Starting phenix.real_space_refine on Thu Mar 21 23:37:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gap_8014/03_2024/5gap_8014.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gap_8014/03_2024/5gap_8014.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gap_8014/03_2024/5gap_8014.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gap_8014/03_2024/5gap_8014.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gap_8014/03_2024/5gap_8014.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gap_8014/03_2024/5gap_8014.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 143 5.49 5 S 121 5.16 5 C 19527 2.51 5 N 5491 2.21 5 O 6294 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 757": "OE1" <-> "OE2" Residue "A GLU 841": "OE1" <-> "OE2" Residue "A GLU 933": "OE1" <-> "OE2" Residue "A GLU 941": "OE1" <-> "OE2" Residue "A GLU 1037": "OE1" <-> "OE2" Residue "A GLU 1129": "OE1" <-> "OE2" Residue "A ARG 1163": "NH1" <-> "NH2" Residue "A GLU 1178": "OE1" <-> "OE2" Residue "A GLU 1180": "OE1" <-> "OE2" Residue "A GLU 1181": "OE1" <-> "OE2" Residue "A GLU 1189": "OE1" <-> "OE2" Residue "A GLU 1479": "OE1" <-> "OE2" Residue "A GLU 1708": "OE1" <-> "OE2" Residue "A GLU 1817": "OE1" <-> "OE2" Residue "A GLU 1927": "OE1" <-> "OE2" Residue "A ARG 1962": "NH1" <-> "NH2" Residue "A GLU 2052": "OE1" <-> "OE2" Residue "A GLU 2062": "OE1" <-> "OE2" Residue "A GLU 2078": "OE1" <-> "OE2" Residue "H GLU 166": "OE1" <-> "OE2" Residue "H ARG 290": "NH1" <-> "NH2" Residue "H ARG 337": "NH1" <-> "NH2" Residue "J GLU 251": "OE1" <-> "OE2" Residue "J GLU 317": "OE1" <-> "OE2" Residue "J ARG 392": "NH1" <-> "NH2" Residue "J GLU 470": "OE1" <-> "OE2" Residue "J GLU 555": "OE1" <-> "OE2" Residue "J ASP 588": "OD1" <-> "OD2" Residue "J ARG 659": "NH1" <-> "NH2" Residue "J GLU 713": "OE1" <-> "OE2" Residue "D GLU 66": "OE1" <-> "OE2" Residue "D GLU 72": "OE1" <-> "OE2" Residue "D ARG 122": "NH1" <-> "NH2" Residue "F ARG 55": "NH1" <-> "NH2" Residue "F GLU 153": "OE1" <-> "OE2" Residue "F GLU 156": "OE1" <-> "OE2" Residue "F GLU 162": "OE1" <-> "OE2" Residue "F GLU 212": "OE1" <-> "OE2" Residue "F GLU 271": "OE1" <-> "OE2" Residue "F GLU 276": "OE1" <-> "OE2" Residue "F GLU 352": "OE1" <-> "OE2" Residue "F ARG 380": "NH1" <-> "NH2" Residue "F GLU 392": "OE1" <-> "OE2" Residue "F GLU 397": "OE1" <-> "OE2" Residue "F GLU 406": "OE1" <-> "OE2" Residue "F ARG 429": "NH1" <-> "NH2" Residue "G GLU 282": "OE1" <-> "OE2" Residue "G GLU 332": "OE1" <-> "OE2" Residue "G ARG 371": "NH1" <-> "NH2" Residue "G GLU 386": "OE1" <-> "OE2" Residue "G GLU 393": "OE1" <-> "OE2" Residue "G GLU 429": "OE1" <-> "OE2" Residue "G GLU 461": "OE1" <-> "OE2" Residue "K ARG 46": "NH1" <-> "NH2" Residue "K GLU 50": "OE1" <-> "OE2" Residue "K GLU 62": "OE1" <-> "OE2" Residue "K GLU 122": "OE1" <-> "OE2" 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: 31576 Number of models: 1 Model: "" Number of chains: 12 Chain: "V" Number of atoms: 1426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1426 Classifications: {'RNA': 67} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 5, 'rna3p_pur': 29, 'rna3p_pyr': 28} Link IDs: {'rna2p': 10, 'rna3p': 56} Chain: "W" Number of atoms: 1190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 1190 Classifications: {'RNA': 56} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 2, 'rna3p_pur': 25, 'rna3p_pyr': 25} Link IDs: {'rna2p': 6, 'rna3p': 49} Chain breaks: 2 Chain: "U" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 414 Classifications: {'RNA': 20} Modifications used: {'rna2p_pyr': 2, 'rna3p_pur': 6, 'rna3p_pyr': 12} Link IDs: {'rna2p': 2, 'rna3p': 17} Chain: "x" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 410 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 82} Link IDs: {'TRANS': 81} Chain breaks: 1 Unresolved non-hydrogen bonds: 164 Unresolved non-hydrogen angles: 246 Unresolved non-hydrogen dihedrals: 82 Planarities with less than four sites: {'UNK:plan-1': 82} Unresolved non-hydrogen planarities: 82 Chain: "A" Number of atoms: 11066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1349, 11066 Classifications: {'peptide': 1349} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 56, 'TRANS': 1289} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 2789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2789 Classifications: {'peptide': 357} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 348} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "J" Number of atoms: 5822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 729, 5822 Classifications: {'peptide': 729} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'CIS': 2, 'PTRANS': 26, 'TRANS': 700} Chain breaks: 4 Unresolved non-hydrogen bonds: 145 Unresolved non-hydrogen angles: 175 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 100 Chain: "D" Number of atoms: 1151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1151 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain: "F" Number of atoms: 3218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3218 Classifications: {'peptide': 415} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 15, 'TRANS': 396} Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 9, 'ARG:plan': 1, 'PHE:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 63 Chain: "G" Number of atoms: 2632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2632 Classifications: {'peptide': 318} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 12, 'TRANS': 305} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "K" Number of atoms: 936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 936 Classifications: {'peptide': 124} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 115} Chain: "B" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 522 Classifications: {'peptide': 71} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 5, 'TRANS': 65} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 37 Time building chain proxies: 15.57, per 1000 atoms: 0.49 Number of scatterers: 31576 At special positions: 0 Unit cell: (183.04, 155.87, 150.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 121 16.00 P 143 15.00 O 6294 8.00 N 5491 7.00 C 19527 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 14.59 Conformation dependent library (CDL) restraints added in 4.8 seconds 6950 Ramachandran restraints generated. 3475 Oldfield, 0 Emsley, 3475 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6876 Finding SS restraints... Secondary structure from input PDB file: 153 helices and 19 sheets defined 59.4% alpha, 9.2% beta 44 base pairs and 69 stacking pairs defined. Time for finding SS restraints: 10.64 Creating SS restraints... Processing helix chain 'x' and resid 21 through 46 Processing helix chain 'x' and resid 53 through 62 Processing helix chain 'x' and resid 102 through 120 Processing helix chain 'A' and resid 752 through 770 removed outlier: 4.196A pdb=" N LEU A 756 " --> pdb=" O ALA A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 774 through 796 removed outlier: 3.664A pdb=" N LYS A 778 " --> pdb=" O ILE A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 837 removed outlier: 3.765A pdb=" N SER A 825 " --> pdb=" O ASP A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 843 through 871 Processing helix chain 'A' and resid 875 through 894 Processing helix chain 'A' and resid 908 through 926 removed outlier: 4.207A pdb=" N VAL A 922 " --> pdb=" O ASP A 918 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N TYR A 923 " --> pdb=" O LEU A 919 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N SER A 925 " --> pdb=" O ASP A 921 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N LYS A 926 " --> pdb=" O VAL A 922 " (cutoff:3.500A) Processing helix chain 'A' and resid 930 through 946 Processing helix chain 'A' and resid 946 through 961 Processing helix chain 'A' and resid 985 through 1007 removed outlier: 3.665A pdb=" N ILE A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N THR A 991 " --> pdb=" O LEU A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1020 through 1034 Processing helix chain 'A' and resid 1057 through 1061 Processing helix chain 'A' and resid 1062 through 1074 removed outlier: 3.520A pdb=" N ILE A1073 " --> pdb=" O LEU A1069 " (cutoff:3.500A) Processing helix chain 'A' and resid 1075 through 1087 Processing helix chain 'A' and resid 1109 through 1127 Processing helix chain 'A' and resid 1127 through 1136 Processing helix chain 'A' and resid 1149 through 1156 removed outlier: 3.611A pdb=" N GLU A1153 " --> pdb=" O SER A1149 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N HIS A1156 " --> pdb=" O VAL A1152 " (cutoff:3.500A) Processing helix chain 'A' and resid 1175 through 1190 Processing helix chain 'A' and resid 1216 through 1234 Processing helix chain 'A' and resid 1273 through 1275 No H-bonds generated for 'chain 'A' and resid 1273 through 1275' Processing helix chain 'A' and resid 1305 through 1321 Processing helix chain 'A' and resid 1327 through 1347 Processing helix chain 'A' and resid 1348 through 1351 Processing helix chain 'A' and resid 1353 through 1376 Processing helix chain 'A' and resid 1385 through 1390 Processing helix chain 'A' and resid 1408 through 1413 removed outlier: 3.553A pdb=" N SER A1413 " --> pdb=" O SER A1410 " (cutoff:3.500A) Processing helix chain 'A' and resid 1439 through 1444 removed outlier: 3.924A pdb=" N ILE A1444 " --> pdb=" O PHE A1441 " (cutoff:3.500A) Processing helix chain 'A' and resid 1446 through 1471 Processing helix chain 'A' and resid 1490 through 1495 removed outlier: 4.227A pdb=" N LEU A1494 " --> pdb=" O ARG A1490 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N PHE A1495 " --> pdb=" O ILE A1491 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1490 through 1495' Processing helix chain 'A' and resid 1498 through 1503 Processing helix chain 'A' and resid 1507 through 1515 Processing helix chain 'A' and resid 1516 through 1518 No H-bonds generated for 'chain 'A' and resid 1516 through 1518' Processing helix chain 'A' and resid 1529 through 1534 Processing helix chain 'A' and resid 1539 through 1550 Processing helix chain 'A' and resid 1551 through 1560 removed outlier: 4.058A pdb=" N THR A1555 " --> pdb=" O GLY A1551 " (cutoff:3.500A) Processing helix chain 'A' and resid 1562 through 1566 Processing helix chain 'A' and resid 1577 through 1586 Processing helix chain 'A' and resid 1591 through 1615 Proline residue: A1602 - end of helix Proline residue: A1612 - end of helix Processing helix chain 'A' and resid 1638 through 1649 Processing helix chain 'A' and resid 1652 through 1672 Processing helix chain 'A' and resid 1672 through 1677 removed outlier: 4.096A pdb=" N LEU A1676 " --> pdb=" O GLU A1672 " (cutoff:3.500A) Processing helix chain 'A' and resid 1687 through 1693 removed outlier: 4.432A pdb=" N SER A1691 " --> pdb=" O PRO A1688 " (cutoff:3.500A) Processing helix chain 'A' and resid 1747 through 1762 removed outlier: 3.709A pdb=" N THR A1761 " --> pdb=" O LEU A1757 " (cutoff:3.500A) Processing helix chain 'A' and resid 1793 through 1809 removed outlier: 3.787A pdb=" N LEU A1797 " --> pdb=" O GLY A1793 " (cutoff:3.500A) Processing helix chain 'A' and resid 1809 through 1824 Processing helix chain 'A' and resid 1840 through 1845 removed outlier: 3.600A pdb=" N ASN A1845 " --> pdb=" O GLU A1842 " (cutoff:3.500A) Processing helix chain 'A' and resid 1895 through 1900 Processing helix chain 'A' and resid 1904 through 1924 Processing helix chain 'A' and resid 1937 through 1939 No H-bonds generated for 'chain 'A' and resid 1937 through 1939' Processing helix chain 'A' and resid 1940 through 1948 Processing helix chain 'A' and resid 1963 through 1969 removed outlier: 4.200A pdb=" N SER A1966 " --> pdb=" O LEU A1963 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N MET A1969 " --> pdb=" O SER A1966 " (cutoff:3.500A) Processing helix chain 'A' and resid 1971 through 1981 Processing helix chain 'A' and resid 1994 through 1998 Processing helix chain 'A' and resid 2000 through 2018 Processing helix chain 'A' and resid 2018 through 2027 Processing helix chain 'A' and resid 2044 through 2068 Processing helix chain 'A' and resid 2074 through 2084 Processing helix chain 'A' and resid 2092 through 2104 Processing helix chain 'H' and resid 114 through 145 removed outlier: 3.890A pdb=" N PHE H 123 " --> pdb=" O PHE H 119 " (cutoff:3.500A) Processing helix chain 'H' and resid 147 through 164 removed outlier: 3.916A pdb=" N GLU H 151 " --> pdb=" O ASN H 147 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU H 152 " --> pdb=" O THR H 148 " (cutoff:3.500A) Processing helix chain 'J' and resid 159 through 170 Processing helix chain 'J' and resid 171 through 177 Processing helix chain 'J' and resid 186 through 198 Proline residue: J 194 - end of helix Processing helix chain 'J' and resid 206 through 210 Processing helix chain 'J' and resid 219 through 236 removed outlier: 3.689A pdb=" N LYS J 225 " --> pdb=" O GLU J 221 " (cutoff:3.500A) Processing helix chain 'J' and resid 241 through 255 removed outlier: 4.319A pdb=" N ARG J 255 " --> pdb=" O GLU J 251 " (cutoff:3.500A) Processing helix chain 'J' and resid 258 through 271 removed outlier: 3.645A pdb=" N ASN J 266 " --> pdb=" O LYS J 262 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU J 270 " --> pdb=" O ASN J 266 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N CYS J 271 " --> pdb=" O GLY J 267 " (cutoff:3.500A) Processing helix chain 'J' and resid 274 through 285 removed outlier: 3.641A pdb=" N TRP J 278 " --> pdb=" O SER J 274 " (cutoff:3.500A) Processing helix chain 'J' and resid 289 through 303 removed outlier: 3.523A pdb=" N ASN J 301 " --> pdb=" O ALA J 297 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE J 302 " --> pdb=" O THR J 298 " (cutoff:3.500A) Processing helix chain 'J' and resid 306 through 317 removed outlier: 4.195A pdb=" N TRP J 310 " --> pdb=" O SER J 306 " (cutoff:3.500A) Processing helix chain 'J' and resid 319 through 334 Processing helix chain 'J' and resid 337 through 348 removed outlier: 4.098A pdb=" N GLU J 348 " --> pdb=" O ALA J 344 " (cutoff:3.500A) Processing helix chain 'J' and resid 351 through 365 Processing helix chain 'J' and resid 368 through 380 removed outlier: 3.763A pdb=" N GLN J 379 " --> pdb=" O TYR J 375 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N SER J 380 " --> pdb=" O THR J 376 " (cutoff:3.500A) Processing helix chain 'J' and resid 381 through 395 removed outlier: 3.520A pdb=" N ILE J 394 " --> pdb=" O SER J 390 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU J 395 " --> pdb=" O PHE J 391 " (cutoff:3.500A) Processing helix chain 'J' and resid 401 through 410 removed outlier: 4.082A pdb=" N SER J 405 " --> pdb=" O ILE J 401 " (cutoff:3.500A) Processing helix chain 'J' and resid 422 through 435 removed outlier: 3.650A pdb=" N LYS J 426 " --> pdb=" O VAL J 422 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU J 432 " --> pdb=" O GLY J 428 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N SER J 433 " --> pdb=" O LEU J 429 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN J 435 " --> pdb=" O GLU J 431 " (cutoff:3.500A) Processing helix chain 'J' and resid 442 through 454 removed outlier: 3.666A pdb=" N LYS J 446 " --> pdb=" O SER J 442 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ALA J 450 " --> pdb=" O LYS J 446 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU J 451 " --> pdb=" O ARG J 447 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA J 454 " --> pdb=" O ALA J 450 " (cutoff:3.500A) Processing helix chain 'J' and resid 457 through 476 removed outlier: 3.589A pdb=" N ALA J 463 " --> pdb=" O LEU J 459 " (cutoff:3.500A) Processing helix chain 'J' and resid 479 through 491 removed outlier: 3.698A pdb=" N ASN J 483 " --> pdb=" O GLU J 479 " (cutoff:3.500A) Processing helix chain 'J' and resid 495 through 509 Processing helix chain 'J' and resid 511 through 526 Processing helix chain 'J' and resid 531 through 543 removed outlier: 3.947A pdb=" N THR J 543 " --> pdb=" O LEU J 539 " (cutoff:3.500A) Processing helix chain 'J' and resid 548 through 557 Processing helix chain 'J' and resid 559 through 572 Processing helix chain 'J' and resid 576 through 589 Processing helix chain 'J' and resid 594 through 608 removed outlier: 4.317A pdb=" N PHE J 598 " --> pdb=" O LEU J 594 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N PHE J 599 " --> pdb=" O ASP J 595 " (cutoff:3.500A) Processing helix chain 'J' and resid 609 through 624 removed outlier: 3.653A pdb=" N SER J 623 " --> pdb=" O GLN J 619 " (cutoff:3.500A) Processing helix chain 'J' and resid 625 through 627 No H-bonds generated for 'chain 'J' and resid 625 through 627' Processing helix chain 'J' and resid 633 through 649 removed outlier: 3.681A pdb=" N TYR J 637 " --> pdb=" O GLU J 633 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR J 639 " --> pdb=" O LEU J 635 " (cutoff:3.500A) Processing helix chain 'J' and resid 652 through 664 removed outlier: 4.380A pdb=" N LEU J 656 " --> pdb=" O ALA J 652 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU J 661 " --> pdb=" O ASN J 657 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LYS J 662 " --> pdb=" O GLU J 658 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE J 664 " --> pdb=" O CYS J 660 " (cutoff:3.500A) Processing helix chain 'J' and resid 667 through 681 removed outlier: 3.846A pdb=" N PHE J 671 " --> pdb=" O CYS J 667 " (cutoff:3.500A) Processing helix chain 'J' and resid 683 through 698 Processing helix chain 'J' and resid 701 through 715 removed outlier: 3.731A pdb=" N TRP J 705 " --> pdb=" O CYS J 701 " (cutoff:3.500A) Processing helix chain 'J' and resid 718 through 733 removed outlier: 3.831A pdb=" N ALA J 722 " --> pdb=" O ASN J 718 " (cutoff:3.500A) Processing helix chain 'J' and resid 737 through 750 Processing helix chain 'J' and resid 753 through 767 Processing helix chain 'J' and resid 770 through 784 removed outlier: 4.133A pdb=" N GLY J 784 " --> pdb=" O LEU J 780 " (cutoff:3.500A) Processing helix chain 'J' and resid 789 through 802 Processing helix chain 'J' and resid 804 through 819 Processing helix chain 'J' and resid 820 through 835 Processing helix chain 'J' and resid 839 through 852 removed outlier: 3.689A pdb=" N VAL J 843 " --> pdb=" O GLY J 839 " (cutoff:3.500A) Processing helix chain 'J' and resid 856 through 863 Processing helix chain 'J' and resid 871 through 880 Processing helix chain 'J' and resid 889 through 898 Processing helix chain 'D' and resid 11 through 22 removed outlier: 3.706A pdb=" N GLU D 22 " --> pdb=" O ALA D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 53 removed outlier: 3.713A pdb=" N GLU D 51 " --> pdb=" O SER D 47 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG D 52 " --> pdb=" O SER D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 127 Processing helix chain 'F' and resid 43 through 45 No H-bonds generated for 'chain 'F' and resid 43 through 45' Processing helix chain 'F' and resid 46 through 58 removed outlier: 3.592A pdb=" N LEU F 57 " --> pdb=" O LEU F 53 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA F 58 " --> pdb=" O PHE F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 78 Proline residue: F 75 - end of helix Processing helix chain 'F' and resid 79 through 87 Processing helix chain 'F' and resid 96 through 121 Proline residue: F 103 - end of helix Processing helix chain 'F' and resid 125 through 131 removed outlier: 4.416A pdb=" N SER F 129 " --> pdb=" O PRO F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 146 Processing helix chain 'F' and resid 155 through 164 removed outlier: 3.505A pdb=" N HIS F 160 " --> pdb=" O GLU F 156 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LEU F 161 " --> pdb=" O LEU F 157 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 182 Processing helix chain 'F' and resid 190 through 226 removed outlier: 4.494A pdb=" N SER F 223 " --> pdb=" O ALA F 219 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N ILE F 224 " --> pdb=" O SER F 220 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE F 225 " --> pdb=" O LYS F 221 " (cutoff:3.500A) Processing helix chain 'F' and resid 226 through 233 Processing helix chain 'F' and resid 234 through 246 Processing helix chain 'F' and resid 247 through 254 Processing helix chain 'F' and resid 255 through 260 removed outlier: 3.508A pdb=" N ILE F 259 " --> pdb=" O PRO F 255 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA F 260 " --> pdb=" O SER F 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 255 through 260' Processing helix chain 'F' and resid 282 through 287 removed outlier: 3.878A pdb=" N PHE F 286 " --> pdb=" O GLU F 282 " (cutoff:3.500A) Processing helix chain 'F' and resid 288 through 293 Processing helix chain 'F' and resid 298 through 320 Processing helix chain 'F' and resid 328 through 346 Processing helix chain 'F' and resid 369 through 380 removed outlier: 3.548A pdb=" N LYS F 374 " --> pdb=" O ARG F 370 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N TYR F 375 " --> pdb=" O LYS F 371 " (cutoff:3.500A) Processing helix chain 'F' and resid 382 through 389 Processing helix chain 'F' and resid 410 through 414 removed outlier: 3.772A pdb=" N SER F 413 " --> pdb=" O LEU F 410 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ASN F 414 " --> pdb=" O GLY F 411 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 410 through 414' Processing helix chain 'F' and resid 415 through 422 Processing helix chain 'F' and resid 438 through 457 Processing helix chain 'G' and resid 151 through 164 removed outlier: 3.697A pdb=" N HIS G 164 " --> pdb=" O TYR G 160 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 189 removed outlier: 3.944A pdb=" N MET G 181 " --> pdb=" O LYS G 177 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 200 removed outlier: 4.337A pdb=" N GLU G 198 " --> pdb=" O LYS G 195 " (cutoff:3.500A) Processing helix chain 'G' and resid 237 through 262 Processing helix chain 'G' and resid 289 through 330 removed outlier: 3.612A pdb=" N GLU G 325 " --> pdb=" O LYS G 321 " (cutoff:3.500A) Processing helix chain 'G' and resid 349 through 363 removed outlier: 3.846A pdb=" N ARG G 353 " --> pdb=" O ASN G 349 " (cutoff:3.500A) Processing helix chain 'G' and resid 385 through 398 Processing helix chain 'G' and resid 447 through 456 Processing helix chain 'G' and resid 457 through 459 No H-bonds generated for 'chain 'G' and resid 457 through 459' Processing helix chain 'K' and resid 13 through 30 Processing helix chain 'K' and resid 36 through 47 Processing helix chain 'K' and resid 60 through 64 Processing helix chain 'K' and resid 65 through 75 removed outlier: 4.240A pdb=" N LEU K 69 " --> pdb=" O LEU K 65 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 92 Processing helix chain 'K' and resid 110 through 126 removed outlier: 4.020A pdb=" N ILE K 126 " --> pdb=" O GLU K 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 370 Processing helix chain 'B' and resid 373 through 389 Processing helix chain 'B' and resid 399 through 407 Processing helix chain 'B' and resid 412 through 423 removed outlier: 4.191A pdb=" N THR B 416 " --> pdb=" O GLU B 412 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS B 417 " --> pdb=" O ALA B 413 " (cutoff:3.500A) Proline residue: B 421 - end of helix Processing helix chain 'B' and resid 425 through 433 Processing sheet with id=AA1, first strand: chain 'A' and resid 981 through 983 removed outlier: 6.293A pdb=" N VAL A 967 " --> pdb=" O ASN A1091 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1013 through 1014 removed outlier: 5.752A pdb=" N ILE A1158 " --> pdb=" O HIS A1173 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N HIS A1173 " --> pdb=" O ILE A1158 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER A1249 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1258 through 1262 Processing sheet with id=AA4, first strand: chain 'A' and resid 1414 through 1417 Processing sheet with id=AA5, first strand: chain 'A' and resid 1825 through 1827 Processing sheet with id=AA6, first strand: chain 'A' and resid 1678 through 1683 removed outlier: 6.776A pdb=" N GLU A1704 " --> pdb=" O GLU A1679 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N VAL A1681 " --> pdb=" O THR A1702 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N THR A1702 " --> pdb=" O VAL A1681 " (cutoff:3.500A) removed outlier: 11.892A pdb=" N ILE A1701 " --> pdb=" O GLN A1737 " (cutoff:3.500A) removed outlier: 11.143A pdb=" N GLN A1737 " --> pdb=" O ILE A1701 " (cutoff:3.500A) removed outlier: 12.291A pdb=" N MET A1703 " --> pdb=" O ASP A1735 " (cutoff:3.500A) removed outlier: 11.282A pdb=" N ASP A1735 " --> pdb=" O MET A1703 " (cutoff:3.500A) removed outlier: 11.289A pdb=" N SER A1705 " --> pdb=" O TRP A1733 " (cutoff:3.500A) removed outlier: 11.735A pdb=" N TRP A1733 " --> pdb=" O SER A1705 " (cutoff:3.500A) removed outlier: 11.031A pdb=" N HIS A1707 " --> pdb=" O LYS A1731 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N LYS A1731 " --> pdb=" O HIS A1707 " (cutoff:3.500A) removed outlier: 8.409A pdb=" N VAL A1773 " --> pdb=" O LYS A1731 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N TRP A1733 " --> pdb=" O VAL A1773 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N ILE A1775 " --> pdb=" O TRP A1733 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N ASP A1735 " --> pdb=" O ILE A1775 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ILE A1777 " --> pdb=" O ASP A1735 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N GLN A1737 " --> pdb=" O ILE A1777 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1955 through 1957 removed outlier: 6.029A pdb=" N LEU A1850 " --> pdb=" O ILE A1934 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N THR A1881 " --> pdb=" O PHE A1890 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 166 through 172 removed outlier: 5.419A pdb=" N LEU H 167 " --> pdb=" O ASN H 465 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N ASN H 465 " --> pdb=" O LEU H 167 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLY H 169 " --> pdb=" O LEU H 463 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N SER H 460 " --> pdb=" O GLY H 456 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLY H 456 " --> pdb=" O SER H 460 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU H 452 " --> pdb=" O TRP H 464 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 180 through 183 removed outlier: 3.622A pdb=" N GLN H 200 " --> pdb=" O THR H 192 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N VAL H 201 " --> pdb=" O LEU H 210 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLN H 208 " --> pdb=" O ASN H 203 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 221 through 225 removed outlier: 4.180A pdb=" N ALA H 223 " --> pdb=" O CYS H 237 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ILE H 243 " --> pdb=" O ASP H 260 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ASP H 260 " --> pdb=" O ILE H 243 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ASN H 245 " --> pdb=" O LEU H 258 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 268 through 273 Processing sheet with id=AB3, first strand: chain 'H' and resid 310 through 315 removed outlier: 3.569A pdb=" N SER H 340 " --> pdb=" O ASP H 335 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 354 through 357 removed outlier: 3.937A pdb=" N VAL H 375 " --> pdb=" O ASN H 387 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ASN H 387 " --> pdb=" O VAL H 375 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 396 through 400 removed outlier: 4.138A pdb=" N GLY H 414 " --> pdb=" O LEU H 418 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N LEU H 418 " --> pdb=" O GLY H 414 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ILE H 419 " --> pdb=" O SER H 432 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N SER H 432 " --> pdb=" O ILE H 419 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL H 421 " --> pdb=" O MET H 430 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 8 through 9 Processing sheet with id=AB7, first strand: chain 'G' and resid 366 through 371 Processing sheet with id=AB8, first strand: chain 'G' and resid 366 through 371 removed outlier: 3.907A pdb=" N TYR G 337 " --> pdb=" O LEU G 432 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 406 through 408 Processing sheet with id=AC1, first strand: chain 'K' and resid 33 through 35 removed outlier: 6.395A pdb=" N ALA K 100 " --> pdb=" O ILE K 52 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ILE K 52 " --> pdb=" O ALA K 100 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N ILE K 102 " --> pdb=" O GLU K 50 " (cutoff:3.500A) removed outlier: 8.745A pdb=" N VAL K 79 " --> pdb=" O GLU K 50 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ILE K 52 " --> pdb=" O VAL K 79 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N VAL K 81 " --> pdb=" O ILE K 52 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N MET K 54 " --> pdb=" O VAL K 81 " (cutoff:3.500A) 1576 hydrogen bonds defined for protein. 4578 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 105 hydrogen bonds 194 hydrogen bond angles 0 basepair planarities 44 basepair parallelities 69 stacking parallelities Total time for adding SS restraints: 16.06 Time building geometry restraints manager: 15.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4941 1.31 - 1.44: 9190 1.44 - 1.56: 17864 1.56 - 1.69: 301 1.69 - 1.82: 208 Bond restraints: 32504 Sorted by residual: bond pdb=" CA ASN A1369 " pdb=" C ASN A1369 " ideal model delta sigma weight residual 1.523 1.455 0.068 1.30e-02 5.92e+03 2.75e+01 bond pdb=" C ASN A1369 " pdb=" O ASN A1369 " ideal model delta sigma weight residual 1.237 1.181 0.056 1.17e-02 7.31e+03 2.28e+01 bond pdb=" CA ASP D 78 " pdb=" CB ASP D 78 " ideal model delta sigma weight residual 1.522 1.554 -0.032 7.00e-03 2.04e+04 2.08e+01 bond pdb=" N ILE F 222 " pdb=" CA ILE F 222 " ideal model delta sigma weight residual 1.461 1.508 -0.048 1.24e-02 6.50e+03 1.47e+01 bond pdb=" N ILE A 882 " pdb=" CA ILE A 882 " ideal model delta sigma weight residual 1.459 1.506 -0.047 1.23e-02 6.61e+03 1.46e+01 ... (remaining 32499 not shown) Histogram of bond angle deviations from ideal: 97.57 - 105.41: 1206 105.41 - 113.25: 17245 113.25 - 121.09: 15577 121.09 - 128.93: 10277 128.93 - 136.77: 354 Bond angle restraints: 44659 Sorted by residual: angle pdb=" C4' C U 95 " pdb=" C3' C U 95 " pdb=" O3' C U 95 " ideal model delta sigma weight residual 109.40 121.52 -12.12 1.50e+00 4.44e-01 6.52e+01 angle pdb=" O3' A W 49 " pdb=" C3' A W 49 " pdb=" C2' A W 49 " ideal model delta sigma weight residual 109.50 121.14 -11.64 1.50e+00 4.44e-01 6.03e+01 angle pdb=" N THR J 239 " pdb=" CA THR J 239 " pdb=" C THR J 239 " ideal model delta sigma weight residual 111.71 120.62 -8.91 1.15e+00 7.56e-01 6.00e+01 angle pdb=" CA ASN A1369 " pdb=" C ASN A1369 " pdb=" O ASN A1369 " ideal model delta sigma weight residual 120.55 112.66 7.89 1.06e+00 8.90e-01 5.55e+01 angle pdb=" O3' A V 17 " pdb=" C3' A V 17 " pdb=" C2' A V 17 " ideal model delta sigma weight residual 113.70 124.74 -11.04 1.50e+00 4.44e-01 5.41e+01 ... (remaining 44654 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.72: 18988 35.72 - 71.45: 855 71.45 - 107.17: 75 107.17 - 142.90: 3 142.90 - 178.62: 9 Dihedral angle restraints: 19930 sinusoidal: 9378 harmonic: 10552 Sorted by residual: dihedral pdb=" C5' G W 31 " pdb=" C4' G W 31 " pdb=" C3' G W 31 " pdb=" O3' G W 31 " ideal model delta sinusoidal sigma weight residual 147.00 72.33 74.67 1 8.00e+00 1.56e-02 1.10e+02 dihedral pdb=" C5' A W 49 " pdb=" C4' A W 49 " pdb=" C3' A W 49 " pdb=" O3' A W 49 " ideal model delta sinusoidal sigma weight residual 147.00 74.90 72.10 1 8.00e+00 1.56e-02 1.04e+02 dihedral pdb=" C5' U W 32 " pdb=" C4' U W 32 " pdb=" C3' U W 32 " pdb=" O3' U W 32 " ideal model delta sinusoidal sigma weight residual 147.00 77.26 69.74 1 8.00e+00 1.56e-02 9.81e+01 ... (remaining 19927 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.134: 4501 0.134 - 0.268: 561 0.268 - 0.401: 57 0.401 - 0.535: 11 0.535 - 0.669: 6 Chirality restraints: 5136 Sorted by residual: chirality pdb=" C3' U V 31 " pdb=" C4' U V 31 " pdb=" O3' U V 31 " pdb=" C2' U V 31 " both_signs ideal model delta sigma weight residual False -2.74 -2.08 -0.67 2.00e-01 2.50e+01 1.12e+01 chirality pdb=" C3' C V 39 " pdb=" C4' C V 39 " pdb=" O3' C V 39 " pdb=" C2' C V 39 " both_signs ideal model delta sigma weight residual False -2.74 -2.16 -0.58 2.00e-01 2.50e+01 8.51e+00 chirality pdb=" C3' C W 84 " pdb=" C4' C W 84 " pdb=" O3' C W 84 " pdb=" C2' C W 84 " both_signs ideal model delta sigma weight residual False -2.74 -2.17 -0.57 2.00e-01 2.50e+01 8.23e+00 ... (remaining 5133 not shown) Planarity restraints: 5181 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 979 " 0.091 5.00e-02 4.00e+02 1.41e-01 3.17e+01 pdb=" N PRO A 980 " -0.243 5.00e-02 4.00e+02 pdb=" CA PRO A 980 " 0.086 5.00e-02 4.00e+02 pdb=" CD PRO A 980 " 0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' G V 44 " 0.078 2.00e-02 2.50e+03 3.17e-02 3.01e+01 pdb=" N9 G V 44 " -0.068 2.00e-02 2.50e+03 pdb=" C8 G V 44 " -0.015 2.00e-02 2.50e+03 pdb=" N7 G V 44 " -0.000 2.00e-02 2.50e+03 pdb=" C5 G V 44 " -0.003 2.00e-02 2.50e+03 pdb=" C6 G V 44 " 0.010 2.00e-02 2.50e+03 pdb=" O6 G V 44 " 0.023 2.00e-02 2.50e+03 pdb=" N1 G V 44 " 0.010 2.00e-02 2.50e+03 pdb=" C2 G V 44 " -0.006 2.00e-02 2.50e+03 pdb=" N2 G V 44 " -0.005 2.00e-02 2.50e+03 pdb=" N3 G V 44 " -0.015 2.00e-02 2.50e+03 pdb=" C4 G V 44 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G V 14 " 0.005 2.00e-02 2.50e+03 2.86e-02 2.45e+01 pdb=" N9 G V 14 " 0.004 2.00e-02 2.50e+03 pdb=" C8 G V 14 " -0.007 2.00e-02 2.50e+03 pdb=" N7 G V 14 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G V 14 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G V 14 " -0.004 2.00e-02 2.50e+03 pdb=" O6 G V 14 " 0.046 2.00e-02 2.50e+03 pdb=" N1 G V 14 " -0.079 2.00e-02 2.50e+03 pdb=" C2 G V 14 " -0.001 2.00e-02 2.50e+03 pdb=" N2 G V 14 " 0.037 2.00e-02 2.50e+03 pdb=" N3 G V 14 " 0.001 2.00e-02 2.50e+03 pdb=" C4 G V 14 " 0.000 2.00e-02 2.50e+03 ... (remaining 5178 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 757 2.69 - 3.25: 33406 3.25 - 3.80: 53173 3.80 - 4.35: 69491 4.35 - 4.90: 107447 Nonbonded interactions: 264274 Sorted by model distance: nonbonded pdb=" O ASP J 199 " pdb=" N LEU J 201 " model vdw 2.143 2.520 nonbonded pdb=" O ALA K 40 " pdb=" OG1 THR K 43 " model vdw 2.207 2.440 nonbonded pdb=" O2' A W 49 " pdb=" OP2 G W 50 " model vdw 2.225 2.440 nonbonded pdb=" OP2 A V 18 " pdb=" NZ LYS F 378 " model vdw 2.240 2.520 nonbonded pdb=" O PHE A1562 " pdb=" OG1 THR A1565 " model vdw 2.255 2.440 ... (remaining 264269 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 13.720 Check model and map are aligned: 0.490 Set scattering table: 0.280 Process input model: 93.640 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.120 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 114.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4837 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 : 0.008 0.071 32504 Z= 0.500 Angle : 1.510 15.387 44659 Z= 1.087 Chirality : 0.092 0.669 5136 Planarity : 0.007 0.141 5181 Dihedral : 18.891 178.621 13054 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 1.47 % Allowed : 8.81 % Favored : 89.73 % Rotamer: Outliers : 4.23 % Allowed : 8.96 % Favored : 86.81 % Cbeta Deviations : 0.76 % Peptide Plane: Cis-proline : 4.38 % Cis-general : 0.09 % Twisted Proline : 1.46 % Twisted General : 0.09 % 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: -1.15 (0.12), residues: 3475 helix: 1.00 (0.09), residues: 1799 sheet: -2.60 (0.23), residues: 371 loop : -2.79 (0.15), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP A 823 HIS 0.009 0.002 HIS G 316 PHE 0.052 0.003 PHE J 617 TYR 0.042 0.003 TYR J 564 ARG 0.018 0.001 ARG A 780 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6950 Ramachandran restraints generated. 3475 Oldfield, 0 Emsley, 3475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6950 Ramachandran restraints generated. 3475 Oldfield, 0 Emsley, 3475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1078 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 948 time to evaluate : 3.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 753 TYR cc_start: 0.4889 (OUTLIER) cc_final: 0.4528 (t80) REVERT: A 770 MET cc_start: 0.6032 (mtt) cc_final: 0.5320 (mtt) REVERT: A 778 LYS cc_start: 0.4636 (mmmt) cc_final: 0.4184 (tppt) REVERT: A 814 ARG cc_start: 0.7570 (tpp80) cc_final: 0.7351 (tpt170) REVERT: A 839 HIS cc_start: 0.6921 (t70) cc_final: 0.6320 (m-70) REVERT: A 868 GLN cc_start: 0.7009 (tp40) cc_final: 0.6668 (tt0) REVERT: A 1046 SER cc_start: 0.5614 (m) cc_final: 0.5270 (p) REVERT: A 1107 LEU cc_start: 0.5572 (mt) cc_final: 0.5259 (mt) REVERT: A 1151 GLU cc_start: 0.6609 (mp0) cc_final: 0.6409 (tm-30) REVERT: A 1166 ASP cc_start: 0.6308 (m-30) cc_final: 0.6053 (m-30) REVERT: A 1168 ILE cc_start: 0.5819 (pt) cc_final: 0.5541 (pt) REVERT: A 1186 TYR cc_start: 0.5540 (t80) cc_final: 0.4739 (t80) REVERT: A 1190 ASN cc_start: 0.6291 (m110) cc_final: 0.5676 (m-40) REVERT: A 1211 SER cc_start: 0.7919 (m) cc_final: 0.7589 (m) REVERT: A 1214 ARG cc_start: 0.6084 (mtt180) cc_final: 0.4894 (mmt180) REVERT: A 1218 GLN cc_start: 0.5694 (tt0) cc_final: 0.5351 (tm-30) REVERT: A 1240 SER cc_start: 0.5954 (t) cc_final: 0.5709 (p) REVERT: A 1253 LYS cc_start: 0.6800 (pttt) cc_final: 0.6504 (tttm) REVERT: A 1266 GLU cc_start: 0.5117 (mm-30) cc_final: 0.4832 (tp30) REVERT: A 1291 GLU cc_start: 0.6476 (mt-10) cc_final: 0.6269 (tp30) REVERT: A 1348 GLU cc_start: 0.6688 (tt0) cc_final: 0.6468 (tp30) REVERT: A 1404 HIS cc_start: 0.7250 (t70) cc_final: 0.7007 (t70) REVERT: A 1413 SER cc_start: 0.7330 (m) cc_final: 0.6960 (p) REVERT: A 1426 ARG cc_start: 0.6999 (mtp85) cc_final: 0.6497 (mtm110) REVERT: A 1458 TRP cc_start: 0.5251 (m100) cc_final: 0.5042 (m100) REVERT: A 1517 TYR cc_start: 0.6262 (m-80) cc_final: 0.5936 (m-80) REVERT: A 1585 MET cc_start: 0.5099 (tpt) cc_final: 0.4873 (tpp) REVERT: A 1586 GLN cc_start: 0.5610 (tt0) cc_final: 0.5387 (tt0) REVERT: A 1684 GLU cc_start: 0.5744 (mm-30) cc_final: 0.5259 (tm-30) REVERT: A 1719 GLU cc_start: 0.7004 (mm-30) cc_final: 0.6724 (tt0) REVERT: A 1721 ASN cc_start: 0.7244 (t0) cc_final: 0.7007 (p0) REVERT: A 1724 PHE cc_start: 0.5371 (m-80) cc_final: 0.4920 (m-80) REVERT: A 1731 LYS cc_start: 0.6378 (ttpt) cc_final: 0.6173 (ttpp) REVERT: A 1733 TRP cc_start: 0.6229 (p-90) cc_final: 0.5423 (p-90) REVERT: A 1747 ASP cc_start: 0.6268 (t0) cc_final: 0.5972 (t0) REVERT: A 1843 LEU cc_start: 0.7129 (mt) cc_final: 0.6859 (mt) REVERT: A 1885 LYS cc_start: 0.6774 (tptt) cc_final: 0.6288 (mmtp) REVERT: A 1915 GLU cc_start: 0.7720 (tt0) cc_final: 0.7306 (tm-30) REVERT: A 1926 LYS cc_start: 0.6250 (mmmt) cc_final: 0.6040 (mmtt) REVERT: A 1928 GLU cc_start: 0.7119 (mt-10) cc_final: 0.6745 (tp30) REVERT: A 1947 HIS cc_start: 0.5183 (m-70) cc_final: 0.4955 (m170) REVERT: A 1948 MET cc_start: 0.6853 (mmm) cc_final: 0.6595 (mmm) REVERT: A 1950 ASP cc_start: 0.7720 (m-30) cc_final: 0.7307 (t0) REVERT: A 1951 PHE cc_start: 0.6775 (m-80) cc_final: 0.6315 (m-80) REVERT: A 1998 ARG cc_start: 0.7802 (mtt180) cc_final: 0.7554 (mmm160) REVERT: A 2055 MET cc_start: 0.6660 (mmt) cc_final: 0.6450 (mmt) REVERT: A 2078 GLU cc_start: 0.6392 (tm-30) cc_final: 0.6142 (tm-30) REVERT: H 127 TYR cc_start: 0.6376 (t80) cc_final: 0.5915 (t80) REVERT: H 139 GLU cc_start: 0.7682 (mm-30) cc_final: 0.7406 (tt0) REVERT: H 158 GLU cc_start: 0.7093 (mt-10) cc_final: 0.6703 (pt0) REVERT: H 172 LEU cc_start: 0.6317 (pp) cc_final: 0.5770 (pp) REVERT: H 234 MET cc_start: 0.6043 (ptm) cc_final: 0.5776 (ppp) REVERT: H 274 HIS cc_start: 0.7097 (t-90) cc_final: 0.6817 (t-90) REVERT: H 280 ILE cc_start: 0.6329 (mt) cc_final: 0.5967 (mp) REVERT: H 331 SER cc_start: 0.8607 (OUTLIER) cc_final: 0.8398 (p) REVERT: H 334 TRP cc_start: 0.7250 (m100) cc_final: 0.6974 (m100) REVERT: H 335 ASP cc_start: 0.7443 (m-30) cc_final: 0.7115 (p0) REVERT: H 372 ILE cc_start: 0.5792 (mt) cc_final: 0.5586 (mt) REVERT: H 388 GLN cc_start: 0.6866 (mt0) cc_final: 0.6613 (mt0) REVERT: J 163 THR cc_start: 0.7637 (p) cc_final: 0.7410 (p) REVERT: J 182 THR cc_start: 0.5374 (p) cc_final: 0.4937 (p) REVERT: J 266 ASN cc_start: 0.6387 (m-40) cc_final: 0.6053 (t0) REVERT: J 290 HIS cc_start: 0.6996 (p-80) cc_final: 0.6575 (t70) REVERT: J 328 ARG cc_start: 0.7837 (ptp90) cc_final: 0.7415 (mtp85) REVERT: J 369 MET cc_start: 0.7075 (ttt) cc_final: 0.6566 (mmm) REVERT: J 492 MET cc_start: 0.5974 (ttm) cc_final: 0.5297 (mmt) REVERT: J 513 THR cc_start: 0.7121 (p) cc_final: 0.6896 (t) REVERT: J 550 ARG cc_start: 0.6284 (ptp-170) cc_final: 0.6045 (ptt-90) REVERT: J 565 VAL cc_start: 0.7544 (t) cc_final: 0.6608 (t) REVERT: J 569 TRP cc_start: 0.6720 (m100) cc_final: 0.6249 (m-10) REVERT: J 578 GLN cc_start: 0.6372 (pt0) cc_final: 0.5631 (mp10) REVERT: J 591 PRO cc_start: 0.4074 (Cg_exo) cc_final: 0.3432 (Cg_endo) REVERT: J 603 LEU cc_start: 0.8139 (mt) cc_final: 0.7821 (mm) REVERT: J 785 ASN cc_start: 0.6288 (m-40) cc_final: 0.5834 (t0) REVERT: J 799 ARG cc_start: 0.7418 (mtt180) cc_final: 0.7213 (mtm110) REVERT: J 809 LEU cc_start: 0.6349 (OUTLIER) cc_final: 0.6129 (tm) REVERT: J 810 GLU cc_start: 0.5810 (tp30) cc_final: 0.5488 (tp30) REVERT: J 873 GLU cc_start: 0.6821 (mt-10) cc_final: 0.6545 (tp30) REVERT: J 874 TRP cc_start: 0.6516 (OUTLIER) cc_final: 0.6030 (t-100) REVERT: D 17 GLN cc_start: 0.6348 (mm-40) cc_final: 0.6043 (tm-30) REVERT: D 22 GLU cc_start: 0.5849 (mm-30) cc_final: 0.5574 (mm-30) REVERT: D 36 ASP cc_start: 0.5889 (t70) cc_final: 0.5631 (t70) REVERT: D 51 GLU cc_start: 0.8024 (mm-30) cc_final: 0.7651 (pt0) REVERT: D 63 ASP cc_start: 0.5634 (t0) cc_final: 0.5195 (t70) REVERT: D 99 ASN cc_start: 0.4877 (t0) cc_final: 0.4628 (t0) REVERT: F 47 LEU cc_start: 0.5734 (pp) cc_final: 0.5509 (pp) REVERT: F 100 GLU cc_start: 0.7750 (tp30) cc_final: 0.7458 (mt-10) REVERT: F 120 TYR cc_start: 0.5991 (OUTLIER) cc_final: 0.4598 (t80) REVERT: F 144 LEU cc_start: 0.7635 (tp) cc_final: 0.7399 (mt) REVERT: F 145 GLU cc_start: 0.7477 (mm-30) cc_final: 0.6535 (pt0) REVERT: F 201 ASN cc_start: 0.6205 (t0) cc_final: 0.5905 (m110) REVERT: F 271 GLU cc_start: 0.6162 (tt0) cc_final: 0.5900 (pt0) REVERT: F 381 LEU cc_start: 0.7208 (mt) cc_final: 0.6962 (mt) REVERT: F 397 GLU cc_start: 0.7680 (mm-30) cc_final: 0.6849 (pt0) REVERT: F 398 GLN cc_start: 0.6061 (OUTLIER) cc_final: 0.5516 (tt0) REVERT: F 412 MET cc_start: 0.5189 (ttm) cc_final: 0.4699 (ttp) REVERT: F 419 GLN cc_start: 0.5720 (OUTLIER) cc_final: 0.5174 (pt0) REVERT: G 181 MET cc_start: 0.4903 (ttm) cc_final: 0.4447 (ttp) REVERT: G 196 LEU cc_start: 0.8395 (mp) cc_final: 0.8048 (mt) REVERT: G 282 GLU cc_start: 0.7319 (mt-10) cc_final: 0.7076 (mp0) REVERT: G 284 ASP cc_start: 0.5657 (m-30) cc_final: 0.5347 (t0) REVERT: G 329 MET cc_start: 0.5371 (OUTLIER) cc_final: 0.4921 (tmm) REVERT: G 353 ARG cc_start: 0.6053 (mtm180) cc_final: 0.5686 (ttm110) REVERT: G 397 MET cc_start: 0.6086 (mmm) cc_final: 0.5872 (mmm) REVERT: G 401 LYS cc_start: 0.7064 (mptt) cc_final: 0.6653 (mmmt) REVERT: G 403 ASN cc_start: 0.5790 (p0) cc_final: 0.5488 (t0) REVERT: G 417 MET cc_start: 0.5867 (mmt) cc_final: 0.5565 (tpp) REVERT: G 419 MET cc_start: 0.4014 (mmm) cc_final: 0.3736 (tpt) REVERT: G 420 HIS cc_start: 0.7548 (p90) cc_final: 0.7014 (p-80) REVERT: G 431 TYR cc_start: 0.6114 (m-80) cc_final: 0.5193 (m-10) REVERT: G 436 LYS cc_start: 0.6534 (mttt) cc_final: 0.6332 (mttp) REVERT: K 7 LYS cc_start: 0.7032 (mtpt) cc_final: 0.6373 (mmmt) REVERT: K 54 MET cc_start: 0.5092 (mtm) cc_final: 0.4441 (mtm) outliers start: 130 outliers final: 32 residues processed: 1036 average time/residue: 0.4825 time to fit residues: 760.8807 Evaluate side-chains 611 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 571 time to evaluate : 3.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 753 TYR Chi-restraints excluded: chain A residue 755 ASP Chi-restraints excluded: chain A residue 950 THR Chi-restraints excluded: chain A residue 1827 GLN Chi-restraints excluded: chain H residue 146 PHE Chi-restraints excluded: chain H residue 232 ASN Chi-restraints excluded: chain H residue 286 ASP Chi-restraints excluded: chain H residue 300 LEU Chi-restraints excluded: chain H residue 322 VAL Chi-restraints excluded: chain H residue 331 SER Chi-restraints excluded: chain H residue 389 ILE Chi-restraints excluded: chain J residue 194 PRO Chi-restraints excluded: chain J residue 239 THR Chi-restraints excluded: chain J residue 459 LEU Chi-restraints excluded: chain J residue 498 GLN Chi-restraints excluded: chain J residue 657 ASN Chi-restraints excluded: chain J residue 661 LEU Chi-restraints excluded: chain J residue 708 LEU Chi-restraints excluded: chain J residue 767 PHE Chi-restraints excluded: chain J residue 782 LYS Chi-restraints excluded: chain J residue 809 LEU Chi-restraints excluded: chain J residue 874 TRP Chi-restraints excluded: chain D residue 39 CYS Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 48 SER Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 117 ILE Chi-restraints excluded: chain F residue 120 TYR Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 391 MET Chi-restraints excluded: chain F residue 398 GLN Chi-restraints excluded: chain F residue 419 GLN Chi-restraints excluded: chain G residue 329 MET Chi-restraints excluded: chain G residue 341 VAL Chi-restraints excluded: chain G residue 395 LEU Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 64 LEU Chi-restraints excluded: chain B residue 390 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 309 optimal weight: 0.9980 chunk 278 optimal weight: 5.9990 chunk 154 optimal weight: 2.9990 chunk 95 optimal weight: 0.5980 chunk 187 optimal weight: 0.0170 chunk 148 optimal weight: 0.0470 chunk 287 optimal weight: 2.9990 chunk 111 optimal weight: 0.6980 chunk 174 optimal weight: 2.9990 chunk 214 optimal weight: 0.0980 chunk 333 optimal weight: 5.9990 overall best weight: 0.2916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 861 GLN A1030 GLN A1086 ASN A1087 ASN A1190 ASN A1368 GLN A1635 HIS A1677 GLN ** A1687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1831 GLN A1856 ASN A1869 ASN A2054 GLN ** H 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 303 GLN H 316 GLN ** H 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 392 HIS J 184 ASN J 363 GLN J 507 GLN J 578 GLN J 676 GLN J 733 ASN ** F 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 148 ASN F 160 HIS F 201 ASN F 270 HIS F 292 GLN F 299 HIS F 320 GLN F 383 HIS F 419 GLN F 451 GLN G 276 ASN K 45 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4847 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 32504 Z= 0.225 Angle : 0.752 13.932 44659 Z= 0.390 Chirality : 0.044 0.320 5136 Planarity : 0.005 0.075 5181 Dihedral : 17.951 179.501 6145 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.27 % Favored : 94.45 % Rotamer: Outliers : 3.91 % Allowed : 13.84 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.38 % Cis-general : 0.09 % Twisted Proline : 1.46 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.15), residues: 3475 helix: 2.81 (0.12), residues: 1823 sheet: -2.13 (0.24), residues: 358 loop : -2.05 (0.16), residues: 1294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 823 HIS 0.018 0.001 HIS J 805 PHE 0.036 0.002 PHE J 616 TYR 0.037 0.002 TYR J 838 ARG 0.011 0.001 ARG J 597 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6950 Ramachandran restraints generated. 3475 Oldfield, 0 Emsley, 3475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6950 Ramachandran restraints generated. 3475 Oldfield, 0 Emsley, 3475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 792 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 672 time to evaluate : 3.780 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 753 TYR cc_start: 0.4752 (OUTLIER) cc_final: 0.4476 (t80) REVERT: A 760 ASN cc_start: 0.6204 (m110) cc_final: 0.5985 (m110) REVERT: A 769 MET cc_start: 0.7169 (mmp) cc_final: 0.6371 (ttm) REVERT: A 778 LYS cc_start: 0.4741 (mmmt) cc_final: 0.3780 (mtmt) REVERT: A 839 HIS cc_start: 0.7147 (t70) cc_final: 0.6447 (m-70) REVERT: A 926 LYS cc_start: 0.5744 (ptpt) cc_final: 0.5468 (mtmm) REVERT: A 1046 SER cc_start: 0.5804 (m) cc_final: 0.5414 (p) REVERT: A 1186 TYR cc_start: 0.5312 (t80) cc_final: 0.4430 (t80) REVERT: A 1190 ASN cc_start: 0.6419 (m-40) cc_final: 0.5853 (m-40) REVERT: A 1214 ARG cc_start: 0.5703 (mtt180) cc_final: 0.4905 (mmt180) REVERT: A 1240 SER cc_start: 0.5994 (t) cc_final: 0.5753 (p) REVERT: A 1253 LYS cc_start: 0.7224 (pttt) cc_final: 0.6607 (tptt) REVERT: A 1272 ARG cc_start: 0.6788 (mmt180) cc_final: 0.6251 (mtm180) REVERT: A 1404 HIS cc_start: 0.7170 (t70) cc_final: 0.6941 (t70) REVERT: A 1413 SER cc_start: 0.7912 (m) cc_final: 0.7397 (p) REVERT: A 1426 ARG cc_start: 0.6896 (mtp85) cc_final: 0.6480 (mtm110) REVERT: A 1458 TRP cc_start: 0.5560 (m100) cc_final: 0.5283 (m100) REVERT: A 1481 GLU cc_start: 0.7928 (tp30) cc_final: 0.7681 (tp30) REVERT: A 1517 TYR cc_start: 0.6127 (m-80) cc_final: 0.5849 (m-80) REVERT: A 1672 GLU cc_start: 0.7572 (mm-30) cc_final: 0.7236 (pm20) REVERT: A 1684 GLU cc_start: 0.6186 (mm-30) cc_final: 0.5443 (tm-30) REVERT: A 1710 GLU cc_start: 0.6064 (pm20) cc_final: 0.5598 (pm20) REVERT: A 1719 GLU cc_start: 0.6545 (mm-30) cc_final: 0.6190 (tt0) REVERT: A 1721 ASN cc_start: 0.7346 (t0) cc_final: 0.7082 (p0) REVERT: A 1724 PHE cc_start: 0.5723 (m-80) cc_final: 0.4911 (m-80) REVERT: A 1730 ASN cc_start: 0.7758 (p0) cc_final: 0.7295 (m-40) REVERT: A 1731 LYS cc_start: 0.6697 (ttpt) cc_final: 0.6160 (ttpp) REVERT: A 1802 MET cc_start: 0.6885 (mmm) cc_final: 0.6376 (mmm) REVERT: A 1809 ASN cc_start: 0.5671 (t0) cc_final: 0.5423 (t0) REVERT: A 1843 LEU cc_start: 0.7282 (mt) cc_final: 0.7060 (mt) REVERT: A 1847 ASP cc_start: 0.6101 (m-30) cc_final: 0.5557 (m-30) REVERT: A 1885 LYS cc_start: 0.6593 (tptt) cc_final: 0.6139 (mmtp) REVERT: A 1915 GLU cc_start: 0.7750 (tt0) cc_final: 0.7363 (tm-30) REVERT: A 1928 GLU cc_start: 0.7057 (mt-10) cc_final: 0.6759 (tp30) REVERT: A 1948 MET cc_start: 0.6852 (mmm) cc_final: 0.6645 (mmm) REVERT: A 1950 ASP cc_start: 0.7725 (m-30) cc_final: 0.7396 (t0) REVERT: A 1998 ARG cc_start: 0.8195 (mtt180) cc_final: 0.7956 (mmm160) REVERT: A 2055 MET cc_start: 0.6606 (mmt) cc_final: 0.6378 (mmt) REVERT: A 2078 GLU cc_start: 0.6449 (tm-30) cc_final: 0.6128 (tm-30) REVERT: H 139 GLU cc_start: 0.7639 (mm-30) cc_final: 0.7292 (tt0) REVERT: H 140 MET cc_start: 0.7894 (tpp) cc_final: 0.7685 (tpp) REVERT: H 143 HIS cc_start: 0.3507 (p-80) cc_final: 0.2982 (p-80) REVERT: H 225 ASP cc_start: 0.6395 (m-30) cc_final: 0.5951 (m-30) REVERT: H 226 TRP cc_start: 0.6777 (m100) cc_final: 0.6337 (m100) REVERT: H 286 ASP cc_start: 0.4344 (OUTLIER) cc_final: 0.4004 (p0) REVERT: H 335 ASP cc_start: 0.7675 (m-30) cc_final: 0.7217 (p0) REVERT: J 163 THR cc_start: 0.7599 (p) cc_final: 0.6864 (p) REVERT: J 170 LEU cc_start: 0.6266 (OUTLIER) cc_final: 0.4587 (mm) REVERT: J 235 LYS cc_start: 0.6700 (ttpt) cc_final: 0.6247 (pttp) REVERT: J 237 ASP cc_start: 0.5658 (OUTLIER) cc_final: 0.4494 (m-30) REVERT: J 269 GLN cc_start: 0.8123 (pt0) cc_final: 0.7880 (pt0) REVERT: J 290 HIS cc_start: 0.7235 (p-80) cc_final: 0.6888 (t70) REVERT: J 328 ARG cc_start: 0.7972 (OUTLIER) cc_final: 0.7574 (mtp85) REVERT: J 358 LEU cc_start: 0.8431 (mm) cc_final: 0.8104 (mt) REVERT: J 386 MET cc_start: 0.6887 (mmp) cc_final: 0.6405 (ptp) REVERT: J 492 MET cc_start: 0.5880 (ttm) cc_final: 0.5298 (mmt) REVERT: J 518 ARG cc_start: 0.7551 (mmm-85) cc_final: 0.6983 (mmm160) REVERT: J 521 MET cc_start: 0.6528 (mmt) cc_final: 0.6164 (mmt) REVERT: J 565 VAL cc_start: 0.7712 (t) cc_final: 0.6832 (m) REVERT: J 569 TRP cc_start: 0.6906 (m100) cc_final: 0.6351 (m-10) REVERT: J 570 LYS cc_start: 0.6483 (mmtt) cc_final: 0.6246 (mmtp) REVERT: J 578 GLN cc_start: 0.6590 (OUTLIER) cc_final: 0.6235 (mp10) REVERT: J 602 LYS cc_start: 0.5891 (mttt) cc_final: 0.5466 (tptm) REVERT: J 603 LEU cc_start: 0.8230 (mt) cc_final: 0.7750 (mm) REVERT: J 785 ASN cc_start: 0.6246 (m-40) cc_final: 0.5683 (t0) REVERT: J 810 GLU cc_start: 0.5864 (tp30) cc_final: 0.5457 (tp30) REVERT: J 826 LYS cc_start: 0.5933 (mttt) cc_final: 0.5673 (mmtt) REVERT: J 829 GLU cc_start: 0.7606 (mt-10) cc_final: 0.7394 (mt-10) REVERT: J 873 GLU cc_start: 0.6660 (mt-10) cc_final: 0.6343 (tp30) REVERT: D 17 GLN cc_start: 0.6346 (mm-40) cc_final: 0.6018 (pp30) REVERT: D 36 ASP cc_start: 0.5409 (t70) cc_final: 0.5157 (t70) REVERT: D 51 GLU cc_start: 0.7442 (mm-30) cc_final: 0.7050 (pt0) REVERT: D 135 TYR cc_start: 0.6726 (m-80) cc_final: 0.6299 (m-80) REVERT: F 120 TYR cc_start: 0.6854 (OUTLIER) cc_final: 0.5273 (t80) REVERT: F 144 LEU cc_start: 0.7723 (OUTLIER) cc_final: 0.7484 (mt) REVERT: F 145 GLU cc_start: 0.7285 (mm-30) cc_final: 0.6436 (pt0) REVERT: F 397 GLU cc_start: 0.7878 (mm-30) cc_final: 0.6966 (pt0) REVERT: F 412 MET cc_start: 0.5023 (ttm) cc_final: 0.4802 (ttp) REVERT: G 181 MET cc_start: 0.4598 (ttm) cc_final: 0.4038 (ttm) REVERT: G 196 LEU cc_start: 0.7986 (mp) cc_final: 0.7771 (mp) REVERT: G 283 ASN cc_start: 0.7394 (t0) cc_final: 0.7045 (t0) REVERT: G 284 ASP cc_start: 0.5505 (m-30) cc_final: 0.5275 (p0) REVERT: G 354 PHE cc_start: 0.6715 (t80) cc_final: 0.6182 (t80) REVERT: G 393 GLU cc_start: 0.6241 (OUTLIER) cc_final: 0.5991 (tm-30) REVERT: G 417 MET cc_start: 0.6089 (mmt) cc_final: 0.5789 (tpp) REVERT: G 420 HIS cc_start: 0.7477 (p90) cc_final: 0.7053 (p-80) REVERT: G 431 TYR cc_start: 0.6193 (m-80) cc_final: 0.5290 (m-10) REVERT: K 7 LYS cc_start: 0.6710 (mtpt) cc_final: 0.6351 (mmmt) REVERT: K 32 GLN cc_start: 0.3441 (tp40) cc_final: 0.3206 (tt0) REVERT: K 54 MET cc_start: 0.5527 (mtm) cc_final: 0.4941 (mtm) REVERT: K 79 VAL cc_start: 0.6346 (OUTLIER) cc_final: 0.5978 (p) REVERT: K 106 ASP cc_start: 0.6913 (OUTLIER) cc_final: 0.6710 (p0) outliers start: 120 outliers final: 50 residues processed: 756 average time/residue: 0.4620 time to fit residues: 548.8972 Evaluate side-chains 582 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 521 time to evaluate : 3.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 753 TYR Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 925 SER Chi-restraints excluded: chain A residue 1199 ILE Chi-restraints excluded: chain A residue 1210 ASP Chi-restraints excluded: chain A residue 1236 THR Chi-restraints excluded: chain A residue 1546 VAL Chi-restraints excluded: chain A residue 1557 LEU Chi-restraints excluded: chain A residue 1804 THR Chi-restraints excluded: chain A residue 1941 LEU Chi-restraints excluded: chain A residue 1979 MET Chi-restraints excluded: chain A residue 1987 VAL Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain H residue 146 PHE Chi-restraints excluded: chain H residue 175 THR Chi-restraints excluded: chain H residue 220 LYS Chi-restraints excluded: chain H residue 232 ASN Chi-restraints excluded: chain H residue 286 ASP Chi-restraints excluded: chain H residue 304 GLU Chi-restraints excluded: chain H residue 349 SER Chi-restraints excluded: chain H residue 389 ILE Chi-restraints excluded: chain H residue 399 VAL Chi-restraints excluded: chain H residue 438 ASP Chi-restraints excluded: chain J residue 170 LEU Chi-restraints excluded: chain J residue 194 PRO Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 237 ASP Chi-restraints excluded: chain J residue 288 ASP Chi-restraints excluded: chain J residue 318 SER Chi-restraints excluded: chain J residue 328 ARG Chi-restraints excluded: chain J residue 395 LEU Chi-restraints excluded: chain J residue 502 LEU Chi-restraints excluded: chain J residue 578 GLN Chi-restraints excluded: chain J residue 624 LEU Chi-restraints excluded: chain J residue 661 LEU Chi-restraints excluded: chain J residue 708 LEU Chi-restraints excluded: chain J residue 767 PHE Chi-restraints excluded: chain J residue 789 LEU Chi-restraints excluded: chain D residue 39 CYS Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain F residue 120 TYR Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 179 MET Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain F residue 391 MET Chi-restraints excluded: chain G residue 261 LYS Chi-restraints excluded: chain G residue 337 TYR Chi-restraints excluded: chain G residue 341 VAL Chi-restraints excluded: chain G residue 347 LEU Chi-restraints excluded: chain G residue 393 GLU Chi-restraints excluded: chain G residue 395 LEU Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 64 LEU Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain K residue 106 ASP Chi-restraints excluded: chain B residue 390 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 185 optimal weight: 0.9980 chunk 103 optimal weight: 0.7980 chunk 277 optimal weight: 0.0870 chunk 226 optimal weight: 0.9990 chunk 91 optimal weight: 5.9990 chunk 333 optimal weight: 7.9990 chunk 360 optimal weight: 0.0270 chunk 297 optimal weight: 0.5980 chunk 331 optimal weight: 0.7980 chunk 113 optimal weight: 6.9990 chunk 267 optimal weight: 3.9990 overall best weight: 0.4616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 976 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1655 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 212 GLN H 232 ASN ** H 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 387 ASN H 388 GLN J 353 GLN J 537 GLN ** J 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 805 HIS ** J 897 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 108 ASN F 163 ASN ** F 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 451 GLN G 276 ASN G 283 ASN G 343 GLN G 433 GLN B 372 ASN B 407 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4854 moved from start: 0.3562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 32504 Z= 0.205 Angle : 0.686 14.427 44659 Z= 0.351 Chirality : 0.043 0.494 5136 Planarity : 0.005 0.157 5181 Dihedral : 17.259 174.577 6100 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.55 % Favored : 94.22 % Rotamer: Outliers : 4.33 % Allowed : 16.35 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.11 % Cis-general : 0.09 % Twisted Proline : 0.73 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.15), residues: 3475 helix: 2.55 (0.12), residues: 1838 sheet: -1.83 (0.24), residues: 357 loop : -1.81 (0.17), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 823 HIS 0.007 0.001 HIS J 805 PHE 0.025 0.002 PHE J 617 TYR 0.019 0.002 TYR H 127 ARG 0.017 0.001 ARG J 644 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6950 Ramachandran restraints generated. 3475 Oldfield, 0 Emsley, 3475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6950 Ramachandran restraints generated. 3475 Oldfield, 0 Emsley, 3475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 722 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 589 time to evaluate : 3.720 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 753 TYR cc_start: 0.4800 (OUTLIER) cc_final: 0.4515 (t80) REVERT: A 778 LYS cc_start: 0.4503 (mmmt) cc_final: 0.3752 (mtmt) REVERT: A 839 HIS cc_start: 0.7129 (t70) cc_final: 0.6431 (m-70) REVERT: A 926 LYS cc_start: 0.5748 (ptpt) cc_final: 0.5530 (mtmm) REVERT: A 1046 SER cc_start: 0.5859 (m) cc_final: 0.5439 (p) REVERT: A 1214 ARG cc_start: 0.5770 (mtt180) cc_final: 0.4965 (mmt-90) REVERT: A 1240 SER cc_start: 0.6301 (t) cc_final: 0.6055 (p) REVERT: A 1253 LYS cc_start: 0.7189 (pttt) cc_final: 0.6665 (tptt) REVERT: A 1413 SER cc_start: 0.7764 (m) cc_final: 0.7226 (p) REVERT: A 1426 ARG cc_start: 0.6864 (mtp85) cc_final: 0.6481 (mtm110) REVERT: A 1458 TRP cc_start: 0.5622 (m100) cc_final: 0.5350 (m100) REVERT: A 1481 GLU cc_start: 0.7902 (tp30) cc_final: 0.7634 (tp30) REVERT: A 1533 ASP cc_start: 0.5534 (m-30) cc_final: 0.5279 (m-30) REVERT: A 1585 MET cc_start: 0.4487 (OUTLIER) cc_final: 0.3649 (mmm) REVERT: A 1684 GLU cc_start: 0.6608 (mm-30) cc_final: 0.6035 (tm-30) REVERT: A 1710 GLU cc_start: 0.5796 (pm20) cc_final: 0.5483 (pm20) REVERT: A 1719 GLU cc_start: 0.6731 (mm-30) cc_final: 0.6392 (tt0) REVERT: A 1721 ASN cc_start: 0.7370 (t0) cc_final: 0.7076 (p0) REVERT: A 1724 PHE cc_start: 0.6043 (m-80) cc_final: 0.5289 (m-80) REVERT: A 1730 ASN cc_start: 0.7696 (p0) cc_final: 0.7166 (m-40) REVERT: A 1731 LYS cc_start: 0.6731 (ttpt) cc_final: 0.6377 (ttmm) REVERT: A 1733 TRP cc_start: 0.6205 (p-90) cc_final: 0.5978 (p-90) REVERT: A 1784 TYR cc_start: 0.6910 (p90) cc_final: 0.5507 (p90) REVERT: A 1802 MET cc_start: 0.6907 (mmm) cc_final: 0.6238 (mmm) REVERT: A 1843 LEU cc_start: 0.7259 (mt) cc_final: 0.7028 (mt) REVERT: A 1847 ASP cc_start: 0.6163 (m-30) cc_final: 0.5532 (m-30) REVERT: A 1885 LYS cc_start: 0.6550 (tptt) cc_final: 0.6086 (mmtp) REVERT: A 1915 GLU cc_start: 0.7798 (tt0) cc_final: 0.7464 (tm-30) REVERT: A 1928 GLU cc_start: 0.7038 (mt-10) cc_final: 0.6747 (tp30) REVERT: A 1948 MET cc_start: 0.7504 (mmm) cc_final: 0.7272 (mmm) REVERT: A 1950 ASP cc_start: 0.8105 (m-30) cc_final: 0.7849 (t0) REVERT: A 2078 GLU cc_start: 0.6452 (tm-30) cc_final: 0.6115 (tm-30) REVERT: H 139 GLU cc_start: 0.7590 (mm-30) cc_final: 0.7131 (tt0) REVERT: H 142 ARG cc_start: 0.7104 (mtp-110) cc_final: 0.6345 (tpt90) REVERT: H 225 ASP cc_start: 0.6296 (m-30) cc_final: 0.5894 (m-30) REVERT: H 226 TRP cc_start: 0.6898 (m100) cc_final: 0.6538 (m100) REVERT: H 257 LEU cc_start: 0.6892 (OUTLIER) cc_final: 0.6679 (tp) REVERT: H 388 GLN cc_start: 0.6461 (mt0) cc_final: 0.6248 (mt0) REVERT: J 237 ASP cc_start: 0.5411 (OUTLIER) cc_final: 0.5182 (m-30) REVERT: J 315 ASP cc_start: 0.7869 (t0) cc_final: 0.7487 (m-30) REVERT: J 328 ARG cc_start: 0.8024 (OUTLIER) cc_final: 0.7658 (mtp85) REVERT: J 386 MET cc_start: 0.6749 (mmt) cc_final: 0.6262 (ptp) REVERT: J 492 MET cc_start: 0.6068 (ttm) cc_final: 0.5473 (mpp) REVERT: J 555 GLU cc_start: 0.5278 (tm-30) cc_final: 0.5017 (pt0) REVERT: J 565 VAL cc_start: 0.7580 (t) cc_final: 0.6646 (m) REVERT: J 569 TRP cc_start: 0.6855 (m100) cc_final: 0.6374 (m-10) REVERT: J 578 GLN cc_start: 0.6600 (OUTLIER) cc_final: 0.5909 (mp10) REVERT: J 603 LEU cc_start: 0.8199 (mt) cc_final: 0.7796 (mm) REVERT: J 785 ASN cc_start: 0.6336 (m-40) cc_final: 0.5867 (t0) REVERT: J 810 GLU cc_start: 0.5975 (tp30) cc_final: 0.5641 (tp30) REVERT: D 17 GLN cc_start: 0.6577 (mm-40) cc_final: 0.6271 (pp30) REVERT: D 36 ASP cc_start: 0.5552 (t70) cc_final: 0.5331 (t70) REVERT: D 51 GLU cc_start: 0.7413 (mm-30) cc_final: 0.6744 (pt0) REVERT: D 54 ARG cc_start: 0.5790 (OUTLIER) cc_final: 0.5383 (ptp-170) REVERT: D 135 TYR cc_start: 0.6761 (m-80) cc_final: 0.6355 (m-80) REVERT: F 70 THR cc_start: 0.7773 (m) cc_final: 0.7481 (p) REVERT: F 120 TYR cc_start: 0.6881 (OUTLIER) cc_final: 0.5383 (t80) REVERT: F 377 GLU cc_start: 0.6084 (tt0) cc_final: 0.5853 (tp30) REVERT: F 397 GLU cc_start: 0.7914 (mm-30) cc_final: 0.6993 (pt0) REVERT: F 412 MET cc_start: 0.5106 (ttm) cc_final: 0.4801 (ttp) REVERT: F 419 GLN cc_start: 0.5292 (OUTLIER) cc_final: 0.4660 (pt0) REVERT: G 181 MET cc_start: 0.4639 (ttm) cc_final: 0.4359 (ttm) REVERT: G 354 PHE cc_start: 0.6613 (t80) cc_final: 0.6292 (t80) REVERT: G 358 MET cc_start: 0.5785 (mmp) cc_final: 0.5446 (mmt) REVERT: G 386 GLU cc_start: 0.5628 (mp0) cc_final: 0.4962 (mp0) REVERT: G 431 TYR cc_start: 0.6030 (m-80) cc_final: 0.4890 (m-10) REVERT: K 7 LYS cc_start: 0.6722 (mtpt) cc_final: 0.6392 (mtpt) REVERT: K 54 MET cc_start: 0.5492 (mtm) cc_final: 0.4949 (mtm) outliers start: 133 outliers final: 59 residues processed: 676 average time/residue: 0.4454 time to fit residues: 482.1673 Evaluate side-chains 558 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 490 time to evaluate : 3.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 753 TYR Chi-restraints excluded: chain A residue 1004 ASP Chi-restraints excluded: chain A residue 1198 SER Chi-restraints excluded: chain A residue 1210 ASP Chi-restraints excluded: chain A residue 1233 ARG Chi-restraints excluded: chain A residue 1546 VAL Chi-restraints excluded: chain A residue 1557 LEU Chi-restraints excluded: chain A residue 1585 MET Chi-restraints excluded: chain A residue 1591 THR Chi-restraints excluded: chain A residue 1677 GLN Chi-restraints excluded: chain A residue 1798 ILE Chi-restraints excluded: chain A residue 1941 LEU Chi-restraints excluded: chain A residue 1979 MET Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 146 PHE Chi-restraints excluded: chain H residue 220 LYS Chi-restraints excluded: chain H residue 232 ASN Chi-restraints excluded: chain H residue 249 SER Chi-restraints excluded: chain H residue 257 LEU Chi-restraints excluded: chain H residue 271 VAL Chi-restraints excluded: chain H residue 291 LEU Chi-restraints excluded: chain H residue 304 GLU Chi-restraints excluded: chain H residue 310 VAL Chi-restraints excluded: chain H residue 327 MET Chi-restraints excluded: chain H residue 331 SER Chi-restraints excluded: chain H residue 397 THR Chi-restraints excluded: chain H residue 399 VAL Chi-restraints excluded: chain H residue 443 LEU Chi-restraints excluded: chain J residue 189 ILE Chi-restraints excluded: chain J residue 194 PRO Chi-restraints excluded: chain J residue 232 SER Chi-restraints excluded: chain J residue 237 ASP Chi-restraints excluded: chain J residue 288 ASP Chi-restraints excluded: chain J residue 318 SER Chi-restraints excluded: chain J residue 328 ARG Chi-restraints excluded: chain J residue 395 LEU Chi-restraints excluded: chain J residue 408 LEU Chi-restraints excluded: chain J residue 502 LEU Chi-restraints excluded: chain J residue 513 THR Chi-restraints excluded: chain J residue 514 VAL Chi-restraints excluded: chain J residue 578 GLN Chi-restraints excluded: chain J residue 661 LEU Chi-restraints excluded: chain J residue 753 LEU Chi-restraints excluded: chain J residue 767 PHE Chi-restraints excluded: chain J residue 783 HIS Chi-restraints excluded: chain J residue 789 LEU Chi-restraints excluded: chain J residue 840 ASP Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 39 CYS Chi-restraints excluded: chain D residue 54 ARG Chi-restraints excluded: chain D residue 71 ASP Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain F residue 120 TYR Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain F residue 222 ILE Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 401 LEU Chi-restraints excluded: chain F residue 419 GLN Chi-restraints excluded: chain G residue 261 LYS Chi-restraints excluded: chain G residue 337 TYR Chi-restraints excluded: chain G residue 341 VAL Chi-restraints excluded: chain G residue 382 VAL Chi-restraints excluded: chain G residue 395 LEU Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 93 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 329 optimal weight: 6.9990 chunk 251 optimal weight: 2.9990 chunk 173 optimal weight: 0.0770 chunk 36 optimal weight: 0.0970 chunk 159 optimal weight: 3.9990 chunk 224 optimal weight: 0.8980 chunk 335 optimal weight: 0.0170 chunk 354 optimal weight: 0.7980 chunk 175 optimal weight: 0.8980 chunk 317 optimal weight: 0.0030 chunk 95 optimal weight: 5.9990 overall best weight: 0.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1655 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 274 HIS ** J 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 578 GLN J 805 HIS J 820 GLN ** J 897 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 187 ASN ** G 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 283 ASN G 300 GLN G 316 HIS G 343 GLN ** G 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4855 moved from start: 0.3917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 32504 Z= 0.184 Angle : 0.652 14.760 44659 Z= 0.331 Chirality : 0.041 0.408 5136 Planarity : 0.004 0.098 5181 Dihedral : 17.002 175.106 6085 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.15 % Favored : 94.65 % Rotamer: Outliers : 3.78 % Allowed : 18.27 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.11 % Cis-general : 0.09 % Twisted Proline : 0.73 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.15), residues: 3475 helix: 2.43 (0.12), residues: 1832 sheet: -1.67 (0.25), residues: 357 loop : -1.62 (0.17), residues: 1286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 823 HIS 0.006 0.001 HIS G 462 PHE 0.026 0.002 PHE J 617 TYR 0.014 0.001 TYR J 564 ARG 0.011 0.000 ARG J 644 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6950 Ramachandran restraints generated. 3475 Oldfield, 0 Emsley, 3475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6950 Ramachandran restraints generated. 3475 Oldfield, 0 Emsley, 3475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 664 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 548 time to evaluate : 3.496 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: A 753 TYR cc_start: 0.4893 (OUTLIER) cc_final: 0.4688 (t80) REVERT: A 778 LYS cc_start: 0.4675 (mmmt) cc_final: 0.3850 (mtmt) REVERT: A 839 HIS cc_start: 0.7042 (t70) cc_final: 0.6500 (m-70) REVERT: A 926 LYS cc_start: 0.5601 (ptpt) cc_final: 0.5344 (mtmm) REVERT: A 933 GLU cc_start: 0.5159 (mt-10) cc_final: 0.4907 (mt-10) REVERT: A 1046 SER cc_start: 0.5843 (m) cc_final: 0.5436 (p) REVERT: A 1049 LEU cc_start: 0.5381 (tp) cc_final: 0.5112 (tp) REVERT: A 1214 ARG cc_start: 0.5795 (mtt180) cc_final: 0.4970 (mmt-90) REVERT: A 1240 SER cc_start: 0.6343 (t) cc_final: 0.6079 (p) REVERT: A 1253 LYS cc_start: 0.7311 (pttt) cc_final: 0.6753 (tptt) REVERT: A 1404 HIS cc_start: 0.7184 (t70) cc_final: 0.6938 (t70) REVERT: A 1413 SER cc_start: 0.7718 (m) cc_final: 0.7152 (p) REVERT: A 1426 ARG cc_start: 0.6766 (mtp85) cc_final: 0.6362 (mtm110) REVERT: A 1481 GLU cc_start: 0.7989 (tp30) cc_final: 0.7729 (tp30) REVERT: A 1585 MET cc_start: 0.4405 (OUTLIER) cc_final: 0.3507 (mmm) REVERT: A 1672 GLU cc_start: 0.7145 (mm-30) cc_final: 0.6502 (mt-10) REVERT: A 1719 GLU cc_start: 0.6727 (mm-30) cc_final: 0.6385 (tt0) REVERT: A 1721 ASN cc_start: 0.7003 (t0) cc_final: 0.6748 (p0) REVERT: A 1730 ASN cc_start: 0.7754 (p0) cc_final: 0.7260 (m-40) REVERT: A 1731 LYS cc_start: 0.6669 (ttpt) cc_final: 0.6325 (ttmm) REVERT: A 1733 TRP cc_start: 0.6261 (p-90) cc_final: 0.6047 (p-90) REVERT: A 1784 TYR cc_start: 0.6873 (p90) cc_final: 0.5642 (p90) REVERT: A 1785 ASP cc_start: 0.5570 (t0) cc_final: 0.5083 (t0) REVERT: A 1802 MET cc_start: 0.6792 (mmm) cc_final: 0.6441 (mmm) REVERT: A 1843 LEU cc_start: 0.7309 (mt) cc_final: 0.7087 (mt) REVERT: A 1847 ASP cc_start: 0.6152 (m-30) cc_final: 0.5511 (m-30) REVERT: A 1885 LYS cc_start: 0.6618 (tptt) cc_final: 0.6086 (mmtp) REVERT: A 1915 GLU cc_start: 0.7782 (tt0) cc_final: 0.7433 (tm-30) REVERT: A 1928 GLU cc_start: 0.7239 (mt-10) cc_final: 0.6970 (tp30) REVERT: A 1948 MET cc_start: 0.6914 (mmm) cc_final: 0.6600 (mmm) REVERT: A 1950 ASP cc_start: 0.8078 (m-30) cc_final: 0.7837 (t0) REVERT: A 2078 GLU cc_start: 0.6451 (tm-30) cc_final: 0.6124 (tm-30) REVERT: H 139 GLU cc_start: 0.7544 (mm-30) cc_final: 0.7117 (tt0) REVERT: H 142 ARG cc_start: 0.7176 (mtp-110) cc_final: 0.6545 (tpt90) REVERT: H 225 ASP cc_start: 0.6072 (OUTLIER) cc_final: 0.5381 (m-30) REVERT: H 226 TRP cc_start: 0.6786 (m100) cc_final: 0.6449 (m100) REVERT: H 273 TYR cc_start: 0.7029 (OUTLIER) cc_final: 0.6422 (m-80) REVERT: H 335 ASP cc_start: 0.6680 (OUTLIER) cc_final: 0.6239 (p0) REVERT: J 163 THR cc_start: 0.7434 (p) cc_final: 0.7223 (t) REVERT: J 226 MET cc_start: 0.4985 (tpp) cc_final: 0.4616 (tpp) REVERT: J 237 ASP cc_start: 0.5288 (OUTLIER) cc_final: 0.4196 (m-30) REVERT: J 328 ARG cc_start: 0.8110 (OUTLIER) cc_final: 0.7809 (mtp85) REVERT: J 471 TRP cc_start: 0.6828 (m100) cc_final: 0.6422 (m100) REVERT: J 492 MET cc_start: 0.6055 (ttm) cc_final: 0.5453 (mpp) REVERT: J 555 GLU cc_start: 0.5578 (tm-30) cc_final: 0.5303 (pt0) REVERT: J 565 VAL cc_start: 0.7801 (t) cc_final: 0.6949 (m) REVERT: J 569 TRP cc_start: 0.6777 (m100) cc_final: 0.6132 (m-10) REVERT: J 578 GLN cc_start: 0.6324 (OUTLIER) cc_final: 0.5851 (mp10) REVERT: J 602 LYS cc_start: 0.5792 (mttt) cc_final: 0.5369 (tptm) REVERT: J 603 LEU cc_start: 0.8157 (mt) cc_final: 0.7684 (mm) REVERT: J 810 GLU cc_start: 0.6131 (tp30) cc_final: 0.5897 (tp30) REVERT: D 17 GLN cc_start: 0.6586 (mm-40) cc_final: 0.6268 (pp30) REVERT: D 36 ASP cc_start: 0.5497 (t70) cc_final: 0.5273 (t70) REVERT: D 51 GLU cc_start: 0.7507 (mm-30) cc_final: 0.7263 (mm-30) REVERT: D 54 ARG cc_start: 0.6117 (OUTLIER) cc_final: 0.5775 (ptp-170) REVERT: D 78 ASP cc_start: 0.7353 (p0) cc_final: 0.6937 (m-30) REVERT: D 135 TYR cc_start: 0.6788 (m-80) cc_final: 0.6298 (m-80) REVERT: F 145 GLU cc_start: 0.6403 (mm-30) cc_final: 0.5679 (pt0) REVERT: F 397 GLU cc_start: 0.7890 (mm-30) cc_final: 0.6963 (pt0) REVERT: F 412 MET cc_start: 0.5084 (ttm) cc_final: 0.4872 (ttp) REVERT: F 419 GLN cc_start: 0.5295 (pt0) cc_final: 0.4718 (pt0) REVERT: G 264 LEU cc_start: 0.4479 (mp) cc_final: 0.4177 (tp) REVERT: G 353 ARG cc_start: 0.5953 (ttm110) cc_final: 0.5720 (mtt90) REVERT: G 354 PHE cc_start: 0.6482 (t80) cc_final: 0.6136 (t80) REVERT: G 358 MET cc_start: 0.5948 (mmp) cc_final: 0.5607 (mmt) REVERT: G 386 GLU cc_start: 0.5632 (mp0) cc_final: 0.5003 (mp0) REVERT: G 431 TYR cc_start: 0.6008 (m-80) cc_final: 0.4884 (m-10) REVERT: K 7 LYS cc_start: 0.6732 (mtpt) cc_final: 0.6376 (mmmt) REVERT: K 54 MET cc_start: 0.5563 (mtm) cc_final: 0.4924 (mtm) REVERT: B 423 ILE cc_start: 0.5225 (OUTLIER) cc_final: 0.5003 (pt) outliers start: 116 outliers final: 68 residues processed: 631 average time/residue: 0.4306 time to fit residues: 435.1908 Evaluate side-chains 558 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 480 time to evaluate : 3.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 753 TYR Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 1004 ASP Chi-restraints excluded: chain A residue 1160 LEU Chi-restraints excluded: chain A residue 1199 ILE Chi-restraints excluded: chain A residue 1210 ASP Chi-restraints excluded: chain A residue 1546 VAL Chi-restraints excluded: chain A residue 1585 MET Chi-restraints excluded: chain A residue 1591 THR Chi-restraints excluded: chain A residue 1624 LEU Chi-restraints excluded: chain A residue 1677 GLN Chi-restraints excluded: chain A residue 1687 HIS Chi-restraints excluded: chain A residue 1742 ASP Chi-restraints excluded: chain A residue 1862 VAL Chi-restraints excluded: chain A residue 1941 LEU Chi-restraints excluded: chain A residue 1979 MET Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 146 PHE Chi-restraints excluded: chain H residue 175 THR Chi-restraints excluded: chain H residue 220 LYS Chi-restraints excluded: chain H residue 225 ASP Chi-restraints excluded: chain H residue 232 ASN Chi-restraints excluded: chain H residue 249 SER Chi-restraints excluded: chain H residue 271 VAL Chi-restraints excluded: chain H residue 273 TYR Chi-restraints excluded: chain H residue 291 LEU Chi-restraints excluded: chain H residue 304 GLU Chi-restraints excluded: chain H residue 310 VAL Chi-restraints excluded: chain H residue 327 MET Chi-restraints excluded: chain H residue 331 SER Chi-restraints excluded: chain H residue 335 ASP Chi-restraints excluded: chain H residue 397 THR Chi-restraints excluded: chain H residue 443 LEU Chi-restraints excluded: chain J residue 189 ILE Chi-restraints excluded: chain J residue 194 PRO Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 232 SER Chi-restraints excluded: chain J residue 237 ASP Chi-restraints excluded: chain J residue 288 ASP Chi-restraints excluded: chain J residue 318 SER Chi-restraints excluded: chain J residue 328 ARG Chi-restraints excluded: chain J residue 395 LEU Chi-restraints excluded: chain J residue 408 LEU Chi-restraints excluded: chain J residue 513 THR Chi-restraints excluded: chain J residue 514 VAL Chi-restraints excluded: chain J residue 578 GLN Chi-restraints excluded: chain J residue 661 LEU Chi-restraints excluded: chain J residue 708 LEU Chi-restraints excluded: chain J residue 753 LEU Chi-restraints excluded: chain J residue 759 LEU Chi-restraints excluded: chain J residue 767 PHE Chi-restraints excluded: chain J residue 789 LEU Chi-restraints excluded: chain J residue 793 ILE Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 39 CYS Chi-restraints excluded: chain D residue 54 ARG Chi-restraints excluded: chain D residue 71 ASP Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 155 ASP Chi-restraints excluded: chain F residue 199 GLU Chi-restraints excluded: chain F residue 222 ILE Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 401 LEU Chi-restraints excluded: chain G residue 194 GLU Chi-restraints excluded: chain G residue 217 VAL Chi-restraints excluded: chain G residue 300 GLN Chi-restraints excluded: chain G residue 337 TYR Chi-restraints excluded: chain G residue 341 VAL Chi-restraints excluded: chain G residue 347 LEU Chi-restraints excluded: chain G residue 385 ASN Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain B residue 423 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 295 optimal weight: 0.0170 chunk 201 optimal weight: 9.9990 chunk 5 optimal weight: 4.9990 chunk 264 optimal weight: 2.9990 chunk 146 optimal weight: 1.9990 chunk 302 optimal weight: 0.6980 chunk 245 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 181 optimal weight: 4.9990 chunk 318 optimal weight: 10.0000 chunk 89 optimal weight: 1.9990 overall best weight: 1.5424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1655 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 274 HIS J 187 ASN ** J 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 805 HIS J 820 GLN ** J 897 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 90 HIS ** F 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 316 HIS G 343 GLN G 348 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4874 moved from start: 0.4125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 32504 Z= 0.290 Angle : 0.677 14.342 44659 Z= 0.344 Chirality : 0.043 0.437 5136 Planarity : 0.005 0.103 5181 Dihedral : 16.826 173.768 6081 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.50 % Favored : 94.30 % Rotamer: Outliers : 4.46 % Allowed : 18.31 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.11 % Cis-general : 0.09 % Twisted Proline : 0.73 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.14), residues: 3475 helix: 2.11 (0.12), residues: 1836 sheet: -1.46 (0.26), residues: 333 loop : -1.59 (0.17), residues: 1306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A1028 HIS 0.006 0.001 HIS J 805 PHE 0.022 0.002 PHE J 541 TYR 0.018 0.002 TYR H 127 ARG 0.009 0.001 ARG G 249 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6950 Ramachandran restraints generated. 3475 Oldfield, 0 Emsley, 3475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6950 Ramachandran restraints generated. 3475 Oldfield, 0 Emsley, 3475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 642 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 505 time to evaluate : 3.476 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 753 TYR cc_start: 0.4953 (OUTLIER) cc_final: 0.4639 (t80) REVERT: A 839 HIS cc_start: 0.6949 (t70) cc_final: 0.6480 (m-70) REVERT: A 926 LYS cc_start: 0.5700 (ptpt) cc_final: 0.5477 (mtmm) REVERT: A 1019 GLU cc_start: 0.6229 (mp0) cc_final: 0.5996 (mp0) REVERT: A 1046 SER cc_start: 0.5773 (m) cc_final: 0.5368 (p) REVERT: A 1049 LEU cc_start: 0.5640 (tp) cc_final: 0.5383 (tp) REVERT: A 1162 THR cc_start: 0.6143 (t) cc_final: 0.5896 (m) REVERT: A 1214 ARG cc_start: 0.5716 (mtt180) cc_final: 0.4901 (mmt180) REVERT: A 1253 LYS cc_start: 0.7286 (pttt) cc_final: 0.6740 (tptt) REVERT: A 1404 HIS cc_start: 0.7189 (t70) cc_final: 0.6830 (t-90) REVERT: A 1413 SER cc_start: 0.7667 (m) cc_final: 0.7313 (p) REVERT: A 1426 ARG cc_start: 0.6661 (mtp85) cc_final: 0.6383 (mtm110) REVERT: A 1570 TRP cc_start: 0.6853 (p90) cc_final: 0.6499 (p-90) REVERT: A 1672 GLU cc_start: 0.7156 (mm-30) cc_final: 0.6428 (pt0) REVERT: A 1719 GLU cc_start: 0.6553 (mm-30) cc_final: 0.6183 (tt0) REVERT: A 1721 ASN cc_start: 0.7006 (t0) cc_final: 0.6741 (p0) REVERT: A 1730 ASN cc_start: 0.7974 (p0) cc_final: 0.7455 (m-40) REVERT: A 1731 LYS cc_start: 0.6581 (ttpt) cc_final: 0.6231 (ttmm) REVERT: A 1742 ASP cc_start: 0.5889 (OUTLIER) cc_final: 0.5479 (p0) REVERT: A 1784 TYR cc_start: 0.6954 (p90) cc_final: 0.6581 (p90) REVERT: A 1785 ASP cc_start: 0.5606 (t0) cc_final: 0.5288 (t0) REVERT: A 1802 MET cc_start: 0.6889 (mmm) cc_final: 0.6582 (mmm) REVERT: A 1847 ASP cc_start: 0.6180 (m-30) cc_final: 0.5563 (m-30) REVERT: A 1885 LYS cc_start: 0.6926 (tptt) cc_final: 0.6401 (mmtp) REVERT: A 1915 GLU cc_start: 0.7809 (tt0) cc_final: 0.7427 (tm-30) REVERT: A 1928 GLU cc_start: 0.7136 (mt-10) cc_final: 0.6858 (tp30) REVERT: A 1948 MET cc_start: 0.6436 (mmm) cc_final: 0.6215 (mmm) REVERT: A 1950 ASP cc_start: 0.7890 (m-30) cc_final: 0.7620 (t0) REVERT: A 2078 GLU cc_start: 0.6612 (tm-30) cc_final: 0.6267 (tm-30) REVERT: H 142 ARG cc_start: 0.7074 (mtp-110) cc_final: 0.6478 (tpt90) REVERT: H 225 ASP cc_start: 0.5740 (OUTLIER) cc_final: 0.5065 (m-30) REVERT: H 226 TRP cc_start: 0.7284 (m100) cc_final: 0.6823 (m100) REVERT: H 273 TYR cc_start: 0.6950 (OUTLIER) cc_final: 0.6293 (m-80) REVERT: H 334 TRP cc_start: 0.6833 (m100) cc_final: 0.6603 (m100) REVERT: H 343 MET cc_start: 0.6389 (ppp) cc_final: 0.6015 (tmm) REVERT: J 315 ASP cc_start: 0.7883 (t0) cc_final: 0.7540 (m-30) REVERT: J 328 ARG cc_start: 0.8110 (OUTLIER) cc_final: 0.7728 (mtp85) REVERT: J 386 MET cc_start: 0.6645 (mmt) cc_final: 0.6055 (ptp) REVERT: J 471 TRP cc_start: 0.6785 (m100) cc_final: 0.6384 (m100) REVERT: J 492 MET cc_start: 0.6002 (ttm) cc_final: 0.5443 (mpp) REVERT: J 555 GLU cc_start: 0.5874 (tm-30) cc_final: 0.5542 (pt0) REVERT: J 565 VAL cc_start: 0.7515 (t) cc_final: 0.6797 (m) REVERT: J 569 TRP cc_start: 0.6812 (m100) cc_final: 0.6005 (m-10) REVERT: J 602 LYS cc_start: 0.5887 (mttt) cc_final: 0.5485 (tptm) REVERT: J 603 LEU cc_start: 0.8106 (mt) cc_final: 0.7163 (mt) REVERT: J 810 GLU cc_start: 0.6273 (tp30) cc_final: 0.5778 (tp30) REVERT: D 17 GLN cc_start: 0.6452 (mm-40) cc_final: 0.6141 (pp30) REVERT: D 51 GLU cc_start: 0.7142 (mm-30) cc_final: 0.6910 (mm-30) REVERT: D 54 ARG cc_start: 0.5715 (OUTLIER) cc_final: 0.5320 (ptp-170) REVERT: D 80 MET cc_start: 0.4711 (OUTLIER) cc_final: 0.4311 (mmt) REVERT: D 135 TYR cc_start: 0.6710 (m-80) cc_final: 0.6366 (m-80) REVERT: F 397 GLU cc_start: 0.7854 (mm-30) cc_final: 0.6926 (pt0) REVERT: F 412 MET cc_start: 0.4697 (ttm) cc_final: 0.4490 (ttp) REVERT: F 419 GLN cc_start: 0.5499 (OUTLIER) cc_final: 0.4971 (pt0) REVERT: G 181 MET cc_start: 0.6546 (ttm) cc_final: 0.6044 (tpt) REVERT: G 354 PHE cc_start: 0.6523 (t80) cc_final: 0.5959 (t80) REVERT: K 7 LYS cc_start: 0.6822 (mtpt) cc_final: 0.6517 (mmmt) REVERT: K 54 MET cc_start: 0.5675 (mtm) cc_final: 0.5006 (mtm) outliers start: 137 outliers final: 82 residues processed: 601 average time/residue: 0.4386 time to fit residues: 424.6333 Evaluate side-chains 550 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 460 time to evaluate : 3.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 753 TYR Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 1004 ASP Chi-restraints excluded: chain A residue 1029 THR Chi-restraints excluded: chain A residue 1198 SER Chi-restraints excluded: chain A residue 1206 CYS Chi-restraints excluded: chain A residue 1210 ASP Chi-restraints excluded: chain A residue 1236 THR Chi-restraints excluded: chain A residue 1501 THR Chi-restraints excluded: chain A residue 1547 ILE Chi-restraints excluded: chain A residue 1591 THR Chi-restraints excluded: chain A residue 1648 ILE Chi-restraints excluded: chain A residue 1687 HIS Chi-restraints excluded: chain A residue 1742 ASP Chi-restraints excluded: chain A residue 1798 ILE Chi-restraints excluded: chain A residue 1838 SER Chi-restraints excluded: chain A residue 1862 VAL Chi-restraints excluded: chain A residue 1875 ILE Chi-restraints excluded: chain A residue 1913 THR Chi-restraints excluded: chain A residue 1941 LEU Chi-restraints excluded: chain A residue 1979 MET Chi-restraints excluded: chain A residue 1987 VAL Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 130 GLU Chi-restraints excluded: chain H residue 146 PHE Chi-restraints excluded: chain H residue 167 LEU Chi-restraints excluded: chain H residue 172 LEU Chi-restraints excluded: chain H residue 186 ASP Chi-restraints excluded: chain H residue 225 ASP Chi-restraints excluded: chain H residue 232 ASN Chi-restraints excluded: chain H residue 249 SER Chi-restraints excluded: chain H residue 271 VAL Chi-restraints excluded: chain H residue 273 TYR Chi-restraints excluded: chain H residue 291 LEU Chi-restraints excluded: chain H residue 304 GLU Chi-restraints excluded: chain H residue 310 VAL Chi-restraints excluded: chain H residue 375 VAL Chi-restraints excluded: chain H residue 389 ILE Chi-restraints excluded: chain H residue 397 THR Chi-restraints excluded: chain H residue 443 LEU Chi-restraints excluded: chain J residue 189 ILE Chi-restraints excluded: chain J residue 194 PRO Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 264 ILE Chi-restraints excluded: chain J residue 269 GLN Chi-restraints excluded: chain J residue 288 ASP Chi-restraints excluded: chain J residue 298 THR Chi-restraints excluded: chain J residue 318 SER Chi-restraints excluded: chain J residue 328 ARG Chi-restraints excluded: chain J residue 395 LEU Chi-restraints excluded: chain J residue 408 LEU Chi-restraints excluded: chain J residue 513 THR Chi-restraints excluded: chain J residue 514 VAL Chi-restraints excluded: chain J residue 661 LEU Chi-restraints excluded: chain J residue 759 LEU Chi-restraints excluded: chain J residue 767 PHE Chi-restraints excluded: chain J residue 788 SER Chi-restraints excluded: chain J residue 789 LEU Chi-restraints excluded: chain J residue 840 ASP Chi-restraints excluded: chain J residue 891 ILE Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 39 CYS Chi-restraints excluded: chain D residue 54 ARG Chi-restraints excluded: chain D residue 69 ASP Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain F residue 222 ILE Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain F residue 259 ILE Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 401 LEU Chi-restraints excluded: chain F residue 419 GLN Chi-restraints excluded: chain G residue 194 GLU Chi-restraints excluded: chain G residue 302 ASP Chi-restraints excluded: chain G residue 337 TYR Chi-restraints excluded: chain G residue 341 VAL Chi-restraints excluded: chain G residue 347 LEU Chi-restraints excluded: chain G residue 395 LEU Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain B residue 380 LYS Chi-restraints excluded: chain B residue 423 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 119 optimal weight: 0.3980 chunk 319 optimal weight: 8.9990 chunk 70 optimal weight: 0.6980 chunk 208 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 355 optimal weight: 1.9990 chunk 294 optimal weight: 0.9980 chunk 164 optimal weight: 0.3980 chunk 29 optimal weight: 1.9990 chunk 117 optimal weight: 6.9990 chunk 186 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1618 ASN ** H 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 285 HIS ** J 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 820 GLN J 897 ASN D 138 ASN ** F 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 276 ASN G 316 HIS G 448 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4867 moved from start: 0.4379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 32504 Z= 0.194 Angle : 0.641 14.154 44659 Z= 0.321 Chirality : 0.041 0.472 5136 Planarity : 0.004 0.110 5181 Dihedral : 16.715 174.941 6081 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.24 % Favored : 94.62 % Rotamer: Outliers : 3.65 % Allowed : 19.61 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.11 % Cis-general : 0.09 % Twisted Proline : 0.73 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.14), residues: 3475 helix: 2.09 (0.12), residues: 1836 sheet: -1.38 (0.25), residues: 337 loop : -1.50 (0.17), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 823 HIS 0.009 0.001 HIS A1658 PHE 0.023 0.002 PHE J 541 TYR 0.016 0.001 TYR J 564 ARG 0.007 0.000 ARG J 644 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6950 Ramachandran restraints generated. 3475 Oldfield, 0 Emsley, 3475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6950 Ramachandran restraints generated. 3475 Oldfield, 0 Emsley, 3475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 517 time to evaluate : 3.234 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 839 HIS cc_start: 0.6937 (t70) cc_final: 0.6462 (m-70) REVERT: A 926 LYS cc_start: 0.5843 (ptpt) cc_final: 0.5635 (mtmm) REVERT: A 1019 GLU cc_start: 0.6243 (mp0) cc_final: 0.6007 (mp0) REVERT: A 1046 SER cc_start: 0.5765 (m) cc_final: 0.5348 (p) REVERT: A 1049 LEU cc_start: 0.5576 (tp) cc_final: 0.5318 (tp) REVERT: A 1214 ARG cc_start: 0.5860 (mtt180) cc_final: 0.5030 (mmt180) REVERT: A 1253 LYS cc_start: 0.7057 (pttt) cc_final: 0.6623 (tptt) REVERT: A 1404 HIS cc_start: 0.7192 (t70) cc_final: 0.6954 (t70) REVERT: A 1413 SER cc_start: 0.7727 (m) cc_final: 0.7290 (p) REVERT: A 1426 ARG cc_start: 0.6703 (mtp85) cc_final: 0.6348 (mtm110) REVERT: A 1570 TRP cc_start: 0.7205 (p90) cc_final: 0.6807 (p-90) REVERT: A 1672 GLU cc_start: 0.6999 (mm-30) cc_final: 0.6389 (pt0) REVERT: A 1719 GLU cc_start: 0.6590 (mm-30) cc_final: 0.6189 (tt0) REVERT: A 1721 ASN cc_start: 0.7014 (t0) cc_final: 0.6748 (p0) REVERT: A 1729 THR cc_start: 0.5539 (m) cc_final: 0.5106 (m) REVERT: A 1730 ASN cc_start: 0.7984 (p0) cc_final: 0.7516 (m-40) REVERT: A 1731 LYS cc_start: 0.6582 (ttpt) cc_final: 0.6057 (ttpp) REVERT: A 1785 ASP cc_start: 0.5559 (t0) cc_final: 0.5210 (t0) REVERT: A 1843 LEU cc_start: 0.7042 (mt) cc_final: 0.6795 (mt) REVERT: A 1847 ASP cc_start: 0.6195 (m-30) cc_final: 0.5579 (m-30) REVERT: A 1885 LYS cc_start: 0.7078 (tptt) cc_final: 0.6569 (mmtp) REVERT: A 1915 GLU cc_start: 0.7809 (tt0) cc_final: 0.7430 (tm-30) REVERT: A 1928 GLU cc_start: 0.7090 (mt-10) cc_final: 0.6818 (tp30) REVERT: A 1948 MET cc_start: 0.6475 (mmm) cc_final: 0.6259 (mmm) REVERT: A 1950 ASP cc_start: 0.7962 (m-30) cc_final: 0.7675 (t0) REVERT: A 2078 GLU cc_start: 0.6625 (tm-30) cc_final: 0.6321 (tm-30) REVERT: H 142 ARG cc_start: 0.6946 (mtp-110) cc_final: 0.6352 (tpt90) REVERT: H 143 HIS cc_start: 0.4115 (p90) cc_final: 0.3875 (p90) REVERT: H 225 ASP cc_start: 0.5753 (OUTLIER) cc_final: 0.5077 (m-30) REVERT: H 226 TRP cc_start: 0.6860 (m100) cc_final: 0.6501 (m100) REVERT: H 273 TYR cc_start: 0.7001 (OUTLIER) cc_final: 0.6334 (m-80) REVERT: H 334 TRP cc_start: 0.6916 (m100) cc_final: 0.6645 (m100) REVERT: H 343 MET cc_start: 0.6655 (ppp) cc_final: 0.6342 (tmm) REVERT: J 315 ASP cc_start: 0.7886 (t0) cc_final: 0.7495 (m-30) REVERT: J 328 ARG cc_start: 0.7911 (OUTLIER) cc_final: 0.7574 (mtp85) REVERT: J 492 MET cc_start: 0.6003 (ttm) cc_final: 0.5494 (mpp) REVERT: J 555 GLU cc_start: 0.5612 (tm-30) cc_final: 0.5285 (pt0) REVERT: J 565 VAL cc_start: 0.7732 (t) cc_final: 0.6838 (m) REVERT: J 569 TRP cc_start: 0.6482 (m100) cc_final: 0.6110 (m-10) REVERT: J 603 LEU cc_start: 0.7949 (mt) cc_final: 0.7626 (mt) REVERT: J 810 GLU cc_start: 0.6376 (tp30) cc_final: 0.5926 (tp30) REVERT: D 17 GLN cc_start: 0.6437 (mm-40) cc_final: 0.6131 (pp30) REVERT: D 54 ARG cc_start: 0.5686 (OUTLIER) cc_final: 0.5350 (ptp-170) REVERT: D 135 TYR cc_start: 0.6736 (m-80) cc_final: 0.6259 (m-80) REVERT: F 397 GLU cc_start: 0.7902 (mm-30) cc_final: 0.7010 (pt0) REVERT: F 412 MET cc_start: 0.4615 (ttm) cc_final: 0.4400 (ttp) REVERT: F 419 GLN cc_start: 0.5431 (OUTLIER) cc_final: 0.4919 (pt0) REVERT: G 276 ASN cc_start: 0.4655 (OUTLIER) cc_final: 0.4311 (t0) REVERT: G 353 ARG cc_start: 0.5865 (mtt90) cc_final: 0.5417 (mtt90) REVERT: G 354 PHE cc_start: 0.6393 (t80) cc_final: 0.5868 (t80) REVERT: G 386 GLU cc_start: 0.5915 (mp0) cc_final: 0.5391 (mt-10) REVERT: K 7 LYS cc_start: 0.6728 (mtpt) cc_final: 0.6451 (mmmt) REVERT: K 54 MET cc_start: 0.5755 (mtm) cc_final: 0.5140 (mtm) REVERT: B 423 ILE cc_start: 0.5361 (OUTLIER) cc_final: 0.5040 (tt) outliers start: 112 outliers final: 71 residues processed: 591 average time/residue: 0.4551 time to fit residues: 427.8977 Evaluate side-chains 546 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 468 time to evaluate : 3.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 768 GLU Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 1004 ASP Chi-restraints excluded: chain A residue 1029 THR Chi-restraints excluded: chain A residue 1160 LEU Chi-restraints excluded: chain A residue 1236 THR Chi-restraints excluded: chain A residue 1383 PHE Chi-restraints excluded: chain A residue 1547 ILE Chi-restraints excluded: chain A residue 1591 THR Chi-restraints excluded: chain A residue 1687 HIS Chi-restraints excluded: chain A residue 1736 VAL Chi-restraints excluded: chain A residue 1757 LEU Chi-restraints excluded: chain A residue 1798 ILE Chi-restraints excluded: chain A residue 1836 ASN Chi-restraints excluded: chain A residue 1862 VAL Chi-restraints excluded: chain A residue 1886 THR Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 130 GLU Chi-restraints excluded: chain H residue 146 PHE Chi-restraints excluded: chain H residue 167 LEU Chi-restraints excluded: chain H residue 175 THR Chi-restraints excluded: chain H residue 220 LYS Chi-restraints excluded: chain H residue 221 ILE Chi-restraints excluded: chain H residue 225 ASP Chi-restraints excluded: chain H residue 232 ASN Chi-restraints excluded: chain H residue 249 SER Chi-restraints excluded: chain H residue 271 VAL Chi-restraints excluded: chain H residue 273 TYR Chi-restraints excluded: chain H residue 291 LEU Chi-restraints excluded: chain H residue 310 VAL Chi-restraints excluded: chain H residue 327 MET Chi-restraints excluded: chain H residue 375 VAL Chi-restraints excluded: chain H residue 397 THR Chi-restraints excluded: chain H residue 443 LEU Chi-restraints excluded: chain J residue 189 ILE Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 264 ILE Chi-restraints excluded: chain J residue 269 GLN Chi-restraints excluded: chain J residue 288 ASP Chi-restraints excluded: chain J residue 318 SER Chi-restraints excluded: chain J residue 328 ARG Chi-restraints excluded: chain J residue 395 LEU Chi-restraints excluded: chain J residue 408 LEU Chi-restraints excluded: chain J residue 513 THR Chi-restraints excluded: chain J residue 514 VAL Chi-restraints excluded: chain J residue 636 TYR Chi-restraints excluded: chain J residue 661 LEU Chi-restraints excluded: chain J residue 759 LEU Chi-restraints excluded: chain J residue 767 PHE Chi-restraints excluded: chain J residue 789 LEU Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 39 CYS Chi-restraints excluded: chain D residue 54 ARG Chi-restraints excluded: chain D residue 71 ASP Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain F residue 222 ILE Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 401 LEU Chi-restraints excluded: chain F residue 419 GLN Chi-restraints excluded: chain G residue 194 GLU Chi-restraints excluded: chain G residue 276 ASN Chi-restraints excluded: chain G residue 341 VAL Chi-restraints excluded: chain G residue 347 LEU Chi-restraints excluded: chain G residue 382 VAL Chi-restraints excluded: chain G residue 385 ASN Chi-restraints excluded: chain G residue 395 LEU Chi-restraints excluded: chain G residue 465 SER Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain B residue 380 LYS Chi-restraints excluded: chain B residue 423 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 342 optimal weight: 4.9990 chunk 40 optimal weight: 0.6980 chunk 202 optimal weight: 4.9990 chunk 259 optimal weight: 0.9980 chunk 200 optimal weight: 2.9990 chunk 298 optimal weight: 0.6980 chunk 198 optimal weight: 2.9990 chunk 353 optimal weight: 0.8980 chunk 221 optimal weight: 3.9990 chunk 215 optimal weight: 3.9990 chunk 163 optimal weight: 3.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1618 ASN ** H 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 156 ASN ** J 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 668 HIS J 820 GLN ** J 897 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 276 ASN G 283 ASN G 300 GLN G 316 HIS K 25 GLN K 38 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4874 moved from start: 0.4532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 32504 Z= 0.255 Angle : 0.658 14.052 44659 Z= 0.331 Chirality : 0.042 0.462 5136 Planarity : 0.005 0.111 5181 Dihedral : 16.629 174.744 6076 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.47 % Favored : 94.39 % Rotamer: Outliers : 3.71 % Allowed : 20.16 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.11 % Cis-general : 0.09 % Twisted Proline : 0.73 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.14), residues: 3475 helix: 1.93 (0.12), residues: 1835 sheet: -1.29 (0.25), residues: 333 loop : -1.44 (0.17), residues: 1307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 823 HIS 0.009 0.001 HIS H 143 PHE 0.028 0.002 PHE F 158 TYR 0.023 0.002 TYR A1992 ARG 0.009 0.000 ARG A2056 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6950 Ramachandran restraints generated. 3475 Oldfield, 0 Emsley, 3475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6950 Ramachandran restraints generated. 3475 Oldfield, 0 Emsley, 3475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 487 time to evaluate : 3.518 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 839 HIS cc_start: 0.6880 (t70) cc_final: 0.6432 (m-70) REVERT: A 926 LYS cc_start: 0.5954 (ptpt) cc_final: 0.5699 (mtmm) REVERT: A 1019 GLU cc_start: 0.6225 (mp0) cc_final: 0.5958 (mp0) REVERT: A 1046 SER cc_start: 0.5622 (m) cc_final: 0.5214 (p) REVERT: A 1049 LEU cc_start: 0.5664 (tp) cc_final: 0.5406 (tp) REVERT: A 1214 ARG cc_start: 0.5865 (mtt180) cc_final: 0.5040 (mmt180) REVERT: A 1253 LYS cc_start: 0.7285 (pttt) cc_final: 0.6894 (tptt) REVERT: A 1404 HIS cc_start: 0.7200 (t70) cc_final: 0.6962 (t70) REVERT: A 1413 SER cc_start: 0.7738 (m) cc_final: 0.7338 (p) REVERT: A 1426 ARG cc_start: 0.6672 (mtp85) cc_final: 0.6371 (mtm110) REVERT: A 1570 TRP cc_start: 0.7160 (p90) cc_final: 0.6770 (p-90) REVERT: A 1672 GLU cc_start: 0.7016 (mm-30) cc_final: 0.6414 (pt0) REVERT: A 1719 GLU cc_start: 0.6604 (mm-30) cc_final: 0.6199 (tt0) REVERT: A 1721 ASN cc_start: 0.6981 (t0) cc_final: 0.6693 (p0) REVERT: A 1729 THR cc_start: 0.5519 (m) cc_final: 0.5040 (m) REVERT: A 1730 ASN cc_start: 0.8030 (p0) cc_final: 0.7573 (m-40) REVERT: A 1731 LYS cc_start: 0.6593 (ttpt) cc_final: 0.6059 (ttpp) REVERT: A 1843 LEU cc_start: 0.7306 (mt) cc_final: 0.6987 (mt) REVERT: A 1847 ASP cc_start: 0.6180 (m-30) cc_final: 0.5574 (m-30) REVERT: A 1885 LYS cc_start: 0.7121 (tptt) cc_final: 0.6595 (mmtp) REVERT: A 1915 GLU cc_start: 0.7823 (tt0) cc_final: 0.7406 (tm-30) REVERT: A 1928 GLU cc_start: 0.7080 (mt-10) cc_final: 0.6816 (tp30) REVERT: A 1948 MET cc_start: 0.6495 (mmm) cc_final: 0.6201 (mmm) REVERT: A 1950 ASP cc_start: 0.8126 (m-30) cc_final: 0.7785 (t0) REVERT: A 2078 GLU cc_start: 0.6783 (tm-30) cc_final: 0.6428 (tm-30) REVERT: H 142 ARG cc_start: 0.6923 (mtp-110) cc_final: 0.6307 (tpt90) REVERT: H 194 SER cc_start: 0.6432 (m) cc_final: 0.6078 (p) REVERT: H 225 ASP cc_start: 0.5734 (OUTLIER) cc_final: 0.5056 (m-30) REVERT: H 226 TRP cc_start: 0.7219 (m100) cc_final: 0.6739 (m100) REVERT: H 273 TYR cc_start: 0.6978 (OUTLIER) cc_final: 0.6309 (m-80) REVERT: H 334 TRP cc_start: 0.6932 (m100) cc_final: 0.6611 (m100) REVERT: J 242 GLN cc_start: 0.6073 (mt0) cc_final: 0.5848 (tt0) REVERT: J 315 ASP cc_start: 0.7884 (t0) cc_final: 0.7498 (m-30) REVERT: J 328 ARG cc_start: 0.7911 (OUTLIER) cc_final: 0.7533 (mtp85) REVERT: J 492 MET cc_start: 0.5910 (ttm) cc_final: 0.5596 (mpp) REVERT: J 555 GLU cc_start: 0.5618 (tm-30) cc_final: 0.5287 (pt0) REVERT: J 565 VAL cc_start: 0.7582 (t) cc_final: 0.6751 (m) REVERT: J 569 TRP cc_start: 0.6498 (m100) cc_final: 0.5987 (m-10) REVERT: J 577 ARG cc_start: 0.7814 (mtt180) cc_final: 0.7334 (tmm160) REVERT: J 578 GLN cc_start: 0.7652 (pm20) cc_final: 0.7208 (pm20) REVERT: J 603 LEU cc_start: 0.8020 (mt) cc_final: 0.7698 (mm) REVERT: J 810 GLU cc_start: 0.6322 (tp30) cc_final: 0.5900 (tp30) REVERT: D 17 GLN cc_start: 0.6375 (mm-40) cc_final: 0.6064 (pp30) REVERT: D 51 GLU cc_start: 0.7146 (mm-30) cc_final: 0.6849 (mm-30) REVERT: D 54 ARG cc_start: 0.5710 (OUTLIER) cc_final: 0.5325 (ptp-170) REVERT: D 80 MET cc_start: 0.4247 (OUTLIER) cc_final: 0.3901 (mmt) REVERT: D 135 TYR cc_start: 0.6713 (m-80) cc_final: 0.6275 (m-80) REVERT: F 397 GLU cc_start: 0.7840 (mm-30) cc_final: 0.6924 (pt0) REVERT: F 412 MET cc_start: 0.4647 (ttm) cc_final: 0.4423 (ttp) REVERT: F 419 GLN cc_start: 0.5348 (OUTLIER) cc_final: 0.4774 (pt0) REVERT: G 353 ARG cc_start: 0.5830 (mtt90) cc_final: 0.5361 (mtt90) REVERT: G 354 PHE cc_start: 0.6290 (t80) cc_final: 0.6039 (t80) REVERT: K 7 LYS cc_start: 0.6822 (mtpt) cc_final: 0.6577 (mmmt) REVERT: K 54 MET cc_start: 0.5709 (mtm) cc_final: 0.5043 (mtm) outliers start: 114 outliers final: 82 residues processed: 570 average time/residue: 0.4451 time to fit residues: 410.2756 Evaluate side-chains 548 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 460 time to evaluate : 3.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 768 GLU Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 1004 ASP Chi-restraints excluded: chain A residue 1029 THR Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1198 SER Chi-restraints excluded: chain A residue 1236 THR Chi-restraints excluded: chain A residue 1379 MET Chi-restraints excluded: chain A residue 1383 PHE Chi-restraints excluded: chain A residue 1501 THR Chi-restraints excluded: chain A residue 1510 ILE Chi-restraints excluded: chain A residue 1547 ILE Chi-restraints excluded: chain A residue 1591 THR Chi-restraints excluded: chain A residue 1648 ILE Chi-restraints excluded: chain A residue 1662 VAL Chi-restraints excluded: chain A residue 1687 HIS Chi-restraints excluded: chain A residue 1736 VAL Chi-restraints excluded: chain A residue 1757 LEU Chi-restraints excluded: chain A residue 1836 ASN Chi-restraints excluded: chain A residue 1838 SER Chi-restraints excluded: chain A residue 1862 VAL Chi-restraints excluded: chain A residue 1886 THR Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 130 GLU Chi-restraints excluded: chain H residue 146 PHE Chi-restraints excluded: chain H residue 167 LEU Chi-restraints excluded: chain H residue 172 LEU Chi-restraints excluded: chain H residue 175 THR Chi-restraints excluded: chain H residue 186 ASP Chi-restraints excluded: chain H residue 225 ASP Chi-restraints excluded: chain H residue 232 ASN Chi-restraints excluded: chain H residue 249 SER Chi-restraints excluded: chain H residue 271 VAL Chi-restraints excluded: chain H residue 273 TYR Chi-restraints excluded: chain H residue 291 LEU Chi-restraints excluded: chain H residue 304 GLU Chi-restraints excluded: chain H residue 310 VAL Chi-restraints excluded: chain H residue 327 MET Chi-restraints excluded: chain H residue 375 VAL Chi-restraints excluded: chain H residue 397 THR Chi-restraints excluded: chain H residue 443 LEU Chi-restraints excluded: chain J residue 189 ILE Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 264 ILE Chi-restraints excluded: chain J residue 269 GLN Chi-restraints excluded: chain J residue 298 THR Chi-restraints excluded: chain J residue 318 SER Chi-restraints excluded: chain J residue 328 ARG Chi-restraints excluded: chain J residue 395 LEU Chi-restraints excluded: chain J residue 408 LEU Chi-restraints excluded: chain J residue 513 THR Chi-restraints excluded: chain J residue 636 TYR Chi-restraints excluded: chain J residue 661 LEU Chi-restraints excluded: chain J residue 759 LEU Chi-restraints excluded: chain J residue 767 PHE Chi-restraints excluded: chain J residue 788 SER Chi-restraints excluded: chain J residue 789 LEU Chi-restraints excluded: chain J residue 840 ASP Chi-restraints excluded: chain J residue 891 ILE Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 54 ARG Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain F residue 197 ILE Chi-restraints excluded: chain F residue 222 ILE Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain F residue 259 ILE Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 401 LEU Chi-restraints excluded: chain F residue 419 GLN Chi-restraints excluded: chain G residue 302 ASP Chi-restraints excluded: chain G residue 341 VAL Chi-restraints excluded: chain G residue 347 LEU Chi-restraints excluded: chain G residue 385 ASN Chi-restraints excluded: chain G residue 395 LEU Chi-restraints excluded: chain G residue 465 SER Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 49 SER Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain B residue 380 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 218 optimal weight: 9.9990 chunk 141 optimal weight: 0.7980 chunk 211 optimal weight: 0.0470 chunk 106 optimal weight: 0.7980 chunk 69 optimal weight: 0.5980 chunk 68 optimal weight: 0.9980 chunk 224 optimal weight: 9.9990 chunk 240 optimal weight: 0.0270 chunk 174 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 278 optimal weight: 4.9990 overall best weight: 0.4536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1500 HIS A1618 ASN J 240 ASN J 897 ASN ** F 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 316 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4868 moved from start: 0.4703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 32504 Z= 0.183 Angle : 0.637 13.933 44659 Z= 0.318 Chirality : 0.041 0.455 5136 Planarity : 0.004 0.115 5181 Dihedral : 16.556 175.540 6075 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.98 % Favored : 94.88 % Rotamer: Outliers : 3.16 % Allowed : 20.75 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.11 % Cis-general : 0.09 % Twisted Proline : 0.73 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.14), residues: 3475 helix: 2.00 (0.12), residues: 1823 sheet: -1.17 (0.25), residues: 333 loop : -1.31 (0.17), residues: 1319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 823 HIS 0.009 0.001 HIS H 143 PHE 0.029 0.001 PHE F 158 TYR 0.022 0.001 TYR H 353 ARG 0.006 0.000 ARG J 550 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6950 Ramachandran restraints generated. 3475 Oldfield, 0 Emsley, 3475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6950 Ramachandran restraints generated. 3475 Oldfield, 0 Emsley, 3475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 598 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 501 time to evaluate : 3.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 839 HIS cc_start: 0.6881 (t70) cc_final: 0.6421 (m-70) REVERT: A 926 LYS cc_start: 0.5912 (ptpt) cc_final: 0.5671 (mtmm) REVERT: A 1019 GLU cc_start: 0.6230 (mp0) cc_final: 0.5953 (mp0) REVERT: A 1046 SER cc_start: 0.5780 (m) cc_final: 0.5384 (p) REVERT: A 1049 LEU cc_start: 0.5697 (tp) cc_final: 0.5451 (tp) REVERT: A 1214 ARG cc_start: 0.5881 (mtt180) cc_final: 0.5030 (mmt180) REVERT: A 1253 LYS cc_start: 0.7360 (pttt) cc_final: 0.6929 (tptt) REVERT: A 1404 HIS cc_start: 0.7204 (t70) cc_final: 0.6950 (t70) REVERT: A 1413 SER cc_start: 0.7762 (m) cc_final: 0.7324 (p) REVERT: A 1426 ARG cc_start: 0.6729 (mtp85) cc_final: 0.6358 (mtm110) REVERT: A 1570 TRP cc_start: 0.7156 (p90) cc_final: 0.6755 (p-90) REVERT: A 1672 GLU cc_start: 0.6955 (mm-30) cc_final: 0.6396 (pt0) REVERT: A 1719 GLU cc_start: 0.6614 (mm-30) cc_final: 0.6226 (tt0) REVERT: A 1721 ASN cc_start: 0.6986 (t0) cc_final: 0.6720 (p0) REVERT: A 1729 THR cc_start: 0.5510 (m) cc_final: 0.5029 (m) REVERT: A 1730 ASN cc_start: 0.8021 (p0) cc_final: 0.7570 (m-40) REVERT: A 1731 LYS cc_start: 0.6570 (ttpt) cc_final: 0.6042 (ttpp) REVERT: A 1785 ASP cc_start: 0.5558 (t0) cc_final: 0.5088 (t0) REVERT: A 1847 ASP cc_start: 0.6191 (m-30) cc_final: 0.5590 (m-30) REVERT: A 1885 LYS cc_start: 0.7111 (tptt) cc_final: 0.6585 (mmtp) REVERT: A 1915 GLU cc_start: 0.7826 (tt0) cc_final: 0.7436 (tm-30) REVERT: A 1928 GLU cc_start: 0.7084 (mt-10) cc_final: 0.6818 (tp30) REVERT: A 2078 GLU cc_start: 0.6831 (tm-30) cc_final: 0.6506 (tm-30) REVERT: H 142 ARG cc_start: 0.6971 (mtp-110) cc_final: 0.6289 (tpt90) REVERT: H 194 SER cc_start: 0.6609 (m) cc_final: 0.6294 (p) REVERT: H 225 ASP cc_start: 0.5758 (OUTLIER) cc_final: 0.4993 (m-30) REVERT: H 226 TRP cc_start: 0.7251 (m100) cc_final: 0.6801 (m100) REVERT: H 273 TYR cc_start: 0.6848 (OUTLIER) cc_final: 0.6074 (m-80) REVERT: H 316 GLN cc_start: 0.5423 (OUTLIER) cc_final: 0.5181 (tm-30) REVERT: H 334 TRP cc_start: 0.6886 (m100) cc_final: 0.6616 (m100) REVERT: H 401 PHE cc_start: 0.6048 (m-80) cc_final: 0.5837 (m-80) REVERT: H 430 MET cc_start: 0.7051 (mmm) cc_final: 0.6653 (mmt) REVERT: J 242 GLN cc_start: 0.6015 (mt0) cc_final: 0.5779 (tt0) REVERT: J 315 ASP cc_start: 0.7953 (t0) cc_final: 0.7582 (m-30) REVERT: J 328 ARG cc_start: 0.7868 (OUTLIER) cc_final: 0.7536 (mtp85) REVERT: J 492 MET cc_start: 0.5948 (ttm) cc_final: 0.5673 (mpp) REVERT: J 555 GLU cc_start: 0.5604 (tm-30) cc_final: 0.5364 (pt0) REVERT: J 565 VAL cc_start: 0.7583 (t) cc_final: 0.6806 (m) REVERT: J 569 TRP cc_start: 0.6563 (m100) cc_final: 0.6152 (m-10) REVERT: J 810 GLU cc_start: 0.6325 (tp30) cc_final: 0.5896 (tp30) REVERT: J 874 TRP cc_start: 0.6416 (t-100) cc_final: 0.6111 (t-100) REVERT: D 17 GLN cc_start: 0.6572 (mm-40) cc_final: 0.6278 (pp30) REVERT: D 51 GLU cc_start: 0.7155 (mm-30) cc_final: 0.6897 (mm-30) REVERT: D 54 ARG cc_start: 0.5329 (OUTLIER) cc_final: 0.5000 (ptp-170) REVERT: D 80 MET cc_start: 0.4194 (OUTLIER) cc_final: 0.3812 (mmt) REVERT: D 135 TYR cc_start: 0.6767 (m-80) cc_final: 0.6171 (m-80) REVERT: F 331 HIS cc_start: 0.5487 (m170) cc_final: 0.5242 (m170) REVERT: F 397 GLU cc_start: 0.7870 (mm-30) cc_final: 0.6987 (pt0) REVERT: F 419 GLN cc_start: 0.5433 (OUTLIER) cc_final: 0.4793 (pt0) REVERT: G 353 ARG cc_start: 0.5913 (mtt90) cc_final: 0.5458 (mtt90) REVERT: G 354 PHE cc_start: 0.6477 (t80) cc_final: 0.5846 (t80) REVERT: G 431 TYR cc_start: 0.5957 (m-80) cc_final: 0.5488 (m-10) REVERT: K 7 LYS cc_start: 0.6967 (mtpt) cc_final: 0.6721 (mmmt) REVERT: K 54 MET cc_start: 0.5761 (mtm) cc_final: 0.5159 (mtm) outliers start: 97 outliers final: 72 residues processed: 568 average time/residue: 0.4529 time to fit residues: 408.2644 Evaluate side-chains 547 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 468 time to evaluate : 3.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 768 GLU Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 1004 ASP Chi-restraints excluded: chain A residue 1029 THR Chi-restraints excluded: chain A residue 1051 GLU Chi-restraints excluded: chain A residue 1233 ARG Chi-restraints excluded: chain A residue 1383 PHE Chi-restraints excluded: chain A residue 1500 HIS Chi-restraints excluded: chain A residue 1510 ILE Chi-restraints excluded: chain A residue 1547 ILE Chi-restraints excluded: chain A residue 1591 THR Chi-restraints excluded: chain A residue 1624 LEU Chi-restraints excluded: chain A residue 1662 VAL Chi-restraints excluded: chain A residue 1687 HIS Chi-restraints excluded: chain A residue 1736 VAL Chi-restraints excluded: chain A residue 1757 LEU Chi-restraints excluded: chain A residue 1825 ILE Chi-restraints excluded: chain A residue 1886 THR Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 130 GLU Chi-restraints excluded: chain H residue 146 PHE Chi-restraints excluded: chain H residue 167 LEU Chi-restraints excluded: chain H residue 175 THR Chi-restraints excluded: chain H residue 186 ASP Chi-restraints excluded: chain H residue 225 ASP Chi-restraints excluded: chain H residue 232 ASN Chi-restraints excluded: chain H residue 249 SER Chi-restraints excluded: chain H residue 271 VAL Chi-restraints excluded: chain H residue 273 TYR Chi-restraints excluded: chain H residue 291 LEU Chi-restraints excluded: chain H residue 304 GLU Chi-restraints excluded: chain H residue 310 VAL Chi-restraints excluded: chain H residue 316 GLN Chi-restraints excluded: chain H residue 327 MET Chi-restraints excluded: chain H residue 335 ASP Chi-restraints excluded: chain H residue 397 THR Chi-restraints excluded: chain H residue 443 LEU Chi-restraints excluded: chain J residue 189 ILE Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 240 ASN Chi-restraints excluded: chain J residue 264 ILE Chi-restraints excluded: chain J residue 269 GLN Chi-restraints excluded: chain J residue 288 ASP Chi-restraints excluded: chain J residue 318 SER Chi-restraints excluded: chain J residue 328 ARG Chi-restraints excluded: chain J residue 395 LEU Chi-restraints excluded: chain J residue 408 LEU Chi-restraints excluded: chain J residue 513 THR Chi-restraints excluded: chain J residue 661 LEU Chi-restraints excluded: chain J residue 759 LEU Chi-restraints excluded: chain J residue 767 PHE Chi-restraints excluded: chain J residue 783 HIS Chi-restraints excluded: chain J residue 789 LEU Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 54 ARG Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 104 ASN Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 401 LEU Chi-restraints excluded: chain F residue 419 GLN Chi-restraints excluded: chain G residue 194 GLU Chi-restraints excluded: chain G residue 341 VAL Chi-restraints excluded: chain G residue 347 LEU Chi-restraints excluded: chain G residue 382 VAL Chi-restraints excluded: chain G residue 385 ASN Chi-restraints excluded: chain G residue 395 LEU Chi-restraints excluded: chain G residue 465 SER Chi-restraints excluded: chain K residue 49 SER Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain B residue 380 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 321 optimal weight: 4.9990 chunk 338 optimal weight: 4.9990 chunk 309 optimal weight: 1.9990 chunk 329 optimal weight: 1.9990 chunk 198 optimal weight: 3.9990 chunk 143 optimal weight: 2.9990 chunk 258 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 chunk 297 optimal weight: 0.7980 chunk 311 optimal weight: 3.9990 chunk 328 optimal weight: 9.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1667 GLN ** J 897 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 114 ASN ** F 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 300 GLN G 316 HIS G 343 GLN K 75 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4880 moved from start: 0.4794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 32504 Z= 0.312 Angle : 0.700 14.105 44659 Z= 0.350 Chirality : 0.043 0.521 5136 Planarity : 0.005 0.119 5181 Dihedral : 16.551 175.984 6073 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.76 % Favored : 94.10 % Rotamer: Outliers : 3.32 % Allowed : 21.43 % Favored : 75.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.11 % Cis-general : 0.09 % Twisted Proline : 0.73 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.14), residues: 3475 helix: 1.79 (0.12), residues: 1825 sheet: -1.14 (0.25), residues: 333 loop : -1.38 (0.17), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A1039 HIS 0.024 0.001 HIS A1500 PHE 0.029 0.002 PHE A1063 TYR 0.027 0.002 TYR H 353 ARG 0.008 0.001 ARG J 550 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6950 Ramachandran restraints generated. 3475 Oldfield, 0 Emsley, 3475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6950 Ramachandran restraints generated. 3475 Oldfield, 0 Emsley, 3475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 475 time to evaluate : 2.824 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 839 HIS cc_start: 0.6511 (t70) cc_final: 0.6077 (m-70) REVERT: A 926 LYS cc_start: 0.6018 (ptpt) cc_final: 0.5746 (mtmm) REVERT: A 1019 GLU cc_start: 0.6279 (mp0) cc_final: 0.5985 (mp0) REVERT: A 1046 SER cc_start: 0.5636 (m) cc_final: 0.5232 (p) REVERT: A 1049 LEU cc_start: 0.5804 (tp) cc_final: 0.5535 (tp) REVERT: A 1214 ARG cc_start: 0.5839 (mtt180) cc_final: 0.5026 (mmt180) REVERT: A 1253 LYS cc_start: 0.7490 (pttt) cc_final: 0.7085 (tptt) REVERT: A 1404 HIS cc_start: 0.7197 (t70) cc_final: 0.6957 (t70) REVERT: A 1413 SER cc_start: 0.7745 (m) cc_final: 0.7297 (p) REVERT: A 1426 ARG cc_start: 0.6669 (mtp85) cc_final: 0.6373 (mtm110) REVERT: A 1570 TRP cc_start: 0.7221 (p90) cc_final: 0.6806 (p-90) REVERT: A 1672 GLU cc_start: 0.6927 (mm-30) cc_final: 0.6345 (pt0) REVERT: A 1719 GLU cc_start: 0.6607 (mm-30) cc_final: 0.6194 (tt0) REVERT: A 1721 ASN cc_start: 0.6983 (t0) cc_final: 0.6654 (p0) REVERT: A 1724 PHE cc_start: 0.5569 (m-10) cc_final: 0.5365 (m-10) REVERT: A 1729 THR cc_start: 0.5531 (m) cc_final: 0.5043 (m) REVERT: A 1730 ASN cc_start: 0.8042 (p0) cc_final: 0.7581 (m-40) REVERT: A 1731 LYS cc_start: 0.6597 (ttpt) cc_final: 0.6069 (ttpp) REVERT: A 1792 ASN cc_start: 0.7118 (t0) cc_final: 0.6577 (p0) REVERT: A 1847 ASP cc_start: 0.6174 (m-30) cc_final: 0.5579 (m-30) REVERT: A 1885 LYS cc_start: 0.7123 (tptt) cc_final: 0.6605 (mmtp) REVERT: A 1915 GLU cc_start: 0.7837 (tt0) cc_final: 0.7525 (tm-30) REVERT: A 1928 GLU cc_start: 0.7071 (mt-10) cc_final: 0.6811 (tp30) REVERT: A 1948 MET cc_start: 0.6108 (mmm) cc_final: 0.5859 (mmm) REVERT: A 2078 GLU cc_start: 0.6717 (tm-30) cc_final: 0.6366 (tm-30) REVERT: H 142 ARG cc_start: 0.6991 (mtp-110) cc_final: 0.6367 (tpt90) REVERT: H 194 SER cc_start: 0.6436 (m) cc_final: 0.6036 (p) REVERT: H 225 ASP cc_start: 0.5657 (OUTLIER) cc_final: 0.4958 (m-30) REVERT: H 226 TRP cc_start: 0.7196 (m100) cc_final: 0.6661 (m100) REVERT: H 273 TYR cc_start: 0.6794 (OUTLIER) cc_final: 0.6222 (m-80) REVERT: H 334 TRP cc_start: 0.6873 (m100) cc_final: 0.6589 (m100) REVERT: H 376 TRP cc_start: 0.5002 (p-90) cc_final: 0.4646 (p-90) REVERT: H 430 MET cc_start: 0.7002 (mmm) cc_final: 0.6568 (mmt) REVERT: J 242 GLN cc_start: 0.6084 (mt0) cc_final: 0.5819 (tt0) REVERT: J 315 ASP cc_start: 0.7956 (t0) cc_final: 0.7586 (m-30) REVERT: J 328 ARG cc_start: 0.7890 (OUTLIER) cc_final: 0.7498 (mtp85) REVERT: J 386 MET cc_start: 0.6641 (mmt) cc_final: 0.6055 (ptp) REVERT: J 492 MET cc_start: 0.5957 (ttm) cc_final: 0.5694 (mpp) REVERT: J 555 GLU cc_start: 0.6241 (tm-30) cc_final: 0.5987 (pt0) REVERT: J 565 VAL cc_start: 0.7574 (t) cc_final: 0.6832 (m) REVERT: J 569 TRP cc_start: 0.6683 (m100) cc_final: 0.6401 (m-10) REVERT: J 577 ARG cc_start: 0.7837 (mtt180) cc_final: 0.7348 (tmm160) REVERT: J 602 LYS cc_start: 0.6305 (mttt) cc_final: 0.5841 (tptm) REVERT: J 810 GLU cc_start: 0.6344 (tp30) cc_final: 0.5932 (tp30) REVERT: J 874 TRP cc_start: 0.6501 (t-100) cc_final: 0.5496 (t-100) REVERT: D 17 GLN cc_start: 0.6470 (mm-40) cc_final: 0.6152 (pp30) REVERT: D 51 GLU cc_start: 0.7078 (mm-30) cc_final: 0.6698 (mm-30) REVERT: D 54 ARG cc_start: 0.5370 (OUTLIER) cc_final: 0.4947 (ptp-170) REVERT: D 80 MET cc_start: 0.4215 (OUTLIER) cc_final: 0.3900 (mmt) REVERT: D 135 TYR cc_start: 0.6753 (m-80) cc_final: 0.6276 (m-80) REVERT: F 397 GLU cc_start: 0.7710 (mm-30) cc_final: 0.6932 (pt0) REVERT: F 419 GLN cc_start: 0.5771 (pt0) cc_final: 0.5199 (pt0) REVERT: G 353 ARG cc_start: 0.5887 (mtt90) cc_final: 0.5426 (mtt90) REVERT: G 421 ASN cc_start: 0.8337 (t0) cc_final: 0.8129 (t0) REVERT: K 54 MET cc_start: 0.5771 (mtm) cc_final: 0.5084 (mtm) REVERT: K 62 GLU cc_start: 0.7810 (mt-10) cc_final: 0.7598 (mp0) outliers start: 102 outliers final: 81 residues processed: 551 average time/residue: 0.4445 time to fit residues: 391.7770 Evaluate side-chains 537 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 451 time to evaluate : 3.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 848 ASN Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 1004 ASP Chi-restraints excluded: chain A residue 1029 THR Chi-restraints excluded: chain A residue 1032 ILE Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1198 SER Chi-restraints excluded: chain A residue 1379 MET Chi-restraints excluded: chain A residue 1383 PHE Chi-restraints excluded: chain A residue 1501 THR Chi-restraints excluded: chain A residue 1510 ILE Chi-restraints excluded: chain A residue 1547 ILE Chi-restraints excluded: chain A residue 1591 THR Chi-restraints excluded: chain A residue 1662 VAL Chi-restraints excluded: chain A residue 1687 HIS Chi-restraints excluded: chain A residue 1736 VAL Chi-restraints excluded: chain A residue 1798 ILE Chi-restraints excluded: chain A residue 1825 ILE Chi-restraints excluded: chain A residue 1838 SER Chi-restraints excluded: chain A residue 1886 THR Chi-restraints excluded: chain A residue 1913 THR Chi-restraints excluded: chain H residue 130 GLU Chi-restraints excluded: chain H residue 146 PHE Chi-restraints excluded: chain H residue 167 LEU Chi-restraints excluded: chain H residue 172 LEU Chi-restraints excluded: chain H residue 175 THR Chi-restraints excluded: chain H residue 186 ASP Chi-restraints excluded: chain H residue 225 ASP Chi-restraints excluded: chain H residue 232 ASN Chi-restraints excluded: chain H residue 249 SER Chi-restraints excluded: chain H residue 271 VAL Chi-restraints excluded: chain H residue 273 TYR Chi-restraints excluded: chain H residue 291 LEU Chi-restraints excluded: chain H residue 304 GLU Chi-restraints excluded: chain H residue 310 VAL Chi-restraints excluded: chain H residue 327 MET Chi-restraints excluded: chain H residue 375 VAL Chi-restraints excluded: chain H residue 397 THR Chi-restraints excluded: chain H residue 443 LEU Chi-restraints excluded: chain J residue 189 ILE Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 264 ILE Chi-restraints excluded: chain J residue 269 GLN Chi-restraints excluded: chain J residue 298 THR Chi-restraints excluded: chain J residue 318 SER Chi-restraints excluded: chain J residue 328 ARG Chi-restraints excluded: chain J residue 395 LEU Chi-restraints excluded: chain J residue 408 LEU Chi-restraints excluded: chain J residue 513 THR Chi-restraints excluded: chain J residue 514 VAL Chi-restraints excluded: chain J residue 661 LEU Chi-restraints excluded: chain J residue 759 LEU Chi-restraints excluded: chain J residue 767 PHE Chi-restraints excluded: chain J residue 788 SER Chi-restraints excluded: chain J residue 789 LEU Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 54 ARG Chi-restraints excluded: chain D residue 69 ASP Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 104 ASN Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain F residue 222 ILE Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 401 LEU Chi-restraints excluded: chain G residue 194 GLU Chi-restraints excluded: chain G residue 300 GLN Chi-restraints excluded: chain G residue 302 ASP Chi-restraints excluded: chain G residue 341 VAL Chi-restraints excluded: chain G residue 347 LEU Chi-restraints excluded: chain G residue 385 ASN Chi-restraints excluded: chain G residue 395 LEU Chi-restraints excluded: chain G residue 444 VAL Chi-restraints excluded: chain G residue 465 SER Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 49 SER Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain B residue 380 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 216 optimal weight: 7.9990 chunk 348 optimal weight: 5.9990 chunk 212 optimal weight: 2.9990 chunk 165 optimal weight: 0.0470 chunk 242 optimal weight: 0.9990 chunk 365 optimal weight: 0.7980 chunk 336 optimal weight: 3.9990 chunk 291 optimal weight: 5.9990 chunk 30 optimal weight: 0.5980 chunk 224 optimal weight: 7.9990 chunk 178 optimal weight: 4.9990 overall best weight: 1.0882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 897 ASN ** F 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 300 GLN G 316 HIS K 75 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4875 moved from start: 0.4914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 32504 Z= 0.238 Angle : 0.679 14.271 44659 Z= 0.337 Chirality : 0.042 0.470 5136 Planarity : 0.005 0.124 5181 Dihedral : 16.574 175.842 6073 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.38 % Favored : 94.50 % Rotamer: Outliers : 3.03 % Allowed : 21.86 % Favored : 75.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.11 % Cis-general : 0.09 % Twisted Proline : 0.73 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.14), residues: 3475 helix: 1.79 (0.12), residues: 1823 sheet: -1.23 (0.25), residues: 335 loop : -1.34 (0.17), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1039 HIS 0.008 0.001 HIS H 143 PHE 0.035 0.002 PHE A1663 TYR 0.034 0.002 TYR H 353 ARG 0.007 0.001 ARG J 550 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6950 Ramachandran restraints generated. 3475 Oldfield, 0 Emsley, 3475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6950 Ramachandran restraints generated. 3475 Oldfield, 0 Emsley, 3475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 466 time to evaluate : 3.541 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 839 HIS cc_start: 0.6538 (t70) cc_final: 0.6092 (m-70) REVERT: A 926 LYS cc_start: 0.6013 (ptpt) cc_final: 0.5762 (mtmm) REVERT: A 1019 GLU cc_start: 0.6300 (mp0) cc_final: 0.5999 (mp0) REVERT: A 1046 SER cc_start: 0.5630 (m) cc_final: 0.5241 (p) REVERT: A 1049 LEU cc_start: 0.5695 (tp) cc_final: 0.5433 (tp) REVERT: A 1214 ARG cc_start: 0.5859 (mtt180) cc_final: 0.5016 (mmt180) REVERT: A 1253 LYS cc_start: 0.7496 (pttt) cc_final: 0.7096 (tptt) REVERT: A 1404 HIS cc_start: 0.7194 (t70) cc_final: 0.6941 (t70) REVERT: A 1413 SER cc_start: 0.7747 (m) cc_final: 0.7320 (p) REVERT: A 1426 ARG cc_start: 0.6728 (mtp85) cc_final: 0.6366 (mtm110) REVERT: A 1570 TRP cc_start: 0.7107 (p90) cc_final: 0.6770 (p-90) REVERT: A 1672 GLU cc_start: 0.7015 (mm-30) cc_final: 0.6520 (pt0) REVERT: A 1719 GLU cc_start: 0.6596 (mm-30) cc_final: 0.6193 (tt0) REVERT: A 1721 ASN cc_start: 0.6988 (t0) cc_final: 0.6665 (p0) REVERT: A 1729 THR cc_start: 0.5518 (m) cc_final: 0.5029 (m) REVERT: A 1730 ASN cc_start: 0.8048 (p0) cc_final: 0.7545 (m-40) REVERT: A 1731 LYS cc_start: 0.6527 (ttpt) cc_final: 0.5998 (ttpp) REVERT: A 1847 ASP cc_start: 0.6191 (m-30) cc_final: 0.5595 (m-30) REVERT: A 1885 LYS cc_start: 0.7123 (tptt) cc_final: 0.6607 (mmtp) REVERT: A 1915 GLU cc_start: 0.7834 (tt0) cc_final: 0.7439 (tm-30) REVERT: A 1928 GLU cc_start: 0.7081 (mt-10) cc_final: 0.6818 (tp30) REVERT: A 1948 MET cc_start: 0.6081 (mmm) cc_final: 0.5858 (mmm) REVERT: A 2078 GLU cc_start: 0.6819 (tm-30) cc_final: 0.6508 (tm-30) REVERT: H 142 ARG cc_start: 0.6938 (mtp-110) cc_final: 0.6297 (tpt90) REVERT: H 194 SER cc_start: 0.6397 (m) cc_final: 0.6053 (p) REVERT: H 225 ASP cc_start: 0.5613 (OUTLIER) cc_final: 0.4838 (m-30) REVERT: H 226 TRP cc_start: 0.7191 (m100) cc_final: 0.6756 (m100) REVERT: H 273 TYR cc_start: 0.7078 (OUTLIER) cc_final: 0.6505 (m-80) REVERT: H 316 GLN cc_start: 0.5383 (OUTLIER) cc_final: 0.5114 (tm-30) REVERT: H 334 TRP cc_start: 0.6892 (m100) cc_final: 0.6616 (m100) REVERT: H 376 TRP cc_start: 0.5019 (p-90) cc_final: 0.4695 (p-90) REVERT: H 430 MET cc_start: 0.7045 (mmm) cc_final: 0.6632 (mmt) REVERT: J 315 ASP cc_start: 0.7953 (t0) cc_final: 0.7586 (m-30) REVERT: J 328 ARG cc_start: 0.7868 (OUTLIER) cc_final: 0.7462 (mtp85) REVERT: J 386 MET cc_start: 0.6638 (mmt) cc_final: 0.6051 (ptp) REVERT: J 492 MET cc_start: 0.6191 (ttm) cc_final: 0.5900 (mpp) REVERT: J 555 GLU cc_start: 0.6256 (tm-30) cc_final: 0.6021 (pt0) REVERT: J 565 VAL cc_start: 0.7568 (t) cc_final: 0.6344 (m) REVERT: J 569 TRP cc_start: 0.6450 (m100) cc_final: 0.6225 (m-10) REVERT: J 577 ARG cc_start: 0.7765 (mtt180) cc_final: 0.7270 (tmm160) REVERT: J 578 GLN cc_start: 0.7624 (pm20) cc_final: 0.5623 (pt0) REVERT: J 602 LYS cc_start: 0.6324 (mttt) cc_final: 0.5844 (tptm) REVERT: J 810 GLU cc_start: 0.6349 (tp30) cc_final: 0.5927 (tp30) REVERT: J 874 TRP cc_start: 0.6531 (t-100) cc_final: 0.5570 (t-100) REVERT: D 17 GLN cc_start: 0.6582 (mm-40) cc_final: 0.6282 (pp30) REVERT: D 51 GLU cc_start: 0.7171 (mm-30) cc_final: 0.6782 (mm-30) REVERT: D 54 ARG cc_start: 0.5577 (OUTLIER) cc_final: 0.5123 (ptp-170) REVERT: D 80 MET cc_start: 0.4226 (OUTLIER) cc_final: 0.3892 (mmt) REVERT: D 135 TYR cc_start: 0.6707 (m-80) cc_final: 0.6113 (m-80) REVERT: F 331 HIS cc_start: 0.5396 (m170) cc_final: 0.5174 (m170) REVERT: F 397 GLU cc_start: 0.7769 (mm-30) cc_final: 0.6970 (pt0) REVERT: F 412 MET cc_start: 0.4631 (ttp) cc_final: 0.4218 (mtp) REVERT: F 419 GLN cc_start: 0.5771 (pt0) cc_final: 0.5173 (pt0) REVERT: G 353 ARG cc_start: 0.5955 (mtt90) cc_final: 0.5635 (mtt90) REVERT: G 354 PHE cc_start: 0.6056 (t80) cc_final: 0.5651 (t80) REVERT: G 421 ASN cc_start: 0.8372 (t0) cc_final: 0.8108 (t0) REVERT: K 54 MET cc_start: 0.5986 (mtm) cc_final: 0.5420 (mtm) outliers start: 93 outliers final: 79 residues processed: 536 average time/residue: 0.4698 time to fit residues: 406.1134 Evaluate side-chains 537 residues out of total 3148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 452 time to evaluate : 3.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 1004 ASP Chi-restraints excluded: chain A residue 1029 THR Chi-restraints excluded: chain A residue 1032 ILE Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1198 SER Chi-restraints excluded: chain A residue 1383 PHE Chi-restraints excluded: chain A residue 1400 ILE Chi-restraints excluded: chain A residue 1510 ILE Chi-restraints excluded: chain A residue 1547 ILE Chi-restraints excluded: chain A residue 1591 THR Chi-restraints excluded: chain A residue 1662 VAL Chi-restraints excluded: chain A residue 1687 HIS Chi-restraints excluded: chain A residue 1736 VAL Chi-restraints excluded: chain A residue 1798 ILE Chi-restraints excluded: chain A residue 1825 ILE Chi-restraints excluded: chain A residue 1838 SER Chi-restraints excluded: chain A residue 1886 THR Chi-restraints excluded: chain A residue 1941 LEU Chi-restraints excluded: chain H residue 130 GLU Chi-restraints excluded: chain H residue 146 PHE Chi-restraints excluded: chain H residue 167 LEU Chi-restraints excluded: chain H residue 175 THR Chi-restraints excluded: chain H residue 186 ASP Chi-restraints excluded: chain H residue 225 ASP Chi-restraints excluded: chain H residue 232 ASN Chi-restraints excluded: chain H residue 249 SER Chi-restraints excluded: chain H residue 271 VAL Chi-restraints excluded: chain H residue 273 TYR Chi-restraints excluded: chain H residue 291 LEU Chi-restraints excluded: chain H residue 304 GLU Chi-restraints excluded: chain H residue 310 VAL Chi-restraints excluded: chain H residue 316 GLN Chi-restraints excluded: chain H residue 327 MET Chi-restraints excluded: chain H residue 335 ASP Chi-restraints excluded: chain H residue 375 VAL Chi-restraints excluded: chain H residue 397 THR Chi-restraints excluded: chain H residue 443 LEU Chi-restraints excluded: chain J residue 189 ILE Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 264 ILE Chi-restraints excluded: chain J residue 269 GLN Chi-restraints excluded: chain J residue 298 THR Chi-restraints excluded: chain J residue 318 SER Chi-restraints excluded: chain J residue 328 ARG Chi-restraints excluded: chain J residue 395 LEU Chi-restraints excluded: chain J residue 408 LEU Chi-restraints excluded: chain J residue 513 THR Chi-restraints excluded: chain J residue 514 VAL Chi-restraints excluded: chain J residue 661 LEU Chi-restraints excluded: chain J residue 759 LEU Chi-restraints excluded: chain J residue 767 PHE Chi-restraints excluded: chain J residue 783 HIS Chi-restraints excluded: chain J residue 788 SER Chi-restraints excluded: chain J residue 789 LEU Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 39 CYS Chi-restraints excluded: chain D residue 54 ARG Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 104 ASN Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain F residue 259 ILE Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 401 LEU Chi-restraints excluded: chain G residue 194 GLU Chi-restraints excluded: chain G residue 300 GLN Chi-restraints excluded: chain G residue 341 VAL Chi-restraints excluded: chain G residue 347 LEU Chi-restraints excluded: chain G residue 385 ASN Chi-restraints excluded: chain G residue 395 LEU Chi-restraints excluded: chain G residue 444 VAL Chi-restraints excluded: chain G residue 465 SER Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 49 SER Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain B residue 380 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 231 optimal weight: 0.0040 chunk 310 optimal weight: 1.9990 chunk 89 optimal weight: 0.5980 chunk 268 optimal weight: 0.4980 chunk 42 optimal weight: 0.4980 chunk 80 optimal weight: 0.7980 chunk 291 optimal weight: 4.9990 chunk 122 optimal weight: 0.9990 chunk 299 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 897 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 244 HIS G 316 HIS K 75 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.152235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.128263 restraints weight = 50506.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.128999 restraints weight = 49453.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.130064 restraints weight = 40729.375| |-----------------------------------------------------------------------------| r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.5060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 32504 Z= 0.189 Angle : 0.659 13.707 44659 Z= 0.327 Chirality : 0.041 0.533 5136 Planarity : 0.005 0.120 5181 Dihedral : 16.524 176.746 6073 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.24 % Favored : 94.65 % Rotamer: Outliers : 2.57 % Allowed : 22.38 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.11 % Cis-general : 0.09 % Twisted Proline : 0.73 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.14), residues: 3475 helix: 1.83 (0.12), residues: 1826 sheet: -1.15 (0.25), residues: 342 loop : -1.24 (0.17), residues: 1307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP F 208 HIS 0.008 0.001 HIS H 143 PHE 0.029 0.001 PHE F 158 TYR 0.029 0.001 TYR H 353 ARG 0.016 0.000 ARG D 25 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8161.07 seconds wall clock time: 151 minutes 34.34 seconds (9094.34 seconds total)