. Residue ILE 265 is missing expected H atoms. Skipping. Residue VAL 266 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue TYR 299 is missing expected H atoms. Skipping. Residue VAL 300 is missing expected H atoms. Skipping. Residue MET 302 is missing expected H atoms. Skipping. Residue SER 304 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue ILE 307 is missing expected H atoms. Skipping. Residue ALA 308 is missing expected H atoms. Skipping. Residue ALA 309 is missing expected H atoms. Skipping. Residue LEU 311 is missing expected H atoms. Skipping. Residue THR 313 is missing expected H atoms. Skipping. Residue VAL 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue VAL 318 is missing expected H atoms. Skipping. Residue ILE 319 is missing expected H atoms. Skipping. Residue VAL 320 is missing expected H atoms. Skipping. Residue VAL 321 is missing expected H atoms. Skipping. Residue THR 326 is missing expected H atoms. Skipping. Residue LEU 328 is missing expected H atoms. Skipping. Residue SER 329 is missing expected H atoms. Skipping. Residue LEU 330 is missing expected H atoms. Skipping. Residue TYR 331 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 336 is missing expected H atoms. Skipping. Residue ALA 337 is missing expected H atoms. Skipping. Residue MET 339 is missing expected H atoms. Skipping. Residue VAL 340 is missing expected H atoms. Skipping. Residue LYS 341 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue VAL 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue LYS 373 is missing expected H atoms. Skipping. Residue ALA 374 is missing expected H atoms. Skipping. Residue LYS 383 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue MET 387 is missing expected H atoms. Skipping. Residue LEU 389 is missing expected H atoms. Skipping. Residue MET 390 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue LEU 394 is missing expected H atoms. Skipping. Residue MET 395 is missing expected H atoms. Skipping. Residue ALA 396 is missing expected H atoms. Skipping. Residue SER 398 is missing expected H atoms. Skipping. Residue LEU 400 is missing expected H atoms. Skipping. Residue SER 424 is missing expected H atoms. Skipping. Residue VAL 426 is missing expected H atoms. Skipping. Residue SER 465 is missing expected H atoms. Skipping. Residue SER 468 is missing expected H atoms. Skipping. Residue LEU 469 is missing expected H atoms. Skipping. Residue VAL 470 is missing expected H atoms. Skipping. Residue SER 471 is missing expected H atoms. Skipping. Residue LYS 472 is missing expected H atoms. Skipping. Residue SER 475 is missing expected H atoms. Skipping. Residue VAL 477 is missing expected H atoms. Skipping. Residue MET 478 is missing expected H atoms. Skipping. Residue THR 491 is missing expected H atoms. Skipping. Residue LYS 493 is missing expected H atoms. Skipping. Residue ALA 499 is missing expected H atoms. Skipping. Residue ALA 500 is missing expected H atoms. Skipping. Residue ILE 502 is missing expected H atoms. Skipping. Residue SER 510 is missing expected H atoms. Skipping. Residue ALA 511 is missing expected H atoms. Skipping. Residue ALA 513 is missing expected H atoms. Skipping. Residue SER 516 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Evaluate side-chains 421 residues out of total 2320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 353 time to evaluate : 2.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 368 MET cc_start: 0.6835 (mmt) cc_final: 0.5580 (ttp) REVERT: A 721 ASP cc_start: 0.6939 (t70) cc_final: 0.6631 (t0) REVERT: A 903 ARG cc_start: 0.6373 (mpt90) cc_final: 0.3475 (tpp-160) REVERT: A 1326 GLN cc_start: 0.8120 (tt0) cc_final: 0.7729 (tt0) REVERT: A 1467 LYS cc_start: 0.7187 (mmtt) cc_final: 0.6697 (mmtt) REVERT: A 1635 ASP cc_start: 0.8189 (m-30) cc_final: 0.7852 (m-30) REVERT: A 1708 TRP cc_start: 0.6878 (m100) cc_final: 0.6558 (m100) REVERT: A 1842 CYS cc_start: 0.7655 (p) cc_final: 0.7118 (m) REVERT: A 1929 CYS cc_start: 0.7444 (m) cc_final: 0.6965 (t) REVERT: A 2207 TRP cc_start: 0.7902 (t-100) cc_final: 0.7369 (t60) REVERT: A 2326 MET cc_start: 0.7890 (mmp) cc_final: 0.7433 (mmp) REVERT: B 190 LYS cc_start: 0.8737 (OUTLIER) cc_final: 0.8315 (mtpt) outliers start: 68 outliers final: 63 residues processed: 390 average time/residue: 0.3346 time to fit residues: 200.3512 Evaluate side-chains 413 residues out of total 2320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 349 time to evaluate : 2.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 325 TRP Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 444 ASN Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 613 PHE Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 809 SER Chi-restraints excluded: chain A residue 833 ASN Chi-restraints excluded: chain A residue 922 GLN Chi-restraints excluded: chain A residue 942 THR Chi-restraints excluded: chain A residue 981 VAL Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 1099 ILE Chi-restraints excluded: chain A residue 1194 TYR Chi-restraints excluded: chain A residue 1309 GLN Chi-restraints excluded: chain A residue 1316 ILE Chi-restraints excluded: chain A residue 1358 SER Chi-restraints excluded: chain A residue 1368 LEU Chi-restraints excluded: chain A residue 1423 GLU Chi-restraints excluded: chain A residue 1521 VAL Chi-restraints excluded: chain A residue 1599 PHE Chi-restraints excluded: chain A residue 1729 VAL Chi-restraints excluded: chain A residue 1753 THR Chi-restraints excluded: chain A residue 1816 THR Chi-restraints excluded: chain A residue 1858 TYR Chi-restraints excluded: chain A residue 2193 TYR Chi-restraints excluded: chain A residue 2279 VAL Chi-restraints excluded: chain A residue 2337 HIS Chi-restraints excluded: chain A residue 2367 VAL Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 190 LYS Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 258 CYS Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 408 PHE Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 538 HIS Chi-restraints excluded: chain B residue 545 HIS Chi-restraints excluded: chain B residue 547 TYR Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 222 SER Chi-restraints excluded: chain C residue 281 HIS Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 380 CYS Chi-restraints excluded: chain C residue 405 THR Chi-restraints excluded: chain C residue 411 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 153 optimal weight: 0.9980 chunk 246 optimal weight: 0.0980 chunk 150 optimal weight: 1.9990 chunk 117 optimal weight: 0.0980 chunk 171 optimal weight: 0.9990 chunk 259 optimal weight: 2.9990 chunk 238 optimal weight: 0.1980 chunk 206 optimal weight: 0.6980 chunk 21 optimal weight: 6.9990 chunk 159 optimal weight: 8.9990 chunk 126 optimal weight: 6.9990 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 ASN A 326 HIS ** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 600 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 922 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 977 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 508 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.3707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 19855 Z= 0.131 Angle : 0.516 12.606 27014 Z= 0.270 Chirality : 0.036 0.174 3267 Planarity : 0.004 0.084 3422 Dihedral : 5.607 107.258 2743 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 67.83 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.16 % Favored : 88.80 % Rotamer: Outliers : 2.96 % Allowed : 18.15 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 1.66 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.18), residues: 2526 helix: 0.66 (0.15), residues: 1422 sheet: -2.47 (0.50), residues: 103 loop : -3.23 (0.19), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1106 HIS 0.002 0.000 HIS A 329 PHE 0.034 0.001 PHE A1015 TYR 0.046 0.001 TYR A1670 ARG 0.005 0.000 ARG B 59 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 5 is missing expected H atoms. Skipping. Residue SER 6 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue VAL 49 is missing expected H atoms. Skipping. Residue VAL 50 is missing expected H atoms. Skipping. Residue ILE 52 is missing expected H atoms. Skipping. Residue LYS 55 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue ALA 57 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue LEU 137 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue ALA 140 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 142 is missing expected H atoms. Skipping. Residue SER 143 is missing expected H atoms. Skipping. Residue SER 146 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue VAL 148 is missing expected H atoms. Skipping. Residue LEU 149 is missing expected H atoms. Skipping. Residue TYR 150 is missing expected H atoms. Skipping. Residue ILE 156 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LEU 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue ALA 165 is missing expected H atoms. Skipping. Residue ALA 185 is missing expected H atoms. Skipping. Residue LYS 194 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue LEU 198 is missing expected H atoms. Skipping. Residue LEU 200 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue TYR 202 is missing expected H atoms. Skipping. Residue LEU 203 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue ILE 209 is missing expected H atoms. Skipping. Residue LEU 210 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue LEU 212 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue THR 216 is missing expected H atoms. Skipping. Residue SER 218 is missing expected H atoms. Skipping. Residue ILE 221 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue TYR 223 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue LEU 233 is missing expected H atoms. Skipping. Residue LYS 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue LEU 238 is missing expected H atoms. Skipping. Residue LEU 240 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue THR 243 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue LEU 300 is missing expected H atoms. Skipping. Residue ALA 303 is missing expected H atoms. Skipping. Residue LEU 304 is missing expected H atoms. Skipping. Residue ILE 308 is missing expected H atoms. Skipping. Residue TYR 309 is missing expected H atoms. Skipping. Residue ILE 311 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue SER 315 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue ALA 334 is missing expected H atoms. Skipping. Residue VAL 336 is missing expected H atoms. Skipping. Residue TYR 337 is missing expected H atoms. Skipping. Residue ILE 338 is missing expected H atoms. Skipping. Residue VAL 339 is missing expected H atoms. Skipping. Residue THR 409 is missing expected H atoms. Skipping. Residue VAL 418 is missing expected H atoms. Skipping. Residue LEU 420 is missing expected H atoms. Skipping. Residue THR 444 is missing expected H atoms. Skipping. Residue TYR 445 is missing expected H atoms. Skipping. Residue LYS 447 is missing expected H atoms. Skipping. Residue ILE 449 is missing expected H atoms. Skipping. Residue SER 450 is missing expected H atoms. Skipping. Residue ALA 451 is missing expected H atoms. Skipping. Residue SER 453 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LEU 455 is missing expected H atoms. Skipping. Residue TYR 456 is missing expected H atoms. Skipping. Residue VAL 458 is missing expected H atoms. Skipping. Residue ALA 459 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue THR 493 is missing expected H atoms. Skipping. Residue LYS 494 is missing expected H atoms. Skipping. Residue SER 496 is missing expected H atoms. Skipping. Residue LEU 528 is missing expected H atoms. Skipping. Residue ALA 529 is missing expected H atoms. Skipping. Residue ALA 531 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue VAL 534 is missing expected H atoms. Skipping. Residue TYR 535 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue ALA 539 is missing expected H atoms. Skipping. Residue ALA 543 is missing expected H atoms. Skipping. Residue LYS 546 is missing expected H atoms. Skipping. Residue TYR 547 is missing expected H atoms. Skipping. Residue ALA 548 is missing expected H atoms. Skipping. Residue MET 549 is missing expected H atoms. Skipping. Residue LEU 551 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue ILE 181 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue LEU 183 is missing expected H atoms. Skipping. Residue VAL 184 is missing expected H atoms. Skipping. Residue MET 188 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue ALA 194 is missing expected H atoms. Skipping. Residue ILE 195 is missing expected H atoms. Skipping. Residue TYR 197 is missing expected H atoms. Skipping. Residue LEU 198 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue THR 202 is missing expected H atoms. Skipping. Residue VAL 204 is missing expected H atoms. Skipping. Residue LEU 205 is missing expected H atoms. Skipping. Residue VAL 207 is missing expected H atoms. Skipping. Residue VAL 209 is missing expected H atoms. Skipping. Residue LEU 210 is missing expected H atoms. Skipping. Residue LEU 212 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue VAL 220 is missing expected H atoms. Skipping. Residue MET 221 is missing expected H atoms. Skipping. Residue SER 225 is missing expected H atoms. Skipping. Residue ALA 226 is missing expected H atoms. Skipping. Residue THR 228 is missing expected H atoms. Skipping. Residue THR 235 is missing expected H atoms. Skipping. Residue ILE 256 is missing expected H atoms. Skipping. Residue ILE 265 is missing expected H atoms. Skipping. Residue VAL 266 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue TYR 299 is missing expected H atoms. Skipping. Residue VAL 300 is missing expected H atoms. Skipping. Residue MET 302 is missing expected H atoms. Skipping. Residue SER 304 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue ILE 307 is missing expected H atoms. Skipping. Residue ALA 308 is missing expected H atoms. Skipping. Residue ALA 309 is missing expected H atoms. Skipping. Residue LEU 311 is missing expected H atoms. Skipping. Residue THR 313 is missing expected H atoms. Skipping. Residue VAL 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue VAL 318 is missing expected H atoms. Skipping. Residue ILE 319 is missing expected H atoms. Skipping. Residue VAL 320 is missing expected H atoms. Skipping. Residue VAL 321 is missing expected H atoms. Skipping. Residue THR 326 is missing expected H atoms. Skipping. Residue LEU 328 is missing expected H atoms. Skipping. Residue SER 329 is missing expected H atoms. Skipping. Residue LEU 330 is missing expected H atoms. Skipping. Residue TYR 331 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue THR 336 is missing expected H atoms. Skipping. Residue ALA 337 is missing expected H atoms. Skipping. Residue MET 339 is missing expected H atoms. Skipping. Residue VAL 340 is missing expected H atoms. Skipping. Residue LYS 341 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue VAL 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue LYS 373 is missing expected H atoms. Skipping. Residue ALA 374 is missing expected H atoms. Skipping. Residue LYS 383 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue MET 387 is missing expected H atoms. Skipping. Residue LEU 389 is missing expected H atoms. Skipping. Residue MET 390 is missing expected H atoms. Skipping. Residue ILE 391 is missing expected H atoms. Skipping. Residue LEU 394 is missing expected H atoms. Skipping. Residue MET 395 is missing expected H atoms. Skipping. Residue ALA 396 is missing expected H atoms. Skipping. Residue SER 398 is missing expected H atoms. Skipping. Residue LEU 400 is missing expected H atoms. Skipping. Residue SER 424 is missing expected H atoms. Skipping. Residue VAL 426 is missing expected H atoms. Skipping. Residue SER 465 is missing expected H atoms. Skipping. Residue SER 468 is missing expected H atoms. Skipping. Residue LEU 469 is missing expected H atoms. Skipping. Residue VAL 470 is missing expected H atoms. Skipping. Residue SER 471 is missing expected H atoms. Skipping. Residue LYS 472 is missing expected H atoms. Skipping. Residue SER 475 is missing expected H atoms. Skipping. Residue VAL 477 is missing expected H atoms. Skipping. Residue MET 478 is missing expected H atoms. Skipping. Residue THR 491 is missing expected H atoms. Skipping. Residue LYS 493 is missing expected H atoms. Skipping. Residue ALA 499 is missing expected H atoms. Skipping. Residue ALA 500 is missing expected H atoms. Skipping. Residue ILE 502 is missing expected H atoms. Skipping. Residue SER 510 is missing expected H atoms. Skipping. Residue ALA 511 is missing expected H atoms. Skipping. Residue ALA 513 is missing expected H atoms. Skipping. Residue SER 516 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Evaluate side-chains 418 residues out of total 2320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 358 time to evaluate : 2.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 368 MET cc_start: 0.6725 (mmt) cc_final: 0.5523 (ttp) REVERT: A 721 ASP cc_start: 0.6995 (t70) cc_final: 0.6684 (t0) REVERT: A 903 ARG cc_start: 0.6209 (mpt90) cc_final: 0.3369 (tpp-160) REVERT: A 1467 LYS cc_start: 0.7175 (mmtt) cc_final: 0.6600 (mmtt) REVERT: A 1635 ASP cc_start: 0.8198 (m-30) cc_final: 0.7865 (m-30) REVERT: A 1708 TRP cc_start: 0.6910 (m100) cc_final: 0.6559 (m100) REVERT: A 1795 LEU cc_start: 0.8665 (tp) cc_final: 0.8353 (tp) REVERT: A 1842 CYS cc_start: 0.7663 (p) cc_final: 0.7116 (m) REVERT: A 1929 CYS cc_start: 0.7436 (m) cc_final: 0.6940 (t) REVERT: A 2207 TRP cc_start: 0.7879 (t-100) cc_final: 0.7357 (t60) REVERT: A 2326 MET cc_start: 0.7793 (mmp) cc_final: 0.7393 (mmp) REVERT: B 190 LYS cc_start: 0.8741 (OUTLIER) cc_final: 0.8328 (mtpt) outliers start: 60 outliers final: 55 residues processed: 389 average time/residue: 0.3306 time to fit residues: 195.3905 Evaluate side-chains 405 residues out of total 2320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 349 time to evaluate : 2.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 257 TYR Chi-restraints excluded: chain A residue 325 TRP Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 444 ASN Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 613 PHE Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 809 SER Chi-restraints excluded: chain A residue 833 ASN Chi-restraints excluded: chain A residue 942 THR Chi-restraints excluded: chain A residue 981 VAL Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 1118 PHE Chi-restraints excluded: chain A residue 1136 ASP Chi-restraints excluded: chain A residue 1316 ILE Chi-restraints excluded: chain A residue 1358 SER Chi-restraints excluded: chain A residue 1368 LEU Chi-restraints excluded: chain A residue 1423 GLU Chi-restraints excluded: chain A residue 1521 VAL Chi-restraints excluded: chain A residue 1599 PHE Chi-restraints excluded: chain A residue 1816 THR Chi-restraints excluded: chain A residue 1858 TYR Chi-restraints excluded: chain A residue 2193 TYR Chi-restraints excluded: chain A residue 2279 VAL Chi-restraints excluded: chain A residue 2337 HIS Chi-restraints excluded: chain A residue 2367 VAL Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 190 LYS Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 258 CYS Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 408 PHE Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 538 HIS Chi-restraints excluded: chain B residue 545 HIS Chi-restraints excluded: chain B residue 547 TYR Chi-restraints excluded: chain C residue 222 SER Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 380 CYS Chi-restraints excluded: chain C residue 405 THR Chi-restraints excluded: chain C residue 411 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 163 optimal weight: 0.8980 chunk 219 optimal weight: 5.9990 chunk 63 optimal weight: 0.8980 chunk 190 optimal weight: 4.9990 chunk 30 optimal weight: 0.0060 chunk 57 optimal weight: 0.4980 chunk 206 optimal weight: 0.6980 chunk 86 optimal weight: 10.0000 chunk 212 optimal weight: 0.1980 chunk 26 optimal weight: 9.9990 chunk 38 optimal weight: 0.0060 overall best weight: 0.2812 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 577 ASN ** A 600 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 922 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 977 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 272 ASN ** B 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 508 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.139400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.118381 restraints weight = 55201.282| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 2.81 r_work: 0.3611 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.3720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 19855 Z= 0.123 Angle : 0.507 12.650 27014 Z= 0.265 Chirality : 0.036 0.206 3267 Planarity : 0.004 0.052 3422 Dihedral : 5.519 107.727 2743 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 68.01 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.81 % Favored : 89.15 % Rotamer: Outliers : 2.96 % Allowed : 18.24 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 1.66 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.18), residues: 2526 helix: 0.80 (0.15), residues: 1426 sheet: -2.33 (0.51), residues: 103 loop : -3.16 (0.20), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1106 HIS 0.004 0.000 HIS A2278 PHE 0.019 0.001 PHE A1015 TYR 0.046 0.001 TYR A1670 ARG 0.005 0.000 ARG A 316 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5306.33 seconds wall clock time: 96 minutes 28.34 seconds (5788.34 seconds total)