Starting phenix.real_space_refine on Mon Jul 22 19:05:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pw8_13678/07_2024/7pw8_13678_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pw8_13678/07_2024/7pw8_13678.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pw8_13678/07_2024/7pw8_13678.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pw8_13678/07_2024/7pw8_13678.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pw8_13678/07_2024/7pw8_13678_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pw8_13678/07_2024/7pw8_13678_neut.cif" } resolution = 2.82 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= 0.005 sd= 0.159 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 1 5.21 5 S 93 5.16 5 C 12179 2.51 5 N 3357 2.21 5 O 3318 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 450": "OE1" <-> "OE2" Residue "A PHE 639": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 862": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 864": "OD1" <-> "OD2" Residue "A TYR 998": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 999": "OE1" <-> "OE2" Residue "A PHE 1015": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1053": "OD1" <-> "OD2" Residue "A GLU 1082": "OE1" <-> "OE2" Residue "A GLU 1124": "OE1" <-> "OE2" Residue "A GLU 1127": "OE1" <-> "OE2" Residue "A GLU 1361": "OE1" <-> "OE2" Residue "A TYR 2152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2299": "OE1" <-> "OE2" Residue "A ASP 2308": "OD1" <-> "OD2" Residue "A TYR 3654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 134": "OD1" <-> "OD2" Residue "B GLU 305": "OE1" <-> "OE2" Residue "B PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 203": "OD1" <-> "OD2" Residue "C GLU 247": "OE1" <-> "OE2" Residue "C PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 280": "OD1" <-> "OD2" Residue "C TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 364": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 18960 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 9176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1295, 9176 Classifications: {'peptide': 1295} Incomplete info: {'truncation_to_alanine': 337} Link IDs: {'PTRANS': 35, 'TRANS': 1259} Chain breaks: 25 Unresolved non-hydrogen bonds: 926 Unresolved non-hydrogen angles: 1214 Unresolved non-hydrogen dihedrals: 672 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 2, 'ASN:plan1': 13, 'TYR:plan': 2, 'UNK:plan-1': 121, 'TRP:plan': 2, 'ASP:plan': 32, 'PHE:plan': 5, 'GLU:plan': 44, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 560 Chain: "A" Number of atoms: 1428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1428 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 98} Link IDs: {'PTRANS': 7, 'TRANS': 208} Chain breaks: 6 Unresolved non-hydrogen bonds: 279 Unresolved non-hydrogen angles: 371 Unresolved non-hydrogen dihedrals: 199 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 1, 'ASN:plan1': 1, 'TYR:plan': 1, 'UNK:plan-1': 42, 'TRP:plan': 1, 'ASP:plan': 6, 'GLU:plan': 7, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 159 Chain: "A" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 196 Classifications: {'peptide': 38} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain breaks: 1 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'TYR:plan': 1, 'UNK:plan-1': 16, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 66 Chain: "A" Number of atoms: 2920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 2920 Classifications: {'peptide': 394} Incomplete info: {'truncation_to_alanine': 73} Link IDs: {'PTRANS': 18, 'TRANS': 375} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 217 Unresolved non-hydrogen angles: 279 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 1, 'UNK:plan-1': 16, 'ASP:plan': 9, 'GLU:plan': 16, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 133 Chain: "B" Number of atoms: 2718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2718 Classifications: {'peptide': 376} Incomplete info: {'truncation_to_alanine': 102} Link IDs: {'PTRANS': 19, 'TRANS': 356} Chain breaks: 8 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 366 Unresolved non-hydrogen angles: 459 Unresolved non-hydrogen dihedrals: 305 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 4, 'TYR:plan': 3, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 13, 'PHE:plan': 3, 'GLU:plan': 15, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 249 Chain: "C" Number of atoms: 2423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2423 Classifications: {'peptide': 310} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 17, 'TRANS': 292} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 117 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 7, 'HIS:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 70 Chain: "A" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'ANP': 1, 'IHP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 10.99, per 1000 atoms: 0.58 Number of scatterers: 18960 At special positions: 0 Unit cell: (130.234, 123.424, 178.752, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 93 16.00 P 12 15.00 Mg 1 11.99 O 3318 8.00 N 3357 7.00 C 12179 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 Time building additional restraints: 7.11 Conformation dependent library (CDL) restraints added in 3.4 seconds 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5074 Finding SS restraints... Secondary structure from input PDB file: 140 helices and 5 sheets defined 75.1% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.62 Creating SS restraints... Processing helix chain 'A' and resid 147 through 156 removed outlier: 3.900A pdb=" N UNK A 154 " --> pdb=" O UNK A 150 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N UNK A 155 " --> pdb=" O UNK A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 175 removed outlier: 3.928A pdb=" N UNK A 172 " --> pdb=" O UNK A 168 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N UNK A 173 " --> pdb=" O UNK A 169 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N UNK A 175 " --> pdb=" O UNK A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 198 Processing helix chain 'A' and resid 199 through 201 No H-bonds generated for 'chain 'A' and resid 199 through 201' Processing helix chain 'A' and resid 208 through 219 Processing helix chain 'A' and resid 230 through 244 removed outlier: 3.558A pdb=" N UNK A 234 " --> pdb=" O UNK A 230 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N UNK A 244 " --> pdb=" O UNK A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 265 removed outlier: 4.076A pdb=" N UNK A 265 " --> pdb=" O UNK A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 283 Processing helix chain 'A' and resid 291 through 302 Processing helix chain 'A' and resid 313 through 322 removed outlier: 4.233A pdb=" N ASP A 317 " --> pdb=" O THR A 313 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N THR A 318 " --> pdb=" O ASN A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 347 removed outlier: 3.804A pdb=" N GLU A 347 " --> pdb=" O LEU A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 374 removed outlier: 3.778A pdb=" N GLY A 362 " --> pdb=" O THR A 358 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLN A 363 " --> pdb=" O THR A 359 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE A 364 " --> pdb=" O LEU A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 412 removed outlier: 4.059A pdb=" N ILE A 412 " --> pdb=" O VAL A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 444 removed outlier: 4.151A pdb=" N VAL A 432 " --> pdb=" O TYR A 428 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ASN A 444 " --> pdb=" O VAL A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 467 removed outlier: 4.354A pdb=" N LEU A 467 " --> pdb=" O LEU A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 487 removed outlier: 4.047A pdb=" N VAL A 478 " --> pdb=" O HIS A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 511 removed outlier: 3.681A pdb=" N SER A 499 " --> pdb=" O ASP A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 524 removed outlier: 4.036A pdb=" N VAL A 520 " --> pdb=" O PRO A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 533 removed outlier: 4.040A pdb=" N PHE A 532 " --> pdb=" O SER A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 536 No H-bonds generated for 'chain 'A' and resid 534 through 536' Processing helix chain 'A' and resid 538 through 553 removed outlier: 3.690A pdb=" N VAL A 542 " --> pdb=" O GLU A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 583 removed outlier: 4.069A pdb=" N THR A 563 " --> pdb=" O PRO A 559 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA A 564 " --> pdb=" O VAL A 560 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A 583 " --> pdb=" O LEU A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 598 removed outlier: 3.567A pdb=" N PHE A 597 " --> pdb=" O HIS A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 623 removed outlier: 3.693A pdb=" N ILE A 612 " --> pdb=" O LYS A 608 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N THR A 620 " --> pdb=" O SER A 616 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ILE A 621 " --> pdb=" O ALA A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 645 Processing helix chain 'A' and resid 646 through 651 Processing helix chain 'A' and resid 652 through 657 removed outlier: 3.743A pdb=" N HIS A 656 " --> pdb=" O ASP A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 674 removed outlier: 3.922A pdb=" N GLN A 661 " --> pdb=" O PHE A 657 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG A 674 " --> pdb=" O SER A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 675 through 679 Processing helix chain 'A' and resid 705 through 719 removed outlier: 3.863A pdb=" N ILE A 709 " --> pdb=" O LYS A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 742 Processing helix chain 'A' and resid 743 through 744 No H-bonds generated for 'chain 'A' and resid 743 through 744' Processing helix chain 'A' and resid 745 through 753 removed outlier: 3.734A pdb=" N TYR A 748 " --> pdb=" O SER A 745 " (cutoff:3.500A) Proline residue: A 750 - end of helix removed outlier: 3.786A pdb=" N SER A 753 " --> pdb=" O PRO A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 767 removed outlier: 3.570A pdb=" N HIS A 758 " --> pdb=" O LEU A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 786 Processing helix chain 'A' and resid 791 through 806 removed outlier: 3.693A pdb=" N ARG A 797 " --> pdb=" O ASP A 793 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASP A 800 " --> pdb=" O GLN A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 810 through 822 removed outlier: 3.682A pdb=" N ARG A 814 " --> pdb=" O GLY A 810 " (cutoff:3.500A) Processing helix chain 'A' and resid 825 through 830 Processing helix chain 'A' and resid 835 through 851 removed outlier: 3.531A pdb=" N GLU A 840 " --> pdb=" O THR A 836 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE A 841 " --> pdb=" O GLU A 837 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER A 842 " --> pdb=" O ILE A 838 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS A 851 " --> pdb=" O SER A 847 " (cutoff:3.500A) Processing helix chain 'A' and resid 858 through 871 Processing helix chain 'A' and resid 882 through 890 Processing helix chain 'A' and resid 902 through 906 Processing helix chain 'A' and resid 908 through 927 Processing helix chain 'A' and resid 935 through 956 removed outlier: 3.687A pdb=" N PHE A 940 " --> pdb=" O ALA A 936 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU A 955 " --> pdb=" O ALA A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 999 removed outlier: 3.847A pdb=" N HIS A 973 " --> pdb=" O ASN A 969 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLY A 974 " --> pdb=" O ASP A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 1009 through 1019 Processing helix chain 'A' and resid 1019 through 1041 removed outlier: 4.700A pdb=" N LEU A1032 " --> pdb=" O THR A1028 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N SER A1033 " --> pdb=" O ARG A1029 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG A1036 " --> pdb=" O LEU A1032 " (cutoff:3.500A) Processing helix chain 'A' and resid 1043 through 1058 removed outlier: 3.755A pdb=" N THR A1047 " --> pdb=" O GLN A1043 " (cutoff:3.500A) Processing helix chain 'A' and resid 1068 through 1083 removed outlier: 3.500A pdb=" N THR A1072 " --> pdb=" O GLU A1068 " (cutoff:3.500A) Processing helix chain 'A' and resid 1085 through 1097 removed outlier: 3.518A pdb=" N ILE A1089 " --> pdb=" O CYS A1085 " (cutoff:3.500A) Processing helix chain 'A' and resid 1106 through 1115 removed outlier: 3.554A pdb=" N GLU A1115 " --> pdb=" O ALA A1111 " (cutoff:3.500A) Processing helix chain 'A' and resid 1117 through 1134 removed outlier: 3.738A pdb=" N VAL A1123 " --> pdb=" O GLU A1119 " (cutoff:3.500A) Processing helix chain 'A' and resid 1143 through 1151 removed outlier: 3.954A pdb=" N LEU A1149 " --> pdb=" O SER A1145 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN A1151 " --> pdb=" O LEU A1147 " (cutoff:3.500A) Processing helix chain 'A' and resid 1179 through 1197 removed outlier: 3.667A pdb=" N ILE A1197 " --> pdb=" O CYS A1193 " (cutoff:3.500A) Processing helix chain 'A' and resid 1199 through 1216 Processing helix chain 'A' and resid 1227 through 1240 Processing helix chain 'A' and resid 1241 through 1250 removed outlier: 3.721A pdb=" N GLU A1250 " --> pdb=" O THR A1246 " (cutoff:3.500A) Processing helix chain 'A' and resid 1281 through 1305 removed outlier: 3.749A pdb=" N ASN A1305 " --> pdb=" O ALA A1301 " (cutoff:3.500A) Processing helix chain 'A' and resid 1317 through 1332 removed outlier: 3.614A pdb=" N VAL A1321 " --> pdb=" O THR A1317 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LYS A1322 " --> pdb=" O GLU A1318 " (cutoff:3.500A) Processing helix chain 'A' and resid 1332 through 1341 removed outlier: 3.764A pdb=" N THR A1339 " --> pdb=" O LEU A1335 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU A1340 " --> pdb=" O ARG A1336 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR A1341 " --> pdb=" O LEU A1337 " (cutoff:3.500A) Processing helix chain 'A' and resid 1347 through 1367 removed outlier: 3.514A pdb=" N THR A1351 " --> pdb=" O PRO A1347 " (cutoff:3.500A) Processing helix chain 'A' and resid 1370 through 1374 removed outlier: 3.629A pdb=" N LEU A1374 " --> pdb=" O GLU A1371 " (cutoff:3.500A) Processing helix chain 'A' and resid 1378 through 1383 removed outlier: 3.584A pdb=" N ARG A1383 " --> pdb=" O GLU A1380 " (cutoff:3.500A) Processing helix chain 'A' and resid 1390 through 1407 removed outlier: 3.697A pdb=" N TYR A1402 " --> pdb=" O ARG A1398 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLN A1403 " --> pdb=" O TYR A1399 " (cutoff:3.500A) Processing helix chain 'A' and resid 1408 through 1410 No H-bonds generated for 'chain 'A' and resid 1408 through 1410' Processing helix chain 'A' and resid 1417 through 1434 Processing helix chain 'A' and resid 1437 through 1450 Processing helix chain 'A' and resid 1458 through 1467 Processing helix chain 'A' and resid 1479 through 1495 Processing helix chain 'A' and resid 1496 through 1512 Processing helix chain 'A' and resid 1517 through 1535 removed outlier: 3.913A pdb=" N VAL A1521 " --> pdb=" O ALA A1517 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ALA A1522 " --> pdb=" O GLU A1518 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA A1534 " --> pdb=" O LYS A1530 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU A1535 " --> pdb=" O TRP A1531 " (cutoff:3.500A) Processing helix chain 'A' and resid 1535 through 1551 removed outlier: 5.135A pdb=" N GLY A1541 " --> pdb=" O LYS A1537 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N GLN A1542 " --> pdb=" O GLU A1538 " (cutoff:3.500A) Processing helix chain 'A' and resid 1559 through 1570 Processing helix chain 'A' and resid 1595 through 1612 removed outlier: 3.517A pdb=" N PHE A1599 " --> pdb=" O GLY A1595 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ILE A1600 " --> pdb=" O GLU A1596 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU A1601 " --> pdb=" O PRO A1597 " (cutoff:3.500A) Processing helix chain 'A' and resid 1615 through 1637 removed outlier: 3.850A pdb=" N TRP A1619 " --> pdb=" O VAL A1615 " (cutoff:3.500A) Processing helix chain 'A' and resid 1647 through 1656 No H-bonds generated for 'chain 'A' and resid 1647 through 1656' Processing helix chain 'A' and resid 1664 through 1674 No H-bonds generated for 'chain 'A' and resid 1664 through 1674' Processing helix chain 'A' and resid 1704 through 1716 No H-bonds generated for 'chain 'A' and resid 1704 through 1716' Processing helix chain 'A' and resid 1728 through 1741 No H-bonds generated for 'chain 'A' and resid 1728 through 1741' Processing helix chain 'A' and resid 1741 through 1757 No H-bonds generated for 'chain 'A' and resid 1741 through 1757' Processing helix chain 'A' and resid 1781 through 1799 No H-bonds generated for 'chain 'A' and resid 1781 through 1799' Processing helix chain 'A' and resid 1803 through 1814 No H-bonds generated for 'chain 'A' and resid 1803 through 1814' Processing helix chain 'A' and resid 1822 through 1829 No H-bonds generated for 'chain 'A' and resid 1822 through 1829' Processing helix chain 'A' and resid 1830 through 1832 No H-bonds generated for 'chain 'A' and resid 1830 through 1832' Processing helix chain 'A' and resid 1835 through 1850 No H-bonds generated for 'chain 'A' and resid 1835 through 1850' Processing helix chain 'A' and resid 1852 through 1855 No H-bonds generated for 'chain 'A' and resid 1852 through 1855' Processing helix chain 'A' and resid 1856 through 1865 No H-bonds generated for 'chain 'A' and resid 1856 through 1865' Processing helix chain 'A' and resid 1924 through 1939 No H-bonds generated for 'chain 'A' and resid 1924 through 1939' Processing helix chain 'A' and resid 1941 through 1958 No H-bonds generated for 'chain 'A' and resid 1941 through 1958' Processing helix chain 'A' and resid 1963 through 1978 No H-bonds generated for 'chain 'A' and resid 1963 through 1978' Processing helix chain 'A' and resid 2007 through 2020 No H-bonds generated for 'chain 'A' and resid 2007 through 2020' Processing helix chain 'A' and resid 2036 through 2045 No H-bonds generated for 'chain 'A' and resid 2036 through 2045' Processing helix chain 'A' and resid 2046 through 2055 No H-bonds generated for 'chain 'A' and resid 2046 through 2055' Processing helix chain 'A' and resid 2069 through 2083 No H-bonds generated for 'chain 'A' and resid 2069 through 2083' Processing helix chain 'A' and resid 2160 through 2176 No H-bonds generated for 'chain 'A' and resid 2160 through 2176' Processing helix chain 'A' and resid 2177 through 2178 No H-bonds generated for 'chain 'A' and resid 2177 through 2178' Processing helix chain 'A' and resid 2179 through 2183 No H-bonds generated for 'chain 'A' and resid 2179 through 2183' Processing helix chain 'A' and resid 2214 through 2232 No H-bonds generated for 'chain 'A' and resid 2214 through 2232' Processing helix chain 'A' and resid 2248 through 2263 No H-bonds generated for 'chain 'A' and resid 2248 through 2263' Processing helix chain 'A' and resid 2276 through 2291 No H-bonds generated for 'chain 'A' and resid 2276 through 2291' Processing helix chain 'A' and resid 2294 through 2304 No H-bonds generated for 'chain 'A' and resid 2294 through 2304' Processing helix chain 'A' and resid 2306 through 2332 No H-bonds generated for 'chain 'A' and resid 2306 through 2332' Processing helix chain 'A' and resid 2360 through 2364 No H-bonds generated for 'chain 'A' and resid 2360 through 2364' Processing helix chain 'A' and resid 2376 through 2382 No H-bonds generated for 'chain 'A' and resid 2376 through 2382' Processing helix chain 'A' and resid 2390 through 2406 No H-bonds generated for 'chain 'A' and resid 2390 through 2406' Processing helix chain 'A' and resid 2406 through 2419 No H-bonds generated for 'chain 'A' and resid 2406 through 2419' Processing helix chain 'A' and resid 3608 through 3621 No H-bonds generated for 'chain 'A' and resid 3608 through 3621' Processing helix chain 'A' and resid 3632 through 3646 No H-bonds generated for 'chain 'A' and resid 3632 through 3646' Processing helix chain 'A' and resid 3646 through 3652 No H-bonds generated for 'chain 'A' and resid 3646 through 3652' Processing helix chain 'A' and resid 3654 through 3658 No H-bonds generated for 'chain 'A' and resid 3654 through 3658' Processing helix chain 'B' and resid 7 through 12 removed outlier: 3.887A pdb=" N MET B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 43 removed outlier: 3.557A pdb=" N ARG B 43 " --> pdb=" O PRO B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 72 removed outlier: 3.525A pdb=" N SER B 66 " --> pdb=" O SER B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 172 removed outlier: 3.683A pdb=" N ARG B 164 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER B 171 " --> pdb=" O ARG B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 204 removed outlier: 3.878A pdb=" N HIS B 186 " --> pdb=" O HIS B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 235 removed outlier: 4.138A pdb=" N ARG B 225 " --> pdb=" O ILE B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 245 Processing helix chain 'B' and resid 251 through 258 removed outlier: 3.748A pdb=" N LYS B 255 " --> pdb=" O GLY B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 315 Processing helix chain 'B' and resid 346 through 359 Processing helix chain 'B' and resid 409 through 423 removed outlier: 4.373A pdb=" N HIS B 417 " --> pdb=" O PHE B 413 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N LEU B 420 " --> pdb=" O GLN B 416 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL B 421 " --> pdb=" O HIS B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 458 removed outlier: 3.672A pdb=" N ALA B 451 " --> pdb=" O LYS B 447 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LYS B 454 " --> pdb=" O SER B 450 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL B 458 " --> pdb=" O LYS B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 483 Processing helix chain 'B' and resid 489 through 509 Proline residue: B 505 - end of helix Processing helix chain 'B' and resid 524 through 539 Processing helix chain 'B' and resid 543 through 558 removed outlier: 3.847A pdb=" N TYR B 547 " --> pdb=" O ALA B 543 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 198 Processing helix chain 'C' and resid 216 through 226 Processing helix chain 'C' and resid 232 through 236 removed outlier: 3.561A pdb=" N TYR C 236 " --> pdb=" O GLN C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 248 removed outlier: 3.844A pdb=" N GLU C 247 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ARG C 248 " --> pdb=" O GLU C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 284 removed outlier: 3.560A pdb=" N ASN C 284 " --> pdb=" O ASP C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 315 removed outlier: 3.647A pdb=" N TYR C 299 " --> pdb=" O LEU C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 340 removed outlier: 3.600A pdb=" N VAL C 340 " --> pdb=" O THR C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 379 Processing helix chain 'C' and resid 380 through 395 Processing helix chain 'C' and resid 418 through 422 Processing helix chain 'C' and resid 453 through 457 Processing helix chain 'C' and resid 465 through 479 removed outlier: 3.682A pdb=" N SER C 479 " --> pdb=" O SER C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 491 through 508 removed outlier: 3.791A pdb=" N PHE C 496 " --> pdb=" O GLU C 492 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N HIS C 497 " --> pdb=" O LYS C 493 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 518 Processing sheet with id=AA1, first strand: chain 'A' and resid 2090 through 2091 WARNING: can't find one or more strands! previous: chain 'A' and resid 2090 through 2091 current: chain 'A' and resid 2127 through 2130 WARNING: can't find one or more strands! previous: chain 'A' and resid 2127 through 2130 current: chain 'A' and resid 2138 through 2144 WARNING: can't find one or more strands! previous: chain 'A' and resid 2138 through 2144 current: chain 'A' and resid 2121 through 2124 No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 2090 through 2091 WARNING: can't find one or more strands! previous: chain 'A' and resid 2090 through 2091 current: chain 'A' and resid 2127 through 2130 WARNING: can't find one or more strands! previous: chain 'A' and resid 2127 through 2130 current: chain 'A' and resid 2138 through 2144 WARNING: can't find one or more strands! previous: chain 'A' and resid 2138 through 2144 current: chain 'A' and resid 2149 through 2155 WARNING: can't find one or more strands! previous: chain 'A' and resid 2149 through 2155 current: chain 'A' and resid 2203 through 2206 WARNING: can't find one or more strands! previous: chain 'A' and resid 2203 through 2206 current: chain 'A' and resid 2195 through 2197 No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 2212 through 2213 WARNING: can't find one or more strands! previous: chain 'A' and resid 2212 through 2213 current: chain 'A' and resid 2341 through 2343 WARNING: can't find one or more strands! previous: chain 'A' and resid 2341 through 2343 current: chain 'A' and resid 2350 through 2352 No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 5 through 6 removed outlier: 3.503A pdb=" N VAL B 148 " --> pdb=" O SER B 143 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N GLY B 54 " --> pdb=" O LEU B 153 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LEU B 210 " --> pdb=" O LEU B 266 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N LEU B 268 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N LEU B 212 " --> pdb=" O LEU B 268 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N GLN B 270 " --> pdb=" O LEU B 212 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N HIS B 214 " --> pdb=" O GLN B 270 " (cutoff:3.500A) removed outlier: 8.769A pdb=" N TYR B 337 " --> pdb=" O LEU B 265 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N PHE B 267 " --> pdb=" O TYR B 337 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N VAL B 339 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N PHE B 269 " --> pdb=" O VAL B 339 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 181 through 184 removed outlier: 6.437A pdb=" N ILE C 256 " --> pdb=" O LEU C 183 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU C 205 " --> pdb=" O VAL C 266 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N LEU C 268 " --> pdb=" O LEU C 205 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL C 207 " --> pdb=" O LEU C 268 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N THR C 270 " --> pdb=" O VAL C 207 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N VAL C 209 " --> pdb=" O THR C 270 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL C 206 " --> pdb=" O VAL C 317 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N ILE C 319 " --> pdb=" O VAL C 206 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N GLY C 208 " --> pdb=" O ILE C 319 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N VAL C 321 " --> pdb=" O GLY C 208 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N LEU C 210 " --> pdb=" O VAL C 321 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N PHE C 429 " --> pdb=" O LEU C 370 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N ASN C 372 " --> pdb=" O PHE C 429 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N VAL C 431 " --> pdb=" O ASN C 372 " (cutoff:3.500A) 915 hydrogen bonds defined for protein. 2667 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: 7.02 Time building geometry restraints manager: 7.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.06 - 1.21: 15 1.21 - 1.36: 6186 1.36 - 1.51: 5220 1.51 - 1.66: 7742 1.66 - 1.81: 142 Bond restraints: 19305 Sorted by residual: bond pdb=" C ILE A 838 " pdb=" O ILE A 838 " ideal model delta sigma weight residual 1.237 1.068 0.169 1.19e-02 7.06e+03 2.03e+02 bond pdb=" C LEU A 830 " pdb=" O LEU A 830 " ideal model delta sigma weight residual 1.235 1.058 0.177 1.32e-02 5.74e+03 1.80e+02 bond pdb=" C HIS A 835 " pdb=" O HIS A 835 " ideal model delta sigma weight residual 1.234 1.082 0.152 1.19e-02 7.06e+03 1.63e+02 bond pdb=" CE1 HIS A 835 " pdb=" NE2 HIS A 835 " ideal model delta sigma weight residual 1.321 1.194 0.127 1.00e-02 1.00e+04 1.62e+02 bond pdb=" C GLN A 839 " pdb=" O GLN A 839 " ideal model delta sigma weight residual 1.236 1.078 0.159 1.26e-02 6.30e+03 1.59e+02 ... (remaining 19300 not shown) Histogram of bond angle deviations from ideal: 99.55 - 107.58: 747 107.58 - 115.60: 11919 115.60 - 123.63: 13161 123.63 - 131.65: 494 131.65 - 139.68: 46 Bond angle restraints: 26367 Sorted by residual: angle pdb=" CA HIS A 835 " pdb=" CB HIS A 835 " pdb=" CG HIS A 835 " ideal model delta sigma weight residual 113.80 121.00 -7.20 1.00e+00 1.00e+00 5.18e+01 angle pdb=" CA ASN A 833 " pdb=" CB ASN A 833 " pdb=" CG ASN A 833 " ideal model delta sigma weight residual 112.60 106.08 6.52 1.00e+00 1.00e+00 4.25e+01 angle pdb=" C ASN A 834 " pdb=" CA ASN A 834 " pdb=" CB ASN A 834 " ideal model delta sigma weight residual 109.51 120.49 -10.98 1.71e+00 3.42e-01 4.12e+01 angle pdb=" N THR C 326 " pdb=" CA THR C 326 " pdb=" C THR C 326 " ideal model delta sigma weight residual 110.91 118.36 -7.45 1.17e+00 7.31e-01 4.05e+01 angle pdb=" C GLN A 839 " pdb=" N GLU A 840 " pdb=" CA GLU A 840 " ideal model delta sigma weight residual 120.28 128.53 -8.25 1.34e+00 5.57e-01 3.79e+01 ... (remaining 26362 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.11: 11298 34.11 - 68.22: 179 68.22 - 102.33: 31 102.33 - 136.44: 7 136.44 - 170.55: 3 Dihedral angle restraints: 11518 sinusoidal: 3797 harmonic: 7721 Sorted by residual: dihedral pdb=" C ASN A 834 " pdb=" N ASN A 834 " pdb=" CA ASN A 834 " pdb=" CB ASN A 834 " ideal model delta harmonic sigma weight residual -122.60 -145.53 22.93 0 2.50e+00 1.60e-01 8.41e+01 dihedral pdb=" N ASN A 834 " pdb=" C ASN A 834 " pdb=" CA ASN A 834 " pdb=" CB ASN A 834 " ideal model delta harmonic sigma weight residual 122.80 144.05 -21.25 0 2.50e+00 1.60e-01 7.23e+01 dihedral pdb=" N ASN A 832 " pdb=" C ASN A 832 " pdb=" CA ASN A 832 " pdb=" CB ASN A 832 " ideal model delta harmonic sigma weight residual 122.80 139.94 -17.14 0 2.50e+00 1.60e-01 4.70e+01 ... (remaining 11515 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.006: 3244 1.006 - 2.012: 0 2.012 - 3.019: 0 3.019 - 4.025: 0 4.025 - 5.031: 3 Chirality restraints: 3247 Sorted by residual: chirality pdb=" C2 IHP A3701 " pdb=" C1 IHP A3701 " pdb=" C3 IHP A3701 " pdb=" O12 IHP A3701 " both_signs ideal model delta sigma weight residual False -2.52 2.51 -5.03 2.00e-01 2.50e+01 6.33e+02 chirality pdb=" C4 IHP A3701 " pdb=" C3 IHP A3701 " pdb=" C5 IHP A3701 " pdb=" O14 IHP A3701 " both_signs ideal model delta sigma weight residual False 2.48 -2.36 4.84 2.00e-01 2.50e+01 5.86e+02 chirality pdb=" C1 IHP A3701 " pdb=" C2 IHP A3701 " pdb=" C6 IHP A3701 " pdb=" O11 IHP A3701 " both_signs ideal model delta sigma weight residual False 2.32 -2.49 4.80 2.00e-01 2.50e+01 5.77e+02 ... (remaining 3244 not shown) Planarity restraints: 3274 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 836 " 0.022 2.00e-02 2.50e+03 4.56e-02 2.08e+01 pdb=" C THR A 836 " -0.079 2.00e-02 2.50e+03 pdb=" O THR A 836 " 0.030 2.00e-02 2.50e+03 pdb=" N GLU A 837 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 839 " 0.010 2.00e-02 2.50e+03 2.09e-02 4.35e+00 pdb=" C GLN A 839 " -0.036 2.00e-02 2.50e+03 pdb=" O GLN A 839 " 0.014 2.00e-02 2.50e+03 pdb=" N GLU A 840 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 833 " -0.009 2.00e-02 2.50e+03 1.83e-02 3.36e+00 pdb=" CG ASN A 833 " 0.032 2.00e-02 2.50e+03 pdb=" OD1 ASN A 833 " -0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN A 833 " -0.011 2.00e-02 2.50e+03 ... (remaining 3271 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 122 2.65 - 3.21: 17274 3.21 - 3.77: 28565 3.77 - 4.34: 38033 4.34 - 4.90: 63323 Nonbonded interactions: 147317 Sorted by model distance: nonbonded pdb=" OG SER C 218 " pdb="MG MG C 602 " model vdw 2.086 2.170 nonbonded pdb=" OG1 THR C 253 " pdb="MG MG C 602 " model vdw 2.128 2.170 nonbonded pdb=" O SER A 616 " pdb=" OG1 THR A 619 " model vdw 2.227 2.440 nonbonded pdb=" OH TYR A2193 " pdb=" O ILE A2353 " model vdw 2.233 2.440 nonbonded pdb=" O1G ANP A3702 " pdb=" O2B ANP A3702 " model vdw 2.239 3.040 ... (remaining 147312 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.960 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: 0.790 Check model and map are aligned: 0.150 Set scattering table: 0.170 Process input model: 52.890 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 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 0.177 19305 Z= 0.318 Angle : 0.749 16.767 26367 Z= 0.433 Chirality : 0.156 5.031 3247 Planarity : 0.004 0.046 3274 Dihedral : 14.194 170.555 6444 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.18 % Allowed : 0.24 % Favored : 99.59 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.18), residues: 2354 helix: 1.87 (0.14), residues: 1493 sheet: 0.19 (0.43), residues: 129 loop : -1.38 (0.23), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A2221 HIS 0.012 0.001 HIS A 706 PHE 0.018 0.001 PHE A 817 TYR 0.015 0.001 TYR A1185 ARG 0.005 0.000 ARG A1820 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 288 time to evaluate : 1.902 Fit side-chains REVERT: A 1547 TYR cc_start: 0.8444 (t80) cc_final: 0.8219 (t80) REVERT: A 2122 HIS cc_start: 0.7356 (t70) cc_final: 0.7098 (t70) REVERT: A 2326 MET cc_start: 0.8635 (mmt) cc_final: 0.8357 (mmt) REVERT: A 3631 MET cc_start: 0.8140 (mtm) cc_final: 0.7895 (mtm) REVERT: C 219 MET cc_start: 0.8536 (ttp) cc_final: 0.8265 (ttm) REVERT: C 221 MET cc_start: 0.8823 (mmm) cc_final: 0.8532 (mmm) outliers start: 3 outliers final: 0 residues processed: 291 average time/residue: 1.3534 time to fit residues: 440.6745 Evaluate side-chains 195 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 195 time to evaluate : 2.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 217 optimal weight: 9.9990 chunk 194 optimal weight: 8.9990 chunk 108 optimal weight: 0.7980 chunk 66 optimal weight: 0.0870 chunk 131 optimal weight: 30.0000 chunk 104 optimal weight: 0.9990 chunk 201 optimal weight: 3.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.9980 chunk 149 optimal weight: 20.0000 chunk 233 optimal weight: 0.0170 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 600 HIS A 833 ASN A 881 ASN A1276 ASN A1344 GLN B 159 ASN ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.1230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 19305 Z= 0.134 Angle : 0.477 11.034 26367 Z= 0.233 Chirality : 0.037 0.529 3247 Planarity : 0.004 0.040 3274 Dihedral : 9.815 120.925 2856 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.41 % Allowed : 8.53 % Favored : 90.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.18), residues: 2354 helix: 2.07 (0.14), residues: 1525 sheet: 0.62 (0.45), residues: 129 loop : -1.33 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1393 HIS 0.006 0.001 HIS A 706 PHE 0.011 0.001 PHE A 868 TYR 0.020 0.001 TYR A 998 ARG 0.003 0.000 ARG A 930 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 214 time to evaluate : 2.091 Fit side-chains REVERT: A 1389 ASP cc_start: 0.6668 (OUTLIER) cc_final: 0.6245 (p0) REVERT: A 2122 HIS cc_start: 0.7385 (t70) cc_final: 0.7119 (t70) REVERT: A 2326 MET cc_start: 0.8693 (mmt) cc_final: 0.8431 (mmt) REVERT: A 3607 SER cc_start: 0.6736 (p) cc_final: 0.6320 (t) REVERT: A 3631 MET cc_start: 0.8295 (mtm) cc_final: 0.7960 (mtm) REVERT: C 221 MET cc_start: 0.8768 (mmm) cc_final: 0.8543 (mmm) REVERT: C 461 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.8184 (ptt180) outliers start: 24 outliers final: 9 residues processed: 225 average time/residue: 1.2163 time to fit residues: 310.5411 Evaluate side-chains 202 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 191 time to evaluate : 1.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 1389 ASP Chi-restraints excluded: chain A residue 1519 TYR Chi-restraints excluded: chain A residue 1589 THR Chi-restraints excluded: chain A residue 1592 ILE Chi-restraints excluded: chain A residue 3645 THR Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 461 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 129 optimal weight: 20.0000 chunk 72 optimal weight: 0.8980 chunk 194 optimal weight: 6.9990 chunk 158 optimal weight: 7.9990 chunk 64 optimal weight: 5.9990 chunk 233 optimal weight: 2.9990 chunk 252 optimal weight: 1.9990 chunk 208 optimal weight: 0.9980 chunk 231 optimal weight: 0.0670 chunk 79 optimal weight: 0.4980 chunk 187 optimal weight: 2.9990 overall best weight: 0.8920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 881 ASN B 159 ASN B 208 HIS ** B 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 GLN ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 19305 Z= 0.148 Angle : 0.463 10.585 26367 Z= 0.230 Chirality : 0.036 0.327 3247 Planarity : 0.004 0.040 3274 Dihedral : 9.040 116.898 2856 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.18 % Allowed : 9.71 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.18), residues: 2354 helix: 2.09 (0.14), residues: 1533 sheet: 0.77 (0.45), residues: 129 loop : -1.31 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1393 HIS 0.007 0.001 HIS A 706 PHE 0.011 0.001 PHE A 609 TYR 0.020 0.001 TYR A 998 ARG 0.003 0.000 ARG A 930 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 192 time to evaluate : 2.076 Fit side-chains REVERT: A 719 LYS cc_start: 0.8456 (OUTLIER) cc_final: 0.8135 (mtpt) REVERT: A 786 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7727 (mt) REVERT: A 1078 GLU cc_start: 0.7983 (tp30) cc_final: 0.7689 (tp30) REVERT: A 1389 ASP cc_start: 0.6941 (OUTLIER) cc_final: 0.6540 (p0) REVERT: A 1829 ARG cc_start: 0.7635 (OUTLIER) cc_final: 0.7042 (mpt180) REVERT: A 2122 HIS cc_start: 0.7410 (t70) cc_final: 0.7143 (t70) REVERT: C 221 MET cc_start: 0.8794 (mmm) cc_final: 0.8513 (mmm) REVERT: C 247 GLU cc_start: 0.7370 (OUTLIER) cc_final: 0.7105 (mt-10) REVERT: C 294 ASN cc_start: 0.7076 (OUTLIER) cc_final: 0.6874 (m-40) REVERT: C 383 LYS cc_start: 0.8399 (OUTLIER) cc_final: 0.8142 (tttt) REVERT: C 461 ARG cc_start: 0.8680 (OUTLIER) cc_final: 0.8329 (ptt180) outliers start: 37 outliers final: 12 residues processed: 214 average time/residue: 1.3079 time to fit residues: 317.4747 Evaluate side-chains 200 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 180 time to evaluate : 1.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 719 LYS Chi-restraints excluded: chain A residue 725 GLN Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 834 ASN Chi-restraints excluded: chain A residue 900 THR Chi-restraints excluded: chain A residue 1317 THR Chi-restraints excluded: chain A residue 1352 LEU Chi-restraints excluded: chain A residue 1389 ASP Chi-restraints excluded: chain A residue 1589 THR Chi-restraints excluded: chain A residue 1829 ARG Chi-restraints excluded: chain A residue 3625 VAL Chi-restraints excluded: chain A residue 3645 THR Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain C residue 247 GLU Chi-restraints excluded: chain C residue 294 ASN Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 383 LYS Chi-restraints excluded: chain C residue 461 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 231 optimal weight: 0.9990 chunk 175 optimal weight: 0.0980 chunk 121 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 156 optimal weight: 6.9990 chunk 234 optimal weight: 0.0870 chunk 248 optimal weight: 5.9990 chunk 122 optimal weight: 1.9990 chunk 222 optimal weight: 8.9990 chunk 66 optimal weight: 4.9990 overall best weight: 1.0364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 881 ASN A1533 GLN ** B 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 19305 Z= 0.158 Angle : 0.467 10.215 26367 Z= 0.231 Chirality : 0.037 0.368 3247 Planarity : 0.004 0.040 3274 Dihedral : 8.854 117.014 2856 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.59 % Allowed : 10.59 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.18), residues: 2354 helix: 2.05 (0.14), residues: 1536 sheet: 0.89 (0.45), residues: 129 loop : -1.29 (0.23), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A3657 HIS 0.008 0.001 HIS A 706 PHE 0.010 0.001 PHE A 609 TYR 0.018 0.001 TYR A 998 ARG 0.003 0.000 ARG C 482 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 189 time to evaluate : 2.081 Fit side-chains REVERT: A 558 ILE cc_start: 0.7937 (OUTLIER) cc_final: 0.7710 (mp) REVERT: A 719 LYS cc_start: 0.8486 (OUTLIER) cc_final: 0.8182 (mtpt) REVERT: A 1078 GLU cc_start: 0.8054 (tp30) cc_final: 0.7749 (tp30) REVERT: A 1389 ASP cc_start: 0.7103 (OUTLIER) cc_final: 0.6636 (p0) REVERT: A 2122 HIS cc_start: 0.7372 (t70) cc_final: 0.7082 (t70) REVERT: A 2405 ARG cc_start: 0.8162 (ttp-110) cc_final: 0.7961 (ttm170) REVERT: C 171 LEU cc_start: 0.6518 (OUTLIER) cc_final: 0.6113 (pp) REVERT: C 221 MET cc_start: 0.8746 (mmm) cc_final: 0.8420 (mmm) REVERT: C 247 GLU cc_start: 0.7338 (mt-10) cc_final: 0.7071 (mt-10) REVERT: C 335 GLN cc_start: 0.8282 (OUTLIER) cc_final: 0.7453 (mt0) REVERT: C 383 LYS cc_start: 0.8380 (OUTLIER) cc_final: 0.8168 (tttt) REVERT: C 461 ARG cc_start: 0.8691 (OUTLIER) cc_final: 0.8347 (ptt180) outliers start: 44 outliers final: 16 residues processed: 219 average time/residue: 1.3153 time to fit residues: 325.2031 Evaluate side-chains 203 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 180 time to evaluate : 2.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 558 ILE Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 719 LYS Chi-restraints excluded: chain A residue 834 ASN Chi-restraints excluded: chain A residue 900 THR Chi-restraints excluded: chain A residue 1047 THR Chi-restraints excluded: chain A residue 1317 THR Chi-restraints excluded: chain A residue 1352 LEU Chi-restraints excluded: chain A residue 1389 ASP Chi-restraints excluded: chain A residue 1439 SER Chi-restraints excluded: chain A residue 1589 THR Chi-restraints excluded: chain A residue 1803 LEU Chi-restraints excluded: chain A residue 3645 THR Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 335 GLN Chi-restraints excluded: chain C residue 383 LYS Chi-restraints excluded: chain C residue 461 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 206 optimal weight: 5.9990 chunk 141 optimal weight: 0.5980 chunk 3 optimal weight: 30.0000 chunk 184 optimal weight: 3.9990 chunk 102 optimal weight: 0.7980 chunk 211 optimal weight: 3.9990 chunk 171 optimal weight: 2.9990 chunk 0 optimal weight: 40.0000 chunk 126 optimal weight: 2.9990 chunk 222 optimal weight: 0.0470 chunk 62 optimal weight: 4.9990 overall best weight: 1.4882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 600 HIS A 881 ASN A1204 GLN A1533 GLN ** B 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19305 Z= 0.199 Angle : 0.500 10.153 26367 Z= 0.249 Chirality : 0.038 0.363 3247 Planarity : 0.004 0.043 3274 Dihedral : 8.900 120.847 2856 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.65 % Allowed : 11.41 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.18), residues: 2354 helix: 1.93 (0.13), residues: 1534 sheet: 0.88 (0.45), residues: 129 loop : -1.33 (0.23), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A3657 HIS 0.009 0.001 HIS A 706 PHE 0.012 0.001 PHE A 857 TYR 0.017 0.001 TYR A 998 ARG 0.004 0.000 ARG C 375 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 189 time to evaluate : 2.067 Fit side-chains REVERT: A 558 ILE cc_start: 0.8004 (OUTLIER) cc_final: 0.7762 (mp) REVERT: A 719 LYS cc_start: 0.8519 (OUTLIER) cc_final: 0.8209 (mtpt) REVERT: A 1078 GLU cc_start: 0.8102 (tp30) cc_final: 0.7779 (tp30) REVERT: A 2122 HIS cc_start: 0.7365 (t70) cc_final: 0.7078 (t70) REVERT: A 2405 ARG cc_start: 0.8154 (ttp-110) cc_final: 0.7938 (ttm170) REVERT: C 171 LEU cc_start: 0.6519 (OUTLIER) cc_final: 0.6061 (pp) REVERT: C 221 MET cc_start: 0.8761 (mmm) cc_final: 0.8539 (mmm) REVERT: C 247 GLU cc_start: 0.7371 (mt-10) cc_final: 0.7097 (mt-10) REVERT: C 335 GLN cc_start: 0.8417 (OUTLIER) cc_final: 0.7461 (mt0) REVERT: C 383 LYS cc_start: 0.8439 (OUTLIER) cc_final: 0.8197 (tttt) REVERT: C 461 ARG cc_start: 0.8745 (OUTLIER) cc_final: 0.8418 (ptt180) outliers start: 45 outliers final: 24 residues processed: 221 average time/residue: 1.3679 time to fit residues: 339.2399 Evaluate side-chains 212 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 182 time to evaluate : 2.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 558 ILE Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 719 LYS Chi-restraints excluded: chain A residue 725 GLN Chi-restraints excluded: chain A residue 834 ASN Chi-restraints excluded: chain A residue 900 THR Chi-restraints excluded: chain A residue 1047 THR Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1317 THR Chi-restraints excluded: chain A residue 1352 LEU Chi-restraints excluded: chain A residue 1439 SER Chi-restraints excluded: chain A residue 1589 THR Chi-restraints excluded: chain A residue 1803 LEU Chi-restraints excluded: chain A residue 2175 THR Chi-restraints excluded: chain A residue 2202 SER Chi-restraints excluded: chain A residue 3607 SER Chi-restraints excluded: chain A residue 3625 VAL Chi-restraints excluded: chain A residue 3645 THR Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 335 GLN Chi-restraints excluded: chain C residue 383 LYS Chi-restraints excluded: chain C residue 461 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 83 optimal weight: 6.9990 chunk 223 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 145 optimal weight: 0.2980 chunk 61 optimal weight: 2.9990 chunk 248 optimal weight: 0.1980 chunk 206 optimal weight: 5.9990 chunk 115 optimal weight: 0.9990 chunk 20 optimal weight: 0.3980 chunk 82 optimal weight: 0.6980 chunk 130 optimal weight: 30.0000 overall best weight: 0.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 881 ASN A1204 GLN A1533 GLN ** B 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 19305 Z= 0.116 Angle : 0.427 8.512 26367 Z= 0.211 Chirality : 0.035 0.291 3247 Planarity : 0.003 0.041 3274 Dihedral : 8.422 115.364 2856 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.24 % Allowed : 12.18 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.18), residues: 2354 helix: 2.15 (0.14), residues: 1538 sheet: 1.00 (0.45), residues: 129 loop : -1.28 (0.23), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A3657 HIS 0.004 0.000 HIS A 706 PHE 0.009 0.001 PHE B 188 TYR 0.016 0.001 TYR A 998 ARG 0.004 0.000 ARG A 930 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 184 time to evaluate : 2.095 Fit side-chains REVERT: A 558 ILE cc_start: 0.7931 (OUTLIER) cc_final: 0.7696 (mp) REVERT: A 719 LYS cc_start: 0.8429 (OUTLIER) cc_final: 0.8144 (mtpt) REVERT: A 1078 GLU cc_start: 0.8093 (tp30) cc_final: 0.7789 (tp30) REVERT: A 1389 ASP cc_start: 0.7042 (OUTLIER) cc_final: 0.6698 (p0) REVERT: A 2122 HIS cc_start: 0.7329 (t70) cc_final: 0.7022 (t70) REVERT: A 3623 ARG cc_start: 0.8085 (OUTLIER) cc_final: 0.7859 (mtt-85) REVERT: C 171 LEU cc_start: 0.6435 (OUTLIER) cc_final: 0.6096 (pp) REVERT: C 221 MET cc_start: 0.8733 (mmm) cc_final: 0.8436 (mmm) REVERT: C 247 GLU cc_start: 0.7286 (mt-10) cc_final: 0.7022 (mt-10) REVERT: C 383 LYS cc_start: 0.8287 (OUTLIER) cc_final: 0.8063 (tttt) REVERT: C 461 ARG cc_start: 0.8608 (OUTLIER) cc_final: 0.8275 (ptt180) outliers start: 38 outliers final: 17 residues processed: 207 average time/residue: 1.3142 time to fit residues: 307.1410 Evaluate side-chains 200 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 176 time to evaluate : 1.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 558 ILE Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 719 LYS Chi-restraints excluded: chain A residue 725 GLN Chi-restraints excluded: chain A residue 834 ASN Chi-restraints excluded: chain A residue 900 THR Chi-restraints excluded: chain A residue 941 GLN Chi-restraints excluded: chain A residue 1047 THR Chi-restraints excluded: chain A residue 1352 LEU Chi-restraints excluded: chain A residue 1389 ASP Chi-restraints excluded: chain A residue 1589 THR Chi-restraints excluded: chain A residue 1803 LEU Chi-restraints excluded: chain A residue 2175 THR Chi-restraints excluded: chain A residue 2202 SER Chi-restraints excluded: chain A residue 3623 ARG Chi-restraints excluded: chain A residue 3625 VAL Chi-restraints excluded: chain A residue 3645 THR Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 383 LYS Chi-restraints excluded: chain C residue 420 ASP Chi-restraints excluded: chain C residue 461 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 239 optimal weight: 0.9990 chunk 28 optimal weight: 7.9990 chunk 141 optimal weight: 3.9990 chunk 181 optimal weight: 2.9990 chunk 140 optimal weight: 0.0570 chunk 209 optimal weight: 2.9990 chunk 138 optimal weight: 6.9990 chunk 247 optimal weight: 3.9990 chunk 155 optimal weight: 0.0870 chunk 151 optimal weight: 9.9990 chunk 114 optimal weight: 2.9990 overall best weight: 1.4282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 881 ASN A1533 GLN ** B 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19305 Z= 0.192 Angle : 0.485 8.451 26367 Z= 0.241 Chirality : 0.037 0.201 3247 Planarity : 0.004 0.044 3274 Dihedral : 8.579 118.978 2856 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.35 % Allowed : 12.35 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.18), residues: 2354 helix: 2.00 (0.13), residues: 1538 sheet: 0.97 (0.44), residues: 129 loop : -1.33 (0.23), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A3657 HIS 0.008 0.001 HIS A 706 PHE 0.011 0.001 PHE A 857 TYR 0.017 0.001 TYR A 998 ARG 0.004 0.000 ARG C 375 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 183 time to evaluate : 2.224 Fit side-chains REVERT: A 558 ILE cc_start: 0.7989 (OUTLIER) cc_final: 0.7761 (mp) REVERT: A 719 LYS cc_start: 0.8513 (OUTLIER) cc_final: 0.8210 (mtpt) REVERT: A 1078 GLU cc_start: 0.8122 (tp30) cc_final: 0.7792 (tp30) REVERT: A 1389 ASP cc_start: 0.7400 (OUTLIER) cc_final: 0.7054 (p0) REVERT: A 2122 HIS cc_start: 0.7349 (t70) cc_final: 0.7017 (t70) REVERT: B 225 ARG cc_start: 0.8105 (OUTLIER) cc_final: 0.7269 (ttt180) REVERT: C 171 LEU cc_start: 0.6583 (OUTLIER) cc_final: 0.6175 (pp) REVERT: C 221 MET cc_start: 0.8747 (mmm) cc_final: 0.8524 (mmm) REVERT: C 247 GLU cc_start: 0.7358 (mt-10) cc_final: 0.7095 (mt-10) REVERT: C 383 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.8197 (tttt) REVERT: C 461 ARG cc_start: 0.8733 (OUTLIER) cc_final: 0.8407 (ptt180) outliers start: 40 outliers final: 20 residues processed: 211 average time/residue: 1.3896 time to fit residues: 330.0286 Evaluate side-chains 204 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 177 time to evaluate : 1.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 558 ILE Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 719 LYS Chi-restraints excluded: chain A residue 725 GLN Chi-restraints excluded: chain A residue 834 ASN Chi-restraints excluded: chain A residue 900 THR Chi-restraints excluded: chain A residue 941 GLN Chi-restraints excluded: chain A residue 1047 THR Chi-restraints excluded: chain A residue 1352 LEU Chi-restraints excluded: chain A residue 1389 ASP Chi-restraints excluded: chain A residue 1439 SER Chi-restraints excluded: chain A residue 1589 THR Chi-restraints excluded: chain A residue 1803 LEU Chi-restraints excluded: chain A residue 2175 THR Chi-restraints excluded: chain A residue 2202 SER Chi-restraints excluded: chain A residue 3607 SER Chi-restraints excluded: chain A residue 3625 VAL Chi-restraints excluded: chain A residue 3645 THR Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 225 ARG Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 383 LYS Chi-restraints excluded: chain C residue 420 ASP Chi-restraints excluded: chain C residue 461 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 153 optimal weight: 6.9990 chunk 98 optimal weight: 0.7980 chunk 147 optimal weight: 0.4980 chunk 74 optimal weight: 0.0060 chunk 48 optimal weight: 0.8980 chunk 47 optimal weight: 0.6980 chunk 157 optimal weight: 2.9990 chunk 168 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 23 optimal weight: 0.0770 chunk 194 optimal weight: 7.9990 overall best weight: 0.4154 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 881 ASN A1533 GLN ** B 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 19305 Z= 0.109 Angle : 0.417 7.442 26367 Z= 0.207 Chirality : 0.035 0.172 3247 Planarity : 0.003 0.041 3274 Dihedral : 8.160 112.928 2856 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.59 % Allowed : 13.29 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.18), residues: 2354 helix: 2.22 (0.14), residues: 1541 sheet: 1.07 (0.44), residues: 129 loop : -1.19 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A3657 HIS 0.004 0.000 HIS A2278 PHE 0.009 0.001 PHE B 188 TYR 0.016 0.001 TYR A 998 ARG 0.003 0.000 ARG C 375 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 189 time to evaluate : 2.263 Fit side-chains REVERT: A 558 ILE cc_start: 0.7920 (OUTLIER) cc_final: 0.7690 (mp) REVERT: A 1078 GLU cc_start: 0.8087 (tp30) cc_final: 0.7786 (tp30) REVERT: A 1389 ASP cc_start: 0.6991 (OUTLIER) cc_final: 0.6680 (p0) REVERT: A 2122 HIS cc_start: 0.7290 (t70) cc_final: 0.6969 (t70) REVERT: C 171 LEU cc_start: 0.6482 (OUTLIER) cc_final: 0.6188 (pp) REVERT: C 221 MET cc_start: 0.8722 (mmm) cc_final: 0.8411 (mmm) REVERT: C 247 GLU cc_start: 0.7231 (mt-10) cc_final: 0.6985 (mt-10) REVERT: C 383 LYS cc_start: 0.8274 (OUTLIER) cc_final: 0.8045 (tttt) REVERT: C 461 ARG cc_start: 0.8588 (OUTLIER) cc_final: 0.8249 (ptt180) outliers start: 27 outliers final: 15 residues processed: 206 average time/residue: 1.3434 time to fit residues: 311.5982 Evaluate side-chains 204 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 184 time to evaluate : 2.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 558 ILE Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 725 GLN Chi-restraints excluded: chain A residue 834 ASN Chi-restraints excluded: chain A residue 900 THR Chi-restraints excluded: chain A residue 941 GLN Chi-restraints excluded: chain A residue 1352 LEU Chi-restraints excluded: chain A residue 1389 ASP Chi-restraints excluded: chain A residue 1589 THR Chi-restraints excluded: chain A residue 1592 ILE Chi-restraints excluded: chain A residue 1803 LEU Chi-restraints excluded: chain A residue 2164 GLU Chi-restraints excluded: chain A residue 2175 THR Chi-restraints excluded: chain A residue 2202 SER Chi-restraints excluded: chain A residue 3625 VAL Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 383 LYS Chi-restraints excluded: chain C residue 461 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 225 optimal weight: 7.9990 chunk 237 optimal weight: 1.9990 chunk 216 optimal weight: 0.7980 chunk 230 optimal weight: 3.9990 chunk 138 optimal weight: 0.7980 chunk 100 optimal weight: 8.9990 chunk 181 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 208 optimal weight: 1.9990 chunk 218 optimal weight: 0.7980 chunk 151 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 881 ASN A1533 GLN B 159 ASN ** B 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 19305 Z= 0.153 Angle : 0.451 8.877 26367 Z= 0.225 Chirality : 0.036 0.200 3247 Planarity : 0.004 0.043 3274 Dihedral : 8.048 114.288 2856 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.65 % Allowed : 13.35 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.18), residues: 2354 helix: 2.15 (0.14), residues: 1537 sheet: 1.14 (0.45), residues: 127 loop : -1.15 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A3657 HIS 0.006 0.001 HIS A 706 PHE 0.010 0.001 PHE A 817 TYR 0.018 0.001 TYR A 998 ARG 0.003 0.000 ARG C 375 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 187 time to evaluate : 2.246 Fit side-chains REVERT: A 1078 GLU cc_start: 0.8122 (tp30) cc_final: 0.7802 (tp30) REVERT: A 1389 ASP cc_start: 0.7345 (OUTLIER) cc_final: 0.7028 (p0) REVERT: A 2122 HIS cc_start: 0.7309 (t70) cc_final: 0.6974 (t70) REVERT: C 171 LEU cc_start: 0.6555 (OUTLIER) cc_final: 0.6232 (pp) REVERT: C 247 GLU cc_start: 0.7273 (mt-10) cc_final: 0.7021 (mt-10) REVERT: C 383 LYS cc_start: 0.8402 (OUTLIER) cc_final: 0.8154 (tttt) REVERT: C 461 ARG cc_start: 0.8698 (OUTLIER) cc_final: 0.8374 (ptt180) outliers start: 28 outliers final: 17 residues processed: 204 average time/residue: 1.3847 time to fit residues: 317.3278 Evaluate side-chains 204 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 183 time to evaluate : 2.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 725 GLN Chi-restraints excluded: chain A residue 834 ASN Chi-restraints excluded: chain A residue 900 THR Chi-restraints excluded: chain A residue 941 GLN Chi-restraints excluded: chain A residue 1047 THR Chi-restraints excluded: chain A residue 1352 LEU Chi-restraints excluded: chain A residue 1389 ASP Chi-restraints excluded: chain A residue 1439 SER Chi-restraints excluded: chain A residue 1589 THR Chi-restraints excluded: chain A residue 1592 ILE Chi-restraints excluded: chain A residue 1803 LEU Chi-restraints excluded: chain A residue 2175 THR Chi-restraints excluded: chain A residue 2202 SER Chi-restraints excluded: chain A residue 3607 SER Chi-restraints excluded: chain A residue 3625 VAL Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 383 LYS Chi-restraints excluded: chain C residue 461 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 55.5729 > 50: distance: 56 - 57: 3.794 distance: 56 - 59: 5.192 distance: 57 - 58: 3.325 distance: 57 - 64: 4.193 distance: 59 - 60: 3.527 distance: 64 - 186: 7.240 distance: 65 - 66: 9.593 distance: 65 - 68: 9.782 distance: 66 - 67: 3.632 distance: 66 - 69: 7.725 distance: 70 - 71: 9.019 distance: 70 - 73: 8.492 distance: 71 - 72: 7.045 distance: 71 - 80: 4.551 distance: 72 - 96: 32.894 distance: 73 - 74: 7.998 distance: 74 - 75: 3.903 distance: 75 - 76: 5.165 distance: 76 - 77: 3.658 distance: 77 - 78: 9.343 distance: 77 - 79: 9.977 distance: 81 - 82: 14.397 distance: 81 - 84: 4.312 distance: 82 - 83: 11.451 distance: 82 - 91: 7.188 distance: 83 - 101: 15.697 distance: 84 - 85: 5.532 distance: 88 - 90: 3.665 distance: 91 - 92: 20.198 distance: 92 - 93: 25.853 distance: 92 - 95: 19.776 distance: 93 - 94: 22.701 distance: 93 - 96: 34.454 distance: 96 - 97: 43.333 distance: 97 - 98: 10.945 distance: 97 - 100: 16.166 distance: 98 - 99: 15.331 distance: 98 - 101: 8.529 distance: 101 - 102: 14.487 distance: 102 - 103: 9.870 distance: 102 - 105: 27.514 distance: 103 - 104: 18.740 distance: 103 - 112: 17.534 distance: 105 - 106: 12.103 distance: 106 - 107: 3.478 distance: 106 - 108: 4.686 distance: 107 - 109: 3.673 distance: 108 - 110: 4.256 distance: 109 - 111: 4.944 distance: 110 - 111: 5.499 distance: 112 - 113: 7.876 distance: 113 - 114: 28.237 distance: 113 - 116: 28.035 distance: 114 - 115: 26.286 distance: 114 - 118: 6.330 distance: 115 - 145: 26.777 distance: 116 - 117: 9.926 distance: 118 - 119: 17.448 distance: 118 - 124: 19.262 distance: 119 - 120: 19.019 distance: 119 - 122: 22.107 distance: 120 - 121: 12.664 distance: 120 - 125: 13.957 distance: 121 - 152: 12.673 distance: 122 - 123: 8.117 distance: 123 - 124: 7.386 distance: 125 - 126: 7.119 distance: 126 - 127: 5.238 distance: 126 - 129: 9.148 distance: 127 - 128: 16.276 distance: 127 - 136: 5.391 distance: 128 - 157: 22.812 distance: 129 - 130: 8.381 distance: 130 - 131: 9.036 distance: 131 - 132: 5.708 distance: 132 - 133: 5.675 distance: 133 - 134: 3.304 distance: 133 - 135: 3.068