Starting phenix.real_space_refine on Tue Jul 23 11:23:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rfe_19118/07_2024/8rfe_19118.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rfe_19118/07_2024/8rfe_19118.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rfe_19118/07_2024/8rfe_19118.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rfe_19118/07_2024/8rfe_19118.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rfe_19118/07_2024/8rfe_19118.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rfe_19118/07_2024/8rfe_19118.cif" } resolution = 3.8 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= 0.004 sd= 0.054 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: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 68 5.16 5 C 13717 2.51 5 N 3864 2.21 5 O 4121 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1245": "OE1" <-> "OE2" Residue "A PHE 1389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1676": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2729": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 21776 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 21580 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 2765, 21558 Classifications: {'peptide': 2765} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 82} Link IDs: {'PTRANS': 114, 'TRANS': 2650} Chain breaks: 5 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 290 Unresolved non-hydrogen angles: 372 Unresolved non-hydrogen dihedrals: 239 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 9, 'ASN:plan1': 3, 'TRP:plan': 2, 'HIS:plan': 1, 'PHE:plan': 4, 'GLU:plan': 6, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 158 Conformer: "B" Number of residues, atoms: 2765, 21558 Classifications: {'peptide': 2765} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 82} Link IDs: {'PTRANS': 114, 'TRANS': 2650} Chain breaks: 5 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 290 Unresolved non-hydrogen angles: 372 Unresolved non-hydrogen dihedrals: 239 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 9, 'ASN:plan1': 3, 'TRP:plan': 2, 'HIS:plan': 1, 'PHE:plan': 4, 'GLU:plan': 6, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 158 bond proxies already assigned to first conformer: 22028 Chain: "B" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 99 Unusual residues: {'BGC': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "A" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 97 Unusual residues: {'UPG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 5 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AARG A 194 " occ=0.60 ... (20 atoms not shown) pdb=" NH2BARG A 194 " occ=0.40 residue: pdb=" N AARG A1355 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A1355 " occ=0.50 Time building chain proxies: 20.61, per 1000 atoms: 0.95 Number of scatterers: 21776 At special positions: 0 Unit cell: (103.777, 120.433, 210.117, 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 68 16.00 P 6 15.00 O 4121 8.00 N 3864 7.00 C 13717 6.00 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 Links applied BETA1-2 " BGC B 1 " - " BGC B 2 " " BGC B 2 " - " BGC B 3 " " BGC B 3 " - " BGC B 4 " " BGC B 4 " - " BGC B 5 " " BGC B 5 " - " BGC B 6 " " BGC B 6 " - " BGC B 7 " " BGC B 7 " - " BGC B 8 " " BGC B 8 " - " BGC B 9 " Time building additional restraints: 8.60 Conformation dependent library (CDL) restraints added in 7.5 seconds 5518 Ramachandran restraints generated. 2759 Oldfield, 0 Emsley, 2759 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5142 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 22 sheets defined 46.5% alpha, 9.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.85 Creating SS restraints... Processing helix chain 'A' and resid 33 through 45 removed outlier: 4.351A pdb=" N ASP A 37 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARG A 44 " --> pdb=" O ALA A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 79 removed outlier: 5.481A pdb=" N THR A 76 " --> pdb=" O VAL A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 96 Processing helix chain 'A' and resid 96 through 104 removed outlier: 3.571A pdb=" N ILE A 100 " --> pdb=" O ASN A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 127 removed outlier: 3.872A pdb=" N GLY A 126 " --> pdb=" O THR A 123 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL A 127 " --> pdb=" O VAL A 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 123 through 127' Processing helix chain 'A' and resid 130 through 142 removed outlier: 3.886A pdb=" N LEU A 138 " --> pdb=" O ALA A 134 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR A 139 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL A 140 " --> pdb=" O GLY A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 161 Processing helix chain 'A' and resid 172 through 212 removed outlier: 3.877A pdb=" N ILE A 176 " --> pdb=" O ALA A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 226 removed outlier: 3.501A pdb=" N ALA A 219 " --> pdb=" O ALA A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 229 No H-bonds generated for 'chain 'A' and resid 227 through 229' Processing helix chain 'A' and resid 231 through 233 No H-bonds generated for 'chain 'A' and resid 231 through 233' Processing helix chain 'A' and resid 234 through 244 removed outlier: 3.661A pdb=" N PHE A 238 " --> pdb=" O PHE A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 262 removed outlier: 3.894A pdb=" N GLU A 258 " --> pdb=" O ALA A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 265 No H-bonds generated for 'chain 'A' and resid 263 through 265' Processing helix chain 'A' and resid 267 through 274 removed outlier: 3.692A pdb=" N GLU A 274 " --> pdb=" O VAL A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 298 Processing helix chain 'A' and resid 300 through 308 Processing helix chain 'A' and resid 308 through 315 removed outlier: 3.706A pdb=" N LYS A 312 " --> pdb=" O SER A 308 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL A 313 " --> pdb=" O HIS A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 322 removed outlier: 4.488A pdb=" N GLU A 321 " --> pdb=" O THR A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 342 Processing helix chain 'A' and resid 345 through 359 Processing helix chain 'A' and resid 373 through 378 removed outlier: 3.501A pdb=" N LEU A 377 " --> pdb=" O VAL A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 390 Processing helix chain 'A' and resid 394 through 406 Processing helix chain 'A' and resid 408 through 430 Proline residue: A 414 - end of helix Processing helix chain 'A' and resid 439 through 448 Processing helix chain 'A' and resid 449 through 467 Processing helix chain 'A' and resid 500 through 515 removed outlier: 3.808A pdb=" N ASN A 515 " --> pdb=" O HIS A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 557 removed outlier: 3.796A pdb=" N ALA A 546 " --> pdb=" O ILE A 542 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA A 551 " --> pdb=" O LYS A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 599 removed outlier: 3.598A pdb=" N ARG A 599 " --> pdb=" O ASN A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 643 Processing helix chain 'A' and resid 644 through 647 Processing helix chain 'A' and resid 700 through 705 Processing helix chain 'A' and resid 719 through 728 Processing helix chain 'A' and resid 737 through 745 Processing helix chain 'A' and resid 763 through 777 removed outlier: 3.667A pdb=" N GLY A 777 " --> pdb=" O ARG A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 787 Processing helix chain 'A' and resid 793 through 824 removed outlier: 3.520A pdb=" N ARG A 797 " --> pdb=" O THR A 793 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N TRP A 798 " --> pdb=" O ALA A 794 " (cutoff:3.500A) Proline residue: A 810 - end of helix removed outlier: 4.261A pdb=" N MET A 824 " --> pdb=" O GLY A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 828 through 849 removed outlier: 3.517A pdb=" N TRP A 832 " --> pdb=" O GLY A 828 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU A 836 " --> pdb=" O TRP A 832 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ILE A 837 " --> pdb=" O GLN A 833 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE A 838 " --> pdb=" O ILE A 834 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU A 840 " --> pdb=" O LEU A 836 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE A 841 " --> pdb=" O ILE A 837 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA A 843 " --> pdb=" O SER A 839 " (cutoff:3.500A) Proline residue: A 844 - end of helix removed outlier: 4.630A pdb=" N SER A 847 " --> pdb=" O ALA A 843 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU A 848 " --> pdb=" O PRO A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 852 No H-bonds generated for 'chain 'A' and resid 850 through 852' Processing helix chain 'A' and resid 867 through 885 removed outlier: 4.200A pdb=" N GLU A 871 " --> pdb=" O THR A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 885 through 903 Processing helix chain 'A' and resid 927 through 936 Processing helix chain 'A' and resid 937 through 951 removed outlier: 3.642A pdb=" N LEU A 951 " --> pdb=" O LEU A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 956 through 969 Proline residue: A 962 - end of helix removed outlier: 3.595A pdb=" N LEU A 969 " --> pdb=" O LEU A 965 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 979 Processing helix chain 'A' and resid 991 through 1005 Processing helix chain 'A' and resid 1005 through 1011 Processing helix chain 'A' and resid 1037 through 1055 Processing helix chain 'A' and resid 1058 through 1075 Processing helix chain 'A' and resid 1102 through 1124 Processing helix chain 'A' and resid 1135 through 1149 removed outlier: 3.637A pdb=" N LYS A1149 " --> pdb=" O ARG A1145 " (cutoff:3.500A) Processing helix chain 'A' and resid 1159 through 1182 removed outlier: 3.547A pdb=" N ARG A1163 " --> pdb=" O ARG A1159 " (cutoff:3.500A) Processing helix chain 'A' and resid 1186 through 1211 removed outlier: 3.525A pdb=" N VAL A1190 " --> pdb=" O ALA A1186 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU A1210 " --> pdb=" O ASN A1206 " (cutoff:3.500A) Processing helix chain 'A' and resid 1215 through 1237 removed outlier: 3.603A pdb=" N VAL A1219 " --> pdb=" O GLN A1215 " (cutoff:3.500A) Processing helix chain 'A' and resid 1244 through 1264 Processing helix chain 'A' and resid 1267 through 1271 Processing helix chain 'A' and resid 1300 through 1311 removed outlier: 3.678A pdb=" N THR A1304 " --> pdb=" O GLU A1300 " (cutoff:3.500A) Processing helix chain 'A' and resid 1316 through 1321 removed outlier: 3.780A pdb=" N TYR A1320 " --> pdb=" O THR A1316 " (cutoff:3.500A) Processing helix chain 'A' and resid 1342 through 1345 Processing helix chain 'A' and resid 1346 through 1352 removed outlier: 3.747A pdb=" N VAL A1351 " --> pdb=" O MET A1347 " (cutoff:3.500A) Processing helix chain 'A' and resid 1358 through 1379 Processing helix chain 'A' and resid 1405 through 1409 removed outlier: 3.896A pdb=" N GLY A1409 " --> pdb=" O PRO A1406 " (cutoff:3.500A) Processing helix chain 'A' and resid 1421 through 1428 removed outlier: 4.191A pdb=" N SER A1425 " --> pdb=" O ALA A1421 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE A1426 " --> pdb=" O PRO A1422 " (cutoff:3.500A) Processing helix chain 'A' and resid 1432 through 1445 Processing helix chain 'A' and resid 1461 through 1465 Processing helix chain 'A' and resid 1479 through 1494 Processing helix chain 'A' and resid 1496 through 1503 Processing helix chain 'A' and resid 1505 through 1513 removed outlier: 3.978A pdb=" N LEU A1513 " --> pdb=" O GLU A1509 " (cutoff:3.500A) Processing helix chain 'A' and resid 1537 through 1542 removed outlier: 3.995A pdb=" N LEU A1542 " --> pdb=" O GLU A1538 " (cutoff:3.500A) Processing helix chain 'A' and resid 1690 through 1696 removed outlier: 3.522A pdb=" N HIS A1696 " --> pdb=" O ASP A1692 " (cutoff:3.500A) Processing helix chain 'A' and resid 1696 through 1703 removed outlier: 3.830A pdb=" N SER A1700 " --> pdb=" O HIS A1696 " (cutoff:3.500A) Processing helix chain 'A' and resid 1751 through 1756 removed outlier: 3.536A pdb=" N GLY A1756 " --> pdb=" O ALA A1752 " (cutoff:3.500A) Processing helix chain 'A' and resid 1764 through 1768 removed outlier: 3.766A pdb=" N PHE A1767 " --> pdb=" O ALA A1764 " (cutoff:3.500A) Processing helix chain 'A' and resid 1813 through 1823 removed outlier: 3.676A pdb=" N ALA A1817 " --> pdb=" O GLU A1813 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N HIS A1823 " --> pdb=" O ASP A1819 " (cutoff:3.500A) Processing helix chain 'A' and resid 1829 through 1845 removed outlier: 3.993A pdb=" N VAL A1845 " --> pdb=" O GLN A1841 " (cutoff:3.500A) Processing helix chain 'A' and resid 1848 through 1864 removed outlier: 3.643A pdb=" N TYR A1861 " --> pdb=" O HIS A1857 " (cutoff:3.500A) Processing helix chain 'A' and resid 1874 through 1878 removed outlier: 3.887A pdb=" N THR A1878 " --> pdb=" O THR A1875 " (cutoff:3.500A) Processing helix chain 'A' and resid 1882 through 1887 Processing helix chain 'A' and resid 1909 through 1925 removed outlier: 3.647A pdb=" N GLU A1913 " --> pdb=" O ASP A1909 " (cutoff:3.500A) Processing helix chain 'A' and resid 1940 through 1953 removed outlier: 3.670A pdb=" N ILE A1951 " --> pdb=" O ALA A1947 " (cutoff:3.500A) Processing helix chain 'A' and resid 1977 through 1988 Processing helix chain 'A' and resid 2001 through 2010 Processing helix chain 'A' and resid 2212 through 2216 removed outlier: 3.797A pdb=" N ILE A2216 " --> pdb=" O ALA A2213 " (cutoff:3.500A) Processing helix chain 'A' and resid 2256 through 2261 Processing helix chain 'A' and resid 2316 through 2330 removed outlier: 3.783A pdb=" N GLN A2329 " --> pdb=" O LYS A2325 " (cutoff:3.500A) Processing helix chain 'A' and resid 2332 through 2348 removed outlier: 3.616A pdb=" N LEU A2336 " --> pdb=" O PHE A2332 " (cutoff:3.500A) Processing helix chain 'A' and resid 2358 through 2363 removed outlier: 3.511A pdb=" N VAL A2363 " --> pdb=" O PHE A2359 " (cutoff:3.500A) Processing helix chain 'A' and resid 2365 through 2375 Processing helix chain 'A' and resid 2391 through 2398 removed outlier: 4.574A pdb=" N THR A2398 " --> pdb=" O GLN A2394 " (cutoff:3.500A) Processing helix chain 'A' and resid 2407 through 2418 Processing helix chain 'A' and resid 2443 through 2460 removed outlier: 4.473A pdb=" N VAL A2447 " --> pdb=" O SER A2443 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU A2449 " --> pdb=" O ASP A2445 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA A2450 " --> pdb=" O VAL A2446 " (cutoff:3.500A) Processing helix chain 'A' and resid 2463 through 2467 Processing helix chain 'A' and resid 2497 through 2512 Processing helix chain 'A' and resid 2542 through 2563 removed outlier: 3.968A pdb=" N ASP A2554 " --> pdb=" O GLY A2550 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N GLU A2557 " --> pdb=" O ARG A2553 " (cutoff:3.500A) Processing helix chain 'A' and resid 2564 through 2585 removed outlier: 4.123A pdb=" N LYS A2570 " --> pdb=" O ASP A2566 " (cutoff:3.500A) Processing helix chain 'A' and resid 2615 through 2625 removed outlier: 4.177A pdb=" N VAL A2622 " --> pdb=" O GLN A2618 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLY A2625 " --> pdb=" O SER A2621 " (cutoff:3.500A) Processing helix chain 'A' and resid 2628 through 2640 Processing helix chain 'A' and resid 2641 through 2644 removed outlier: 3.676A pdb=" N VAL A2644 " --> pdb=" O GLU A2641 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2641 through 2644' Processing helix chain 'A' and resid 2667 through 2671 Processing helix chain 'A' and resid 2683 through 2697 removed outlier: 3.644A pdb=" N TRP A2688 " --> pdb=" O HIS A2684 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY A2697 " --> pdb=" O LEU A2693 " (cutoff:3.500A) Processing helix chain 'A' and resid 2698 through 2710 Processing helix chain 'A' and resid 2738 through 2742 removed outlier: 3.983A pdb=" N TYR A2741 " --> pdb=" O GLU A2738 " (cutoff:3.500A) Processing helix chain 'A' and resid 2753 through 2764 Processing sheet with id=AA1, first strand: chain 'A' and resid 565 through 569 removed outlier: 9.314A pdb=" N TYR A 566 " --> pdb=" O ILE A 520 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N PHE A 522 " --> pdb=" O TYR A 566 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N LEU A 568 " --> pdb=" O PHE A 522 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N LEU A 524 " --> pdb=" O LEU A 568 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N THR A 487 " --> pdb=" O TYR A 521 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N SER A 523 " --> pdb=" O THR A 487 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N VAL A 489 " --> pdb=" O SER A 523 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N VAL A 525 " --> pdb=" O VAL A 489 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N VAL A 491 " --> pdb=" O VAL A 525 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 628 through 629 removed outlier: 3.847A pdb=" N VAL A 757 " --> pdb=" O ARG A 628 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 663 through 665 Processing sheet with id=AA4, first strand: chain 'A' and resid 1023 through 1025 Processing sheet with id=AA5, first strand: chain 'A' and resid 1035 through 1036 Processing sheet with id=AA6, first strand: chain 'A' and resid 1099 through 1101 Processing sheet with id=AA7, first strand: chain 'A' and resid 1326 through 1329 removed outlier: 3.520A pdb=" N GLN A1332 " --> pdb=" O ILE A1329 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1419 through 1420 Processing sheet with id=AA9, first strand: chain 'A' and resid 1449 through 1450 removed outlier: 3.535A pdb=" N GLY A1453 " --> pdb=" O GLY A1450 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1548 through 1550 removed outlier: 3.516A pdb=" N ARG A1548 " --> pdb=" O PHE A1632 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1560 through 1564 removed outlier: 6.581A pdb=" N SER A1580 " --> pdb=" O ILE A1587 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN A1585 " --> pdb=" O TRP A1582 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N GLN A1585 " --> pdb=" O ALA A1688 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N ALA A1688 " --> pdb=" O GLN A1585 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1613 through 1615 removed outlier: 3.505A pdb=" N LEU A1787 " --> pdb=" O SER A1681 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1968 through 1972 removed outlier: 6.023A pdb=" N PHE A1898 " --> pdb=" O VAL A1931 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N VAL A1933 " --> pdb=" O PHE A1898 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LEU A1900 " --> pdb=" O VAL A1933 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU A1992 " --> pdb=" O SER A1899 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 2051 through 2053 Processing sheet with id=AB6, first strand: chain 'A' and resid 2076 through 2080 removed outlier: 3.974A pdb=" N PHE A2083 " --> pdb=" O ASN A2080 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 2119 through 2120 removed outlier: 3.504A pdb=" N ALA A2199 " --> pdb=" O LEU A2293 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 2351 through 2352 Processing sheet with id=AB9, first strand: chain 'A' and resid 2389 through 2390 removed outlier: 3.567A pdb=" N TRP A2430 " --> pdb=" O PHE A2389 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 2473 through 2474 Processing sheet with id=AC2, first strand: chain 'A' and resid 2540 through 2541 Processing sheet with id=AC3, first strand: chain 'A' and resid 2681 through 2682 removed outlier: 3.649A pdb=" N VAL A2735 " --> pdb=" O GLN A2681 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N THR A2732 " --> pdb=" O SER A2748 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N SER A2748 " --> pdb=" O THR A2732 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 2768 through 2770 997 hydrogen bonds defined for protein. 2848 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: 11.68 Time building geometry restraints manager: 9.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7327 1.34 - 1.46: 5131 1.46 - 1.58: 9686 1.58 - 1.70: 12 1.70 - 1.82: 121 Bond restraints: 22277 Sorted by residual: bond pdb=" C1 BGC B 2 " pdb=" O5 BGC B 2 " ideal model delta sigma weight residual 1.408 1.476 -0.068 2.00e-02 2.50e+03 1.15e+01 bond pdb=" C1 BGC B 9 " pdb=" O5 BGC B 9 " ideal model delta sigma weight residual 1.408 1.466 -0.058 2.00e-02 2.50e+03 8.33e+00 bond pdb=" N GLU A1228 " pdb=" CA GLU A1228 " ideal model delta sigma weight residual 1.459 1.490 -0.030 1.23e-02 6.61e+03 6.11e+00 bond pdb=" O3B UPG A2903 " pdb=" PB UPG A2903 " ideal model delta sigma weight residual 1.652 1.604 0.048 2.00e-02 2.50e+03 5.87e+00 bond pdb=" O3B UPG A2902 " pdb=" PB UPG A2902 " ideal model delta sigma weight residual 1.652 1.604 0.048 2.00e-02 2.50e+03 5.79e+00 ... (remaining 22272 not shown) Histogram of bond angle deviations from ideal: 98.34 - 105.48: 379 105.48 - 112.63: 11758 112.63 - 119.78: 7277 119.78 - 126.92: 10547 126.92 - 134.07: 328 Bond angle restraints: 30289 Sorted by residual: angle pdb=" N PRO A2030 " pdb=" CA PRO A2030 " pdb=" CB PRO A2030 " ideal model delta sigma weight residual 102.79 109.83 -7.04 6.60e-01 2.30e+00 1.14e+02 angle pdb=" N PRO A2033 " pdb=" CA PRO A2033 " pdb=" CB PRO A2033 " ideal model delta sigma weight residual 103.25 110.86 -7.61 1.05e+00 9.07e-01 5.26e+01 angle pdb=" N PRO A1524 " pdb=" CA PRO A1524 " pdb=" CB PRO A1524 " ideal model delta sigma weight residual 103.25 110.82 -7.57 1.05e+00 9.07e-01 5.20e+01 angle pdb=" N PRO A1888 " pdb=" CA PRO A1888 " pdb=" CB PRO A1888 " ideal model delta sigma weight residual 103.25 110.18 -6.93 1.05e+00 9.07e-01 4.36e+01 angle pdb=" N PRO A2028 " pdb=" CA PRO A2028 " pdb=" CB PRO A2028 " ideal model delta sigma weight residual 103.25 110.08 -6.83 1.05e+00 9.07e-01 4.23e+01 ... (remaining 30284 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.70: 12584 25.70 - 51.40: 663 51.40 - 77.11: 58 77.11 - 102.81: 34 102.81 - 128.51: 34 Dihedral angle restraints: 13373 sinusoidal: 5384 harmonic: 7989 Sorted by residual: dihedral pdb=" CA VAL A 72 " pdb=" C VAL A 72 " pdb=" N TYR A 73 " pdb=" CA TYR A 73 " ideal model delta harmonic sigma weight residual 180.00 140.21 39.79 0 5.00e+00 4.00e-02 6.33e+01 dihedral pdb=" CA ALA A1519 " pdb=" C ALA A1519 " pdb=" N PRO A1520 " pdb=" CA PRO A1520 " ideal model delta harmonic sigma weight residual -180.00 -156.65 -23.35 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" C2 BGC B 1 " pdb=" C1 BGC B 1 " pdb=" O5 BGC B 1 " pdb=" C5 BGC B 1 " ideal model delta sinusoidal sigma weight residual -65.02 63.49 -128.51 1 3.00e+01 1.11e-03 1.73e+01 ... (remaining 13370 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2776 0.053 - 0.105: 506 0.105 - 0.158: 68 0.158 - 0.210: 6 0.210 - 0.263: 6 Chirality restraints: 3362 Sorted by residual: chirality pdb=" CA PRO A1888 " pdb=" N PRO A1888 " pdb=" C PRO A1888 " pdb=" CB PRO A1888 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CA PRO A2037 " pdb=" N PRO A2037 " pdb=" C PRO A2037 " pdb=" CB PRO A2037 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA PRO A2030 " pdb=" N PRO A2030 " pdb=" C PRO A2030 " pdb=" CB PRO A2030 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.25 2.00e-01 2.50e+01 1.56e+00 ... (remaining 3359 not shown) Planarity restraints: 3929 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 821 " -0.025 2.00e-02 2.50e+03 2.58e-02 1.66e+01 pdb=" CG TRP A 821 " 0.069 2.00e-02 2.50e+03 pdb=" CD1 TRP A 821 " -0.034 2.00e-02 2.50e+03 pdb=" CD2 TRP A 821 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 821 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 821 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 821 " -0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 821 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 821 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP A 821 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A1865 " 0.019 2.00e-02 2.50e+03 3.77e-02 1.42e+01 pdb=" C PRO A1865 " -0.065 2.00e-02 2.50e+03 pdb=" O PRO A1865 " 0.024 2.00e-02 2.50e+03 pdb=" N ASP A1866 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A1519 " 0.019 2.00e-02 2.50e+03 3.75e-02 1.40e+01 pdb=" C ALA A1519 " -0.065 2.00e-02 2.50e+03 pdb=" O ALA A1519 " 0.024 2.00e-02 2.50e+03 pdb=" N PRO A1520 " 0.021 2.00e-02 2.50e+03 ... (remaining 3926 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 628 2.70 - 3.25: 22321 3.25 - 3.80: 35439 3.80 - 4.35: 44179 4.35 - 4.90: 72335 Nonbonded interactions: 174902 Sorted by model distance: nonbonded pdb=" O VAL A2077 " pdb=" OH TYR A2369 " model vdw 2.148 2.440 nonbonded pdb=" O ASN A1417 " pdb=" OG1 THR A1461 " model vdw 2.158 2.440 nonbonded pdb=" O PRO A 844 " pdb=" OG SER A 847 " model vdw 2.180 2.440 nonbonded pdb=" O ALA A 552 " pdb=" OG SER A 555 " model vdw 2.192 2.440 nonbonded pdb=" O HIS A2580 " pdb=" OG1 THR A2584 " model vdw 2.196 2.440 ... (remaining 174897 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=0.40 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: 2.010 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: 0.010 Extract box with map and model: 0.690 Check model and map are aligned: 0.150 Set scattering table: 0.180 Process input model: 76.600 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.130 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:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 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 : 0.003 0.068 22277 Z= 0.188 Angle : 0.607 9.305 30289 Z= 0.327 Chirality : 0.042 0.263 3362 Planarity : 0.003 0.053 3929 Dihedral : 16.601 128.510 8231 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.84 % Allowed : 7.56 % Favored : 91.61 % Rotamer: Outliers : 0.14 % Allowed : 0.14 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.17), residues: 2759 helix: 1.23 (0.16), residues: 1154 sheet: 0.21 (0.30), residues: 329 loop : -2.58 (0.16), residues: 1276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.001 TRP A 821 HIS 0.004 0.001 HIS A1209 PHE 0.012 0.001 PHE A2547 TYR 0.015 0.001 TYR A 73 ARG 0.005 0.000 ARG A1163 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5518 Ramachandran restraints generated. 2759 Oldfield, 0 Emsley, 2759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5518 Ramachandran restraints generated. 2759 Oldfield, 0 Emsley, 2759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 2287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 2.478 Fit side-chains REVERT: A 423 MET cc_start: 0.9236 (ptp) cc_final: 0.9003 (ppp) REVERT: A 621 MET cc_start: 0.8428 (tpt) cc_final: 0.8214 (tpt) REVERT: A 824 MET cc_start: 0.8763 (pmm) cc_final: 0.8308 (pmm) REVERT: A 1244 MET cc_start: 0.8449 (mmp) cc_final: 0.8118 (mmm) REVERT: A 2135 CYS cc_start: 0.8873 (m) cc_final: 0.8611 (m) REVERT: A 2636 MET cc_start: 0.8856 (mmp) cc_final: 0.7899 (ptm) REVERT: A 2640 MET cc_start: 0.9071 (mmp) cc_final: 0.8784 (mmm) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.3160 time to fit residues: 63.2161 Evaluate side-chains 90 residues out of total 2287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 2.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 233 optimal weight: 0.1980 chunk 209 optimal weight: 6.9990 chunk 116 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 141 optimal weight: 4.9990 chunk 111 optimal weight: 4.9990 chunk 216 optimal weight: 0.0770 chunk 83 optimal weight: 5.9990 chunk 131 optimal weight: 0.9980 chunk 161 optimal weight: 7.9990 chunk 250 optimal weight: 4.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.0608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 22277 Z= 0.154 Angle : 0.597 11.889 30289 Z= 0.291 Chirality : 0.042 0.226 3362 Planarity : 0.003 0.053 3929 Dihedral : 12.420 121.241 3364 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.73 % Allowed : 7.81 % Favored : 91.46 % Rotamer: Outliers : 0.50 % Allowed : 4.66 % Favored : 94.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.17), residues: 2759 helix: 1.26 (0.16), residues: 1190 sheet: 0.34 (0.29), residues: 333 loop : -2.72 (0.16), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP A 821 HIS 0.005 0.001 HIS A1829 PHE 0.024 0.001 PHE A2547 TYR 0.012 0.001 TYR A 619 ARG 0.008 0.000 ARG A1221 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5518 Ramachandran restraints generated. 2759 Oldfield, 0 Emsley, 2759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5518 Ramachandran restraints generated. 2759 Oldfield, 0 Emsley, 2759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 2287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 91 time to evaluate : 2.469 Fit side-chains REVERT: A 271 MET cc_start: 0.9341 (mmm) cc_final: 0.8725 (mpp) REVERT: A 596 MET cc_start: 0.9170 (mtm) cc_final: 0.8600 (mpp) REVERT: A 629 LEU cc_start: 0.9179 (tp) cc_final: 0.8973 (tp) REVERT: A 824 MET cc_start: 0.8823 (pmm) cc_final: 0.8336 (pmm) REVERT: A 1244 MET cc_start: 0.8477 (mmp) cc_final: 0.8120 (mmm) REVERT: A 1908 MET cc_start: 0.6526 (mmp) cc_final: 0.6304 (mmm) REVERT: A 2135 CYS cc_start: 0.8857 (m) cc_final: 0.8526 (m) REVERT: A 2145 MET cc_start: 0.8299 (tpp) cc_final: 0.7736 (tpt) REVERT: A 2640 MET cc_start: 0.9029 (mmp) cc_final: 0.8662 (mmm) outliers start: 8 outliers final: 5 residues processed: 94 average time/residue: 0.2958 time to fit residues: 49.2020 Evaluate side-chains 95 residues out of total 2287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 90 time to evaluate : 2.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 687 ILE Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain A residue 2311 LEU Chi-restraints excluded: chain A residue 2498 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 139 optimal weight: 0.7980 chunk 77 optimal weight: 0.0980 chunk 208 optimal weight: 4.9990 chunk 170 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 chunk 251 optimal weight: 0.0870 chunk 271 optimal weight: 8.9990 chunk 223 optimal weight: 0.0870 chunk 248 optimal weight: 1.9990 chunk 85 optimal weight: 7.9990 chunk 201 optimal weight: 3.9990 overall best weight: 0.3536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.0854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 22277 Z= 0.140 Angle : 0.577 11.905 30289 Z= 0.280 Chirality : 0.042 0.389 3362 Planarity : 0.003 0.052 3929 Dihedral : 9.476 125.028 3364 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.69 % Allowed : 7.66 % Favored : 91.65 % Rotamer: Outliers : 0.45 % Allowed : 6.25 % Favored : 93.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.17), residues: 2759 helix: 1.35 (0.16), residues: 1190 sheet: 0.41 (0.30), residues: 328 loop : -2.66 (0.16), residues: 1241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP A 821 HIS 0.005 0.000 HIS A1829 PHE 0.021 0.001 PHE A2547 TYR 0.012 0.001 TYR A 73 ARG 0.004 0.000 ARG A1221 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5518 Ramachandran restraints generated. 2759 Oldfield, 0 Emsley, 2759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5518 Ramachandran restraints generated. 2759 Oldfield, 0 Emsley, 2759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 2287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 96 time to evaluate : 2.281 Fit side-chains REVERT: A 271 MET cc_start: 0.9383 (mmm) cc_final: 0.8770 (mpp) REVERT: A 596 MET cc_start: 0.9204 (mtm) cc_final: 0.8462 (mpp) REVERT: A 824 MET cc_start: 0.8835 (pmm) cc_final: 0.8194 (pmm) REVERT: A 1244 MET cc_start: 0.8492 (mmp) cc_final: 0.8089 (mmm) REVERT: A 2135 CYS cc_start: 0.8846 (m) cc_final: 0.8509 (m) REVERT: A 2636 MET cc_start: 0.8879 (mmp) cc_final: 0.7951 (ptm) REVERT: A 2640 MET cc_start: 0.9022 (mmp) cc_final: 0.8691 (mmm) outliers start: 7 outliers final: 6 residues processed: 97 average time/residue: 0.2978 time to fit residues: 51.0667 Evaluate side-chains 95 residues out of total 2287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 89 time to evaluate : 2.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 621 MET Chi-restraints excluded: chain A residue 935 MET Chi-restraints excluded: chain A residue 965 LEU Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain A residue 1806 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 248 optimal weight: 10.0000 chunk 188 optimal weight: 6.9990 chunk 130 optimal weight: 7.9990 chunk 27 optimal weight: 4.9990 chunk 119 optimal weight: 4.9990 chunk 168 optimal weight: 4.9990 chunk 251 optimal weight: 0.3980 chunk 266 optimal weight: 3.9990 chunk 131 optimal weight: 3.9990 chunk 238 optimal weight: 10.0000 chunk 71 optimal weight: 7.9990 overall best weight: 3.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 HIS ** A1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1040 ASN ** A1107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1174 ASN ** A1209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1233 HIS ** A1451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1955 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2527 ASN ** A2678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2714 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.125 22277 Z= 0.418 Angle : 0.760 9.215 30289 Z= 0.389 Chirality : 0.045 0.396 3362 Planarity : 0.005 0.079 3929 Dihedral : 8.109 103.984 3364 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 20.98 Ramachandran Plot: Outliers : 0.80 % Allowed : 9.77 % Favored : 89.43 % Rotamer: Outliers : 1.13 % Allowed : 8.33 % Favored : 90.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.16), residues: 2759 helix: 1.02 (0.16), residues: 1193 sheet: 0.19 (0.29), residues: 357 loop : -2.74 (0.16), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP A1122 HIS 0.012 0.002 HIS A 643 PHE 0.031 0.002 PHE A1307 TYR 0.030 0.003 TYR A1398 ARG 0.008 0.001 ARG A1392 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5518 Ramachandran restraints generated. 2759 Oldfield, 0 Emsley, 2759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5518 Ramachandran restraints generated. 2759 Oldfield, 0 Emsley, 2759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 2287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 84 time to evaluate : 2.805 Fit side-chains REVERT: A 271 MET cc_start: 0.9442 (mmm) cc_final: 0.8765 (mpp) REVERT: A 824 MET cc_start: 0.8834 (pmm) cc_final: 0.8615 (pmm) REVERT: A 1244 MET cc_start: 0.8618 (mmp) cc_final: 0.8082 (mmm) REVERT: A 1842 MET cc_start: 0.8527 (tpp) cc_final: 0.8321 (tpt) REVERT: A 1908 MET cc_start: 0.7205 (mmm) cc_final: 0.6443 (mmm) REVERT: A 2135 CYS cc_start: 0.8954 (m) cc_final: 0.8616 (m) REVERT: A 2640 MET cc_start: 0.9054 (mmp) cc_final: 0.8726 (mmm) outliers start: 22 outliers final: 13 residues processed: 96 average time/residue: 0.3118 time to fit residues: 52.6377 Evaluate side-chains 93 residues out of total 2287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 80 time to evaluate : 2.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 621 MET Chi-restraints excluded: chain A residue 687 ILE Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 965 LEU Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1107 ASN Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain A residue 1306 LEU Chi-restraints excluded: chain A residue 1427 LEU Chi-restraints excluded: chain A residue 2255 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 222 optimal weight: 0.7980 chunk 151 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 198 optimal weight: 7.9990 chunk 110 optimal weight: 5.9990 chunk 227 optimal weight: 1.9990 chunk 184 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 136 optimal weight: 4.9990 chunk 239 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1017 ASN A1040 ASN ** A1107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1955 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2420 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 22277 Z= 0.242 Angle : 0.634 15.798 30289 Z= 0.315 Chirality : 0.042 0.402 3362 Planarity : 0.004 0.053 3929 Dihedral : 7.011 97.753 3364 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.80 % Allowed : 8.17 % Favored : 91.03 % Rotamer: Outliers : 0.81 % Allowed : 9.60 % Favored : 89.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.16), residues: 2759 helix: 1.28 (0.16), residues: 1192 sheet: 0.11 (0.28), residues: 363 loop : -2.68 (0.17), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A1122 HIS 0.007 0.001 HIS A1503 PHE 0.021 0.001 PHE A1307 TYR 0.014 0.001 TYR A 545 ARG 0.005 0.000 ARG A 570 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5518 Ramachandran restraints generated. 2759 Oldfield, 0 Emsley, 2759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5518 Ramachandran restraints generated. 2759 Oldfield, 0 Emsley, 2759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 2287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 89 time to evaluate : 2.486 Fit side-chains REVERT: A 596 MET cc_start: 0.9176 (mtm) cc_final: 0.8547 (mpp) REVERT: A 1244 MET cc_start: 0.8353 (mmp) cc_final: 0.7914 (mmm) REVERT: A 1908 MET cc_start: 0.7476 (mmm) cc_final: 0.7056 (mmm) REVERT: A 2135 CYS cc_start: 0.8917 (m) cc_final: 0.8587 (m) REVERT: A 2145 MET cc_start: 0.8332 (tpp) cc_final: 0.7744 (tpt) REVERT: A 2640 MET cc_start: 0.9072 (mmp) cc_final: 0.8777 (mmm) outliers start: 15 outliers final: 14 residues processed: 97 average time/residue: 0.2907 time to fit residues: 49.6889 Evaluate side-chains 99 residues out of total 2287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 85 time to evaluate : 2.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 621 MET Chi-restraints excluded: chain A residue 687 ILE Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 940 VAL Chi-restraints excluded: chain A residue 965 LEU Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain A residue 1306 LEU Chi-restraints excluded: chain A residue 1398 TYR Chi-restraints excluded: chain A residue 1427 LEU Chi-restraints excluded: chain A residue 2255 THR Chi-restraints excluded: chain A residue 2655 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 89 optimal weight: 7.9990 chunk 240 optimal weight: 0.7980 chunk 52 optimal weight: 0.8980 chunk 156 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 chunk 267 optimal weight: 0.9990 chunk 221 optimal weight: 4.9990 chunk 123 optimal weight: 0.3980 chunk 22 optimal weight: 9.9990 chunk 88 optimal weight: 10.0000 chunk 140 optimal weight: 3.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 833 GLN ** A1107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1955 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 22277 Z= 0.197 Angle : 0.611 15.119 30289 Z= 0.300 Chirality : 0.041 0.360 3362 Planarity : 0.004 0.054 3929 Dihedral : 6.628 97.926 3364 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.69 % Allowed : 8.50 % Favored : 90.81 % Rotamer: Outliers : 0.63 % Allowed : 10.82 % Favored : 88.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.17), residues: 2759 helix: 1.41 (0.16), residues: 1194 sheet: 0.10 (0.29), residues: 345 loop : -2.60 (0.17), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A1122 HIS 0.004 0.001 HIS A2574 PHE 0.018 0.001 PHE A1307 TYR 0.013 0.001 TYR A2383 ARG 0.004 0.000 ARG A 570 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5518 Ramachandran restraints generated. 2759 Oldfield, 0 Emsley, 2759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5518 Ramachandran restraints generated. 2759 Oldfield, 0 Emsley, 2759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 2287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 92 time to evaluate : 2.379 Fit side-chains revert: symmetry clash REVERT: A 271 MET cc_start: 0.9443 (mmm) cc_final: 0.8793 (mpp) REVERT: A 423 MET cc_start: 0.9373 (ptp) cc_final: 0.9154 (ppp) REVERT: A 1244 MET cc_start: 0.8312 (mmp) cc_final: 0.7905 (mmm) REVERT: A 1342 MET cc_start: 0.8564 (mpp) cc_final: 0.8025 (mpp) REVERT: A 1908 MET cc_start: 0.7426 (mmm) cc_final: 0.7036 (mmm) REVERT: A 2135 CYS cc_start: 0.8936 (m) cc_final: 0.8606 (m) REVERT: A 2145 MET cc_start: 0.8309 (tpp) cc_final: 0.7853 (tpt) REVERT: A 2246 LEU cc_start: 0.8739 (tp) cc_final: 0.8043 (tp) REVERT: A 2640 MET cc_start: 0.9055 (mmp) cc_final: 0.8773 (mmm) outliers start: 11 outliers final: 9 residues processed: 98 average time/residue: 0.3328 time to fit residues: 56.4901 Evaluate side-chains 95 residues out of total 2287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 86 time to evaluate : 2.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 687 ILE Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 742 GLU Chi-restraints excluded: chain A residue 833 GLN Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain A residue 2255 THR Chi-restraints excluded: chain A residue 2655 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 257 optimal weight: 8.9990 chunk 30 optimal weight: 4.9990 chunk 152 optimal weight: 6.9990 chunk 195 optimal weight: 6.9990 chunk 151 optimal weight: 0.0570 chunk 224 optimal weight: 8.9990 chunk 149 optimal weight: 20.0000 chunk 266 optimal weight: 6.9990 chunk 166 optimal weight: 7.9990 chunk 162 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 overall best weight: 4.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1040 ASN ** A1107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1397 ASN ** A1451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1955 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.114 22277 Z= 0.443 Angle : 0.776 13.715 30289 Z= 0.395 Chirality : 0.045 0.337 3362 Planarity : 0.005 0.069 3929 Dihedral : 6.873 92.369 3364 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 21.65 Ramachandran Plot: Outliers : 0.87 % Allowed : 10.35 % Favored : 88.78 % Rotamer: Outliers : 0.91 % Allowed : 11.36 % Favored : 87.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.16), residues: 2759 helix: 0.96 (0.15), residues: 1205 sheet: 0.04 (0.30), residues: 334 loop : -2.69 (0.16), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP A1122 HIS 0.009 0.002 HIS A 643 PHE 0.025 0.002 PHE A1307 TYR 0.026 0.002 TYR A1398 ARG 0.016 0.001 ARG A 806 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5518 Ramachandran restraints generated. 2759 Oldfield, 0 Emsley, 2759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5518 Ramachandran restraints generated. 2759 Oldfield, 0 Emsley, 2759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 2287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 80 time to evaluate : 2.366 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1244 MET cc_start: 0.8366 (mmp) cc_final: 0.7898 (mmm) REVERT: A 1342 MET cc_start: 0.8763 (mpp) cc_final: 0.8160 (mpp) REVERT: A 1699 PHE cc_start: 0.6432 (OUTLIER) cc_final: 0.5255 (t80) REVERT: A 2135 CYS cc_start: 0.9016 (m) cc_final: 0.8686 (m) REVERT: A 2145 MET cc_start: 0.8332 (tpp) cc_final: 0.7992 (tpp) REVERT: A 2246 LEU cc_start: 0.8920 (tp) cc_final: 0.8388 (tp) REVERT: A 2640 MET cc_start: 0.9057 (mmp) cc_final: 0.8801 (mmm) outliers start: 17 outliers final: 12 residues processed: 91 average time/residue: 0.3119 time to fit residues: 49.0881 Evaluate side-chains 92 residues out of total 2287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 79 time to evaluate : 2.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 621 MET Chi-restraints excluded: chain A residue 687 ILE Chi-restraints excluded: chain A residue 742 GLU Chi-restraints excluded: chain A residue 833 GLN Chi-restraints excluded: chain A residue 940 VAL Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain A residue 1306 LEU Chi-restraints excluded: chain A residue 1398 TYR Chi-restraints excluded: chain A residue 1427 LEU Chi-restraints excluded: chain A residue 1699 PHE Chi-restraints excluded: chain A residue 2255 THR Chi-restraints excluded: chain A residue 2655 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 164 optimal weight: 0.9990 chunk 106 optimal weight: 0.9980 chunk 158 optimal weight: 3.9990 chunk 80 optimal weight: 9.9990 chunk 52 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 169 optimal weight: 6.9990 chunk 181 optimal weight: 6.9990 chunk 131 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 209 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1040 ASN ** A1107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1955 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 22277 Z= 0.226 Angle : 0.644 14.071 30289 Z= 0.318 Chirality : 0.042 0.298 3362 Planarity : 0.004 0.055 3929 Dihedral : 6.501 87.708 3364 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 16.81 Ramachandran Plot: Outliers : 0.80 % Allowed : 8.72 % Favored : 90.48 % Rotamer: Outliers : 0.81 % Allowed : 11.72 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.16), residues: 2759 helix: 1.25 (0.16), residues: 1204 sheet: 0.14 (0.30), residues: 311 loop : -2.56 (0.16), residues: 1244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A1122 HIS 0.005 0.001 HIS A 97 PHE 0.017 0.001 PHE A1307 TYR 0.014 0.001 TYR A 73 ARG 0.008 0.000 ARG A 806 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5518 Ramachandran restraints generated. 2759 Oldfield, 0 Emsley, 2759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5518 Ramachandran restraints generated. 2759 Oldfield, 0 Emsley, 2759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 2287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 88 time to evaluate : 2.601 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1244 MET cc_start: 0.8277 (mmp) cc_final: 0.7807 (mmm) REVERT: A 1342 MET cc_start: 0.8744 (mpp) cc_final: 0.8108 (mpp) REVERT: A 2135 CYS cc_start: 0.8957 (m) cc_final: 0.8630 (m) REVERT: A 2145 MET cc_start: 0.8288 (tpp) cc_final: 0.7966 (tpt) REVERT: A 2246 LEU cc_start: 0.8904 (tp) cc_final: 0.8202 (tp) REVERT: A 2640 MET cc_start: 0.9049 (mmp) cc_final: 0.8799 (mmm) outliers start: 15 outliers final: 12 residues processed: 99 average time/residue: 0.3155 time to fit residues: 53.2808 Evaluate side-chains 97 residues out of total 2287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 85 time to evaluate : 2.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 687 ILE Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 742 GLU Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain A residue 1306 LEU Chi-restraints excluded: chain A residue 1427 LEU Chi-restraints excluded: chain A residue 2255 THR Chi-restraints excluded: chain A residue 2335 VAL Chi-restraints excluded: chain A residue 2555 PHE Chi-restraints excluded: chain A residue 2655 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 241 optimal weight: 6.9990 chunk 254 optimal weight: 3.9990 chunk 232 optimal weight: 7.9990 chunk 247 optimal weight: 0.0060 chunk 149 optimal weight: 20.0000 chunk 107 optimal weight: 0.7980 chunk 194 optimal weight: 0.7980 chunk 76 optimal weight: 0.9980 chunk 224 optimal weight: 3.9990 chunk 234 optimal weight: 0.9990 chunk 162 optimal weight: 0.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1451 GLN ** A2351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 22277 Z= 0.161 Angle : 0.626 14.002 30289 Z= 0.303 Chirality : 0.041 0.244 3362 Planarity : 0.004 0.056 3929 Dihedral : 6.014 72.762 3364 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.73 % Allowed : 8.39 % Favored : 90.88 % Rotamer: Outliers : 0.81 % Allowed : 11.86 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.17), residues: 2759 helix: 1.42 (0.16), residues: 1200 sheet: 0.12 (0.30), residues: 330 loop : -2.45 (0.17), residues: 1229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A1122 HIS 0.005 0.001 HIS A1829 PHE 0.014 0.001 PHE A1307 TYR 0.017 0.001 TYR A 73 ARG 0.009 0.000 ARG A 806 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5518 Ramachandran restraints generated. 2759 Oldfield, 0 Emsley, 2759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5518 Ramachandran restraints generated. 2759 Oldfield, 0 Emsley, 2759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 2287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 89 time to evaluate : 2.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1244 MET cc_start: 0.8306 (mmp) cc_final: 0.7817 (mmm) REVERT: A 1908 MET cc_start: 0.7479 (mmm) cc_final: 0.6954 (mmm) REVERT: A 2135 CYS cc_start: 0.8932 (m) cc_final: 0.8604 (m) REVERT: A 2145 MET cc_start: 0.8368 (tpp) cc_final: 0.8057 (tpp) REVERT: A 2246 LEU cc_start: 0.8853 (tp) cc_final: 0.8053 (tp) REVERT: A 2640 MET cc_start: 0.9061 (mmp) cc_final: 0.8818 (mmm) outliers start: 15 outliers final: 12 residues processed: 98 average time/residue: 0.2981 time to fit residues: 50.4407 Evaluate side-chains 100 residues out of total 2287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 88 time to evaluate : 2.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 687 ILE Chi-restraints excluded: chain A residue 742 GLU Chi-restraints excluded: chain A residue 965 LEU Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain A residue 1427 LEU Chi-restraints excluded: chain A residue 1473 VAL Chi-restraints excluded: chain A residue 2335 VAL Chi-restraints excluded: chain A residue 2530 MET Chi-restraints excluded: chain A residue 2555 PHE Chi-restraints excluded: chain A residue 2655 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 262 optimal weight: 2.9990 chunk 159 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 182 optimal weight: 2.9990 chunk 274 optimal weight: 0.7980 chunk 253 optimal weight: 4.9990 chunk 218 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 169 optimal weight: 9.9990 chunk 134 optimal weight: 0.0570 chunk 173 optimal weight: 4.9990 overall best weight: 1.5704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 803 ASN ** A1107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22277 Z= 0.211 Angle : 0.633 13.607 30289 Z= 0.311 Chirality : 0.041 0.222 3362 Planarity : 0.004 0.056 3929 Dihedral : 5.766 59.300 3364 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.73 % Allowed : 8.57 % Favored : 90.70 % Rotamer: Outliers : 0.68 % Allowed : 12.00 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.17), residues: 2759 helix: 1.38 (0.16), residues: 1202 sheet: 0.15 (0.30), residues: 321 loop : -2.42 (0.17), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A1122 HIS 0.005 0.001 HIS A 97 PHE 0.016 0.001 PHE A1307 TYR 0.015 0.001 TYR A 73 ARG 0.007 0.000 ARG A 806 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5518 Ramachandran restraints generated. 2759 Oldfield, 0 Emsley, 2759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5518 Ramachandran restraints generated. 2759 Oldfield, 0 Emsley, 2759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 2287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 87 time to evaluate : 2.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1244 MET cc_start: 0.8340 (mmp) cc_final: 0.7812 (mmm) REVERT: A 1908 MET cc_start: 0.7577 (mmm) cc_final: 0.7078 (mmm) REVERT: A 2135 CYS cc_start: 0.8963 (m) cc_final: 0.8637 (m) REVERT: A 2145 MET cc_start: 0.8214 (tpp) cc_final: 0.7885 (tpp) REVERT: A 2246 LEU cc_start: 0.8873 (tp) cc_final: 0.8100 (tp) REVERT: A 2383 TYR cc_start: 0.8194 (m-80) cc_final: 0.7936 (m-10) REVERT: A 2640 MET cc_start: 0.9059 (mmp) cc_final: 0.8822 (mmm) outliers start: 12 outliers final: 12 residues processed: 95 average time/residue: 0.3084 time to fit residues: 50.5567 Evaluate side-chains 99 residues out of total 2287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 87 time to evaluate : 2.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 687 ILE Chi-restraints excluded: chain A residue 742 GLU Chi-restraints excluded: chain A residue 940 VAL Chi-restraints excluded: chain A residue 965 LEU Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain A residue 1427 LEU Chi-restraints excluded: chain A residue 1473 VAL Chi-restraints excluded: chain A residue 2335 VAL Chi-restraints excluded: chain A residue 2555 PHE Chi-restraints excluded: chain A residue 2655 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 233 optimal weight: 0.5980 chunk 67 optimal weight: 5.9990 chunk 201 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 219 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 225 optimal weight: 7.9990 chunk 27 optimal weight: 0.8980 chunk 40 optimal weight: 7.9990 chunk 192 optimal weight: 7.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2351 GLN ** 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 = 0.3370 r_free = 0.3370 target = 0.048673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.038246 restraints weight = 296315.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.039710 restraints weight = 144364.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.040730 restraints weight = 90623.674| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3128 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3128 r_free = 0.3128 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3128 r_free = 0.3128 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3128 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22277 Z= 0.212 Angle : 0.642 14.876 30289 Z= 0.315 Chirality : 0.041 0.197 3362 Planarity : 0.004 0.056 3929 Dihedral : 5.614 57.505 3364 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 16.25 Ramachandran Plot: Outliers : 0.73 % Allowed : 8.68 % Favored : 90.59 % Rotamer: Outliers : 0.72 % Allowed : 11.91 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.17), residues: 2759 helix: 1.41 (0.16), residues: 1194 sheet: 0.17 (0.30), residues: 320 loop : -2.42 (0.17), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A1122 HIS 0.005 0.001 HIS A 97 PHE 0.016 0.001 PHE A1307 TYR 0.015 0.001 TYR A 73 ARG 0.007 0.000 ARG A 806 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3358.13 seconds wall clock time: 61 minutes 49.38 seconds (3709.38 seconds total)