Starting phenix.real_space_refine on Sun Jul 5 08:29:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7yfn_33794/07_2026/7yfn_33794.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yfn_33794/07_2026/7yfn_33794.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7yfn_33794/07_2026/7yfn_33794.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yfn_33794/07_2026/7yfn_33794.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yfn_33794/07_2026/7yfn_33794.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yfn_33794/07_2026/7yfn_33794.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7yfn_33794/07_2026/7yfn_33794.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7yfn_33794/07_2026/7yfn_33794.cif" } resolution = 3.8 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= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 31 atoms to isotropic. 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 3 5.49 5 S 100 5.16 5 C 16894 2.51 5 N 4503 2.21 5 O 4897 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 62 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26397 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2904 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Chain: "B" Number of atoms: 3172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3172 Classifications: {'peptide': 402} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 382} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 3777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3777 Classifications: {'peptide': 454} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 22, 'TRANS': 431} Chain breaks: 2 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 1668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1668 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 193} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "T" Number of atoms: 13822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1688, 13822 Classifications: {'peptide': 1688} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 13} Link IDs: {'CIS': 1, 'PTRANS': 79, 'TRANS': 1607} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'PHE:plan': 2, 'ARG:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 53 Chain: "F" Number of atoms: 1023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1023 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 8, 'TRANS': 115} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.96, per 1000 atoms: 0.19 Number of scatterers: 26397 At special positions: 0 Unit cell: (137.28, 164.34, 172.26, 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 100 16.00 P 3 15.00 O 4897 8.00 N 4503 7.00 C 16894 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.09 Conformation dependent library (CDL) restraints added in 942.9 milliseconds 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6236 Finding SS restraints... Secondary structure from input PDB file: 143 helices and 24 sheets defined 58.2% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 54 through 61 removed outlier: 3.789A pdb=" N ALA A 58 " --> pdb=" O VAL A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 92 Processing helix chain 'A' and resid 97 through 101 removed outlier: 4.297A pdb=" N GLU A 100 " --> pdb=" O ALA A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 128 removed outlier: 4.016A pdb=" N THR A 120 " --> pdb=" O ARG A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 146 Processing helix chain 'A' and resid 181 through 196 removed outlier: 4.844A pdb=" N ASP A 187 " --> pdb=" O ARG A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 216 Processing helix chain 'A' and resid 222 through 233 Processing helix chain 'A' and resid 252 through 263 Proline residue: A 258 - end of helix removed outlier: 4.444A pdb=" N LEU A 261 " --> pdb=" O ALA A 257 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N PHE A 262 " --> pdb=" O PRO A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 285 Processing helix chain 'A' and resid 287 through 296 removed outlier: 3.921A pdb=" N LYS A 291 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N GLU A 292 " --> pdb=" O ASP A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 321 Processing helix chain 'A' and resid 337 through 349 Processing helix chain 'A' and resid 350 through 355 Processing helix chain 'A' and resid 358 through 365 Processing helix chain 'A' and resid 366 through 368 No H-bonds generated for 'chain 'A' and resid 366 through 368' Processing helix chain 'A' and resid 369 through 374 Processing helix chain 'B' and resid 82 through 97 removed outlier: 4.680A pdb=" N GLU B 88 " --> pdb=" O ASP B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 131 Processing helix chain 'B' and resid 142 through 151 Processing helix chain 'B' and resid 186 through 198 removed outlier: 4.675A pdb=" N HIS B 192 " --> pdb=" O LYS B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 237 Processing helix chain 'B' and resid 237 through 244 Processing helix chain 'B' and resid 254 through 257 Processing helix chain 'B' and resid 258 through 263 Processing helix chain 'B' and resid 281 through 294 removed outlier: 4.432A pdb=" N ALA B 289 " --> pdb=" O ARG B 285 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LEU B 292 " --> pdb=" O PHE B 288 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE B 293 " --> pdb=" O ALA B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 396 Processing helix chain 'B' and resid 400 through 407 Processing helix chain 'B' and resid 413 through 417 Processing helix chain 'B' and resid 419 through 432 removed outlier: 4.278A pdb=" N MET B 425 " --> pdb=" O SER B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 449 Processing helix chain 'B' and resid 450 through 462 Processing helix chain 'B' and resid 471 through 479 removed outlier: 4.123A pdb=" N GLY B 479 " --> pdb=" O TYR B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 487 Processing helix chain 'D' and resid 25 through 48 Processing helix chain 'D' and resid 69 through 74 Processing helix chain 'D' and resid 286 through 297 Processing helix chain 'D' and resid 302 through 306 Processing helix chain 'D' and resid 311 through 336 Processing helix chain 'D' and resid 357 through 398 Processing helix chain 'D' and resid 562 through 566 Processing helix chain 'D' and resid 638 through 642 Processing helix chain 'D' and resid 651 through 666 removed outlier: 3.567A pdb=" N LYS D 660 " --> pdb=" O GLN D 656 " (cutoff:3.500A) Processing helix chain 'D' and resid 668 through 677 Processing helix chain 'D' and resid 692 through 704 Processing helix chain 'D' and resid 708 through 712 Processing helix chain 'D' and resid 716 through 735 removed outlier: 3.509A pdb=" N GLN D 734 " --> pdb=" O PHE D 730 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASN D 735 " --> pdb=" O GLN D 731 " (cutoff:3.500A) Processing helix chain 'D' and resid 754 through 772 removed outlier: 4.358A pdb=" N PHE D 761 " --> pdb=" O TRP D 757 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N GLU D 762 " --> pdb=" O ALA D 758 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LYS D 766 " --> pdb=" O GLU D 762 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS D 770 " --> pdb=" O LYS D 766 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 103 removed outlier: 3.746A pdb=" N ILE E 102 " --> pdb=" O SER E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 165 through 177 removed outlier: 4.232A pdb=" N ASN E 174 " --> pdb=" O GLU E 170 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N LEU E 175 " --> pdb=" O TYR E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 190 removed outlier: 3.966A pdb=" N ASP E 188 " --> pdb=" O PHE E 184 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 217 Processing helix chain 'E' and resid 221 through 226 Processing helix chain 'E' and resid 229 through 246 Processing helix chain 'E' and resid 247 through 266 Processing helix chain 'E' and resid 270 through 279 Processing helix chain 'E' and resid 280 through 284 removed outlier: 3.678A pdb=" N ASP E 283 " --> pdb=" O ARG E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 299 through 308 Processing helix chain 'T' and resid 837 through 846 removed outlier: 4.517A pdb=" N GLN T 844 " --> pdb=" O GLN T 840 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N MET T 845 " --> pdb=" O SER T 841 " (cutoff:3.500A) Processing helix chain 'T' and resid 855 through 865 Processing helix chain 'T' and resid 879 through 890 Processing helix chain 'T' and resid 893 through 905 removed outlier: 3.642A pdb=" N ILE T 905 " --> pdb=" O LEU T 901 " (cutoff:3.500A) Processing helix chain 'T' and resid 912 through 932 removed outlier: 3.694A pdb=" N ILE T 916 " --> pdb=" O TYR T 912 " (cutoff:3.500A) Proline residue: T 919 - end of helix removed outlier: 4.681A pdb=" N ASP T 922 " --> pdb=" O GLU T 918 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ASP T 923 " --> pdb=" O PRO T 919 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LYS T 926 " --> pdb=" O ASP T 922 " (cutoff:3.500A) Processing helix chain 'T' and resid 938 through 952 removed outlier: 3.816A pdb=" N LEU T 952 " --> pdb=" O ILE T 948 " (cutoff:3.500A) Processing helix chain 'T' and resid 970 through 974 Processing helix chain 'T' and resid 996 through 1006 removed outlier: 4.006A pdb=" N ASN T1002 " --> pdb=" O GLN T 998 " (cutoff:3.500A) Processing helix chain 'T' and resid 1010 through 1034 removed outlier: 4.638A pdb=" N SER T1031 " --> pdb=" O LEU T1027 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N SER T1032 " --> pdb=" O MET T1028 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLU T1034 " --> pdb=" O LYS T1030 " (cutoff:3.500A) Processing helix chain 'T' and resid 1038 through 1052 removed outlier: 4.158A pdb=" N LYS T1051 " --> pdb=" O VAL T1047 " (cutoff:3.500A) Processing helix chain 'T' and resid 1068 through 1091 removed outlier: 3.951A pdb=" N SER T1091 " --> pdb=" O PHE T1087 " (cutoff:3.500A) Processing helix chain 'T' and resid 1095 through 1125 removed outlier: 4.058A pdb=" N ASN T1116 " --> pdb=" O LEU T1112 " (cutoff:3.500A) Processing helix chain 'T' and resid 1143 through 1155 Proline residue: T1150 - end of helix Processing helix chain 'T' and resid 1157 through 1180 Processing helix chain 'T' and resid 1181 through 1188 Processing helix chain 'T' and resid 1189 through 1203 Processing helix chain 'T' and resid 1205 through 1224 Processing helix chain 'T' and resid 1228 through 1233 Processing helix chain 'T' and resid 1234 through 1247 Processing helix chain 'T' and resid 2416 through 2424 removed outlier: 3.500A pdb=" N PHE T2420 " --> pdb=" O MET T2416 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR T2424 " --> pdb=" O PHE T2420 " (cutoff:3.500A) Processing helix chain 'T' and resid 2428 through 2443 removed outlier: 3.790A pdb=" N ARG T2434 " --> pdb=" O GLY T2430 " (cutoff:3.500A) Processing helix chain 'T' and resid 2446 through 2457 Processing helix chain 'T' and resid 2468 through 2480 removed outlier: 3.925A pdb=" N ALA T2472 " --> pdb=" O TRP T2468 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE T2480 " --> pdb=" O LEU T2476 " (cutoff:3.500A) Processing helix chain 'T' and resid 2496 through 2502 removed outlier: 3.871A pdb=" N LEU T2500 " --> pdb=" O PRO T2496 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU T2502 " --> pdb=" O SER T2498 " (cutoff:3.500A) Processing helix chain 'T' and resid 2503 through 2508 removed outlier: 6.372A pdb=" N GLU T2506 " --> pdb=" O TYR T2503 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASN T2507 " --> pdb=" O LEU T2504 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA T2508 " --> pdb=" O PRO T2505 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 2503 through 2508' Processing helix chain 'T' and resid 2518 through 2535 removed outlier: 3.624A pdb=" N ARG T2535 " --> pdb=" O GLN T2531 " (cutoff:3.500A) Processing helix chain 'T' and resid 2537 through 2552 removed outlier: 3.530A pdb=" N PHE T2541 " --> pdb=" O ILE T2537 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU T2547 " --> pdb=" O ASP T2543 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE T2548 " --> pdb=" O SER T2544 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N TYR T2550 " --> pdb=" O ILE T2546 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLN T2551 " --> pdb=" O GLU T2547 " (cutoff:3.500A) Processing helix chain 'T' and resid 2552 through 2562 removed outlier: 4.235A pdb=" N ILE T2556 " --> pdb=" O ASP T2552 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N HIS T2557 " --> pdb=" O PRO T2553 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG T2558 " --> pdb=" O LYS T2554 " (cutoff:3.500A) Processing helix chain 'T' and resid 2563 through 2569 Processing helix chain 'T' and resid 2575 through 2588 Processing helix chain 'T' and resid 2603 through 2614 removed outlier: 4.239A pdb=" N GLU T2614 " --> pdb=" O ILE T2610 " (cutoff:3.500A) Processing helix chain 'T' and resid 2623 through 2630 removed outlier: 4.011A pdb=" N ILE T2628 " --> pdb=" O TYR T2625 " (cutoff:3.500A) Processing helix chain 'T' and resid 2632 through 2647 removed outlier: 3.561A pdb=" N LEU T2640 " --> pdb=" O SER T2636 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLN T2644 " --> pdb=" O LEU T2640 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N SER T2645 " --> pdb=" O GLU T2641 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N THR T2647 " --> pdb=" O ILE T2643 " (cutoff:3.500A) Processing helix chain 'T' and resid 2652 through 2670 removed outlier: 3.802A pdb=" N ASP T2660 " --> pdb=" O GLU T2656 " (cutoff:3.500A) Processing helix chain 'T' and resid 2671 through 2683 removed outlier: 3.706A pdb=" N TYR T2676 " --> pdb=" O GLU T2672 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N GLY T2677 " --> pdb=" O ASP T2673 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TRP T2679 " --> pdb=" O PHE T2675 " (cutoff:3.500A) Processing helix chain 'T' and resid 2685 through 2698 removed outlier: 3.527A pdb=" N ASN T2689 " --> pdb=" O TYR T2685 " (cutoff:3.500A) Processing helix chain 'T' and resid 2699 through 2714 removed outlier: 3.538A pdb=" N GLN T2705 " --> pdb=" O ASP T2701 " (cutoff:3.500A) Processing helix chain 'T' and resid 2724 through 2741 Processing helix chain 'T' and resid 2746 through 2753 removed outlier: 3.771A pdb=" N HIS T2752 " --> pdb=" O GLU T2748 " (cutoff:3.500A) Processing helix chain 'T' and resid 2754 through 2761 Processing helix chain 'T' and resid 2772 through 2783 removed outlier: 3.502A pdb=" N SER T2779 " --> pdb=" O ALA T2775 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL T2783 " --> pdb=" O SER T2779 " (cutoff:3.500A) Processing helix chain 'T' and resid 2788 through 2806 removed outlier: 3.905A pdb=" N PHE T2794 " --> pdb=" O ARG T2790 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS T2795 " --> pdb=" O ARG T2791 " (cutoff:3.500A) Processing helix chain 'T' and resid 2812 through 2831 Processing helix chain 'T' and resid 2836 through 2865 removed outlier: 4.001A pdb=" N LYS T2840 " --> pdb=" O THR T2836 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N TRP T2841 " --> pdb=" O PRO T2837 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU T2842 " --> pdb=" O ALA T2838 " (cutoff:3.500A) Processing helix chain 'T' and resid 2873 through 2887 Processing helix chain 'T' and resid 2895 through 2917 Processing helix chain 'T' and resid 2918 through 2920 No H-bonds generated for 'chain 'T' and resid 2918 through 2920' Processing helix chain 'T' and resid 2941 through 2958 removed outlier: 4.353A pdb=" N TRP T2945 " --> pdb=" O HIS T2941 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N HIS T2957 " --> pdb=" O VAL T2953 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASN T2958 " --> pdb=" O ALA T2954 " (cutoff:3.500A) Processing helix chain 'T' and resid 2959 through 2968 removed outlier: 4.427A pdb=" N CYS T2963 " --> pdb=" O MET T2959 " (cutoff:3.500A) Processing helix chain 'T' and resid 2979 through 2994 removed outlier: 4.128A pdb=" N GLN T2994 " --> pdb=" O LYS T2990 " (cutoff:3.500A) Processing helix chain 'T' and resid 2995 through 2999 Processing helix chain 'T' and resid 3018 through 3033 removed outlier: 3.714A pdb=" N PHE T3022 " --> pdb=" O GLN T3018 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU T3033 " --> pdb=" O PHE T3029 " (cutoff:3.500A) Processing helix chain 'T' and resid 3036 through 3051 removed outlier: 3.844A pdb=" N ASP T3050 " --> pdb=" O ALA T3046 " (cutoff:3.500A) Processing helix chain 'T' and resid 3053 through 3071 removed outlier: 3.655A pdb=" N TRP T3057 " --> pdb=" O LEU T3053 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLU T3071 " --> pdb=" O ARG T3067 " (cutoff:3.500A) Processing helix chain 'T' and resid 3078 through 3092 removed outlier: 3.503A pdb=" N TYR T3092 " --> pdb=" O ALA T3088 " (cutoff:3.500A) Processing helix chain 'T' and resid 3097 through 3109 removed outlier: 3.587A pdb=" N ILE T3104 " --> pdb=" O LEU T3100 " (cutoff:3.500A) Processing helix chain 'T' and resid 3115 through 3124 Processing helix chain 'T' and resid 3129 through 3135 removed outlier: 3.812A pdb=" N THR T3135 " --> pdb=" O TYR T3132 " (cutoff:3.500A) Processing helix chain 'T' and resid 3136 through 3146 removed outlier: 3.559A pdb=" N LEU T3140 " --> pdb=" O PHE T3136 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N SER T3145 " --> pdb=" O LEU T3141 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N HIS T3146 " --> pdb=" O THR T3142 " (cutoff:3.500A) Processing helix chain 'T' and resid 3151 through 3163 removed outlier: 3.839A pdb=" N ILE T3155 " --> pdb=" O MET T3151 " (cutoff:3.500A) Processing helix chain 'T' and resid 3163 through 3182 removed outlier: 4.510A pdb=" N LEU T3167 " --> pdb=" O TYR T3163 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N PHE T3169 " --> pdb=" O GLN T3165 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N GLN T3170 " --> pdb=" O ALA T3166 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR T3173 " --> pdb=" O PHE T3169 " (cutoff:3.500A) Processing helix chain 'T' and resid 3203 through 3218 removed outlier: 4.388A pdb=" N TYR T3207 " --> pdb=" O GLN T3203 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU T3208 " --> pdb=" O PRO T3204 " (cutoff:3.500A) Processing helix chain 'T' and resid 3219 through 3237 Processing helix chain 'T' and resid 3240 through 3263 removed outlier: 4.854A pdb=" N LEU T3263 " --> pdb=" O ASN T3259 " (cutoff:3.500A) Processing helix chain 'T' and resid 3273 through 3283 removed outlier: 3.504A pdb=" N VAL T3281 " --> pdb=" O GLU T3277 " (cutoff:3.500A) Processing helix chain 'T' and resid 3288 through 3300 removed outlier: 4.207A pdb=" N ILE T3292 " --> pdb=" O LEU T3288 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ARG T3293 " --> pdb=" O ALA T3289 " (cutoff:3.500A) Proline residue: T3294 - end of helix removed outlier: 3.784A pdb=" N ASP T3299 " --> pdb=" O LYS T3295 " (cutoff:3.500A) Processing helix chain 'T' and resid 3308 through 3328 Processing helix chain 'T' and resid 3333 through 3338 Processing helix chain 'T' and resid 3338 through 3343 removed outlier: 3.903A pdb=" N SER T3342 " --> pdb=" O CYS T3338 " (cutoff:3.500A) Processing helix chain 'T' and resid 3412 through 3433 removed outlier: 3.593A pdb=" N PHE T3426 " --> pdb=" O LEU T3422 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LYS T3428 " --> pdb=" O ARG T3424 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N SER T3429 " --> pdb=" O LEU T3425 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASN T3433 " --> pdb=" O SER T3429 " (cutoff:3.500A) Processing helix chain 'T' and resid 3467 through 3478 removed outlier: 3.608A pdb=" N LYS T3478 " --> pdb=" O PHE T3474 " (cutoff:3.500A) Processing helix chain 'T' and resid 3481 through 3497 removed outlier: 4.035A pdb=" N ILE T3485 " --> pdb=" O ASP T3481 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N GLN T3486 " --> pdb=" O PRO T3482 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N HIS T3497 " --> pdb=" O LEU T3493 " (cutoff:3.500A) Processing helix chain 'T' and resid 3505 through 3521 removed outlier: 3.840A pdb=" N LEU T3509 " --> pdb=" O ASP T3505 " (cutoff:3.500A) Processing helix chain 'T' and resid 3525 through 3535 Processing helix chain 'T' and resid 3537 through 3561 removed outlier: 3.893A pdb=" N PHE T3541 " --> pdb=" O GLN T3537 " (cutoff:3.500A) Processing helix chain 'T' and resid 3568 through 3570 No H-bonds generated for 'chain 'T' and resid 3568 through 3570' Processing helix chain 'T' and resid 3625 through 3633 Processing helix chain 'T' and resid 3633 through 3640 removed outlier: 3.611A pdb=" N GLU T3638 " --> pdb=" O ASP T3634 " (cutoff:3.500A) Processing helix chain 'T' and resid 3640 through 3654 removed outlier: 3.970A pdb=" N GLU T3654 " --> pdb=" O ARG T3650 " (cutoff:3.500A) Processing helix chain 'T' and resid 3658 through 3678 removed outlier: 3.684A pdb=" N LEU T3665 " --> pdb=" O THR T3661 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N PHE T3666 " --> pdb=" O TYR T3662 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU T3670 " --> pdb=" O PHE T3666 " (cutoff:3.500A) Processing helix chain 'T' and resid 3685 through 3707 removed outlier: 4.253A pdb=" N ARG T3689 " --> pdb=" O ASN T3685 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU T3690 " --> pdb=" O PRO T3686 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU T3706 " --> pdb=" O LYS T3702 " (cutoff:3.500A) Processing helix chain 'T' and resid 3717 through 3729 Processing helix chain 'T' and resid 3729 through 3735 Processing helix chain 'T' and resid 3736 through 3741 removed outlier: 6.414A pdb=" N ASN T3739 " --> pdb=" O THR T3736 " (cutoff:3.500A) Processing helix chain 'F' and resid 521 through 535 removed outlier: 3.891A pdb=" N GLU F 525 " --> pdb=" O GLN F 521 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 3.519A pdb=" N ALA A 29 " --> pdb=" O ALA A 19 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA A 19 " --> pdb=" O ALA A 29 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY A 20 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL A 9 " --> pdb=" O GLY A 20 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 71 through 72 removed outlier: 3.789A pdb=" N GLU A 72 " --> pdb=" O ILE A 75 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE A 75 " --> pdb=" O GLU A 72 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 106 through 107 Processing sheet with id=AA4, first strand: chain 'A' and resid 176 through 178 removed outlier: 5.769A pdb=" N LEU A 153 " --> pdb=" O SER A 300 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 238 through 242 Processing sheet with id=AA6, first strand: chain 'B' and resid 38 through 41 removed outlier: 3.572A pdb=" N THR B 111 " --> pdb=" O ILE B 19 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 45 through 47 Processing sheet with id=AA8, first strand: chain 'B' and resid 75 through 76 Processing sheet with id=AA9, first strand: chain 'B' and resid 174 through 175 Processing sheet with id=AB1, first strand: chain 'B' and resid 174 through 175 removed outlier: 5.885A pdb=" N LEU B 156 " --> pdb=" O VAL B 409 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N THR B 411 " --> pdb=" O LEU B 156 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N VAL B 158 " --> pdb=" O THR B 411 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL B 408 " --> pdb=" O LEU B 440 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 209 through 212 Processing sheet with id=AB3, first strand: chain 'B' and resid 270 through 271 Processing sheet with id=AB4, first strand: chain 'D' and resid 268 through 270 Processing sheet with id=AB5, first strand: chain 'D' and resid 273 through 274 Processing sheet with id=AB6, first strand: chain 'D' and resid 280 through 282 Processing sheet with id=AB7, first strand: chain 'D' and resid 568 through 569 removed outlier: 3.506A pdb=" N ILE D 569 " --> pdb=" O LYS F 640 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL F 642 " --> pdb=" O ILE D 569 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG F 639 " --> pdb=" O ASP F 651 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE F 647 " --> pdb=" O GLY F 643 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 649 through 650 Processing sheet with id=AB9, first strand: chain 'E' and resid 78 through 83 Processing sheet with id=AC1, first strand: chain 'T' and resid 977 through 980 Processing sheet with id=AC2, first strand: chain 'T' and resid 3331 through 3332 removed outlier: 3.501A pdb=" N ARG T3373 " --> pdb=" O ARG T3394 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'T' and resid 3331 through 3332 removed outlier: 3.886A pdb=" N ARG T3389 " --> pdb=" O VAL T3405 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'T' and resid 3464 through 3466 Processing sheet with id=AC5, first strand: chain 'T' and resid 3590 through 3591 Processing sheet with id=AC6, first strand: chain 'F' and resid 546 through 548 removed outlier: 3.739A pdb=" N GLN F 571 " --> pdb=" O VAL F 546 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ASP F 548 " --> pdb=" O LYS F 569 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LYS F 569 " --> pdb=" O ASP F 548 " (cutoff:3.500A) 1303 hydrogen bonds defined for protein. 3756 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.49 Time building geometry restraints manager: 2.81 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: 4764 1.32 - 1.45: 6871 1.45 - 1.57: 15197 1.57 - 1.69: 6 1.69 - 1.81: 165 Bond restraints: 27003 Sorted by residual: bond pdb=" N PRO T2620 " pdb=" CA PRO T2620 " ideal model delta sigma weight residual 1.469 1.666 -0.197 1.28e-02 6.10e+03 2.37e+02 bond pdb=" C4 ATP B 501 " pdb=" C5 ATP B 501 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.96e+01 bond pdb=" C5 ATP B 501 " pdb=" C6 ATP B 501 " ideal model delta sigma weight residual 1.409 1.476 -0.067 1.00e-02 1.00e+04 4.56e+01 bond pdb=" C PRO T2619 " pdb=" N PRO T2620 " ideal model delta sigma weight residual 1.334 1.453 -0.119 2.34e-02 1.83e+03 2.60e+01 bond pdb=" N MET T2959 " pdb=" CA MET T2959 " ideal model delta sigma weight residual 1.458 1.494 -0.037 7.40e-03 1.83e+04 2.46e+01 ... (remaining 26998 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.02: 35956 4.02 - 8.04: 597 8.04 - 12.05: 23 12.05 - 16.07: 5 16.07 - 20.09: 4 Bond angle restraints: 36585 Sorted by residual: angle pdb=" PB ATP B 501 " pdb=" O3B ATP B 501 " pdb=" PG ATP B 501 " ideal model delta sigma weight residual 139.87 121.22 18.65 1.00e+00 1.00e+00 3.48e+02 angle pdb=" PA ATP B 501 " pdb=" O3A ATP B 501 " pdb=" PB ATP B 501 " ideal model delta sigma weight residual 136.83 119.92 16.91 1.00e+00 1.00e+00 2.86e+02 angle pdb=" C PRO T2619 " pdb=" N PRO T2620 " pdb=" CA PRO T2620 " ideal model delta sigma weight residual 119.84 139.65 -19.81 1.25e+00 6.40e-01 2.51e+02 angle pdb=" CA PRO T2620 " pdb=" N PRO T2620 " pdb=" CD PRO T2620 " ideal model delta sigma weight residual 112.00 91.91 20.09 1.40e+00 5.10e-01 2.06e+02 angle pdb=" N PRO T2619 " pdb=" CA PRO T2619 " pdb=" C PRO T2619 " ideal model delta sigma weight residual 110.70 122.44 -11.74 1.22e+00 6.72e-01 9.27e+01 ... (remaining 36580 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.31: 15373 25.31 - 50.63: 896 50.63 - 75.94: 68 75.94 - 101.26: 5 101.26 - 126.57: 1 Dihedral angle restraints: 16343 sinusoidal: 6751 harmonic: 9592 Sorted by residual: dihedral pdb=" CA ASP T3112 " pdb=" C ASP T3112 " pdb=" N ALA T3113 " pdb=" CA ALA T3113 " ideal model delta harmonic sigma weight residual -180.00 -53.43 -126.57 0 5.00e+00 4.00e-02 6.41e+02 dihedral pdb=" CA ALA D 540 " pdb=" C ALA D 540 " pdb=" N PRO D 541 " pdb=" CA PRO D 541 " ideal model delta harmonic sigma weight residual -180.00 -122.30 -57.70 0 5.00e+00 4.00e-02 1.33e+02 dihedral pdb=" CA LEU T 847 " pdb=" C LEU T 847 " pdb=" N THR T 848 " pdb=" CA THR T 848 " ideal model delta harmonic sigma weight residual 0.00 -33.59 33.59 0 5.00e+00 4.00e-02 4.51e+01 ... (remaining 16340 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 3399 0.094 - 0.189: 554 0.189 - 0.283: 79 0.283 - 0.377: 5 0.377 - 0.472: 1 Chirality restraints: 4038 Sorted by residual: chirality pdb=" CA TYR T2721 " pdb=" N TYR T2721 " pdb=" C TYR T2721 " pdb=" CB TYR T2721 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.56e+00 chirality pdb=" CA PRO T2620 " pdb=" N PRO T2620 " pdb=" C PRO T2620 " pdb=" CB PRO T2620 " both_signs ideal model delta sigma weight residual False 2.72 3.08 -0.36 2.00e-01 2.50e+01 3.26e+00 chirality pdb=" CA ASN T3710 " pdb=" N ASN T3710 " pdb=" C ASN T3710 " pdb=" CB ASN T3710 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.36 2.00e-01 2.50e+01 3.15e+00 ... (remaining 4035 not shown) Planarity restraints: 4692 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO D 541 " 0.102 5.00e-02 4.00e+02 1.54e-01 3.81e+01 pdb=" N PRO D 542 " -0.267 5.00e-02 4.00e+02 pdb=" CA PRO D 542 " 0.086 5.00e-02 4.00e+02 pdb=" CD PRO D 542 " 0.079 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN T3442 " -0.028 2.00e-02 2.50e+03 5.73e-02 3.29e+01 pdb=" C GLN T3442 " 0.099 2.00e-02 2.50e+03 pdb=" O GLN T3442 " -0.036 2.00e-02 2.50e+03 pdb=" N PHE T3443 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE T2697 " 0.027 2.00e-02 2.50e+03 5.66e-02 3.20e+01 pdb=" C ILE T2697 " -0.098 2.00e-02 2.50e+03 pdb=" O ILE T2697 " 0.037 2.00e-02 2.50e+03 pdb=" N GLY T2698 " 0.034 2.00e-02 2.50e+03 ... (remaining 4689 not shown) Histogram of nonbonded interaction distances: 1.13 - 1.88: 6 1.88 - 2.64: 573 2.64 - 3.39: 38785 3.39 - 4.15: 58673 4.15 - 4.90: 105885 Nonbonded interactions: 203922 Sorted by model distance: nonbonded pdb=" CD2 TYR T1013 " pdb=" OE1 GLN T2551 " model vdw 1.130 3.340 nonbonded pdb=" CD1 ILE D 277 " pdb=" OH TYR F 577 " model vdw 1.552 3.460 nonbonded pdb=" CE2 TYR T1013 " pdb=" OE1 GLN T2551 " model vdw 1.610 3.340 nonbonded pdb=" NE ARG T3315 " pdb=" OD2 ASP T3483 " model vdw 1.750 3.120 nonbonded pdb=" CG PRO F 582 " pdb=" CE1 TYR F 584 " model vdw 1.752 3.740 ... (remaining 203917 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: 11.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.020 Extract box with map and model: 0.750 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 24.370 Find NCS groups from input model: 0.150 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 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 : 0.008 0.197 27004 Z= 0.609 Angle : 1.322 20.088 36585 Z= 0.962 Chirality : 0.069 0.472 4038 Planarity : 0.007 0.154 4692 Dihedral : 14.659 126.570 10107 Min Nonbonded Distance : 1.130 Molprobity Statistics. All-atom Clashscore : 19.42 Ramachandran Plot: Outliers : 0.56 % Allowed : 9.23 % Favored : 90.21 % Rotamer: Outliers : 3.57 % Allowed : 8.86 % Favored : 87.56 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.96 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.63 (0.14), residues: 3207 helix: -0.19 (0.12), residues: 1636 sheet: -2.79 (0.33), residues: 193 loop : -3.65 (0.14), residues: 1378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG T2599 TYR 0.044 0.002 TYR T3092 PHE 0.056 0.002 PHE T3464 TRP 0.031 0.002 TRP B 469 HIS 0.010 0.001 HIS T2621 Details of bonding type rmsd/Z covalent geometry : bond 0.00849 / 0.61 (27003) covalent geometry : angle 1.32221 / 0.96 (36585) hydrogen bonds : bond 0.17698 / 11.83 ( 1295) hydrogen bonds : angle 6.17404 / 4.35 ( 3756) Misc. bond : bond 0.00028 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 694 residues out of total 2938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 590 time to evaluate : 0.979 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: symmetry clash revert: symmetry clash REVERT: A 143 TYR cc_start: 0.8714 (m-10) cc_final: 0.8422 (m-80) REVERT: A 148 THR cc_start: 0.8522 (p) cc_final: 0.8166 (p) REVERT: A 190 MET cc_start: 0.8908 (ttm) cc_final: 0.8452 (tpt) REVERT: A 293 LEU cc_start: 0.8215 (tp) cc_final: 0.8013 (tp) REVERT: A 296 ASN cc_start: 0.8587 (m-40) cc_final: 0.8081 (m110) REVERT: B 399 ASP cc_start: 0.8593 (p0) cc_final: 0.8353 (p0) REVERT: B 427 GLU cc_start: 0.8157 (tp30) cc_final: 0.7916 (tt0) REVERT: D 292 TYR cc_start: 0.7631 (t80) cc_final: 0.7359 (t80) REVERT: D 339 LEU cc_start: 0.7888 (mt) cc_final: 0.7149 (pp) REVERT: D 602 GLU cc_start: 0.7967 (tt0) cc_final: 0.7402 (tt0) REVERT: D 640 ARG cc_start: 0.8700 (mtt180) cc_final: 0.8494 (tmt170) REVERT: D 644 ASN cc_start: 0.8831 (m110) cc_final: 0.8052 (t0) REVERT: D 657 GLU cc_start: 0.8755 (tt0) cc_final: 0.8363 (tt0) REVERT: D 676 MET cc_start: 0.8277 (mmm) cc_final: 0.7999 (mmt) REVERT: D 691 ARG cc_start: 0.8311 (mmt-90) cc_final: 0.7187 (mmt90) REVERT: D 726 GLU cc_start: 0.7798 (tp30) cc_final: 0.7318 (tp30) REVERT: E 181 LEU cc_start: 0.8936 (tp) cc_final: 0.8473 (tt) REVERT: E 208 THR cc_start: 0.9330 (p) cc_final: 0.9129 (p) REVERT: E 271 THR cc_start: 0.8581 (m) cc_final: 0.8326 (p) REVERT: T 1147 ASP cc_start: 0.8389 (t0) cc_final: 0.8127 (t0) REVERT: T 1206 TYR cc_start: 0.8018 (p90) cc_final: 0.6044 (p90) REVERT: T 1231 LYS cc_start: 0.7827 (mtpt) cc_final: 0.7464 (tttp) REVERT: T 2443 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8145 (tt) REVERT: T 2643 ILE cc_start: 0.8601 (OUTLIER) cc_final: 0.8357 (mt) REVERT: T 2656 GLU cc_start: 0.8229 (mm-30) cc_final: 0.7803 (tp30) REVERT: T 2684 LYS cc_start: 0.8238 (tttp) cc_final: 0.7721 (ttpt) REVERT: T 2715 ARG cc_start: 0.7877 (OUTLIER) cc_final: 0.7454 (ptp90) REVERT: T 2721 TYR cc_start: 0.7354 (OUTLIER) cc_final: 0.6962 (p90) REVERT: T 2723 GLN cc_start: 0.7440 (tp40) cc_final: 0.7190 (tp-100) REVERT: T 2904 TRP cc_start: 0.3682 (m100) cc_final: 0.2610 (m100) REVERT: T 3080 ASN cc_start: 0.7898 (OUTLIER) cc_final: 0.7427 (p0) REVERT: T 3086 LEU cc_start: 0.9419 (mt) cc_final: 0.9208 (mt) REVERT: T 3134 ILE cc_start: 0.9254 (mt) cc_final: 0.9048 (mm) REVERT: T 3205 TRP cc_start: 0.6842 (p-90) cc_final: 0.6371 (p-90) REVERT: T 3209 GLN cc_start: 0.8893 (mt0) cc_final: 0.8673 (mt0) REVERT: T 3232 GLN cc_start: 0.8275 (mm-40) cc_final: 0.7620 (mm-40) REVERT: T 3436 THR cc_start: 0.9263 (OUTLIER) cc_final: 0.8999 (m) REVERT: T 3534 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8970 (tp) REVERT: T 3661 THR cc_start: 0.8472 (m) cc_final: 0.8166 (t) REVERT: T 3721 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8785 (mm) outliers start: 104 outliers final: 44 residues processed: 664 average time/residue: 0.1722 time to fit residues: 179.2185 Evaluate side-chains 460 residues out of total 2938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 408 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 2424 THR Chi-restraints excluded: chain T residue 2443 LEU Chi-restraints excluded: chain T residue 2455 ILE Chi-restraints excluded: chain T residue 2459 ASN Chi-restraints excluded: chain T residue 2545 LEU Chi-restraints excluded: chain T residue 2556 ILE Chi-restraints excluded: chain T residue 2600 THR Chi-restraints excluded: chain T residue 2602 VAL Chi-restraints excluded: chain T residue 2621 HIS Chi-restraints excluded: chain T residue 2626 LEU Chi-restraints excluded: chain T residue 2643 ILE Chi-restraints excluded: chain T residue 2715 ARG Chi-restraints excluded: chain T residue 2721 TYR Chi-restraints excluded: chain T residue 2788 THR Chi-restraints excluded: chain T residue 2962 VAL Chi-restraints excluded: chain T residue 2970 ILE Chi-restraints excluded: chain T residue 2975 ASN Chi-restraints excluded: chain T residue 2978 ILE Chi-restraints excluded: chain T residue 2997 ASN Chi-restraints excluded: chain T residue 3006 ILE Chi-restraints excluded: chain T residue 3012 VAL Chi-restraints excluded: chain T residue 3053 LEU Chi-restraints excluded: chain T residue 3059 GLN Chi-restraints excluded: chain T residue 3074 ASN Chi-restraints excluded: chain T residue 3080 ASN Chi-restraints excluded: chain T residue 3167 LEU Chi-restraints excluded: chain T residue 3338 CYS Chi-restraints excluded: chain T residue 3349 PHE Chi-restraints excluded: chain T residue 3361 ASN Chi-restraints excluded: chain T residue 3365 ASN Chi-restraints excluded: chain T residue 3369 ILE Chi-restraints excluded: chain T residue 3410 VAL Chi-restraints excluded: chain T residue 3434 VAL Chi-restraints excluded: chain T residue 3436 THR Chi-restraints excluded: chain T residue 3449 ILE Chi-restraints excluded: chain T residue 3457 ILE Chi-restraints excluded: chain T residue 3494 ASN Chi-restraints excluded: chain T residue 3505 ASP Chi-restraints excluded: chain T residue 3511 VAL Chi-restraints excluded: chain T residue 3534 LEU Chi-restraints excluded: chain T residue 3564 ILE Chi-restraints excluded: chain T residue 3572 ILE Chi-restraints excluded: chain T residue 3624 LEU Chi-restraints excluded: chain T residue 3625 THR Chi-restraints excluded: chain T residue 3682 ILE Chi-restraints excluded: chain T residue 3709 LEU Chi-restraints excluded: chain T residue 3721 LEU Chi-restraints excluded: chain F residue 572 ILE Chi-restraints excluded: chain F residue 577 TYR Chi-restraints excluded: chain F residue 588 ILE Chi-restraints excluded: chain F residue 591 ASP Chi-restraints excluded: chain F residue 593 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.7980 chunk 298 optimal weight: 0.0030 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 37 GLN ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 675 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 728 HIS E 241 GLN E 289 GLN E 298 GLN ** T 956 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T1075 GLN ** T1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T1239 ASN T2470 ASN T2515 ASN T2638 ASN T2741 GLN T2792 GLN T2811 GLN T2844 HIS T2899 ASN T2992 HIS T3119 ASN ** T3261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T3695 ASN T3732 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.126912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.104215 restraints weight = 64564.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.107401 restraints weight = 31387.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.109280 restraints weight = 18858.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.109457 restraints weight = 15183.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.109795 restraints weight = 14283.853| |-----------------------------------------------------------------------------| r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 27004 Z= 0.171 Angle : 0.771 12.179 36585 Z= 0.398 Chirality : 0.045 0.241 4038 Planarity : 0.006 0.146 4692 Dihedral : 7.004 66.821 3640 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.37 % Allowed : 7.86 % Favored : 91.77 % Rotamer: Outliers : 2.78 % Allowed : 14.39 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 1.31 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.55 (0.14), residues: 3207 helix: 0.66 (0.12), residues: 1643 sheet: -2.26 (0.36), residues: 172 loop : -3.09 (0.15), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 305 TYR 0.027 0.002 TYR T2492 PHE 0.025 0.002 PHE T3464 TRP 0.024 0.002 TRP A 340 HIS 0.015 0.001 HIS D 675 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.17 (27003) covalent geometry : angle 0.77120 / 0.40 (36585) hydrogen bonds : bond 0.05364 / 3.62 ( 1295) hydrogen bonds : angle 4.94854 / 3.46 ( 3756) Misc. bond : bond 0.00090 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 2938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 467 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 MET cc_start: 0.8960 (ttm) cc_final: 0.8551 (tpt) REVERT: A 296 ASN cc_start: 0.8548 (m-40) cc_final: 0.8079 (m-40) REVERT: A 299 MET cc_start: 0.7353 (tmm) cc_final: 0.7047 (tmm) REVERT: A 364 GLU cc_start: 0.8979 (tm-30) cc_final: 0.8487 (tm-30) REVERT: B 399 ASP cc_start: 0.8435 (p0) cc_final: 0.8126 (p0) REVERT: D 273 MET cc_start: 0.8246 (mtp) cc_final: 0.7847 (mtp) REVERT: D 294 SER cc_start: 0.8860 (m) cc_final: 0.8438 (p) REVERT: D 332 GLU cc_start: 0.8102 (tm-30) cc_final: 0.7847 (tm-30) REVERT: D 339 LEU cc_start: 0.7889 (OUTLIER) cc_final: 0.6918 (pp) REVERT: D 553 ASN cc_start: 0.7780 (m-40) cc_final: 0.7127 (p0) REVERT: D 602 GLU cc_start: 0.8086 (tt0) cc_final: 0.7514 (tm-30) REVERT: D 640 ARG cc_start: 0.8692 (mtt180) cc_final: 0.8296 (tmt170) REVERT: D 650 TRP cc_start: 0.9346 (m100) cc_final: 0.8948 (m100) REVERT: D 656 GLN cc_start: 0.8154 (tp40) cc_final: 0.7917 (tp-100) REVERT: D 676 MET cc_start: 0.8699 (mmm) cc_final: 0.8288 (mmt) REVERT: D 726 GLU cc_start: 0.7875 (tp30) cc_final: 0.7382 (tp30) REVERT: E 181 LEU cc_start: 0.9084 (tp) cc_final: 0.8596 (tt) REVERT: E 266 MET cc_start: 0.8642 (mtt) cc_final: 0.8313 (mtt) REVERT: E 271 THR cc_start: 0.8532 (m) cc_final: 0.8273 (m) REVERT: E 300 MET cc_start: 0.7622 (mmt) cc_final: 0.7150 (mmt) REVERT: T 1206 TYR cc_start: 0.7606 (p90) cc_final: 0.7387 (p90) REVERT: T 1231 LYS cc_start: 0.7888 (mtpt) cc_final: 0.7486 (tttp) REVERT: T 2443 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.8074 (tt) REVERT: T 2575 GLU cc_start: 0.8325 (mp0) cc_final: 0.7857 (mp0) REVERT: T 2684 LYS cc_start: 0.8698 (tttp) cc_final: 0.8363 (ttpt) REVERT: T 2695 GLU cc_start: 0.8751 (tp30) cc_final: 0.8470 (tp30) REVERT: T 2721 TYR cc_start: 0.7960 (p90) cc_final: 0.7628 (p90) REVERT: T 2778 GLN cc_start: 0.7877 (pp30) cc_final: 0.6904 (tm-30) REVERT: T 2904 TRP cc_start: 0.3918 (m100) cc_final: 0.2461 (m100) REVERT: T 2948 ASN cc_start: 0.8849 (t0) cc_final: 0.8231 (t0) REVERT: T 3022 PHE cc_start: 0.8754 (m-80) cc_final: 0.8549 (m-80) REVERT: T 3093 LYS cc_start: 0.8326 (ptmt) cc_final: 0.8096 (mtmm) REVERT: T 3127 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7458 (tt0) REVERT: T 3232 GLN cc_start: 0.8320 (mm-40) cc_final: 0.8118 (mm-40) REVERT: T 3283 PHE cc_start: 0.7621 (m-80) cc_final: 0.7394 (m-80) REVERT: F 649 TYR cc_start: 0.8818 (m-10) cc_final: 0.8531 (m-10) outliers start: 81 outliers final: 38 residues processed: 520 average time/residue: 0.1648 time to fit residues: 137.3853 Evaluate side-chains 417 residues out of total 2938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 376 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 HIS Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 415 SER Chi-restraints excluded: chain B residue 469 TRP Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain D residue 283 GLN Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 663 ASN Chi-restraints excluded: chain D residue 678 HIS Chi-restraints excluded: chain D residue 735 ASN Chi-restraints excluded: chain D residue 752 HIS Chi-restraints excluded: chain T residue 939 HIS Chi-restraints excluded: chain T residue 2424 THR Chi-restraints excluded: chain T residue 2426 VAL Chi-restraints excluded: chain T residue 2443 LEU Chi-restraints excluded: chain T residue 2455 ILE Chi-restraints excluded: chain T residue 2556 ILE Chi-restraints excluded: chain T residue 2621 HIS Chi-restraints excluded: chain T residue 2870 LEU Chi-restraints excluded: chain T residue 2963 CYS Chi-restraints excluded: chain T residue 3012 VAL Chi-restraints excluded: chain T residue 3127 GLU Chi-restraints excluded: chain T residue 3167 LEU Chi-restraints excluded: chain T residue 3208 LEU Chi-restraints excluded: chain T residue 3349 PHE Chi-restraints excluded: chain T residue 3375 LEU Chi-restraints excluded: chain T residue 3410 VAL Chi-restraints excluded: chain T residue 3457 ILE Chi-restraints excluded: chain T residue 3494 ASN Chi-restraints excluded: chain T residue 3505 ASP Chi-restraints excluded: chain T residue 3509 LEU Chi-restraints excluded: chain T residue 3586 MET Chi-restraints excluded: chain T residue 3624 LEU Chi-restraints excluded: chain F residue 550 SER Chi-restraints excluded: chain F residue 551 LEU Chi-restraints excluded: chain F residue 572 ILE Chi-restraints excluded: chain F residue 627 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 186 optimal weight: 5.9990 chunk 39 optimal weight: 7.9990 chunk 174 optimal weight: 3.9990 chunk 223 optimal weight: 0.0980 chunk 206 optimal weight: 4.9990 chunk 234 optimal weight: 4.9990 chunk 128 optimal weight: 9.9990 chunk 8 optimal weight: 5.9990 chunk 56 optimal weight: 8.9990 chunk 281 optimal weight: 0.6980 chunk 216 optimal weight: 6.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 GLN B 234 ASN ** B 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 644 ASN D 675 HIS D 728 HIS E 298 GLN ** T 956 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T2458 GLN T2711 GLN ** T2847 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2863 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T2869 ASN T2992 HIS T3064 ASN T3094 ASN ** T3261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T3365 ASN T3367 HIS T3412 HIS T3471 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.119228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.096321 restraints weight = 64885.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.099197 restraints weight = 33807.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.101566 restraints weight = 20438.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.101641 restraints weight = 15989.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.101731 restraints weight = 14872.867| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 27004 Z= 0.244 Angle : 0.752 10.445 36585 Z= 0.388 Chirality : 0.046 0.259 4038 Planarity : 0.006 0.143 4692 Dihedral : 6.263 68.497 3568 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.04 % Favored : 90.77 % Rotamer: Outliers : 3.85 % Allowed : 16.83 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.31 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.15), residues: 3207 helix: 0.90 (0.13), residues: 1640 sheet: -1.93 (0.35), residues: 191 loop : -2.94 (0.16), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 206 TYR 0.038 0.002 TYR T1013 PHE 0.028 0.002 PHE T3464 TRP 0.026 0.002 TRP B 469 HIS 0.008 0.001 HIS T2592 Details of bonding type rmsd/Z covalent geometry : bond 0.00570 / 0.24 (27003) covalent geometry : angle 0.75152 / 0.39 (36585) hydrogen bonds : bond 0.05062 / 3.40 ( 1295) hydrogen bonds : angle 4.89673 / 3.43 ( 3756) Misc. bond : bond 0.00037 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 2938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 409 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 GLU cc_start: 0.8756 (pt0) cc_final: 0.8536 (pt0) REVERT: A 143 TYR cc_start: 0.8954 (m-10) cc_final: 0.8443 (m-80) REVERT: A 154 ASP cc_start: 0.8874 (t0) cc_final: 0.8611 (t0) REVERT: A 190 MET cc_start: 0.8986 (ttm) cc_final: 0.8597 (tpt) REVERT: A 296 ASN cc_start: 0.8506 (m-40) cc_final: 0.8147 (m-40) REVERT: A 299 MET cc_start: 0.7969 (tmm) cc_final: 0.7679 (tmm) REVERT: B 37 GLN cc_start: 0.8893 (OUTLIER) cc_final: 0.8497 (tm-30) REVERT: B 399 ASP cc_start: 0.8505 (p0) cc_final: 0.8126 (p0) REVERT: D 36 ARG cc_start: 0.7518 (OUTLIER) cc_final: 0.7305 (pmt-80) REVERT: D 294 SER cc_start: 0.8899 (m) cc_final: 0.8503 (p) REVERT: D 339 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7024 (pp) REVERT: D 553 ASN cc_start: 0.7756 (m-40) cc_final: 0.7036 (p0) REVERT: D 602 GLU cc_start: 0.8264 (tt0) cc_final: 0.7446 (tt0) REVERT: D 640 ARG cc_start: 0.8723 (mtt180) cc_final: 0.8360 (tmt170) REVERT: D 650 TRP cc_start: 0.9242 (m100) cc_final: 0.9003 (m100) REVERT: D 656 GLN cc_start: 0.8321 (tp40) cc_final: 0.8104 (tp-100) REVERT: D 726 GLU cc_start: 0.8088 (tp30) cc_final: 0.7468 (tp30) REVERT: D 764 ILE cc_start: 0.9100 (OUTLIER) cc_final: 0.8745 (mt) REVERT: D 767 CYS cc_start: 0.8739 (t) cc_final: 0.8051 (t) REVERT: E 181 LEU cc_start: 0.9185 (tp) cc_final: 0.8607 (tt) REVERT: E 300 MET cc_start: 0.7435 (mmt) cc_final: 0.7060 (mmt) REVERT: T 1203 ASP cc_start: 0.8774 (t0) cc_final: 0.8483 (t0) REVERT: T 1204 GLU cc_start: 0.7392 (pt0) cc_final: 0.7163 (pt0) REVERT: T 1231 LYS cc_start: 0.7997 (mtpt) cc_final: 0.7543 (tttp) REVERT: T 2443 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.7946 (tt) REVERT: T 2663 LEU cc_start: 0.9368 (OUTLIER) cc_final: 0.9001 (mp) REVERT: T 2721 TYR cc_start: 0.8240 (p90) cc_final: 0.7777 (p90) REVERT: T 2778 GLN cc_start: 0.8050 (pp30) cc_final: 0.7076 (tm-30) REVERT: T 3041 GLN cc_start: 0.7419 (tp-100) cc_final: 0.6837 (tm-30) REVERT: T 3059 GLN cc_start: 0.9153 (OUTLIER) cc_final: 0.8936 (mm-40) REVERT: T 3093 LYS cc_start: 0.8462 (ptmt) cc_final: 0.8162 (ttpt) REVERT: T 3232 GLN cc_start: 0.8419 (mm-40) cc_final: 0.8162 (mm-40) REVERT: T 3407 TYR cc_start: 0.7521 (t80) cc_final: 0.7282 (t80) REVERT: F 639 ARG cc_start: 0.7610 (ttp-170) cc_final: 0.7401 (ttp-170) outliers start: 112 outliers final: 66 residues processed: 483 average time/residue: 0.1541 time to fit residues: 119.5083 Evaluate side-chains 443 residues out of total 2938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 370 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 HIS Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain B residue 37 GLN Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 415 SER Chi-restraints excluded: chain B residue 469 TRP Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 36 ARG Chi-restraints excluded: chain D residue 283 GLN Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 678 HIS Chi-restraints excluded: chain D residue 701 VAL Chi-restraints excluded: chain D residue 735 ASN Chi-restraints excluded: chain D residue 752 HIS Chi-restraints excluded: chain D residue 764 ILE Chi-restraints excluded: chain E residue 251 ILE Chi-restraints excluded: chain T residue 878 PHE Chi-restraints excluded: chain T residue 939 HIS Chi-restraints excluded: chain T residue 1200 LEU Chi-restraints excluded: chain T residue 1242 LEU Chi-restraints excluded: chain T residue 2416 MET Chi-restraints excluded: chain T residue 2424 THR Chi-restraints excluded: chain T residue 2426 VAL Chi-restraints excluded: chain T residue 2443 LEU Chi-restraints excluded: chain T residue 2455 ILE Chi-restraints excluded: chain T residue 2537 ILE Chi-restraints excluded: chain T residue 2574 ASN Chi-restraints excluded: chain T residue 2600 THR Chi-restraints excluded: chain T residue 2613 ILE Chi-restraints excluded: chain T residue 2663 LEU Chi-restraints excluded: chain T residue 2679 TRP Chi-restraints excluded: chain T residue 2689 ASN Chi-restraints excluded: chain T residue 2706 LEU Chi-restraints excluded: chain T residue 2709 VAL Chi-restraints excluded: chain T residue 2719 LEU Chi-restraints excluded: chain T residue 2870 LEU Chi-restraints excluded: chain T residue 2962 VAL Chi-restraints excluded: chain T residue 2963 CYS Chi-restraints excluded: chain T residue 3009 THR Chi-restraints excluded: chain T residue 3012 VAL Chi-restraints excluded: chain T residue 3059 GLN Chi-restraints excluded: chain T residue 3101 LEU Chi-restraints excluded: chain T residue 3167 LEU Chi-restraints excluded: chain T residue 3208 LEU Chi-restraints excluded: chain T residue 3336 VAL Chi-restraints excluded: chain T residue 3349 PHE Chi-restraints excluded: chain T residue 3352 ILE Chi-restraints excluded: chain T residue 3359 LEU Chi-restraints excluded: chain T residue 3375 LEU Chi-restraints excluded: chain T residue 3410 VAL Chi-restraints excluded: chain T residue 3436 THR Chi-restraints excluded: chain T residue 3457 ILE Chi-restraints excluded: chain T residue 3505 ASP Chi-restraints excluded: chain T residue 3511 VAL Chi-restraints excluded: chain T residue 3563 MET Chi-restraints excluded: chain T residue 3564 ILE Chi-restraints excluded: chain T residue 3568 THR Chi-restraints excluded: chain T residue 3624 LEU Chi-restraints excluded: chain T residue 3709 LEU Chi-restraints excluded: chain T residue 3712 THR Chi-restraints excluded: chain F residue 550 SER Chi-restraints excluded: chain F residue 551 LEU Chi-restraints excluded: chain F residue 572 ILE Chi-restraints excluded: chain F residue 591 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 159 optimal weight: 4.9990 chunk 180 optimal weight: 2.9990 chunk 182 optimal weight: 5.9990 chunk 137 optimal weight: 1.9990 chunk 114 optimal weight: 0.7980 chunk 227 optimal weight: 0.0670 chunk 57 optimal weight: 9.9990 chunk 269 optimal weight: 5.9990 chunk 207 optimal weight: 1.9990 chunk 299 optimal weight: 0.6980 chunk 216 optimal weight: 4.9990 overall best weight: 1.1122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 240 GLN E 241 GLN T2948 ASN T2992 HIS T3261 ASN ** T3357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T3365 ASN T3412 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.122914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.099747 restraints weight = 64673.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.103002 restraints weight = 33836.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.105414 restraints weight = 19440.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.105409 restraints weight = 14876.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.105604 restraints weight = 14164.611| |-----------------------------------------------------------------------------| r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 27004 Z= 0.144 Angle : 0.672 11.314 36585 Z= 0.346 Chirality : 0.043 0.307 4038 Planarity : 0.005 0.137 4692 Dihedral : 5.986 67.327 3562 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.42 % Favored : 91.39 % Rotamer: Outliers : 3.64 % Allowed : 18.00 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 1.31 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.15), residues: 3207 helix: 1.14 (0.13), residues: 1624 sheet: -1.75 (0.35), residues: 195 loop : -2.75 (0.16), residues: 1388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG T3327 TYR 0.023 0.001 TYR T2492 PHE 0.021 0.001 PHE T3464 TRP 0.024 0.001 TRP B 469 HIS 0.007 0.001 HIS D 675 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (27003) covalent geometry : angle 0.67197 / 0.35 (36585) hydrogen bonds : bond 0.04326 / 2.91 ( 1295) hydrogen bonds : angle 4.60493 / 3.21 ( 3756) Misc. bond : bond 0.00097 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 2938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 431 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 GLU cc_start: 0.8752 (pt0) cc_final: 0.8536 (pt0) REVERT: A 143 TYR cc_start: 0.8875 (m-10) cc_final: 0.8411 (m-80) REVERT: A 190 MET cc_start: 0.9016 (ttm) cc_final: 0.8641 (tpt) REVERT: A 296 ASN cc_start: 0.8422 (m-40) cc_final: 0.8029 (m-40) REVERT: A 299 MET cc_start: 0.8059 (tmm) cc_final: 0.7754 (tmm) REVERT: B 37 GLN cc_start: 0.8855 (OUTLIER) cc_final: 0.8451 (tm-30) REVERT: B 89 GLN cc_start: 0.8568 (OUTLIER) cc_final: 0.8230 (tm-30) REVERT: B 399 ASP cc_start: 0.8459 (p0) cc_final: 0.8053 (p0) REVERT: D 36 ARG cc_start: 0.7392 (OUTLIER) cc_final: 0.7135 (pmt-80) REVERT: D 321 GLU cc_start: 0.8269 (tm-30) cc_final: 0.8032 (tm-30) REVERT: D 332 GLU cc_start: 0.8203 (tm-30) cc_final: 0.7967 (tm-30) REVERT: D 339 LEU cc_start: 0.7982 (mt) cc_final: 0.6950 (pp) REVERT: D 553 ASN cc_start: 0.7647 (m-40) cc_final: 0.6884 (p0) REVERT: D 602 GLU cc_start: 0.8224 (tt0) cc_final: 0.7410 (tt0) REVERT: D 640 ARG cc_start: 0.8695 (mtt180) cc_final: 0.8328 (tmt170) REVERT: D 650 TRP cc_start: 0.9162 (m100) cc_final: 0.8899 (m-10) REVERT: D 657 GLU cc_start: 0.8870 (tt0) cc_final: 0.8644 (tt0) REVERT: D 726 GLU cc_start: 0.8073 (tp30) cc_final: 0.7553 (tp30) REVERT: D 764 ILE cc_start: 0.9087 (OUTLIER) cc_final: 0.8742 (mt) REVERT: D 767 CYS cc_start: 0.8549 (t) cc_final: 0.7889 (t) REVERT: E 173 PHE cc_start: 0.8497 (m-80) cc_final: 0.8210 (m-80) REVERT: E 181 LEU cc_start: 0.9150 (tp) cc_final: 0.8562 (tt) REVERT: T 1138 PHE cc_start: 0.8609 (m-80) cc_final: 0.8328 (m-80) REVERT: T 1147 ASP cc_start: 0.8425 (t0) cc_final: 0.8076 (t0) REVERT: T 1151 PHE cc_start: 0.7858 (t80) cc_final: 0.7637 (t80) REVERT: T 1203 ASP cc_start: 0.8762 (t0) cc_final: 0.8557 (t0) REVERT: T 1231 LYS cc_start: 0.7950 (mtpt) cc_final: 0.7524 (tttp) REVERT: T 2443 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7840 (tt) REVERT: T 2575 GLU cc_start: 0.8470 (mp0) cc_final: 0.7873 (mp0) REVERT: T 2662 LEU cc_start: 0.9270 (OUTLIER) cc_final: 0.8969 (tt) REVERT: T 2778 GLN cc_start: 0.7974 (pp30) cc_final: 0.6965 (tm-30) REVERT: T 3041 GLN cc_start: 0.7286 (tp-100) cc_final: 0.6721 (tm-30) REVERT: T 3093 LYS cc_start: 0.8431 (ptmt) cc_final: 0.8136 (ttmt) REVERT: T 3232 GLN cc_start: 0.8395 (mm-40) cc_final: 0.8165 (mm-40) REVERT: T 3407 TYR cc_start: 0.7451 (t80) cc_final: 0.7182 (t80) outliers start: 106 outliers final: 68 residues processed: 507 average time/residue: 0.1463 time to fit residues: 120.8082 Evaluate side-chains 469 residues out of total 2938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 395 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 HIS Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain B residue 37 GLN Chi-restraints excluded: chain B residue 89 GLN Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 415 SER Chi-restraints excluded: chain B residue 434 SER Chi-restraints excluded: chain B residue 469 TRP Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 36 ARG Chi-restraints excluded: chain D residue 283 GLN Chi-restraints excluded: chain D residue 289 GLU Chi-restraints excluded: chain D residue 531 GLU Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 663 ASN Chi-restraints excluded: chain D residue 678 HIS Chi-restraints excluded: chain D residue 701 VAL Chi-restraints excluded: chain D residue 735 ASN Chi-restraints excluded: chain D residue 752 HIS Chi-restraints excluded: chain D residue 764 ILE Chi-restraints excluded: chain E residue 92 ARG Chi-restraints excluded: chain T residue 878 PHE Chi-restraints excluded: chain T residue 939 HIS Chi-restraints excluded: chain T residue 1080 LEU Chi-restraints excluded: chain T residue 1242 LEU Chi-restraints excluded: chain T residue 2424 THR Chi-restraints excluded: chain T residue 2426 VAL Chi-restraints excluded: chain T residue 2443 LEU Chi-restraints excluded: chain T residue 2455 ILE Chi-restraints excluded: chain T residue 2561 VAL Chi-restraints excluded: chain T residue 2596 ILE Chi-restraints excluded: chain T residue 2662 LEU Chi-restraints excluded: chain T residue 2679 TRP Chi-restraints excluded: chain T residue 2689 ASN Chi-restraints excluded: chain T residue 2706 LEU Chi-restraints excluded: chain T residue 2709 VAL Chi-restraints excluded: chain T residue 2719 LEU Chi-restraints excluded: chain T residue 2734 ILE Chi-restraints excluded: chain T residue 2870 LEU Chi-restraints excluded: chain T residue 2962 VAL Chi-restraints excluded: chain T residue 2963 CYS Chi-restraints excluded: chain T residue 2978 ILE Chi-restraints excluded: chain T residue 3006 ILE Chi-restraints excluded: chain T residue 3009 THR Chi-restraints excluded: chain T residue 3012 VAL Chi-restraints excluded: chain T residue 3101 LEU Chi-restraints excluded: chain T residue 3127 GLU Chi-restraints excluded: chain T residue 3167 LEU Chi-restraints excluded: chain T residue 3208 LEU Chi-restraints excluded: chain T residue 3336 VAL Chi-restraints excluded: chain T residue 3349 PHE Chi-restraints excluded: chain T residue 3352 ILE Chi-restraints excluded: chain T residue 3359 LEU Chi-restraints excluded: chain T residue 3375 LEU Chi-restraints excluded: chain T residue 3384 THR Chi-restraints excluded: chain T residue 3410 VAL Chi-restraints excluded: chain T residue 3425 LEU Chi-restraints excluded: chain T residue 3457 ILE Chi-restraints excluded: chain T residue 3460 ASP Chi-restraints excluded: chain T residue 3505 ASP Chi-restraints excluded: chain T residue 3563 MET Chi-restraints excluded: chain T residue 3586 MET Chi-restraints excluded: chain T residue 3624 LEU Chi-restraints excluded: chain T residue 3682 ILE Chi-restraints excluded: chain T residue 3709 LEU Chi-restraints excluded: chain T residue 3712 THR Chi-restraints excluded: chain F residue 550 SER Chi-restraints excluded: chain F residue 551 LEU Chi-restraints excluded: chain F residue 572 ILE Chi-restraints excluded: chain F residue 627 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 193 optimal weight: 10.0000 chunk 98 optimal weight: 3.9990 chunk 162 optimal weight: 9.9990 chunk 247 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 20 optimal weight: 7.9990 chunk 151 optimal weight: 0.9980 chunk 102 optimal weight: 0.0030 chunk 250 optimal weight: 5.9990 chunk 97 optimal weight: 6.9990 chunk 297 optimal weight: 6.9990 overall best weight: 1.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 ASN ** B 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 241 GLN ** T2847 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T2863 HIS T2875 GLN T2948 ASN T2992 HIS ** T3357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T3365 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.120738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.097842 restraints weight = 64202.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.100694 restraints weight = 34340.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.103197 restraints weight = 20601.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.103356 restraints weight = 14789.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.103597 restraints weight = 14318.127| |-----------------------------------------------------------------------------| r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.3474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 27004 Z= 0.167 Angle : 0.675 10.941 36585 Z= 0.345 Chirality : 0.043 0.221 4038 Planarity : 0.005 0.105 4692 Dihedral : 5.833 50.085 3562 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.73 % Favored : 91.11 % Rotamer: Outliers : 3.92 % Allowed : 18.76 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.65 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.15), residues: 3207 helix: 1.19 (0.13), residues: 1632 sheet: -1.73 (0.36), residues: 197 loop : -2.67 (0.16), residues: 1378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 210 TYR 0.023 0.001 TYR T2492 PHE 0.025 0.001 PHE T3464 TRP 0.043 0.002 TRP A 340 HIS 0.007 0.001 HIS T2592 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.17 (27003) covalent geometry : angle 0.67538 / 0.35 (36585) hydrogen bonds : bond 0.04299 / 2.90 ( 1295) hydrogen bonds : angle 4.55210 / 3.18 ( 3756) Misc. bond : bond 0.00061 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 2938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 423 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 GLU cc_start: 0.8788 (pt0) cc_final: 0.8543 (pt0) REVERT: A 143 TYR cc_start: 0.8885 (m-10) cc_final: 0.8463 (m-80) REVERT: A 190 MET cc_start: 0.8990 (ttm) cc_final: 0.8634 (tpt) REVERT: A 296 ASN cc_start: 0.8436 (m-40) cc_final: 0.8083 (m-40) REVERT: A 299 MET cc_start: 0.8215 (tmm) cc_final: 0.7960 (tmm) REVERT: B 37 GLN cc_start: 0.8882 (OUTLIER) cc_final: 0.8465 (tm-30) REVERT: B 89 GLN cc_start: 0.8632 (OUTLIER) cc_final: 0.8304 (tm-30) REVERT: B 399 ASP cc_start: 0.8453 (p0) cc_final: 0.7980 (p0) REVERT: D 36 ARG cc_start: 0.7439 (OUTLIER) cc_final: 0.7179 (pmt-80) REVERT: D 332 GLU cc_start: 0.8231 (tm-30) cc_final: 0.8008 (tm-30) REVERT: D 339 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.6975 (pp) REVERT: D 553 ASN cc_start: 0.7631 (m-40) cc_final: 0.7003 (p0) REVERT: D 602 GLU cc_start: 0.8253 (tt0) cc_final: 0.7462 (tt0) REVERT: D 640 ARG cc_start: 0.8722 (mtt180) cc_final: 0.8369 (tmt170) REVERT: D 650 TRP cc_start: 0.9170 (m100) cc_final: 0.8925 (m-10) REVERT: D 657 GLU cc_start: 0.8943 (tt0) cc_final: 0.8707 (tt0) REVERT: D 676 MET cc_start: 0.9266 (mmp) cc_final: 0.9037 (mmp) REVERT: D 726 GLU cc_start: 0.8154 (tp30) cc_final: 0.7597 (tp30) REVERT: D 764 ILE cc_start: 0.9128 (OUTLIER) cc_final: 0.8816 (mt) REVERT: D 767 CYS cc_start: 0.8607 (t) cc_final: 0.7961 (t) REVERT: E 173 PHE cc_start: 0.8540 (m-80) cc_final: 0.8301 (m-80) REVERT: E 181 LEU cc_start: 0.9169 (tp) cc_final: 0.8568 (tt) REVERT: T 1138 PHE cc_start: 0.8632 (m-80) cc_final: 0.8289 (m-80) REVERT: T 1147 ASP cc_start: 0.8445 (t0) cc_final: 0.8087 (t0) REVERT: T 1220 ILE cc_start: 0.9185 (pt) cc_final: 0.8916 (mt) REVERT: T 1231 LYS cc_start: 0.8003 (mtpt) cc_final: 0.7607 (tttp) REVERT: T 2443 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7818 (tt) REVERT: T 2643 ILE cc_start: 0.8045 (OUTLIER) cc_final: 0.7792 (tt) REVERT: T 2662 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.8984 (tt) REVERT: T 2778 GLN cc_start: 0.8037 (pp30) cc_final: 0.7033 (tm-30) REVERT: T 2980 GLU cc_start: 0.7470 (mp0) cc_final: 0.7164 (mp0) REVERT: T 3041 GLN cc_start: 0.7249 (tp-100) cc_final: 0.6661 (tm-30) REVERT: T 3232 GLN cc_start: 0.8454 (mm-40) cc_final: 0.8242 (mm-40) REVERT: T 3326 ASP cc_start: 0.8816 (t0) cc_final: 0.8514 (t0) REVERT: T 3377 THR cc_start: 0.8629 (p) cc_final: 0.8399 (p) REVERT: F 649 TYR cc_start: 0.9007 (m-10) cc_final: 0.8790 (m-10) outliers start: 114 outliers final: 70 residues processed: 500 average time/residue: 0.1499 time to fit residues: 122.4040 Evaluate side-chains 465 residues out of total 2938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 387 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 HIS Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain B residue 37 GLN Chi-restraints excluded: chain B residue 89 GLN Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 415 SER Chi-restraints excluded: chain B residue 434 SER Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 469 TRP Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 36 ARG Chi-restraints excluded: chain D residue 289 GLU Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 531 GLU Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 701 VAL Chi-restraints excluded: chain D residue 735 ASN Chi-restraints excluded: chain D residue 752 HIS Chi-restraints excluded: chain D residue 764 ILE Chi-restraints excluded: chain E residue 92 ARG Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain T residue 878 PHE Chi-restraints excluded: chain T residue 939 HIS Chi-restraints excluded: chain T residue 1080 LEU Chi-restraints excluded: chain T residue 1177 LEU Chi-restraints excluded: chain T residue 1242 LEU Chi-restraints excluded: chain T residue 2424 THR Chi-restraints excluded: chain T residue 2426 VAL Chi-restraints excluded: chain T residue 2443 LEU Chi-restraints excluded: chain T residue 2455 ILE Chi-restraints excluded: chain T residue 2458 GLN Chi-restraints excluded: chain T residue 2490 ASN Chi-restraints excluded: chain T residue 2561 VAL Chi-restraints excluded: chain T residue 2588 SER Chi-restraints excluded: chain T residue 2596 ILE Chi-restraints excluded: chain T residue 2600 THR Chi-restraints excluded: chain T residue 2643 ILE Chi-restraints excluded: chain T residue 2662 LEU Chi-restraints excluded: chain T residue 2679 TRP Chi-restraints excluded: chain T residue 2689 ASN Chi-restraints excluded: chain T residue 2706 LEU Chi-restraints excluded: chain T residue 2719 LEU Chi-restraints excluded: chain T residue 2734 ILE Chi-restraints excluded: chain T residue 2823 LEU Chi-restraints excluded: chain T residue 2870 LEU Chi-restraints excluded: chain T residue 2963 CYS Chi-restraints excluded: chain T residue 2978 ILE Chi-restraints excluded: chain T residue 3006 ILE Chi-restraints excluded: chain T residue 3009 THR Chi-restraints excluded: chain T residue 3012 VAL Chi-restraints excluded: chain T residue 3101 LEU Chi-restraints excluded: chain T residue 3167 LEU Chi-restraints excluded: chain T residue 3208 LEU Chi-restraints excluded: chain T residue 3336 VAL Chi-restraints excluded: chain T residue 3349 PHE Chi-restraints excluded: chain T residue 3352 ILE Chi-restraints excluded: chain T residue 3359 LEU Chi-restraints excluded: chain T residue 3375 LEU Chi-restraints excluded: chain T residue 3410 VAL Chi-restraints excluded: chain T residue 3425 LEU Chi-restraints excluded: chain T residue 3457 ILE Chi-restraints excluded: chain T residue 3460 ASP Chi-restraints excluded: chain T residue 3505 ASP Chi-restraints excluded: chain T residue 3525 ASN Chi-restraints excluded: chain T residue 3563 MET Chi-restraints excluded: chain T residue 3568 THR Chi-restraints excluded: chain T residue 3682 ILE Chi-restraints excluded: chain T residue 3709 LEU Chi-restraints excluded: chain T residue 3712 THR Chi-restraints excluded: chain F residue 550 SER Chi-restraints excluded: chain F residue 551 LEU Chi-restraints excluded: chain F residue 572 ILE Chi-restraints excluded: chain F residue 627 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 117 optimal weight: 10.0000 chunk 103 optimal weight: 6.9990 chunk 227 optimal weight: 0.0870 chunk 43 optimal weight: 6.9990 chunk 10 optimal weight: 7.9990 chunk 83 optimal weight: 8.9990 chunk 314 optimal weight: 0.9980 chunk 113 optimal weight: 0.7980 chunk 184 optimal weight: 7.9990 chunk 230 optimal weight: 0.9990 chunk 257 optimal weight: 9.9990 overall best weight: 1.9762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 241 GLN ** T1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T2526 HIS T2723 GLN T2875 GLN ** T2948 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T2992 HIS ** T3357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T3412 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.120409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.096643 restraints weight = 64491.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.099581 restraints weight = 33932.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.101439 restraints weight = 22391.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.102640 restraints weight = 17204.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.103322 restraints weight = 14533.188| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.3692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 27004 Z= 0.174 Angle : 0.674 10.514 36585 Z= 0.345 Chirality : 0.043 0.209 4038 Planarity : 0.005 0.056 4692 Dihedral : 5.762 47.507 3560 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.22 % Allowed : 9.14 % Favored : 90.65 % Rotamer: Outliers : 4.43 % Allowed : 19.79 % Favored : 75.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.65 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.15), residues: 3207 helix: 1.16 (0.13), residues: 1653 sheet: -1.66 (0.35), residues: 203 loop : -2.69 (0.16), residues: 1351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG T2879 TYR 0.023 0.001 TYR T2492 PHE 0.026 0.001 PHE T3464 TRP 0.036 0.002 TRP A 340 HIS 0.008 0.001 HIS T2592 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.17 (27003) covalent geometry : angle 0.67434 / 0.35 (36585) hydrogen bonds : bond 0.04244 / 2.86 ( 1295) hydrogen bonds : angle 4.53335 / 3.16 ( 3756) Misc. bond : bond 0.00058 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 2938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 412 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 GLU cc_start: 0.8789 (pt0) cc_final: 0.8524 (pt0) REVERT: A 143 TYR cc_start: 0.8897 (m-10) cc_final: 0.8476 (m-80) REVERT: A 190 MET cc_start: 0.9044 (ttm) cc_final: 0.8654 (tpt) REVERT: A 296 ASN cc_start: 0.8414 (m-40) cc_final: 0.8064 (m-40) REVERT: A 299 MET cc_start: 0.8274 (tmm) cc_final: 0.8016 (tmm) REVERT: B 37 GLN cc_start: 0.8931 (OUTLIER) cc_final: 0.8488 (tm-30) REVERT: B 89 GLN cc_start: 0.8674 (OUTLIER) cc_final: 0.8329 (tm-30) REVERT: B 399 ASP cc_start: 0.8454 (p0) cc_final: 0.7978 (p0) REVERT: D 36 ARG cc_start: 0.7451 (OUTLIER) cc_final: 0.7183 (pmt-80) REVERT: D 332 GLU cc_start: 0.8255 (tm-30) cc_final: 0.8033 (tm-30) REVERT: D 339 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.6963 (pp) REVERT: D 553 ASN cc_start: 0.7647 (m-40) cc_final: 0.6966 (p0) REVERT: D 573 ARG cc_start: 0.6734 (OUTLIER) cc_final: 0.6289 (ptt180) REVERT: D 602 GLU cc_start: 0.8254 (tt0) cc_final: 0.7508 (tt0) REVERT: D 640 ARG cc_start: 0.8716 (mtt180) cc_final: 0.8347 (tmt170) REVERT: D 656 GLN cc_start: 0.9048 (tt0) cc_final: 0.8423 (tm-30) REVERT: D 657 GLU cc_start: 0.8993 (tt0) cc_final: 0.8671 (tt0) REVERT: D 726 GLU cc_start: 0.8195 (tp30) cc_final: 0.7613 (tp30) REVERT: D 764 ILE cc_start: 0.9157 (OUTLIER) cc_final: 0.8856 (mt) REVERT: D 767 CYS cc_start: 0.8609 (t) cc_final: 0.7923 (t) REVERT: E 173 PHE cc_start: 0.8495 (m-80) cc_final: 0.8275 (m-80) REVERT: E 181 LEU cc_start: 0.9142 (tp) cc_final: 0.8551 (tt) REVERT: E 289 GLN cc_start: 0.6472 (OUTLIER) cc_final: 0.5498 (tm130) REVERT: T 885 PHE cc_start: 0.7957 (m-80) cc_final: 0.7393 (t80) REVERT: T 1147 ASP cc_start: 0.8459 (t0) cc_final: 0.8092 (t0) REVERT: T 1220 ILE cc_start: 0.9179 (pt) cc_final: 0.8913 (mt) REVERT: T 1231 LYS cc_start: 0.8000 (mtpt) cc_final: 0.7635 (pttt) REVERT: T 2443 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7773 (tt) REVERT: T 2575 GLU cc_start: 0.8511 (mp0) cc_final: 0.8169 (mp0) REVERT: T 2643 ILE cc_start: 0.7992 (OUTLIER) cc_final: 0.7745 (tt) REVERT: T 2662 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.8886 (tt) REVERT: T 2778 GLN cc_start: 0.8032 (pp30) cc_final: 0.7023 (tm-30) REVERT: T 2959 MET cc_start: 0.8765 (ptp) cc_final: 0.8447 (ptp) REVERT: T 3041 GLN cc_start: 0.7250 (tp-100) cc_final: 0.6679 (tm-30) REVERT: T 3059 GLN cc_start: 0.9189 (OUTLIER) cc_final: 0.8594 (mm-40) REVERT: T 3093 LYS cc_start: 0.8390 (ptmt) cc_final: 0.8136 (ttmt) REVERT: T 3131 TRP cc_start: 0.8877 (t60) cc_final: 0.8604 (t60) REVERT: T 3377 THR cc_start: 0.8627 (p) cc_final: 0.8376 (p) outliers start: 129 outliers final: 93 residues processed: 499 average time/residue: 0.1438 time to fit residues: 116.1287 Evaluate side-chains 493 residues out of total 2938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 389 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 HIS Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain B residue 37 GLN Chi-restraints excluded: chain B residue 89 GLN Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 280 PHE Chi-restraints excluded: chain B residue 383 ILE Chi-restraints excluded: chain B residue 415 SER Chi-restraints excluded: chain B residue 434 SER Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 469 TRP Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 36 ARG Chi-restraints excluded: chain D residue 45 CYS Chi-restraints excluded: chain D residue 283 GLN Chi-restraints excluded: chain D residue 293 MET Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 531 GLU Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 573 ARG Chi-restraints excluded: chain D residue 701 VAL Chi-restraints excluded: chain D residue 735 ASN Chi-restraints excluded: chain D residue 752 HIS Chi-restraints excluded: chain D residue 764 ILE Chi-restraints excluded: chain E residue 92 ARG Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain E residue 289 GLN Chi-restraints excluded: chain T residue 878 PHE Chi-restraints excluded: chain T residue 939 HIS Chi-restraints excluded: chain T residue 952 LEU Chi-restraints excluded: chain T residue 970 THR Chi-restraints excluded: chain T residue 1023 CYS Chi-restraints excluded: chain T residue 1117 THR Chi-restraints excluded: chain T residue 1144 LEU Chi-restraints excluded: chain T residue 1242 LEU Chi-restraints excluded: chain T residue 2424 THR Chi-restraints excluded: chain T residue 2426 VAL Chi-restraints excluded: chain T residue 2443 LEU Chi-restraints excluded: chain T residue 2455 ILE Chi-restraints excluded: chain T residue 2458 GLN Chi-restraints excluded: chain T residue 2517 LEU Chi-restraints excluded: chain T residue 2537 ILE Chi-restraints excluded: chain T residue 2556 ILE Chi-restraints excluded: chain T residue 2561 VAL Chi-restraints excluded: chain T residue 2574 ASN Chi-restraints excluded: chain T residue 2588 SER Chi-restraints excluded: chain T residue 2596 ILE Chi-restraints excluded: chain T residue 2600 THR Chi-restraints excluded: chain T residue 2643 ILE Chi-restraints excluded: chain T residue 2654 ILE Chi-restraints excluded: chain T residue 2662 LEU Chi-restraints excluded: chain T residue 2679 TRP Chi-restraints excluded: chain T residue 2689 ASN Chi-restraints excluded: chain T residue 2695 GLU Chi-restraints excluded: chain T residue 2706 LEU Chi-restraints excluded: chain T residue 2719 LEU Chi-restraints excluded: chain T residue 2734 ILE Chi-restraints excluded: chain T residue 2788 THR Chi-restraints excluded: chain T residue 2793 MET Chi-restraints excluded: chain T residue 2823 LEU Chi-restraints excluded: chain T residue 2870 LEU Chi-restraints excluded: chain T residue 2963 CYS Chi-restraints excluded: chain T residue 2978 ILE Chi-restraints excluded: chain T residue 3006 ILE Chi-restraints excluded: chain T residue 3009 THR Chi-restraints excluded: chain T residue 3012 VAL Chi-restraints excluded: chain T residue 3059 GLN Chi-restraints excluded: chain T residue 3101 LEU Chi-restraints excluded: chain T residue 3117 LEU Chi-restraints excluded: chain T residue 3127 GLU Chi-restraints excluded: chain T residue 3167 LEU Chi-restraints excluded: chain T residue 3208 LEU Chi-restraints excluded: chain T residue 3255 ASP Chi-restraints excluded: chain T residue 3336 VAL Chi-restraints excluded: chain T residue 3349 PHE Chi-restraints excluded: chain T residue 3352 ILE Chi-restraints excluded: chain T residue 3359 LEU Chi-restraints excluded: chain T residue 3375 LEU Chi-restraints excluded: chain T residue 3410 VAL Chi-restraints excluded: chain T residue 3425 LEU Chi-restraints excluded: chain T residue 3431 SER Chi-restraints excluded: chain T residue 3457 ILE Chi-restraints excluded: chain T residue 3460 ASP Chi-restraints excluded: chain T residue 3505 ASP Chi-restraints excluded: chain T residue 3509 LEU Chi-restraints excluded: chain T residue 3511 VAL Chi-restraints excluded: chain T residue 3525 ASN Chi-restraints excluded: chain T residue 3563 MET Chi-restraints excluded: chain T residue 3568 THR Chi-restraints excluded: chain T residue 3581 VAL Chi-restraints excluded: chain T residue 3586 MET Chi-restraints excluded: chain T residue 3703 VAL Chi-restraints excluded: chain T residue 3709 LEU Chi-restraints excluded: chain T residue 3712 THR Chi-restraints excluded: chain F residue 550 SER Chi-restraints excluded: chain F residue 551 LEU Chi-restraints excluded: chain F residue 560 VAL Chi-restraints excluded: chain F residue 572 ILE Chi-restraints excluded: chain F residue 627 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 11 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 116 optimal weight: 9.9990 chunk 192 optimal weight: 3.9990 chunk 132 optimal weight: 9.9990 chunk 313 optimal weight: 1.9990 chunk 58 optimal weight: 8.9990 chunk 165 optimal weight: 0.6980 chunk 244 optimal weight: 1.9990 chunk 83 optimal weight: 9.9990 chunk 215 optimal weight: 6.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 444 HIS ** T2948 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T2992 HIS ** T3357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T3365 ASN T3412 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.119597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.096439 restraints weight = 63967.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.098884 restraints weight = 35748.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.101626 restraints weight = 21960.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.102222 restraints weight = 15488.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.102228 restraints weight = 14064.129| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.3846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 27004 Z= 0.153 Angle : 0.665 10.568 36585 Z= 0.340 Chirality : 0.043 0.206 4038 Planarity : 0.005 0.053 4692 Dihedral : 5.696 48.183 3560 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.07 % Favored : 90.74 % Rotamer: Outliers : 4.43 % Allowed : 20.68 % Favored : 74.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.65 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.15), residues: 3207 helix: 1.23 (0.13), residues: 1646 sheet: -1.55 (0.36), residues: 201 loop : -2.61 (0.17), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG E 210 TYR 0.021 0.001 TYR T2492 PHE 0.026 0.001 PHE T3464 TRP 0.026 0.001 TRP A 340 HIS 0.007 0.001 HIS T2592 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 (27003) covalent geometry : angle 0.66547 / 0.34 (36585) hydrogen bonds : bond 0.04087 / 2.76 ( 1295) hydrogen bonds : angle 4.46792 / 3.11 ( 3756) Misc. bond : bond 0.00067 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 2938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 422 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 GLU cc_start: 0.8771 (pt0) cc_final: 0.8474 (pt0) REVERT: A 143 TYR cc_start: 0.8862 (m-10) cc_final: 0.8576 (m-80) REVERT: A 155 SER cc_start: 0.8978 (m) cc_final: 0.7724 (p) REVERT: A 180 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8689 (tp) REVERT: A 190 MET cc_start: 0.8997 (ttm) cc_final: 0.8640 (tpt) REVERT: A 296 ASN cc_start: 0.8386 (m-40) cc_final: 0.8024 (m110) REVERT: A 299 MET cc_start: 0.8319 (tmm) cc_final: 0.8061 (tmm) REVERT: B 37 GLN cc_start: 0.8935 (OUTLIER) cc_final: 0.8500 (tm-30) REVERT: B 89 GLN cc_start: 0.8686 (OUTLIER) cc_final: 0.8357 (tm-30) REVERT: B 399 ASP cc_start: 0.8453 (p0) cc_final: 0.7958 (p0) REVERT: D 36 ARG cc_start: 0.7417 (OUTLIER) cc_final: 0.7128 (pmt-80) REVERT: D 332 GLU cc_start: 0.8262 (tm-30) cc_final: 0.8043 (tm-30) REVERT: D 339 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.6950 (pp) REVERT: D 553 ASN cc_start: 0.7632 (m-40) cc_final: 0.7070 (p0) REVERT: D 573 ARG cc_start: 0.6834 (OUTLIER) cc_final: 0.6396 (ptt180) REVERT: D 602 GLU cc_start: 0.8270 (tt0) cc_final: 0.7561 (tt0) REVERT: D 656 GLN cc_start: 0.9034 (tt0) cc_final: 0.8425 (tm-30) REVERT: D 678 HIS cc_start: 0.8713 (OUTLIER) cc_final: 0.8204 (p-80) REVERT: D 726 GLU cc_start: 0.8195 (tp30) cc_final: 0.7611 (tp30) REVERT: D 764 ILE cc_start: 0.9161 (OUTLIER) cc_final: 0.8861 (mt) REVERT: D 767 CYS cc_start: 0.8551 (t) cc_final: 0.7898 (t) REVERT: E 173 PHE cc_start: 0.8572 (m-80) cc_final: 0.8304 (m-80) REVERT: E 181 LEU cc_start: 0.9137 (tp) cc_final: 0.8553 (tt) REVERT: E 220 ASN cc_start: 0.6341 (t0) cc_final: 0.6102 (t0) REVERT: E 289 GLN cc_start: 0.6386 (OUTLIER) cc_final: 0.5215 (tm130) REVERT: T 845 MET cc_start: 0.8238 (tmm) cc_final: 0.8026 (tmm) REVERT: T 1147 ASP cc_start: 0.8483 (t0) cc_final: 0.8079 (t0) REVERT: T 1220 ILE cc_start: 0.9126 (pt) cc_final: 0.8914 (mt) REVERT: T 1231 LYS cc_start: 0.8099 (mtpt) cc_final: 0.7698 (pttt) REVERT: T 2443 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7810 (tt) REVERT: T 2471 GLN cc_start: 0.5330 (OUTLIER) cc_final: 0.4567 (mm-40) REVERT: T 2662 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.8890 (tt) REVERT: T 2778 GLN cc_start: 0.8019 (pp30) cc_final: 0.7010 (tm-30) REVERT: T 2847 GLN cc_start: 0.9049 (OUTLIER) cc_final: 0.7857 (tt0) REVERT: T 3041 GLN cc_start: 0.7178 (tp-100) cc_final: 0.6625 (tm-30) REVERT: T 3059 GLN cc_start: 0.9205 (OUTLIER) cc_final: 0.8609 (mm-40) REVERT: T 3093 LYS cc_start: 0.8410 (ptmt) cc_final: 0.8173 (ttpt) REVERT: T 3232 GLN cc_start: 0.8307 (mm-40) cc_final: 0.7769 (tp-100) REVERT: T 3288 LEU cc_start: 0.6763 (OUTLIER) cc_final: 0.6452 (tp) REVERT: T 3377 THR cc_start: 0.8563 (p) cc_final: 0.8329 (p) REVERT: T 3680 ARG cc_start: 0.7796 (mtm110) cc_final: 0.7238 (ptt90) outliers start: 129 outliers final: 90 residues processed: 514 average time/residue: 0.1486 time to fit residues: 124.5810 Evaluate side-chains 497 residues out of total 2938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 392 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 HIS Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain B residue 37 GLN Chi-restraints excluded: chain B residue 89 GLN Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 280 PHE Chi-restraints excluded: chain B residue 383 ILE Chi-restraints excluded: chain B residue 434 SER Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 469 TRP Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 36 ARG Chi-restraints excluded: chain D residue 283 GLN Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 573 ARG Chi-restraints excluded: chain D residue 601 LEU Chi-restraints excluded: chain D residue 678 HIS Chi-restraints excluded: chain D residue 701 VAL Chi-restraints excluded: chain D residue 735 ASN Chi-restraints excluded: chain D residue 752 HIS Chi-restraints excluded: chain D residue 764 ILE Chi-restraints excluded: chain E residue 92 ARG Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain E residue 289 GLN Chi-restraints excluded: chain T residue 878 PHE Chi-restraints excluded: chain T residue 952 LEU Chi-restraints excluded: chain T residue 970 THR Chi-restraints excluded: chain T residue 1023 CYS Chi-restraints excluded: chain T residue 1043 LEU Chi-restraints excluded: chain T residue 1080 LEU Chi-restraints excluded: chain T residue 1117 THR Chi-restraints excluded: chain T residue 1144 LEU Chi-restraints excluded: chain T residue 1242 LEU Chi-restraints excluded: chain T residue 2424 THR Chi-restraints excluded: chain T residue 2426 VAL Chi-restraints excluded: chain T residue 2443 LEU Chi-restraints excluded: chain T residue 2455 ILE Chi-restraints excluded: chain T residue 2458 GLN Chi-restraints excluded: chain T residue 2471 GLN Chi-restraints excluded: chain T residue 2490 ASN Chi-restraints excluded: chain T residue 2517 LEU Chi-restraints excluded: chain T residue 2556 ILE Chi-restraints excluded: chain T residue 2561 VAL Chi-restraints excluded: chain T residue 2574 ASN Chi-restraints excluded: chain T residue 2588 SER Chi-restraints excluded: chain T residue 2596 ILE Chi-restraints excluded: chain T residue 2600 THR Chi-restraints excluded: chain T residue 2626 LEU Chi-restraints excluded: chain T residue 2654 ILE Chi-restraints excluded: chain T residue 2662 LEU Chi-restraints excluded: chain T residue 2679 TRP Chi-restraints excluded: chain T residue 2689 ASN Chi-restraints excluded: chain T residue 2706 LEU Chi-restraints excluded: chain T residue 2719 LEU Chi-restraints excluded: chain T residue 2734 ILE Chi-restraints excluded: chain T residue 2788 THR Chi-restraints excluded: chain T residue 2793 MET Chi-restraints excluded: chain T residue 2823 LEU Chi-restraints excluded: chain T residue 2847 GLN Chi-restraints excluded: chain T residue 2870 LEU Chi-restraints excluded: chain T residue 2963 CYS Chi-restraints excluded: chain T residue 2978 ILE Chi-restraints excluded: chain T residue 3009 THR Chi-restraints excluded: chain T residue 3012 VAL Chi-restraints excluded: chain T residue 3059 GLN Chi-restraints excluded: chain T residue 3101 LEU Chi-restraints excluded: chain T residue 3117 LEU Chi-restraints excluded: chain T residue 3127 GLU Chi-restraints excluded: chain T residue 3167 LEU Chi-restraints excluded: chain T residue 3208 LEU Chi-restraints excluded: chain T residue 3255 ASP Chi-restraints excluded: chain T residue 3288 LEU Chi-restraints excluded: chain T residue 3336 VAL Chi-restraints excluded: chain T residue 3349 PHE Chi-restraints excluded: chain T residue 3352 ILE Chi-restraints excluded: chain T residue 3366 VAL Chi-restraints excluded: chain T residue 3375 LEU Chi-restraints excluded: chain T residue 3410 VAL Chi-restraints excluded: chain T residue 3425 LEU Chi-restraints excluded: chain T residue 3431 SER Chi-restraints excluded: chain T residue 3457 ILE Chi-restraints excluded: chain T residue 3460 ASP Chi-restraints excluded: chain T residue 3505 ASP Chi-restraints excluded: chain T residue 3509 LEU Chi-restraints excluded: chain T residue 3563 MET Chi-restraints excluded: chain T residue 3581 VAL Chi-restraints excluded: chain T residue 3624 LEU Chi-restraints excluded: chain T residue 3682 ILE Chi-restraints excluded: chain T residue 3703 VAL Chi-restraints excluded: chain T residue 3709 LEU Chi-restraints excluded: chain T residue 3712 THR Chi-restraints excluded: chain F residue 550 SER Chi-restraints excluded: chain F residue 551 LEU Chi-restraints excluded: chain F residue 560 VAL Chi-restraints excluded: chain F residue 572 ILE Chi-restraints excluded: chain F residue 627 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 62 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 chunk 123 optimal weight: 5.9990 chunk 75 optimal weight: 0.7980 chunk 120 optimal weight: 4.9990 chunk 178 optimal weight: 6.9990 chunk 139 optimal weight: 3.9990 chunk 65 optimal weight: 6.9990 chunk 59 optimal weight: 0.0570 chunk 220 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 overall best weight: 1.2700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 444 HIS E 241 GLN T 843 ASN T 939 HIS ** T2948 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T2992 HIS ** T3357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T3365 ASN T3412 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.120009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.096944 restraints weight = 63939.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.099857 restraints weight = 33955.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.102410 restraints weight = 20482.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.102658 restraints weight = 14861.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.102814 restraints weight = 14230.015| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.4021 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: