Starting phenix.real_space_refine on Tue Dec 12 14:28:15 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p05_13144/12_2023/7p05_13144_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p05_13144/12_2023/7p05_13144.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p05_13144/12_2023/7p05_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_13144/12_2023/7p05_13144_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p05_13144/12_2023/7p05_13144_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p05_13144/12_2023/7p05_13144.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p05_13144/12_2023/7p05_13144.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p05_13144/12_2023/7p05_13144_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p05_13144/12_2023/7p05_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-1.21rc1-5172/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: 10.00, per 1000 atoms: 0.46 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: 19.20 Conformation dependent library (CDL) restraints added in 2.2 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: 4.63 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: 9.46 Time building geometry restraints manager: 19.70 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: 9646 21.63 - 43.26: 426 43.26 - 64.89: 44 64.89 - 86.53: 29 86.53 - 108.16: 4 Dihedral angle restraints: 10149 sinusoidal: 5251 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 10146 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: 5.810 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: 0.340 Extract box with map and model: 30.340 Check model and map are aligned: 0.330 Set scattering table: 0.210 Process input model: 75.460 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.060 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 115.950 ------------------------------------------------------------------------------- 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 : 1.818 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 110 average time/residue: 0.6228 time to fit residues: 94.8904 Evaluate side-chains 91 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 2.074 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2536 ------------------------------------------------------------------------------- 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: 3.9990 chunk 56 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 78 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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: 0.8108 moved from start: 0.0530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11185 Z= 0.286 Angle : 0.583 11.843 15170 Z= 0.306 Chirality : 0.041 0.409 1647 Planarity : 0.005 0.050 1905 Dihedral : 8.202 105.054 1531 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 0.69 % Allowed : 3.18 % Favored : 96.13 % 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: 0.45 (0.23), residues: 1341 helix: 0.91 (0.19), residues: 759 sheet: -0.14 (0.55), residues: 86 loop : -0.44 (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 561 TYR 0.014 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 99 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 91 time to evaluate : 1.683 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 7 residues processed: 97 average time/residue: 0.5500 time to fit residues: 76.2980 Evaluate side-chains 96 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 89 time to evaluate : 1.756 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2664 time to fit residues: 5.6270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 102 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 122 optimal weight: 4.9990 chunk 132 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 A1138 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.0817 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= 0.235 Angle : 0.542 11.882 15170 Z= 0.277 Chirality : 0.040 0.403 1647 Planarity : 0.004 0.043 1905 Dihedral : 7.790 99.585 1531 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 0.09 % Allowed : 4.48 % Favored : 95.44 % 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: 0.53 (0.24), residues: 1341 helix: 0.97 (0.19), residues: 756 sheet: -0.23 (0.55), residues: 87 loop : -0.37 (0.29), 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 0.011 0.001 PHE A1242 TYR 0.012 0.001 TYR A 591 ARG 0.004 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 93 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 92 time to evaluate : 1.718 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 92 average time/residue: 0.5866 time to fit residues: 76.1548 Evaluate side-chains 87 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 86 time to evaluate : 1.740 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3063 time to fit residues: 2.7208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 63 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 123 optimal weight: 0.8980 chunk 130 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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: 0.8098 moved from start: 0.0972 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= 0.234 Angle : 0.530 12.164 15170 Z= 0.270 Chirality : 0.040 0.400 1647 Planarity : 0.004 0.041 1905 Dihedral : 7.590 96.404 1531 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.26 % Allowed : 5.85 % Favored : 93.89 % 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 : -0.34 (0.29), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1200 HIS 0.003 0.001 HIS A 251 PHE 0.012 0.001 PHE A1248 TYR 0.013 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 97 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 94 time to evaluate : 1.796 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 96 average time/residue: 0.5884 time to fit residues: 80.0181 Evaluate side-chains 91 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 88 time to evaluate : 1.769 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2913 time to fit residues: 3.6792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 108 optimal weight: 1.9990 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: 3.9990 chunk 90 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 117 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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: 0.8118 moved from start: 0.1100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 11185 Z= 0.309 Angle : 0.552 12.121 15170 Z= 0.283 Chirality : 0.041 0.401 1647 Planarity : 0.004 0.041 1905 Dihedral : 7.665 94.758 1531 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 0.17 % Allowed : 6.71 % 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: 0.49 (0.24), residues: 1341 helix: 0.94 (0.19), residues: 755 sheet: -0.34 (0.55), residues: 87 loop : -0.36 (0.29), 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 0.013 0.001 PHE A1242 TYR 0.015 0.001 TYR A 591 ARG 0.002 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 91 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 89 time to evaluate : 1.731 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 91 average time/residue: 0.5468 time to fit residues: 71.7037 Evaluate side-chains 88 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 87 time to evaluate : 1.740 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2498 time to fit residues: 2.7469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 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: 0.8980 chunk 10 optimal weight: 3.9990 chunk 68 optimal weight: 0.6980 chunk 125 optimal weight: 0.6980 overall best weight: 1.1982 ------------------------------------------------------------------------------- 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: 0.8093 moved from start: 0.1215 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= 0.188 Angle : 0.514 12.111 15170 Z= 0.260 Chirality : 0.039 0.399 1647 Planarity : 0.004 0.042 1905 Dihedral : 7.347 92.676 1531 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 0.34 % Allowed : 7.57 % Favored : 92.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.24), residues: 1341 helix: 1.09 (0.19), residues: 755 sheet: -0.32 (0.54), residues: 87 loop : -0.21 (0.30), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1200 HIS 0.003 0.001 HIS A 251 PHE 0.010 0.001 PHE A1248 TYR 0.012 0.001 TYR A 591 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 97 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 93 time to evaluate : 1.642 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 95 average time/residue: 0.5228 time to fit residues: 71.8788 Evaluate side-chains 90 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 87 time to evaluate : 1.875 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2750 time to fit residues: 3.6967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 chunk 109 optimal weight: 2.9990 chunk 72 optimal weight: 10.0000 chunk 130 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 79 optimal weight: 0.4980 chunk 60 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 overall best weight: 1.6184 ------------------------------------------------------------------------------- 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: 0.8105 moved from start: 0.1341 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= 0.241 Angle : 0.523 12.152 15170 Z= 0.265 Chirality : 0.040 0.398 1647 Planarity : 0.004 0.042 1905 Dihedral : 7.326 91.863 1531 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 0.17 % Allowed : 7.75 % Favored : 92.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.24), residues: 1341 helix: 1.10 (0.19), residues: 755 sheet: -0.33 (0.54), residues: 87 loop : -0.24 (0.30), residues: 499 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 93 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 91 time to evaluate : 1.971 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 92 average time/residue: 0.5821 time to fit residues: 76.6723 Evaluate side-chains 89 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 88 time to evaluate : 1.807 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2474 time to fit residues: 2.7852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 51 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 25 optimal weight: 0.2980 chunk 82 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 chunk 124 optimal weight: 0.6980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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: 0.8082 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 11185 Z= 0.161 Angle : 0.503 12.141 15170 Z= 0.252 Chirality : 0.039 0.398 1647 Planarity : 0.004 0.042 1905 Dihedral : 7.057 89.240 1531 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.17 % Allowed : 8.09 % Favored : 91.74 % 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: 0.83 (0.24), residues: 1341 helix: 1.18 (0.20), residues: 760 sheet: -0.27 (0.55), residues: 87 loop : -0.14 (0.30), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1200 HIS 0.002 0.000 HIS A 251 PHE 0.009 0.001 PHE A1248 TYR 0.020 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 99 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 97 time to evaluate : 1.769 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 98 average time/residue: 0.6181 time to fit residues: 84.9537 Evaluate side-chains 89 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 87 time to evaluate : 1.836 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2553 time to fit residues: 3.2585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 72 optimal weight: 10.0000 chunk 52 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 chunk 114 optimal weight: 0.5980 chunk 120 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN A 211 HIS A 952 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.1544 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= 0.185 Angle : 0.507 12.105 15170 Z= 0.254 Chirality : 0.039 0.399 1647 Planarity : 0.004 0.042 1905 Dihedral : 6.970 87.414 1531 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 0.09 % Allowed : 8.86 % Favored : 91.05 % 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: 0.92 (0.24), residues: 1341 helix: 1.27 (0.20), residues: 753 sheet: -0.24 (0.55), residues: 87 loop : -0.12 (0.30), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1200 HIS 0.003 0.001 HIS A 211 PHE 0.010 0.001 PHE A1242 TYR 0.021 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 90 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 89 time to evaluate : 1.758 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 90 average time/residue: 0.5563 time to fit residues: 72.7456 Evaluate side-chains 87 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 1.725 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 128 optimal weight: 0.6980 chunk 78 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 134 optimal weight: 0.9990 chunk 123 optimal weight: 0.0470 chunk 107 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 65 optimal weight: 0.2980 chunk 85 optimal weight: 0.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- 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: 0.8065 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 11185 Z= 0.137 Angle : 0.491 12.113 15170 Z= 0.245 Chirality : 0.038 0.397 1647 Planarity : 0.004 0.042 1905 Dihedral : 6.712 85.158 1531 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.00 % Allowed : 9.21 % Favored : 90.79 % 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: 1.08 (0.24), residues: 1341 helix: 1.38 (0.20), residues: 761 sheet: -0.21 (0.55), residues: 87 loop : -0.03 (0.30), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 693 HIS 0.002 0.000 HIS A 251 PHE 0.010 0.001 PHE A 967 TYR 0.018 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 95 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 1.945 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.5787 time to fit residues: 79.7581 Evaluate side-chains 88 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 1.752 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 98 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 110 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1138 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.102201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.090014 restraints weight = 59037.855| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.06 r_work: 0.3156 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11185 Z= 0.223 Angle : 0.512 12.018 15170 Z= 0.258 Chirality : 0.039 0.400 1647 Planarity : 0.004 0.042 1905 Dihedral : 6.849 84.773 1531 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 0.09 % Allowed : 9.47 % Favored : 90.45 % 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: 1.03 (0.24), residues: 1341 helix: 1.35 (0.20), residues: 755 sheet: -0.20 (0.55), residues: 87 loop : -0.06 (0.30), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A1475 HIS 0.002 0.001 HIS A 595 PHE 0.012 0.001 PHE A1242 TYR 0.019 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: 4712.21 seconds wall clock time: 84 minutes 49.35 seconds (5089.35 seconds total)