Starting phenix.real_space_refine (version: 1.21rc1) on Tue Oct 10 12:34:21 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6skz_10232/10_2023/6skz_10232_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6skz_10232/10_2023/6skz_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_10232/10_2023/6skz_10232.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6skz_10232/10_2023/6skz_10232.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6skz_10232/10_2023/6skz_10232_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6skz_10232/10_2023/6skz_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: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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: 11.03, per 1000 atoms: 0.53 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: 8.36 Conformation dependent library (CDL) restraints added in 2.9 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: 8.00 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: 8.96 Time building geometry restraints manager: 8.92 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: 11680 17.94 - 35.87: 1013 35.87 - 53.81: 242 53.81 - 71.75: 51 71.75 - 89.68: 18 Dihedral angle restraints: 13004 sinusoidal: 5247 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 13001 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: 2.560 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: 9.830 Check model and map are aligned: 0.290 Set scattering table: 0.190 Process input model: 56.190 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.570 ------------------------------------------------------------------------------- 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 : 14.815 89.682 7937 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 *********************** 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 : 2.511 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 outliers start: 123 outliers final: 76 residues processed: 524 average time/residue: 0.3812 time to fit residues: 296.3425 Evaluate side-chains 290 residues out of total 2281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 214 time to evaluate : 2.351 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "THR A 27 " (corrupted residue). Skipping it. outliers start: 76 outliers final: 1 residues processed: 76 average time/residue: 0.2033 time to fit residues: 32.0069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 68 optimal weight: 0.9980 chunk 134 optimal weight: 0.4980 chunk 106 optimal weight: 0.9980 chunk 206 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 125 optimal weight: 0.7980 chunk 154 optimal weight: 0.7980 chunk 239 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 376 ASN A 394 HIS A 519 HIS A 528 GLN A 612 HIS A 632 HIS A 658 GLN ** A1027 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1028 ASN A1062 GLN A1096 HIS A1175 GLN A1200 ASN A1242 GLN A1300 HIS 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 A2925 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2112 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= 0.201 Angle : 0.572 12.987 28910 Z= 0.292 Chirality : 0.039 0.270 3315 Planarity : 0.005 0.060 3686 Dihedral : 5.223 78.908 2864 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.35 % Favored : 95.61 % Rotamer: Outliers : 2.76 % Allowed : 15.21 % Favored : 82.03 % 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: -1.00 (0.16), residues: 2596 helix: 0.15 (0.12), residues: 1846 sheet: -0.39 (0.97), residues: 31 loop : -2.73 (0.21), residues: 719 *********************** 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 326 residues out of total 2281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 263 time to evaluate : 2.502 Fit side-chains TARDY: cannot create tardy model for: "THR A 27 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash outliers start: 63 outliers final: 32 residues processed: 313 average time/residue: 0.3422 time to fit residues: 167.5397 Evaluate side-chains 240 residues out of total 2281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 208 time to evaluate : 2.313 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "THR A 27 " (corrupted residue). Skipping it. outliers start: 32 outliers final: 1 residues processed: 32 average time/residue: 0.2312 time to fit residues: 16.9678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 133 optimal weight: 0.6980 chunk 74 optimal weight: 0.1980 chunk 199 optimal weight: 2.9990 chunk 163 optimal weight: 0.3980 chunk 66 optimal weight: 3.9990 chunk 240 optimal weight: 0.6980 chunk 259 optimal weight: 0.8980 chunk 213 optimal weight: 1.9990 chunk 238 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 192 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 HIS A 528 GLN A1000 ASN A1106 HIS A1161 HIS A1245 GLN ** A1761 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21339 Z= 0.175 Angle : 0.537 11.263 28910 Z= 0.267 Chirality : 0.038 0.243 3315 Planarity : 0.004 0.052 3686 Dihedral : 4.909 79.933 2864 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.12 % Favored : 95.84 % Rotamer: Outliers : 2.54 % Allowed : 16.22 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.12 (0.16), residues: 2596 helix: 0.82 (0.12), residues: 1853 sheet: -0.09 (1.01), residues: 31 loop : -2.47 (0.21), residues: 712 *********************** 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 280 residues out of total 2281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 222 time to evaluate : 2.519 Fit side-chains TARDY: cannot create tardy model for: "THR A 27 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 58 outliers final: 29 residues processed: 263 average time/residue: 0.3479 time to fit residues: 143.1154 Evaluate side-chains 235 residues out of total 2281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 206 time to evaluate : 2.198 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "THR A 27 " (corrupted residue). Skipping it. outliers start: 29 outliers final: 1 residues processed: 29 average time/residue: 0.1930 time to fit residues: 13.6752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 237 optimal weight: 0.8980 chunk 180 optimal weight: 0.5980 chunk 124 optimal weight: 6.9990 chunk 26 optimal weight: 7.9990 chunk 114 optimal weight: 5.9990 chunk 161 optimal weight: 0.5980 chunk 241 optimal weight: 0.8980 chunk 255 optimal weight: 1.9990 chunk 125 optimal weight: 0.8980 chunk 228 optimal weight: 0.0010 chunk 68 optimal weight: 0.9980 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 607 GLN A 635 HIS ** A1027 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1245 GLN ** A1761 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1870 ASN A2380 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21339 Z= 0.170 Angle : 0.518 10.040 28910 Z= 0.256 Chirality : 0.037 0.155 3315 Planarity : 0.004 0.047 3686 Dihedral : 4.715 80.884 2864 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.08 % Favored : 95.88 % Rotamer: Outliers : 1.36 % Allowed : 17.36 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.17), residues: 2596 helix: 1.18 (0.12), residues: 1865 sheet: 0.13 (1.03), residues: 31 loop : -2.25 (0.21), residues: 700 *********************** 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 269 residues out of total 2281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 238 time to evaluate : 2.398 Fit side-chains TARDY: cannot create tardy model for: "THR A 27 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 15 residues processed: 262 average time/residue: 0.3527 time to fit residues: 141.9510 Evaluate side-chains 224 residues out of total 2281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 209 time to evaluate : 2.346 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "THR A 27 " (corrupted residue). Skipping it. outliers start: 15 outliers final: 1 residues processed: 15 average time/residue: 0.2004 time to fit residues: 8.8930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 105 optimal weight: 6.9990 chunk 217 optimal weight: 4.9990 chunk 176 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 130 optimal weight: 2.9990 chunk 229 optimal weight: 0.0870 chunk 64 optimal weight: 4.9990 overall best weight: 1.7964 ------------------------------------------------------------------------------- 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 A 839 HIS ** A1027 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1245 GLN A1574 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 21339 Z= 0.355 Angle : 0.621 10.196 28910 Z= 0.308 Chirality : 0.042 0.180 3315 Planarity : 0.004 0.044 3686 Dihedral : 4.984 78.105 2864 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.01 % Favored : 94.95 % Rotamer: Outliers : 2.06 % Allowed : 18.19 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.17), residues: 2596 helix: 1.04 (0.12), residues: 1864 sheet: -0.12 (0.95), residues: 31 loop : -2.27 (0.22), residues: 701 *********************** 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 261 residues out of total 2281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 214 time to evaluate : 2.472 Fit side-chains TARDY: cannot create tardy model for: "THR A 27 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 47 outliers final: 32 residues processed: 252 average time/residue: 0.3421 time to fit residues: 135.6835 Evaluate side-chains 226 residues out of total 2281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 194 time to evaluate : 2.344 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "THR A 27 " (corrupted residue). Skipping it. outliers start: 32 outliers final: 1 residues processed: 32 average time/residue: 0.2013 time to fit residues: 15.4562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 85 optimal weight: 0.9990 chunk 229 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 149 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 255 optimal weight: 0.7980 chunk 212 optimal weight: 0.8980 chunk 118 optimal weight: 1.9990 chunk 21 optimal weight: 0.0980 chunk 84 optimal weight: 0.9980 chunk 134 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 528 GLN ** A1027 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1245 GLN A1764 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 21339 Z= 0.187 Angle : 0.528 10.344 28910 Z= 0.263 Chirality : 0.038 0.151 3315 Planarity : 0.004 0.043 3686 Dihedral : 4.754 78.516 2864 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.58 % Favored : 96.38 % Rotamer: Outliers : 1.18 % Allowed : 18.98 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.17), residues: 2596 helix: 1.35 (0.12), residues: 1862 sheet: 0.11 (0.95), residues: 31 loop : -2.18 (0.22), residues: 703 *********************** 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 245 residues out of total 2281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 218 time to evaluate : 2.542 Fit side-chains TARDY: cannot create tardy model for: "THR A 27 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 27 outliers final: 16 residues processed: 240 average time/residue: 0.3610 time to fit residues: 136.4936 Evaluate side-chains 213 residues out of total 2281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 197 time to evaluate : 2.391 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "THR A 27 " (corrupted residue). Skipping it. outliers start: 16 outliers final: 1 residues processed: 16 average time/residue: 0.2006 time to fit residues: 9.1700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 246 optimal weight: 0.6980 chunk 28 optimal weight: 4.9990 chunk 145 optimal weight: 2.9990 chunk 186 optimal weight: 1.9990 chunk 144 optimal weight: 0.7980 chunk 215 optimal weight: 0.3980 chunk 142 optimal weight: 0.2980 chunk 254 optimal weight: 1.9990 chunk 159 optimal weight: 0.4980 chunk 155 optimal weight: 0.8980 chunk 117 optimal weight: 3.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 528 GLN ** A1027 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1245 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.3386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 21339 Z= 0.164 Angle : 0.518 10.391 28910 Z= 0.257 Chirality : 0.038 0.471 3315 Planarity : 0.004 0.042 3686 Dihedral : 4.606 79.069 2864 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.83 % Allowed : 19.55 % Favored : 79.61 % 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: 0.91 (0.17), residues: 2596 helix: 1.58 (0.12), residues: 1851 sheet: 0.35 (0.95), residues: 31 loop : -2.07 (0.22), residues: 714 *********************** 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 226 residues out of total 2281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 207 time to evaluate : 2.220 Fit side-chains TARDY: cannot create tardy model for: "THR A 27 " (corrupted residue). Skipping it. outliers start: 19 outliers final: 11 residues processed: 223 average time/residue: 0.3371 time to fit residues: 119.0893 Evaluate side-chains 202 residues out of total 2281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 191 time to evaluate : 2.401 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "THR A 27 " (corrupted residue). Skipping it. outliers start: 11 outliers final: 1 residues processed: 11 average time/residue: 0.2185 time to fit residues: 8.0368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 157 optimal weight: 0.4980 chunk 101 optimal weight: 0.3980 chunk 151 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 161 optimal weight: 0.6980 chunk 173 optimal weight: 0.9990 chunk 125 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 200 optimal weight: 0.9990 chunk 231 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 528 GLN ** A1027 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.3496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 21339 Z= 0.187 Angle : 0.528 10.349 28910 Z= 0.262 Chirality : 0.038 0.407 3315 Planarity : 0.004 0.041 3686 Dihedral : 4.562 78.842 2864 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.70 % Allowed : 20.39 % Favored : 78.91 % 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: 0.99 (0.17), residues: 2596 helix: 1.63 (0.12), residues: 1854 sheet: 0.43 (0.97), residues: 31 loop : -2.01 (0.22), residues: 711 *********************** 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 221 residues out of total 2281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 205 time to evaluate : 2.486 Fit side-chains TARDY: cannot create tardy model for: "THR A 27 " (corrupted residue). Skipping it. outliers start: 16 outliers final: 8 residues processed: 213 average time/residue: 0.3593 time to fit residues: 122.9692 Evaluate side-chains 202 residues out of total 2281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 194 time to evaluate : 2.485 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "THR A 27 " (corrupted residue). Skipping it. outliers start: 8 outliers final: 1 residues processed: 8 average time/residue: 0.2233 time to fit residues: 6.7725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0370 chunk 237 optimal weight: 0.9980 chunk 142 optimal weight: 0.0370 chunk 103 optimal weight: 7.9990 chunk 186 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 214 optimal weight: 4.9990 chunk 224 optimal weight: 2.9990 chunk 236 optimal weight: 0.7980 chunk 155 optimal weight: 0.0980 overall best weight: 0.3936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 528 GLN ** A1027 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1764 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.3651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 21339 Z= 0.146 Angle : 0.515 10.388 28910 Z= 0.254 Chirality : 0.037 0.424 3315 Planarity : 0.004 0.041 3686 Dihedral : 4.425 79.275 2864 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.39 % Allowed : 20.78 % Favored : 78.83 % 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: 1.24 (0.17), residues: 2596 helix: 1.80 (0.12), residues: 1851 sheet: 0.47 (0.96), residues: 31 loop : -1.87 (0.22), residues: 714 *********************** 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 215 residues out of total 2281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 206 time to evaluate : 2.355 Fit side-chains TARDY: cannot create tardy model for: "THR A 27 " (corrupted residue). Skipping it. outliers start: 9 outliers final: 4 residues processed: 210 average time/residue: 0.3413 time to fit residues: 114.8376 Evaluate side-chains 195 residues out of total 2281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 191 time to evaluate : 2.916 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "THR A 27 " (corrupted residue). Skipping it. outliers start: 4 outliers final: 1 residues processed: 4 average time/residue: 0.2250 time to fit residues: 4.8972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 250 optimal weight: 0.8980 chunk 153 optimal weight: 0.5980 chunk 118 optimal weight: 1.9990 chunk 174 optimal weight: 0.6980 chunk 263 optimal weight: 0.7980 chunk 242 optimal weight: 0.8980 chunk 209 optimal weight: 3.9990 chunk 21 optimal weight: 0.0170 chunk 161 optimal weight: 0.0050 chunk 128 optimal weight: 0.7980 chunk 166 optimal weight: 0.5980 overall best weight: 0.3832 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 528 GLN ** A1027 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.3764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 21339 Z= 0.149 Angle : 0.516 10.366 28910 Z= 0.254 Chirality : 0.037 0.434 3315 Planarity : 0.004 0.041 3686 Dihedral : 4.343 79.016 2864 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.13 % Allowed : 21.26 % Favored : 78.61 % 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: 1.92 (0.12), residues: 1850 sheet: 0.56 (0.96), residues: 31 loop : -1.78 (0.22), residues: 715 ********************** 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 209 residues out of total 2281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 206 time to evaluate : 2.415 Fit side-chains TARDY: cannot create tardy model for: "THR A 27 " (corrupted residue). Skipping it. outliers start: 3 outliers final: 2 residues processed: 209 average time/residue: 0.3368 time to fit residues: 114.1543 Evaluate side-chains 189 residues out of total 2281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 187 time to evaluate : 2.572 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "THR A 27 " (corrupted residue). Skipping it. outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 0.2050 time to fit residues: 4.1346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 223 optimal weight: 0.0870 chunk 64 optimal weight: 2.9990 chunk 193 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 209 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 215 optimal weight: 0.6980 chunk 26 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 184 optimal weight: 0.7980 overall best weight: 0.9162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 528 GLN ** A1027 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1028 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.144923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.120388 restraints weight = 31339.734| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 1.90 r_work: 0.3281 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21339 Z= 0.212 Angle : 0.543 11.095 28910 Z= 0.267 Chirality : 0.039 0.528 3315 Planarity : 0.004 0.040 3686 Dihedral : 4.415 77.603 2864 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.31 % Allowed : 21.22 % Favored : 78.47 % 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: 1.33 (0.17), residues: 2596 helix: 1.86 (0.12), residues: 1850 sheet: 0.38 (0.95), residues: 31 loop : -1.77 (0.22), residues: 715 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4380.11 seconds wall clock time: 80 minutes 9.39 seconds (4809.39 seconds total)