Starting phenix.real_space_refine on Sun Feb 18 05:19:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6skz_10232/02_2024/6skz_10232_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6skz_10232/02_2024/6skz_10232.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6skz_10232/02_2024/6skz_10232.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6skz_10232/02_2024/6skz_10232.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6skz_10232/02_2024/6skz_10232_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6skz_10232/02_2024/6skz_10232_updated.pdb" } resolution = 3.4 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 1 5.21 5 S 95 5.16 5 C 13302 2.51 5 N 3643 2.21 5 O 3886 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 317": "NH1" <-> "NH2" Residue "A TYR 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 348": "OE1" <-> "OE2" Residue "A GLU 349": "OE1" <-> "OE2" Residue "A TYR 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 361": "NH1" <-> "NH2" Residue "A ARG 366": "NH1" <-> "NH2" Residue "A PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 544": "NH1" <-> "NH2" Residue "A PHE 663": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 680": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 721": "NH1" <-> "NH2" Residue "A PHE 728": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 791": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 811": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 843": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 854": "NH1" <-> "NH2" Residue "A ARG 891": "NH1" <-> "NH2" Residue "A TYR 898": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 903": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 913": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 947": "NH1" <-> "NH2" Residue "A PHE 949": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 954": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 970": "OE1" <-> "OE2" Residue "A TYR 979": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 985": "OE1" <-> "OE2" Residue "A ASP 993": "OD1" <-> "OD2" Residue "A ASP 996": "OD1" <-> "OD2" Residue "A PHE 998": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1004": "OD1" <-> "OD2" Residue "A PHE 1007": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1051": "OE1" <-> "OE2" Residue "A TYR 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1079": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1088": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1137": "NH1" <-> "NH2" Residue "A PHE 1143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1287": "NH1" <-> "NH2" Residue "A PHE 1303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1379": "OE1" <-> "OE2" Residue "A ARG 1461": "NH1" <-> "NH2" Residue "A TYR 1465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1468": "NH1" <-> "NH2" Residue "A PHE 1501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1518": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1536": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1641": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1694": "OE1" <-> "OE2" Residue "A TYR 1733": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1769": "NH1" <-> "NH2" Residue "A PHE 1830": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1857": "OE1" <-> "OE2" Residue "A ASP 1862": "OD1" <-> "OD2" Residue "A ARG 1863": "NH1" <-> "NH2" Residue "A ARG 1880": "NH1" <-> "NH2" Residue "A TYR 1931": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1945": "NH1" <-> "NH2" Residue "A TYR 1948": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1959": "NH1" <-> "NH2" Residue "A TYR 1963": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2015": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2019": "NH1" <-> "NH2" Residue "A ARG 2056": "NH1" <-> "NH2" Residue "A ARG 2068": "NH1" <-> "NH2" Residue "A ARG 2081": "NH1" <-> "NH2" Residue "A ARG 2100": "NH1" <-> "NH2" Residue "A GLU 2113": "OE1" <-> "OE2" Residue "A ARG 2115": "NH1" <-> "NH2" Residue "A ARG 2123": "NH1" <-> "NH2" Residue "A ARG 2134": "NH1" <-> "NH2" Residue "A ARG 2158": "NH1" <-> "NH2" Residue "A ARG 2163": "NH1" <-> "NH2" Residue "A ARG 2173": "NH1" <-> "NH2" Residue "A ARG 2176": "NH1" <-> "NH2" Residue "A ARG 2178": "NH1" <-> "NH2" Residue "A ASP 2216": "OD1" <-> "OD2" Residue "A GLU 2219": "OE1" <-> "OE2" Residue "A ARG 2225": "NH1" <-> "NH2" Residue "A ARG 2245": "NH1" <-> "NH2" Residue "A TYR 2254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2260": "NH1" <-> "NH2" Residue "A ARG 2286": "NH1" <-> "NH2" Residue "A ARG 2314": "NH1" <-> "NH2" Residue "A ARG 2364": "NH1" <-> "NH2" Residue "A ARG 2365": "NH1" <-> "NH2" Residue "A ARG 2370": "NH1" <-> "NH2" Residue "A ASP 2394": "OD1" <-> "OD2" Residue "A ARG 2397": "NH1" <-> "NH2" Residue "A ARG 2425": "NH1" <-> "NH2" Residue "A PHE 2445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2455": "NH1" <-> "NH2" Residue "A ARG 2473": "NH1" <-> "NH2" Residue "A ARG 2515": "NH1" <-> "NH2" Residue "A PHE 2579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2603": "NH1" <-> "NH2" Residue "A ARG 2617": "NH1" <-> "NH2" Residue "A ARG 2637": "NH1" <-> "NH2" Residue "A ARG 2640": "NH1" <-> "NH2" Residue "A ARG 2642": "NH1" <-> "NH2" Residue "A ARG 2647": "NH1" <-> "NH2" Residue "A TYR 2649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2662": "OE1" <-> "OE2" Residue "A ARG 2680": "NH1" <-> "NH2" Residue "A ARG 2706": "NH1" <-> "NH2" Residue "A TYR 2710": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2711": "NH1" <-> "NH2" Residue "A ARG 2712": "NH1" <-> "NH2" Residue "A ARG 2716": "NH1" <-> "NH2" Residue "A ARG 2722": "NH1" <-> "NH2" Residue "A TYR 2723": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2728": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2739": "NH1" <-> "NH2" Residue "A TYR 2742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2744": "NH1" <-> "NH2" Residue "A ARG 2761": "NH1" <-> "NH2" Residue "A ARG 2788": "NH1" <-> "NH2" Residue "A PHE 2798": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2799": "NH1" <-> "NH2" Residue "A ARG 2818": "NH1" <-> "NH2" Residue "A ARG 2819": "NH1" <-> "NH2" Residue "A ARG 2829": "NH1" <-> "NH2" Residue "A ARG 2843": "NH1" <-> "NH2" Residue "A ARG 2901": "NH1" <-> "NH2" Residue "A TYR 2943": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 20930 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 20930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2640, 20930 Unusual residues: {' MG': 1, 'AGS': 1} Inner-chain residues flagged as termini: ['pdbres="ALA A2944 "'] Classifications: {'peptide': 2638, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 111, 'TRANS': 2526, None: 2} Not linked: pdbres="ALA A2944 " pdbres="AGS A3001 " Not linked: pdbres="AGS A3001 " pdbres=" MG A3002 " Chain breaks: 20 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Time building chain proxies: 10.90, per 1000 atoms: 0.52 Number of scatterers: 20930 At special positions: 0 Unit cell: (108.018, 138.729, 205.446, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 95 16.00 P 3 15.00 Mg 1 11.99 O 3886 8.00 N 3643 7.00 C 13302 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A1408 " - pdb=" SG CYS A1447 " distance=2.05 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: 7.25 Conformation dependent library (CDL) restraints added in 3.7 seconds 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5064 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 137 helices and 3 sheets defined 65.8% alpha, 1.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.11 Creating SS restraints... Processing helix chain 'A' and resid 15 through 21 Processing helix chain 'A' and resid 26 through 39 WARNING: missing atoms! Processing helix chain 'A' and resid 56 through 72 Processing helix chain 'A' and resid 86 through 102 Proline residue: A 95 - end of helix Processing helix chain 'A' and resid 111 through 124 Processing helix chain 'A' and resid 137 through 149 Processing helix chain 'A' and resid 151 through 158 removed outlier: 3.989A pdb=" N ALA A 158 " --> pdb=" O ALA A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 178 Processing helix chain 'A' and resid 219 through 232 Processing helix chain 'A' and resid 245 through 253 Processing helix chain 'A' and resid 263 through 280 Processing helix chain 'A' and resid 284 through 294 Processing helix chain 'A' and resid 313 through 326 Processing helix chain 'A' and resid 328 through 336 removed outlier: 3.859A pdb=" N GLN A 332 " --> pdb=" O ARG A 328 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG A 336 " --> pdb=" O GLN A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 359 Processing helix chain 'A' and resid 399 through 415 Processing helix chain 'A' and resid 448 through 453 Processing helix chain 'A' and resid 458 through 474 removed outlier: 4.196A pdb=" N ILE A 468 " --> pdb=" O ALA A 464 " (cutoff:3.500A) Proline residue: A 469 - end of helix removed outlier: 4.136A pdb=" N HIS A 474 " --> pdb=" O PHE A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 492 Processing helix chain 'A' and resid 498 through 513 removed outlier: 4.494A pdb=" N ILE A 513 " --> pdb=" O SER A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 534 removed outlier: 6.145A pdb=" N SER A 524 " --> pdb=" O SER A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 556 Processing helix chain 'A' and resid 566 through 574 Processing helix chain 'A' and resid 585 through 601 Processing helix chain 'A' and resid 607 through 620 Processing helix chain 'A' and resid 626 through 631 Processing helix chain 'A' and resid 638 through 649 Processing helix chain 'A' and resid 666 through 675 Processing helix chain 'A' and resid 678 through 684 Processing helix chain 'A' and resid 716 through 742 Proline residue: A 730 - end of helix removed outlier: 3.835A pdb=" N TRP A 742 " --> pdb=" O LEU A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 770 Processing helix chain 'A' and resid 784 through 802 Processing helix chain 'A' and resid 810 through 821 Proline residue: A 820 - end of helix Processing helix chain 'A' and resid 827 through 832 Processing helix chain 'A' and resid 838 through 857 Processing helix chain 'A' and resid 896 through 898 No H-bonds generated for 'chain 'A' and resid 896 through 898' Processing helix chain 'A' and resid 900 through 920 Processing helix chain 'A' and resid 929 through 935 Processing helix chain 'A' and resid 945 through 955 removed outlier: 4.345A pdb=" N GLU A 948 " --> pdb=" O CYS A 945 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG A 951 " --> pdb=" O GLU A 948 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N THR A 955 " --> pdb=" O GLU A 952 " (cutoff:3.500A) Processing helix chain 'A' and resid 962 through 976 removed outlier: 4.035A pdb=" N VAL A 976 " --> pdb=" O ALA A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 997 Processing helix chain 'A' and resid 999 through 1002 No H-bonds generated for 'chain 'A' and resid 999 through 1002' Processing helix chain 'A' and resid 1010 through 1022 Processing helix chain 'A' and resid 1032 through 1047 removed outlier: 4.136A pdb=" N GLU A1047 " --> pdb=" O LEU A1043 " (cutoff:3.500A) Processing helix chain 'A' and resid 1052 through 1055 No H-bonds generated for 'chain 'A' and resid 1052 through 1055' Processing helix chain 'A' and resid 1061 through 1070 Processing helix chain 'A' and resid 1074 through 1083 Processing helix chain 'A' and resid 1087 through 1089 No H-bonds generated for 'chain 'A' and resid 1087 through 1089' Processing helix chain 'A' and resid 1093 through 1106 removed outlier: 4.144A pdb=" N HIS A1096 " --> pdb=" O LEU A1093 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N ASP A1097 " --> pdb=" O LYS A1094 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ASP A1098 " --> pdb=" O THR A1095 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE A1099 " --> pdb=" O HIS A1096 " (cutoff:3.500A) Processing helix chain 'A' and resid 1114 through 1130 Processing helix chain 'A' and resid 1135 through 1145 removed outlier: 3.851A pdb=" N ILE A1145 " --> pdb=" O HIS A1141 " (cutoff:3.500A) Processing helix chain 'A' and resid 1162 through 1177 removed outlier: 3.508A pdb=" N LEU A1177 " --> pdb=" O ILE A1173 " (cutoff:3.500A) Processing helix chain 'A' and resid 1183 through 1200 removed outlier: 4.218A pdb=" N LEU A1188 " --> pdb=" O GLU A1184 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE A1189 " --> pdb=" O LEU A1185 " (cutoff:3.500A) Proline residue: A1191 - end of helix removed outlier: 4.896A pdb=" N ASN A1200 " --> pdb=" O THR A1196 " (cutoff:3.500A) Processing helix chain 'A' and resid 1203 through 1205 No H-bonds generated for 'chain 'A' and resid 1203 through 1205' Processing helix chain 'A' and resid 1216 through 1234 removed outlier: 3.719A pdb=" N ARG A1221 " --> pdb=" O LEU A1217 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLU A1222 " --> pdb=" O ASP A1218 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N THR A1225 " --> pdb=" O ARG A1221 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N GLU A1226 " --> pdb=" O GLU A1222 " (cutoff:3.500A) Processing helix chain 'A' and resid 1237 through 1247 Processing helix chain 'A' and resid 1251 through 1257 Processing helix chain 'A' and resid 1259 through 1268 Processing helix chain 'A' and resid 1283 through 1287 Processing helix chain 'A' and resid 1295 through 1301 Processing helix chain 'A' and resid 1303 through 1313 removed outlier: 3.622A pdb=" N ILE A1313 " --> pdb=" O THR A1309 " (cutoff:3.500A) Processing helix chain 'A' and resid 1319 through 1323 Processing helix chain 'A' and resid 1333 through 1343 Processing helix chain 'A' and resid 1360 through 1371 Proline residue: A1364 - end of helix Processing helix chain 'A' and resid 1384 through 1397 Processing helix chain 'A' and resid 1406 through 1421 Processing helix chain 'A' and resid 1429 through 1442 removed outlier: 3.648A pdb=" N SER A1437 " --> pdb=" O MET A1433 " (cutoff:3.500A) Processing helix chain 'A' and resid 1449 through 1466 removed outlier: 3.616A pdb=" N GLY A1453 " --> pdb=" O ASP A1449 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASP A1463 " --> pdb=" O ILE A1459 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N GLU A1464 " --> pdb=" O LYS A1460 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N TYR A1465 " --> pdb=" O ARG A1461 " (cutoff:3.500A) Processing helix chain 'A' and resid 1470 through 1489 removed outlier: 3.624A pdb=" N GLY A1475 " --> pdb=" O SER A1471 " (cutoff:3.500A) Processing helix chain 'A' and resid 1498 through 1521 removed outlier: 3.923A pdb=" N LYS A1502 " --> pdb=" O GLU A1498 " (cutoff:3.500A) Processing helix chain 'A' and resid 1530 through 1545 removed outlier: 3.758A pdb=" N HIS A1545 " --> pdb=" O GLU A1541 " (cutoff:3.500A) Processing helix chain 'A' and resid 1557 through 1569 Processing helix chain 'A' and resid 1578 through 1588 Processing helix chain 'A' and resid 1606 through 1619 removed outlier: 5.078A pdb=" N ALA A1614 " --> pdb=" O ILE A1610 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N VAL A1615 " --> pdb=" O LYS A1611 " (cutoff:3.500A) Processing helix chain 'A' and resid 1627 through 1644 Processing helix chain 'A' and resid 1649 through 1651 No H-bonds generated for 'chain 'A' and resid 1649 through 1651' Processing helix chain 'A' and resid 1657 through 1663 Processing helix chain 'A' and resid 1670 through 1683 removed outlier: 3.777A pdb=" N LEU A1681 " --> pdb=" O LEU A1677 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR A1682 " --> pdb=" O ILE A1678 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ILE A1683 " --> pdb=" O LYS A1679 " (cutoff:3.500A) Processing helix chain 'A' and resid 1687 through 1706 Processing helix chain 'A' and resid 1710 through 1719 removed outlier: 3.574A pdb=" N GLU A1718 " --> pdb=" O SER A1714 " (cutoff:3.500A) Processing helix chain 'A' and resid 1722 through 1726 Processing helix chain 'A' and resid 1762 through 1773 removed outlier: 3.850A pdb=" N SER A1773 " --> pdb=" O ARG A1769 " (cutoff:3.500A) Processing helix chain 'A' and resid 1778 through 1781 No H-bonds generated for 'chain 'A' and resid 1778 through 1781' Processing helix chain 'A' and resid 1784 through 1787 No H-bonds generated for 'chain 'A' and resid 1784 through 1787' Processing helix chain 'A' and resid 1793 through 1810 Proline residue: A1799 - end of helix removed outlier: 3.658A pdb=" N LEU A1810 " --> pdb=" O LEU A1806 " (cutoff:3.500A) Processing helix chain 'A' and resid 1815 through 1827 removed outlier: 4.096A pdb=" N GLN A1825 " --> pdb=" O SER A1821 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N GLU A1826 " --> pdb=" O GLU A1822 " (cutoff:3.500A) Processing helix chain 'A' and resid 1836 through 1851 removed outlier: 3.759A pdb=" N LEU A1841 " --> pdb=" O GLU A1837 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR A1851 " --> pdb=" O LEU A1847 " (cutoff:3.500A) Processing helix chain 'A' and resid 1860 through 1862 No H-bonds generated for 'chain 'A' and resid 1860 through 1862' Processing helix chain 'A' and resid 1871 through 1880 Processing helix chain 'A' and resid 1884 through 1898 Processing helix chain 'A' and resid 1916 through 1923 removed outlier: 3.720A pdb=" N ASN A1923 " --> pdb=" O GLU A1919 " (cutoff:3.500A) Processing helix chain 'A' and resid 1929 through 1932 Processing helix chain 'A' and resid 1939 through 1948 Processing helix chain 'A' and resid 1953 through 1968 removed outlier: 3.799A pdb=" N PHE A1958 " --> pdb=" O LYS A1954 " (cutoff:3.500A) Processing helix chain 'A' and resid 1972 through 1988 removed outlier: 3.806A pdb=" N ARG A1975 " --> pdb=" O LEU A1972 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU A1988 " --> pdb=" O LEU A1985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1991 through 2000 removed outlier: 3.623A pdb=" N SER A2000 " --> pdb=" O SER A1996 " (cutoff:3.500A) Processing helix chain 'A' and resid 2009 through 2021 removed outlier: 3.954A pdb=" N PHE A2015 " --> pdb=" O LEU A2011 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N THR A2017 " --> pdb=" O ALA A2013 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ALA A2018 " --> pdb=" O THR A2014 " (cutoff:3.500A) Processing helix chain 'A' and resid 2035 through 2047 Processing helix chain 'A' and resid 2052 through 2071 Processing helix chain 'A' and resid 2077 through 2098 removed outlier: 3.629A pdb=" N ASN A2098 " --> pdb=" O ASP A2094 " (cutoff:3.500A) Processing helix chain 'A' and resid 2102 through 2121 removed outlier: 4.977A pdb=" N SER A2121 " --> pdb=" O LYS A2117 " (cutoff:3.500A) Processing helix chain 'A' and resid 2124 through 2143 Processing helix chain 'A' and resid 2154 through 2174 Processing helix chain 'A' and resid 2178 through 2196 removed outlier: 3.817A pdb=" N LEU A2191 " --> pdb=" O ALA A2187 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE A2192 " --> pdb=" O LEU A2188 " (cutoff:3.500A) Proline residue: A2193 - end of helix Processing helix chain 'A' and resid 2203 through 2217 Processing helix chain 'A' and resid 2220 through 2232 Processing helix chain 'A' and resid 2245 through 2258 Processing helix chain 'A' and resid 2264 through 2270 removed outlier: 3.919A pdb=" N GLN A2268 " --> pdb=" O PRO A2264 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS A2269 " --> pdb=" O ASP A2265 " (cutoff:3.500A) Processing helix chain 'A' and resid 2272 through 2278 Processing helix chain 'A' and resid 2286 through 2303 Processing helix chain 'A' and resid 2306 through 2329 Processing helix chain 'A' and resid 2349 through 2385 Processing helix chain 'A' and resid 2394 through 2404 Processing helix chain 'A' and resid 2409 through 2421 removed outlier: 5.239A pdb=" N ASN A2420 " --> pdb=" O LYS A2416 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N LYS A2421 " --> pdb=" O LYS A2417 " (cutoff:3.500A) Processing helix chain 'A' and resid 2424 through 2426 No H-bonds generated for 'chain 'A' and resid 2424 through 2426' Processing helix chain 'A' and resid 2431 through 2434 No H-bonds generated for 'chain 'A' and resid 2431 through 2434' Processing helix chain 'A' and resid 2444 through 2459 removed outlier: 3.685A pdb=" N ASP A2451 " --> pdb=" O LYS A2447 " (cutoff:3.500A) Processing helix chain 'A' and resid 2461 through 2472 removed outlier: 5.841A pdb=" N TYR A2466 " --> pdb=" O TYR A2462 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N HIS A2467 " --> pdb=" O HIS A2463 " (cutoff:3.500A) Processing helix chain 'A' and resid 2483 through 2499 removed outlier: 3.913A pdb=" N LYS A2499 " --> pdb=" O LYS A2495 " (cutoff:3.500A) Processing helix chain 'A' and resid 2507 through 2522 Processing helix chain 'A' and resid 2541 through 2552 Processing helix chain 'A' and resid 2616 through 2635 removed outlier: 3.929A pdb=" N LYS A2634 " --> pdb=" O SER A2630 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N LEU A2635 " --> pdb=" O GLU A2631 " (cutoff:3.500A) Processing helix chain 'A' and resid 2637 through 2641 Processing helix chain 'A' and resid 2670 through 2681 Proline residue: A2676 - end of helix removed outlier: 3.933A pdb=" N GLU A2679 " --> pdb=" O MET A2675 " (cutoff:3.500A) Processing helix chain 'A' and resid 2688 through 2699 removed outlier: 3.880A pdb=" N ALA A2698 " --> pdb=" O GLU A2694 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLN A2699 " --> pdb=" O ILE A2695 " (cutoff:3.500A) Processing helix chain 'A' and resid 2703 through 2716 removed outlier: 3.903A pdb=" N ARG A2716 " --> pdb=" O ARG A2712 " (cutoff:3.500A) Processing helix chain 'A' and resid 2721 through 2728 removed outlier: 3.792A pdb=" N PHE A2725 " --> pdb=" O ARG A2722 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLU A2727 " --> pdb=" O PHE A2724 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N TYR A2728 " --> pdb=" O PHE A2725 " (cutoff:3.500A) Processing helix chain 'A' and resid 2732 through 2755 Processing helix chain 'A' and resid 2763 through 2765 No H-bonds generated for 'chain 'A' and resid 2763 through 2765' Processing helix chain 'A' and resid 2786 through 2789 removed outlier: 3.675A pdb=" N VAL A2789 " --> pdb=" O MET A2786 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2786 through 2789' Processing helix chain 'A' and resid 2802 through 2808 removed outlier: 4.501A pdb=" N MET A2808 " --> pdb=" O ILE A2804 " (cutoff:3.500A) Processing helix chain 'A' and resid 2816 through 2828 Processing helix chain 'A' and resid 2832 through 2843 Processing helix chain 'A' and resid 2854 through 2860 Processing helix chain 'A' and resid 2898 through 2909 Processing helix chain 'A' and resid 2916 through 2927 Processing helix chain 'A' and resid 2930 through 2935 removed outlier: 4.434A pdb=" N VAL A2935 " --> pdb=" O SER A2931 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 2534 through 2536 Processing sheet with id= B, first strand: chain 'A' and resid 2651 through 2655 removed outlier: 6.706A pdb=" N SER A2658 " --> pdb=" O LEU A2654 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS A2593 " --> pdb=" O VAL A2609 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 2667 through 2669 1116 hydrogen bonds defined for protein. 3216 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.24 Time building geometry restraints manager: 7.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 7232 1.36 - 1.51: 6915 1.51 - 1.65: 7043 1.65 - 1.80: 130 1.80 - 1.95: 19 Bond restraints: 21339 Sorted by residual: bond pdb=" C ILE A1084 " pdb=" N PRO A1085 " ideal model delta sigma weight residual 1.337 1.364 -0.027 9.80e-03 1.04e+04 7.68e+00 bond pdb=" CG LEU A1917 " pdb=" CD2 LEU A1917 " ideal model delta sigma weight residual 1.521 1.431 0.090 3.30e-02 9.18e+02 7.39e+00 bond pdb=" CB THR A2740 " pdb=" CG2 THR A2740 " ideal model delta sigma weight residual 1.521 1.438 0.083 3.30e-02 9.18e+02 6.35e+00 bond pdb=" CB THR A2743 " pdb=" CG2 THR A2743 " ideal model delta sigma weight residual 1.521 1.440 0.081 3.30e-02 9.18e+02 6.02e+00 bond pdb=" CB VAL A2256 " pdb=" CG1 VAL A2256 " ideal model delta sigma weight residual 1.521 1.454 0.067 3.30e-02 9.18e+02 4.08e+00 ... (remaining 21334 not shown) Histogram of bond angle deviations from ideal: 97.80 - 105.11: 373 105.11 - 112.42: 11378 112.42 - 119.73: 7482 119.73 - 127.04: 9413 127.04 - 134.36: 264 Bond angle restraints: 28910 Sorted by residual: angle pdb=" N SER A2007 " pdb=" CA SER A2007 " pdb=" CB SER A2007 " ideal model delta sigma weight residual 110.49 98.97 11.52 1.69e+00 3.50e-01 4.65e+01 angle pdb=" N GLY A 162 " pdb=" CA GLY A 162 " pdb=" C GLY A 162 " ideal model delta sigma weight residual 115.64 107.75 7.89 1.46e+00 4.69e-01 2.92e+01 angle pdb=" C GLY A2006 " pdb=" N SER A2007 " pdb=" CA SER A2007 " ideal model delta sigma weight residual 121.54 128.53 -6.99 1.91e+00 2.74e-01 1.34e+01 angle pdb=" N TYR A1332 " pdb=" CA TYR A1332 " pdb=" C TYR A1332 " ideal model delta sigma weight residual 114.56 110.04 4.52 1.27e+00 6.20e-01 1.27e+01 angle pdb=" C ASP A2005 " pdb=" N GLY A2006 " pdb=" CA GLY A2006 " ideal model delta sigma weight residual 121.41 128.09 -6.68 1.96e+00 2.60e-01 1.16e+01 ... (remaining 28905 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 11686 17.94 - 35.87: 1013 35.87 - 53.81: 245 53.81 - 71.75: 53 71.75 - 89.68: 18 Dihedral angle restraints: 13015 sinusoidal: 5258 harmonic: 7757 Sorted by residual: dihedral pdb=" CA GLY A2006 " pdb=" C GLY A2006 " pdb=" N SER A2007 " pdb=" CA SER A2007 " ideal model delta harmonic sigma weight residual -180.00 -144.06 -35.94 0 5.00e+00 4.00e-02 5.17e+01 dihedral pdb=" CA MET A 259 " pdb=" C MET A 259 " pdb=" N LYS A 260 " pdb=" CA LYS A 260 " ideal model delta harmonic sigma weight residual 180.00 -147.20 -32.80 0 5.00e+00 4.00e-02 4.30e+01 dihedral pdb=" CA ALA A 159 " pdb=" C ALA A 159 " pdb=" N LEU A 160 " pdb=" CA LEU A 160 " ideal model delta harmonic sigma weight residual 180.00 -147.59 -32.41 0 5.00e+00 4.00e-02 4.20e+01 ... (remaining 13012 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1897 0.039 - 0.078: 1081 0.078 - 0.117: 268 0.117 - 0.156: 64 0.156 - 0.196: 5 Chirality restraints: 3315 Sorted by residual: chirality pdb=" CA PRO A 666 " pdb=" N PRO A 666 " pdb=" C PRO A 666 " pdb=" CB PRO A 666 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 9.56e-01 chirality pdb=" CB ILE A 233 " pdb=" CA ILE A 233 " pdb=" CG1 ILE A 233 " pdb=" CG2 ILE A 233 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.37e-01 chirality pdb=" CA ILE A2004 " pdb=" N ILE A2004 " pdb=" C ILE A2004 " pdb=" CB ILE A2004 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.92e-01 ... (remaining 3312 not shown) Planarity restraints: 3686 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A1854 " -0.051 5.00e-02 4.00e+02 7.79e-02 9.70e+00 pdb=" N PRO A1855 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO A1855 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A1855 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 383 " -0.048 5.00e-02 4.00e+02 7.33e-02 8.61e+00 pdb=" N PRO A 384 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO A 384 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 384 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER A2007 " 0.013 2.00e-02 2.50e+03 2.54e-02 6.48e+00 pdb=" C SER A2007 " -0.044 2.00e-02 2.50e+03 pdb=" O SER A2007 " 0.016 2.00e-02 2.50e+03 pdb=" N SER A2008 " 0.015 2.00e-02 2.50e+03 ... (remaining 3683 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.48: 107 2.48 - 3.08: 14990 3.08 - 3.69: 30499 3.69 - 4.29: 45542 4.29 - 4.90: 76745 Nonbonded interactions: 167883 Sorted by model distance: nonbonded pdb=" OD1 ASP A2012 " pdb=" OG SER A2034 " model vdw 1.872 2.440 nonbonded pdb=" NZ LYS A1528 " pdb=" OD1 ASN A1573 " model vdw 1.963 2.520 nonbonded pdb=" ND2 ASN A2702 " pdb=" OE1 GLU A2704 " model vdw 1.998 2.520 nonbonded pdb=" OH TYR A 852 " pdb=" OE1 GLN A 934 " model vdw 2.109 2.440 nonbonded pdb=" O SER A1024 " pdb=" OG SER A1029 " model vdw 2.144 2.440 ... (remaining 167878 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.450 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: 10.060 Check model and map are aligned: 0.320 Set scattering table: 0.190 Process input model: 54.540 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.070 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:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 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 : 0.011 0.090 21339 Z= 0.701 Angle : 0.816 14.198 28910 Z= 0.442 Chirality : 0.048 0.196 3315 Planarity : 0.005 0.078 3686 Dihedral : 14.876 89.682 7948 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.43 % Favored : 92.49 % Rotamer: Outliers : 5.39 % Allowed : 10.35 % Favored : 84.26 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.09 (0.14), residues: 2596 helix: -1.48 (0.10), residues: 1837 sheet: -0.93 (0.91), residues: 31 loop : -3.27 (0.19), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP A2735 HIS 0.007 0.001 HIS A1512 PHE 0.020 0.003 PHE A 791 TYR 0.026 0.003 TYR A1295 ARG 0.005 0.001 ARG A2173 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 2281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 415 time to evaluate : 2.696 Fit side-chains TARDY: cannot create tardy model for: "THR A 27 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 GLN cc_start: 0.6900 (OUTLIER) cc_final: 0.6336 (mt0) REVERT: A 325 TYR cc_start: 0.7078 (OUTLIER) cc_final: 0.5981 (m-10) REVERT: A 328 ARG cc_start: 0.7308 (ptt180) cc_final: 0.6787 (ptm160) REVERT: A 395 HIS cc_start: 0.8557 (OUTLIER) cc_final: 0.7956 (t-90) REVERT: A 522 LEU cc_start: 0.8068 (OUTLIER) cc_final: 0.7406 (pp) REVERT: A 549 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8351 (tt) REVERT: A 607 GLN cc_start: 0.8543 (OUTLIER) cc_final: 0.8119 (mp10) REVERT: A 660 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8334 (mt) REVERT: A 826 ILE cc_start: 0.8677 (pt) cc_final: 0.8470 (pt) REVERT: A 1022 LYS cc_start: 0.8043 (ttpt) cc_final: 0.7839 (tptp) REVERT: A 1221 ARG cc_start: 0.7744 (OUTLIER) cc_final: 0.7162 (mtp180) REVERT: A 1342 LYS cc_start: 0.6634 (tttt) cc_final: 0.6143 (mtmt) REVERT: A 1376 TYR cc_start: 0.7491 (OUTLIER) cc_final: 0.4940 (m-80) REVERT: A 1406 HIS cc_start: 0.7957 (OUTLIER) cc_final: 0.7090 (t70) REVERT: A 1708 ASN cc_start: 0.7015 (m-40) cc_final: 0.5880 (t0) REVERT: A 1854 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8673 (tm) REVERT: A 1968 ARG cc_start: 0.7756 (ttm-80) cc_final: 0.6484 (mmt-90) REVERT: A 2126 ASP cc_start: 0.7019 (OUTLIER) cc_final: 0.6579 (m-30) REVERT: A 2608 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8442 (mt) REVERT: A 2751 MET cc_start: 0.8024 (mmp) cc_final: 0.7380 (mmp) REVERT: A 2826 ASP cc_start: 0.7959 (t0) cc_final: 0.7459 (t0) outliers start: 123 outliers final: 76 residues processed: 524 average time/residue: 0.3788 time to fit residues: 293.7681 Evaluate side-chains 304 residues out of total 2281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 215 time to evaluate : 2.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 56 TYR Chi-restraints excluded: chain A residue 66 CYS Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 293 GLN Chi-restraints excluded: chain A residue 325 TYR Chi-restraints excluded: chain A residue 356 CYS Chi-restraints excluded: chain A residue 362 GLU Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 395 HIS Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 602 PHE Chi-restraints excluded: chain A residue 607 GLN Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 658 GLN Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 741 SER Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 809 ASN Chi-restraints excluded: chain A residue 834 LYS Chi-restraints excluded: chain A residue 855 SER Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 907 THR Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 915 ASP Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain A residue 941 GLU Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 983 CYS Chi-restraints excluded: chain A residue 998 PHE Chi-restraints excluded: chain A residue 1002 TRP Chi-restraints excluded: chain A residue 1009 ILE Chi-restraints excluded: chain A residue 1024 SER Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1068 ILE Chi-restraints excluded: chain A residue 1098 ASP Chi-restraints excluded: chain A residue 1104 LEU Chi-restraints excluded: chain A residue 1162 SER Chi-restraints excluded: chain A residue 1200 ASN Chi-restraints excluded: chain A residue 1215 SER Chi-restraints excluded: chain A residue 1221 ARG Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1254 LEU Chi-restraints excluded: chain A residue 1255 VAL Chi-restraints excluded: chain A residue 1314 PHE Chi-restraints excluded: chain A residue 1320 ILE Chi-restraints excluded: chain A residue 1324 PHE Chi-restraints excluded: chain A residue 1376 TYR Chi-restraints excluded: chain A residue 1380 ASN Chi-restraints excluded: chain A residue 1397 THR Chi-restraints excluded: chain A residue 1398 ILE Chi-restraints excluded: chain A residue 1399 HIS Chi-restraints excluded: chain A residue 1406 HIS Chi-restraints excluded: chain A residue 1408 CYS Chi-restraints excluded: chain A residue 1410 VAL Chi-restraints excluded: chain A residue 1411 LEU Chi-restraints excluded: chain A residue 1414 ILE Chi-restraints excluded: chain A residue 1427 SER Chi-restraints excluded: chain A residue 1443 VAL Chi-restraints excluded: chain A residue 1568 ASP Chi-restraints excluded: chain A residue 1575 LEU Chi-restraints excluded: chain A residue 1585 LEU Chi-restraints excluded: chain A residue 1608 ASP Chi-restraints excluded: chain A residue 1743 VAL Chi-restraints excluded: chain A residue 1854 LEU Chi-restraints excluded: chain A residue 2126 ASP Chi-restraints excluded: chain A residue 2443 THR Chi-restraints excluded: chain A residue 2465 MET Chi-restraints excluded: chain A residue 2514 SER Chi-restraints excluded: chain A residue 2608 LEU Chi-restraints excluded: chain A residue 2805 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 222 optimal weight: 3.9990 chunk 200 optimal weight: 0.5980 chunk 111 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 134 optimal weight: 0.6980 chunk 106 optimal weight: 0.6980 chunk 206 optimal weight: 0.9980 chunk 80 optimal weight: 0.6980 chunk 125 optimal weight: 0.6980 chunk 154 optimal weight: 0.9980 chunk 239 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 HIS A 376 ASN A 394 HIS A 395 HIS A 519 HIS A 528 GLN A 612 HIS A 632 HIS A 658 GLN A 670 HIS A1028 ASN A1062 GLN A1096 HIS A1175 GLN A1242 GLN A1369 HIS A1512 HIS ** A1761 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1844 ASN A2065 ASN A2179 GLN A2239 GLN A2255 GLN A2294 GLN A2354 GLN A2356 GLN A2446 GLN ** A2544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2624 GLN A2678 HIS A2754 HIS A2925 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21339 Z= 0.197 Angle : 0.566 12.867 28910 Z= 0.289 Chirality : 0.039 0.266 3315 Planarity : 0.005 0.061 3686 Dihedral : 9.320 79.128 3036 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.24 % Favored : 95.72 % Rotamer: Outliers : 5.13 % Allowed : 14.03 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.96 (0.16), residues: 2596 helix: 0.17 (0.12), residues: 1850 sheet: -0.39 (0.97), residues: 31 loop : -2.70 (0.21), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A2118 HIS 0.009 0.001 HIS A1512 PHE 0.016 0.001 PHE A 791 TYR 0.016 0.001 TYR A 145 ARG 0.008 0.000 ARG A 926 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 257 time to evaluate : 2.284 Fit side-chains TARDY: cannot create tardy model for: "THR A 27 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 325 TYR cc_start: 0.6893 (OUTLIER) cc_final: 0.6163 (m-80) REVERT: A 328 ARG cc_start: 0.7099 (ptt180) cc_final: 0.6715 (ptm160) REVERT: A 415 TYR cc_start: 0.7281 (t80) cc_final: 0.6891 (t80) REVERT: A 522 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7354 (pp) REVERT: A 660 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8306 (mt) REVERT: A 842 LYS cc_start: 0.8743 (mtmt) cc_final: 0.8520 (mtmm) REVERT: A 846 LYS cc_start: 0.8005 (mttt) cc_final: 0.7628 (mmtt) REVERT: A 1122 PHE cc_start: 0.8436 (t80) cc_final: 0.8115 (t80) REVERT: A 1342 LYS cc_start: 0.6674 (tttt) cc_final: 0.6150 (mtmt) REVERT: A 1376 TYR cc_start: 0.7152 (OUTLIER) cc_final: 0.4642 (m-80) REVERT: A 1405 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7847 (mp) REVERT: A 1406 HIS cc_start: 0.7496 (OUTLIER) cc_final: 0.6810 (t70) REVERT: A 1585 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.7898 (mp) REVERT: A 1608 ASP cc_start: 0.7395 (OUTLIER) cc_final: 0.7160 (m-30) REVERT: A 1708 ASN cc_start: 0.6991 (m-40) cc_final: 0.5888 (t0) REVERT: A 1854 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8448 (tm) REVERT: A 1968 ARG cc_start: 0.7698 (ttm-80) cc_final: 0.6442 (mmt-90) REVERT: A 2751 MET cc_start: 0.7984 (mmp) cc_final: 0.7595 (mmp) outliers start: 117 outliers final: 72 residues processed: 356 average time/residue: 0.3400 time to fit residues: 189.8445 Evaluate side-chains 285 residues out of total 2281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 204 time to evaluate : 2.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 56 TYR Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 325 TYR Chi-restraints excluded: chain A residue 362 GLU Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 535 ARG Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 607 GLN Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 658 GLN Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 809 ASN Chi-restraints excluded: chain A residue 834 LYS Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 899 THR Chi-restraints excluded: chain A residue 955 THR Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1002 TRP Chi-restraints excluded: chain A residue 1047 GLU Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1068 ILE Chi-restraints excluded: chain A residue 1071 ASP Chi-restraints excluded: chain A residue 1098 ASP Chi-restraints excluded: chain A residue 1104 LEU Chi-restraints excluded: chain A residue 1200 ASN Chi-restraints excluded: chain A residue 1215 SER Chi-restraints excluded: chain A residue 1254 LEU Chi-restraints excluded: chain A residue 1255 VAL Chi-restraints excluded: chain A residue 1314 PHE Chi-restraints excluded: chain A residue 1320 ILE Chi-restraints excluded: chain A residue 1324 PHE Chi-restraints excluded: chain A residue 1376 TYR Chi-restraints excluded: chain A residue 1397 THR Chi-restraints excluded: chain A residue 1398 ILE Chi-restraints excluded: chain A residue 1399 HIS Chi-restraints excluded: chain A residue 1405 LEU Chi-restraints excluded: chain A residue 1406 HIS Chi-restraints excluded: chain A residue 1410 VAL Chi-restraints excluded: chain A residue 1411 LEU Chi-restraints excluded: chain A residue 1414 ILE Chi-restraints excluded: chain A residue 1568 ASP Chi-restraints excluded: chain A residue 1575 LEU Chi-restraints excluded: chain A residue 1585 LEU Chi-restraints excluded: chain A residue 1591 VAL Chi-restraints excluded: chain A residue 1608 ASP Chi-restraints excluded: chain A residue 1644 SER Chi-restraints excluded: chain A residue 1684 SER Chi-restraints excluded: chain A residue 1719 SER Chi-restraints excluded: chain A residue 1737 LEU Chi-restraints excluded: chain A residue 1837 GLU Chi-restraints excluded: chain A residue 1854 LEU Chi-restraints excluded: chain A residue 1934 SER Chi-restraints excluded: chain A residue 2052 LEU Chi-restraints excluded: chain A residue 2118 TRP Chi-restraints excluded: chain A residue 2126 ASP Chi-restraints excluded: chain A residue 2135 GLU Chi-restraints excluded: chain A residue 2443 THR Chi-restraints excluded: chain A residue 2656 SER Chi-restraints excluded: chain A residue 2792 VAL Chi-restraints excluded: chain A residue 2805 VAL Chi-restraints excluded: chain A residue 2814 GLU Chi-restraints excluded: chain A residue 2855 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 133 optimal weight: 0.7980 chunk 74 optimal weight: 0.9990 chunk 199 optimal weight: 1.9990 chunk 163 optimal weight: 1.9990 chunk 66 optimal weight: 0.0970 chunk 240 optimal weight: 0.6980 chunk 259 optimal weight: 0.8980 chunk 213 optimal weight: 1.9990 chunk 238 optimal weight: 2.9990 chunk 81 optimal weight: 0.2980 chunk 192 optimal weight: 0.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 528 GLN A 635 HIS A 839 HIS ** A 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 HIS A1245 GLN A1380 ASN ** A1761 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2380 ASN ** A2544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 21339 Z= 0.173 Angle : 0.525 12.448 28910 Z= 0.262 Chirality : 0.038 0.178 3315 Planarity : 0.004 0.051 3686 Dihedral : 8.174 80.210 2981 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.28 % Favored : 95.69 % Rotamer: Outliers : 4.25 % Allowed : 15.91 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.17), residues: 2596 helix: 0.88 (0.12), residues: 1856 sheet: -0.03 (1.02), residues: 31 loop : -2.36 (0.21), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A2118 HIS 0.005 0.001 HIS A 824 PHE 0.016 0.001 PHE A 171 TYR 0.024 0.001 TYR A 145 ARG 0.005 0.000 ARG A1755 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 222 time to evaluate : 2.366 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 230 MET cc_start: 0.7998 (mtm) cc_final: 0.7545 (mtm) REVERT: A 325 TYR cc_start: 0.6795 (OUTLIER) cc_final: 0.6141 (m-10) REVERT: A 328 ARG cc_start: 0.7024 (ptt180) cc_final: 0.6671 (ptm160) REVERT: A 522 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7449 (pp) REVERT: A 660 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8413 (mt) REVERT: A 846 LYS cc_start: 0.8115 (mttt) cc_final: 0.7727 (mmtt) REVERT: A 1342 LYS cc_start: 0.6743 (tttt) cc_final: 0.6180 (mtmt) REVERT: A 1376 TYR cc_start: 0.7181 (OUTLIER) cc_final: 0.4640 (m-80) REVERT: A 1405 LEU cc_start: 0.8161 (OUTLIER) cc_final: 0.7843 (mp) REVERT: A 1708 ASN cc_start: 0.7098 (m-40) cc_final: 0.5868 (t0) REVERT: A 1854 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8394 (tm) REVERT: A 2465 MET cc_start: 0.7249 (OUTLIER) cc_final: 0.6985 (ttm) REVERT: A 2751 MET cc_start: 0.7934 (mmp) cc_final: 0.7659 (mmp) outliers start: 97 outliers final: 69 residues processed: 303 average time/residue: 0.3480 time to fit residues: 165.9656 Evaluate side-chains 276 residues out of total 2281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 200 time to evaluate : 2.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 56 TYR Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 325 TYR Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 607 GLN Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 658 GLN Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 809 ASN Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 983 CYS Chi-restraints excluded: chain A residue 1002 TRP Chi-restraints excluded: chain A residue 1047 GLU Chi-restraints excluded: chain A residue 1071 ASP Chi-restraints excluded: chain A residue 1098 ASP Chi-restraints excluded: chain A residue 1104 LEU Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1200 ASN Chi-restraints excluded: chain A residue 1254 LEU Chi-restraints excluded: chain A residue 1255 VAL Chi-restraints excluded: chain A residue 1314 PHE Chi-restraints excluded: chain A residue 1320 ILE Chi-restraints excluded: chain A residue 1324 PHE Chi-restraints excluded: chain A residue 1376 TYR Chi-restraints excluded: chain A residue 1380 ASN Chi-restraints excluded: chain A residue 1398 ILE Chi-restraints excluded: chain A residue 1399 HIS Chi-restraints excluded: chain A residue 1405 LEU Chi-restraints excluded: chain A residue 1411 LEU Chi-restraints excluded: chain A residue 1414 ILE Chi-restraints excluded: chain A residue 1449 ASP Chi-restraints excluded: chain A residue 1568 ASP Chi-restraints excluded: chain A residue 1575 LEU Chi-restraints excluded: chain A residue 1591 VAL Chi-restraints excluded: chain A residue 1644 SER Chi-restraints excluded: chain A residue 1647 VAL Chi-restraints excluded: chain A residue 1684 SER Chi-restraints excluded: chain A residue 1737 LEU Chi-restraints excluded: chain A residue 1837 GLU Chi-restraints excluded: chain A residue 1854 LEU Chi-restraints excluded: chain A residue 1915 ASP Chi-restraints excluded: chain A residue 1918 LEU Chi-restraints excluded: chain A residue 2118 TRP Chi-restraints excluded: chain A residue 2126 ASP Chi-restraints excluded: chain A residue 2135 GLU Chi-restraints excluded: chain A residue 2233 ASP Chi-restraints excluded: chain A residue 2234 SER Chi-restraints excluded: chain A residue 2307 ASP Chi-restraints excluded: chain A residue 2318 LEU Chi-restraints excluded: chain A residue 2349 LEU Chi-restraints excluded: chain A residue 2443 THR Chi-restraints excluded: chain A residue 2465 MET Chi-restraints excluded: chain A residue 2482 VAL Chi-restraints excluded: chain A residue 2567 ASN Chi-restraints excluded: chain A residue 2666 ASN Chi-restraints excluded: chain A residue 2805 VAL Chi-restraints excluded: chain A residue 2814 GLU Chi-restraints excluded: chain A residue 2855 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 237 optimal weight: 1.9990 chunk 180 optimal weight: 0.9990 chunk 124 optimal weight: 0.0270 chunk 26 optimal weight: 7.9990 chunk 114 optimal weight: 1.9990 chunk 161 optimal weight: 0.9980 chunk 241 optimal weight: 0.5980 chunk 255 optimal weight: 1.9990 chunk 125 optimal weight: 0.8980 chunk 228 optimal weight: 4.9990 chunk 68 optimal weight: 0.9980 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1161 HIS A1245 GLN ** A1761 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1870 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21339 Z= 0.182 Angle : 0.518 11.234 28910 Z= 0.257 Chirality : 0.038 0.453 3315 Planarity : 0.004 0.046 3686 Dihedral : 7.725 80.813 2958 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.28 % Favored : 95.69 % Rotamer: Outliers : 4.78 % Allowed : 15.83 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.17), residues: 2596 helix: 1.20 (0.12), residues: 1863 sheet: 0.11 (0.96), residues: 36 loop : -2.21 (0.22), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1382 HIS 0.004 0.001 HIS A 839 PHE 0.016 0.001 PHE A1122 TYR 0.023 0.001 TYR A 145 ARG 0.005 0.000 ARG A2314 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 226 time to evaluate : 2.426 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 325 TYR cc_start: 0.6482 (OUTLIER) cc_final: 0.4491 (t80) REVERT: A 328 ARG cc_start: 0.6973 (ptt180) cc_final: 0.6639 (ptm160) REVERT: A 415 TYR cc_start: 0.7297 (t80) cc_final: 0.6962 (t80) REVERT: A 522 LEU cc_start: 0.8034 (OUTLIER) cc_final: 0.7555 (pp) REVERT: A 564 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7719 (pp) REVERT: A 660 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8439 (mt) REVERT: A 846 LYS cc_start: 0.8105 (mttt) cc_final: 0.7707 (mmtt) REVERT: A 1224 GLN cc_start: 0.8538 (mt0) cc_final: 0.8335 (mt0) REVERT: A 1342 LYS cc_start: 0.6783 (tttt) cc_final: 0.6294 (mtmt) REVERT: A 1376 TYR cc_start: 0.7143 (OUTLIER) cc_final: 0.4490 (m-80) REVERT: A 1708 ASN cc_start: 0.7222 (m-40) cc_final: 0.5917 (t0) REVERT: A 1854 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8430 (tm) outliers start: 109 outliers final: 82 residues processed: 318 average time/residue: 0.3352 time to fit residues: 167.7905 Evaluate side-chains 295 residues out of total 2281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 207 time to evaluate : 2.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 56 TYR Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 325 TYR Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 607 GLN Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 658 GLN Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 809 ASN Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 897 SER Chi-restraints excluded: chain A residue 899 THR Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 983 CYS Chi-restraints excluded: chain A residue 1002 TRP Chi-restraints excluded: chain A residue 1047 GLU Chi-restraints excluded: chain A residue 1068 ILE Chi-restraints excluded: chain A residue 1071 ASP Chi-restraints excluded: chain A residue 1098 ASP Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1200 ASN Chi-restraints excluded: chain A residue 1232 MET Chi-restraints excluded: chain A residue 1254 LEU Chi-restraints excluded: chain A residue 1255 VAL Chi-restraints excluded: chain A residue 1300 HIS Chi-restraints excluded: chain A residue 1314 PHE Chi-restraints excluded: chain A residue 1320 ILE Chi-restraints excluded: chain A residue 1324 PHE Chi-restraints excluded: chain A residue 1376 TYR Chi-restraints excluded: chain A residue 1397 THR Chi-restraints excluded: chain A residue 1398 ILE Chi-restraints excluded: chain A residue 1408 CYS Chi-restraints excluded: chain A residue 1411 LEU Chi-restraints excluded: chain A residue 1414 ILE Chi-restraints excluded: chain A residue 1443 VAL Chi-restraints excluded: chain A residue 1449 ASP Chi-restraints excluded: chain A residue 1568 ASP Chi-restraints excluded: chain A residue 1575 LEU Chi-restraints excluded: chain A residue 1591 VAL Chi-restraints excluded: chain A residue 1628 GLU Chi-restraints excluded: chain A residue 1644 SER Chi-restraints excluded: chain A residue 1684 SER Chi-restraints excluded: chain A residue 1719 SER Chi-restraints excluded: chain A residue 1777 ILE Chi-restraints excluded: chain A residue 1779 THR Chi-restraints excluded: chain A residue 1837 GLU Chi-restraints excluded: chain A residue 1854 LEU Chi-restraints excluded: chain A residue 1918 LEU Chi-restraints excluded: chain A residue 2096 ILE Chi-restraints excluded: chain A residue 2118 TRP Chi-restraints excluded: chain A residue 2126 ASP Chi-restraints excluded: chain A residue 2135 GLU Chi-restraints excluded: chain A residue 2216 ASP Chi-restraints excluded: chain A residue 2233 ASP Chi-restraints excluded: chain A residue 2234 SER Chi-restraints excluded: chain A residue 2307 ASP Chi-restraints excluded: chain A residue 2349 LEU Chi-restraints excluded: chain A residue 2443 THR Chi-restraints excluded: chain A residue 2482 VAL Chi-restraints excluded: chain A residue 2567 ASN Chi-restraints excluded: chain A residue 2651 VAL Chi-restraints excluded: chain A residue 2656 SER Chi-restraints excluded: chain A residue 2666 ASN Chi-restraints excluded: chain A residue 2715 GLU Chi-restraints excluded: chain A residue 2733 ASP Chi-restraints excluded: chain A residue 2805 VAL Chi-restraints excluded: chain A residue 2813 THR Chi-restraints excluded: chain A residue 2814 GLU Chi-restraints excluded: chain A residue 2855 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 212 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 190 optimal weight: 7.9990 chunk 105 optimal weight: 5.9990 chunk 217 optimal weight: 0.0040 chunk 176 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 130 optimal weight: 2.9990 chunk 229 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 overall best weight: 1.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 528 GLN A 664 ASN A1245 GLN A1656 GLN ** A1761 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1829 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 21339 Z= 0.320 Angle : 0.585 10.544 28910 Z= 0.290 Chirality : 0.041 0.210 3315 Planarity : 0.004 0.043 3686 Dihedral : 7.684 78.986 2951 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.89 % Favored : 95.07 % Rotamer: Outliers : 4.87 % Allowed : 17.05 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.17), residues: 2596 helix: 1.15 (0.12), residues: 1858 sheet: -0.28 (0.96), residues: 31 loop : -2.18 (0.22), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A2118 HIS 0.005 0.001 HIS A2518 PHE 0.018 0.002 PHE A 171 TYR 0.023 0.002 TYR A 145 ARG 0.006 0.000 ARG A2314 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 217 time to evaluate : 2.404 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 283 ASP cc_start: 0.6762 (t0) cc_final: 0.6516 (t70) REVERT: A 325 TYR cc_start: 0.6526 (OUTLIER) cc_final: 0.4498 (t80) REVERT: A 328 ARG cc_start: 0.7035 (ptt180) cc_final: 0.6654 (ptm160) REVERT: A 415 TYR cc_start: 0.7382 (t80) cc_final: 0.6989 (t80) REVERT: A 522 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7641 (pp) REVERT: A 607 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.7924 (mp10) REVERT: A 660 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8472 (mt) REVERT: A 755 MET cc_start: 0.7456 (tpp) cc_final: 0.6851 (tpp) REVERT: A 846 LYS cc_start: 0.8154 (mttt) cc_final: 0.7785 (mmtt) REVERT: A 1224 GLN cc_start: 0.8567 (mt0) cc_final: 0.8351 (mt0) REVERT: A 1313 ILE cc_start: 0.9072 (OUTLIER) cc_final: 0.8817 (pp) REVERT: A 1342 LYS cc_start: 0.6806 (tttt) cc_final: 0.6325 (mtmt) REVERT: A 1376 TYR cc_start: 0.7125 (OUTLIER) cc_final: 0.4413 (m-80) REVERT: A 1405 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7729 (mp) REVERT: A 1608 ASP cc_start: 0.7351 (OUTLIER) cc_final: 0.7051 (m-30) REVERT: A 1667 VAL cc_start: 0.6379 (t) cc_final: 0.6143 (t) REVERT: A 1854 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8532 (tm) REVERT: A 2751 MET cc_start: 0.7822 (mmp) cc_final: 0.7341 (mmp) outliers start: 111 outliers final: 88 residues processed: 309 average time/residue: 0.3273 time to fit residues: 160.6592 Evaluate side-chains 295 residues out of total 2281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 198 time to evaluate : 2.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 56 TYR Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 325 TYR Chi-restraints excluded: chain A residue 362 GLU Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 466 GLN Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 607 GLN Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 658 GLN Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 894 ILE Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 897 SER Chi-restraints excluded: chain A residue 899 THR Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 983 CYS Chi-restraints excluded: chain A residue 1002 TRP Chi-restraints excluded: chain A residue 1047 GLU Chi-restraints excluded: chain A residue 1068 ILE Chi-restraints excluded: chain A residue 1071 ASP Chi-restraints excluded: chain A residue 1098 ASP Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1200 ASN Chi-restraints excluded: chain A residue 1232 MET Chi-restraints excluded: chain A residue 1254 LEU Chi-restraints excluded: chain A residue 1255 VAL Chi-restraints excluded: chain A residue 1313 ILE Chi-restraints excluded: chain A residue 1314 PHE Chi-restraints excluded: chain A residue 1320 ILE Chi-restraints excluded: chain A residue 1324 PHE Chi-restraints excluded: chain A residue 1376 TYR Chi-restraints excluded: chain A residue 1397 THR Chi-restraints excluded: chain A residue 1398 ILE Chi-restraints excluded: chain A residue 1399 HIS Chi-restraints excluded: chain A residue 1405 LEU Chi-restraints excluded: chain A residue 1408 CYS Chi-restraints excluded: chain A residue 1414 ILE Chi-restraints excluded: chain A residue 1443 VAL Chi-restraints excluded: chain A residue 1449 ASP Chi-restraints excluded: chain A residue 1568 ASP Chi-restraints excluded: chain A residue 1575 LEU Chi-restraints excluded: chain A residue 1591 VAL Chi-restraints excluded: chain A residue 1608 ASP Chi-restraints excluded: chain A residue 1628 GLU Chi-restraints excluded: chain A residue 1684 SER Chi-restraints excluded: chain A residue 1713 LEU Chi-restraints excluded: chain A residue 1719 SER Chi-restraints excluded: chain A residue 1777 ILE Chi-restraints excluded: chain A residue 1779 THR Chi-restraints excluded: chain A residue 1837 GLU Chi-restraints excluded: chain A residue 1854 LEU Chi-restraints excluded: chain A residue 1915 ASP Chi-restraints excluded: chain A residue 1918 LEU Chi-restraints excluded: chain A residue 1924 ILE Chi-restraints excluded: chain A residue 2052 LEU Chi-restraints excluded: chain A residue 2058 MET Chi-restraints excluded: chain A residue 2096 ILE Chi-restraints excluded: chain A residue 2118 TRP Chi-restraints excluded: chain A residue 2233 ASP Chi-restraints excluded: chain A residue 2234 SER Chi-restraints excluded: chain A residue 2307 ASP Chi-restraints excluded: chain A residue 2349 LEU Chi-restraints excluded: chain A residue 2443 THR Chi-restraints excluded: chain A residue 2465 MET Chi-restraints excluded: chain A residue 2482 VAL Chi-restraints excluded: chain A residue 2491 ASP Chi-restraints excluded: chain A residue 2516 VAL Chi-restraints excluded: chain A residue 2621 ILE Chi-restraints excluded: chain A residue 2656 SER Chi-restraints excluded: chain A residue 2666 ASN Chi-restraints excluded: chain A residue 2715 GLU Chi-restraints excluded: chain A residue 2805 VAL Chi-restraints excluded: chain A residue 2813 THR Chi-restraints excluded: chain A residue 2814 GLU Chi-restraints excluded: chain A residue 2855 VAL Chi-restraints excluded: chain A residue 2917 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 85 optimal weight: 0.5980 chunk 229 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 149 optimal weight: 0.0070 chunk 62 optimal weight: 0.3980 chunk 255 optimal weight: 0.7980 chunk 212 optimal weight: 0.0370 chunk 118 optimal weight: 0.6980 chunk 21 optimal weight: 0.0980 chunk 84 optimal weight: 0.9980 chunk 134 optimal weight: 2.9990 overall best weight: 0.2276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 528 GLN ** A 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1245 GLN A1574 GLN A1764 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 21339 Z= 0.131 Angle : 0.497 9.741 28910 Z= 0.246 Chirality : 0.036 0.225 3315 Planarity : 0.004 0.042 3686 Dihedral : 7.224 80.343 2943 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.51 % Favored : 96.46 % Rotamer: Outliers : 3.68 % Allowed : 18.81 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.17), residues: 2596 helix: 1.56 (0.12), residues: 1856 sheet: -0.03 (0.97), residues: 31 loop : -2.11 (0.22), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A2118 HIS 0.004 0.001 HIS A 824 PHE 0.018 0.001 PHE A1122 TYR 0.026 0.001 TYR A 145 ARG 0.006 0.000 ARG A2314 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 233 time to evaluate : 2.805 Fit side-chains revert: symmetry clash REVERT: A 325 TYR cc_start: 0.6488 (OUTLIER) cc_final: 0.4600 (t80) REVERT: A 328 ARG cc_start: 0.6875 (ptt180) cc_final: 0.6581 (ptm160) REVERT: A 415 TYR cc_start: 0.7332 (t80) cc_final: 0.6951 (t80) REVERT: A 522 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7677 (pp) REVERT: A 564 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7120 (pp) REVERT: A 568 ILE cc_start: 0.8693 (OUTLIER) cc_final: 0.8440 (mp) REVERT: A 660 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8376 (mt) REVERT: A 755 MET cc_start: 0.7358 (tpp) cc_final: 0.6950 (tpp) REVERT: A 846 LYS cc_start: 0.8071 (mttt) cc_final: 0.7703 (mmtt) REVERT: A 1224 GLN cc_start: 0.8548 (mt0) cc_final: 0.8319 (mt0) REVERT: A 1342 LYS cc_start: 0.6773 (tttt) cc_final: 0.6303 (mtmt) REVERT: A 1376 TYR cc_start: 0.6741 (OUTLIER) cc_final: 0.4154 (m-80) REVERT: A 1649 GLU cc_start: 0.7399 (tm-30) cc_final: 0.7181 (tm-30) REVERT: A 1667 VAL cc_start: 0.6471 (t) cc_final: 0.6206 (t) REVERT: A 1854 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8405 (tm) REVERT: A 2751 MET cc_start: 0.7744 (mmp) cc_final: 0.7197 (mmp) outliers start: 84 outliers final: 60 residues processed: 298 average time/residue: 0.3273 time to fit residues: 154.8950 Evaluate side-chains 267 residues out of total 2281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 200 time to evaluate : 2.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 56 TYR Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 325 TYR Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 658 GLN Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 897 SER Chi-restraints excluded: chain A residue 899 THR Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1002 TRP Chi-restraints excluded: chain A residue 1047 GLU Chi-restraints excluded: chain A residue 1071 ASP Chi-restraints excluded: chain A residue 1098 ASP Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1232 MET Chi-restraints excluded: chain A residue 1254 LEU Chi-restraints excluded: chain A residue 1255 VAL Chi-restraints excluded: chain A residue 1314 PHE Chi-restraints excluded: chain A residue 1324 PHE Chi-restraints excluded: chain A residue 1376 TYR Chi-restraints excluded: chain A residue 1398 ILE Chi-restraints excluded: chain A residue 1399 HIS Chi-restraints excluded: chain A residue 1408 CYS Chi-restraints excluded: chain A residue 1411 LEU Chi-restraints excluded: chain A residue 1414 ILE Chi-restraints excluded: chain A residue 1449 ASP Chi-restraints excluded: chain A residue 1568 ASP Chi-restraints excluded: chain A residue 1591 VAL Chi-restraints excluded: chain A residue 1628 GLU Chi-restraints excluded: chain A residue 1777 ILE Chi-restraints excluded: chain A residue 1837 GLU Chi-restraints excluded: chain A residue 1854 LEU Chi-restraints excluded: chain A residue 1915 ASP Chi-restraints excluded: chain A residue 2096 ILE Chi-restraints excluded: chain A residue 2118 TRP Chi-restraints excluded: chain A residue 2126 ASP Chi-restraints excluded: chain A residue 2216 ASP Chi-restraints excluded: chain A residue 2233 ASP Chi-restraints excluded: chain A residue 2234 SER Chi-restraints excluded: chain A residue 2307 ASP Chi-restraints excluded: chain A residue 2443 THR Chi-restraints excluded: chain A residue 2516 VAL Chi-restraints excluded: chain A residue 2656 SER Chi-restraints excluded: chain A residue 2666 ASN Chi-restraints excluded: chain A residue 2715 GLU Chi-restraints excluded: chain A residue 2733 ASP Chi-restraints excluded: chain A residue 2814 GLU Chi-restraints excluded: chain A residue 2846 THR Chi-restraints excluded: chain A residue 2855 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 246 optimal weight: 0.5980 chunk 28 optimal weight: 4.9990 chunk 145 optimal weight: 2.9990 chunk 186 optimal weight: 0.5980 chunk 144 optimal weight: 0.7980 chunk 215 optimal weight: 0.9980 chunk 142 optimal weight: 2.9990 chunk 254 optimal weight: 0.6980 chunk 159 optimal weight: 3.9990 chunk 155 optimal weight: 0.8980 chunk 117 optimal weight: 0.0020 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 528 GLN A 569 ASN A1000 ASN A1245 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.3299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21339 Z= 0.163 Angle : 0.515 9.732 28910 Z= 0.253 Chirality : 0.038 0.529 3315 Planarity : 0.004 0.041 3686 Dihedral : 6.934 80.512 2931 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.81 % Favored : 96.15 % Rotamer: Outliers : 3.73 % Allowed : 19.38 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.17), residues: 2596 helix: 1.67 (0.12), residues: 1858 sheet: 0.03 (0.97), residues: 31 loop : -2.06 (0.22), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A2118 HIS 0.004 0.001 HIS A 839 PHE 0.018 0.001 PHE A 171 TYR 0.026 0.001 TYR A1017 ARG 0.007 0.000 ARG A2314 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 210 time to evaluate : 2.282 Fit side-chains revert: symmetry clash REVERT: A 106 VAL cc_start: 0.7344 (OUTLIER) cc_final: 0.6932 (t) REVERT: A 170 ASP cc_start: 0.6933 (p0) cc_final: 0.6039 (p0) REVERT: A 325 TYR cc_start: 0.6433 (OUTLIER) cc_final: 0.5858 (m-10) REVERT: A 328 ARG cc_start: 0.6832 (ptt180) cc_final: 0.6542 (ptm160) REVERT: A 415 TYR cc_start: 0.7334 (t80) cc_final: 0.6949 (t80) REVERT: A 522 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7675 (pp) REVERT: A 564 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7066 (pp) REVERT: A 568 ILE cc_start: 0.8703 (OUTLIER) cc_final: 0.8435 (mp) REVERT: A 660 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8421 (mt) REVERT: A 755 MET cc_start: 0.7406 (tpp) cc_final: 0.7038 (tpp) REVERT: A 802 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7849 (mm) REVERT: A 846 LYS cc_start: 0.8103 (mttt) cc_final: 0.7722 (mmtt) REVERT: A 1224 GLN cc_start: 0.8546 (mt0) cc_final: 0.8328 (mt0) REVERT: A 1342 LYS cc_start: 0.6814 (tttt) cc_final: 0.6296 (mtmt) REVERT: A 1376 TYR cc_start: 0.6784 (OUTLIER) cc_final: 0.4067 (m-80) REVERT: A 1405 LEU cc_start: 0.7921 (OUTLIER) cc_final: 0.7608 (mp) REVERT: A 1411 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8477 (tt) REVERT: A 1649 GLU cc_start: 0.7411 (tm-30) cc_final: 0.7176 (tm-30) REVERT: A 1667 VAL cc_start: 0.6337 (t) cc_final: 0.6088 (t) REVERT: A 1854 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8428 (tm) REVERT: A 2751 MET cc_start: 0.7782 (mmp) cc_final: 0.7215 (mmp) outliers start: 85 outliers final: 60 residues processed: 282 average time/residue: 0.3155 time to fit residues: 141.5429 Evaluate side-chains 271 residues out of total 2281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 200 time to evaluate : 2.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 56 TYR Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 325 TYR Chi-restraints excluded: chain A residue 362 GLU Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 658 GLN Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 897 SER Chi-restraints excluded: chain A residue 899 THR Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 983 CYS Chi-restraints excluded: chain A residue 1002 TRP Chi-restraints excluded: chain A residue 1047 GLU Chi-restraints excluded: chain A residue 1071 ASP Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1200 ASN Chi-restraints excluded: chain A residue 1232 MET Chi-restraints excluded: chain A residue 1254 LEU Chi-restraints excluded: chain A residue 1255 VAL Chi-restraints excluded: chain A residue 1314 PHE Chi-restraints excluded: chain A residue 1324 PHE Chi-restraints excluded: chain A residue 1376 TYR Chi-restraints excluded: chain A residue 1398 ILE Chi-restraints excluded: chain A residue 1399 HIS Chi-restraints excluded: chain A residue 1405 LEU Chi-restraints excluded: chain A residue 1408 CYS Chi-restraints excluded: chain A residue 1411 LEU Chi-restraints excluded: chain A residue 1414 ILE Chi-restraints excluded: chain A residue 1449 ASP Chi-restraints excluded: chain A residue 1450 ASP Chi-restraints excluded: chain A residue 1568 ASP Chi-restraints excluded: chain A residue 1591 VAL Chi-restraints excluded: chain A residue 1628 GLU Chi-restraints excluded: chain A residue 1777 ILE Chi-restraints excluded: chain A residue 1854 LEU Chi-restraints excluded: chain A residue 1918 LEU Chi-restraints excluded: chain A residue 2058 MET Chi-restraints excluded: chain A residue 2096 ILE Chi-restraints excluded: chain A residue 2118 TRP Chi-restraints excluded: chain A residue 2126 ASP Chi-restraints excluded: chain A residue 2216 ASP Chi-restraints excluded: chain A residue 2233 ASP Chi-restraints excluded: chain A residue 2234 SER Chi-restraints excluded: chain A residue 2307 ASP Chi-restraints excluded: chain A residue 2349 LEU Chi-restraints excluded: chain A residue 2516 VAL Chi-restraints excluded: chain A residue 2656 SER Chi-restraints excluded: chain A residue 2666 ASN Chi-restraints excluded: chain A residue 2715 GLU Chi-restraints excluded: chain A residue 2733 ASP Chi-restraints excluded: chain A residue 2814 GLU Chi-restraints excluded: chain A residue 2855 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 157 optimal weight: 3.9990 chunk 101 optimal weight: 0.2980 chunk 151 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 161 optimal weight: 0.5980 chunk 173 optimal weight: 0.9980 chunk 125 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 200 optimal weight: 0.9990 chunk 231 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 528 GLN A 569 ASN A1245 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21339 Z= 0.179 Angle : 0.521 9.937 28910 Z= 0.255 Chirality : 0.038 0.470 3315 Planarity : 0.004 0.040 3686 Dihedral : 6.762 79.213 2925 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.73 % Allowed : 19.42 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.17), residues: 2596 helix: 1.74 (0.12), residues: 1853 sheet: 0.10 (0.97), residues: 31 loop : -1.95 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A2118 HIS 0.004 0.001 HIS A 824 PHE 0.027 0.001 PHE A 602 TYR 0.024 0.001 TYR A 145 ARG 0.007 0.000 ARG A2314 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 206 time to evaluate : 2.260 Fit side-chains REVERT: A 61 GLU cc_start: 0.7370 (pp20) cc_final: 0.6909 (pp20) REVERT: A 106 VAL cc_start: 0.7314 (OUTLIER) cc_final: 0.6900 (t) REVERT: A 170 ASP cc_start: 0.6491 (p0) cc_final: 0.6266 (p0) REVERT: A 283 ASP cc_start: 0.6549 (t0) cc_final: 0.6169 (t70) REVERT: A 325 TYR cc_start: 0.6429 (OUTLIER) cc_final: 0.5856 (m-10) REVERT: A 328 ARG cc_start: 0.6814 (ptt180) cc_final: 0.6559 (ptm160) REVERT: A 415 TYR cc_start: 0.7313 (t80) cc_final: 0.6935 (t80) REVERT: A 522 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7617 (pp) REVERT: A 564 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7652 (pp) REVERT: A 602 PHE cc_start: 0.7794 (m-10) cc_final: 0.7514 (m-80) REVERT: A 660 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8394 (mt) REVERT: A 677 MET cc_start: 0.7212 (ttm) cc_final: 0.6883 (ttp) REVERT: A 755 MET cc_start: 0.7428 (tpp) cc_final: 0.7089 (tpp) REVERT: A 802 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7816 (mm) REVERT: A 846 LYS cc_start: 0.8106 (mttt) cc_final: 0.7729 (mmtt) REVERT: A 1076 LEU cc_start: 0.7985 (tt) cc_final: 0.7652 (tt) REVERT: A 1224 GLN cc_start: 0.8574 (mt0) cc_final: 0.8358 (mt0) REVERT: A 1342 LYS cc_start: 0.6954 (tttt) cc_final: 0.6364 (mtmt) REVERT: A 1376 TYR cc_start: 0.6808 (OUTLIER) cc_final: 0.4097 (m-80) REVERT: A 1405 LEU cc_start: 0.8013 (OUTLIER) cc_final: 0.7692 (mp) REVERT: A 1411 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8563 (tt) REVERT: A 1649 GLU cc_start: 0.7408 (tm-30) cc_final: 0.7169 (tm-30) REVERT: A 1667 VAL cc_start: 0.6353 (t) cc_final: 0.6101 (t) REVERT: A 1854 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8413 (tm) REVERT: A 2751 MET cc_start: 0.7796 (mmp) cc_final: 0.7223 (mmp) outliers start: 85 outliers final: 67 residues processed: 275 average time/residue: 0.3023 time to fit residues: 134.5458 Evaluate side-chains 273 residues out of total 2281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 196 time to evaluate : 2.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 56 TYR Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 325 TYR Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 658 GLN Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 809 ASN Chi-restraints excluded: chain A residue 894 ILE Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 897 SER Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 983 CYS Chi-restraints excluded: chain A residue 1002 TRP Chi-restraints excluded: chain A residue 1047 GLU Chi-restraints excluded: chain A residue 1071 ASP Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1200 ASN Chi-restraints excluded: chain A residue 1232 MET Chi-restraints excluded: chain A residue 1254 LEU Chi-restraints excluded: chain A residue 1255 VAL Chi-restraints excluded: chain A residue 1314 PHE Chi-restraints excluded: chain A residue 1324 PHE Chi-restraints excluded: chain A residue 1376 TYR Chi-restraints excluded: chain A residue 1398 ILE Chi-restraints excluded: chain A residue 1399 HIS Chi-restraints excluded: chain A residue 1405 LEU Chi-restraints excluded: chain A residue 1408 CYS Chi-restraints excluded: chain A residue 1411 LEU Chi-restraints excluded: chain A residue 1414 ILE Chi-restraints excluded: chain A residue 1449 ASP Chi-restraints excluded: chain A residue 1568 ASP Chi-restraints excluded: chain A residue 1591 VAL Chi-restraints excluded: chain A residue 1628 GLU Chi-restraints excluded: chain A residue 1684 SER Chi-restraints excluded: chain A residue 1777 ILE Chi-restraints excluded: chain A residue 1854 LEU Chi-restraints excluded: chain A residue 1915 ASP Chi-restraints excluded: chain A residue 1918 LEU Chi-restraints excluded: chain A residue 2052 LEU Chi-restraints excluded: chain A residue 2058 MET Chi-restraints excluded: chain A residue 2096 ILE Chi-restraints excluded: chain A residue 2118 TRP Chi-restraints excluded: chain A residue 2126 ASP Chi-restraints excluded: chain A residue 2216 ASP Chi-restraints excluded: chain A residue 2233 ASP Chi-restraints excluded: chain A residue 2234 SER Chi-restraints excluded: chain A residue 2307 ASP Chi-restraints excluded: chain A residue 2349 LEU Chi-restraints excluded: chain A residue 2516 VAL Chi-restraints excluded: chain A residue 2656 SER Chi-restraints excluded: chain A residue 2664 VAL Chi-restraints excluded: chain A residue 2666 ASN Chi-restraints excluded: chain A residue 2715 GLU Chi-restraints excluded: chain A residue 2733 ASP Chi-restraints excluded: chain A residue 2813 THR Chi-restraints excluded: chain A residue 2855 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 243 optimal weight: 1.9990 chunk 222 optimal weight: 2.9990 chunk 237 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 186 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 214 optimal weight: 4.9990 chunk 224 optimal weight: 2.9990 chunk 236 optimal weight: 0.4980 chunk 155 optimal weight: 0.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 528 GLN A 569 ASN A1764 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.3434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 21339 Z= 0.264 Angle : 0.563 9.797 28910 Z= 0.279 Chirality : 0.040 0.448 3315 Planarity : 0.004 0.039 3686 Dihedral : 6.808 76.756 2925 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.77 % Allowed : 19.82 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.17), residues: 2596 helix: 1.62 (0.12), residues: 1854 sheet: 0.01 (0.97), residues: 31 loop : -1.95 (0.22), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A2118 HIS 0.004 0.001 HIS A 824 PHE 0.019 0.001 PHE A 602 TYR 0.024 0.002 TYR A 145 ARG 0.006 0.000 ARG A2314 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 200 time to evaluate : 2.309 Fit side-chains REVERT: A 283 ASP cc_start: 0.6602 (t0) cc_final: 0.6363 (t70) REVERT: A 325 TYR cc_start: 0.6510 (OUTLIER) cc_final: 0.5857 (m-10) REVERT: A 328 ARG cc_start: 0.6895 (ptt180) cc_final: 0.6624 (ptm160) REVERT: A 522 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7555 (pp) REVERT: A 564 LEU cc_start: 0.8119 (OUTLIER) cc_final: 0.7658 (pp) REVERT: A 660 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8437 (mt) REVERT: A 677 MET cc_start: 0.7326 (ttm) cc_final: 0.7114 (ttp) REVERT: A 755 MET cc_start: 0.7426 (tpp) cc_final: 0.7104 (tpp) REVERT: A 802 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7738 (mm) REVERT: A 846 LYS cc_start: 0.8114 (mttt) cc_final: 0.7734 (mmtt) REVERT: A 1224 GLN cc_start: 0.8552 (mt0) cc_final: 0.8340 (mt0) REVERT: A 1342 LYS cc_start: 0.7000 (tttt) cc_final: 0.6398 (mtmt) REVERT: A 1376 TYR cc_start: 0.6823 (OUTLIER) cc_final: 0.3795 (m-80) REVERT: A 1405 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7713 (mp) REVERT: A 1411 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8637 (tt) REVERT: A 1649 GLU cc_start: 0.7459 (tm-30) cc_final: 0.7227 (tm-30) REVERT: A 1667 VAL cc_start: 0.6445 (t) cc_final: 0.6211 (t) REVERT: A 1854 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8469 (tm) REVERT: A 2751 MET cc_start: 0.7863 (mmp) cc_final: 0.7382 (mmp) outliers start: 86 outliers final: 70 residues processed: 270 average time/residue: 0.3144 time to fit residues: 136.5868 Evaluate side-chains 277 residues out of total 2281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 198 time to evaluate : 2.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 56 TYR Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 325 TYR Chi-restraints excluded: chain A residue 362 GLU Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 658 GLN Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 809 ASN Chi-restraints excluded: chain A residue 894 ILE Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 897 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 983 CYS Chi-restraints excluded: chain A residue 1002 TRP Chi-restraints excluded: chain A residue 1047 GLU Chi-restraints excluded: chain A residue 1071 ASP Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1200 ASN Chi-restraints excluded: chain A residue 1232 MET Chi-restraints excluded: chain A residue 1254 LEU Chi-restraints excluded: chain A residue 1255 VAL Chi-restraints excluded: chain A residue 1314 PHE Chi-restraints excluded: chain A residue 1324 PHE Chi-restraints excluded: chain A residue 1376 TYR Chi-restraints excluded: chain A residue 1398 ILE Chi-restraints excluded: chain A residue 1399 HIS Chi-restraints excluded: chain A residue 1405 LEU Chi-restraints excluded: chain A residue 1408 CYS Chi-restraints excluded: chain A residue 1411 LEU Chi-restraints excluded: chain A residue 1443 VAL Chi-restraints excluded: chain A residue 1449 ASP Chi-restraints excluded: chain A residue 1568 ASP Chi-restraints excluded: chain A residue 1591 VAL Chi-restraints excluded: chain A residue 1628 GLU Chi-restraints excluded: chain A residue 1684 SER Chi-restraints excluded: chain A residue 1777 ILE Chi-restraints excluded: chain A residue 1854 LEU Chi-restraints excluded: chain A residue 1915 ASP Chi-restraints excluded: chain A residue 1918 LEU Chi-restraints excluded: chain A residue 2052 LEU Chi-restraints excluded: chain A residue 2054 THR Chi-restraints excluded: chain A residue 2058 MET Chi-restraints excluded: chain A residue 2096 ILE Chi-restraints excluded: chain A residue 2118 TRP Chi-restraints excluded: chain A residue 2216 ASP Chi-restraints excluded: chain A residue 2233 ASP Chi-restraints excluded: chain A residue 2234 SER Chi-restraints excluded: chain A residue 2307 ASP Chi-restraints excluded: chain A residue 2349 LEU Chi-restraints excluded: chain A residue 2443 THR Chi-restraints excluded: chain A residue 2491 ASP Chi-restraints excluded: chain A residue 2516 VAL Chi-restraints excluded: chain A residue 2656 SER Chi-restraints excluded: chain A residue 2664 VAL Chi-restraints excluded: chain A residue 2666 ASN Chi-restraints excluded: chain A residue 2715 GLU Chi-restraints excluded: chain A residue 2813 THR Chi-restraints excluded: chain A residue 2846 THR Chi-restraints excluded: chain A residue 2855 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 250 optimal weight: 0.0370 chunk 153 optimal weight: 0.8980 chunk 118 optimal weight: 0.6980 chunk 174 optimal weight: 0.5980 chunk 263 optimal weight: 0.0020 chunk 242 optimal weight: 0.7980 chunk 209 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 161 optimal weight: 0.0980 chunk 128 optimal weight: 2.9990 chunk 166 optimal weight: 0.8980 overall best weight: 0.2866 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 528 GLN A 569 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.3631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 21339 Z= 0.143 Angle : 0.510 9.789 28910 Z= 0.252 Chirality : 0.037 0.420 3315 Planarity : 0.003 0.040 3686 Dihedral : 6.499 78.925 2921 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.38 % Allowed : 20.21 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.17), residues: 2596 helix: 1.87 (0.12), residues: 1853 sheet: 0.09 (0.96), residues: 31 loop : -1.85 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A2118 HIS 0.003 0.001 HIS A 824 PHE 0.019 0.001 PHE A1122 TYR 0.025 0.001 TYR A 145 ARG 0.006 0.000 ARG A2314 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 206 time to evaluate : 2.456 Fit side-chains REVERT: A 31 ASP cc_start: 0.6458 (OUTLIER) cc_final: 0.6093 (t0) REVERT: A 283 ASP cc_start: 0.6483 (t0) cc_final: 0.6128 (t70) REVERT: A 325 TYR cc_start: 0.6455 (OUTLIER) cc_final: 0.5940 (m-10) REVERT: A 328 ARG cc_start: 0.6800 (ptt180) cc_final: 0.6496 (ptm160) REVERT: A 415 TYR cc_start: 0.7234 (t80) cc_final: 0.6928 (t80) REVERT: A 522 LEU cc_start: 0.8013 (OUTLIER) cc_final: 0.7583 (pp) REVERT: A 564 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7499 (pp) REVERT: A 602 PHE cc_start: 0.7797 (m-80) cc_final: 0.7520 (m-80) REVERT: A 660 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8367 (mt) REVERT: A 677 MET cc_start: 0.7219 (ttm) cc_final: 0.6994 (ttp) REVERT: A 755 MET cc_start: 0.7332 (tpp) cc_final: 0.7025 (tpp) REVERT: A 802 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7772 (mm) REVERT: A 846 LYS cc_start: 0.8096 (mttt) cc_final: 0.7733 (mmtt) REVERT: A 1209 GLU cc_start: 0.7579 (mm-30) cc_final: 0.7251 (mp0) REVERT: A 1342 LYS cc_start: 0.6927 (tttt) cc_final: 0.6333 (mtmt) REVERT: A 1376 TYR cc_start: 0.6903 (OUTLIER) cc_final: 0.4104 (m-80) REVERT: A 1405 LEU cc_start: 0.7842 (OUTLIER) cc_final: 0.7575 (mp) REVERT: A 1411 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8594 (tt) REVERT: A 1587 MET cc_start: 0.9061 (tmm) cc_final: 0.8763 (tmm) REVERT: A 1649 GLU cc_start: 0.7406 (tm-30) cc_final: 0.7197 (tm-30) REVERT: A 1667 VAL cc_start: 0.6397 (t) cc_final: 0.6157 (t) REVERT: A 1854 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8378 (tm) REVERT: A 2751 MET cc_start: 0.7746 (mmp) cc_final: 0.7371 (mmp) outliers start: 77 outliers final: 59 residues processed: 268 average time/residue: 0.3084 time to fit residues: 134.1170 Evaluate side-chains 267 residues out of total 2281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 198 time to evaluate : 3.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 56 TYR Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 325 TYR Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 658 GLN Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 894 ILE Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1002 TRP Chi-restraints excluded: chain A residue 1025 LEU Chi-restraints excluded: chain A residue 1071 ASP Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1200 ASN Chi-restraints excluded: chain A residue 1232 MET Chi-restraints excluded: chain A residue 1254 LEU Chi-restraints excluded: chain A residue 1255 VAL Chi-restraints excluded: chain A residue 1314 PHE Chi-restraints excluded: chain A residue 1324 PHE Chi-restraints excluded: chain A residue 1376 TYR Chi-restraints excluded: chain A residue 1398 ILE Chi-restraints excluded: chain A residue 1399 HIS Chi-restraints excluded: chain A residue 1405 LEU Chi-restraints excluded: chain A residue 1408 CYS Chi-restraints excluded: chain A residue 1411 LEU Chi-restraints excluded: chain A residue 1449 ASP Chi-restraints excluded: chain A residue 1568 ASP Chi-restraints excluded: chain A residue 1591 VAL Chi-restraints excluded: chain A residue 1628 GLU Chi-restraints excluded: chain A residue 1719 SER Chi-restraints excluded: chain A residue 1777 ILE Chi-restraints excluded: chain A residue 1854 LEU Chi-restraints excluded: chain A residue 1918 LEU Chi-restraints excluded: chain A residue 2052 LEU Chi-restraints excluded: chain A residue 2054 THR Chi-restraints excluded: chain A residue 2058 MET Chi-restraints excluded: chain A residue 2096 ILE Chi-restraints excluded: chain A residue 2118 TRP Chi-restraints excluded: chain A residue 2216 ASP Chi-restraints excluded: chain A residue 2233 ASP Chi-restraints excluded: chain A residue 2234 SER Chi-restraints excluded: chain A residue 2307 ASP Chi-restraints excluded: chain A residue 2443 THR Chi-restraints excluded: chain A residue 2491 ASP Chi-restraints excluded: chain A residue 2516 VAL Chi-restraints excluded: chain A residue 2656 SER Chi-restraints excluded: chain A residue 2664 VAL Chi-restraints excluded: chain A residue 2666 ASN Chi-restraints excluded: chain A residue 2715 GLU Chi-restraints excluded: chain A residue 2733 ASP Chi-restraints excluded: chain A residue 2813 THR Chi-restraints excluded: chain A residue 2855 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 223 optimal weight: 0.6980 chunk 64 optimal weight: 4.9990 chunk 193 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 58 optimal weight: 0.3980 chunk 209 optimal weight: 4.9990 chunk 87 optimal weight: 0.0170 chunk 215 optimal weight: 0.7980 chunk 26 optimal weight: 6.9990 chunk 38 optimal weight: 0.7980 chunk 184 optimal weight: 0.9980 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 528 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.145240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.121667 restraints weight = 31257.935| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 1.78 r_work: 0.3307 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.3684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21339 Z= 0.166 Angle : 0.517 10.870 28910 Z= 0.256 Chirality : 0.038 0.466 3315 Planarity : 0.003 0.040 3686 Dihedral : 6.351 78.286 2921 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.16 % Allowed : 20.52 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.17), residues: 2596 helix: 1.95 (0.12), residues: 1845 sheet: 0.12 (0.96), residues: 31 loop : -1.80 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A2118 HIS 0.004 0.001 HIS A 824 PHE 0.034 0.001 PHE A 171 TYR 0.020 0.001 TYR A 145 ARG 0.005 0.000 ARG A2314 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4669.16 seconds wall clock time: 85 minutes 11.41 seconds (5111.41 seconds total)