Starting phenix.real_space_refine (version: dev) on Thu Apr 7 08:14:02 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u5o_20651/04_2022/6u5o_20651.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u5o_20651/04_2022/6u5o_20651.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u5o_20651/04_2022/6u5o_20651.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u5o_20651/04_2022/6u5o_20651.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u5o_20651/04_2022/6u5o_20651.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u5o_20651/04_2022/6u5o_20651.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.001 sd= 0.030 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "L ASP 15": "OD1" <-> "OD2" Residue "L ASP 43": "OD1" <-> "OD2" Residue "L TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 359": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 364": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ASP 370": "OD1" <-> "OD2" Residue "L PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 408": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 431": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 437": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 448": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 488": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L GLU 495": "OE1" <-> "OE2" Residue "L PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 521": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ASP 524": "OD1" <-> "OD2" Residue "L TYR 541": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ASP 544": "OD1" <-> "OD2" Residue "L PHE 590": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 597": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ASP 601": "OD1" <-> "OD2" Residue "L TYR 626": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L GLU 691": "OE1" <-> "OE2" Residue "L TYR 704": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 706": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ASP 728": "OD1" <-> "OD2" Residue "L ARG 783": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L GLU 793": "OE1" <-> "OE2" Residue "L PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 899": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 900": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ASP 910": "OD1" <-> "OD2" Residue "L TYR 928": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 931": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ASP 937": "OD1" <-> "OD2" Residue "L PHE 938": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 965": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ASP 985": "OD1" <-> "OD2" Residue "L ASP 1020": "OD1" <-> "OD2" Residue "L GLU 1030": "OE1" <-> "OE2" Residue "L GLU 1037": "OE1" <-> "OE2" Residue "L TYR 1224": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 1261": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 1281": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 1286": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 1288": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 1301": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 1310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L GLU 1325": "OE1" <-> "OE2" Residue "L PHE 1352": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 1356": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 1358": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ASP 1377": "OD1" <-> "OD2" Residue "P GLU 181": "OE1" <-> "OE2" Residue "P GLU 216": "OE1" <-> "OE2" Residue "P GLU 232": "OE1" <-> "OE2" Residue "P ASP 264": "OD1" <-> "OD2" Residue "P GLU 265": "OE1" <-> "OE2" Residue "Q ARG 208": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q ASP 209": "OD1" <-> "OD2" Residue "Q GLU 225": "OE1" <-> "OE2" Residue "Q GLU 232": "OE1" <-> "OE2" Residue "Q GLU 236": "OE1" <-> "OE2" Residue "R GLU 173": "OE1" <-> "OE2" Residue "R GLU 180": "OE1" <-> "OE2" Residue "R ARG 208": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ASP 209": "OD1" <-> "OD2" Residue "R ARG 215": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R GLU 216": "OE1" <-> "OE2" Residue "S GLU 177": "OE1" <-> "OE2" Residue "S GLU 181": "OE1" <-> "OE2" Residue "S ARG 215": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "S ASP 221": "OD1" <-> "OD2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 26316 Number of models: 1 Model: "" Number of chains: 5 Chain: "L" Number of atoms: 22107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1354, 22107 Classifications: {'peptide': 1354} Link IDs: {'PTRANS': 50, 'TRANS': 1302, 'PCIS': 1} Chain breaks: 1 Chain: "P" Number of atoms: 1531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 1531 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 1, 'TRANS': 96} Chain: "Q" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 1022 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 1, 'TRANS': 64} Chain: "R" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 806 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 1, 'TRANS': 50} Chain: "S" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 850 Classifications: {'peptide': 53} Link IDs: {'TRANS': 52} Chain breaks: 1 Time building chain proxies: 11.34, per 1000 atoms: 0.43 Number of scatterers: 26316 At special positions: 0 Unit cell: (109.12, 120.28, 101.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 72 16.00 O 2426 8.00 N 2231 7.00 C 8248 6.00 H 13339 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 21.34 Conformation dependent library (CDL) restraints added in 2.2 seconds 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3090 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 9 sheets defined 58.5% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'L' and resid 24 through 36 removed outlier: 3.951A pdb=" N LEU L 34 " --> pdb=" O ILE L 30 " (cutoff:3.500A) Processing helix chain 'L' and resid 43 through 52 removed outlier: 3.620A pdb=" N LYS L 47 " --> pdb=" O ASP L 43 " (cutoff:3.500A) Processing helix chain 'L' and resid 54 through 67 Processing helix chain 'L' and resid 77 through 80 Processing helix chain 'L' and resid 81 through 86 Processing helix chain 'L' and resid 93 through 120 removed outlier: 3.841A pdb=" N TRP L 118 " --> pdb=" O MET L 114 " (cutoff:3.500A) Processing helix chain 'L' and resid 135 through 139 removed outlier: 3.501A pdb=" N ILE L 139 " --> pdb=" O VAL L 136 " (cutoff:3.500A) Processing helix chain 'L' and resid 143 through 167 removed outlier: 4.114A pdb=" N ASN L 149 " --> pdb=" O ASN L 145 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE L 166 " --> pdb=" O ARG L 162 " (cutoff:3.500A) Processing helix chain 'L' and resid 207 through 231 removed outlier: 3.676A pdb=" N CYS L 222 " --> pdb=" O ASN L 218 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE L 223 " --> pdb=" O ALA L 219 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER L 226 " --> pdb=" O CYS L 222 " (cutoff:3.500A) Processing helix chain 'L' and resid 243 through 261 Processing helix chain 'L' and resid 264 through 270 Processing helix chain 'L' and resid 270 through 285 removed outlier: 4.422A pdb=" N GLY L 274 " --> pdb=" O LYS L 270 " (cutoff:3.500A) Processing helix chain 'L' and resid 286 through 316 removed outlier: 4.747A pdb=" N ARG L 292 " --> pdb=" O GLN L 288 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASN L 299 " --> pdb=" O ASN L 295 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLY L 300 " --> pdb=" O THR L 296 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LYS L 309 " --> pdb=" O LEU L 305 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ASN L 310 " --> pdb=" O THR L 306 " (cutoff:3.500A) Processing helix chain 'L' and resid 328 through 347 removed outlier: 3.824A pdb=" N VAL L 332 " --> pdb=" O MET L 328 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE L 347 " --> pdb=" O ILE L 343 " (cutoff:3.500A) Processing helix chain 'L' and resid 352 through 357 Processing helix chain 'L' and resid 359 through 364 removed outlier: 3.910A pdb=" N PHE L 364 " --> pdb=" O ILE L 360 " (cutoff:3.500A) Processing helix chain 'L' and resid 372 through 383 removed outlier: 3.793A pdb=" N LEU L 380 " --> pdb=" O ASP L 376 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ASN L 381 " --> pdb=" O ALA L 377 " (cutoff:3.500A) Processing helix chain 'L' and resid 390 through 412 removed outlier: 3.614A pdb=" N ARG L 397 " --> pdb=" O LEU L 393 " (cutoff:3.500A) Processing helix chain 'L' and resid 425 through 435 Processing helix chain 'L' and resid 444 through 452 removed outlier: 3.534A pdb=" N PHE L 448 " --> pdb=" O SER L 444 " (cutoff:3.500A) Processing helix chain 'L' and resid 467 through 472 Processing helix chain 'L' and resid 484 through 488 Processing helix chain 'L' and resid 494 through 505 Processing helix chain 'L' and resid 509 through 514 removed outlier: 3.739A pdb=" N LYS L 513 " --> pdb=" O ASP L 510 " (cutoff:3.500A) Processing helix chain 'L' and resid 516 through 523 Processing helix chain 'L' and resid 530 through 539 removed outlier: 3.773A pdb=" N SER L 534 " --> pdb=" O LYS L 530 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL L 537 " --> pdb=" O LYS L 533 " (cutoff:3.500A) Processing helix chain 'L' and resid 568 through 586 removed outlier: 3.663A pdb=" N ILE L 574 " --> pdb=" O LYS L 570 " (cutoff:3.500A) Processing helix chain 'L' and resid 590 through 595 removed outlier: 4.091A pdb=" N LEU L 594 " --> pdb=" O PHE L 590 " (cutoff:3.500A) Processing helix chain 'L' and resid 599 through 604 removed outlier: 3.731A pdb=" N GLN L 603 " --> pdb=" O ASP L 599 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG L 604 " --> pdb=" O LEU L 600 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 599 through 604' Processing helix chain 'L' and resid 639 through 643 removed outlier: 3.891A pdb=" N PHE L 643 " --> pdb=" O ASN L 640 " (cutoff:3.500A) Processing helix chain 'L' and resid 644 through 660 removed outlier: 4.989A pdb=" N ILE L 650 " --> pdb=" O GLU L 646 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N CYS L 651 " --> pdb=" O THR L 647 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL L 654 " --> pdb=" O ILE L 650 " (cutoff:3.500A) Processing helix chain 'L' and resid 666 through 671 Processing helix chain 'L' and resid 672 through 675 Processing helix chain 'L' and resid 715 through 734 removed outlier: 4.204A pdb=" N LEU L 727 " --> pdb=" O ALA L 723 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASP L 728 " --> pdb=" O ILE L 724 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL L 729 " --> pdb=" O SER L 725 " (cutoff:3.500A) Processing helix chain 'L' and resid 763 through 784 Processing helix chain 'L' and resid 802 through 806 removed outlier: 3.847A pdb=" N LYS L 805 " --> pdb=" O PHE L 802 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL L 806 " --> pdb=" O ILE L 803 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 802 through 806' Processing helix chain 'L' and resid 820 through 824 removed outlier: 4.145A pdb=" N ARG L 823 " --> pdb=" O LYS L 820 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N VAL L 824 " --> pdb=" O VAL L 821 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 820 through 824' Processing helix chain 'L' and resid 834 through 847 Processing helix chain 'L' and resid 847 through 852 Processing helix chain 'L' and resid 855 through 872 removed outlier: 3.932A pdb=" N TRP L 866 " --> pdb=" O LEU L 862 " (cutoff:3.500A) Processing helix chain 'L' and resid 883 through 901 Processing helix chain 'L' and resid 907 through 914 Processing helix chain 'L' and resid 916 through 920 Processing helix chain 'L' and resid 937 through 953 Processing helix chain 'L' and resid 962 through 970 removed outlier: 3.782A pdb=" N LYS L 966 " --> pdb=" O VAL L 962 " (cutoff:3.500A) Processing helix chain 'L' and resid 979 through 985 Processing helix chain 'L' and resid 997 through 1012 removed outlier: 4.318A pdb=" N THR L1004 " --> pdb=" O ASP L1000 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N ALA L1005 " --> pdb=" O ILE L1001 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU L1012 " --> pdb=" O SER L1008 " (cutoff:3.500A) Processing helix chain 'L' and resid 1015 through 1024 removed outlier: 3.741A pdb=" N HIS L1024 " --> pdb=" O ASP L1020 " (cutoff:3.500A) Processing helix chain 'L' and resid 1024 through 1036 removed outlier: 4.417A pdb=" N GLY L1033 " --> pdb=" O GLU L1029 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ILE L1034 " --> pdb=" O GLU L1030 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE L1035 " --> pdb=" O GLU L1031 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ALA L1036 " --> pdb=" O VAL L1032 " (cutoff:3.500A) Processing helix chain 'L' and resid 1043 through 1054 removed outlier: 3.628A pdb=" N LEU L1054 " --> pdb=" O LEU L1050 " (cutoff:3.500A) Processing helix chain 'L' and resid 1055 through 1068 removed outlier: 3.699A pdb=" N ALA L1059 " --> pdb=" O PRO L1055 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLY L1068 " --> pdb=" O ASN L1064 " (cutoff:3.500A) Processing helix chain 'L' and resid 1084 through 1099 removed outlier: 3.700A pdb=" N LEU L1098 " --> pdb=" O MET L1094 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLY L1099 " --> pdb=" O LEU L1095 " (cutoff:3.500A) Processing helix chain 'L' and resid 1099 through 1105 Processing helix chain 'L' and resid 1124 through 1136 removed outlier: 3.909A pdb=" N THR L1130 " --> pdb=" O GLN L1126 " (cutoff:3.500A) Processing helix chain 'L' and resid 1207 through 1224 Processing helix chain 'L' and resid 1229 through 1242 Processing helix chain 'L' and resid 1249 through 1253 Processing helix chain 'L' and resid 1260 through 1265 Processing helix chain 'L' and resid 1279 through 1284 Processing helix chain 'L' and resid 1290 through 1292 No H-bonds generated for 'chain 'L' and resid 1290 through 1292' Processing helix chain 'L' and resid 1293 through 1301 Processing helix chain 'L' and resid 1309 through 1328 Processing helix chain 'L' and resid 1359 through 1368 removed outlier: 3.984A pdb=" N LYS L1363 " --> pdb=" O LYS L1359 " (cutoff:3.500A) Processing helix chain 'P' and resid 173 through 193 removed outlier: 3.771A pdb=" N GLU P 177 " --> pdb=" O GLU P 173 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU P 181 " --> pdb=" O GLU P 177 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N THR P 192 " --> pdb=" O GLY P 188 " (cutoff:3.500A) Processing helix chain 'P' and resid 214 through 226 Processing helix chain 'P' and resid 227 through 238 removed outlier: 3.747A pdb=" N ALA P 231 " --> pdb=" O LYS P 227 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLU P 232 " --> pdb=" O GLY P 228 " (cutoff:3.500A) Processing helix chain 'P' and resid 254 through 264 removed outlier: 4.277A pdb=" N LEU P 258 " --> pdb=" O LYS P 254 " (cutoff:3.500A) Processing helix chain 'Q' and resid 173 through 197 removed outlier: 3.879A pdb=" N GLU Q 177 " --> pdb=" O GLU Q 173 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N SER Q 178 " --> pdb=" O ALA Q 174 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ILE Q 179 " --> pdb=" O ARG Q 175 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE Q 186 " --> pdb=" O LYS Q 182 " (cutoff:3.500A) Processing helix chain 'Q' and resid 199 through 204 Processing helix chain 'Q' and resid 207 through 213 Processing helix chain 'Q' and resid 217 through 232 Processing helix chain 'Q' and resid 233 through 236 removed outlier: 3.873A pdb=" N GLU Q 236 " --> pdb=" O MET Q 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 233 through 236' Processing helix chain 'R' and resid 173 through 191 Processing helix chain 'R' and resid 200 through 205 removed outlier: 4.257A pdb=" N ASP R 205 " --> pdb=" O THR R 201 " (cutoff:3.500A) Processing helix chain 'R' and resid 205 through 218 removed outlier: 4.365A pdb=" N ASP R 209 " --> pdb=" O ASP R 205 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ALA R 210 " --> pdb=" O GLY R 206 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ARG R 215 " --> pdb=" O MET R 211 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLU R 216 " --> pdb=" O ILE R 212 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU R 218 " --> pdb=" O ILE R 214 " (cutoff:3.500A) Processing helix chain 'S' and resid 171 through 191 removed outlier: 4.130A pdb=" N LEU S 176 " --> pdb=" O ILE S 172 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N GLU S 177 " --> pdb=" O GLU S 173 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER S 178 " --> pdb=" O ALA S 174 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N SER S 184 " --> pdb=" O GLU S 180 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N MET S 185 " --> pdb=" O GLU S 181 " (cutoff:3.500A) Processing helix chain 'S' and resid 205 through 231 removed outlier: 3.777A pdb=" N ASP S 209 " --> pdb=" O ASP S 205 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ARG S 215 " --> pdb=" O MET S 211 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLU S 217 " --> pdb=" O GLY S 213 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE S 219 " --> pdb=" O ARG S 215 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ALA S 220 " --> pdb=" O GLU S 216 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS S 224 " --> pdb=" O ALA S 220 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS S 229 " --> pdb=" O GLU S 225 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 10 through 11 Processing sheet with id=AA2, first strand: chain 'L' and resid 172 through 174 removed outlier: 3.649A pdb=" N ARG L 197 " --> pdb=" O SER L 192 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 387 through 389 Processing sheet with id=AA4, first strand: chain 'L' and resid 550 through 551 Processing sheet with id=AA5, first strand: chain 'L' and resid 737 through 741 Processing sheet with id=AA6, first strand: chain 'L' and resid 807 through 809 removed outlier: 3.671A pdb=" N ILE L 807 " --> pdb=" O HIS L 814 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 1154 through 1157 Processing sheet with id=AA8, first strand: chain 'L' and resid 1196 through 1197 removed outlier: 3.651A pdb=" N LEU L1197 " --> pdb=" O ARG L1255 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ARG L1255 " --> pdb=" O LEU L1197 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'P' and resid 199 through 200 621 hydrogen bonds defined for protein. 1791 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: 10.16 Time building geometry restraints manager: 22.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 13318 1.03 - 1.23: 25 1.23 - 1.42: 5266 1.42 - 1.62: 7792 1.62 - 1.81: 123 Bond restraints: 26524 Sorted by residual: bond pdb=" CB VAL P 262 " pdb=" CG1 VAL P 262 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.88e+00 bond pdb=" CG GLU P 263 " pdb=" CD GLU P 263 " ideal model delta sigma weight residual 1.516 1.553 -0.037 2.50e-02 1.60e+03 2.15e+00 bond pdb=" CB ILE L 363 " pdb=" CG2 ILE L 363 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.60e+00 bond pdb=" CG PRO L1041 " pdb=" CD PRO L1041 " ideal model delta sigma weight residual 1.512 1.478 0.034 2.70e-02 1.37e+03 1.59e+00 bond pdb=" C ASP L 762 " pdb=" N GLU L 763 " ideal model delta sigma weight residual 1.324 1.354 -0.030 2.56e-02 1.53e+03 1.39e+00 ... (remaining 26519 not shown) Histogram of bond angle deviations from ideal: 99.28 - 106.23: 365 106.23 - 113.19: 32145 113.19 - 120.15: 8215 120.15 - 127.11: 7294 127.11 - 134.07: 119 Bond angle restraints: 48138 Sorted by residual: angle pdb=" C PHE L1171 " pdb=" CA PHE L1171 " pdb=" CB PHE L1171 " ideal model delta sigma weight residual 109.55 102.40 7.15 2.03e+00 2.43e-01 1.24e+01 angle pdb=" CA THR L1192 " pdb=" CB THR L1192 " pdb=" CG2 THR L1192 " ideal model delta sigma weight residual 110.50 116.00 -5.50 1.70e+00 3.46e-01 1.05e+01 angle pdb=" C ASN L1138 " pdb=" N MET L1139 " pdb=" CA MET L1139 " ideal model delta sigma weight residual 122.54 127.86 -5.32 1.65e+00 3.67e-01 1.04e+01 angle pdb=" C VAL L 75 " pdb=" N VAL L 76 " pdb=" CA VAL L 76 " ideal model delta sigma weight residual 121.71 126.45 -4.74 1.50e+00 4.44e-01 1.00e+01 angle pdb=" C VAL L 672 " pdb=" CA VAL L 672 " pdb=" CB VAL L 672 " ideal model delta sigma weight residual 114.00 110.39 3.61 1.31e+00 5.83e-01 7.59e+00 ... (remaining 48133 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 9315 17.70 - 35.40: 1097 35.40 - 53.10: 147 53.10 - 70.80: 27 70.80 - 88.50: 7 Dihedral angle restraints: 10593 sinusoidal: 5200 harmonic: 5393 Sorted by residual: dihedral pdb=" CA ILE L 130 " pdb=" C ILE L 130 " pdb=" N LEU L 131 " pdb=" CA LEU L 131 " ideal model delta harmonic sigma weight residual 180.00 -152.82 -27.18 0 5.00e+00 4.00e-02 2.96e+01 dihedral pdb=" CA ARG L1264 " pdb=" C ARG L1264 " pdb=" N LEU L1265 " pdb=" CA LEU L1265 " ideal model delta harmonic sigma weight residual -180.00 -153.75 -26.25 0 5.00e+00 4.00e-02 2.76e+01 dihedral pdb=" CA ASN L 204 " pdb=" C ASN L 204 " pdb=" N GLN L 205 " pdb=" CA GLN L 205 " ideal model delta harmonic sigma weight residual 180.00 -154.02 -25.98 0 5.00e+00 4.00e-02 2.70e+01 ... (remaining 10590 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1589 0.049 - 0.097: 359 0.097 - 0.146: 98 0.146 - 0.194: 7 0.194 - 0.243: 2 Chirality restraints: 2055 Sorted by residual: chirality pdb=" CA TRP L1136 " pdb=" N TRP L1136 " pdb=" C TRP L1136 " pdb=" CB TRP L1136 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CA ASN L1137 " pdb=" N ASN L1137 " pdb=" C ASN L1137 " pdb=" CB ASN L1137 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.94e-01 chirality pdb=" CA ILE L 182 " pdb=" N ILE L 182 " pdb=" C ILE L 182 " pdb=" CB ILE L 182 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.96e-01 ... (remaining 2052 not shown) Planarity restraints: 3810 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN L 890 " 0.023 2.00e-02 2.50e+03 4.58e-02 2.10e+01 pdb=" C ASN L 890 " -0.079 2.00e-02 2.50e+03 pdb=" O ASN L 890 " 0.029 2.00e-02 2.50e+03 pdb=" N LYS L 891 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER Q 178 " 0.020 2.00e-02 2.50e+03 4.06e-02 1.65e+01 pdb=" C SER Q 178 " -0.070 2.00e-02 2.50e+03 pdb=" O SER Q 178 " 0.026 2.00e-02 2.50e+03 pdb=" N ILE Q 179 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP L 209 " 0.017 2.00e-02 2.50e+03 3.39e-02 1.15e+01 pdb=" C TRP L 209 " -0.059 2.00e-02 2.50e+03 pdb=" O TRP L 209 " 0.022 2.00e-02 2.50e+03 pdb=" N LYS L 210 " 0.020 2.00e-02 2.50e+03 ... (remaining 3807 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.22: 2095 2.22 - 2.81: 58288 2.81 - 3.41: 69002 3.41 - 4.00: 92038 4.00 - 4.60: 145820 Nonbonded interactions: 367243 Sorted by model distance: nonbonded pdb=" OE2 GLU L 279 " pdb=" HZ2 LYS L 344 " model vdw 1.621 1.850 nonbonded pdb=" H LYS L 790 " pdb=" OE2 GLU L 793 " model vdw 1.678 1.850 nonbonded pdb=" O GLU L1133 " pdb=" H ASN L1138 " model vdw 1.680 1.850 nonbonded pdb="HH21 ARG L 294 " pdb=" OD1 ASN P 259 " model vdw 1.680 1.850 nonbonded pdb=" O THR L1130 " pdb=" HG1 THR L1134 " model vdw 1.686 1.850 ... (remaining 367238 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 Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 72 5.16 5 C 8248 2.51 5 N 2231 2.21 5 O 2426 1.98 5 H 13339 0.53 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.070 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: 0.480 Extract box with map and model: 2.990 Check model and map are aligned: 0.430 Convert atoms to be neutral: 0.240 Process input model: 78.950 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 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 : 0.005 0.056 13185 Z= 0.315 Angle : 0.782 9.206 17778 Z= 0.442 Chirality : 0.045 0.243 2055 Planarity : 0.006 0.067 2248 Dihedral : 14.702 88.498 5062 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: -4.22 (0.17), residues: 1609 helix: -2.36 (0.14), residues: 849 sheet: -2.20 (0.54), residues: 80 loop : -3.39 (0.19), residues: 680 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 319 time to evaluate : 2.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 319 average time/residue: 0.6552 time to fit residues: 290.1770 Evaluate side-chains 235 residues out of total 1461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 235 time to evaluate : 2.034 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.7206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 20.0000 chunk 121 optimal weight: 6.9990 chunk 67 optimal weight: 10.0000 chunk 41 optimal weight: 9.9990 chunk 81 optimal weight: 8.9990 chunk 64 optimal weight: 5.9990 chunk 125 optimal weight: 10.0000 chunk 48 optimal weight: 9.9990 chunk 76 optimal weight: 10.0000 chunk 93 optimal weight: 9.9990 chunk 145 optimal weight: 7.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 42 ASN L 149 ASN L 348 ASN L 420 ASN L 585 ASN L 683 HIS ** L 707 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L1097 ASN L1119 ASN L1303 ASN P 240 GLN ** P 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.069 13185 Z= 0.430 Angle : 0.728 6.863 17778 Z= 0.396 Chirality : 0.045 0.211 2055 Planarity : 0.006 0.099 2248 Dihedral : 5.439 20.094 1758 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.14 % Favored : 91.80 % Rotamer Outliers : 1.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: -2.61 (0.19), residues: 1609 helix: -0.88 (0.17), residues: 856 sheet: -2.19 (0.51), residues: 81 loop : -2.79 (0.21), residues: 672 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 278 time to evaluate : 1.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 11 residues processed: 287 average time/residue: 0.6614 time to fit residues: 265.8215 Evaluate side-chains 249 residues out of total 1461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 238 time to evaluate : 2.222 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 11 outliers final: 1 residues processed: 11 average time/residue: 0.3983 time to fit residues: 10.0724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 80 optimal weight: 5.9990 chunk 45 optimal weight: 9.9990 chunk 120 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 145 optimal weight: 10.0000 chunk 157 optimal weight: 20.0000 chunk 129 optimal weight: 4.9990 chunk 144 optimal weight: 8.9990 chunk 49 optimal weight: 8.9990 chunk 116 optimal weight: 10.0000 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 42 ASN ** L 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 420 ASN L 525 ASN ** L 707 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L1119 ASN L1260 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.3506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 13185 Z= 0.213 Angle : 0.555 7.122 17778 Z= 0.297 Chirality : 0.039 0.145 2055 Planarity : 0.005 0.085 2248 Dihedral : 5.079 19.436 1758 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer Outliers : 0.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: -1.82 (0.20), residues: 1609 helix: -0.19 (0.17), residues: 855 sheet: -1.95 (0.51), residues: 81 loop : -2.46 (0.22), residues: 673 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 259 time to evaluate : 2.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 265 average time/residue: 0.6475 time to fit residues: 247.2725 Evaluate side-chains 243 residues out of total 1461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 239 time to evaluate : 2.262 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 4 average time/residue: 0.3104 time to fit residues: 5.2647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 143 optimal weight: 10.0000 chunk 109 optimal weight: 10.0000 chunk 75 optimal weight: 9.9990 chunk 16 optimal weight: 9.9990 chunk 69 optimal weight: 9.9990 chunk 97 optimal weight: 10.0000 chunk 146 optimal weight: 9.9990 chunk 154 optimal weight: 20.0000 chunk 76 optimal weight: 9.9990 chunk 138 optimal weight: 10.0000 chunk 41 optimal weight: 10.0000 overall best weight: 9.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 348 ASN L 420 ASN L 473 ASN ** L 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 707 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 829 ASN L1119 ASN L1303 ASN P 240 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.4304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.062 13185 Z= 0.498 Angle : 0.691 6.316 17778 Z= 0.378 Chirality : 0.046 0.160 2055 Planarity : 0.005 0.093 2248 Dihedral : 5.330 20.581 1758 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer Outliers : 1.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: -2.03 (0.20), residues: 1609 helix: -0.37 (0.17), residues: 854 sheet: -1.77 (0.54), residues: 82 loop : -2.58 (0.21), residues: 673 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 259 time to evaluate : 2.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 19 residues processed: 272 average time/residue: 0.6096 time to fit residues: 236.8174 Evaluate side-chains 263 residues out of total 1461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 244 time to evaluate : 2.052 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 19 outliers final: 1 residues processed: 19 average time/residue: 0.3424 time to fit residues: 14.6922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 128 optimal weight: 6.9990 chunk 87 optimal weight: 0.9990 chunk 2 optimal weight: 5.9990 chunk 115 optimal weight: 10.0000 chunk 63 optimal weight: 6.9990 chunk 131 optimal weight: 5.9990 chunk 106 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 78 optimal weight: 8.9990 chunk 138 optimal weight: 7.9990 chunk 39 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 42 ASN L 420 ASN L 473 ASN ** L 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 707 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L1119 ASN L1312 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.4581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.066 13185 Z= 0.272 Angle : 0.578 6.113 17778 Z= 0.309 Chirality : 0.040 0.143 2055 Planarity : 0.004 0.071 2248 Dihedral : 5.101 21.817 1758 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer Outliers : 0.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: -1.68 (0.20), residues: 1609 helix: -0.07 (0.18), residues: 861 sheet: -1.68 (0.50), residues: 90 loop : -2.45 (0.22), residues: 658 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 248 time to evaluate : 2.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 7 residues processed: 250 average time/residue: 0.6267 time to fit residues: 222.7230 Evaluate side-chains 243 residues out of total 1461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 236 time to evaluate : 2.122 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 7 average time/residue: 0.4645 time to fit residues: 7.8761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 2.9990 chunk 139 optimal weight: 3.9990 chunk 30 optimal weight: 8.9990 chunk 90 optimal weight: 8.9990 chunk 38 optimal weight: 5.9990 chunk 154 optimal weight: 6.9990 chunk 128 optimal weight: 7.9990 chunk 71 optimal weight: 8.9990 chunk 12 optimal weight: 8.9990 chunk 51 optimal weight: 7.9990 chunk 81 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 348 ASN L 420 ASN ** L 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 707 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L1119 ASN L1312 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.4838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.075 13185 Z= 0.305 Angle : 0.586 6.316 17778 Z= 0.314 Chirality : 0.040 0.141 2055 Planarity : 0.004 0.068 2248 Dihedral : 5.036 22.214 1758 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % Rotamer Outliers : 1.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: -1.60 (0.20), residues: 1609 helix: 0.01 (0.18), residues: 860 sheet: -1.56 (0.51), residues: 89 loop : -2.46 (0.22), residues: 660 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 244 time to evaluate : 2.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 10 residues processed: 251 average time/residue: 0.6447 time to fit residues: 229.3372 Evaluate side-chains 245 residues out of total 1461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 235 time to evaluate : 2.110 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 10 outliers final: 1 residues processed: 10 average time/residue: 0.3267 time to fit residues: 8.6858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 149 optimal weight: 9.9990 chunk 17 optimal weight: 8.9990 chunk 88 optimal weight: 6.9990 chunk 113 optimal weight: 10.0000 chunk 87 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 86 optimal weight: 0.8980 chunk 154 optimal weight: 30.0000 chunk 96 optimal weight: 9.9990 chunk 94 optimal weight: 9.9990 chunk 71 optimal weight: 5.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 420 ASN ** L 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 707 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 994 GLN L1119 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.4931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.168 13185 Z= 0.241 Angle : 0.565 11.668 17778 Z= 0.304 Chirality : 0.039 0.147 2055 Planarity : 0.005 0.114 2248 Dihedral : 4.935 22.012 1758 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer Outliers : 0.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: -1.46 (0.20), residues: 1609 helix: 0.12 (0.18), residues: 864 sheet: -1.48 (0.51), residues: 89 loop : -2.40 (0.22), residues: 656 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 240 time to evaluate : 2.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 242 average time/residue: 0.6359 time to fit residues: 217.2208 Evaluate side-chains 239 residues out of total 1461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 234 time to evaluate : 2.081 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 5 average time/residue: 0.3062 time to fit residues: 5.5236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 10.0000 chunk 61 optimal weight: 9.9990 chunk 92 optimal weight: 5.9990 chunk 46 optimal weight: 10.0000 chunk 30 optimal weight: 8.9990 chunk 29 optimal weight: 8.9990 chunk 98 optimal weight: 0.2980 chunk 105 optimal weight: 9.9990 chunk 76 optimal weight: 9.9990 chunk 14 optimal weight: 7.9990 chunk 121 optimal weight: 6.9990 overall best weight: 6.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 707 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 994 GLN L1119 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.5064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.098 13185 Z= 0.319 Angle : 0.587 9.373 17778 Z= 0.316 Chirality : 0.040 0.160 2055 Planarity : 0.005 0.089 2248 Dihedral : 4.952 22.577 1758 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer Outliers : 0.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: -1.49 (0.20), residues: 1609 helix: 0.10 (0.18), residues: 861 sheet: -1.43 (0.52), residues: 90 loop : -2.42 (0.22), residues: 658 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 239 time to evaluate : 2.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 243 average time/residue: 0.6261 time to fit residues: 216.5149 Evaluate side-chains 237 residues out of total 1461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 232 time to evaluate : 2.058 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 5 average time/residue: 0.3392 time to fit residues: 5.6913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 140 optimal weight: 10.0000 chunk 147 optimal weight: 8.9990 chunk 134 optimal weight: 5.9990 chunk 143 optimal weight: 6.9990 chunk 86 optimal weight: 8.9990 chunk 62 optimal weight: 4.9990 chunk 112 optimal weight: 10.0000 chunk 44 optimal weight: 9.9990 chunk 129 optimal weight: 6.9990 chunk 135 optimal weight: 20.0000 chunk 94 optimal weight: 9.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 145 ASN ** L 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 707 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 994 GLN L1119 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.5280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.100 13185 Z= 0.359 Angle : 0.610 6.558 17778 Z= 0.329 Chirality : 0.041 0.160 2055 Planarity : 0.006 0.108 2248 Dihedral : 5.037 23.552 1758 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.32 % Favored : 90.68 % Rotamer Outliers : 0.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: -1.60 (0.20), residues: 1609 helix: -0.00 (0.18), residues: 861 sheet: -1.34 (0.53), residues: 89 loop : -2.47 (0.22), residues: 659 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 238 time to evaluate : 2.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 239 average time/residue: 0.6659 time to fit residues: 226.6525 Evaluate side-chains 231 residues out of total 1461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 226 time to evaluate : 2.079 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 5 average time/residue: 0.3173 time to fit residues: 5.6258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 151 optimal weight: 7.9990 chunk 92 optimal weight: 4.9990 chunk 72 optimal weight: 9.9990 chunk 105 optimal weight: 6.9990 chunk 159 optimal weight: 20.0000 chunk 146 optimal weight: 9.9990 chunk 126 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 chunk 98 optimal weight: 6.9990 chunk 77 optimal weight: 7.9990 chunk 100 optimal weight: 6.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 286 HIS ** L 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 707 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 994 GLN L1119 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.5406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.115 13185 Z= 0.327 Angle : 0.607 14.362 17778 Z= 0.332 Chirality : 0.041 0.189 2055 Planarity : 0.006 0.116 2248 Dihedral : 5.016 22.845 1758 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.32 % Favored : 90.68 % Rotamer Outliers : 0.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: -1.58 (0.20), residues: 1609 helix: 0.01 (0.18), residues: 864 sheet: -1.33 (0.54), residues: 89 loop : -2.46 (0.22), residues: 656 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 237 time to evaluate : 2.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 237 average time/residue: 0.6340 time to fit residues: 213.1949 Evaluate side-chains 227 residues out of total 1461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 225 time to evaluate : 2.106 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 0.2848 time to fit residues: 3.8277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 0.3980 chunk 38 optimal weight: 7.9990 chunk 117 optimal weight: 7.9990 chunk 18 optimal weight: 5.9990 chunk 35 optimal weight: 0.8980 chunk 127 optimal weight: 10.0000 chunk 53 optimal weight: 5.9990 chunk 130 optimal weight: 10.0000 chunk 16 optimal weight: 7.9990 chunk 23 optimal weight: 7.9990 chunk 111 optimal weight: 10.0000 overall best weight: 4.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 707 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.144927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.129525 restraints weight = 45389.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.130117 restraints weight = 36830.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.130955 restraints weight = 33907.829| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.5472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.117 13185 Z= 0.261 Angle : 0.568 9.792 17778 Z= 0.306 Chirality : 0.039 0.144 2055 Planarity : 0.005 0.097 2248 Dihedral : 4.913 22.885 1758 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % Rotamer Outliers : 0.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: -1.39 (0.21), residues: 1609 helix: 0.15 (0.18), residues: 863 sheet: -1.21 (0.54), residues: 89 loop : -2.36 (0.22), residues: 657 =============================================================================== Job complete usr+sys time: 5288.08 seconds wall clock time: 94 minutes 50.82 seconds (5690.82 seconds total)