Starting phenix.real_space_refine on Wed Mar 4 14:50:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7d3u_30567/03_2026/7d3u_30567.cif Found real_map, /net/cci-nas-00/data/ceres_data/7d3u_30567/03_2026/7d3u_30567.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7d3u_30567/03_2026/7d3u_30567.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7d3u_30567/03_2026/7d3u_30567.map" model { file = "/net/cci-nas-00/data/ceres_data/7d3u_30567/03_2026/7d3u_30567.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7d3u_30567/03_2026/7d3u_30567.cif" } resolution = 3.0 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 57 5.16 5 C 9488 2.51 5 N 2293 2.21 5 O 2495 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14333 Number of models: 1 Model: "" Number of chains: 9 Chain: "D" Number of atoms: 3897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 534, 3897 Classifications: {'peptide': 534} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 26, 'TRANS': 507} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "A" Number of atoms: 6661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 904, 6661 Classifications: {'peptide': 904} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 40, 'TRANS': 863} Chain breaks: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 19 Chain: "C" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 938 Classifications: {'peptide': 129} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 117} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 629 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 2, 'TRANS': 82} Chain: "G" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 799 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 4, 'TRANS': 106} Chain: "E" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 892 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 101} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 201 Unusual residues: {'LMT': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 200 Unresolved non-hydrogen angles: 296 Unresolved non-hydrogen dihedrals: 416 Unresolved non-hydrogen chiralities: 80 Chain: "A" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 292 Unusual residues: {'LMT': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 253 Unresolved non-hydrogen angles: 373 Unresolved non-hydrogen dihedrals: 523 Unresolved non-hydrogen chiralities: 100 Chain: "C" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'LMT': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 104 Unresolved non-hydrogen chiralities: 20 Time building chain proxies: 2.93, per 1000 atoms: 0.20 Number of scatterers: 14333 At special positions: 0 Unit cell: (86.32, 86.32, 161.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 57 16.00 O 2495 8.00 N 2293 7.00 C 9488 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.41 Conformation dependent library (CDL) restraints added in 389.6 milliseconds 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3402 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 5 sheets defined 72.7% alpha, 2.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'D' and resid 4 through 7 Processing helix chain 'D' and resid 8 through 24 Proline residue: D 14 - end of helix removed outlier: 3.748A pdb=" N ALA D 23 " --> pdb=" O GLY D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 50 removed outlier: 3.630A pdb=" N PHE D 36 " --> pdb=" O LEU D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 66 No H-bonds generated for 'chain 'D' and resid 64 through 66' Processing helix chain 'D' and resid 79 through 102 removed outlier: 3.704A pdb=" N ALA D 100 " --> pdb=" O ALA D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 126 Processing helix chain 'D' and resid 128 through 147 removed outlier: 3.563A pdb=" N PHE D 132 " --> pdb=" O ASP D 128 " (cutoff:3.500A) Proline residue: D 142 - end of helix Processing helix chain 'D' and resid 156 through 188 removed outlier: 3.774A pdb=" N SER D 163 " --> pdb=" O GLY D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 197 Processing helix chain 'D' and resid 203 through 222 removed outlier: 3.750A pdb=" N ALA D 209 " --> pdb=" O ALA D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 232 Processing helix chain 'D' and resid 238 through 246 removed outlier: 3.517A pdb=" N ALA D 243 " --> pdb=" O PRO D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 264 Processing helix chain 'D' and resid 271 through 293 removed outlier: 4.022A pdb=" N GLY D 275 " --> pdb=" O TYR D 271 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL D 287 " --> pdb=" O MET D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 317 removed outlier: 3.666A pdb=" N LEU D 300 " --> pdb=" O PRO D 296 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA D 301 " --> pdb=" O ARG D 297 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N PHE D 302 " --> pdb=" O SER D 298 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLY D 314 " --> pdb=" O TYR D 310 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N VAL D 315 " --> pdb=" O ILE D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 351 removed outlier: 3.748A pdb=" N THR D 324 " --> pdb=" O PRO D 320 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE D 335 " --> pdb=" O LEU D 331 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG D 350 " --> pdb=" O ALA D 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 366 Processing helix chain 'D' and resid 366 through 381 removed outlier: 3.622A pdb=" N SER D 376 " --> pdb=" O ALA D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 402 removed outlier: 4.402A pdb=" N VAL D 390 " --> pdb=" O PHE D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 430 removed outlier: 4.466A pdb=" N SER D 415 " --> pdb=" O ALA D 411 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ILE D 416 " --> pdb=" O VAL D 412 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU D 417 " --> pdb=" O VAL D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 458 through 462 removed outlier: 3.863A pdb=" N ASP D 461 " --> pdb=" O ASP D 458 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N VAL D 462 " --> pdb=" O GLY D 459 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 458 through 462' Processing helix chain 'D' and resid 527 through 547 Proline residue: D 533 - end of helix removed outlier: 3.539A pdb=" N LEU D 537 " --> pdb=" O PRO D 533 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER D 538 " --> pdb=" O ALA D 534 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N THR D 541 " --> pdb=" O LEU D 537 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU D 542 " --> pdb=" O SER D 538 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLY D 545 " --> pdb=" O THR D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 560 removed outlier: 3.504A pdb=" N LEU D 554 " --> pdb=" O LEU D 550 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 573 removed outlier: 3.674A pdb=" N ALA D 571 " --> pdb=" O THR D 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 2 through 24 removed outlier: 3.655A pdb=" N ALA A 14 " --> pdb=" O ALA A 10 " (cutoff:3.500A) Proline residue: A 18 - end of helix Processing helix chain 'A' and resid 28 through 46 removed outlier: 3.501A pdb=" N LEU A 32 " --> pdb=" O ALA A 28 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLY A 38 " --> pdb=" O ALA A 34 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU A 39 " --> pdb=" O MET A 35 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 95 removed outlier: 3.966A pdb=" N MET A 78 " --> pdb=" O ARG A 74 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE A 83 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ARG A 93 " --> pdb=" O ALA A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 120 removed outlier: 3.849A pdb=" N LEU A 107 " --> pdb=" O GLY A 103 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU A 110 " --> pdb=" O GLY A 106 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA A 112 " --> pdb=" O MET A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 143 Processing helix chain 'A' and resid 145 through 148 removed outlier: 3.581A pdb=" N LYS A 148 " --> pdb=" O ALA A 145 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 145 through 148' Processing helix chain 'A' and resid 149 through 165 Processing helix chain 'A' and resid 165 through 179 Processing helix chain 'A' and resid 182 through 187 Processing helix chain 'A' and resid 190 through 195 removed outlier: 3.602A pdb=" N ASP A 195 " --> pdb=" O VAL A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 214 removed outlier: 3.765A pdb=" N ALA A 199 " --> pdb=" O ASP A 195 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL A 201 " --> pdb=" O ALA A 197 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR A 212 " --> pdb=" O MET A 208 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LYS A 213 " --> pdb=" O ALA A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 229 Processing helix chain 'A' and resid 230 through 240 Processing helix chain 'A' and resid 242 through 253 removed outlier: 3.799A pdb=" N GLY A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ILE A 247 " --> pdb=" O VAL A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 256 No H-bonds generated for 'chain 'A' and resid 254 through 256' Processing helix chain 'A' and resid 260 through 285 removed outlier: 3.679A pdb=" N CYS A 270 " --> pdb=" O LEU A 266 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N PHE A 281 " --> pdb=" O LEU A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 309 removed outlier: 3.514A pdb=" N ALA A 293 " --> pdb=" O LYS A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 342 removed outlier: 3.759A pdb=" N VAL A 316 " --> pdb=" O PRO A 312 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA A 317 " --> pdb=" O ALA A 313 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N SER A 330 " --> pdb=" O ALA A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 374 removed outlier: 3.744A pdb=" N VAL A 365 " --> pdb=" O THR A 361 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA A 370 " --> pdb=" O GLY A 366 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N SER A 371 " --> pdb=" O LEU A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 392 removed outlier: 4.146A pdb=" N VAL A 382 " --> pdb=" O LEU A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 424 removed outlier: 3.657A pdb=" N PHE A 410 " --> pdb=" O ALA A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 472 Proline residue: A 462 - end of helix removed outlier: 3.545A pdb=" N LEU A 467 " --> pdb=" O ALA A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 475 No H-bonds generated for 'chain 'A' and resid 473 through 475' Processing helix chain 'A' and resid 476 through 485 Processing helix chain 'A' and resid 503 through 521 removed outlier: 4.501A pdb=" N SER A 509 " --> pdb=" O GLU A 505 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N VAL A 512 " --> pdb=" O MET A 508 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE A 513 " --> pdb=" O SER A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 531 Processing helix chain 'A' and resid 539 through 541 No H-bonds generated for 'chain 'A' and resid 539 through 541' Processing helix chain 'A' and resid 542 through 559 Processing helix chain 'A' and resid 560 through 562 No H-bonds generated for 'chain 'A' and resid 560 through 562' Processing helix chain 'A' and resid 565 through 570 removed outlier: 3.642A pdb=" N HIS A 569 " --> pdb=" O ARG A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 588 removed outlier: 3.560A pdb=" N VAL A 576 " --> pdb=" O ALA A 572 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL A 586 " --> pdb=" O ALA A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 601 No H-bonds generated for 'chain 'A' and resid 599 through 601' Processing helix chain 'A' and resid 602 through 618 Processing helix chain 'A' and resid 621 through 643 Processing helix chain 'A' and resid 645 through 668 removed outlier: 3.620A pdb=" N VAL A 662 " --> pdb=" O LEU A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 702 removed outlier: 3.503A pdb=" N VAL A 691 " --> pdb=" O ALA A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 719 Processing helix chain 'A' and resid 728 through 736 Processing helix chain 'A' and resid 738 through 763 removed outlier: 3.770A pdb=" N THR A 742 " --> pdb=" O ARG A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 788 Processing helix chain 'A' and resid 788 through 813 removed outlier: 4.093A pdb=" N ARG A 796 " --> pdb=" O ARG A 792 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE A 797 " --> pdb=" O THR A 793 " (cutoff:3.500A) Proline residue: A 800 - end of helix removed outlier: 3.667A pdb=" N VAL A 811 " --> pdb=" O LEU A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 820 through 838 removed outlier: 3.681A pdb=" N GLY A 830 " --> pdb=" O ILE A 826 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA A 838 " --> pdb=" O TYR A 834 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 867 Processing helix chain 'A' and resid 868 through 871 Processing helix chain 'A' and resid 889 through 913 removed outlier: 3.568A pdb=" N LEU A 912 " --> pdb=" O ALA A 908 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 18 removed outlier: 3.769A pdb=" N VAL C 7 " --> pdb=" O LEU C 3 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 45 removed outlier: 3.898A pdb=" N GLY C 29 " --> pdb=" O ARG C 25 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLY C 45 " --> pdb=" O LEU C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 91 removed outlier: 4.032A pdb=" N GLN C 69 " --> pdb=" O ASP C 65 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL C 77 " --> pdb=" O LEU C 73 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL C 91 " --> pdb=" O LEU C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 108 Processing helix chain 'F' and resid 2 through 24 Processing helix chain 'F' and resid 29 through 53 removed outlier: 3.721A pdb=" N ALA F 35 " --> pdb=" O ARG F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 58 through 66 removed outlier: 3.561A pdb=" N THR F 66 " --> pdb=" O VAL F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 81 removed outlier: 4.275A pdb=" N LEU F 76 " --> pdb=" O SER F 72 " (cutoff:3.500A) Processing helix chain 'G' and resid 4 through 29 Processing helix chain 'G' and resid 34 through 61 removed outlier: 3.570A pdb=" N ARG G 38 " --> pdb=" O ASP G 34 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ALA G 44 " --> pdb=" O SER G 40 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLY G 47 " --> pdb=" O GLY G 43 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU G 50 " --> pdb=" O ALA G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 96 removed outlier: 3.875A pdb=" N ALA G 73 " --> pdb=" O LYS G 69 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE G 75 " --> pdb=" O ALA G 71 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA G 85 " --> pdb=" O SER G 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 34 removed outlier: 3.520A pdb=" N TRP E 13 " --> pdb=" O LEU E 9 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N THR E 25 " --> pdb=" O GLN E 21 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE E 34 " --> pdb=" O VAL E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 67 removed outlier: 3.659A pdb=" N VAL E 57 " --> pdb=" O SER E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 112 Processing sheet with id=AA1, first strand: chain 'D' and resid 59 through 62 Processing sheet with id=AA2, first strand: chain 'D' and resid 437 through 438 Processing sheet with id=AA3, first strand: chain 'A' and resid 52 through 58 removed outlier: 5.172A pdb=" N SER A 54 " --> pdb=" O LEU A 67 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N LEU A 67 " --> pdb=" O SER A 54 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N GLU A 56 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N LEU A 65 " --> pdb=" O GLU A 56 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 880 through 882 Processing sheet with id=AA5, first strand: chain 'G' and resid 105 through 106 removed outlier: 6.471A pdb=" N TYR G 105 " --> pdb=" O PHE E 44 " (cutoff:3.500A) removed outlier: 8.714A pdb=" N ARG E 46 " --> pdb=" O TYR G 105 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N GLU E 85 " --> pdb=" O ALA E 75 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N ALA E 75 " --> pdb=" O GLU E 85 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL E 87 " --> pdb=" O LEU E 73 " (cutoff:3.500A) 948 hydrogen bonds defined for protein. 2802 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: 2.45 Time building geometry restraints manager: 1.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4268 1.34 - 1.45: 1894 1.45 - 1.57: 8351 1.57 - 1.69: 0 1.69 - 1.81: 109 Bond restraints: 14622 Sorted by residual: bond pdb=" C5 LMT A1207 " pdb=" C6 LMT A1207 " ideal model delta sigma weight residual 1.527 1.263 0.264 2.00e-02 2.50e+03 1.74e+02 bond pdb=" C6 LMT A1207 " pdb=" C7 LMT A1207 " ideal model delta sigma weight residual 1.527 1.316 0.211 2.00e-02 2.50e+03 1.11e+02 bond pdb=" C8 LMT A1210 " pdb=" C9 LMT A1210 " ideal model delta sigma weight residual 1.531 1.367 0.164 2.00e-02 2.50e+03 6.76e+01 bond pdb=" C7 LMT A1210 " pdb=" C8 LMT A1210 " ideal model delta sigma weight residual 1.529 1.374 0.155 2.00e-02 2.50e+03 6.02e+01 bond pdb=" C2 LMT A1207 " pdb=" C3 LMT A1207 " ideal model delta sigma weight residual 1.529 1.376 0.153 2.00e-02 2.50e+03 5.86e+01 ... (remaining 14617 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.90: 19773 5.90 - 11.80: 108 11.80 - 17.70: 3 17.70 - 23.61: 2 23.61 - 29.51: 2 Bond angle restraints: 19888 Sorted by residual: angle pdb=" C6 LMT A1210 " pdb=" C7 LMT A1210 " pdb=" C8 LMT A1210 " ideal model delta sigma weight residual 117.26 87.75 29.51 3.00e+00 1.11e-01 9.67e+01 angle pdb=" C5 LMT A1207 " pdb=" C6 LMT A1207 " pdb=" C7 LMT A1207 " ideal model delta sigma weight residual 115.22 89.90 25.32 3.00e+00 1.11e-01 7.12e+01 angle pdb=" N PRO D 517 " pdb=" CA PRO D 517 " pdb=" CB PRO D 517 " ideal model delta sigma weight residual 103.00 110.44 -7.44 1.10e+00 8.26e-01 4.58e+01 angle pdb=" C4 LMT A1207 " pdb=" C5 LMT A1207 " pdb=" C6 LMT A1207 " ideal model delta sigma weight residual 115.09 94.85 20.24 3.00e+00 1.11e-01 4.55e+01 angle pdb=" C3 LMT A1207 " pdb=" C4 LMT A1207 " pdb=" C5 LMT A1207 " ideal model delta sigma weight residual 115.20 133.51 -18.31 3.00e+00 1.11e-01 3.72e+01 ... (remaining 19883 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.53: 8277 25.53 - 51.05: 439 51.05 - 76.58: 73 76.58 - 102.11: 42 102.11 - 127.64: 46 Dihedral angle restraints: 8877 sinusoidal: 3569 harmonic: 5308 Sorted by residual: dihedral pdb=" N TRP E 84 " pdb=" C TRP E 84 " pdb=" CA TRP E 84 " pdb=" CB TRP E 84 " ideal model delta harmonic sigma weight residual 122.80 135.47 -12.67 0 2.50e+00 1.60e-01 2.57e+01 dihedral pdb=" C1' LMT A1206 " pdb=" C5' LMT A1206 " pdb=" O5' LMT A1206 " pdb=" C4' LMT A1206 " ideal model delta sinusoidal sigma weight residual -62.78 64.86 -127.64 1 3.00e+01 1.11e-03 1.72e+01 dihedral pdb=" CA ASP A 919 " pdb=" C ASP A 919 " pdb=" N GLU A 920 " pdb=" CA GLU A 920 " ideal model delta harmonic sigma weight residual 180.00 159.69 20.31 0 5.00e+00 4.00e-02 1.65e+01 ... (remaining 8874 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.114: 2436 0.114 - 0.228: 42 0.228 - 0.342: 7 0.342 - 0.456: 0 0.456 - 0.570: 2 Chirality restraints: 2487 Sorted by residual: chirality pdb=" C5' LMT A1206 " pdb=" C4' LMT A1206 " pdb=" C6' LMT A1206 " pdb=" O5' LMT A1206 " both_signs ideal model delta sigma weight residual False -2.51 -1.94 -0.57 2.00e-01 2.50e+01 8.13e+00 chirality pdb=" CA TRP E 84 " pdb=" N TRP E 84 " pdb=" C TRP E 84 " pdb=" CB TRP E 84 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.15e+00 chirality pdb=" C3B LMT A1214 " pdb=" C2B LMT A1214 " pdb=" C4B LMT A1214 " pdb=" O3B LMT A1214 " both_signs ideal model delta sigma weight residual False 2.50 2.22 0.28 2.00e-01 2.50e+01 1.90e+00 ... (remaining 2484 not shown) Planarity restraints: 2395 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE D 383 " -0.042 5.00e-02 4.00e+02 6.27e-02 6.29e+00 pdb=" N PRO D 384 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO D 384 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 384 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 920 " 0.032 5.00e-02 4.00e+02 4.86e-02 3.78e+00 pdb=" N PRO A 921 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 921 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 921 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 535 " 0.009 2.00e-02 2.50e+03 1.81e-02 3.28e+00 pdb=" C ALA A 535 " -0.031 2.00e-02 2.50e+03 pdb=" O ALA A 535 " 0.011 2.00e-02 2.50e+03 pdb=" N PRO A 536 " 0.011 2.00e-02 2.50e+03 ... (remaining 2392 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 247 2.68 - 3.23: 14641 3.23 - 3.79: 23380 3.79 - 4.34: 31853 4.34 - 4.90: 52658 Nonbonded interactions: 122779 Sorted by model distance: nonbonded pdb=" O ASP E 83 " pdb=" O TRP E 84 " model vdw 2.119 3.040 nonbonded pdb=" O LEU A 734 " pdb=" OG1 THR A 742 " model vdw 2.230 3.040 nonbonded pdb=" NE2 GLN A 284 " pdb=" CD1 LEU A 530 " model vdw 2.239 3.540 nonbonded pdb=" O ARG A 681 " pdb=" OG SER A 685 " model vdw 2.257 3.040 nonbonded pdb=" O ASP D 77 " pdb=" ND2 ASN D 561 " model vdw 2.268 3.120 ... (remaining 122774 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 individual isotropic 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: 3.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.560 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 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 0.264 14622 Z= 0.384 Angle : 1.029 29.508 19888 Z= 0.441 Chirality : 0.049 0.570 2487 Planarity : 0.004 0.063 2395 Dihedral : 19.880 127.635 5475 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 18.66 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.71 % Favored : 94.24 % Rotamer: Outliers : 0.50 % Allowed : 16.23 % Favored : 83.27 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.05 (0.17), residues: 1857 helix: -1.49 (0.13), residues: 1281 sheet: -2.25 (0.86), residues: 30 loop : -2.99 (0.24), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 707 TYR 0.023 0.001 TYR A 418 PHE 0.028 0.001 PHE A 328 TRP 0.013 0.001 TRP A 263 HIS 0.006 0.001 HIS G 61 Details of bonding type rmsd covalent geometry : bond 0.00781 (14622) covalent geometry : angle 1.02872 (19888) hydrogen bonds : bond 0.13817 ( 948) hydrogen bonds : angle 6.27001 ( 2802) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 248 time to evaluate : 0.511 Fit side-chains REVERT: D 1 MET cc_start: 0.7004 (mmm) cc_final: 0.6736 (mmm) REVERT: D 77 ASP cc_start: 0.8151 (p0) cc_final: 0.7824 (p0) REVERT: D 332 HIS cc_start: 0.8783 (OUTLIER) cc_final: 0.8563 (t-90) REVERT: D 364 LYS cc_start: 0.8759 (tttm) cc_final: 0.8468 (tttp) REVERT: D 570 GLN cc_start: 0.8649 (tm-30) cc_final: 0.8044 (tp-100) REVERT: A 88 MET cc_start: 0.8994 (mmt) cc_final: 0.8693 (mmp) REVERT: A 148 LYS cc_start: 0.9105 (mmtt) cc_final: 0.8798 (tptm) REVERT: A 281 PHE cc_start: 0.8506 (m-80) cc_final: 0.8297 (m-10) REVERT: A 488 ILE cc_start: 0.7863 (pt) cc_final: 0.7619 (pt) REVERT: A 523 ARG cc_start: 0.7325 (ttp-110) cc_final: 0.6823 (ptp-170) REVERT: A 785 GLN cc_start: 0.8877 (tm-30) cc_final: 0.8496 (tm-30) REVERT: A 814 HIS cc_start: 0.9018 (OUTLIER) cc_final: 0.8723 (t-90) REVERT: C 59 ASP cc_start: 0.8301 (t70) cc_final: 0.7907 (t0) REVERT: C 121 ASP cc_start: 0.8501 (t0) cc_final: 0.7946 (p0) REVERT: F 24 ARG cc_start: 0.7763 (ttt-90) cc_final: 0.7467 (tpp80) REVERT: G 64 TRP cc_start: 0.8411 (t-100) cc_final: 0.8160 (m100) REVERT: E 112 ARG cc_start: 0.8376 (ttm170) cc_final: 0.8008 (ttm-80) outliers start: 7 outliers final: 2 residues processed: 255 average time/residue: 0.5174 time to fit residues: 146.9520 Evaluate side-chains 176 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 172 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 332 HIS Chi-restraints excluded: chain A residue 639 TRP Chi-restraints excluded: chain A residue 814 HIS Chi-restraints excluded: chain C residue 101 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 42 GLN D 121 ASN D 131 ASN D 227 HIS D 249 HIS D 450 HIS A 151 GLN ** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 284 GLN A 342 GLN A 675 HIS C 69 GLN F 27 HIS G 61 HIS ** G 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 22 GLN E 109 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.104212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.085012 restraints weight = 20669.655| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 2.18 r_work: 0.2879 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14622 Z= 0.160 Angle : 0.696 8.891 19888 Z= 0.333 Chirality : 0.043 0.251 2487 Planarity : 0.005 0.072 2395 Dihedral : 14.650 102.790 2668 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 3.97 % Allowed : 19.99 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.19), residues: 1857 helix: -0.12 (0.14), residues: 1286 sheet: -1.93 (0.81), residues: 35 loop : -2.53 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 421 TYR 0.025 0.002 TYR A 418 PHE 0.027 0.001 PHE A 328 TRP 0.017 0.001 TRP A 263 HIS 0.009 0.001 HIS E 109 Details of bonding type rmsd covalent geometry : bond 0.00366 (14622) covalent geometry : angle 0.69550 (19888) hydrogen bonds : bond 0.04024 ( 948) hydrogen bonds : angle 4.35904 ( 2802) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 206 time to evaluate : 0.389 Fit side-chains REVERT: D 1 MET cc_start: 0.7056 (mmm) cc_final: 0.6849 (mmm) REVERT: D 77 ASP cc_start: 0.8702 (p0) cc_final: 0.8245 (p0) REVERT: D 364 LYS cc_start: 0.8863 (tttm) cc_final: 0.8549 (tttp) REVERT: D 570 GLN cc_start: 0.8866 (tm-30) cc_final: 0.8211 (tp-100) REVERT: A 58 MET cc_start: 0.8526 (mtm) cc_final: 0.8323 (mtt) REVERT: A 358 MET cc_start: 0.7364 (mtp) cc_final: 0.6522 (mmm) REVERT: A 454 SER cc_start: 0.8683 (p) cc_final: 0.8440 (m) REVERT: A 523 ARG cc_start: 0.7064 (ttp-110) cc_final: 0.6406 (ptp-170) REVERT: A 583 VAL cc_start: 0.8467 (OUTLIER) cc_final: 0.8259 (p) REVERT: A 636 MET cc_start: 0.8800 (mmm) cc_final: 0.8492 (mmm) REVERT: A 719 ASN cc_start: 0.8069 (m110) cc_final: 0.7733 (m-40) REVERT: A 769 ARG cc_start: 0.7290 (ttp80) cc_final: 0.6995 (ptt-90) REVERT: A 776 HIS cc_start: 0.6564 (p-80) cc_final: 0.6340 (p-80) REVERT: A 785 GLN cc_start: 0.8806 (tm-30) cc_final: 0.8239 (tm-30) REVERT: A 879 HIS cc_start: 0.8826 (OUTLIER) cc_final: 0.8289 (p90) REVERT: C 59 ASP cc_start: 0.8026 (t70) cc_final: 0.7607 (t0) REVERT: C 103 ASP cc_start: 0.7781 (t0) cc_final: 0.7473 (t0) REVERT: C 105 ASP cc_start: 0.8156 (OUTLIER) cc_final: 0.7948 (p0) REVERT: C 108 ASP cc_start: 0.8393 (OUTLIER) cc_final: 0.8182 (t0) REVERT: C 121 ASP cc_start: 0.8499 (t0) cc_final: 0.7922 (p0) REVERT: F 24 ARG cc_start: 0.7439 (ttt-90) cc_final: 0.6974 (tpp80) REVERT: G 64 TRP cc_start: 0.8565 (t-100) cc_final: 0.8208 (m100) REVERT: E 112 ARG cc_start: 0.8440 (ttm170) cc_final: 0.8062 (ttm-80) outliers start: 56 outliers final: 27 residues processed: 247 average time/residue: 0.5134 time to fit residues: 141.3660 Evaluate side-chains 203 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 172 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 201 SER Chi-restraints excluded: chain D residue 332 HIS Chi-restraints excluded: chain D residue 520 VAL Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 399 TRP Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 639 TRP Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 879 HIS Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 105 ASP Chi-restraints excluded: chain C residue 108 ASP Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 76 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 147 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 56 optimal weight: 0.6980 chunk 60 optimal weight: 0.8980 chunk 173 optimal weight: 1.9990 chunk 110 optimal weight: 4.9990 chunk 81 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 chunk 156 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.107290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.088144 restraints weight = 21078.994| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 2.21 r_work: 0.2902 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14622 Z= 0.145 Angle : 0.632 8.994 19888 Z= 0.309 Chirality : 0.041 0.268 2487 Planarity : 0.004 0.074 2395 Dihedral : 11.226 95.254 2664 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 4.68 % Allowed : 21.19 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.20), residues: 1857 helix: 0.42 (0.14), residues: 1294 sheet: -1.38 (0.84), residues: 35 loop : -2.22 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 421 TYR 0.023 0.001 TYR A 418 PHE 0.029 0.001 PHE A 328 TRP 0.014 0.001 TRP A 263 HIS 0.007 0.001 HIS A 776 Details of bonding type rmsd covalent geometry : bond 0.00336 (14622) covalent geometry : angle 0.63179 (19888) hydrogen bonds : bond 0.03808 ( 948) hydrogen bonds : angle 4.11716 ( 2802) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 188 time to evaluate : 0.483 Fit side-chains REVERT: D 323 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8328 (mm) REVERT: D 332 HIS cc_start: 0.8738 (OUTLIER) cc_final: 0.8335 (t-90) REVERT: D 364 LYS cc_start: 0.8774 (tttm) cc_final: 0.8466 (tttp) REVERT: D 570 GLN cc_start: 0.8850 (tm-30) cc_final: 0.8108 (tp-100) REVERT: A 88 MET cc_start: 0.8534 (OUTLIER) cc_final: 0.7504 (mpm) REVERT: A 283 MET cc_start: 0.8651 (ttp) cc_final: 0.8220 (ttm) REVERT: A 358 MET cc_start: 0.7484 (mtp) cc_final: 0.6911 (mmm) REVERT: A 454 SER cc_start: 0.8690 (p) cc_final: 0.8411 (m) REVERT: A 500 HIS cc_start: 0.7417 (OUTLIER) cc_final: 0.7034 (t70) REVERT: A 523 ARG cc_start: 0.7057 (ttp-110) cc_final: 0.6407 (ptp-170) REVERT: A 583 VAL cc_start: 0.8445 (OUTLIER) cc_final: 0.8230 (p) REVERT: A 636 MET cc_start: 0.8767 (mmm) cc_final: 0.8562 (mmm) REVERT: A 719 ASN cc_start: 0.8107 (m110) cc_final: 0.7759 (m-40) REVERT: A 769 ARG cc_start: 0.7526 (ttp80) cc_final: 0.7215 (ptt-90) REVERT: A 785 GLN cc_start: 0.8858 (tm-30) cc_final: 0.8474 (tm-30) REVERT: A 898 TYR cc_start: 0.8321 (t80) cc_final: 0.8096 (t80) REVERT: C 112 GLU cc_start: 0.8783 (tm-30) cc_final: 0.8398 (tt0) REVERT: C 121 ASP cc_start: 0.8424 (t0) cc_final: 0.7875 (p0) REVERT: F 24 ARG cc_start: 0.7471 (ttt-90) cc_final: 0.7044 (tpp80) REVERT: G 64 TRP cc_start: 0.8581 (t-100) cc_final: 0.8221 (m100) REVERT: E 110 MET cc_start: 0.8418 (ttp) cc_final: 0.8153 (ttt) REVERT: E 112 ARG cc_start: 0.8315 (ttm170) cc_final: 0.7961 (ttm-80) REVERT: E 115 ARG cc_start: 0.7146 (mtt90) cc_final: 0.6536 (mtt90) outliers start: 66 outliers final: 35 residues processed: 230 average time/residue: 0.5215 time to fit residues: 133.8490 Evaluate side-chains 217 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 177 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 201 SER Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 332 HIS Chi-restraints excluded: chain D residue 520 VAL Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 387 MET Chi-restraints excluded: chain A residue 399 TRP Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 500 HIS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 639 TRP Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 915 ASP Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain G residue 2 SER Chi-restraints excluded: chain G residue 6 VAL Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain E residue 76 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 179 optimal weight: 0.9990 chunk 38 optimal weight: 0.2980 chunk 32 optimal weight: 0.0970 chunk 11 optimal weight: 0.6980 chunk 181 optimal weight: 0.9980 chunk 183 optimal weight: 5.9990 chunk 123 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 107 optimal weight: 0.2980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 42 GLN ** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.109276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.090058 restraints weight = 20861.062| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 2.22 r_work: 0.2938 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14622 Z= 0.126 Angle : 0.605 11.364 19888 Z= 0.296 Chirality : 0.041 0.291 2487 Planarity : 0.004 0.072 2395 Dihedral : 9.064 59.870 2664 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 4.04 % Allowed : 22.25 % Favored : 73.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.20), residues: 1857 helix: 0.87 (0.15), residues: 1282 sheet: -1.09 (0.82), residues: 37 loop : -1.97 (0.27), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 50 TYR 0.023 0.001 TYR A 418 PHE 0.027 0.001 PHE A 328 TRP 0.011 0.001 TRP A 263 HIS 0.008 0.001 HIS A 776 Details of bonding type rmsd covalent geometry : bond 0.00285 (14622) covalent geometry : angle 0.60491 (19888) hydrogen bonds : bond 0.03565 ( 948) hydrogen bonds : angle 3.94715 ( 2802) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 211 time to evaluate : 0.488 Fit side-chains REVERT: D 323 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8326 (mm) REVERT: D 364 LYS cc_start: 0.8820 (tttm) cc_final: 0.8508 (tttp) REVERT: D 570 GLN cc_start: 0.8801 (tm-30) cc_final: 0.8037 (tp-100) REVERT: A 88 MET cc_start: 0.8611 (OUTLIER) cc_final: 0.7602 (mpm) REVERT: A 283 MET cc_start: 0.8650 (ttp) cc_final: 0.8306 (ttm) REVERT: A 358 MET cc_start: 0.7562 (mtp) cc_final: 0.7037 (mmm) REVERT: A 363 ILE cc_start: 0.7652 (pt) cc_final: 0.7409 (mt) REVERT: A 454 SER cc_start: 0.8662 (p) cc_final: 0.8393 (m) REVERT: A 523 ARG cc_start: 0.7030 (ttp-110) cc_final: 0.6422 (ptp-170) REVERT: A 556 ARG cc_start: 0.6736 (mtp180) cc_final: 0.6519 (ttp80) REVERT: A 636 MET cc_start: 0.8765 (mmm) cc_final: 0.8559 (mmm) REVERT: A 719 ASN cc_start: 0.8149 (m110) cc_final: 0.7824 (m-40) REVERT: A 785 GLN cc_start: 0.8899 (tm-30) cc_final: 0.8619 (tm-30) REVERT: A 898 TYR cc_start: 0.8318 (t80) cc_final: 0.8030 (t80) REVERT: C 59 ASP cc_start: 0.8136 (t70) cc_final: 0.7755 (t70) REVERT: C 97 ASP cc_start: 0.8476 (p0) cc_final: 0.8272 (p0) REVERT: C 112 GLU cc_start: 0.8758 (tm-30) cc_final: 0.8535 (tm-30) REVERT: C 121 ASP cc_start: 0.8301 (t0) cc_final: 0.7703 (p0) REVERT: F 24 ARG cc_start: 0.7408 (ttt-90) cc_final: 0.7031 (tpp80) REVERT: G 64 TRP cc_start: 0.8574 (t-100) cc_final: 0.8216 (m100) REVERT: E 28 LYS cc_start: 0.8152 (ttmm) cc_final: 0.7182 (tppt) REVERT: E 52 ARG cc_start: 0.8521 (mtt90) cc_final: 0.8275 (ptp90) REVERT: E 112 ARG cc_start: 0.8156 (ttm170) cc_final: 0.7834 (ttm-80) outliers start: 57 outliers final: 33 residues processed: 249 average time/residue: 0.5073 time to fit residues: 141.4704 Evaluate side-chains 216 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 181 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 201 SER Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 332 HIS Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 387 MET Chi-restraints excluded: chain A residue 399 TRP Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 639 TRP Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 915 ASP Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain G residue 2 SER Chi-restraints excluded: chain G residue 6 VAL Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 95 SER Chi-restraints excluded: chain E residue 76 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 128 optimal weight: 8.9990 chunk 14 optimal weight: 0.9980 chunk 180 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 57 optimal weight: 0.6980 chunk 148 optimal weight: 0.0030 chunk 160 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 157 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 42 GLN ** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 284 GLN ** G 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.108991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.089981 restraints weight = 20958.445| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 2.20 r_work: 0.2913 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14622 Z= 0.135 Angle : 0.600 8.727 19888 Z= 0.296 Chirality : 0.040 0.259 2487 Planarity : 0.004 0.072 2395 Dihedral : 8.400 59.853 2664 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 4.54 % Allowed : 23.03 % Favored : 72.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.20), residues: 1857 helix: 1.03 (0.15), residues: 1284 sheet: -0.73 (0.84), residues: 37 loop : -1.86 (0.28), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 115 TYR 0.022 0.001 TYR A 418 PHE 0.026 0.001 PHE A 328 TRP 0.011 0.001 TRP A 263 HIS 0.007 0.001 HIS A 776 Details of bonding type rmsd covalent geometry : bond 0.00310 (14622) covalent geometry : angle 0.59975 (19888) hydrogen bonds : bond 0.03575 ( 948) hydrogen bonds : angle 3.90859 ( 2802) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 191 time to evaluate : 0.514 Fit side-chains REVERT: D 30 LEU cc_start: 0.7867 (OUTLIER) cc_final: 0.7620 (tp) REVERT: D 323 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8309 (mm) REVERT: D 364 LYS cc_start: 0.8841 (tttm) cc_final: 0.8522 (tttp) REVERT: D 570 GLN cc_start: 0.8768 (tm-30) cc_final: 0.7982 (tp-100) REVERT: A 35 MET cc_start: 0.8159 (mtp) cc_final: 0.7903 (mtp) REVERT: A 88 MET cc_start: 0.8559 (OUTLIER) cc_final: 0.7576 (mpm) REVERT: A 283 MET cc_start: 0.8673 (ttp) cc_final: 0.8337 (ttm) REVERT: A 358 MET cc_start: 0.7568 (mtp) cc_final: 0.6704 (mmm) REVERT: A 363 ILE cc_start: 0.7464 (pt) cc_final: 0.7256 (mt) REVERT: A 454 SER cc_start: 0.8656 (p) cc_final: 0.8396 (m) REVERT: A 500 HIS cc_start: 0.7240 (OUTLIER) cc_final: 0.6923 (t70) REVERT: A 523 ARG cc_start: 0.7009 (ttp-110) cc_final: 0.6373 (ptp-170) REVERT: A 556 ARG cc_start: 0.6702 (mtp180) cc_final: 0.6487 (ttp80) REVERT: A 636 MET cc_start: 0.8798 (mmm) cc_final: 0.8439 (mmm) REVERT: A 719 ASN cc_start: 0.8164 (m110) cc_final: 0.7839 (m-40) REVERT: A 785 GLN cc_start: 0.8910 (tm-30) cc_final: 0.8659 (tm-30) REVERT: A 898 TYR cc_start: 0.8301 (t80) cc_final: 0.8024 (t80) REVERT: C 105 ASP cc_start: 0.7941 (OUTLIER) cc_final: 0.7713 (p0) REVERT: C 112 GLU cc_start: 0.8736 (tm-30) cc_final: 0.8348 (tt0) REVERT: C 121 ASP cc_start: 0.8287 (t0) cc_final: 0.7682 (p0) REVERT: F 24 ARG cc_start: 0.7357 (ttt-90) cc_final: 0.6998 (tpp80) REVERT: G 64 TRP cc_start: 0.8580 (t-100) cc_final: 0.8216 (m100) REVERT: E 49 THR cc_start: 0.7395 (OUTLIER) cc_final: 0.7171 (m) REVERT: E 112 ARG cc_start: 0.8095 (ttm170) cc_final: 0.7752 (ttm-80) outliers start: 64 outliers final: 40 residues processed: 232 average time/residue: 0.5262 time to fit residues: 136.4667 Evaluate side-chains 236 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 190 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 42 GLN Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 201 SER Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 332 HIS Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 387 MET Chi-restraints excluded: chain A residue 399 TRP Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 500 HIS Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 639 TRP Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 915 ASP Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 105 ASP Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain G residue 6 VAL Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 95 SER Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 76 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 158 optimal weight: 1.9990 chunk 70 optimal weight: 0.3980 chunk 61 optimal weight: 0.7980 chunk 151 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 168 optimal weight: 0.6980 chunk 184 optimal weight: 0.9980 chunk 41 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 42 GLN ** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 61 HIS ** G 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.106815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.088469 restraints weight = 21080.902| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 2.16 r_work: 0.2890 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14622 Z= 0.136 Angle : 0.605 10.839 19888 Z= 0.298 Chirality : 0.040 0.227 2487 Planarity : 0.004 0.072 2395 Dihedral : 8.113 59.749 2664 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 4.32 % Allowed : 23.88 % Favored : 71.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.20), residues: 1857 helix: 1.13 (0.15), residues: 1280 sheet: -0.65 (0.84), residues: 37 loop : -1.73 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 115 TYR 0.022 0.001 TYR A 418 PHE 0.025 0.001 PHE A 328 TRP 0.013 0.001 TRP A 263 HIS 0.007 0.001 HIS A 776 Details of bonding type rmsd covalent geometry : bond 0.00318 (14622) covalent geometry : angle 0.60482 (19888) hydrogen bonds : bond 0.03603 ( 948) hydrogen bonds : angle 3.88279 ( 2802) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 199 time to evaluate : 0.535 Fit side-chains REVERT: D 30 LEU cc_start: 0.7896 (OUTLIER) cc_final: 0.7647 (tp) REVERT: D 137 GLU cc_start: 0.8568 (mm-30) cc_final: 0.8278 (mm-30) REVERT: D 310 TYR cc_start: 0.8632 (m-80) cc_final: 0.8378 (m-80) REVERT: D 323 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8400 (mm) REVERT: D 364 LYS cc_start: 0.8830 (tttm) cc_final: 0.8507 (tttp) REVERT: D 570 GLN cc_start: 0.8781 (tm-30) cc_final: 0.7972 (tp-100) REVERT: A 35 MET cc_start: 0.8235 (mtp) cc_final: 0.8005 (mtp) REVERT: A 88 MET cc_start: 0.8559 (OUTLIER) cc_final: 0.7608 (mpm) REVERT: A 283 MET cc_start: 0.8693 (ttp) cc_final: 0.8377 (ttm) REVERT: A 358 MET cc_start: 0.7608 (mtp) cc_final: 0.6732 (mmm) REVERT: A 454 SER cc_start: 0.8641 (p) cc_final: 0.8364 (m) REVERT: A 523 ARG cc_start: 0.7084 (ttp-110) cc_final: 0.6391 (ptp-170) REVERT: A 556 ARG cc_start: 0.6714 (mtp180) cc_final: 0.6496 (ttp80) REVERT: A 636 MET cc_start: 0.8813 (mmm) cc_final: 0.8462 (mmm) REVERT: A 719 ASN cc_start: 0.8199 (m110) cc_final: 0.7855 (m-40) REVERT: A 898 TYR cc_start: 0.8328 (t80) cc_final: 0.8009 (t80) REVERT: C 59 ASP cc_start: 0.8168 (t70) cc_final: 0.7759 (t0) REVERT: C 103 ASP cc_start: 0.7816 (t0) cc_final: 0.7462 (t0) REVERT: C 105 ASP cc_start: 0.7930 (OUTLIER) cc_final: 0.7659 (p0) REVERT: C 112 GLU cc_start: 0.8738 (tm-30) cc_final: 0.8502 (tm-30) REVERT: C 121 ASP cc_start: 0.8300 (t0) cc_final: 0.7693 (p0) REVERT: F 24 ARG cc_start: 0.7311 (ttt-90) cc_final: 0.6947 (tpp80) REVERT: G 48 LEU cc_start: 0.7597 (OUTLIER) cc_final: 0.7081 (tp) REVERT: G 64 TRP cc_start: 0.8625 (t-100) cc_final: 0.8242 (m100) REVERT: E 28 LYS cc_start: 0.8091 (ttmm) cc_final: 0.7146 (tppt) REVERT: E 112 ARG cc_start: 0.8064 (ttm170) cc_final: 0.7695 (ttm-80) outliers start: 61 outliers final: 40 residues processed: 240 average time/residue: 0.5015 time to fit residues: 134.3372 Evaluate side-chains 231 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 186 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 201 SER Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 332 HIS Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 387 MET Chi-restraints excluded: chain A residue 399 TRP Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 639 TRP Chi-restraints excluded: chain A residue 669 ARG Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 769 ARG Chi-restraints excluded: chain A residue 888 THR Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 915 ASP Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 105 ASP Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain G residue 6 VAL Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain E residue 76 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 43 optimal weight: 0.9990 chunk 107 optimal weight: 0.8980 chunk 166 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 111 optimal weight: 0.3980 chunk 38 optimal weight: 4.9990 chunk 142 optimal weight: 0.3980 chunk 82 optimal weight: 0.9980 chunk 93 optimal weight: 0.9990 chunk 110 optimal weight: 0.5980 chunk 48 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.107672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.089341 restraints weight = 20835.144| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 2.14 r_work: 0.2903 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14622 Z= 0.129 Angle : 0.602 9.783 19888 Z= 0.297 Chirality : 0.040 0.191 2487 Planarity : 0.004 0.071 2395 Dihedral : 7.856 59.266 2664 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 4.04 % Allowed : 24.88 % Favored : 71.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.20), residues: 1857 helix: 1.23 (0.15), residues: 1290 sheet: -0.55 (0.85), residues: 37 loop : -1.78 (0.28), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 115 TYR 0.023 0.001 TYR A 418 PHE 0.029 0.001 PHE A 328 TRP 0.013 0.001 TRP A 263 HIS 0.006 0.001 HIS A 776 Details of bonding type rmsd covalent geometry : bond 0.00298 (14622) covalent geometry : angle 0.60157 (19888) hydrogen bonds : bond 0.03536 ( 948) hydrogen bonds : angle 3.82109 ( 2802) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 204 time to evaluate : 0.525 Fit side-chains revert: symmetry clash REVERT: D 30 LEU cc_start: 0.7866 (OUTLIER) cc_final: 0.7617 (tp) REVERT: D 137 GLU cc_start: 0.8481 (mm-30) cc_final: 0.8221 (mm-30) REVERT: D 323 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8402 (mm) REVERT: D 364 LYS cc_start: 0.8828 (tttm) cc_final: 0.8496 (tttp) REVERT: D 570 GLN cc_start: 0.8738 (tm-30) cc_final: 0.7903 (tp-100) REVERT: A 35 MET cc_start: 0.8245 (mtp) cc_final: 0.8037 (mtp) REVERT: A 88 MET cc_start: 0.8543 (OUTLIER) cc_final: 0.7527 (mpm) REVERT: A 283 MET cc_start: 0.8685 (ttp) cc_final: 0.8372 (ttm) REVERT: A 358 MET cc_start: 0.7536 (mtp) cc_final: 0.6764 (mmm) REVERT: A 454 SER cc_start: 0.8613 (p) cc_final: 0.8329 (m) REVERT: A 523 ARG cc_start: 0.7124 (ttp-110) cc_final: 0.6415 (ptp-170) REVERT: A 556 ARG cc_start: 0.6632 (mtp180) cc_final: 0.6428 (ttp80) REVERT: A 719 ASN cc_start: 0.8157 (m110) cc_final: 0.7799 (m-40) REVERT: A 898 TYR cc_start: 0.8188 (t80) cc_final: 0.7833 (t80) REVERT: C 59 ASP cc_start: 0.8133 (t70) cc_final: 0.7705 (t70) REVERT: C 103 ASP cc_start: 0.7672 (t0) cc_final: 0.7438 (t0) REVERT: C 112 GLU cc_start: 0.8719 (tm-30) cc_final: 0.8478 (tm-30) REVERT: C 121 ASP cc_start: 0.8289 (t0) cc_final: 0.7684 (p0) REVERT: F 24 ARG cc_start: 0.7269 (ttt-90) cc_final: 0.6902 (tpp80) REVERT: G 48 LEU cc_start: 0.7565 (OUTLIER) cc_final: 0.7050 (tp) REVERT: G 64 TRP cc_start: 0.8626 (t-100) cc_final: 0.8243 (m100) REVERT: E 28 LYS cc_start: 0.8107 (ttmm) cc_final: 0.7188 (tppt) REVERT: E 112 ARG cc_start: 0.8005 (ttm170) cc_final: 0.7623 (ttm-80) outliers start: 57 outliers final: 36 residues processed: 242 average time/residue: 0.5108 time to fit residues: 138.3703 Evaluate side-chains 226 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 186 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 201 SER Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 332 HIS Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 387 MET Chi-restraints excluded: chain A residue 399 TRP Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 639 TRP Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 888 THR Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 915 ASP Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain G residue 2 SER Chi-restraints excluded: chain G residue 6 VAL Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain E residue 76 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 137 optimal weight: 0.6980 chunk 123 optimal weight: 7.9990 chunk 87 optimal weight: 0.9980 chunk 159 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 125 optimal weight: 0.6980 chunk 85 optimal weight: 0.6980 chunk 102 optimal weight: 2.9990 chunk 126 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 113 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 121 ASN ** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.106038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.087184 restraints weight = 20689.307| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 2.15 r_work: 0.2901 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14622 Z= 0.138 Angle : 0.609 9.400 19888 Z= 0.301 Chirality : 0.040 0.165 2487 Planarity : 0.004 0.071 2395 Dihedral : 7.742 59.671 2664 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 3.83 % Allowed : 25.09 % Favored : 71.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.20), residues: 1857 helix: 1.27 (0.15), residues: 1289 sheet: -0.47 (0.85), residues: 37 loop : -1.75 (0.28), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 115 TYR 0.022 0.001 TYR A 418 PHE 0.024 0.001 PHE A 328 TRP 0.015 0.001 TRP D 52 HIS 0.006 0.001 HIS A 776 Details of bonding type rmsd covalent geometry : bond 0.00324 (14622) covalent geometry : angle 0.60882 (19888) hydrogen bonds : bond 0.03580 ( 948) hydrogen bonds : angle 3.81922 ( 2802) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 194 time to evaluate : 0.521 Fit side-chains revert: symmetry clash REVERT: D 30 LEU cc_start: 0.7918 (OUTLIER) cc_final: 0.7672 (tp) REVERT: D 137 GLU cc_start: 0.8488 (mm-30) cc_final: 0.8216 (mm-30) REVERT: D 190 THR cc_start: 0.8960 (p) cc_final: 0.8418 (t) REVERT: D 310 TYR cc_start: 0.8580 (m-80) cc_final: 0.8358 (m-80) REVERT: D 323 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8423 (mm) REVERT: D 364 LYS cc_start: 0.8787 (tttm) cc_final: 0.8446 (tttp) REVERT: D 570 GLN cc_start: 0.8717 (tm-30) cc_final: 0.7879 (tp-100) REVERT: A 35 MET cc_start: 0.8290 (mtp) cc_final: 0.8082 (mtp) REVERT: A 88 MET cc_start: 0.8553 (OUTLIER) cc_final: 0.7528 (mpm) REVERT: A 111 PHE cc_start: 0.8282 (OUTLIER) cc_final: 0.8075 (t80) REVERT: A 283 MET cc_start: 0.8742 (ttp) cc_final: 0.8375 (ttm) REVERT: A 358 MET cc_start: 0.7562 (mtp) cc_final: 0.6757 (mmm) REVERT: A 454 SER cc_start: 0.8611 (p) cc_final: 0.8307 (m) REVERT: A 523 ARG cc_start: 0.7051 (ttp-110) cc_final: 0.6383 (ptp-170) REVERT: A 719 ASN cc_start: 0.8153 (m110) cc_final: 0.7785 (m-40) REVERT: A 898 TYR cc_start: 0.8196 (t80) cc_final: 0.7822 (t80) REVERT: C 105 ASP cc_start: 0.7808 (OUTLIER) cc_final: 0.7518 (p0) REVERT: C 112 GLU cc_start: 0.8742 (tm-30) cc_final: 0.8506 (tm-30) REVERT: C 121 ASP cc_start: 0.8295 (t0) cc_final: 0.7689 (p0) REVERT: F 24 ARG cc_start: 0.7271 (ttt-90) cc_final: 0.6903 (tpp80) REVERT: G 48 LEU cc_start: 0.7583 (OUTLIER) cc_final: 0.7082 (tp) REVERT: G 64 TRP cc_start: 0.8675 (t-100) cc_final: 0.8241 (m100) REVERT: E 28 LYS cc_start: 0.8096 (ttmm) cc_final: 0.7145 (tppt) REVERT: E 112 ARG cc_start: 0.7945 (ttm170) cc_final: 0.7564 (ttm-80) outliers start: 54 outliers final: 34 residues processed: 235 average time/residue: 0.5459 time to fit residues: 142.8564 Evaluate side-chains 227 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 187 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 201 SER Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 332 HIS Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 111 PHE Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 387 MET Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 639 TRP Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 769 ARG Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 105 ASP Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain G residue 2 SER Chi-restraints excluded: chain G residue 6 VAL Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain E residue 76 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 174 optimal weight: 6.9990 chunk 161 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 chunk 64 optimal weight: 0.9980 chunk 107 optimal weight: 0.7980 chunk 94 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 23 optimal weight: 0.0970 chunk 17 optimal weight: 0.9980 chunk 145 optimal weight: 0.9990 chunk 104 optimal weight: 0.0020 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.108144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.089148 restraints weight = 20984.045| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 2.19 r_work: 0.2915 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14622 Z= 0.128 Angle : 0.600 9.486 19888 Z= 0.297 Chirality : 0.040 0.162 2487 Planarity : 0.004 0.070 2395 Dihedral : 7.571 58.166 2664 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 3.12 % Allowed : 26.44 % Favored : 70.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.20), residues: 1857 helix: 1.37 (0.15), residues: 1287 sheet: -0.41 (0.86), residues: 37 loop : -1.75 (0.28), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 792 TYR 0.023 0.001 TYR A 418 PHE 0.027 0.001 PHE A 328 TRP 0.013 0.001 TRP D 52 HIS 0.006 0.001 HIS A 776 Details of bonding type rmsd covalent geometry : bond 0.00294 (14622) covalent geometry : angle 0.60047 (19888) hydrogen bonds : bond 0.03469 ( 948) hydrogen bonds : angle 3.77661 ( 2802) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 200 time to evaluate : 0.511 Fit side-chains REVERT: D 30 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7714 (tp) REVERT: D 137 GLU cc_start: 0.8496 (mm-30) cc_final: 0.8220 (mm-30) REVERT: D 190 THR cc_start: 0.8919 (p) cc_final: 0.8398 (t) REVERT: D 323 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8428 (mm) REVERT: D 364 LYS cc_start: 0.8788 (tttm) cc_final: 0.8445 (tttp) REVERT: D 570 GLN cc_start: 0.8718 (tm-30) cc_final: 0.7877 (tp-100) REVERT: A 88 MET cc_start: 0.8567 (OUTLIER) cc_final: 0.7595 (mpm) REVERT: A 283 MET cc_start: 0.8761 (ttp) cc_final: 0.8365 (ttm) REVERT: A 358 MET cc_start: 0.7523 (mtp) cc_final: 0.6705 (mmm) REVERT: A 454 SER cc_start: 0.8598 (p) cc_final: 0.8286 (m) REVERT: A 523 ARG cc_start: 0.7054 (ttp-110) cc_final: 0.6390 (ptp-170) REVERT: A 719 ASN cc_start: 0.8176 (m110) cc_final: 0.7805 (m-40) REVERT: A 898 TYR cc_start: 0.8260 (t80) cc_final: 0.7921 (t80) REVERT: A 920 GLU cc_start: 0.7342 (tp30) cc_final: 0.7075 (pm20) REVERT: C 103 ASP cc_start: 0.7614 (t0) cc_final: 0.7033 (t0) REVERT: C 105 ASP cc_start: 0.7719 (OUTLIER) cc_final: 0.7389 (p0) REVERT: C 121 ASP cc_start: 0.8294 (t0) cc_final: 0.7684 (p0) REVERT: F 24 ARG cc_start: 0.7289 (ttt-90) cc_final: 0.6923 (tpp80) REVERT: F 55 SER cc_start: 0.8523 (t) cc_final: 0.8307 (p) REVERT: G 48 LEU cc_start: 0.7606 (OUTLIER) cc_final: 0.7105 (tp) REVERT: G 64 TRP cc_start: 0.8681 (t-100) cc_final: 0.8256 (m100) REVERT: E 28 LYS cc_start: 0.8070 (ttmm) cc_final: 0.7118 (tppt) REVERT: E 112 ARG cc_start: 0.7926 (ttm170) cc_final: 0.7506 (ttm-80) outliers start: 44 outliers final: 29 residues processed: 229 average time/residue: 0.5230 time to fit residues: 133.9539 Evaluate side-chains 223 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 189 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 201 SER Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 332 HIS Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 387 MET Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 105 ASP Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain G residue 6 VAL Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain E residue 76 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 109 optimal weight: 0.8980 chunk 130 optimal weight: 0.8980 chunk 154 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 148 optimal weight: 0.1980 chunk 95 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 159 optimal weight: 0.8980 chunk 85 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 HIS ** G 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.107950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.088961 restraints weight = 20986.917| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 2.18 r_work: 0.2914 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14622 Z= 0.134 Angle : 0.618 9.549 19888 Z= 0.303 Chirality : 0.040 0.174 2487 Planarity : 0.004 0.070 2395 Dihedral : 7.406 57.498 2662 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.98 % Allowed : 26.58 % Favored : 70.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.20), residues: 1857 helix: 1.38 (0.15), residues: 1291 sheet: -0.40 (0.86), residues: 37 loop : -1.75 (0.28), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 115 TYR 0.022 0.001 TYR A 418 PHE 0.023 0.001 PHE A 328 TRP 0.013 0.001 TRP D 52 HIS 0.005 0.001 HIS A 776 Details of bonding type rmsd covalent geometry : bond 0.00312 (14622) covalent geometry : angle 0.61816 (19888) hydrogen bonds : bond 0.03491 ( 948) hydrogen bonds : angle 3.79026 ( 2802) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 190 time to evaluate : 0.513 Fit side-chains REVERT: D 30 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7715 (tp) REVERT: D 137 GLU cc_start: 0.8504 (mm-30) cc_final: 0.8227 (mm-30) REVERT: D 190 THR cc_start: 0.8916 (p) cc_final: 0.8390 (t) REVERT: D 323 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8436 (mm) REVERT: D 364 LYS cc_start: 0.8778 (tttm) cc_final: 0.8422 (tttp) REVERT: D 570 GLN cc_start: 0.8710 (tm-30) cc_final: 0.7860 (tp-100) REVERT: A 16 ILE cc_start: 0.7622 (tt) cc_final: 0.7378 (pp) REVERT: A 88 MET cc_start: 0.8584 (OUTLIER) cc_final: 0.7595 (mpm) REVERT: A 115 MET cc_start: 0.8229 (mmm) cc_final: 0.7861 (mmm) REVERT: A 283 MET cc_start: 0.8763 (ttp) cc_final: 0.8367 (ttm) REVERT: A 358 MET cc_start: 0.7562 (mtp) cc_final: 0.6748 (mmm) REVERT: A 454 SER cc_start: 0.8591 (p) cc_final: 0.8282 (m) REVERT: A 508 MET cc_start: 0.7870 (ppp) cc_final: 0.7434 (ptt) REVERT: A 523 ARG cc_start: 0.7111 (ttp-110) cc_final: 0.6450 (ptp-170) REVERT: A 898 TYR cc_start: 0.8245 (t80) cc_final: 0.7923 (t80) REVERT: C 59 ASP cc_start: 0.8128 (t70) cc_final: 0.7692 (t70) REVERT: C 103 ASP cc_start: 0.7619 (t0) cc_final: 0.6999 (t0) REVERT: C 105 ASP cc_start: 0.7801 (OUTLIER) cc_final: 0.7429 (p0) REVERT: C 112 GLU cc_start: 0.8658 (tm-30) cc_final: 0.8386 (tm-30) REVERT: C 121 ASP cc_start: 0.8293 (t0) cc_final: 0.7682 (p0) REVERT: F 24 ARG cc_start: 0.7423 (ttt-90) cc_final: 0.7058 (tpp80) REVERT: G 48 LEU cc_start: 0.7612 (OUTLIER) cc_final: 0.7108 (tp) REVERT: G 64 TRP cc_start: 0.8676 (t-100) cc_final: 0.8244 (m100) REVERT: E 28 LYS cc_start: 0.8049 (ttmm) cc_final: 0.7101 (tppt) REVERT: E 100 THR cc_start: 0.7132 (m) cc_final: 0.6900 (m) REVERT: E 112 ARG cc_start: 0.7938 (ttm170) cc_final: 0.7524 (ttm-80) outliers start: 42 outliers final: 29 residues processed: 220 average time/residue: 0.5125 time to fit residues: 126.2274 Evaluate side-chains 220 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 186 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 201 SER Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 332 HIS Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 387 MET Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 888 THR Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 105 ASP Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain G residue 6 VAL Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain E residue 76 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 47 optimal weight: 4.9990 chunk 88 optimal weight: 0.0870 chunk 105 optimal weight: 0.0010 chunk 180 optimal weight: 0.7980 chunk 99 optimal weight: 3.9990 chunk 14 optimal weight: 0.6980 chunk 123 optimal weight: 7.9990 chunk 7 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 chunk 18 optimal weight: 0.8980 overall best weight: 0.4964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.108093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.089261 restraints weight = 20681.316| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 2.16 r_work: 0.2943 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14622 Z= 0.126 Angle : 0.619 9.500 19888 Z= 0.302 Chirality : 0.040 0.182 2487 Planarity : 0.004 0.069 2395 Dihedral : 7.291 57.024 2662 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.83 % Allowed : 26.65 % Favored : 70.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.20), residues: 1857 helix: 1.46 (0.15), residues: 1281 sheet: -0.34 (0.86), residues: 37 loop : -1.72 (0.27), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 115 TYR 0.023 0.001 TYR A 418 PHE 0.025 0.001 PHE A 328 TRP 0.012 0.001 TRP D 52 HIS 0.005 0.001 HIS A 776 Details of bonding type rmsd covalent geometry : bond 0.00289 (14622) covalent geometry : angle 0.61899 (19888) hydrogen bonds : bond 0.03436 ( 948) hydrogen bonds : angle 3.76199 ( 2802) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4617.66 seconds wall clock time: 79 minutes 32.23 seconds (4772.23 seconds total)