Starting phenix.real_space_refine on Mon Jun 9 23:39:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6gte_0063/06_2025/6gte_0063.cif Found real_map, /net/cci-nas-00/data/ceres_data/6gte_0063/06_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_0063/06_2025/6gte_0063.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6gte_0063/06_2025/6gte_0063.map" model { file = "/net/cci-nas-00/data/ceres_data/6gte_0063/06_2025/6gte_0063.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6gte_0063/06_2025/6gte_0063.cif" } resolution = 4.07 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 67 5.49 5 S 17 5.16 5 C 6602 2.51 5 N 1906 2.21 5 O 2280 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 10872 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1274, 9475 Classifications: {'peptide': 1274} Incomplete info: {'backbone_only': 239, 'truncation_to_alanine': 10} Link IDs: {'CIS': 5, 'PTRANS': 28, 'TRANS': 1240} Chain breaks: 4 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 1078 Unresolved non-hydrogen angles: 1539 Unresolved non-hydrogen dihedrals: 691 Unresolved non-hydrogen chiralities: 308 Planarities with less than four sites: {'GLN:plan1': 16, 'ARG:plan': 4, 'TYR:plan': 9, 'ASN:plan1': 16, 'TRP:plan': 1, 'ASP:plan': 24, 'PHE:plan': 14, 'GLU:plan': 21, 'HIS:plan': 4} Unresolved non-hydrogen planarities: 526 Chain: "B" Number of atoms: 616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 616 Classifications: {'RNA': 29} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 4, 'rna3p_pur': 11, 'rna3p_pyr': 10} Link IDs: {'rna2p': 8, 'rna3p': 20} Chain: "C" Number of atoms: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 427 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Chain: "D" Number of atoms: 354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 354 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Time building chain proxies: 6.77, per 1000 atoms: 0.62 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: 3.02 Conformation dependent library (CDL) restraints added in 1.5 seconds 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1968 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 6 sheets defined 38.7% alpha, 7.2% beta 5 base pairs and 31 stacking pairs defined. Time for finding SS restraints: 3.82 Creating SS restraints... Processing helix chain 'A' and resid 26 through 32 removed outlier: 3.506A pdb=" N ASN A 30 " --> pdb=" O LYS A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 53 removed outlier: 3.755A pdb=" N GLN A 52 " --> pdb=" O LYS A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 63 Processing helix chain 'A' and resid 75 through 85 removed outlier: 3.652A pdb=" N VAL A 82 " --> pdb=" O ASN A 78 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TYR A 83 " --> pdb=" O TYR A 79 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE A 84 " --> pdb=" O SER A 80 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LYS A 85 " --> pdb=" O ASP A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 114 removed outlier: 3.920A pdb=" N ALA A 101 " --> pdb=" O ASP A 97 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS A 106 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LYS A 107 " --> pdb=" O ASP A 103 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N TYR A 112 " --> pdb=" O GLN A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 123 removed outlier: 3.553A pdb=" N LEU A 122 " --> pdb=" O PHE A 119 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N PHE A 123 " --> pdb=" O LYS A 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 119 through 123' Processing helix chain 'A' and resid 136 through 143 Processing helix chain 'A' and resid 161 through 171 removed outlier: 4.115A pdb=" N GLU A 167 " --> pdb=" O ASP A 163 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE A 168 " --> pdb=" O GLU A 164 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER A 171 " --> pdb=" O GLU A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 207 Processing helix chain 'A' and resid 211 through 220 removed outlier: 3.608A pdb=" N LYS A 217 " --> pdb=" O GLU A 213 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU A 219 " --> pdb=" O LYS A 215 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N SER A 220 " --> pdb=" O ALA A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 234 removed outlier: 3.834A pdb=" N GLN A 233 " --> pdb=" O ILE A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 269 removed outlier: 3.851A pdb=" N PHE A 269 " --> pdb=" O ILE A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 285 removed outlier: 3.532A pdb=" N ILE A 278 " --> pdb=" O ASN A 274 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LYS A 280 " --> pdb=" O SER A 276 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N THR A 283 " --> pdb=" O THR A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 302 Processing helix chain 'A' and resid 303 through 308 removed outlier: 3.618A pdb=" N SER A 308 " --> pdb=" O ILE A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 320 removed outlier: 3.907A pdb=" N LYS A 317 " --> pdb=" O LYS A 314 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS A 318 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N TYR A 319 " --> pdb=" O LEU A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 357 removed outlier: 4.262A pdb=" N MET A 352 " --> pdb=" O VAL A 348 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU A 357 " --> pdb=" O GLN A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 362 removed outlier: 3.837A pdb=" N ALA A 361 " --> pdb=" O GLU A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 378 removed outlier: 6.112A pdb=" N LEU A 376 " --> pdb=" O GLU A 372 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU A 377 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE A 378 " --> pdb=" O LEU A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 399 No H-bonds generated for 'chain 'A' and resid 397 through 399' Processing helix chain 'A' and resid 400 through 407 Processing helix chain 'A' and resid 412 through 416 removed outlier: 3.638A pdb=" N THR A 415 " --> pdb=" O VAL A 412 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ALA A 416 " --> pdb=" O ILE A 413 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 412 through 416' Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 453 through 460 Processing helix chain 'A' and resid 460 through 465 removed outlier: 3.920A pdb=" N LYS A 465 " --> pdb=" O GLU A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 495 removed outlier: 4.169A pdb=" N PHE A 489 " --> pdb=" O ILE A 485 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ASP A 490 " --> pdb=" O PRO A 486 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLU A 491 " --> pdb=" O MET A 487 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ILE A 492 " --> pdb=" O ILE A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 498 No H-bonds generated for 'chain 'A' and resid 496 through 498' Processing helix chain 'A' and resid 499 through 506 Processing helix chain 'A' and resid 516 through 521 removed outlier: 4.848A pdb=" N ASP A 521 " --> pdb=" O SER A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 528 Processing helix chain 'A' and resid 529 through 532 removed outlier: 3.942A pdb=" N GLN A 532 " --> pdb=" O LEU A 529 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 529 through 532' Processing helix chain 'A' and resid 533 through 540 removed outlier: 3.768A pdb=" N LEU A 537 " --> pdb=" O THR A 533 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N HIS A 538 " --> pdb=" O ASN A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 544 removed outlier: 4.009A pdb=" N HIS A 544 " --> pdb=" O LYS A 541 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 541 through 544' Processing helix chain 'A' and resid 564 through 569 removed outlier: 3.748A pdb=" N CYS A 568 " --> pdb=" O VAL A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 573 removed outlier: 3.930A pdb=" N ALA A 573 " --> pdb=" O PHE A 570 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 570 through 573' Processing helix chain 'A' and resid 574 through 580 Processing helix chain 'A' and resid 582 through 588 removed outlier: 4.068A pdb=" N ILE A 586 " --> pdb=" O ILE A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 612 No H-bonds generated for 'chain 'A' and resid 610 through 612' Processing helix chain 'A' and resid 613 through 618 Processing helix chain 'A' and resid 643 through 648 removed outlier: 3.528A pdb=" N LYS A 647 " --> pdb=" O ASP A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 673 removed outlier: 3.887A pdb=" N LEU A 669 " --> pdb=" O ALA A 665 " (cutoff:3.500A) Proline residue: A 670 - end of helix removed outlier: 3.719A pdb=" N PHE A 673 " --> pdb=" O LEU A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 683 Processing helix chain 'A' and resid 685 through 695 removed outlier: 3.606A pdb=" N LEU A 689 " --> pdb=" O SER A 685 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N HIS A 694 " --> pdb=" O ARG A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 725 removed outlier: 3.529A pdb=" N LYS A 719 " --> pdb=" O GLU A 715 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N PHE A 720 " --> pdb=" O ASP A 716 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE A 723 " --> pdb=" O LYS A 719 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N TYR A 724 " --> pdb=" O PHE A 720 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS A 725 " --> pdb=" O ILE A 721 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 738 removed outlier: 3.597A pdb=" N PHE A 737 " --> pdb=" O TRP A 734 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLY A 738 " --> pdb=" O LYS A 735 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 747 removed outlier: 3.872A pdb=" N TYR A 747 " --> pdb=" O THR A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 755 removed outlier: 3.608A pdb=" N ARG A 755 " --> pdb=" O ASP A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 781 removed outlier: 3.514A pdb=" N VAL A 777 " --> pdb=" O TYR A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 812 removed outlier: 4.092A pdb=" N PHE A 812 " --> pdb=" O TRP A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 905 removed outlier: 3.671A pdb=" N ASN A 901 " --> pdb=" O ASN A 897 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU A 904 " --> pdb=" O ILE A 900 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS A 905 " --> pdb=" O ASN A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 953 through 961 removed outlier: 3.987A pdb=" N ALA A 959 " --> pdb=" O ASP A 955 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE A 960 " --> pdb=" O LYS A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 979 through 999 removed outlier: 4.560A pdb=" N LEU A 985 " --> pdb=" O LYS A 981 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N SER A 986 " --> pdb=" O GLU A 982 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLN A 987 " --> pdb=" O GLY A 983 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL A 988 " --> pdb=" O TYR A 984 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N HIS A 990 " --> pdb=" O SER A 986 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU A 995 " --> pdb=" O GLU A 991 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU A 998 " --> pdb=" O LYS A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 1025 through 1033 removed outlier: 3.629A pdb=" N MET A1030 " --> pdb=" O LYS A1026 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE A1032 " --> pdb=" O GLU A1028 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU A1033 " --> pdb=" O LYS A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1102 through 1111 removed outlier: 3.713A pdb=" N GLN A1106 " --> pdb=" O VAL A1102 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLU A1107 " --> pdb=" O SER A1103 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N PHE A1108 " --> pdb=" O LYS A1104 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE A1109 " --> pdb=" O SER A1105 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS A1111 " --> pdb=" O GLU A1107 " (cutoff:3.500A) Processing helix chain 'A' and resid 1129 through 1133 removed outlier: 3.687A pdb=" N ASN A1132 " --> pdb=" O ASP A1129 " (cutoff:3.500A) Processing helix chain 'A' and resid 1169 through 1178 removed outlier: 3.569A pdb=" N GLU A1173 " --> pdb=" O TYR A1169 " (cutoff:3.500A) Processing helix chain 'A' and resid 1191 through 1198 removed outlier: 3.539A pdb=" N ILE A1195 " --> pdb=" O ILE A1191 " (cutoff:3.500A) Processing helix chain 'A' and resid 1200 through 1213 removed outlier: 3.814A pdb=" N PHE A1204 " --> pdb=" O ASP A1200 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA A1205 " --> pdb=" O LYS A1201 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS A1206 " --> pdb=" O LYS A1202 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SER A1209 " --> pdb=" O ALA A1205 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N VAL A1210 " --> pdb=" O LYS A1206 " (cutoff:3.500A) Processing helix chain 'A' and resid 1242 through 1246 Processing helix chain 'A' and resid 1256 through 1261 removed outlier: 4.079A pdb=" N HIS A1261 " --> pdb=" O ASN A1257 " (cutoff:3.500A) Processing helix chain 'A' and resid 1261 through 1266 Processing helix chain 'A' and resid 1268 through 1274 removed outlier: 3.747A pdb=" N ILE A1273 " --> pdb=" O LEU A1269 " (cutoff:3.500A) Processing helix chain 'A' and resid 1287 through 1295 removed outlier: 3.670A pdb=" N TYR A1291 " --> pdb=" O LYS A1287 " (cutoff:3.500A) Processing helix chain 'A' and resid 1296 through 1298 No H-bonds generated for 'chain 'A' and resid 1296 through 1298' Processing sheet with id=AA1, first strand: chain 'A' and resid 596 through 598 removed outlier: 3.566A pdb=" N PHE A 596 " --> pdb=" O TYR A 832 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU A 830 " --> pdb=" O LEU A 598 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU A 829 " --> pdb=" O HIS A 881 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N HIS A 881 " --> pdb=" O GLU A 829 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS A 877 " --> pdb=" O ARG A 833 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N PHE A 878 " --> pdb=" O LEU A 21 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU A 17 " --> pdb=" O CYS A 882 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU A 20 " --> pdb=" O TYR A 789 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N TYR A 628 " --> pdb=" O ILE A 788 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N LEU A 621 " --> pdb=" O ILE A 657 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE A 657 " --> pdb=" O LEU A 621 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 596 through 598 removed outlier: 3.566A pdb=" N PHE A 596 " --> pdb=" O TYR A 832 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU A 830 " --> pdb=" O LEU A 598 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU A 829 " --> pdb=" O HIS A 881 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N HIS A 881 " --> pdb=" O GLU A 829 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS A 877 " --> pdb=" O ARG A 833 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N PHE A 878 " --> pdb=" O LEU A 21 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU A 17 " --> pdb=" O CYS A 882 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU A 20 " --> pdb=" O TYR A 789 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N TYR A 628 " --> pdb=" O ILE A 788 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N LEU A 621 " --> pdb=" O ILE A 657 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE A 657 " --> pdb=" O LEU A 621 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 822 through 824 Processing sheet with id=AA4, first strand: chain 'A' and resid 912 through 913 removed outlier: 6.513A pdb=" N HIS A 912 " --> pdb=" O ILE A1002 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 925 through 929 removed outlier: 7.389A pdb=" N TYR A 926 " --> pdb=" O GLN A 938 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N GLN A 938 " --> pdb=" O TYR A 926 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N LEU A 928 " --> pdb=" O ILE A 936 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1125 through 1126 210 hydrogen bonds defined for protein. 582 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 10 hydrogen bonds 16 hydrogen bond angles 0 basepair planarities 5 basepair parallelities 31 stacking parallelities Total time for adding SS restraints: 4.27 Time building geometry restraints manager: 3.46 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: 0.910 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: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 31.260 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.000 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.76 (0.17), residues: 1264 helix: -4.51 (0.11), residues: 419 sheet: -3.43 (0.45), residues: 112 loop : -3.59 (0.18), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.004 TRP A1142 HIS 0.012 0.003 HIS A 183 PHE 0.040 0.004 PHE A1240 TYR 0.042 0.004 TYR A1037 ARG 0.010 0.001 ARG A 918 Details of bonding type rmsd hydrogen bonds : bond 0.31380 ( 199) hydrogen bonds : angle 13.01689 ( 598) covalent geometry : bond 0.00925 (11212) covalent geometry : angle 1.10661 (15276) *********************** 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 : 1.098 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: 0.8483 (mmtm) REVERT: A 166 LEU cc_start: 0.9040 (mm) cc_final: 0.8685 (mm) REVERT: A 638 ASN cc_start: 0.8333 (p0) cc_final: 0.8074 (p0) REVERT: A 758 GLU cc_start: 0.7695 (mt-10) cc_final: 0.7243 (tp30) REVERT: A 791 LYS cc_start: 0.8231 (mttt) cc_final: 0.7994 (mtpt) REVERT: A 918 ARG cc_start: 0.6039 (mmt90) cc_final: 0.2908 (tpt170) REVERT: A 1204 PHE cc_start: 0.7098 (m-80) cc_final: 0.6615 (m-80) REVERT: A 1206 LYS cc_start: 0.8518 (mmpt) cc_final: 0.8258 (ptmt) REVERT: A 1235 ASP cc_start: 0.8756 (p0) cc_final: 0.8384 (p0) REVERT: A 1241 PHE cc_start: 0.6424 (t80) cc_final: 0.6183 (t80) outliers start: 7 outliers final: 1 residues processed: 255 average time/residue: 0.2784 time to fit residues: 95.7891 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 : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 7.9990 chunk 100 optimal weight: 0.5980 chunk 55 optimal weight: 50.0000 chunk 34 optimal weight: 0.9990 chunk 67 optimal weight: 6.9990 chunk 53 optimal weight: 0.2980 chunk 103 optimal weight: 0.0000 chunk 40 optimal weight: 50.0000 chunk 62 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 119 optimal weight: 10.0000 overall best weight: 0.5788 ------------------------------------------------------------------------------- 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 = 0.4144 r_free = 0.4144 target = 0.154644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.118619 restraints weight = 17518.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.120348 restraints weight = 12870.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.121868 restraints weight = 8524.189| |-----------------------------------------------------------------------------| r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6797 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11212 Z= 0.135 Angle : 0.640 7.674 15276 Z= 0.354 Chirality : 0.044 0.177 1525 Planarity : 0.005 0.067 1805 Dihedral : 19.506 89.126 2207 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.84 (0.19), residues: 1264 helix: -3.33 (0.18), residues: 411 sheet: -3.02 (0.44), residues: 111 loop : -3.29 (0.20), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 175 HIS 0.004 0.001 HIS A 954 PHE 0.018 0.002 PHE A 7 TYR 0.017 0.001 TYR A 591 ARG 0.005 0.001 ARG A 872 Details of bonding type rmsd hydrogen bonds : bond 0.04411 ( 199) hydrogen bonds : angle 6.90992 ( 598) covalent geometry : bond 0.00282 (11212) covalent geometry : angle 0.63972 (15276) *********************** 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 212 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 1.285 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 112 TYR cc_start: 0.7226 (t80) cc_final: 0.6978 (t80) REVERT: A 126 ASN cc_start: 0.8203 (t0) cc_final: 0.7950 (t0) REVERT: A 169 ILE cc_start: 0.9140 (pt) cc_final: 0.8704 (tp) REVERT: A 873 PHE cc_start: 0.5062 (m-10) cc_final: 0.4591 (m-80) REVERT: A 918 ARG cc_start: 0.5993 (mmt90) cc_final: 0.2981 (tpt170) REVERT: A 949 MET cc_start: 0.7093 (tpt) cc_final: 0.6713 (tpt) REVERT: A 1204 PHE cc_start: 0.6753 (m-80) cc_final: 0.6478 (m-80) REVERT: A 1206 LYS cc_start: 0.8309 (mmpt) cc_final: 0.7875 (ttpt) REVERT: A 1235 ASP cc_start: 0.8507 (p0) cc_final: 0.7976 (p0) REVERT: A 1250 MET cc_start: 0.8639 (mmm) cc_final: 0.8292 (mmm) outliers start: 0 outliers final: 0 residues processed: 212 average time/residue: 0.3164 time to fit residues: 95.2339 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 : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 109 optimal weight: 10.0000 chunk 21 optimal weight: 9.9990 chunk 66 optimal weight: 4.9990 chunk 102 optimal weight: 0.9980 chunk 42 optimal weight: 50.0000 chunk 122 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 89 optimal weight: 6.9990 chunk 93 optimal weight: 7.9990 chunk 97 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 ASN 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.148152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.113458 restraints weight = 18459.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.113936 restraints weight = 14856.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.114878 restraints weight = 12018.329| |-----------------------------------------------------------------------------| r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6978 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 11212 Z= 0.223 Angle : 0.682 7.663 15276 Z= 0.371 Chirality : 0.046 0.181 1525 Planarity : 0.004 0.054 1805 Dihedral : 19.625 88.911 2207 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.03 % Favored : 87.97 % Rotamer: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.40 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.42 (0.20), residues: 1264 helix: -2.77 (0.20), residues: 438 sheet: -3.07 (0.45), residues: 100 loop : -3.12 (0.21), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 808 HIS 0.005 0.001 HIS A1261 PHE 0.020 0.002 PHE A 888 TYR 0.020 0.002 TYR A 591 ARG 0.005 0.000 ARG A 872 Details of bonding type rmsd hydrogen bonds : bond 0.05547 ( 199) hydrogen bonds : angle 6.26302 ( 598) covalent geometry : bond 0.00498 (11212) covalent geometry : angle 0.68197 (15276) *********************** 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 173 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 1.214 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: 0.8819 (mp) cc_final: 0.8482 (mp) REVERT: A 126 ASN cc_start: 0.8494 (t0) cc_final: 0.8212 (t0) REVERT: A 625 ASP cc_start: 0.7045 (m-30) cc_final: 0.6800 (p0) REVERT: A 918 ARG cc_start: 0.6259 (mmt90) cc_final: 0.3189 (tpt170) REVERT: A 949 MET cc_start: 0.7095 (tpt) cc_final: 0.6841 (tpt) REVERT: A 953 TYR cc_start: 0.6046 (m-80) cc_final: 0.5827 (m-80) REVERT: A 1006 GLN cc_start: 0.7951 (mm110) cc_final: 0.7685 (mm110) REVERT: A 1206 LYS cc_start: 0.8368 (mmpt) cc_final: 0.8044 (pttm) REVERT: A 1230 ILE cc_start: 0.7529 (pt) cc_final: 0.7011 (pt) REVERT: A 1235 ASP cc_start: 0.8707 (p0) cc_final: 0.8265 (p0) REVERT: A 1250 MET cc_start: 0.8692 (mmm) cc_final: 0.8458 (mmm) outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.2081 time to fit residues: 53.4510 Evaluate side-chains 133 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 10 optimal weight: 9.9990 chunk 32 optimal weight: 2.9990 chunk 35 optimal weight: 0.0050 chunk 62 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 121 optimal weight: 0.0070 chunk 5 optimal weight: 0.7980 chunk 106 optimal weight: 0.5980 chunk 103 optimal weight: 0.1980 chunk 118 optimal weight: 9.9990 chunk 47 optimal weight: 10.0000 overall best weight: 0.3212 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 637 ASN ** A 780 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 942 ASN A 954 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.155046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.119391 restraints weight = 17407.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.121725 restraints weight = 11483.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.122929 restraints weight = 7112.494| |-----------------------------------------------------------------------------| r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6743 moved from start: 0.3875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11212 Z= 0.116 Angle : 0.567 7.348 15276 Z= 0.312 Chirality : 0.042 0.266 1525 Planarity : 0.003 0.056 1805 Dihedral : 19.122 87.783 2207 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.78 (0.21), residues: 1264 helix: -2.13 (0.22), residues: 422 sheet: -2.74 (0.46), residues: 102 loop : -2.81 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 609 HIS 0.004 0.001 HIS A 954 PHE 0.016 0.001 PHE A1005 TYR 0.016 0.001 TYR A 926 ARG 0.002 0.000 ARG A 872 Details of bonding type rmsd hydrogen bonds : bond 0.03608 ( 199) hydrogen bonds : angle 5.47104 ( 598) covalent geometry : bond 0.00243 (11212) covalent geometry : angle 0.56686 (15276) *********************** 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 179 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 1.202 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: 0.7315 (t80) cc_final: 0.7079 (t80) REVERT: A 126 ASN cc_start: 0.8258 (t0) cc_final: 0.7678 (t0) REVERT: A 682 TYR cc_start: 0.8049 (m-80) cc_final: 0.7669 (m-80) REVERT: A 918 ARG cc_start: 0.5744 (mmt90) cc_final: 0.2853 (tpt170) REVERT: A 1206 LYS cc_start: 0.8262 (mmpt) cc_final: 0.7918 (pttm) REVERT: A 1235 ASP cc_start: 0.8433 (p0) cc_final: 0.7999 (p0) REVERT: A 1250 MET cc_start: 0.8630 (mmm) cc_final: 0.8424 (mmm) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.2219 time to fit residues: 57.7980 Evaluate side-chains 130 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 124 optimal weight: 8.9990 chunk 62 optimal weight: 10.0000 chunk 85 optimal weight: 9.9990 chunk 126 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 19 optimal weight: 10.0000 chunk 114 optimal weight: 10.0000 chunk 123 optimal weight: 3.9990 chunk 107 optimal weight: 8.9990 chunk 100 optimal weight: 1.9990 chunk 26 optimal weight: 9.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 637 ASN A 649 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.148497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.113946 restraints weight = 18267.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.115322 restraints weight = 13783.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.116880 restraints weight = 9240.902| |-----------------------------------------------------------------------------| r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6955 moved from start: 0.3786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 11212 Z= 0.231 Angle : 0.675 8.254 15276 Z= 0.363 Chirality : 0.047 0.204 1525 Planarity : 0.004 0.048 1805 Dihedral : 19.443 88.627 2207 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.47 % Favored : 88.53 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.84 (0.22), residues: 1264 helix: -2.16 (0.22), residues: 439 sheet: -3.23 (0.44), residues: 102 loop : -2.77 (0.22), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 808 HIS 0.004 0.001 HIS A 183 PHE 0.024 0.002 PHE A 896 TYR 0.019 0.002 TYR A 178 ARG 0.006 0.001 ARG A 872 Details of bonding type rmsd hydrogen bonds : bond 0.04905 ( 199) hydrogen bonds : angle 5.69803 ( 598) covalent geometry : bond 0.00522 (11212) covalent geometry : angle 0.67513 (15276) *********************** 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 162 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 1.113 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: 0.8342 (t0) cc_final: 0.8121 (t0) REVERT: A 682 TYR cc_start: 0.8088 (m-80) cc_final: 0.7772 (m-80) REVERT: A 825 ASN cc_start: 0.8464 (m-40) cc_final: 0.8106 (m-40) REVERT: A 918 ARG cc_start: 0.6165 (mmt90) cc_final: 0.3176 (tpt170) REVERT: A 1024 TYR cc_start: 0.3763 (m-80) cc_final: 0.3227 (m-80) REVERT: A 1206 LYS cc_start: 0.8251 (mmpt) cc_final: 0.7889 (pttm) REVERT: A 1230 ILE cc_start: 0.7648 (pt) cc_final: 0.7339 (pt) REVERT: A 1235 ASP cc_start: 0.8665 (p0) cc_final: 0.8246 (p0) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.2120 time to fit residues: 51.6114 Evaluate side-chains 127 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 65 optimal weight: 2.9990 chunk 42 optimal weight: 0.0970 chunk 21 optimal weight: 9.9990 chunk 71 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 9 optimal weight: 9.9990 chunk 129 optimal weight: 8.9990 chunk 15 optimal weight: 0.0370 chunk 86 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 83 optimal weight: 0.0070 overall best weight: 0.3674 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 881 HIS ** 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 = 0.4175 r_free = 0.4175 target = 0.156936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.121403 restraints weight = 17975.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.122246 restraints weight = 11453.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.123027 restraints weight = 9080.811| |-----------------------------------------------------------------------------| r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6756 moved from start: 0.4414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11212 Z= 0.109 Angle : 0.559 8.095 15276 Z= 0.304 Chirality : 0.041 0.188 1525 Planarity : 0.003 0.055 1805 Dihedral : 18.964 87.380 2207 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.40 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.46 (0.22), residues: 1264 helix: -1.83 (0.23), residues: 445 sheet: -2.78 (0.48), residues: 95 loop : -2.62 (0.22), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 609 HIS 0.003 0.001 HIS A 697 PHE 0.029 0.001 PHE A 7 TYR 0.013 0.001 TYR A 112 ARG 0.002 0.000 ARG A 872 Details of bonding type rmsd hydrogen bonds : bond 0.03632 ( 199) hydrogen bonds : angle 5.22669 ( 598) covalent geometry : bond 0.00233 (11212) covalent geometry : angle 0.55885 (15276) *********************** 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 164 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 1.167 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: 0.8163 (t0) cc_final: 0.7703 (t0) REVERT: A 172 PHE cc_start: 0.7987 (m-80) cc_final: 0.7773 (m-80) REVERT: A 682 TYR cc_start: 0.8009 (m-80) cc_final: 0.7681 (m-80) REVERT: A 825 ASN cc_start: 0.8151 (m-40) cc_final: 0.7721 (m-40) REVERT: A 918 ARG cc_start: 0.5744 (mmt90) cc_final: 0.2892 (tpt170) REVERT: A 950 LYS cc_start: 0.6471 (mmtp) cc_final: 0.5937 (mptt) REVERT: A 1230 ILE cc_start: 0.7639 (pt) cc_final: 0.7121 (pt) REVERT: A 1235 ASP cc_start: 0.8492 (p0) cc_final: 0.8112 (p0) REVERT: A 1250 MET cc_start: 0.8694 (mmm) cc_final: 0.8387 (mmm) REVERT: A 1268 MET cc_start: 0.7259 (ptt) cc_final: 0.6844 (ptt) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.2187 time to fit residues: 52.5181 Evaluate side-chains 123 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 67 optimal weight: 0.0870 chunk 21 optimal weight: 8.9990 chunk 42 optimal weight: 50.0000 chunk 88 optimal weight: 5.9990 chunk 95 optimal weight: 0.0870 chunk 47 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 70 optimal weight: 8.9990 chunk 117 optimal weight: 20.0000 chunk 59 optimal weight: 4.9990 overall best weight: 2.2342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 637 ASN ** 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 = 0.4107 r_free = 0.4107 target = 0.151509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.117039 restraints weight = 18255.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.118724 restraints weight = 13345.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.119740 restraints weight = 8821.670| |-----------------------------------------------------------------------------| r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6867 moved from start: 0.4346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11212 Z= 0.174 Angle : 0.609 7.522 15276 Z= 0.330 Chirality : 0.044 0.173 1525 Planarity : 0.004 0.051 1805 Dihedral : 19.156 88.320 2207 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.97 % Favored : 90.03 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.45 (0.22), residues: 1264 helix: -1.76 (0.23), residues: 451 sheet: -2.98 (0.48), residues: 97 loop : -2.62 (0.22), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 609 HIS 0.005 0.001 HIS A1261 PHE 0.031 0.002 PHE A 888 TYR 0.021 0.002 TYR A 112 ARG 0.004 0.000 ARG A 872 Details of bonding type rmsd hydrogen bonds : bond 0.04250 ( 199) hydrogen bonds : angle 5.35947 ( 598) covalent geometry : bond 0.00392 (11212) covalent geometry : angle 0.60921 (15276) *********************** 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 151 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 1.321 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: 0.8257 (t0) cc_final: 0.8011 (t0) REVERT: A 201 TYR cc_start: 0.6107 (t80) cc_final: 0.5893 (t80) REVERT: A 682 TYR cc_start: 0.8021 (m-80) cc_final: 0.7775 (m-80) REVERT: A 825 ASN cc_start: 0.8632 (m-40) cc_final: 0.8267 (m-40) REVERT: A 873 PHE cc_start: 0.4680 (m-10) cc_final: 0.4475 (m-10) REVERT: A 918 ARG cc_start: 0.6076 (mmt90) cc_final: 0.3102 (tpt170) REVERT: A 1024 TYR cc_start: 0.3616 (m-80) cc_final: 0.3149 (m-80) REVERT: A 1206 LYS cc_start: 0.8149 (mmpt) cc_final: 0.7817 (pttm) REVERT: A 1230 ILE cc_start: 0.7608 (pt) cc_final: 0.7135 (pt) REVERT: A 1235 ASP cc_start: 0.8624 (p0) cc_final: 0.8234 (p0) REVERT: A 1250 MET cc_start: 0.8725 (mmm) cc_final: 0.8355 (mmm) REVERT: A 1268 MET cc_start: 0.7346 (ptt) cc_final: 0.7063 (ptt) outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.2543 time to fit residues: 56.6430 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 : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 69 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 chunk 123 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 40 optimal weight: 40.0000 chunk 66 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 125 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 37 optimal weight: 0.0670 chunk 33 optimal weight: 20.0000 overall best weight: 1.1724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 759 ASN ** 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 = 0.4145 r_free = 0.4145 target = 0.154626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.118216 restraints weight = 18122.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.121112 restraints weight = 13224.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.122174 restraints weight = 8364.954| |-----------------------------------------------------------------------------| r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6796 moved from start: 0.4581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11212 Z= 0.123 Angle : 0.555 7.649 15276 Z= 0.302 Chirality : 0.042 0.176 1525 Planarity : 0.003 0.055 1805 Dihedral : 18.952 89.150 2207 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % Rotamer: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.40 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.26 (0.23), residues: 1264 helix: -1.56 (0.24), residues: 451 sheet: -2.88 (0.47), residues: 100 loop : -2.53 (0.23), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 609 HIS 0.004 0.001 HIS A1261 PHE 0.026 0.001 PHE A 888 TYR 0.015 0.001 TYR A 201 ARG 0.003 0.000 ARG A 872 Details of bonding type rmsd hydrogen bonds : bond 0.03459 ( 199) hydrogen bonds : angle 5.15896 ( 598) covalent geometry : bond 0.00277 (11212) covalent geometry : angle 0.55502 (15276) *********************** 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 143 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 1.132 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: 0.8164 (t0) cc_final: 0.7723 (t0) REVERT: A 640 ILE cc_start: 0.8296 (pt) cc_final: 0.7966 (mt) REVERT: A 682 TYR cc_start: 0.7984 (m-80) cc_final: 0.7696 (m-80) REVERT: A 825 ASN cc_start: 0.8540 (m-40) cc_final: 0.8110 (m-40) REVERT: A 873 PHE cc_start: 0.4601 (m-10) cc_final: 0.4362 (m-10) REVERT: A 918 ARG cc_start: 0.5849 (mmt90) cc_final: 0.2940 (tpt170) REVERT: A 1024 TYR cc_start: 0.3240 (m-80) cc_final: 0.2835 (m-80) REVERT: A 1034 LYS cc_start: 0.7508 (mptt) cc_final: 0.6979 (mptt) REVERT: A 1230 ILE cc_start: 0.7590 (pt) cc_final: 0.7141 (pt) REVERT: A 1235 ASP cc_start: 0.8574 (p0) cc_final: 0.8193 (p0) REVERT: A 1250 MET cc_start: 0.8702 (mmm) cc_final: 0.8373 (mmm) REVERT: A 1268 MET cc_start: 0.7359 (ptt) cc_final: 0.6943 (ptt) outliers start: 0 outliers final: 0 residues processed: 143 average time/residue: 0.2229 time to fit residues: 47.0765 Evaluate side-chains 116 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 42 optimal weight: 50.0000 chunk 53 optimal weight: 0.0370 chunk 47 optimal weight: 20.0000 chunk 54 optimal weight: 1.9990 chunk 34 optimal weight: 20.0000 chunk 6 optimal weight: 5.9990 chunk 22 optimal weight: 0.0470 chunk 50 optimal weight: 0.8980 chunk 2 optimal weight: 0.0070 chunk 25 optimal weight: 6.9990 chunk 75 optimal weight: 6.9990 overall best weight: 0.5976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4191 r_free = 0.4191 target = 0.158608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.122586 restraints weight = 18168.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.122807 restraints weight = 10630.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.123764 restraints weight = 8057.640| |-----------------------------------------------------------------------------| r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6759 moved from start: 0.4918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11212 Z= 0.108 Angle : 0.547 8.354 15276 Z= 0.296 Chirality : 0.042 0.166 1525 Planarity : 0.003 0.055 1805 Dihedral : 18.816 88.868 2207 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % 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 : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.12 (0.23), residues: 1264 helix: -1.41 (0.24), residues: 460 sheet: -2.49 (0.47), residues: 106 loop : -2.53 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 609 HIS 0.004 0.001 HIS A1261 PHE 0.025 0.001 PHE A1203 TYR 0.011 0.001 TYR A 591 ARG 0.003 0.000 ARG A 872 Details of bonding type rmsd hydrogen bonds : bond 0.03375 ( 199) hydrogen bonds : angle 5.07861 ( 598) covalent geometry : bond 0.00238 (11212) covalent geometry : angle 0.54737 (15276) *********************** 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 147 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 ASN cc_start: 0.8074 (t0) cc_final: 0.7458 (t0) REVERT: A 640 ILE cc_start: 0.8201 (pt) cc_final: 0.7871 (mt) REVERT: A 682 TYR cc_start: 0.7974 (m-80) cc_final: 0.7638 (m-80) REVERT: A 825 ASN cc_start: 0.8367 (m-40) cc_final: 0.7977 (m-40) REVERT: A 873 PHE cc_start: 0.4521 (m-10) cc_final: 0.4316 (m-10) REVERT: A 918 ARG cc_start: 0.5788 (mmt90) cc_final: 0.2887 (tpt170) REVERT: A 1024 TYR cc_start: 0.3121 (m-80) cc_final: 0.2704 (m-80) REVERT: A 1034 LYS cc_start: 0.7480 (mptt) cc_final: 0.7028 (mptt) REVERT: A 1230 ILE cc_start: 0.7558 (pt) cc_final: 0.7203 (pt) REVERT: A 1235 ASP cc_start: 0.8535 (p0) cc_final: 0.8170 (p0) REVERT: A 1250 MET cc_start: 0.8657 (mmm) cc_final: 0.8353 (mmm) REVERT: A 1268 MET cc_start: 0.7297 (ptt) cc_final: 0.6936 (ptt) outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 0.2322 time to fit residues: 49.7603 Evaluate side-chains 119 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 83 optimal weight: 6.9990 chunk 39 optimal weight: 10.0000 chunk 47 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 70 optimal weight: 8.9990 chunk 32 optimal weight: 10.0000 chunk 111 optimal weight: 20.0000 chunk 5 optimal weight: 4.9990 chunk 113 optimal weight: 10.0000 chunk 56 optimal weight: 50.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 599 ASN A 607 ASN A 637 ASN A 745 GLN ** A 887 ASN ** 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 = 0.4062 r_free = 0.4062 target = 0.148056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.107259 restraints weight = 18990.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.110337 restraints weight = 11181.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.112347 restraints weight = 7957.842| |-----------------------------------------------------------------------------| r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.4449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.094 11212 Z= 0.358 Angle : 0.825 8.783 15276 Z= 0.438 Chirality : 0.054 0.223 1525 Planarity : 0.005 0.046 1805 Dihedral : 19.584 89.739 2207 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 17.39 Ramachandran Plot: Outliers : 0.08 % Allowed : 13.13 % Favored : 86.79 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.40 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.53 (0.22), residues: 1264 helix: -1.89 (0.23), residues: 457 sheet: -3.18 (0.46), residues: 110 loop : -2.56 (0.23), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.004 TRP A 609 HIS 0.008 0.002 HIS A 881 PHE 0.025 0.003 PHE A1240 TYR 0.040 0.003 TYR A 984 ARG 0.003 0.001 ARG A 833 Details of bonding type rmsd hydrogen bonds : bond 0.06343 ( 199) hydrogen bonds : angle 5.83532 ( 598) covalent geometry : bond 0.00804 (11212) covalent geometry : angle 0.82520 (15276) ********************** 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 : 1.175 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 102 LYS cc_start: 0.7960 (ttmt) cc_final: 0.7645 (ttpp) REVERT: A 126 ASN cc_start: 0.8439 (t0) cc_final: 0.8238 (t0) REVERT: A 682 TYR cc_start: 0.8084 (m-80) cc_final: 0.7873 (m-80) REVERT: A 825 ASN cc_start: 0.8788 (m-40) cc_final: 0.8255 (m-40) REVERT: A 918 ARG cc_start: 0.6233 (mmt90) cc_final: 0.3230 (tpt170) REVERT: A 1024 TYR cc_start: 0.3804 (m-80) cc_final: 0.3326 (m-80) REVERT: A 1034 LYS cc_start: 0.7804 (mptt) cc_final: 0.7322 (mptt) REVERT: A 1230 ILE cc_start: 0.7664 (pt) cc_final: 0.7045 (pt) REVERT: A 1235 ASP cc_start: 0.8763 (p0) cc_final: 0.8385 (p0) REVERT: A 1268 MET cc_start: 0.7723 (ptt) cc_final: 0.7239 (ptt) outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.2280 time to fit residues: 50.9797 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 : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 104 optimal weight: 0.4980 chunk 22 optimal weight: 8.9990 chunk 108 optimal weight: 1.9990 chunk 3 optimal weight: 0.1980 chunk 68 optimal weight: 4.9990 chunk 92 optimal weight: 8.9990 chunk 18 optimal weight: 0.6980 chunk 40 optimal weight: 40.0000 chunk 13 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 chunk 109 optimal weight: 10.0000 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 637 ASN ** A 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 942 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.152985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.117244 restraints weight = 18340.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.119641 restraints weight = 14815.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.120692 restraints weight = 9613.127| |-----------------------------------------------------------------------------| r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6856 moved from start: 0.4681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 11212 Z= 0.151 Angle : 0.614 7.186 15276 Z= 0.332 Chirality : 0.044 0.178 1525 Planarity : 0.004 0.077 1805 Dihedral : 19.230 88.944 2207 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.02 % Favored : 90.98 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.40 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.29 (0.23), residues: 1264 helix: -1.57 (0.23), residues: 464 sheet: -2.87 (0.47), residues: 107 loop : -2.57 (0.23), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 971 HIS 0.005 0.001 HIS A1261 PHE 0.022 0.002 PHE A 888 TYR 0.023 0.002 TYR A 11 ARG 0.003 0.000 ARG A1150 Details of bonding type rmsd hydrogen bonds : bond 0.03773 ( 199) hydrogen bonds : angle 5.40189 ( 598) covalent geometry : bond 0.00344 (11212) covalent geometry : angle 0.61423 (15276) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3586.70 seconds wall clock time: 63 minutes 21.33 seconds (3801.33 seconds total)