Starting phenix.real_space_refine on Wed Sep 17 20:21:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6gte_0063/09_2025/6gte_0063.cif Found real_map, /net/cci-nas-00/data/ceres_data/6gte_0063/09_2025/6gte_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_2025/6gte_0063.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6gte_0063/09_2025/6gte_0063.map" model { file = "/net/cci-nas-00/data/ceres_data/6gte_0063/09_2025/6gte_0063.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6gte_0063/09_2025/6gte_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-2.0-5805/lib/python3.9/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: {'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: 2.91, per 1000 atoms: 0.27 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: 0.97 Conformation dependent library (CDL) restraints added in 524.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 1.31 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: 2.20 Time building geometry restraints manager: 1.31 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: 0.00 - 2.54: 14691 2.54 - 5.09: 505 5.09 - 7.63: 67 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=" 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: 5566 17.84 - 35.68: 488 35.68 - 53.52: 210 53.52 - 71.36: 88 71.36 - 89.20: 15 Dihedral angle restraints: 6367 sinusoidal: 3072 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 6364 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 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: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.960 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: 0.000 Load rotamer database and sin/cos tables:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.430 ------------------------------------------------------------------------------- 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= 0.412 Angle : 1.107 12.715 15276 Z= 0.601 Chirality : 0.064 0.471 1525 Planarity : 0.007 0.096 1805 Dihedral : 17.327 89.200 4399 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 aren 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 covalent geometry : bond 0.00925 (11212) covalent geometry : angle 1.10661 (15276) hydrogen bonds : bond 0.31380 ( 199) hydrogen bonds : angle 13.01689 ( 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 : 0.422 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: 0.8333 (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: 0.6424 (t80) cc_final: 0.6186 (t80) outliers start: 7 outliers final: 1 residues processed: 255 average time/residue: 0.1243 time to fit residues: 42.8995 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 : 0.407 ------------------------------------------------------------------------------- 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: 2.9990 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... Flipped N/Q/H residues before XYZ refinement: A 183 HIS A 214 ASN 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.153886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.114193 restraints weight = 17590.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.117462 restraints weight = 9911.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.119507 restraints weight = 6868.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.120863 restraints weight = 5478.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.121535 restraints weight = 4750.174| |-----------------------------------------------------------------------------| r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6821 moved from start: 0.2843 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= 0.135 Angle : 0.647 7.602 15276 Z= 0.358 Chirality : 0.044 0.177 1525 Planarity : 0.005 0.067 1805 Dihedral : 19.555 88.985 2207 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.94 % Favored : 91.06 % Rotamer: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % 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 aren not related in a simple way. whole: -4.86 (0.19), residues: 1264 helix: -3.37 (0.18), residues: 412 sheet: -3.06 (0.44), residues: 111 loop : -3.29 (0.20), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 872 TYR 0.017 0.002 TYR A 591 PHE 0.021 0.002 PHE A 7 TRP 0.008 0.001 TRP A 734 HIS 0.004 0.001 HIS A 694 Details of bonding type rmsd covalent geometry : bond 0.00285 (11212) covalent geometry : angle 0.64658 (15276) hydrogen bonds : bond 0.04519 ( 199) hydrogen bonds : angle 7.03187 ( 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 202 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 ASN cc_start: 0.8185 (t0) cc_final: 0.7951 (t0) REVERT: A 169 ILE cc_start: 0.9091 (pt) cc_final: 0.8641 (tp) REVERT: A 918 ARG cc_start: 0.6185 (mmt90) cc_final: 0.2989 (tmt-80) REVERT: A 949 MET cc_start: 0.7186 (tpt) cc_final: 0.6804 (tpt) REVERT: A 1204 PHE cc_start: 0.6696 (m-80) cc_final: 0.6492 (m-80) REVERT: A 1206 LYS cc_start: 0.8330 (mmpt) cc_final: 0.7905 (ttpt) REVERT: A 1235 ASP cc_start: 0.8497 (p0) cc_final: 0.8004 (p0) REVERT: A 1250 MET cc_start: 0.8621 (mmm) cc_final: 0.8252 (mmm) outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.1160 time to fit residues: 32.6694 Evaluate side-chains 134 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.301 ------------------------------------------------------------------------------- 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: 9.9990 chunk 7 optimal weight: 9.9990 chunk 63 optimal weight: 1.9990 chunk 93 optimal weight: 7.9990 chunk 51 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 52 optimal weight: 30.0000 chunk 10 optimal weight: 2.9990 chunk 55 optimal weight: 50.0000 chunk 47 optimal weight: 0.0070 chunk 88 optimal weight: 2.9990 overall best weight: 1.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 GLN A 637 ASN A 694 HIS ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.152043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.117341 restraints weight = 17892.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.119037 restraints weight = 13538.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.120077 restraints weight = 9514.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.120238 restraints weight = 7099.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.120487 restraints weight = 6909.300| |-----------------------------------------------------------------------------| r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6842 moved from start: 0.3383 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= 0.152 Angle : 0.611 7.375 15276 Z= 0.335 Chirality : 0.044 0.168 1525 Planarity : 0.004 0.056 1805 Dihedral : 19.377 87.968 2207 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.97 % Favored : 90.03 % Rotamer: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % 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 aren not related in a simple way. whole: -4.34 (0.20), residues: 1264 helix: -2.70 (0.20), residues: 429 sheet: -2.92 (0.45), residues: 100 loop : -3.11 (0.20), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 872 TYR 0.017 0.002 TYR A 591 PHE 0.016 0.002 PHE A1240 TRP 0.009 0.001 TRP A 609 HIS 0.004 0.001 HIS A1261 Details of bonding type rmsd covalent geometry : bond 0.00339 (11212) covalent geometry : angle 0.61053 (15276) hydrogen bonds : bond 0.04454 ( 199) hydrogen bonds : angle 6.04035 ( 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 182 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 0.378 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: 0.8388 (t0) cc_final: 0.7965 (t0) REVERT: A 140 LEU cc_start: 0.9156 (mt) cc_final: 0.8430 (pp) REVERT: A 625 ASP cc_start: 0.7199 (m-30) cc_final: 0.6873 (p0) REVERT: A 918 ARG cc_start: 0.6113 (mmt90) cc_final: 0.2961 (tmt-80) REVERT: A 949 MET cc_start: 0.6849 (tpt) cc_final: 0.6591 (tpt) REVERT: A 999 TYR cc_start: 0.5903 (m-80) cc_final: 0.5683 (m-80) REVERT: A 1006 GLN cc_start: 0.7892 (mm110) cc_final: 0.7653 (mm110) REVERT: A 1206 LYS cc_start: 0.8294 (mmpt) cc_final: 0.8034 (pttm) REVERT: A 1230 ILE cc_start: 0.7494 (pt) cc_final: 0.6928 (pt) REVERT: A 1235 ASP cc_start: 0.8586 (p0) cc_final: 0.8093 (p0) REVERT: A 1250 MET cc_start: 0.8647 (mmm) cc_final: 0.8280 (mmm) outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.0992 time to fit residues: 26.1796 Evaluate side-chains 136 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.439 ------------------------------------------------------------------------------- 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: 6.9990 chunk 79 optimal weight: 0.9980 chunk 48 optimal weight: 5.9990 chunk 114 optimal weight: 0.5980 chunk 128 optimal weight: 6.9990 chunk 9 optimal weight: 10.0000 chunk 89 optimal weight: 0.4980 chunk 68 optimal weight: 9.9990 chunk 99 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 637 ASN ** A 881 HIS ** 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 = 0.4078 r_free = 0.4078 target = 0.149423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.114779 restraints weight = 18102.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.116824 restraints weight = 14106.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.117883 restraints weight = 9421.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.117941 restraints weight = 7053.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.118576 restraints weight = 6946.328| |-----------------------------------------------------------------------------| r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6891 moved from start: 0.3619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11212 Z= 0.176 Angle : 0.629 7.980 15276 Z= 0.344 Chirality : 0.045 0.261 1525 Planarity : 0.004 0.054 1805 Dihedral : 19.369 89.685 2207 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.52 % Favored : 89.48 % Rotamer: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % 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 aren not related in a simple way. whole: -4.01 (0.21), residues: 1264 helix: -2.31 (0.22), residues: 440 sheet: -3.06 (0.45), residues: 100 loop : -2.93 (0.22), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 872 TYR 0.017 0.002 TYR A 591 PHE 0.016 0.002 PHE A1240 TRP 0.010 0.002 TRP A1142 HIS 0.004 0.001 HIS A1261 Details of bonding type rmsd covalent geometry : bond 0.00394 (11212) covalent geometry : angle 0.62889 (15276) hydrogen bonds : bond 0.04353 ( 199) hydrogen bonds : angle 5.72052 ( 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 171 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 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: symmetry clash revert: symmetry clash REVERT: A 126 ASN cc_start: 0.8389 (t0) cc_final: 0.8185 (t0) REVERT: A 635 LYS cc_start: 0.7021 (tppt) cc_final: 0.6807 (tppt) REVERT: A 682 TYR cc_start: 0.8040 (m-80) cc_final: 0.7629 (m-80) REVERT: A 918 ARG cc_start: 0.6187 (mmt90) cc_final: 0.3017 (tmt-80) REVERT: A 950 LYS cc_start: 0.6653 (mmtp) cc_final: 0.6167 (mptt) REVERT: A 1206 LYS cc_start: 0.8272 (mmpt) cc_final: 0.7962 (pttm) REVERT: A 1230 ILE cc_start: 0.7563 (pt) cc_final: 0.7090 (pt) REVERT: A 1235 ASP cc_start: 0.8592 (p0) cc_final: 0.8151 (p0) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.1032 time to fit residues: 25.5472 Evaluate side-chains 134 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.391 ------------------------------------------------------------------------------- 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: 0.4980 chunk 31 optimal weight: 7.9990 chunk 17 optimal weight: 6.9990 chunk 20 optimal weight: 8.9990 chunk 48 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 68 optimal weight: 9.9990 chunk 120 optimal weight: 3.9990 chunk 101 optimal weight: 0.8980 chunk 75 optimal weight: 7.9990 chunk 37 optimal weight: 0.0020 overall best weight: 1.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 637 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.151981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.117448 restraints weight = 17975.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.119383 restraints weight = 13065.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.120710 restraints weight = 8610.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.120810 restraints weight = 6473.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.121009 restraints weight = 6432.427| |-----------------------------------------------------------------------------| r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6823 moved from start: 0.3989 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= 0.138 Angle : 0.581 7.992 15276 Z= 0.317 Chirality : 0.043 0.206 1525 Planarity : 0.003 0.054 1805 Dihedral : 19.196 89.046 2207 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % 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 aren not related in a simple way. whole: -3.72 (0.22), residues: 1264 helix: -2.01 (0.23), residues: 440 sheet: -3.06 (0.46), residues: 100 loop : -2.77 (0.22), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 872 TYR 0.015 0.001 TYR A 178 PHE 0.017 0.002 PHE A1240 TRP 0.004 0.001 TRP A 734 HIS 0.004 0.001 HIS A1261 Details of bonding type rmsd covalent geometry : bond 0.00307 (11212) covalent geometry : angle 0.58128 (15276) hydrogen bonds : bond 0.03605 ( 199) hydrogen bonds : angle 5.36277 ( 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 165 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 0.412 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 112 TYR cc_start: 0.7094 (t80) cc_final: 0.6818 (t80) REVERT: A 126 ASN cc_start: 0.8236 (t0) cc_final: 0.8031 (t0) REVERT: A 682 TYR cc_start: 0.8005 (m-80) cc_final: 0.7660 (m-80) REVERT: A 918 ARG cc_start: 0.5998 (mmt90) cc_final: 0.3009 (tpt170) REVERT: A 950 LYS cc_start: 0.6652 (mmtp) cc_final: 0.6137 (mptt) REVERT: A 1036 ASN cc_start: 0.7524 (m-40) cc_final: 0.7300 (m-40) REVERT: A 1206 LYS cc_start: 0.8212 (mmpt) cc_final: 0.7848 (pttm) REVERT: A 1235 ASP cc_start: 0.8539 (p0) cc_final: 0.8090 (p0) REVERT: A 1250 MET cc_start: 0.8706 (mmm) cc_final: 0.8331 (mmm) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.0999 time to fit residues: 24.2629 Evaluate side-chains 135 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.388 ------------------------------------------------------------------------------- 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: 0.0070 chunk 6 optimal weight: 5.9990 chunk 111 optimal weight: 5.9990 chunk 89 optimal weight: 0.1980 chunk 85 optimal weight: 2.9990 chunk 131 optimal weight: 10.0000 chunk 107 optimal weight: 7.9990 chunk 124 optimal weight: 2.9990 chunk 40 optimal weight: 50.0000 chunk 1 optimal weight: 0.9980 chunk 118 optimal weight: 0.7980 overall best weight: 1.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 ASN A 637 ASN ** A 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1056 GLN ** 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 = 0.4144 r_free = 0.4144 target = 0.154432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.118590 restraints weight = 18264.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.119852 restraints weight = 12815.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.121643 restraints weight = 8465.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.121791 restraints weight = 6862.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.122139 restraints weight = 6465.017| |-----------------------------------------------------------------------------| r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6792 moved from start: 0.4318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11212 Z= 0.120 Angle : 0.563 8.541 15276 Z= 0.308 Chirality : 0.042 0.183 1525 Planarity : 0.003 0.053 1805 Dihedral : 19.033 89.535 2207 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % Rotamer: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % 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 aren not related in a simple way. whole: -3.52 (0.22), residues: 1264 helix: -1.82 (0.23), residues: 440 sheet: -2.96 (0.46), residues: 102 loop : -2.65 (0.22), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 872 TYR 0.019 0.001 TYR A 926 PHE 0.017 0.001 PHE A 258 TRP 0.003 0.001 TRP A 141 HIS 0.003 0.001 HIS A 697 Details of bonding type rmsd covalent geometry : bond 0.00268 (11212) covalent geometry : angle 0.56312 (15276) hydrogen bonds : bond 0.03521 ( 199) hydrogen bonds : angle 5.17691 ( 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 160 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 TYR cc_start: 0.7107 (t80) cc_final: 0.6829 (t80) REVERT: A 126 ASN cc_start: 0.8162 (t0) cc_final: 0.7824 (t0) REVERT: A 682 TYR cc_start: 0.7958 (m-80) cc_final: 0.7632 (m-80) REVERT: A 918 ARG cc_start: 0.5956 (mmt90) cc_final: 0.2921 (tpt170) REVERT: A 950 LYS cc_start: 0.6633 (mmtp) cc_final: 0.6025 (mptt) REVERT: A 1206 LYS cc_start: 0.8159 (mmpt) cc_final: 0.7809 (pttm) REVERT: A 1230 ILE cc_start: 0.7553 (pt) cc_final: 0.7070 (pt) REVERT: A 1235 ASP cc_start: 0.8499 (p0) cc_final: 0.8088 (p0) REVERT: A 1250 MET cc_start: 0.8704 (mmm) cc_final: 0.8322 (mmm) REVERT: A 1268 MET cc_start: 0.7278 (ptt) cc_final: 0.6897 (ptt) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.0980 time to fit residues: 23.1719 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 : 0.419 ------------------------------------------------------------------------------- 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: 0.9990 chunk 121 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 chunk 6 optimal weight: 0.0270 chunk 83 optimal weight: 9.9990 chunk 3 optimal weight: 7.9990 chunk 44 optimal weight: 50.0000 chunk 107 optimal weight: 9.9990 chunk 39 optimal weight: 20.0000 chunk 120 optimal weight: 3.9990 chunk 105 optimal weight: 0.0060 overall best weight: 1.6060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 ASN A 637 ASN ** A 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 HIS ** A1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.152666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.117516 restraints weight = 17982.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.118939 restraints weight = 13692.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.120718 restraints weight = 9178.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.120616 restraints weight = 6981.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.120764 restraints weight = 7024.479| |-----------------------------------------------------------------------------| r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6829 moved from start: 0.4409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 11212 Z= 0.141 Angle : 0.579 7.980 15276 Z= 0.314 Chirality : 0.043 0.204 1525 Planarity : 0.003 0.054 1805 Dihedral : 19.043 88.574 2207 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % 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 aren not related in a simple way. whole: -3.38 (0.22), residues: 1264 helix: -1.68 (0.23), residues: 446 sheet: -2.93 (0.45), residues: 106 loop : -2.57 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1150 TYR 0.023 0.002 TYR A 659 PHE 0.024 0.002 PHE A1203 TRP 0.005 0.001 TRP A 609 HIS 0.003 0.001 HIS A 954 Details of bonding type rmsd covalent geometry : bond 0.00319 (11212) covalent geometry : angle 0.57922 (15276) hydrogen bonds : bond 0.03673 ( 199) hydrogen bonds : angle 5.09244 ( 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 158 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 0.341 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: 0.8215 (t0) cc_final: 0.7873 (t0) REVERT: A 640 ILE cc_start: 0.8503 (pt) cc_final: 0.8046 (mt) REVERT: A 682 TYR cc_start: 0.7977 (m-80) cc_final: 0.7700 (m-80) REVERT: A 918 ARG cc_start: 0.6011 (mmt90) cc_final: 0.2901 (tpt170) REVERT: A 1206 LYS cc_start: 0.8076 (mmpt) cc_final: 0.7768 (pttm) REVERT: A 1230 ILE cc_start: 0.7611 (pt) cc_final: 0.7196 (pt) REVERT: A 1235 ASP cc_start: 0.8589 (p0) cc_final: 0.8207 (p0) REVERT: A 1250 MET cc_start: 0.8688 (mmm) cc_final: 0.8479 (mmt) REVERT: A 1268 MET cc_start: 0.7469 (ptt) cc_final: 0.7064 (ptt) outliers start: 0 outliers final: 0 residues processed: 158 average time/residue: 0.0872 time to fit residues: 20.5587 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 : 0.398 ------------------------------------------------------------------------------- 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: 4.9990 chunk 14 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 83 optimal weight: 7.9990 chunk 130 optimal weight: 6.9990 chunk 116 optimal weight: 20.0000 chunk 44 optimal weight: 50.0000 chunk 31 optimal weight: 9.9990 chunk 45 optimal weight: 4.9990 chunk 51 optimal weight: 8.9990 chunk 110 optimal weight: 10.0000 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 ASN A 599 ASN A 637 ASN A 649 ASN ** A 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 HIS ** A1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.147250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.108477 restraints weight = 18742.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.110138 restraints weight = 11548.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.110947 restraints weight = 8482.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.111658 restraints weight = 7375.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.111882 restraints weight = 6651.129| |-----------------------------------------------------------------------------| r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.4244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 11212 Z= 0.280 Angle : 0.747 7.503 15276 Z= 0.399 Chirality : 0.050 0.191 1525 Planarity : 0.004 0.049 1805 Dihedral : 19.542 87.938 2207 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.47 % Favored : 88.53 % 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 aren not related in a simple way. whole: -3.69 (0.22), residues: 1264 helix: -1.96 (0.22), residues: 455 sheet: -3.31 (0.43), residues: 111 loop : -2.69 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1244 TYR 0.037 0.003 TYR A 659 PHE 0.023 0.003 PHE A 888 TRP 0.027 0.003 TRP A 609 HIS 0.006 0.002 HIS A 183 Details of bonding type rmsd covalent geometry : bond 0.00630 (11212) covalent geometry : angle 0.74675 (15276) hydrogen bonds : bond 0.05513 ( 199) hydrogen bonds : angle 5.57762 ( 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 162 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.393 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: 0.8456 (t0) cc_final: 0.8179 (t0) REVERT: A 201 TYR cc_start: 0.5900 (t80) cc_final: 0.5647 (t80) REVERT: A 682 TYR cc_start: 0.8130 (m-80) cc_final: 0.7860 (m-80) REVERT: A 825 ASN cc_start: 0.8583 (m-40) cc_final: 0.8227 (m-40) REVERT: A 918 ARG cc_start: 0.6304 (mmt90) cc_final: 0.3163 (tpt170) REVERT: A 1206 LYS cc_start: 0.8143 (mmpt) cc_final: 0.7756 (pttm) REVERT: A 1235 ASP cc_start: 0.8764 (p0) cc_final: 0.8377 (p0) REVERT: A 1250 MET cc_start: 0.8741 (mmm) cc_final: 0.8477 (mmm) REVERT: A 1268 MET cc_start: 0.7625 (ptt) cc_final: 0.7174 (ptt) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.0912 time to fit residues: 22.2269 Evaluate side-chains 131 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.413 ------------------------------------------------------------------------------- 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: 0.9990 chunk 71 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 8 optimal weight: 0.2980 chunk 102 optimal weight: 0.5980 chunk 2 optimal weight: 0.7980 chunk 25 optimal weight: 20.0000 chunk 42 optimal weight: 50.0000 chunk 21 optimal weight: 0.7980 chunk 17 optimal weight: 0.0370 chunk 72 optimal weight: 0.9990 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 ASN A 881 HIS ** A1056 GLN ** 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 = 0.4159 r_free = 0.4159 target = 0.155655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.121629 restraints weight = 17520.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.121944 restraints weight = 12011.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.123105 restraints weight = 9421.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.123811 restraints weight = 6989.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.123916 restraints weight = 6792.715| |-----------------------------------------------------------------------------| r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6757 moved from start: 0.4797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11212 Z= 0.115 Angle : 0.581 8.516 15276 Z= 0.313 Chirality : 0.043 0.166 1525 Planarity : 0.004 0.066 1805 Dihedral : 18.957 88.352 2207 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % 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 aren not related in a simple way. whole: -3.33 (0.22), residues: 1264 helix: -1.50 (0.23), residues: 461 sheet: -3.02 (0.45), residues: 101 loop : -2.65 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 872 TYR 0.015 0.002 TYR A 659 PHE 0.020 0.001 PHE A1203 TRP 0.007 0.001 TRP A 609 HIS 0.003 0.001 HIS A 697 Details of bonding type rmsd covalent geometry : bond 0.00253 (11212) covalent geometry : angle 0.58129 (15276) hydrogen bonds : bond 0.03509 ( 199) hydrogen bonds : angle 5.10684 ( 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 158 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 0.434 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 112 TYR cc_start: 0.7131 (t80) cc_final: 0.6926 (t80) REVERT: A 126 ASN cc_start: 0.8096 (t0) cc_final: 0.7643 (t0) REVERT: A 682 TYR cc_start: 0.7874 (m-80) cc_final: 0.7587 (m-80) REVERT: A 825 ASN cc_start: 0.8268 (m-40) cc_final: 0.8059 (m-40) REVERT: A 873 PHE cc_start: 0.4427 (m-10) cc_final: 0.4216 (m-10) REVERT: A 918 ARG cc_start: 0.5822 (mmt90) cc_final: 0.2872 (tpt170) REVERT: A 1034 LYS cc_start: 0.7518 (mptt) cc_final: 0.7113 (mptt) REVERT: A 1230 ILE cc_start: 0.7363 (pt) cc_final: 0.6924 (pt) REVERT: A 1235 ASP cc_start: 0.8543 (p0) cc_final: 0.8113 (p0) REVERT: A 1268 MET cc_start: 0.7385 (ptt) cc_final: 0.6983 (ptt) outliers start: 0 outliers final: 0 residues processed: 158 average time/residue: 0.0956 time to fit residues: 22.6578 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 : 0.395 ------------------------------------------------------------------------------- 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: 5.9990 chunk 86 optimal weight: 0.4980 chunk 0 optimal weight: 8.9990 chunk 96 optimal weight: 0.3980 chunk 10 optimal weight: 0.0670 chunk 44 optimal weight: 8.9990 chunk 53 optimal weight: 30.0000 chunk 51 optimal weight: 9.9990 chunk 94 optimal weight: 3.9990 chunk 116 optimal weight: 20.0000 chunk 46 optimal weight: 40.0000 overall best weight: 2.1922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 607 ASN A 637 ASN A 942 ASN A 954 HIS ** A1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.151210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.116028 restraints weight = 18399.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.118582 restraints weight = 14528.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.119405 restraints weight = 9216.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.119386 restraints weight = 7075.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.119541 restraints weight = 7003.997| |-----------------------------------------------------------------------------| r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6864 moved from start: 0.4682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 11212 Z= 0.173 Angle : 0.624 7.448 15276 Z= 0.335 Chirality : 0.045 0.336 1525 Planarity : 0.004 0.058 1805 Dihedral : 19.074 88.178 2207 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.49 % Favored : 90.51 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % 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 aren not related in a simple way. whole: -3.32 (0.23), residues: 1264 helix: -1.52 (0.24), residues: 452 sheet: -3.09 (0.43), residues: 119 loop : -2.56 (0.23), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 872 TYR 0.027 0.002 TYR A 659 PHE 0.021 0.002 PHE A1204 TRP 0.011 0.002 TRP A 175 HIS 0.005 0.001 HIS A 954 Details of bonding type rmsd covalent geometry : bond 0.00396 (11212) covalent geometry : angle 0.62372 (15276) hydrogen bonds : bond 0.04062 ( 199) hydrogen bonds : angle 5.20886 ( 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 145 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 TYR cc_start: 0.7343 (t80) cc_final: 0.7107 (t80) REVERT: A 126 ASN cc_start: 0.8251 (t0) cc_final: 0.7845 (t0) REVERT: A 640 ILE cc_start: 0.8502 (pt) cc_final: 0.8080 (mt) REVERT: A 682 TYR cc_start: 0.8025 (m-80) cc_final: 0.7733 (m-80) REVERT: A 873 PHE cc_start: 0.4407 (m-10) cc_final: 0.4182 (m-10) REVERT: A 918 ARG cc_start: 0.6035 (mmt90) cc_final: 0.2733 (tpt170) REVERT: A 1034 LYS cc_start: 0.7680 (mptt) cc_final: 0.7190 (mptt) REVERT: A 1230 ILE cc_start: 0.7617 (pt) cc_final: 0.7160 (pt) REVERT: A 1235 ASP cc_start: 0.8652 (p0) cc_final: 0.8260 (p0) outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 0.0912 time to fit residues: 20.2568 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 : 0.402 ------------------------------------------------------------------------------- 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: 5.9990 chunk 15 optimal weight: 4.9990 chunk 73 optimal weight: 0.0270 chunk 20 optimal weight: 6.9990 chunk 128 optimal weight: 6.9990 chunk 86 optimal weight: 0.0870 chunk 109 optimal weight: 9.9990 chunk 4 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 overall best weight: 0.7618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 ASN ** A1056 GLN ** 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 = 0.4167 r_free = 0.4167 target = 0.156057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.121001 restraints weight = 18026.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.122749 restraints weight = 14022.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.124179 restraints weight = 9047.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.124407 restraints weight = 6937.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.124758 restraints weight = 6624.631| |-----------------------------------------------------------------------------| r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6735 moved from start: 0.5022 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= 0.114 Angle : 0.566 7.218 15276 Z= 0.303 Chirality : 0.043 0.330 1525 Planarity : 0.003 0.058 1805 Dihedral : 18.849 89.041 2207 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % 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 aren not related in a simple way. whole: -3.11 (0.23), residues: 1264 helix: -1.24 (0.24), residues: 454 sheet: -2.94 (0.46), residues: 102 loop : -2.56 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 872 TYR 0.027 0.002 TYR A 984 PHE 0.015 0.001 PHE A1203 TRP 0.005 0.001 TRP A1142 HIS 0.002 0.001 HIS A1261 Details of bonding type rmsd covalent geometry : bond 0.00258 (11212) covalent geometry : angle 0.56569 (15276) hydrogen bonds : bond 0.03309 ( 199) hydrogen bonds : angle 4.96836 ( 598) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1810.31 seconds wall clock time: 32 minutes 11.43 seconds (1931.43 seconds total)