Starting phenix.real_space_refine on Mon Mar 18 17:05:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p05_13144/03_2024/7p05_13144_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p05_13144/03_2024/7p05_13144.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p05_13144/03_2024/7p05_13144_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p05_13144/03_2024/7p05_13144_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p05_13144/03_2024/7p05_13144_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p05_13144/03_2024/7p05_13144.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p05_13144/03_2024/7p05_13144.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p05_13144/03_2024/7p05_13144_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p05_13144/03_2024/7p05_13144_trim_updated.pdb" } resolution = 3.13 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 5 5.49 5 S 68 5.16 5 C 7050 2.51 5 N 1796 2.21 5 O 1982 1.98 5 H 10675 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 37": "OE1" <-> "OE2" Residue "A ASP 96": "OD1" <-> "OD2" Residue "A GLU 100": "OE1" <-> "OE2" Residue "A PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 162": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 187": "OE1" <-> "OE2" Residue "A PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 229": "OD1" <-> "OD2" Residue "A GLU 238": "OE1" <-> "OE2" Residue "A GLU 244": "OE1" <-> "OE2" Residue "A GLU 256": "OE1" <-> "OE2" Residue "A GLU 346": "OE1" <-> "OE2" Residue "A TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 395": "OD1" <-> "OD2" Residue "A ARG 517": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 591": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 607": "OE1" <-> "OE2" Residue "A TYR 623": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 630": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 647": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 705": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 714": "OE1" <-> "OE2" Residue "A GLU 724": "OE1" <-> "OE2" Residue "A TYR 725": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 732": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 795": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 810": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 866": "OE1" <-> "OE2" Residue "A ARG 872": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 877": "OE1" <-> "OE2" Residue "A ASP 916": "OD1" <-> "OD2" Residue "A GLU 920": "OE1" <-> "OE2" Residue "A TYR 948": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 953": "OD1" <-> "OD2" Residue "A GLU 963": "OE1" <-> "OE2" Residue "A GLU 980": "OE1" <-> "OE2" Residue "A TYR 985": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 998": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 1008": "OE1" <-> "OE2" Residue "A GLU 1013": "OE1" <-> "OE2" Residue "A PHE 1033": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 1042": "OD1" <-> "OD2" Residue "A GLU 1077": "OE1" <-> "OE2" Residue "A GLU 1123": "OE1" <-> "OE2" Residue "A GLU 1127": "OE1" <-> "OE2" Residue "A TYR 1141": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 1146": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 1149": "OE1" <-> "OE2" Residue "A GLU 1150": "OE1" <-> "OE2" Residue "A GLU 1162": "OE1" <-> "OE2" Residue "A GLU 1179": "OE1" <-> "OE2" Residue "A PHE 1215": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 1224": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 1242": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 1244": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 1267": "OE1" <-> "OE2" Residue "A ARG 1274": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 1287": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 1304": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 1311": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 1323": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 1385": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 1415": "OE1" <-> "OE2" Residue "A PHE 1419": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 1442": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 1473": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 21576 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 21576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1356, 21576 Unusual residues: {'ADP': 1, 'ATP': 1, 'RHQ': 1} Classifications: {'peptide': 1353, 'undetermined': 3} Link IDs: {'PTRANS': 52, 'TRANS': 1300, None: 3} Not linked: pdbres="PRO A1502 " pdbres="ATP A1601 " Not linked: pdbres="ATP A1601 " pdbres="ADP A1602 " Not linked: pdbres="ADP A1602 " pdbres="RHQ A1603 " Chain breaks: 5 Time building chain proxies: 9.52, per 1000 atoms: 0.44 Number of scatterers: 21576 At special positions: 0 Unit cell: (104.32, 95.844, 148.656, 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 68 16.00 P 5 15.00 O 1982 8.00 N 1796 7.00 C 7050 6.00 H 10675 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 722 " - pdb=" SG CYS A 742 " distance=2.03 Simple disulfide: pdb=" SG CYS A1411 " - pdb=" SG CYS A1455 " distance=2.04 Simple disulfide: pdb=" SG CYS A1427 " - pdb=" SG CYS A1452 " distance=2.02 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: 18.56 Conformation dependent library (CDL) restraints added in 2.0 seconds 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2534 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 59 helices and 7 sheets defined 55.6% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.35 Creating SS restraints... Processing helix chain 'A' and resid 37 through 55 Processing helix chain 'A' and resid 104 through 115 Processing helix chain 'A' and resid 152 through 164 Processing helix chain 'A' and resid 199 through 206 Processing helix chain 'A' and resid 228 through 233 Processing helix chain 'A' and resid 254 through 265 removed outlier: 3.820A pdb=" N VAL A 261 " --> pdb=" O THR A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 290 Processing helix chain 'A' and resid 294 through 296 No H-bonds generated for 'chain 'A' and resid 294 through 296' Processing helix chain 'A' and resid 311 through 325 Processing helix chain 'A' and resid 341 through 358 Processing helix chain 'A' and resid 371 through 376 removed outlier: 3.913A pdb=" N LEU A 376 " --> pdb=" O ASP A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 404 removed outlier: 4.467A pdb=" N LYS A 398 " --> pdb=" O ASP A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 422 removed outlier: 4.404A pdb=" N THR A 422 " --> pdb=" O LEU A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 435 Processing helix chain 'A' and resid 444 through 453 Processing helix chain 'A' and resid 455 through 469 removed outlier: 3.573A pdb=" N GLN A 466 " --> pdb=" O LYS A 462 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG A 467 " --> pdb=" O GLU A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 518 Processing helix chain 'A' and resid 520 through 540 Processing helix chain 'A' and resid 544 through 546 No H-bonds generated for 'chain 'A' and resid 544 through 546' Processing helix chain 'A' and resid 550 through 568 removed outlier: 4.923A pdb=" N TYR A 554 " --> pdb=" O SER A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 590 removed outlier: 3.940A pdb=" N PHE A 576 " --> pdb=" O LEU A 573 " (cutoff:3.500A) Proline residue: A 583 - end of helix Processing helix chain 'A' and resid 596 through 626 removed outlier: 3.520A pdb=" N GLU A 607 " --> pdb=" O SER A 603 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE A 608 " --> pdb=" O VAL A 604 " (cutoff:3.500A) Proline residue: A 609 - end of helix removed outlier: 3.653A pdb=" N PHE A 624 " --> pdb=" O ILE A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 659 removed outlier: 3.536A pdb=" N LEU A 659 " --> pdb=" O CYS A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 681 removed outlier: 4.559A pdb=" N VAL A 668 " --> pdb=" O SER A 664 " (cutoff:3.500A) Proline residue: A 669 - end of helix Processing helix chain 'A' and resid 692 through 700 removed outlier: 3.728A pdb=" N LYS A 695 " --> pdb=" O ARG A 692 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N TRP A 696 " --> pdb=" O TRP A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 715 Processing helix chain 'A' and resid 730 through 732 No H-bonds generated for 'chain 'A' and resid 730 through 732' Processing helix chain 'A' and resid 737 through 739 No H-bonds generated for 'chain 'A' and resid 737 through 739' Processing helix chain 'A' and resid 756 through 763 Processing helix chain 'A' and resid 768 through 795 removed outlier: 4.657A pdb=" N TRP A 772 " --> pdb=" O LYS A 769 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY A 774 " --> pdb=" O LYS A 771 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE A 775 " --> pdb=" O TRP A 772 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE A 785 " --> pdb=" O VAL A 782 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR A 795 " --> pdb=" O LEU A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 810 through 813 No H-bonds generated for 'chain 'A' and resid 810 through 813' Processing helix chain 'A' and resid 911 through 918 Processing helix chain 'A' and resid 942 through 945 No H-bonds generated for 'chain 'A' and resid 942 through 945' Processing helix chain 'A' and resid 961 through 972 Processing helix chain 'A' and resid 979 through 993 Processing helix chain 'A' and resid 996 through 998 No H-bonds generated for 'chain 'A' and resid 996 through 998' Processing helix chain 'A' and resid 1012 through 1024 removed outlier: 3.511A pdb=" N GLU A1023 " --> pdb=" O THR A1019 " (cutoff:3.500A) Processing helix chain 'A' and resid 1043 through 1059 Processing helix chain 'A' and resid 1072 through 1076 removed outlier: 3.695A pdb=" N GLN A1076 " --> pdb=" O ALA A1072 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1072 through 1076' Processing helix chain 'A' and resid 1098 through 1110 removed outlier: 5.768A pdb=" N THR A1102 " --> pdb=" O GLY A1099 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N SER A1109 " --> pdb=" O TYR A1106 " (cutoff:3.500A) Processing helix chain 'A' and resid 1121 through 1128 Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'A' and resid 1149 through 1163 Processing helix chain 'A' and resid 1184 through 1199 Processing helix chain 'A' and resid 1203 through 1223 Processing helix chain 'A' and resid 1231 through 1245 removed outlier: 3.658A pdb=" N GLN A1235 " --> pdb=" O LEU A1231 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N THR A1245 " --> pdb=" O VAL A1241 " (cutoff:3.500A) Processing helix chain 'A' and resid 1248 through 1269 Proline residue: A1257 - end of helix Processing helix chain 'A' and resid 1278 through 1308 Proline residue: A1291 - end of helix removed outlier: 4.316A pdb=" N TYR A1306 " --> pdb=" O PHE A1302 " (cutoff:3.500A) Proline residue: A1307 - end of helix Processing helix chain 'A' and resid 1310 through 1316 Processing helix chain 'A' and resid 1320 through 1346 Processing helix chain 'A' and resid 1352 through 1368 Processing helix chain 'A' and resid 1376 through 1378 No H-bonds generated for 'chain 'A' and resid 1376 through 1378' Processing helix chain 'A' and resid 1381 through 1389 removed outlier: 3.517A pdb=" N ILE A1384 " --> pdb=" O ARG A1381 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N PHE A1385 " --> pdb=" O PHE A1382 " (cutoff:3.500A) Processing helix chain 'A' and resid 1391 through 1404 Processing helix chain 'A' and resid 1413 through 1415 No H-bonds generated for 'chain 'A' and resid 1413 through 1415' Processing helix chain 'A' and resid 1427 through 1430 No H-bonds generated for 'chain 'A' and resid 1427 through 1430' Processing helix chain 'A' and resid 1432 through 1437 removed outlier: 3.638A pdb=" N LEU A1437 " --> pdb=" O PRO A1433 " (cutoff:3.500A) Processing helix chain 'A' and resid 1460 through 1467 Processing helix chain 'A' and resid 1474 through 1499 Processing sheet with id= A, first strand: chain 'A' and resid 129 through 132 Processing sheet with id= B, first strand: chain 'A' and resid 387 through 393 removed outlier: 6.606A pdb=" N VAL A 382 " --> pdb=" O ILE A 389 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N TYR A 391 " --> pdb=" O VAL A 380 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL A 380 " --> pdb=" O TYR A 391 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ALA A 362 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N VAL A 191 " --> pdb=" O ALA A 362 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL A 364 " --> pdb=" O VAL A 191 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 719 through 721 Processing sheet with id= D, first strand: chain 'A' and resid 893 through 895 Processing sheet with id= E, first strand: chain 'A' and resid 926 through 928 removed outlier: 7.867A pdb=" N TYR A 876 " --> pdb=" O ASN A 889 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N ASN A 889 " --> pdb=" O TYR A 876 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 1089 through 1094 removed outlier: 6.325A pdb=" N PHE A1083 " --> pdb=" O VAL A1091 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N PHE A1093 " --> pdb=" O LEU A1081 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N LEU A1081 " --> pdb=" O PHE A1093 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ILE A1063 " --> pdb=" O THR A 901 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N LEU A 903 " --> pdb=" O ILE A1063 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N CYS A1065 " --> pdb=" O LEU A 903 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N VAL A1032 " --> pdb=" O LEU A1064 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N THR A1066 " --> pdb=" O VAL A1032 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LEU A1034 " --> pdb=" O THR A1066 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N GLY A 947 " --> pdb=" O PHE A1033 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N ASP A1035 " --> pdb=" O GLY A 947 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N CYS A 949 " --> pdb=" O ASP A1035 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 1417 through 1419 530 hydrogen bonds defined for protein. 1344 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: 8.90 Time building geometry restraints manager: 19.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 10653 1.04 - 1.23: 669 1.23 - 1.43: 4286 1.43 - 1.63: 6144 1.63 - 1.83: 108 Bond restraints: 21860 Sorted by residual: bond pdb=" C2 RHQ A1603 " pdb=" C3 RHQ A1603 " ideal model delta sigma weight residual 1.158 1.422 -0.264 2.00e-02 2.50e+03 1.74e+02 bond pdb=" C4 RHQ A1603 " pdb=" C5 RHQ A1603 " ideal model delta sigma weight residual 1.641 1.427 0.214 2.00e-02 2.50e+03 1.14e+02 bond pdb=" C5 RHQ A1603 " pdb=" C6 RHQ A1603 " ideal model delta sigma weight residual 1.618 1.406 0.212 2.00e-02 2.50e+03 1.12e+02 bond pdb=" C1 RHQ A1603 " pdb=" C2 RHQ A1603 " ideal model delta sigma weight residual 1.200 1.396 -0.196 2.00e-02 2.50e+03 9.64e+01 bond pdb=" C4 ATP A1601 " pdb=" C5 ATP A1601 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.46e+01 ... (remaining 21855 not shown) Histogram of bond angle deviations from ideal: 73.57 - 86.12: 6 86.12 - 98.67: 1 98.67 - 111.22: 23509 111.22 - 123.77: 14125 123.77 - 136.32: 1687 Bond angle restraints: 39328 Sorted by residual: angle pdb=" PB ATP A1601 " pdb=" O3B ATP A1601 " pdb=" PG ATP A1601 " ideal model delta sigma weight residual 139.87 119.75 20.12 1.00e+00 1.00e+00 4.05e+02 angle pdb=" PA ATP A1601 " pdb=" O3A ATP A1601 " pdb=" PB ATP A1601 " ideal model delta sigma weight residual 136.83 120.62 16.21 1.00e+00 1.00e+00 2.63e+02 angle pdb=" C6 RHQ A1603 " pdb=" C5 RHQ A1603 " pdb=" N2 RHQ A1603 " ideal model delta sigma weight residual 72.13 116.94 -44.81 3.00e+00 1.11e-01 2.23e+02 angle pdb=" C ASP A 120 " pdb=" CA ASP A 120 " pdb=" HA ASP A 120 " ideal model delta sigma weight residual 109.00 73.57 35.43 3.00e+00 1.11e-01 1.39e+02 angle pdb=" C ARG A 517 " pdb=" CA ARG A 517 " pdb=" HA ARG A 517 " ideal model delta sigma weight residual 109.00 74.08 34.92 3.00e+00 1.11e-01 1.35e+02 ... (remaining 39323 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.63: 9757 21.63 - 43.26: 470 43.26 - 64.89: 128 64.89 - 86.53: 29 86.53 - 108.16: 4 Dihedral angle restraints: 10388 sinusoidal: 5490 harmonic: 4898 Sorted by residual: dihedral pdb=" C2' ADP A1602 " pdb=" C1' ADP A1602 " pdb=" N9 ADP A1602 " pdb=" C4 ADP A1602 " ideal model delta sinusoidal sigma weight residual 91.55 -160.30 -108.16 1 2.00e+01 2.50e-03 3.15e+01 dihedral pdb=" CA PRO A 267 " pdb=" C PRO A 267 " pdb=" N GLN A 268 " pdb=" CA GLN A 268 " ideal model delta harmonic sigma weight residual 180.00 -153.68 -26.32 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CA TYR A1199 " pdb=" C TYR A1199 " pdb=" N TRP A1200 " pdb=" CA TRP A1200 " ideal model delta harmonic sigma weight residual 180.00 154.34 25.66 0 5.00e+00 4.00e-02 2.63e+01 ... (remaining 10385 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 1555 0.084 - 0.167: 88 0.167 - 0.251: 2 0.251 - 0.334: 0 0.334 - 0.418: 2 Chirality restraints: 1647 Sorted by residual: chirality pdb=" CA ARG A 517 " pdb=" N ARG A 517 " pdb=" C ARG A 517 " pdb=" CB ARG A 517 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.37e+00 chirality pdb=" CA ASP A 120 " pdb=" N ASP A 120 " pdb=" C ASP A 120 " pdb=" CB ASP A 120 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.41e+00 chirality pdb=" CA CYS A1411 " pdb=" N CYS A1411 " pdb=" C CYS A1411 " pdb=" CB CYS A1411 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 1644 not shown) Planarity restraints: 3201 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 RHQ A1603 " 0.039 2.00e-02 2.50e+03 2.90e-01 2.31e+03 pdb=" C2 RHQ A1603 " -0.098 2.00e-02 2.50e+03 pdb=" C21 RHQ A1603 " 0.140 2.00e-02 2.50e+03 pdb=" C24 RHQ A1603 " -0.743 2.00e-02 2.50e+03 pdb=" C3 RHQ A1603 " -0.055 2.00e-02 2.50e+03 pdb=" C4 RHQ A1603 " 0.108 2.00e-02 2.50e+03 pdb=" C5 RHQ A1603 " 0.244 2.00e-02 2.50e+03 pdb=" C6 RHQ A1603 " 0.207 2.00e-02 2.50e+03 pdb=" C9 RHQ A1603 " -0.260 2.00e-02 2.50e+03 pdb=" N2 RHQ A1603 " 0.397 2.00e-02 2.50e+03 pdb=" O1 RHQ A1603 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 882 " -0.013 2.00e-02 2.50e+03 2.57e-02 6.63e+00 pdb=" N GLU A 883 " 0.044 2.00e-02 2.50e+03 pdb=" CA GLU A 883 " -0.011 2.00e-02 2.50e+03 pdb=" H GLU A 883 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 808 " -0.035 5.00e-02 4.00e+02 5.24e-02 4.40e+00 pdb=" N PRO A 809 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 809 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 809 " -0.029 5.00e-02 4.00e+02 ... (remaining 3198 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 1030 2.18 - 2.78: 43498 2.78 - 3.39: 62673 3.39 - 3.99: 81720 3.99 - 4.60: 128246 Nonbonded interactions: 317167 Sorted by model distance: nonbonded pdb="HH12 ARG A 962 " pdb=" OE2 GLU A 987 " model vdw 1.572 1.850 nonbonded pdb=" O GLN A1182 " pdb="HE21 GLN A1187 " model vdw 1.573 1.850 nonbonded pdb=" OE1 GLU A 238 " pdb=" HZ2 LYS A 328 " model vdw 1.604 1.850 nonbonded pdb=" OE1 GLN A1044 " pdb=" H GLN A1044 " model vdw 1.612 1.850 nonbonded pdb=" HA ASP A 120 " pdb=" HB3 ASP A 120 " model vdw 1.634 1.952 ... (remaining 317162 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: 8.160 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: 0.320 Extract box with map and model: 30.640 Check model and map are aligned: 0.340 Set scattering table: 0.220 Process input model: 73.930 Find NCS groups from input model: 0.420 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: 0.010 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 117.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.264 11185 Z= 0.480 Angle : 0.865 44.810 15170 Z= 0.481 Chirality : 0.042 0.418 1647 Planarity : 0.008 0.290 1905 Dihedral : 13.903 108.156 4036 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.09 % Allowed : 0.34 % Favored : 99.57 % 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: 0.57 (0.23), residues: 1341 helix: 1.03 (0.19), residues: 764 sheet: -0.17 (0.55), residues: 86 loop : -0.44 (0.30), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 451 HIS 0.004 0.001 HIS A 234 PHE 0.021 0.002 PHE A 35 TYR 0.012 0.002 TYR A1335 ARG 0.016 0.001 ARG A 297 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 882 is missing expected H atoms. Skipping. Evaluate side-chains 110 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 109 time to evaluate : 1.724 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 154 TYR cc_start: 0.8069 (t80) cc_final: 0.7866 (t80) REVERT: A 580 GLU cc_start: 0.8178 (tt0) cc_final: 0.7906 (tt0) REVERT: A 1264 ASP cc_start: 0.7935 (m-30) cc_final: 0.7565 (m-30) outliers start: 1 outliers final: 0 residues processed: 110 average time/residue: 0.5738 time to fit residues: 88.6596 Evaluate side-chains 92 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 1.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 64 optimal weight: 0.2980 chunk 78 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 GLN A 388 GLN A 952 GLN A1138 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.0556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11185 Z= 0.268 Angle : 0.577 12.462 15170 Z= 0.300 Chirality : 0.041 0.406 1647 Planarity : 0.005 0.049 1905 Dihedral : 8.181 104.645 1531 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 0.69 % Allowed : 3.01 % Favored : 96.30 % 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: 0.47 (0.23), residues: 1341 helix: 0.93 (0.19), residues: 758 sheet: -0.22 (0.54), residues: 87 loop : -0.43 (0.30), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1200 HIS 0.003 0.001 HIS A 595 PHE 0.012 0.001 PHE A 653 TYR 0.013 0.001 TYR A 591 ARG 0.005 0.000 ARG A 297 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 882 is missing expected H atoms. Skipping. Evaluate side-chains 101 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 93 time to evaluate : 1.779 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 580 GLU cc_start: 0.8015 (tt0) cc_final: 0.7810 (tt0) REVERT: A 1264 ASP cc_start: 0.7925 (m-30) cc_final: 0.7458 (m-30) outliers start: 8 outliers final: 7 residues processed: 99 average time/residue: 0.5430 time to fit residues: 76.6314 Evaluate side-chains 94 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 87 time to evaluate : 1.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 1044 GLN Chi-restraints excluded: chain A residue 1138 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 68 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 102 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 122 optimal weight: 0.6980 chunk 132 optimal weight: 3.9990 chunk 109 optimal weight: 0.8980 chunk 121 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 952 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.0842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11185 Z= 0.187 Angle : 0.531 12.107 15170 Z= 0.271 Chirality : 0.039 0.398 1647 Planarity : 0.004 0.044 1905 Dihedral : 7.749 100.020 1531 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.60 % Allowed : 3.70 % Favored : 95.70 % 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: 0.63 (0.24), residues: 1341 helix: 1.05 (0.19), residues: 756 sheet: -0.19 (0.55), residues: 87 loop : -0.31 (0.30), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 451 HIS 0.003 0.001 HIS A 251 PHE 0.010 0.001 PHE A 967 TYR 0.010 0.001 TYR A 591 ARG 0.003 0.000 ARG A 297 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 882 is missing expected H atoms. Skipping. Evaluate side-chains 100 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 93 time to evaluate : 1.705 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1264 ASP cc_start: 0.7902 (m-30) cc_final: 0.7445 (m-30) outliers start: 7 outliers final: 7 residues processed: 97 average time/residue: 0.5472 time to fit residues: 75.9307 Evaluate side-chains 95 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 88 time to evaluate : 1.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 924 MET Chi-restraints excluded: chain A residue 1136 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 121 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 123 optimal weight: 0.8980 chunk 130 optimal weight: 4.9990 chunk 64 optimal weight: 0.7980 chunk 116 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN A 952 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.0958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11185 Z= 0.262 Angle : 0.538 11.990 15170 Z= 0.274 Chirality : 0.040 0.400 1647 Planarity : 0.004 0.042 1905 Dihedral : 7.658 96.905 1531 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 0.69 % Allowed : 5.34 % Favored : 93.98 % 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: 0.59 (0.24), residues: 1341 helix: 1.02 (0.19), residues: 756 sheet: -0.28 (0.55), residues: 87 loop : -0.32 (0.29), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 772 HIS 0.003 0.001 HIS A 234 PHE 0.012 0.001 PHE A1248 TYR 0.014 0.001 TYR A 591 ARG 0.005 0.000 ARG A 276 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 882 is missing expected H atoms. Skipping. Evaluate side-chains 98 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 90 time to evaluate : 1.609 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1264 ASP cc_start: 0.7876 (m-30) cc_final: 0.7426 (m-30) outliers start: 8 outliers final: 8 residues processed: 96 average time/residue: 0.5258 time to fit residues: 73.0666 Evaluate side-chains 97 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 89 time to evaluate : 1.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 928 THR Chi-restraints excluded: chain A residue 1136 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 108 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 66 optimal weight: 0.5980 chunk 117 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 ASN A 952 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11185 Z= 0.287 Angle : 0.544 12.204 15170 Z= 0.278 Chirality : 0.040 0.401 1647 Planarity : 0.004 0.041 1905 Dihedral : 7.626 94.610 1531 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 0.86 % Allowed : 6.02 % Favored : 93.12 % 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: 0.55 (0.24), residues: 1341 helix: 0.97 (0.19), residues: 755 sheet: -0.30 (0.55), residues: 87 loop : -0.30 (0.30), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 772 HIS 0.003 0.001 HIS A 234 PHE 0.012 0.001 PHE A1242 TYR 0.014 0.001 TYR A 591 ARG 0.003 0.000 ARG A 276 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 882 is missing expected H atoms. Skipping. Evaluate side-chains 104 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 94 time to evaluate : 1.603 Fit side-chains revert: symmetry clash REVERT: A 154 TYR cc_start: 0.7906 (t80) cc_final: 0.7681 (t80) REVERT: A 1264 ASP cc_start: 0.7872 (m-30) cc_final: 0.7429 (m-30) outliers start: 10 outliers final: 8 residues processed: 102 average time/residue: 0.5439 time to fit residues: 79.3897 Evaluate side-chains 96 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 88 time to evaluate : 1.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 928 THR Chi-restraints excluded: chain A residue 1136 HIS Chi-restraints excluded: chain A residue 1362 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 43 optimal weight: 0.6980 chunk 117 optimal weight: 2.9990 chunk 25 optimal weight: 0.4980 chunk 76 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 68 optimal weight: 0.6980 chunk 125 optimal weight: 0.8980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 ASN A 952 GLN A1138 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11185 Z= 0.183 Angle : 0.510 12.096 15170 Z= 0.257 Chirality : 0.039 0.399 1647 Planarity : 0.004 0.041 1905 Dihedral : 7.300 92.131 1531 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.77 % Allowed : 6.71 % Favored : 92.51 % 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: 0.75 (0.24), residues: 1341 helix: 1.13 (0.19), residues: 755 sheet: -0.34 (0.55), residues: 87 loop : -0.19 (0.30), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1200 HIS 0.003 0.000 HIS A 251 PHE 0.010 0.001 PHE A1248 TYR 0.012 0.001 TYR A1414 ARG 0.002 0.000 ARG A 276 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 882 is missing expected H atoms. Skipping. Evaluate side-chains 107 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 98 time to evaluate : 1.662 Fit side-chains revert: symmetry clash REVERT: A 154 TYR cc_start: 0.7931 (t80) cc_final: 0.7661 (t80) REVERT: A 528 LEU cc_start: 0.7381 (tp) cc_final: 0.7039 (mp) REVERT: A 1023 GLU cc_start: 0.7187 (mp0) cc_final: 0.6879 (mp0) REVERT: A 1264 ASP cc_start: 0.7854 (m-30) cc_final: 0.7416 (m-30) outliers start: 9 outliers final: 8 residues processed: 105 average time/residue: 0.5336 time to fit residues: 79.9372 Evaluate side-chains 99 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 91 time to evaluate : 1.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASN Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 1136 HIS Chi-restraints excluded: chain A residue 1362 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 14 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 73 optimal weight: 0.7980 chunk 109 optimal weight: 2.9990 chunk 72 optimal weight: 9.9990 chunk 130 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 79 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 ASN A 211 HIS A 952 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 11185 Z= 0.278 Angle : 0.534 12.211 15170 Z= 0.272 Chirality : 0.040 0.402 1647 Planarity : 0.004 0.041 1905 Dihedral : 7.363 91.329 1531 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 0.86 % Allowed : 7.14 % Favored : 92.00 % 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: 0.70 (0.24), residues: 1341 helix: 1.11 (0.19), residues: 749 sheet: -0.31 (0.55), residues: 87 loop : -0.24 (0.30), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1200 HIS 0.003 0.001 HIS A 234 PHE 0.012 0.001 PHE A1242 TYR 0.013 0.001 TYR A 591 ARG 0.002 0.000 ARG A 276 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 882 is missing expected H atoms. Skipping. Evaluate side-chains 101 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 91 time to evaluate : 1.828 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1023 GLU cc_start: 0.7224 (mp0) cc_final: 0.6870 (mp0) REVERT: A 1264 ASP cc_start: 0.7868 (m-30) cc_final: 0.7435 (m-30) outliers start: 10 outliers final: 9 residues processed: 98 average time/residue: 0.5668 time to fit residues: 78.4483 Evaluate side-chains 99 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 90 time to evaluate : 1.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 928 THR Chi-restraints excluded: chain A residue 1136 HIS Chi-restraints excluded: chain A residue 1362 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 51 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 ASN A 952 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 11185 Z= 0.231 Angle : 0.519 12.141 15170 Z= 0.263 Chirality : 0.039 0.401 1647 Planarity : 0.004 0.041 1905 Dihedral : 7.278 89.952 1531 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 0.86 % Allowed : 7.49 % Favored : 91.65 % 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: 0.76 (0.24), residues: 1341 helix: 1.14 (0.19), residues: 752 sheet: -0.27 (0.55), residues: 87 loop : -0.19 (0.30), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1200 HIS 0.003 0.001 HIS A 234 PHE 0.011 0.001 PHE A1248 TYR 0.019 0.001 TYR A1414 ARG 0.002 0.000 ARG A 276 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 882 is missing expected H atoms. Skipping. Evaluate side-chains 102 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 92 time to evaluate : 1.757 Fit side-chains revert: symmetry clash REVERT: A 154 TYR cc_start: 0.7919 (t80) cc_final: 0.7690 (t80) REVERT: A 1023 GLU cc_start: 0.7227 (mp0) cc_final: 0.6891 (mp0) REVERT: A 1264 ASP cc_start: 0.7843 (m-30) cc_final: 0.7408 (m-30) outliers start: 10 outliers final: 9 residues processed: 100 average time/residue: 0.5951 time to fit residues: 83.4615 Evaluate side-chains 98 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 89 time to evaluate : 1.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 928 THR Chi-restraints excluded: chain A residue 930 ASP Chi-restraints excluded: chain A residue 1136 HIS Chi-restraints excluded: chain A residue 1362 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 72 optimal weight: 9.9990 chunk 52 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 114 optimal weight: 0.4980 chunk 120 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 ASN A 952 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 11185 Z= 0.225 Angle : 0.516 12.114 15170 Z= 0.261 Chirality : 0.039 0.401 1647 Planarity : 0.004 0.041 1905 Dihedral : 7.184 88.555 1531 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 0.77 % Allowed : 7.92 % Favored : 91.31 % 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: 0.81 (0.24), residues: 1341 helix: 1.19 (0.19), residues: 751 sheet: -0.27 (0.55), residues: 87 loop : -0.17 (0.30), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1200 HIS 0.003 0.001 HIS A 251 PHE 0.011 0.001 PHE A1248 TYR 0.022 0.001 TYR A1414 ARG 0.003 0.000 ARG A 194 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 882 is missing expected H atoms. Skipping. Evaluate side-chains 102 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 93 time to evaluate : 3.339 Fit side-chains revert: symmetry clash REVERT: A 154 TYR cc_start: 0.7923 (t80) cc_final: 0.7691 (t80) REVERT: A 1023 GLU cc_start: 0.7217 (mp0) cc_final: 0.6884 (mp0) REVERT: A 1264 ASP cc_start: 0.7857 (m-30) cc_final: 0.7425 (m-30) outliers start: 9 outliers final: 8 residues processed: 101 average time/residue: 0.6037 time to fit residues: 87.2342 Evaluate side-chains 96 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 88 time to evaluate : 1.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 928 THR Chi-restraints excluded: chain A residue 1136 HIS Chi-restraints excluded: chain A residue 1362 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 128 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 89 optimal weight: 0.0980 chunk 134 optimal weight: 0.8980 chunk 123 optimal weight: 0.2980 chunk 107 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 65 optimal weight: 0.3980 chunk 85 optimal weight: 1.9990 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 31 ASN A 101 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 11185 Z= 0.133 Angle : 0.489 12.141 15170 Z= 0.244 Chirality : 0.038 0.400 1647 Planarity : 0.004 0.041 1905 Dihedral : 6.834 86.166 1531 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.69 % Allowed : 8.18 % Favored : 91.14 % 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: 1.05 (0.24), residues: 1341 helix: 1.39 (0.20), residues: 752 sheet: -0.26 (0.55), residues: 87 loop : -0.08 (0.30), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 693 HIS 0.002 0.000 HIS A 234 PHE 0.010 0.001 PHE A 967 TYR 0.020 0.001 TYR A1414 ARG 0.002 0.000 ARG A 194 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 882 is missing expected H atoms. Skipping. Evaluate side-chains 103 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 95 time to evaluate : 2.000 Fit side-chains revert: symmetry clash REVERT: A 154 TYR cc_start: 0.7909 (t80) cc_final: 0.7675 (t80) REVERT: A 1023 GLU cc_start: 0.7137 (mp0) cc_final: 0.6852 (mp0) REVERT: A 1264 ASP cc_start: 0.7814 (m-30) cc_final: 0.7367 (m-30) outliers start: 8 outliers final: 6 residues processed: 102 average time/residue: 0.5678 time to fit residues: 82.5719 Evaluate side-chains 93 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 87 time to evaluate : 1.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 930 ASP Chi-restraints excluded: chain A residue 1136 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 114 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 110 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.101350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.089297 restraints weight = 59301.354| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 2.02 r_work: 0.3145 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 11185 Z= 0.257 Angle : 0.520 12.023 15170 Z= 0.263 Chirality : 0.040 0.401 1647 Planarity : 0.004 0.041 1905 Dihedral : 7.001 86.010 1531 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 0.60 % Allowed : 8.52 % Favored : 90.88 % 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: 0.96 (0.24), residues: 1341 helix: 1.32 (0.20), residues: 752 sheet: -0.24 (0.56), residues: 87 loop : -0.13 (0.30), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1475 HIS 0.002 0.001 HIS A 251 PHE 0.012 0.001 PHE A1242 TYR 0.020 0.001 TYR A1414 ARG 0.002 0.000 ARG A 194 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4907.93 seconds wall clock time: 87 minutes 33.51 seconds (5253.51 seconds total)