Starting phenix.real_space_refine (version: 1.21rc1) on Sat Aug 12 02:20:55 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gte_0063/08_2023/6gte_0063.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gte_0063/08_2023/6gte_0063.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gte_0063/08_2023/6gte_0063.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gte_0063/08_2023/6gte_0063.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gte_0063/08_2023/6gte_0063.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gte_0063/08_2023/6gte_0063.pdb" } resolution = 4.07 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 67 5.49 5 S 17 5.16 5 C 6602 2.51 5 N 1906 2.21 5 O 2280 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 583": "NH1" <-> "NH2" Residue "A PHE 641": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 740": "NH1" <-> "NH2" Residue "A ARG 746": "NH1" <-> "NH2" Residue "A TYR 822": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 865": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 925": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 926": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1228": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 10872 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1274, 9475 Classifications: {'peptide': 1274} Incomplete info: {'backbone_only': 239, 'truncation_to_alanine': 10} Link IDs: {'CIS': 5, 'PTRANS': 28, 'TRANS': 1240} Chain breaks: 4 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 1078 Unresolved non-hydrogen angles: 1539 Unresolved non-hydrogen dihedrals: 691 Unresolved non-hydrogen chiralities: 308 Planarities with less than four sites: {'GLN:plan1': 16, 'ARG:plan': 4, 'TYR:plan': 9, 'ASN:plan1': 16, 'TRP:plan': 1, 'ASP:plan': 24, 'PHE:plan': 14, 'GLU:plan': 21, 'HIS:plan': 4} Unresolved non-hydrogen planarities: 526 Chain: "B" Number of atoms: 616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 616 Classifications: {'RNA': 29} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 4, 'rna3p_pur': 11, 'rna3p_pyr': 10} Link IDs: {'rna2p': 8, 'rna3p': 20} Chain: "C" Number of atoms: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 427 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Chain: "D" Number of atoms: 354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 354 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Time building chain proxies: 5.89, per 1000 atoms: 0.54 Number of scatterers: 10872 At special positions: 0 Unit cell: (99.008, 133.12, 103.168, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 17 16.00 P 67 15.00 O 2280 8.00 N 1906 7.00 C 6602 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: 4.87 Conformation dependent library (CDL) restraints added in 1.6 seconds 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1968 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 6 sheets defined 38.7% alpha, 7.2% beta 5 base pairs and 31 stacking pairs defined. Time for finding SS restraints: 3.56 Creating SS restraints... Processing helix chain 'A' and resid 26 through 32 removed outlier: 3.506A pdb=" N ASN A 30 " --> pdb=" O LYS A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 53 removed outlier: 3.755A pdb=" N GLN A 52 " --> pdb=" O LYS A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 63 Processing helix chain 'A' and resid 75 through 85 removed outlier: 3.652A pdb=" N VAL A 82 " --> pdb=" O ASN A 78 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TYR A 83 " --> pdb=" O TYR A 79 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE A 84 " --> pdb=" O SER A 80 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LYS A 85 " --> pdb=" O ASP A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 114 removed outlier: 3.920A pdb=" N ALA A 101 " --> pdb=" O ASP A 97 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS A 106 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LYS A 107 " --> pdb=" O ASP A 103 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N TYR A 112 " --> pdb=" O GLN A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 123 removed outlier: 3.553A pdb=" N LEU A 122 " --> pdb=" O PHE A 119 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N PHE A 123 " --> pdb=" O LYS A 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 119 through 123' Processing helix chain 'A' and resid 136 through 143 Processing helix chain 'A' and resid 161 through 171 removed outlier: 4.115A pdb=" N GLU A 167 " --> pdb=" O ASP A 163 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE A 168 " --> pdb=" O GLU A 164 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER A 171 " --> pdb=" O GLU A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 207 Processing helix chain 'A' and resid 211 through 220 removed outlier: 3.608A pdb=" N LYS A 217 " --> pdb=" O GLU A 213 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU A 219 " --> pdb=" O LYS A 215 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N SER A 220 " --> pdb=" O ALA A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 234 removed outlier: 3.834A pdb=" N GLN A 233 " --> pdb=" O ILE A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 269 removed outlier: 3.851A pdb=" N PHE A 269 " --> pdb=" O ILE A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 285 removed outlier: 3.532A pdb=" N ILE A 278 " --> pdb=" O ASN A 274 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LYS A 280 " --> pdb=" O SER A 276 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N THR A 283 " --> pdb=" O THR A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 302 Processing helix chain 'A' and resid 303 through 308 removed outlier: 3.618A pdb=" N SER A 308 " --> pdb=" O ILE A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 320 removed outlier: 3.907A pdb=" N LYS A 317 " --> pdb=" O LYS A 314 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS A 318 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N TYR A 319 " --> pdb=" O LEU A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 357 removed outlier: 4.262A pdb=" N MET A 352 " --> pdb=" O VAL A 348 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU A 357 " --> pdb=" O GLN A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 362 removed outlier: 3.837A pdb=" N ALA A 361 " --> pdb=" O GLU A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 378 removed outlier: 6.112A pdb=" N LEU A 376 " --> pdb=" O GLU A 372 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU A 377 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE A 378 " --> pdb=" O LEU A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 399 No H-bonds generated for 'chain 'A' and resid 397 through 399' Processing helix chain 'A' and resid 400 through 407 Processing helix chain 'A' and resid 412 through 416 removed outlier: 3.638A pdb=" N THR A 415 " --> pdb=" O VAL A 412 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ALA A 416 " --> pdb=" O ILE A 413 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 412 through 416' Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 453 through 460 Processing helix chain 'A' and resid 460 through 465 removed outlier: 3.920A pdb=" N LYS A 465 " --> pdb=" O GLU A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 495 removed outlier: 4.169A pdb=" N PHE A 489 " --> pdb=" O ILE A 485 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ASP A 490 " --> pdb=" O PRO A 486 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLU A 491 " --> pdb=" O MET A 487 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ILE A 492 " --> pdb=" O ILE A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 498 No H-bonds generated for 'chain 'A' and resid 496 through 498' Processing helix chain 'A' and resid 499 through 506 Processing helix chain 'A' and resid 516 through 521 removed outlier: 4.848A pdb=" N ASP A 521 " --> pdb=" O SER A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 528 Processing helix chain 'A' and resid 529 through 532 removed outlier: 3.942A pdb=" N GLN A 532 " --> pdb=" O LEU A 529 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 529 through 532' Processing helix chain 'A' and resid 533 through 540 removed outlier: 3.768A pdb=" N LEU A 537 " --> pdb=" O THR A 533 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N HIS A 538 " --> pdb=" O ASN A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 544 removed outlier: 4.009A pdb=" N HIS A 544 " --> pdb=" O LYS A 541 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 541 through 544' Processing helix chain 'A' and resid 564 through 569 removed outlier: 3.748A pdb=" N CYS A 568 " --> pdb=" O VAL A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 573 removed outlier: 3.930A pdb=" N ALA A 573 " --> pdb=" O PHE A 570 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 570 through 573' Processing helix chain 'A' and resid 574 through 580 Processing helix chain 'A' and resid 582 through 588 removed outlier: 4.068A pdb=" N ILE A 586 " --> pdb=" O ILE A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 612 No H-bonds generated for 'chain 'A' and resid 610 through 612' Processing helix chain 'A' and resid 613 through 618 Processing helix chain 'A' and resid 643 through 648 removed outlier: 3.528A pdb=" N LYS A 647 " --> pdb=" O ASP A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 673 removed outlier: 3.887A pdb=" N LEU A 669 " --> pdb=" O ALA A 665 " (cutoff:3.500A) Proline residue: A 670 - end of helix removed outlier: 3.719A pdb=" N PHE A 673 " --> pdb=" O LEU A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 683 Processing helix chain 'A' and resid 685 through 695 removed outlier: 3.606A pdb=" N LEU A 689 " --> pdb=" O SER A 685 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N HIS A 694 " --> pdb=" O ARG A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 725 removed outlier: 3.529A pdb=" N LYS A 719 " --> pdb=" O GLU A 715 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N PHE A 720 " --> pdb=" O ASP A 716 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE A 723 " --> pdb=" O LYS A 719 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N TYR A 724 " --> pdb=" O PHE A 720 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS A 725 " --> pdb=" O ILE A 721 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 738 removed outlier: 3.597A pdb=" N PHE A 737 " --> pdb=" O TRP A 734 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLY A 738 " --> pdb=" O LYS A 735 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 747 removed outlier: 3.872A pdb=" N TYR A 747 " --> pdb=" O THR A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 755 removed outlier: 3.608A pdb=" N ARG A 755 " --> pdb=" O ASP A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 781 removed outlier: 3.514A pdb=" N VAL A 777 " --> pdb=" O TYR A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 812 removed outlier: 4.092A pdb=" N PHE A 812 " --> pdb=" O TRP A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 905 removed outlier: 3.671A pdb=" N ASN A 901 " --> pdb=" O ASN A 897 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU A 904 " --> pdb=" O ILE A 900 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS A 905 " --> pdb=" O ASN A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 953 through 961 removed outlier: 3.987A pdb=" N ALA A 959 " --> pdb=" O ASP A 955 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE A 960 " --> pdb=" O LYS A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 979 through 999 removed outlier: 4.560A pdb=" N LEU A 985 " --> pdb=" O LYS A 981 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N SER A 986 " --> pdb=" O GLU A 982 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLN A 987 " --> pdb=" O GLY A 983 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL A 988 " --> pdb=" O TYR A 984 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N HIS A 990 " --> pdb=" O SER A 986 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU A 995 " --> pdb=" O GLU A 991 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU A 998 " --> pdb=" O LYS A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 1025 through 1033 removed outlier: 3.629A pdb=" N MET A1030 " --> pdb=" O LYS A1026 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE A1032 " --> pdb=" O GLU A1028 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU A1033 " --> pdb=" O LYS A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1102 through 1111 removed outlier: 3.713A pdb=" N GLN A1106 " --> pdb=" O VAL A1102 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLU A1107 " --> pdb=" O SER A1103 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N PHE A1108 " --> pdb=" O LYS A1104 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE A1109 " --> pdb=" O SER A1105 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS A1111 " --> pdb=" O GLU A1107 " (cutoff:3.500A) Processing helix chain 'A' and resid 1129 through 1133 removed outlier: 3.687A pdb=" N ASN A1132 " --> pdb=" O ASP A1129 " (cutoff:3.500A) Processing helix chain 'A' and resid 1169 through 1178 removed outlier: 3.569A pdb=" N GLU A1173 " --> pdb=" O TYR A1169 " (cutoff:3.500A) Processing helix chain 'A' and resid 1191 through 1198 removed outlier: 3.539A pdb=" N ILE A1195 " --> pdb=" O ILE A1191 " (cutoff:3.500A) Processing helix chain 'A' and resid 1200 through 1213 removed outlier: 3.814A pdb=" N PHE A1204 " --> pdb=" O ASP A1200 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA A1205 " --> pdb=" O LYS A1201 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS A1206 " --> pdb=" O LYS A1202 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SER A1209 " --> pdb=" O ALA A1205 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N VAL A1210 " --> pdb=" O LYS A1206 " (cutoff:3.500A) Processing helix chain 'A' and resid 1242 through 1246 Processing helix chain 'A' and resid 1256 through 1261 removed outlier: 4.079A pdb=" N HIS A1261 " --> pdb=" O ASN A1257 " (cutoff:3.500A) Processing helix chain 'A' and resid 1261 through 1266 Processing helix chain 'A' and resid 1268 through 1274 removed outlier: 3.747A pdb=" N ILE A1273 " --> pdb=" O LEU A1269 " (cutoff:3.500A) Processing helix chain 'A' and resid 1287 through 1295 removed outlier: 3.670A pdb=" N TYR A1291 " --> pdb=" O LYS A1287 " (cutoff:3.500A) Processing helix chain 'A' and resid 1296 through 1298 No H-bonds generated for 'chain 'A' and resid 1296 through 1298' Processing sheet with id=AA1, first strand: chain 'A' and resid 596 through 598 removed outlier: 3.566A pdb=" N PHE A 596 " --> pdb=" O TYR A 832 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU A 830 " --> pdb=" O LEU A 598 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU A 829 " --> pdb=" O HIS A 881 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N HIS A 881 " --> pdb=" O GLU A 829 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS A 877 " --> pdb=" O ARG A 833 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N PHE A 878 " --> pdb=" O LEU A 21 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU A 17 " --> pdb=" O CYS A 882 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU A 20 " --> pdb=" O TYR A 789 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N TYR A 628 " --> pdb=" O ILE A 788 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N LEU A 621 " --> pdb=" O ILE A 657 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE A 657 " --> pdb=" O LEU A 621 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 596 through 598 removed outlier: 3.566A pdb=" N PHE A 596 " --> pdb=" O TYR A 832 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU A 830 " --> pdb=" O LEU A 598 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU A 829 " --> pdb=" O HIS A 881 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N HIS A 881 " --> pdb=" O GLU A 829 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS A 877 " --> pdb=" O ARG A 833 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N PHE A 878 " --> pdb=" O LEU A 21 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU A 17 " --> pdb=" O CYS A 882 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU A 20 " --> pdb=" O TYR A 789 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N TYR A 628 " --> pdb=" O ILE A 788 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N LEU A 621 " --> pdb=" O ILE A 657 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE A 657 " --> pdb=" O LEU A 621 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 822 through 824 Processing sheet with id=AA4, first strand: chain 'A' and resid 912 through 913 removed outlier: 6.513A pdb=" N HIS A 912 " --> pdb=" O ILE A1002 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 925 through 929 removed outlier: 7.389A pdb=" N TYR A 926 " --> pdb=" O GLN A 938 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N GLN A 938 " --> pdb=" O TYR A 926 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N LEU A 928 " --> pdb=" O ILE A 936 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1125 through 1126 210 hydrogen bonds defined for protein. 582 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 10 hydrogen bonds 16 hydrogen bond angles 0 basepair planarities 5 basepair parallelities 31 stacking parallelities Total time for adding SS restraints: 4.09 Time building geometry restraints manager: 5.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1951 1.32 - 1.44: 3219 1.44 - 1.56: 5884 1.56 - 1.69: 131 1.69 - 1.81: 27 Bond restraints: 11212 Sorted by residual: bond pdb=" CB ASP A 917 " pdb=" CG ASP A 917 " ideal model delta sigma weight residual 1.516 1.440 0.076 2.50e-02 1.60e+03 9.25e+00 bond pdb=" CB TRP A 808 " pdb=" CG TRP A 808 " ideal model delta sigma weight residual 1.498 1.416 0.082 3.10e-02 1.04e+03 6.98e+00 bond pdb=" C THR A 885 " pdb=" N ILE A 886 " ideal model delta sigma weight residual 1.327 1.257 0.070 2.97e-02 1.13e+03 5.54e+00 bond pdb=" CG LEU A 824 " pdb=" CD1 LEU A 824 " ideal model delta sigma weight residual 1.521 1.444 0.077 3.30e-02 9.18e+02 5.47e+00 bond pdb=" CB PHE A 19 " pdb=" CG PHE A 19 " ideal model delta sigma weight residual 1.502 1.450 0.052 2.30e-02 1.89e+03 5.15e+00 ... (remaining 11207 not shown) Histogram of bond angle deviations from ideal: 98.13 - 105.37: 418 105.37 - 112.60: 5210 112.60 - 119.84: 4396 119.84 - 127.08: 5043 127.08 - 134.32: 209 Bond angle restraints: 15276 Sorted by residual: angle pdb=" C ASP A1135 " pdb=" N LYS A1136 " pdb=" CA LYS A1136 " ideal model delta sigma weight residual 121.70 132.51 -10.81 1.80e+00 3.09e-01 3.61e+01 angle pdb=" N THR A 805 " pdb=" CA THR A 805 " pdb=" C THR A 805 " ideal model delta sigma weight residual 114.64 106.33 8.31 1.52e+00 4.33e-01 2.99e+01 angle pdb=" C PHE A1045 " pdb=" N ASP A1046 " pdb=" CA ASP A1046 " ideal model delta sigma weight residual 121.54 130.24 -8.70 1.91e+00 2.74e-01 2.08e+01 angle pdb=" N THR A1224 " pdb=" CA THR A1224 " pdb=" C THR A1224 " ideal model delta sigma weight residual 111.00 123.71 -12.71 2.80e+00 1.28e-01 2.06e+01 angle pdb=" CA TYR A 178 " pdb=" CB TYR A 178 " pdb=" CG TYR A 178 " ideal model delta sigma weight residual 113.90 121.01 -7.11 1.80e+00 3.09e-01 1.56e+01 ... (remaining 15271 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 5524 17.84 - 35.68: 461 35.68 - 53.52: 183 53.52 - 71.36: 55 71.36 - 89.20: 12 Dihedral angle restraints: 6235 sinusoidal: 2940 harmonic: 3295 Sorted by residual: dihedral pdb=" CA ARG A 921 " pdb=" C ARG A 921 " pdb=" N HIS A 922 " pdb=" CA HIS A 922 " ideal model delta harmonic sigma weight residual 180.00 141.01 38.99 0 5.00e+00 4.00e-02 6.08e+01 dihedral pdb=" CA LYS A1034 " pdb=" C LYS A1034 " pdb=" N LEU A1035 " pdb=" CA LEU A1035 " ideal model delta harmonic sigma weight residual 180.00 151.07 28.93 0 5.00e+00 4.00e-02 3.35e+01 dihedral pdb=" CA THR A 176 " pdb=" C THR A 176 " pdb=" N THR A 177 " pdb=" CA THR A 177 " ideal model delta harmonic sigma weight residual 180.00 153.26 26.74 0 5.00e+00 4.00e-02 2.86e+01 ... (remaining 6232 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 1317 0.094 - 0.189: 195 0.189 - 0.283: 12 0.283 - 0.377: 0 0.377 - 0.471: 1 Chirality restraints: 1525 Sorted by residual: chirality pdb=" CB ILE A 974 " pdb=" CA ILE A 974 " pdb=" CG1 ILE A 974 " pdb=" CG2 ILE A 974 " both_signs ideal model delta sigma weight residual False 2.64 2.17 0.47 2.00e-01 2.50e+01 5.56e+00 chirality pdb=" CB ILE A 234 " pdb=" CA ILE A 234 " pdb=" CG1 ILE A 234 " pdb=" CG2 ILE A 234 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" CB ILE A 53 " pdb=" CA ILE A 53 " pdb=" CG1 ILE A 53 " pdb=" CG2 ILE A 53 " both_signs ideal model delta sigma weight residual False 2.64 2.92 -0.27 2.00e-01 2.50e+01 1.85e+00 ... (remaining 1522 not shown) Planarity restraints: 1805 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 669 " -0.064 5.00e-02 4.00e+02 9.59e-02 1.47e+01 pdb=" N PRO A 670 " 0.166 5.00e-02 4.00e+02 pdb=" CA PRO A 670 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO A 670 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 195 " -0.053 5.00e-02 4.00e+02 7.98e-02 1.02e+01 pdb=" N PRO A 196 " 0.138 5.00e-02 4.00e+02 pdb=" CA PRO A 196 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 196 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 856 " -0.048 5.00e-02 4.00e+02 7.38e-02 8.72e+00 pdb=" N PRO A 857 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO A 857 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 857 " -0.041 5.00e-02 4.00e+02 ... (remaining 1802 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2277 2.77 - 3.30: 9630 3.30 - 3.83: 17809 3.83 - 4.37: 20879 4.37 - 4.90: 33206 Nonbonded interactions: 83801 Sorted by model distance: nonbonded pdb=" NH2 ARG A 833 " pdb=" OP1 U B -15 " model vdw 2.232 2.520 nonbonded pdb=" OG SER A 749 " pdb=" OD1 ASP A 751 " model vdw 2.249 2.440 nonbonded pdb=" O GLY A 608 " pdb=" ND2 ASN A 617 " model vdw 2.301 2.520 nonbonded pdb=" NZ LYS A 709 " pdb=" O PHE A 710 " model vdw 2.314 2.520 nonbonded pdb=" OE1 GLU A1033 " pdb=" ND2 ASN A1036 " model vdw 2.322 2.520 ... (remaining 83796 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.240 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: 0.000 Extract box with map and model: 2.690 Check model and map are aligned: 0.180 Set scattering table: 0.100 Process input model: 33.910 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 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:3.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7020 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 : 0.009 0.082 11212 Z= 0.566 Angle : 1.107 12.715 15276 Z= 0.601 Chirality : 0.064 0.471 1525 Planarity : 0.007 0.096 1805 Dihedral : 16.151 89.200 4267 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.08 % Allowed : 15.59 % Favored : 84.34 % Rotamer Outliers : 0.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.40 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -5.76 (0.17), residues: 1264 helix: -4.51 (0.11), residues: 419 sheet: -3.43 (0.45), residues: 112 loop : -3.59 (0.18), residues: 733 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 251 time to evaluate : 1.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 255 average time/residue: 0.2716 time to fit residues: 93.4511 Evaluate side-chains 141 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 140 time to evaluate : 1.113 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1054 time to fit residues: 1.7268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 7.9990 chunk 100 optimal weight: 2.9990 chunk 55 optimal weight: 30.0000 chunk 34 optimal weight: 0.0980 chunk 67 optimal weight: 6.9990 chunk 53 optimal weight: 50.0000 chunk 103 optimal weight: 0.0040 chunk 40 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 119 optimal weight: 9.9990 overall best weight: 0.9796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 HIS A 214 ASN A 327 GLN A 637 ASN A 779 ASN ** A 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 938 GLN A 942 ASN A1006 GLN A1252 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6858 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 11212 Z= 0.177 Angle : 0.636 7.842 15276 Z= 0.353 Chirality : 0.044 0.178 1525 Planarity : 0.004 0.064 1805 Dihedral : 17.660 89.788 2075 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.78 % Favored : 91.22 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.40 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.84 (0.19), residues: 1264 helix: -3.42 (0.17), residues: 419 sheet: -2.85 (0.45), residues: 105 loop : -3.26 (0.20), residues: 740 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 197 time to evaluate : 1.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 198 average time/residue: 0.2465 time to fit residues: 68.4972 Evaluate side-chains 128 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 127 time to evaluate : 1.198 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0984 time to fit residues: 1.7433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 66 optimal weight: 5.9990 chunk 37 optimal weight: 40.0000 chunk 99 optimal weight: 2.9990 chunk 81 optimal weight: 7.9990 chunk 33 optimal weight: 30.0000 chunk 120 optimal weight: 3.9990 chunk 129 optimal weight: 8.9990 chunk 106 optimal weight: 10.0000 chunk 119 optimal weight: 0.9990 chunk 40 optimal weight: 50.0000 chunk 96 optimal weight: 8.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 ASN ** A 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 637 ASN A 649 ASN ** A 694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1070 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.057 11212 Z= 0.402 Angle : 0.775 8.636 15276 Z= 0.418 Chirality : 0.050 0.247 1525 Planarity : 0.005 0.062 1805 Dihedral : 17.969 88.174 2075 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 20.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.00 % Favored : 86.00 % Rotamer Outliers : 0.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.40 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.45 (0.20), residues: 1264 helix: -2.91 (0.19), residues: 427 sheet: -3.25 (0.43), residues: 105 loop : -3.03 (0.21), residues: 732 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 162 time to evaluate : 1.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 163 average time/residue: 0.2148 time to fit residues: 51.4572 Evaluate side-chains 131 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 129 time to evaluate : 1.132 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1113 time to fit residues: 1.9424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 10.0000 chunk 90 optimal weight: 7.9990 chunk 62 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 chunk 57 optimal weight: 10.0000 chunk 80 optimal weight: 2.9990 chunk 120 optimal weight: 10.0000 chunk 127 optimal weight: 5.9990 chunk 114 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 637 ASN A 694 HIS ** A 780 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1070 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6948 moved from start: 0.3500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 11212 Z= 0.220 Angle : 0.616 7.858 15276 Z= 0.338 Chirality : 0.044 0.200 1525 Planarity : 0.004 0.062 1805 Dihedral : 17.660 88.628 2075 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 16.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.73 % Favored : 90.27 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.40 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.09 (0.21), residues: 1264 helix: -2.44 (0.21), residues: 437 sheet: -2.94 (0.44), residues: 100 loop : -2.96 (0.22), residues: 727 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 1.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.2253 time to fit residues: 57.0046 Evaluate side-chains 135 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 1.172 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 95 optimal weight: 10.0000 chunk 52 optimal weight: 9.9990 chunk 108 optimal weight: 5.9990 chunk 88 optimal weight: 8.9990 chunk 0 optimal weight: 7.9990 chunk 65 optimal weight: 5.9990 chunk 114 optimal weight: 10.0000 chunk 32 optimal weight: 2.9990 chunk 42 optimal weight: 50.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 637 ASN A 731 HIS A 804 HIS ** A 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 HIS ** A1297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7124 moved from start: 0.3746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.058 11212 Z= 0.448 Angle : 0.818 8.490 15276 Z= 0.437 Chirality : 0.052 0.196 1525 Planarity : 0.005 0.069 1805 Dihedral : 18.152 89.624 2075 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 23.54 Ramachandran Plot: Outliers : 0.08 % Allowed : 15.11 % Favored : 84.81 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.40 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.11 (0.21), residues: 1264 helix: -2.44 (0.22), residues: 443 sheet: -3.34 (0.42), residues: 103 loop : -2.91 (0.22), residues: 718 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 1.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.2000 time to fit residues: 48.0210 Evaluate side-chains 125 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 1.202 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 31 optimal weight: 9.9990 chunk 127 optimal weight: 4.9990 chunk 106 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 chunk 10 optimal weight: 6.9990 chunk 42 optimal weight: 50.0000 chunk 67 optimal weight: 6.9990 chunk 123 optimal weight: 0.6980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 637 ASN A 779 ASN ** A 780 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6873 moved from start: 0.4116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 11212 Z= 0.173 Angle : 0.599 8.260 15276 Z= 0.325 Chirality : 0.043 0.190 1525 Planarity : 0.004 0.065 1805 Dihedral : 17.568 89.630 2075 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.26 % Favored : 90.74 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.40 % 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: -3.67 (0.22), residues: 1264 helix: -1.99 (0.23), residues: 440 sheet: -3.06 (0.44), residues: 101 loop : -2.72 (0.22), residues: 723 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 1.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.2164 time to fit residues: 55.9207 Evaluate side-chains 128 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 1.175 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 7.9990 chunk 72 optimal weight: 3.9990 chunk 93 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 71 optimal weight: 7.9990 chunk 127 optimal weight: 7.9990 chunk 79 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 50 optimal weight: 9.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 ASN A 637 ASN A 804 HIS ** A 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6895 moved from start: 0.4308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 11212 Z= 0.180 Angle : 0.583 8.249 15276 Z= 0.315 Chirality : 0.043 0.186 1525 Planarity : 0.003 0.055 1805 Dihedral : 17.446 89.128 2075 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.05 % Favored : 89.95 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.40 % 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: -3.40 (0.22), residues: 1264 helix: -1.62 (0.24), residues: 435 sheet: -2.85 (0.45), residues: 102 loop : -2.66 (0.22), residues: 727 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 161 time to evaluate : 1.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 161 average time/residue: 0.2178 time to fit residues: 51.5014 Evaluate side-chains 126 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 1.163 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 1.9990 chunk 38 optimal weight: 50.0000 chunk 24 optimal weight: 7.9990 chunk 80 optimal weight: 2.9990 chunk 86 optimal weight: 8.9990 chunk 62 optimal weight: 7.9990 chunk 11 optimal weight: 0.8980 chunk 100 optimal weight: 4.9990 chunk 115 optimal weight: 10.0000 chunk 121 optimal weight: 3.9990 chunk 111 optimal weight: 7.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 637 ASN ** A 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7004 moved from start: 0.4321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.042 11212 Z= 0.295 Angle : 0.677 7.291 15276 Z= 0.365 Chirality : 0.047 0.196 1525 Planarity : 0.004 0.053 1805 Dihedral : 17.653 88.530 2075 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 18.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.42 % Favored : 87.58 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.40 % 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: -3.41 (0.22), residues: 1264 helix: -1.66 (0.24), residues: 444 sheet: -2.96 (0.44), residues: 110 loop : -2.61 (0.23), residues: 710 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.2148 time to fit residues: 51.9649 Evaluate side-chains 126 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 1.204 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 0.8980 chunk 121 optimal weight: 0.5980 chunk 71 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 chunk 93 optimal weight: 4.9990 chunk 36 optimal weight: 40.0000 chunk 107 optimal weight: 3.9990 chunk 112 optimal weight: 7.9990 chunk 77 optimal weight: 0.5980 chunk 125 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 ASN A 637 ASN ** A 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6924 moved from start: 0.4505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.063 11212 Z= 0.221 Angle : 0.609 9.343 15276 Z= 0.330 Chirality : 0.044 0.191 1525 Planarity : 0.004 0.065 1805 Dihedral : 17.503 89.294 2075 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 16.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.21 % Favored : 89.79 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.40 % 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: -3.30 (0.23), residues: 1264 helix: -1.59 (0.24), residues: 452 sheet: -2.75 (0.46), residues: 106 loop : -2.58 (0.23), residues: 706 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 160 time to evaluate : 1.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 160 average time/residue: 0.2118 time to fit residues: 50.0210 Evaluate side-chains 126 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 1.127 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 0.1980 chunk 87 optimal weight: 2.9990 chunk 131 optimal weight: 10.0000 chunk 121 optimal weight: 0.5980 chunk 104 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 80 optimal weight: 0.4980 chunk 64 optimal weight: 0.9990 chunk 83 optimal weight: 7.9990 chunk 111 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6844 moved from start: 0.4710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 11212 Z= 0.172 Angle : 0.572 7.084 15276 Z= 0.309 Chirality : 0.043 0.330 1525 Planarity : 0.003 0.057 1805 Dihedral : 17.270 88.551 2075 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.57 % Favored : 90.43 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.40 % 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: -3.15 (0.23), residues: 1264 helix: -1.35 (0.24), residues: 446 sheet: -2.78 (0.44), residues: 116 loop : -2.53 (0.23), residues: 702 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 1.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 0.2192 time to fit residues: 50.3077 Evaluate side-chains 122 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 1.169 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 0.0970 chunk 15 optimal weight: 0.0980 chunk 29 optimal weight: 20.0000 chunk 104 optimal weight: 0.9980 chunk 43 optimal weight: 30.0000 chunk 107 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 19 optimal weight: 0.5980 chunk 92 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 75 optimal weight: 7.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 ASN A 804 HIS ** A 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1187 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.157484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.119894 restraints weight = 18088.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.118977 restraints weight = 11021.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.120307 restraints weight = 8826.483| |-----------------------------------------------------------------------------| r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6848 moved from start: 0.5020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 11212 Z= 0.151 Angle : 0.552 7.284 15276 Z= 0.296 Chirality : 0.042 0.326 1525 Planarity : 0.003 0.057 1805 Dihedral : 17.049 88.657 2075 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.40 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.93 (0.23), residues: 1264 helix: -1.09 (0.25), residues: 442 sheet: -2.70 (0.42), residues: 128 loop : -2.43 (0.24), residues: 694 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2087.69 seconds wall clock time: 39 minutes 2.30 seconds (2342.30 seconds total)