Starting phenix.real_space_refine on Fri Sep 11 06:31:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6ppl_20442/09_2026/6ppl_20442.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ppl_20442/09_2026/6ppl_20442.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6ppl_20442/09_2026/6ppl_20442.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6ppl_20442/09_2026/6ppl_20442.cif" model { file = "/net/cci-nas-00/data/ceres_data/6ppl_20442/09_2026/6ppl_20442.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ppl_20442/09_2026/6ppl_20442.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ppl_20442/09_2026/6ppl_20442.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ppl_20442/09_2026/6ppl_20442.map" } resolution = 3.02 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 53 5.16 5 C 5178 2.51 5 N 1384 2.21 5 O 1528 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8155 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1260 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 4, 'TRANS': 150} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "B" Number of atoms: 5470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 665, 5470 Classifications: {'peptide': 665} Link IDs: {'PTRANS': 27, 'TRANS': 637} Chain breaks: 1 Chain: "C" Number of atoms: 1287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1287 Unusual residues: {'ACE': 1} Classifications: {'peptide': 160, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'ACE_C-N': 1, 'PTRANS': 6, 'TRANS': 153} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 23 Chain: "A" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'ACO': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'ACO': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.65, per 1000 atoms: 0.20 Number of scatterers: 8155 At special positions: 0 Unit cell: (89.856, 107.328, 108.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 53 16.00 P 12 15.00 O 1528 8.00 N 1384 7.00 C 5178 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.60 Conformation dependent library (CDL) restraints added in 411.8 milliseconds 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1894 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 2 sheets defined 67.3% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 15 through 27 removed outlier: 3.520A pdb=" N LEU A 19 " --> pdb=" O ASN A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 39 removed outlier: 3.650A pdb=" N TYR A 36 " --> pdb=" O ASN A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 42 No H-bonds generated for 'chain 'A' and resid 40 through 42' Processing helix chain 'A' and resid 81 through 84 removed outlier: 3.831A pdb=" N ARG A 84 " --> pdb=" O ALA A 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 81 through 84' Processing helix chain 'A' and resid 87 through 104 Processing helix chain 'A' and resid 117 through 125 removed outlier: 3.635A pdb=" N ILE A 121 " --> pdb=" O ASN A 117 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASP A 122 " --> pdb=" O GLU A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 128 No H-bonds generated for 'chain 'A' and resid 126 through 128' Processing helix chain 'B' and resid 117 through 128 removed outlier: 3.773A pdb=" N GLN B 126 " --> pdb=" O LEU B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 142 removed outlier: 3.505A pdb=" N THR B 136 " --> pdb=" O GLY B 132 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLN B 139 " --> pdb=" O GLU B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 160 removed outlier: 4.069A pdb=" N TRP B 151 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE B 152 " --> pdb=" O ARG B 148 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TYR B 154 " --> pdb=" O SER B 150 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE B 156 " --> pdb=" O ILE B 152 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA B 157 " --> pdb=" O GLY B 153 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N TYR B 158 " --> pdb=" O TYR B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 176 removed outlier: 4.807A pdb=" N LYS B 169 " --> pdb=" O GLU B 165 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU B 172 " --> pdb=" O ALA B 168 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU B 173 " --> pdb=" O LYS B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 203 removed outlier: 3.966A pdb=" N LEU B 192 " --> pdb=" O GLU B 188 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR B 195 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLN B 198 " --> pdb=" O LEU B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 217 removed outlier: 3.834A pdb=" N LEU B 210 " --> pdb=" O TYR B 206 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR B 215 " --> pdb=" O GLU B 211 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TYR B 216 " --> pdb=" O HIS B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 237 removed outlier: 3.883A pdb=" N LEU B 235 " --> pdb=" O GLY B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 254 removed outlier: 4.026A pdb=" N ASP B 245 " --> pdb=" O GLU B 241 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL B 246 " --> pdb=" O ASP B 242 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLY B 249 " --> pdb=" O ASP B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 269 removed outlier: 3.752A pdb=" N LEU B 264 " --> pdb=" O TYR B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 287 removed outlier: 3.560A pdb=" N LEU B 277 " --> pdb=" O MET B 273 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LYS B 278 " --> pdb=" O LEU B 274 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ILE B 279 " --> pdb=" O GLU B 275 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N TYR B 280 " --> pdb=" O ARG B 276 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ALA B 283 " --> pdb=" O ILE B 279 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N THR B 285 " --> pdb=" O GLU B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 296 Processing helix chain 'B' and resid 297 through 300 Processing helix chain 'B' and resid 303 through 321 removed outlier: 3.694A pdb=" N LYS B 312 " --> pdb=" O GLU B 308 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N MET B 316 " --> pdb=" O LYS B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 329 removed outlier: 3.722A pdb=" N LEU B 329 " --> pdb=" O VAL B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 334 removed outlier: 4.303A pdb=" N LYS B 334 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 354 removed outlier: 3.907A pdb=" N VAL B 339 " --> pdb=" O ASP B 335 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA B 340 " --> pdb=" O LYS B 336 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE B 341 " --> pdb=" O GLU B 337 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL B 347 " --> pdb=" O GLU B 343 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER B 352 " --> pdb=" O GLY B 348 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS B 354 " --> pdb=" O GLU B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 388 removed outlier: 4.406A pdb=" N LEU B 373 " --> pdb=" O PRO B 369 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU B 374 " --> pdb=" O PRO B 370 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN B 382 " --> pdb=" O TYR B 378 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N TYR B 384 " --> pdb=" O LEU B 380 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP B 385 " --> pdb=" O ALA B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 402 Processing helix chain 'B' and resid 408 through 422 removed outlier: 3.657A pdb=" N VAL B 413 " --> pdb=" O GLU B 409 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS B 414 " --> pdb=" O LEU B 410 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS B 416 " --> pdb=" O LEU B 412 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS B 419 " --> pdb=" O ALA B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 438 removed outlier: 3.587A pdb=" N ARG B 429 " --> pdb=" O LYS B 425 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N TRP B 430 " --> pdb=" O GLU B 426 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN B 435 " --> pdb=" O MET B 431 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA B 436 " --> pdb=" O ASP B 432 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU B 437 " --> pdb=" O GLU B 433 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASP B 438 " --> pdb=" O ALA B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 455 removed outlier: 3.620A pdb=" N CYS B 448 " --> pdb=" O ILE B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 466 removed outlier: 3.529A pdb=" N MET B 464 " --> pdb=" O GLU B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 469 No H-bonds generated for 'chain 'B' and resid 467 through 469' Processing helix chain 'B' and resid 474 through 482 removed outlier: 3.579A pdb=" N ASN B 478 " --> pdb=" O SER B 474 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU B 479 " --> pdb=" O ALA B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 498 removed outlier: 3.550A pdb=" N GLU B 490 " --> pdb=" O TRP B 486 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA B 492 " --> pdb=" O GLN B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 520 removed outlier: 3.551A pdb=" N LYS B 507 " --> pdb=" O GLU B 503 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU B 517 " --> pdb=" O ARG B 513 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR B 519 " --> pdb=" O PHE B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 525 removed outlier: 3.971A pdb=" N ASP B 524 " --> pdb=" O ASP B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 527 through 532 Processing helix chain 'B' and resid 534 through 545 Processing helix chain 'B' and resid 546 through 550 removed outlier: 5.383A pdb=" N ARG B 549 " --> pdb=" O ASP B 546 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN B 550 " --> pdb=" O VAL B 547 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 546 through 550' Processing helix chain 'B' and resid 551 through 571 removed outlier: 3.662A pdb=" N PHE B 555 " --> pdb=" O HIS B 551 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA B 557 " --> pdb=" O PHE B 553 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ILE B 560 " --> pdb=" O LYS B 556 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS B 567 " --> pdb=" O GLU B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 643 through 649 removed outlier: 3.500A pdb=" N ALA B 648 " --> pdb=" O PRO B 644 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS B 649 " --> pdb=" O GLU B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 658 Processing helix chain 'B' and resid 661 through 668 removed outlier: 3.583A pdb=" N ASN B 666 " --> pdb=" O THR B 662 " (cutoff:3.500A) Processing helix chain 'B' and resid 671 through 684 removed outlier: 4.290A pdb=" N HIS B 675 " --> pdb=" O LYS B 671 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE B 681 " --> pdb=" O PHE B 677 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG B 684 " --> pdb=" O GLU B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 700 removed outlier: 3.586A pdb=" N ALA B 700 " --> pdb=" O LYS B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 721 removed outlier: 3.563A pdb=" N GLU B 710 " --> pdb=" O PRO B 706 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG B 714 " --> pdb=" O GLU B 710 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N THR B 718 " --> pdb=" O ARG B 714 " (cutoff:3.500A) Processing helix chain 'B' and resid 727 through 742 removed outlier: 4.032A pdb=" N VAL B 733 " --> pdb=" O THR B 729 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LYS B 735 " --> pdb=" O ARG B 731 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N GLN B 736 " --> pdb=" O THR B 732 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N GLU B 737 " --> pdb=" O VAL B 733 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N MET B 738 " --> pdb=" O LEU B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 758 removed outlier: 3.523A pdb=" N PHE B 750 " --> pdb=" O ASN B 746 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASN B 758 " --> pdb=" O PHE B 754 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 775 removed outlier: 3.643A pdb=" N MET B 771 " --> pdb=" O SER B 767 " (cutoff:3.500A) Processing helix chain 'B' and resid 779 through 788 removed outlier: 3.506A pdb=" N ALA B 783 " --> pdb=" O SER B 779 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 807 removed outlier: 3.791A pdb=" N GLU B 804 " --> pdb=" O GLN B 800 " (cutoff:3.500A) Processing helix chain 'B' and resid 819 through 832 removed outlier: 3.814A pdb=" N ILE B 823 " --> pdb=" O GLU B 819 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ARG B 825 " --> pdb=" O ALA B 821 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LYS B 830 " --> pdb=" O ALA B 826 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU B 831 " --> pdb=" O ASN B 827 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 9 No H-bonds generated for 'chain 'C' and resid 7 through 9' Processing helix chain 'C' and resid 10 through 21 removed outlier: 3.700A pdb=" N HIS C 16 " --> pdb=" O MET C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 35 removed outlier: 3.888A pdb=" N TYR C 31 " --> pdb=" O GLN C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 41 removed outlier: 3.659A pdb=" N LEU C 41 " --> pdb=" O TRP C 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 38 through 41' Processing helix chain 'C' and resid 79 through 82 removed outlier: 3.578A pdb=" N ARG C 82 " --> pdb=" O ARG C 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 79 through 82' Processing helix chain 'C' and resid 87 through 103 removed outlier: 3.663A pdb=" N GLN C 93 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASN C 101 " --> pdb=" O ALA C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 123 Processing helix chain 'C' and resid 152 through 160 removed outlier: 3.790A pdb=" N GLU C 157 " --> pdb=" O GLN C 153 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU C 158 " --> pdb=" O MET C 154 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG C 159 " --> pdb=" O ALA C 155 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 6 through 10 removed outlier: 6.509A pdb=" N PHE A 51 " --> pdb=" O ALA A 55 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N ALA A 55 " --> pdb=" O PHE A 51 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N VAL A 56 " --> pdb=" O CYS A 79 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N CYS A 79 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N ALA A 58 " --> pdb=" O LEU A 77 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LEU A 77 " --> pdb=" O ALA A 58 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N CYS A 60 " --> pdb=" O MET A 75 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN A 108 " --> pdb=" O LYS A 70 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N HIS A 112 " --> pdb=" O ILE A 74 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N THR A 76 " --> pdb=" O HIS A 112 " (cutoff:3.500A) removed outlier: 12.689A pdb=" N GLN A 114 " --> pdb=" O THR A 76 " (cutoff:3.500A) removed outlier: 13.672A pdb=" N GLY A 78 " --> pdb=" O GLN A 114 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU A 133 " --> pdb=" O VAL A 149 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N GLN A 151 " --> pdb=" O ILE A 131 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N ILE A 131 " --> pdb=" O GLN A 151 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 2 through 5 removed outlier: 3.537A pdb=" N GLY C 54 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N VAL C 53 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL C 77 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N TYR C 55 " --> pdb=" O LEU C 75 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N LEU C 75 " --> pdb=" O TYR C 55 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LEU C 57 " --> pdb=" O THR C 73 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N HIS C 69 " --> pdb=" O GLU C 61 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N HIS C 110 " --> pdb=" O ILE C 72 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N SER C 74 " --> pdb=" O HIS C 110 " (cutoff:3.500A) removed outlier: 12.575A pdb=" N ARG C 112 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 14.111A pdb=" N ALA C 76 " --> pdb=" O ARG C 112 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ALA C 144 " --> pdb=" O VAL C 133 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N VAL C 133 " --> pdb=" O ALA C 144 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ALA C 146 " --> pdb=" O SER C 131 " (cutoff:3.500A) 381 hydrogen bonds defined for protein. 1116 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: 1.35 Time building geometry restraints manager: 0.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1342 1.30 - 1.43: 2164 1.43 - 1.57: 4714 1.57 - 1.70: 20 1.70 - 1.83: 87 Bond restraints: 8327 Sorted by residual: bond pdb=" C1B ACO A 201 " pdb=" O4B ACO A 201 " ideal model delta sigma weight residual 1.416 1.655 -0.239 1.40e-02 5.10e+03 2.91e+02 bond pdb=" C1B ACO C 901 " pdb=" O4B ACO C 901 " ideal model delta sigma weight residual 1.416 1.654 -0.238 1.40e-02 5.10e+03 2.89e+02 bond pdb=" C1B ACO C 901 " pdb=" C2B ACO C 901 " ideal model delta sigma weight residual 1.531 1.337 0.194 1.20e-02 6.94e+03 2.60e+02 bond pdb=" C1B ACO A 201 " pdb=" C2B ACO A 201 " ideal model delta sigma weight residual 1.531 1.339 0.192 1.20e-02 6.94e+03 2.56e+02 bond pdb=" C5P ACO C 901 " pdb=" N4P ACO C 901 " ideal model delta sigma weight residual 1.331 1.499 -0.168 1.20e-02 6.94e+03 1.96e+02 ... (remaining 8322 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.74: 10999 2.74 - 5.47: 201 5.47 - 8.20: 36 8.20 - 10.94: 13 10.94 - 13.67: 7 Bond angle restraints: 11256 Sorted by residual: angle pdb=" P1A ACO A 201 " pdb=" O3A ACO A 201 " pdb=" P2A ACO A 201 " ideal model delta sigma weight residual 136.83 123.92 12.91 1.00e+00 1.00e+00 1.67e+02 angle pdb=" N1A ACO A 201 " pdb=" C6A ACO A 201 " pdb=" N6A ACO A 201 " ideal model delta sigma weight residual 118.11 104.44 13.67 1.23e+00 6.64e-01 1.24e+02 angle pdb=" N1A ACO C 901 " pdb=" C6A ACO C 901 " pdb=" N6A ACO C 901 " ideal model delta sigma weight residual 118.11 104.47 13.64 1.23e+00 6.64e-01 1.24e+02 angle pdb=" C5A ACO A 201 " pdb=" C6A ACO A 201 " pdb=" N6A ACO A 201 " ideal model delta sigma weight residual 123.59 135.25 -11.66 1.08e+00 8.64e-01 1.17e+02 angle pdb=" C5A ACO C 901 " pdb=" C6A ACO C 901 " pdb=" N6A ACO C 901 " ideal model delta sigma weight residual 123.59 134.91 -11.32 1.08e+00 8.64e-01 1.11e+02 ... (remaining 11251 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.31: 4478 17.31 - 34.62: 456 34.62 - 51.93: 100 51.93 - 69.24: 11 69.24 - 86.55: 5 Dihedral angle restraints: 5050 sinusoidal: 2126 harmonic: 2924 Sorted by residual: dihedral pdb=" CA CYS C 21 " pdb=" C CYS C 21 " pdb=" N LEU C 22 " pdb=" CA LEU C 22 " ideal model delta harmonic sigma weight residual 180.00 157.79 22.21 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" CA THR B 534 " pdb=" C THR B 534 " pdb=" N LEU B 535 " pdb=" CA LEU B 535 " ideal model delta harmonic sigma weight residual -180.00 -158.92 -21.08 0 5.00e+00 4.00e-02 1.78e+01 dihedral pdb=" CA GLU A 143 " pdb=" C GLU A 143 " pdb=" N PRO A 144 " pdb=" CA PRO A 144 " ideal model delta harmonic sigma weight residual 180.00 162.45 17.55 0 5.00e+00 4.00e-02 1.23e+01 ... (remaining 5047 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.989: 1213 0.989 - 1.978: 0 1.978 - 2.967: 0 2.967 - 3.956: 0 3.956 - 4.945: 3 Chirality restraints: 1216 Sorted by residual: chirality pdb=" C4 IHP B 901 " pdb=" C3 IHP B 901 " pdb=" C5 IHP B 901 " pdb=" O14 IHP B 901 " both_signs ideal model delta sigma weight residual False 2.48 -2.47 4.94 2.00e-01 2.50e+01 6.11e+02 chirality pdb=" C2 IHP B 901 " pdb=" C1 IHP B 901 " pdb=" C3 IHP B 901 " pdb=" O12 IHP B 901 " both_signs ideal model delta sigma weight residual False -2.52 2.41 -4.92 2.00e-01 2.50e+01 6.06e+02 chirality pdb=" C1 IHP B 901 " pdb=" C2 IHP B 901 " pdb=" C6 IHP B 901 " pdb=" O11 IHP B 901 " both_signs ideal model delta sigma weight residual False 2.32 -2.40 4.71 2.00e-01 2.50e+01 5.56e+02 ... (remaining 1213 not shown) Planarity restraints: 1423 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 296 " 0.049 5.00e-02 4.00e+02 7.27e-02 8.46e+00 pdb=" N PRO B 297 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO B 297 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 297 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 746 " 0.047 5.00e-02 4.00e+02 7.04e-02 7.93e+00 pdb=" N PRO B 747 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO B 747 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 747 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 12 " -0.043 5.00e-02 4.00e+02 6.56e-02 6.89e+00 pdb=" N PRO A 13 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO A 13 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 13 " -0.036 5.00e-02 4.00e+02 ... (remaining 1420 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.51: 42 2.51 - 3.11: 4861 3.11 - 3.71: 12175 3.71 - 4.30: 18169 4.30 - 4.90: 29927 Nonbonded interactions: 65174 Sorted by model distance: nonbonded pdb=" OH TYR B 333 " pdb=" ND1 HIS B 383 " model vdw 1.917 3.120 nonbonded pdb=" OG SER C 114 " pdb=" OE2 GLU C 142 " model vdw 2.305 3.040 nonbonded pdb=" OE2 GLU B 228 " pdb=" OH TYR B 260 " model vdw 2.308 3.040 nonbonded pdb=" O4B ACO C 901 " pdb=" O5B ACO C 901 " model vdw 2.309 2.432 nonbonded pdb=" O ASN B 749 " pdb=" OG1 THR B 753 " model vdw 2.336 3.040 ... (remaining 65169 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: 1.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.210 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 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 : 0.010 0.239 8329 Z= 0.677 Angle : 0.992 13.675 11256 Z= 0.626 Chirality : 0.247 4.945 1216 Planarity : 0.006 0.073 1423 Dihedral : 14.173 86.548 3156 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.23 % Allowed : 4.63 % Favored : 95.14 % 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: -6.00 (0.18), residues: 972 helix: -4.69 (0.07), residues: 610 sheet: -1.43 (0.50), residues: 71 loop : -2.28 (0.32), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 79 TYR 0.010 0.002 TYR A 110 PHE 0.019 0.002 PHE B 300 TRP 0.013 0.002 TRP C 38 HIS 0.011 0.001 HIS B 514 Details of bonding type rmsd/Z covalent geometry : bond 0.00991 / 0.68 ( 8327) covalent geometry : angle 0.99164 / 0.63 (11256) hydrogen bonds : bond 0.34967 / 22.56 ( 381) hydrogen bonds : angle 9.94690 / 6.93 ( 1116) Misc. bond : bond 0.00467 / 0.24 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 157 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ASP cc_start: 0.7524 (m-30) cc_final: 0.7310 (m-30) REVERT: B 145 PRO cc_start: 0.8857 (Cg_endo) cc_final: 0.8282 (Cg_exo) REVERT: B 304 GLU cc_start: 0.7273 (tp30) cc_final: 0.7034 (tp30) REVERT: B 464 MET cc_start: 0.8769 (tpt) cc_final: 0.8545 (tpp) REVERT: B 571 ASN cc_start: 0.8174 (m110) cc_final: 0.7407 (p0) REVERT: B 776 ASP cc_start: 0.7526 (p0) cc_final: 0.6997 (p0) outliers start: 2 outliers final: 1 residues processed: 159 average time/residue: 0.0979 time to fit residues: 20.5204 Evaluate side-chains 121 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 120 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 334 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 0.1980 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 74 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 24 GLN A 69 GLN A 108 ASN B 142 GLN B 445 ASN B 514 HIS B 693 GLN B 705 HIS B 739 ASN C 27 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.149600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.122539 restraints weight = 9649.087| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.79 r_work: 0.3201 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 8329 Z= 0.143 Angle : 0.622 11.285 11256 Z= 0.312 Chirality : 0.044 0.368 1216 Planarity : 0.005 0.057 1423 Dihedral : 7.005 55.907 1117 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.50 % Allowed : 8.10 % Favored : 90.39 % 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: -3.66 (0.23), residues: 972 helix: -2.69 (0.16), residues: 621 sheet: -0.63 (0.54), residues: 69 loop : -1.64 (0.36), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 134 TYR 0.013 0.001 TYR A 50 PHE 0.013 0.001 PHE B 300 TRP 0.011 0.002 TRP B 430 HIS 0.007 0.001 HIS B 514 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 ( 8327) covalent geometry : angle 0.62236 / 0.31 (11256) hydrogen bonds : bond 0.05028 / 3.43 ( 381) hydrogen bonds : angle 4.87673 / 3.49 ( 1116) Misc. bond : bond 0.00247 / 0.12 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 149 time to evaluate : 0.241 Fit side-chains revert: symmetry clash REVERT: A 38 ASP cc_start: 0.7765 (m-30) cc_final: 0.7382 (m-30) REVERT: B 273 MET cc_start: 0.7500 (ttp) cc_final: 0.7250 (ttt) REVERT: B 452 MET cc_start: 0.8142 (mmt) cc_final: 0.7847 (mtt) REVERT: B 571 ASN cc_start: 0.8315 (m110) cc_final: 0.7281 (p0) REVERT: B 776 ASP cc_start: 0.8001 (p0) cc_final: 0.7566 (p0) REVERT: B 819 GLU cc_start: 0.8310 (tp30) cc_final: 0.8079 (mp0) outliers start: 13 outliers final: 8 residues processed: 157 average time/residue: 0.0928 time to fit residues: 19.5087 Evaluate side-chains 140 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 132 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain B residue 431 MET Chi-restraints excluded: chain B residue 466 SER Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain B residue 789 THR Chi-restraints excluded: chain B residue 791 ASP Chi-restraints excluded: chain C residue 74 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 95 optimal weight: 0.3980 chunk 41 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 68 optimal weight: 0.5980 overall best weight: 0.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 ASN A 69 GLN A 108 ASN ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 GLN B 693 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.148629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.119423 restraints weight = 9589.517| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 1.88 r_work: 0.3194 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 8329 Z= 0.124 Angle : 0.557 9.432 11256 Z= 0.277 Chirality : 0.043 0.310 1216 Planarity : 0.004 0.055 1423 Dihedral : 6.479 56.887 1113 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.97 % Allowed : 9.38 % Favored : 88.66 % 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: -2.27 (0.25), residues: 972 helix: -1.52 (0.19), residues: 628 sheet: -0.19 (0.56), residues: 70 loop : -1.31 (0.38), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 148 TYR 0.017 0.001 TYR B 206 PHE 0.012 0.001 PHE B 300 TRP 0.010 0.001 TRP B 430 HIS 0.003 0.001 HIS A 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.12 ( 8327) covalent geometry : angle 0.55743 / 0.28 (11256) hydrogen bonds : bond 0.04264 / 2.89 ( 381) hydrogen bonds : angle 4.27827 / 3.07 ( 1116) Misc. bond : bond 0.00202 / 0.10 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 135 time to evaluate : 0.235 Fit side-chains revert: symmetry clash REVERT: A 38 ASP cc_start: 0.7799 (m-30) cc_final: 0.7416 (m-30) REVERT: B 235 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8375 (mp) REVERT: B 452 MET cc_start: 0.8180 (mmt) cc_final: 0.7861 (mtt) REVERT: B 571 ASN cc_start: 0.8354 (m110) cc_final: 0.7422 (p0) REVERT: B 776 ASP cc_start: 0.7923 (p0) cc_final: 0.7500 (p0) REVERT: B 819 GLU cc_start: 0.8295 (tp30) cc_final: 0.8051 (mp0) outliers start: 17 outliers final: 9 residues processed: 148 average time/residue: 0.0875 time to fit residues: 17.6785 Evaluate side-chains 137 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 127 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 431 MET Chi-restraints excluded: chain B residue 466 SER Chi-restraints excluded: chain B residue 789 THR Chi-restraints excluded: chain B residue 791 ASP Chi-restraints excluded: chain C residue 74 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 13 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 89 optimal weight: 0.7980 chunk 88 optimal weight: 0.5980 chunk 25 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 75 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN B 693 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.147882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.120906 restraints weight = 9716.983| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 1.92 r_work: 0.3209 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 8329 Z= 0.138 Angle : 0.563 8.724 11256 Z= 0.278 Chirality : 0.044 0.277 1216 Planarity : 0.004 0.053 1423 Dihedral : 6.401 57.662 1113 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.85 % Allowed : 10.88 % Favored : 87.27 % 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: -1.54 (0.26), residues: 972 helix: -0.93 (0.20), residues: 630 sheet: -0.05 (0.57), residues: 70 loop : -1.06 (0.39), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 79 TYR 0.010 0.001 TYR B 247 PHE 0.013 0.001 PHE B 300 TRP 0.009 0.001 TRP B 430 HIS 0.003 0.001 HIS A 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 ( 8327) covalent geometry : angle 0.56301 / 0.28 (11256) hydrogen bonds : bond 0.04095 / 2.77 ( 381) hydrogen bonds : angle 4.09287 / 2.93 ( 1116) Misc. bond : bond 0.00218 / 0.11 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 140 time to evaluate : 0.214 Fit side-chains REVERT: A 38 ASP cc_start: 0.7832 (m-30) cc_final: 0.7475 (m-30) REVERT: B 235 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8312 (mp) REVERT: B 452 MET cc_start: 0.8229 (mmt) cc_final: 0.7921 (mtt) REVERT: B 530 MET cc_start: 0.7880 (mtm) cc_final: 0.7665 (mtt) REVERT: B 571 ASN cc_start: 0.8411 (m110) cc_final: 0.7550 (p0) REVERT: B 776 ASP cc_start: 0.7850 (p0) cc_final: 0.7442 (p0) outliers start: 16 outliers final: 12 residues processed: 148 average time/residue: 0.0887 time to fit residues: 17.9596 Evaluate side-chains 148 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 135 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 431 MET Chi-restraints excluded: chain B residue 466 SER Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain B residue 789 THR Chi-restraints excluded: chain C residue 74 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 14 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 23 ASN A 108 ASN ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 148 HIS B 693 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.144647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.118026 restraints weight = 9715.273| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 1.73 r_work: 0.3150 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 8329 Z= 0.233 Angle : 0.647 10.305 11256 Z= 0.318 Chirality : 0.049 0.342 1216 Planarity : 0.005 0.053 1423 Dihedral : 6.715 57.613 1113 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.31 % Allowed : 12.15 % Favored : 85.53 % 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: -1.48 (0.26), residues: 972 helix: -0.84 (0.20), residues: 630 sheet: -0.04 (0.58), residues: 69 loop : -1.14 (0.39), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 79 TYR 0.012 0.002 TYR B 247 PHE 0.016 0.002 PHE B 300 TRP 0.009 0.002 TRP B 430 HIS 0.004 0.001 HIS B 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00575 / 0.23 ( 8327) covalent geometry : angle 0.64734 / 0.32 (11256) hydrogen bonds : bond 0.04966 / 3.35 ( 381) hydrogen bonds : angle 4.27439 / 3.06 ( 1116) Misc. bond : bond 0.00318 / 0.16 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 134 time to evaluate : 0.314 Fit side-chains REVERT: A 38 ASP cc_start: 0.7731 (m-30) cc_final: 0.7377 (m-30) REVERT: B 235 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8374 (mp) REVERT: B 452 MET cc_start: 0.8309 (mmt) cc_final: 0.7865 (mtt) REVERT: B 530 MET cc_start: 0.7966 (mtm) cc_final: 0.7695 (mtt) REVERT: B 531 ARG cc_start: 0.7232 (mtt180) cc_final: 0.7006 (mmt180) REVERT: B 571 ASN cc_start: 0.8417 (m110) cc_final: 0.7557 (p0) REVERT: B 776 ASP cc_start: 0.7989 (p0) cc_final: 0.7575 (p0) REVERT: B 822 GLU cc_start: 0.7960 (tp30) cc_final: 0.7742 (mm-30) outliers start: 20 outliers final: 15 residues processed: 147 average time/residue: 0.0863 time to fit residues: 17.1755 Evaluate side-chains 143 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 127 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 126 LYS Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 431 MET Chi-restraints excluded: chain B residue 466 SER Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain B residue 789 THR Chi-restraints excluded: chain C residue 74 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 10 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 60 optimal weight: 0.6980 chunk 88 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 18 optimal weight: 0.1980 chunk 5 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 693 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.148204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.121164 restraints weight = 9653.814| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 1.83 r_work: 0.3240 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 8329 Z= 0.113 Angle : 0.539 8.541 11256 Z= 0.268 Chirality : 0.043 0.258 1216 Planarity : 0.004 0.053 1423 Dihedral : 6.323 58.332 1113 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.74 % Allowed : 12.62 % Favored : 85.65 % 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: -0.90 (0.27), residues: 972 helix: -0.38 (0.20), residues: 627 sheet: 0.06 (0.57), residues: 70 loop : -0.91 (0.40), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 697 TYR 0.010 0.001 TYR B 154 PHE 0.011 0.001 PHE B 300 TRP 0.009 0.001 TRP B 430 HIS 0.002 0.001 HIS A 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.11 ( 8327) covalent geometry : angle 0.53876 / 0.27 (11256) hydrogen bonds : bond 0.03592 / 2.42 ( 381) hydrogen bonds : angle 3.93004 / 2.83 ( 1116) Misc. bond : bond 0.00170 / 0.08 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 135 time to evaluate : 0.299 Fit side-chains REVERT: A 38 ASP cc_start: 0.7759 (m-30) cc_final: 0.7419 (m-30) REVERT: A 94 ASN cc_start: 0.8652 (m-40) cc_final: 0.8375 (m-40) REVERT: B 235 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8273 (mp) REVERT: B 452 MET cc_start: 0.8233 (mmt) cc_final: 0.7913 (mtt) REVERT: B 530 MET cc_start: 0.7882 (mtm) cc_final: 0.7666 (mtt) REVERT: B 531 ARG cc_start: 0.7289 (mtt180) cc_final: 0.7072 (mmt180) REVERT: B 571 ASN cc_start: 0.8378 (m110) cc_final: 0.7553 (p0) REVERT: B 771 MET cc_start: 0.8974 (mmp) cc_final: 0.8714 (mmp) REVERT: B 776 ASP cc_start: 0.7945 (p0) cc_final: 0.7543 (p0) REVERT: B 822 GLU cc_start: 0.7864 (tp30) cc_final: 0.7654 (tp30) outliers start: 15 outliers final: 14 residues processed: 145 average time/residue: 0.0905 time to fit residues: 17.4505 Evaluate side-chains 141 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 126 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASN Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 126 LYS Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 273 MET Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 431 MET Chi-restraints excluded: chain B residue 466 SER Chi-restraints excluded: chain B residue 476 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 74 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 60 optimal weight: 0.5980 chunk 70 optimal weight: 8.9990 chunk 9 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 693 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.145711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.118351 restraints weight = 9892.140| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 1.86 r_work: 0.3145 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 8329 Z= 0.202 Angle : 0.613 9.551 11256 Z= 0.301 Chirality : 0.047 0.312 1216 Planarity : 0.004 0.052 1423 Dihedral : 6.548 58.318 1113 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.08 % Allowed : 12.62 % Favored : 85.30 % 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: -0.86 (0.27), residues: 972 helix: -0.33 (0.20), residues: 626 sheet: 0.03 (0.57), residues: 70 loop : -0.93 (0.40), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 79 TYR 0.011 0.001 TYR B 247 PHE 0.015 0.002 PHE B 300 TRP 0.009 0.001 TRP B 430 HIS 0.004 0.001 HIS B 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00501 / 0.20 ( 8327) covalent geometry : angle 0.61251 / 0.30 (11256) hydrogen bonds : bond 0.04481 / 3.01 ( 381) hydrogen bonds : angle 4.08800 / 2.93 ( 1116) Misc. bond : bond 0.00285 / 0.14 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 127 time to evaluate : 0.319 Fit side-chains REVERT: A 38 ASP cc_start: 0.7758 (m-30) cc_final: 0.7403 (m-30) REVERT: B 235 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8394 (mp) REVERT: B 452 MET cc_start: 0.8258 (mmt) cc_final: 0.7874 (mtt) REVERT: B 530 MET cc_start: 0.7894 (mtm) cc_final: 0.7666 (mtt) REVERT: B 531 ARG cc_start: 0.7248 (mtt180) cc_final: 0.7036 (mmt180) REVERT: B 571 ASN cc_start: 0.8434 (m110) cc_final: 0.7548 (p0) REVERT: B 776 ASP cc_start: 0.7994 (p0) cc_final: 0.7605 (p0) REVERT: B 822 GLU cc_start: 0.7948 (tp30) cc_final: 0.7719 (tp30) outliers start: 18 outliers final: 15 residues processed: 138 average time/residue: 0.0872 time to fit residues: 16.1594 Evaluate side-chains 140 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 124 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 126 LYS Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 273 MET Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 431 MET Chi-restraints excluded: chain B residue 466 SER Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain B residue 789 THR Chi-restraints excluded: chain C residue 74 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 27 optimal weight: 0.1980 chunk 57 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 18 optimal weight: 7.9990 chunk 21 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 chunk 13 optimal weight: 7.9990 chunk 51 optimal weight: 0.4980 chunk 32 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN A 114 GLN B 693 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.146959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.119892 restraints weight = 9730.421| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.90 r_work: 0.3189 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 8329 Z= 0.131 Angle : 0.563 8.479 11256 Z= 0.277 Chirality : 0.044 0.263 1216 Planarity : 0.004 0.053 1423 Dihedral : 6.382 58.429 1113 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.85 % Allowed : 12.73 % Favored : 85.42 % 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: -0.60 (0.27), residues: 972 helix: -0.09 (0.20), residues: 626 sheet: 0.04 (0.57), residues: 69 loop : -0.91 (0.40), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 697 TYR 0.010 0.001 TYR B 206 PHE 0.012 0.001 PHE B 300 TRP 0.010 0.001 TRP B 430 HIS 0.003 0.001 HIS B 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.13 ( 8327) covalent geometry : angle 0.56313 / 0.28 (11256) hydrogen bonds : bond 0.03821 / 2.57 ( 381) hydrogen bonds : angle 3.93945 / 2.83 ( 1116) Misc. bond : bond 0.00212 / 0.10 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 135 time to evaluate : 0.324 Fit side-chains REVERT: A 38 ASP cc_start: 0.7729 (m-30) cc_final: 0.7373 (m-30) REVERT: A 94 ASN cc_start: 0.8681 (m-40) cc_final: 0.8366 (m-40) REVERT: B 235 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8352 (mp) REVERT: B 452 MET cc_start: 0.8227 (mmt) cc_final: 0.7867 (mtt) REVERT: B 530 MET cc_start: 0.7844 (mtm) cc_final: 0.7625 (mtt) REVERT: B 531 ARG cc_start: 0.7271 (mtt180) cc_final: 0.7060 (mmt180) REVERT: B 571 ASN cc_start: 0.8383 (m110) cc_final: 0.7512 (p0) REVERT: B 776 ASP cc_start: 0.7949 (p0) cc_final: 0.7573 (p0) REVERT: B 822 GLU cc_start: 0.7869 (tp30) cc_final: 0.7653 (tp30) outliers start: 16 outliers final: 14 residues processed: 146 average time/residue: 0.0932 time to fit residues: 18.4369 Evaluate side-chains 146 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 131 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 126 LYS Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 273 MET Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 431 MET Chi-restraints excluded: chain B residue 466 SER Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain B residue 789 THR Chi-restraints excluded: chain C residue 74 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 48 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 36 optimal weight: 0.4980 chunk 22 optimal weight: 4.9990 chunk 34 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 96 optimal weight: 0.6980 chunk 1 optimal weight: 0.4980 chunk 33 optimal weight: 0.0050 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 693 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.148660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.121636 restraints weight = 9646.738| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.86 r_work: 0.3259 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 8329 Z= 0.105 Angle : 0.539 8.137 11256 Z= 0.266 Chirality : 0.042 0.235 1216 Planarity : 0.004 0.054 1423 Dihedral : 6.206 58.432 1113 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.62 % Allowed : 13.19 % Favored : 85.19 % 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: -0.31 (0.27), residues: 972 helix: 0.16 (0.21), residues: 630 sheet: 0.14 (0.57), residues: 70 loop : -0.89 (0.40), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 697 TYR 0.014 0.001 TYR B 158 PHE 0.010 0.001 PHE B 300 TRP 0.010 0.001 TRP B 430 HIS 0.002 0.001 HIS A 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 ( 8327) covalent geometry : angle 0.53883 / 0.27 (11256) hydrogen bonds : bond 0.03378 / 2.28 ( 381) hydrogen bonds : angle 3.81297 / 2.75 ( 1116) Misc. bond : bond 0.00171 / 0.09 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 135 time to evaluate : 0.317 Fit side-chains REVERT: A 38 ASP cc_start: 0.7780 (m-30) cc_final: 0.7434 (m-30) REVERT: B 235 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8320 (mp) REVERT: B 452 MET cc_start: 0.8201 (mmt) cc_final: 0.7930 (mtt) REVERT: B 477 GLU cc_start: 0.6950 (mp0) cc_final: 0.6595 (pm20) REVERT: B 571 ASN cc_start: 0.8384 (m110) cc_final: 0.7513 (p0) REVERT: B 776 ASP cc_start: 0.7866 (p0) cc_final: 0.7512 (p0) REVERT: B 822 GLU cc_start: 0.7837 (tp30) cc_final: 0.7628 (tp30) outliers start: 14 outliers final: 11 residues processed: 144 average time/residue: 0.0930 time to fit residues: 18.1048 Evaluate side-chains 144 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 132 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 126 LYS Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 273 MET Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 431 MET Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain B residue 789 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 96 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 693 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.148445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.122245 restraints weight = 9668.430| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.69 r_work: 0.3249 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 8329 Z= 0.135 Angle : 0.568 8.399 11256 Z= 0.279 Chirality : 0.043 0.262 1216 Planarity : 0.004 0.052 1423 Dihedral : 6.246 58.500 1113 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.74 % Allowed : 12.50 % Favored : 85.76 % 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: -0.21 (0.27), residues: 972 helix: 0.26 (0.21), residues: 630 sheet: 0.08 (0.56), residues: 70 loop : -0.86 (0.40), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 148 TYR 0.010 0.001 TYR B 206 PHE 0.012 0.001 PHE B 300 TRP 0.009 0.001 TRP B 430 HIS 0.003 0.001 HIS B 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.13 ( 8327) covalent geometry : angle 0.56787 / 0.28 (11256) hydrogen bonds : bond 0.03734 / 2.50 ( 381) hydrogen bonds : angle 3.89294 / 2.80 ( 1116) Misc. bond : bond 0.00208 / 0.10 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 135 time to evaluate : 0.281 Fit side-chains REVERT: A 38 ASP cc_start: 0.7829 (m-30) cc_final: 0.7502 (m-30) REVERT: B 235 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8424 (mp) REVERT: B 452 MET cc_start: 0.8281 (mmt) cc_final: 0.8028 (mtt) REVERT: B 477 GLU cc_start: 0.6984 (mp0) cc_final: 0.6615 (pm20) REVERT: B 571 ASN cc_start: 0.8426 (m110) cc_final: 0.7558 (p0) REVERT: B 776 ASP cc_start: 0.7843 (p0) cc_final: 0.7505 (p0) REVERT: B 822 GLU cc_start: 0.7860 (tp30) cc_final: 0.7643 (tp30) outliers start: 15 outliers final: 13 residues processed: 145 average time/residue: 0.0885 time to fit residues: 17.3861 Evaluate side-chains 144 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 130 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 126 LYS Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 273 MET Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 431 MET Chi-restraints excluded: chain B residue 466 SER Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain B residue 789 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 1 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 22 optimal weight: 0.5980 chunk 65 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 70 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 62 optimal weight: 0.0060 overall best weight: 0.8998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN A 114 GLN B 693 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.148450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.121500 restraints weight = 9651.339| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 1.76 r_work: 0.3218 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 8329 Z= 0.132 Angle : 0.557 8.436 11256 Z= 0.275 Chirality : 0.043 0.259 1216 Planarity : 0.004 0.053 1423 Dihedral : 6.238 58.418 1113 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.74 % Allowed : 12.85 % Favored : 85.42 % 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: -0.12 (0.27), residues: 972 helix: 0.34 (0.21), residues: 630 sheet: 0.06 (0.56), residues: 70 loop : -0.84 (0.40), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 148 TYR 0.010 0.001 TYR B 206 PHE 0.012 0.001 PHE B 300 TRP 0.009 0.001 TRP B 430 HIS 0.003 0.001 HIS A 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.13 ( 8327) covalent geometry : angle 0.55736 / 0.28 (11256) hydrogen bonds : bond 0.03668 / 2.46 ( 381) hydrogen bonds : angle 3.87642 / 2.79 ( 1116) Misc. bond : bond 0.00199 / 0.10 ( 2) =============================================================================== Job complete usr+sys time: 2057.69 seconds wall clock time: 35 minutes 48.36 seconds (2148.36 seconds total)