Starting phenix.real_space_refine on Fri Sep 11 19:08:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6gte_0063/09_2026/6gte_0063.cif Found real_map, /net/cci-nas-00/data/ceres_data/6gte_0063/09_2026/6gte_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/cci-nas-00/data/ceres_data/6gte_0063/09_2026/6gte_0063.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6gte_0063/09_2026/6gte_0063.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6gte_0063/09_2026/6gte_0063.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6gte_0063/09_2026/6gte_0063.cif" model { file = "/net/cci-nas-00/data/ceres_data/6gte_0063/09_2026/6gte_0063.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6gte_0063/09_2026/6gte_0063.cif" } resolution = 4.07 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/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: {'GLU:plan': 21, 'ASP:plan': 24, 'GLN:plan1': 16, 'PHE:plan': 14, 'TYR:plan': 9, 'ASN:plan1': 16, 'HIS:plan': 4, 'ARG:plan': 4, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 526 Chain: "B" Number of atoms: 616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 616 Classifications: {'RNAv2': 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: 2.70, per 1000 atoms: 0.25 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 - 3.00 Amino acid : True - 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: 0.98 Conformation dependent library (CDL) restraints added in 515.1 milliseconds 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: 1.36 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: 2.22 Time building geometry restraints manager: 1.32 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=" C3' DG D 0 " pdb=" O3' DG D 0 " ideal model delta sigma weight residual 1.435 1.366 0.069 1.30e-02 5.92e+03 2.80e+01 bond pdb=" C3' DT C -1 " pdb=" O3' DT C -1 " ideal model delta sigma weight residual 1.435 1.383 0.052 1.30e-02 5.92e+03 1.61e+01 bond pdb=" N9 DA C 3 " pdb=" C4 DA C 3 " ideal model delta sigma weight residual 1.374 1.352 0.022 6.00e-03 2.78e+04 1.34e+01 bond pdb=" N9 DA C 3 " pdb=" C8 DA C 3 " ideal model delta sigma weight residual 1.373 1.344 0.029 8.00e-03 1.56e+04 1.29e+01 bond pdb=" N7 DA D -1 " pdb=" C5 DA D -1 " ideal model delta sigma weight residual 1.388 1.367 0.021 6.00e-03 2.78e+04 1.27e+01 ... (remaining 11207 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.54: 14614 2.54 - 5.09: 569 5.09 - 7.63: 80 7.63 - 10.17: 7 10.17 - 12.71: 6 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=" O4' DC D -7 " pdb=" C4' DC D -7 " pdb=" C3' DC D -7 " ideal model delta sigma weight residual 106.00 102.84 3.16 6.00e-01 2.78e+00 2.77e+01 angle pdb=" O4' DG D -4 " pdb=" C4' DG D -4 " pdb=" C3' DG D -4 " ideal model delta sigma weight residual 106.00 103.12 2.88 6.00e-01 2.78e+00 2.30e+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 ... (remaining 15271 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 5471 17.84 - 35.68: 496 35.68 - 53.52: 210 53.52 - 71.36: 80 71.36 - 89.20: 18 Dihedral angle restraints: 6275 sinusoidal: 2980 harmonic: 3295 Sorted by residual: dihedral pdb=" C4' U B -7 " pdb=" C3' U B -7 " pdb=" C2' U B -7 " pdb=" C1' U B -7 " ideal model delta sinusoidal sigma weight residual 36.34 -38.81 75.15 1 3.10e+00 1.04e-01 7.43e+02 dihedral pdb=" C4' U B -10 " pdb=" C3' U B -10 " pdb=" C2' U B -10 " pdb=" C1' U B -10 " ideal model delta sinusoidal sigma weight residual 36.35 -37.54 73.88 1 3.10e+00 1.04e-01 7.22e+02 dihedral pdb=" C4' G B -9 " pdb=" C3' G B -9 " pdb=" C2' G B -9 " pdb=" C1' G B -9 " ideal model delta sinusoidal sigma weight residual 36.35 -37.53 73.88 1 3.10e+00 1.04e-01 7.22e+02 ... (remaining 6272 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 1268 0.094 - 0.189: 206 0.189 - 0.283: 40 0.283 - 0.377: 9 0.377 - 0.471: 2 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=" P U B -1 " pdb=" OP1 U B -1 " pdb=" OP2 U B -1 " pdb=" O5' U B -1 " both_signs ideal model delta sigma weight residual True 2.17 -2.56 -0.39 2.00e-01 2.50e+01 3.83e+00 chirality pdb=" C2' A B -19 " pdb=" C3' A B -19 " pdb=" O2' A B -19 " pdb=" C1' A B -19 " both_signs ideal model delta sigma weight residual False -2.79 -2.48 -0.31 2.00e-01 2.50e+01 2.46e+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 3.120 nonbonded pdb=" OG SER A 749 " pdb=" OD1 ASP A 751 " model vdw 2.249 3.040 nonbonded pdb=" O GLY A 608 " pdb=" ND2 ASN A 617 " model vdw 2.301 3.120 nonbonded pdb=" NZ LYS A 709 " pdb=" O PHE A 710 " model vdw 2.314 3.120 nonbonded pdb=" OE1 GLU A1033 " pdb=" ND2 ASN A1036 " model vdw 2.322 3.120 ... (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 Time spend for trying shortcut: 0.00 ========== 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: 1.470 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: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 12.440 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 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= 0.504 Angle : 1.155 12.715 15276 Z= 0.655 Chirality : 0.078 0.471 1525 Planarity : 0.007 0.096 1805 Dihedral : 17.424 89.200 4307 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 % Allowed : 6.03 % Favored : 93.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.40 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 918 TYR 0.042 0.004 TYR A1037 PHE 0.040 0.004 PHE A1240 TRP 0.016 0.004 TRP A1142 HIS 0.012 0.003 HIS A 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00942 / 0.50 (11212) covalent geometry : angle 1.15488 / 0.65 (15276) hydrogen bonds : bond 0.31380 / 20.48 ( 199) hydrogen bonds : angle 13.01689 / 8.68 ( 598) *********************** 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 to be fit. rotamer outliers: 7 poor density : 251 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 LYS cc_start: 0.8959 (mttp) cc_final: 0.8484 (mmtm) REVERT: A 166 LEU cc_start: 0.9040 (mm) cc_final: 0.8687 (mm) REVERT: A 638 ASN cc_start: 0.8332 (p0) cc_final: 0.8071 (p0) REVERT: A 758 GLU cc_start: 0.7695 (mt-10) cc_final: 0.7114 (tp30) REVERT: A 791 LYS cc_start: 0.8231 (mttt) cc_final: 0.7996 (mtpt) REVERT: A 918 ARG cc_start: 0.6039 (mmt90) cc_final: 0.2812 (tpt170) REVERT: A 1204 PHE cc_start: 0.7098 (m-80) cc_final: 0.6618 (m-80) REVERT: A 1206 LYS cc_start: 0.8518 (mmpt) cc_final: 0.8255 (ptmt) REVERT: A 1235 ASP cc_start: 0.8756 (p0) cc_final: 0.8385 (p0) REVERT: A 1241 PHE cc_start: 0.6425 (t80) cc_final: 0.6186 (t80) outliers start: 7 outliers final: 1 residues processed: 255 average time/residue: 0.1179 time to fit residues: 40.9378 Evaluate side-chains 148 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 147 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.2980 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.0000 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 50.0000 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 183 HIS A 214 ASN A 327 GLN A 637 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.154425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.118189 restraints weight = 17783.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.117443 restraints weight = 13144.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.119461 restraints weight = 10645.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.119721 restraints weight = 7951.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.120860 restraints weight = 8024.814| |-----------------------------------------------------------------------------| r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6897 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 11212 Z= 0.193 Angle : 0.956 19.588 15276 Z= 0.462 Chirality : 0.085 1.368 1525 Planarity : 0.005 0.072 1805 Dihedral : 19.733 156.888 2115 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.13 % Favored : 89.87 % Rotamer: Outliers : 0.11 % Allowed : 2.91 % Favored : 96.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.40 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.03 (0.19), residues: 1264 helix: -3.62 (0.16), residues: 420 sheet: -3.05 (0.43), residues: 106 loop : -3.34 (0.20), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1150 TYR 0.022 0.002 TYR A 248 PHE 0.028 0.002 PHE A 7 TRP 0.008 0.001 TRP A 734 HIS 0.004 0.001 HIS A 881 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.19 (11212) covalent geometry : angle 0.95587 / 0.46 (15276) hydrogen bonds : bond 0.06942 / 4.36 ( 199) hydrogen bonds : angle 7.88779 / 5.31 ( 598) *********************** 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 to be fit. rotamer outliers: 1 poor density : 197 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ILE cc_start: 0.8726 (mp) cc_final: 0.8515 (mp) REVERT: A 107 LYS cc_start: 0.8595 (mttp) cc_final: 0.8371 (ttpp) REVERT: A 126 ASN cc_start: 0.8284 (t0) cc_final: 0.8013 (t0) REVERT: A 166 LEU cc_start: 0.9065 (mm) cc_final: 0.8583 (pp) REVERT: A 918 ARG cc_start: 0.6259 (mmt90) cc_final: 0.2899 (tmt-80) REVERT: A 1204 PHE cc_start: 0.6723 (m-80) cc_final: 0.6353 (m-80) REVERT: A 1206 LYS cc_start: 0.8385 (mmpt) cc_final: 0.7941 (ttpt) REVERT: A 1235 ASP cc_start: 0.8585 (p0) cc_final: 0.8130 (p0) outliers start: 1 outliers final: 1 residues processed: 198 average time/residue: 0.1093 time to fit residues: 30.6952 Evaluate side-chains 130 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 129 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 3 optimal weight: 10.0000 chunk 7 optimal weight: 0.9980 chunk 63 optimal weight: 6.9990 chunk 93 optimal weight: 7.9990 chunk 51 optimal weight: 7.9990 chunk 19 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 chunk 55 optimal weight: 50.0000 chunk 47 optimal weight: 0.0980 chunk 88 optimal weight: 0.0870 overall best weight: 1.2160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 637 ASN A 704 GLN ** A 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.153092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.118954 restraints weight = 17922.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.119812 restraints weight = 13711.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.121060 restraints weight = 10736.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.121348 restraints weight = 7884.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.121573 restraints weight = 7549.969| |-----------------------------------------------------------------------------| r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6856 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11212 Z= 0.153 Angle : 0.774 12.110 15276 Z= 0.392 Chirality : 0.065 0.677 1525 Planarity : 0.004 0.056 1805 Dihedral : 19.639 157.552 2115 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.00 % Favored : 89.00 % Rotamer: Outliers : 0.11 % Allowed : 3.77 % Favored : 96.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.40 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.55 (0.20), residues: 1264 helix: -3.02 (0.19), residues: 426 sheet: -3.09 (0.42), residues: 110 loop : -3.11 (0.21), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 692 TYR 0.031 0.002 TYR A 178 PHE 0.017 0.002 PHE A 153 TRP 0.013 0.002 TRP A 175 HIS 0.005 0.001 HIS A1261 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 (11212) covalent geometry : angle 0.77426 / 0.39 (15276) hydrogen bonds : bond 0.04743 / 2.88 ( 199) hydrogen bonds : angle 6.76981 / 4.58 ( 598) *********************** 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 171 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 170 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 ASN cc_start: 0.8329 (t0) cc_final: 0.7493 (t0) REVERT: A 169 ILE cc_start: 0.9187 (pt) cc_final: 0.8875 (tp) REVERT: A 918 ARG cc_start: 0.6220 (mmt90) cc_final: 0.2944 (tmt-80) REVERT: A 949 MET cc_start: 0.7101 (tpt) cc_final: 0.6604 (tpt) REVERT: A 1206 LYS cc_start: 0.8362 (mmpt) cc_final: 0.8117 (pttm) REVERT: A 1235 ASP cc_start: 0.8558 (p0) cc_final: 0.8103 (p0) REVERT: A 1250 MET cc_start: 0.8809 (mmm) cc_final: 0.8489 (mmm) outliers start: 1 outliers final: 0 residues processed: 171 average time/residue: 0.0967 time to fit residues: 24.2275 Evaluate side-chains 126 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 55 optimal weight: 50.0000 chunk 78 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 chunk 48 optimal weight: 20.0000 chunk 114 optimal weight: 3.9990 chunk 128 optimal weight: 4.9990 chunk 9 optimal weight: 9.9990 chunk 89 optimal weight: 0.1980 chunk 68 optimal weight: 9.9990 chunk 99 optimal weight: 4.9990 chunk 103 optimal weight: 5.9990 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 694 HIS ** A 704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 780 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.151540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.116964 restraints weight = 18298.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.116743 restraints weight = 15428.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.118325 restraints weight = 11767.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.118506 restraints weight = 8596.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.118697 restraints weight = 8432.469| |-----------------------------------------------------------------------------| r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6934 moved from start: 0.3272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11212 Z= 0.185 Angle : 0.767 11.382 15276 Z= 0.389 Chirality : 0.063 0.534 1525 Planarity : 0.004 0.051 1805 Dihedral : 19.497 154.674 2115 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.00 % Favored : 89.00 % Rotamer: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.40 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.28 (0.20), residues: 1264 helix: -2.61 (0.21), residues: 429 sheet: -3.21 (0.42), residues: 110 loop : -3.02 (0.21), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 872 TYR 0.020 0.002 TYR A 926 PHE 0.026 0.002 PHE A1204 TRP 0.009 0.002 TRP A 609 HIS 0.006 0.001 HIS A1261 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.19 (11212) covalent geometry : angle 0.76680 / 0.39 (15276) hydrogen bonds : bond 0.04987 / 2.93 ( 199) hydrogen bonds : angle 6.36576 / 4.30 ( 598) *********************** 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 164 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 ASN cc_start: 0.8426 (t0) cc_final: 0.7892 (t0) REVERT: A 169 ILE cc_start: 0.9235 (pt) cc_final: 0.8841 (tp) REVERT: A 918 ARG cc_start: 0.6182 (mmt90) cc_final: 0.2930 (tmt-80) REVERT: A 949 MET cc_start: 0.7057 (tpt) cc_final: 0.6649 (tpt) REVERT: A 1206 LYS cc_start: 0.8334 (mmpt) cc_final: 0.8018 (pttm) REVERT: A 1230 ILE cc_start: 0.7596 (pt) cc_final: 0.6976 (pt) REVERT: A 1235 ASP cc_start: 0.8586 (p0) cc_final: 0.8135 (p0) REVERT: A 1250 MET cc_start: 0.8789 (mmm) cc_final: 0.8464 (mmm) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.0886 time to fit residues: 21.6134 Evaluate side-chains 125 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 46 optimal weight: 40.0000 chunk 31 optimal weight: 20.0000 chunk 17 optimal weight: 6.9990 chunk 20 optimal weight: 0.0370 chunk 48 optimal weight: 0.0370 chunk 63 optimal weight: 7.9990 chunk 68 optimal weight: 10.0000 chunk 120 optimal weight: 5.9990 chunk 101 optimal weight: 0.9980 chunk 75 optimal weight: 5.9990 chunk 37 optimal weight: 0.0980 overall best weight: 1.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 704 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.153232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.116430 restraints weight = 17969.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.117453 restraints weight = 13648.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.118740 restraints weight = 9691.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.119143 restraints weight = 7328.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.119447 restraints weight = 6977.358| |-----------------------------------------------------------------------------| r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6922 moved from start: 0.3492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11212 Z= 0.144 Angle : 0.705 10.351 15276 Z= 0.357 Chirality : 0.058 0.423 1525 Planarity : 0.004 0.050 1805 Dihedral : 19.389 152.331 2115 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.89 % Favored : 90.11 % Rotamer: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.40 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.06 (0.21), residues: 1264 helix: -2.34 (0.22), residues: 424 sheet: -3.15 (0.42), residues: 110 loop : -2.93 (0.21), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 872 TYR 0.018 0.002 TYR A 659 PHE 0.025 0.002 PHE A 258 TRP 0.005 0.001 TRP A 609 HIS 0.005 0.001 HIS A1261 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (11212) covalent geometry : angle 0.70511 / 0.36 (15276) hydrogen bonds : bond 0.04258 / 2.54 ( 199) hydrogen bonds : angle 6.02231 / 4.09 ( 598) *********************** 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 164 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 ASN cc_start: 0.8358 (t0) cc_final: 0.7848 (t0) REVERT: A 169 ILE cc_start: 0.9167 (pt) cc_final: 0.8787 (tp) REVERT: A 918 ARG cc_start: 0.6217 (mmt90) cc_final: 0.2811 (tmt170) REVERT: A 949 MET cc_start: 0.6864 (tpt) cc_final: 0.6512 (tpt) REVERT: A 1206 LYS cc_start: 0.8287 (mmpt) cc_final: 0.7930 (pttm) REVERT: A 1230 ILE cc_start: 0.7646 (pt) cc_final: 0.6969 (pt) REVERT: A 1235 ASP cc_start: 0.8520 (p0) cc_final: 0.8043 (p0) REVERT: A 1250 MET cc_start: 0.8776 (mmm) cc_final: 0.8414 (mmm) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.0885 time to fit residues: 21.4443 Evaluate side-chains 125 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 35 optimal weight: 0.0170 chunk 6 optimal weight: 0.9990 chunk 111 optimal weight: 7.9990 chunk 89 optimal weight: 0.0670 chunk 85 optimal weight: 3.9990 chunk 131 optimal weight: 30.0000 chunk 107 optimal weight: 0.9990 chunk 124 optimal weight: 0.6980 chunk 40 optimal weight: 30.0000 chunk 1 optimal weight: 0.7980 chunk 118 optimal weight: 1.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 704 GLN ** A 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.155319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.120342 restraints weight = 17747.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.120426 restraints weight = 12100.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.121845 restraints weight = 8819.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.122104 restraints weight = 7062.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.122263 restraints weight = 6553.660| |-----------------------------------------------------------------------------| r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6834 moved from start: 0.3851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11212 Z= 0.123 Angle : 0.681 9.656 15276 Z= 0.348 Chirality : 0.056 0.441 1525 Planarity : 0.004 0.051 1805 Dihedral : 19.265 149.592 2115 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.41 % Favored : 90.59 % Rotamer: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.40 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.80 (0.21), residues: 1264 helix: -2.07 (0.23), residues: 414 sheet: -2.81 (0.46), residues: 102 loop : -2.86 (0.21), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A1150 TYR 0.024 0.002 TYR A 926 PHE 0.016 0.002 PHE A1005 TRP 0.006 0.001 TRP A 175 HIS 0.006 0.001 HIS A1261 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (11212) covalent geometry : angle 0.68071 / 0.35 (15276) hydrogen bonds : bond 0.03722 / 2.27 ( 199) hydrogen bonds : angle 5.72509 / 3.92 ( 598) *********************** 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 172 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 ASN cc_start: 0.8303 (t0) cc_final: 0.7581 (t0) REVERT: A 918 ARG cc_start: 0.5996 (mmt90) cc_final: 0.3608 (mmt90) REVERT: A 1206 LYS cc_start: 0.8250 (mmpt) cc_final: 0.7851 (pttm) REVERT: A 1230 ILE cc_start: 0.7214 (pt) cc_final: 0.6974 (pt) REVERT: A 1235 ASP cc_start: 0.8469 (p0) cc_final: 0.8007 (p0) REVERT: A 1250 MET cc_start: 0.8717 (mmm) cc_final: 0.8409 (mmm) outliers start: 0 outliers final: 0 residues processed: 172 average time/residue: 0.0865 time to fit residues: 21.9287 Evaluate side-chains 120 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 90 optimal weight: 1.9990 chunk 121 optimal weight: 0.0770 chunk 20 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 83 optimal weight: 0.0670 chunk 3 optimal weight: 4.9990 chunk 44 optimal weight: 7.9990 chunk 107 optimal weight: 4.9990 chunk 39 optimal weight: 6.9990 chunk 120 optimal weight: 0.8980 chunk 105 optimal weight: 3.9990 overall best weight: 1.0080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 759 ASN A 881 HIS ** A 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.155358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.119076 restraints weight = 17628.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.121043 restraints weight = 11780.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.122530 restraints weight = 7468.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.122536 restraints weight = 6119.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.122818 restraints weight = 5778.168| |-----------------------------------------------------------------------------| r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6836 moved from start: 0.4016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11212 Z= 0.130 Angle : 0.666 9.412 15276 Z= 0.338 Chirality : 0.055 0.422 1525 Planarity : 0.003 0.050 1805 Dihedral : 19.216 147.611 2115 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.40 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.71 (0.21), residues: 1264 helix: -1.90 (0.24), residues: 417 sheet: -2.91 (0.44), residues: 114 loop : -2.82 (0.21), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1150 TYR 0.014 0.001 TYR A 178 PHE 0.017 0.002 PHE A 7 TRP 0.006 0.001 TRP A 808 HIS 0.003 0.001 HIS A1261 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (11212) covalent geometry : angle 0.66564 / 0.34 (15276) hydrogen bonds : bond 0.03684 / 2.23 ( 199) hydrogen bonds : angle 5.53619 / 3.79 ( 598) *********************** 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 161 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 ASN cc_start: 0.8302 (t0) cc_final: 0.7720 (t0) REVERT: A 918 ARG cc_start: 0.5693 (mmt90) cc_final: 0.2697 (tpt170) REVERT: A 991 GLU cc_start: 0.6602 (mm-30) cc_final: 0.6314 (mm-30) REVERT: A 1206 LYS cc_start: 0.8233 (mmpt) cc_final: 0.7860 (pttm) REVERT: A 1230 ILE cc_start: 0.7698 (pt) cc_final: 0.6806 (pt) REVERT: A 1235 ASP cc_start: 0.8434 (p0) cc_final: 0.7965 (p0) REVERT: A 1250 MET cc_start: 0.8735 (mmm) cc_final: 0.8390 (mmm) outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.0899 time to fit residues: 21.7531 Evaluate side-chains 124 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 73 optimal weight: 0.3980 chunk 14 optimal weight: 5.9990 chunk 23 optimal weight: 0.0050 chunk 83 optimal weight: 0.9980 chunk 130 optimal weight: 9.9990 chunk 116 optimal weight: 7.9990 chunk 44 optimal weight: 50.0000 chunk 31 optimal weight: 6.9990 chunk 45 optimal weight: 5.9990 chunk 51 optimal weight: 9.9990 chunk 110 optimal weight: 9.9990 overall best weight: 2.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 599 ASN ** A 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 759 ASN ** A 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.152265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.115450 restraints weight = 18464.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.117236 restraints weight = 13671.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.118479 restraints weight = 8986.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.118536 restraints weight = 6948.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.118746 restraints weight = 6666.216| |-----------------------------------------------------------------------------| r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6943 moved from start: 0.3994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11212 Z= 0.200 Angle : 0.733 9.652 15276 Z= 0.371 Chirality : 0.057 0.383 1525 Planarity : 0.004 0.047 1805 Dihedral : 19.203 149.424 2115 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.00 % Favored : 89.00 % Rotamer: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.40 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.75 (0.22), residues: 1264 helix: -1.91 (0.23), residues: 427 sheet: -3.13 (0.42), residues: 118 loop : -2.83 (0.21), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 872 TYR 0.031 0.002 TYR A 178 PHE 0.029 0.002 PHE A1203 TRP 0.007 0.002 TRP A 609 HIS 0.004 0.001 HIS A 697 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.20 (11212) covalent geometry : angle 0.73267 / 0.37 (15276) hydrogen bonds : bond 0.04472 / 2.70 ( 199) hydrogen bonds : angle 5.69820 / 3.87 ( 598) *********************** 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 153 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 ASN cc_start: 0.8411 (t0) cc_final: 0.7843 (t0) REVERT: A 825 ASN cc_start: 0.8563 (m-40) cc_final: 0.8199 (m-40) REVERT: A 918 ARG cc_start: 0.6018 (mmt90) cc_final: 0.3023 (tpt170) REVERT: A 1206 LYS cc_start: 0.8191 (mmpt) cc_final: 0.7840 (pttm) REVERT: A 1235 ASP cc_start: 0.8573 (p0) cc_final: 0.8134 (p0) REVERT: A 1250 MET cc_start: 0.8761 (mmm) cc_final: 0.8388 (mmm) outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.0804 time to fit residues: 18.8482 Evaluate side-chains 126 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 13 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 1 optimal weight: 0.7980 chunk 8 optimal weight: 5.9990 chunk 102 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 25 optimal weight: 7.9990 chunk 42 optimal weight: 50.0000 chunk 21 optimal weight: 9.9990 chunk 17 optimal weight: 6.9990 chunk 72 optimal weight: 0.9980 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 ASN ** A 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 759 ASN ** A 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.150414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.115513 restraints weight = 18268.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.113462 restraints weight = 14181.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.115242 restraints weight = 10881.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.115894 restraints weight = 8056.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.116119 restraints weight = 7403.819| |-----------------------------------------------------------------------------| r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7009 moved from start: 0.4011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 11212 Z= 0.222 Angle : 0.766 9.447 15276 Z= 0.387 Chirality : 0.059 0.386 1525 Planarity : 0.004 0.046 1805 Dihedral : 19.250 147.295 2115 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.31 % Favored : 88.69 % Rotamer: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.40 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.75 (0.22), residues: 1264 helix: -1.91 (0.23), residues: 427 sheet: -3.30 (0.41), residues: 118 loop : -2.79 (0.22), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 872 TYR 0.019 0.002 TYR A 178 PHE 0.026 0.003 PHE A1203 TRP 0.009 0.002 TRP A 609 HIS 0.004 0.001 HIS A 697 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.22 (11212) covalent geometry : angle 0.76592 / 0.39 (15276) hydrogen bonds : bond 0.04512 / 2.73 ( 199) hydrogen bonds : angle 5.72772 / 3.90 ( 598) *********************** 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 152 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 ASN cc_start: 0.8403 (t0) cc_final: 0.7887 (t0) REVERT: A 918 ARG cc_start: 0.6200 (mmt90) cc_final: 0.3150 (tpt170) REVERT: A 1206 LYS cc_start: 0.8220 (mmpt) cc_final: 0.7869 (pttm) REVERT: A 1230 ILE cc_start: 0.7592 (pt) cc_final: 0.7116 (pt) REVERT: A 1235 ASP cc_start: 0.8573 (p0) cc_final: 0.8124 (p0) REVERT: A 1250 MET cc_start: 0.8713 (mmm) cc_final: 0.8432 (mmm) outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.0868 time to fit residues: 19.9843 Evaluate side-chains 121 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 89 optimal weight: 6.9990 chunk 86 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 96 optimal weight: 7.9990 chunk 10 optimal weight: 7.9990 chunk 44 optimal weight: 50.0000 chunk 53 optimal weight: 30.0000 chunk 51 optimal weight: 10.0000 chunk 94 optimal weight: 0.9990 chunk 116 optimal weight: 0.0870 chunk 46 optimal weight: 50.0000 overall best weight: 4.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 649 ASN A 759 ASN ** A 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.148244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.106641 restraints weight = 18912.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.109782 restraints weight = 10861.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.111715 restraints weight = 7652.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.112956 restraints weight = 6192.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.113493 restraints weight = 5433.412| |-----------------------------------------------------------------------------| r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 moved from start: 0.4027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 11212 Z= 0.307 Angle : 0.881 10.627 15276 Z= 0.442 Chirality : 0.063 0.415 1525 Planarity : 0.005 0.052 1805 Dihedral : 19.398 147.698 2115 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 16.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.45 % Favored : 86.55 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.40 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.87 (0.22), residues: 1264 helix: -2.05 (0.23), residues: 444 sheet: -3.44 (0.43), residues: 104 loop : -2.85 (0.22), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 872 TYR 0.025 0.003 TYR A 984 PHE 0.028 0.003 PHE A 888 TRP 0.023 0.003 TRP A 609 HIS 0.007 0.002 HIS A 843 Details of bonding type rmsd/Z covalent geometry : bond 0.00689 / 0.31 (11212) covalent geometry : angle 0.88130 / 0.44 (15276) hydrogen bonds : bond 0.05587 / 3.28 ( 199) hydrogen bonds : angle 5.98355 / 4.04 ( 598) ********************** 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 153 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 ASN cc_start: 0.8550 (t0) cc_final: 0.8282 (t0) REVERT: A 918 ARG cc_start: 0.6296 (mmt90) cc_final: 0.3095 (tpt170) REVERT: A 1206 LYS cc_start: 0.8181 (mmpt) cc_final: 0.7837 (pttm) REVERT: A 1230 ILE cc_start: 0.7872 (pt) cc_final: 0.7401 (pt) REVERT: A 1235 ASP cc_start: 0.8707 (p0) cc_final: 0.8289 (p0) REVERT: A 1250 MET cc_start: 0.8742 (mmm) cc_final: 0.8366 (mmm) REVERT: A 1268 MET cc_start: 0.7670 (ptt) cc_final: 0.7061 (ptt) outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.0859 time to fit residues: 19.9245 Evaluate side-chains 118 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 65 optimal weight: 0.6980 chunk 3 optimal weight: 0.0870 chunk 15 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 128 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 109 optimal weight: 10.0000 chunk 4 optimal weight: 0.8980 chunk 122 optimal weight: 0.4980 chunk 90 optimal weight: 2.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 9 ASN ** A 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 780 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.154026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.118505 restraints weight = 18128.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.119690 restraints weight = 12870.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.121354 restraints weight = 8627.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.121445 restraints weight = 6869.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.121785 restraints weight = 6586.604| |-----------------------------------------------------------------------------| r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6857 moved from start: 0.4260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11212 Z= 0.132 Angle : 0.704 10.320 15276 Z= 0.355 Chirality : 0.054 0.416 1525 Planarity : 0.004 0.071 1805 Dihedral : 19.230 142.911 2115 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.10 % Favored : 90.90 % Rotamer: Outliers : 0.11 % Allowed : 0.65 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.40 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.51 (0.22), residues: 1264 helix: -1.76 (0.23), residues: 439 sheet: -3.04 (0.45), residues: 107 loop : -2.66 (0.22), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1150 TYR 0.026 0.002 TYR A 112 PHE 0.031 0.002 PHE A1203 TRP 0.007 0.001 TRP A 734 HIS 0.004 0.001 HIS A1261 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (11212) covalent geometry : angle 0.70449 / 0.36 (15276) hydrogen bonds : bond 0.03620 / 2.23 ( 199) hydrogen bonds : angle 5.55104 / 3.82 ( 598) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1674.31 seconds wall clock time: 29 minutes 52.32 seconds (1792.32 seconds total)