Starting phenix.real_space_refine on Wed Feb 12 19:11:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ppl_20442/02_2025/6ppl_20442.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ppl_20442/02_2025/6ppl_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6ppl_20442/02_2025/6ppl_20442.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ppl_20442/02_2025/6ppl_20442.map" model { file = "/net/cci-nas-00/data/ceres_data/6ppl_20442/02_2025/6ppl_20442.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ppl_20442/02_2025/6ppl_20442.cif" } resolution = 3.02 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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, 'ARG:plan': 3, 'ASP:plan': 2} 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: 5.24, per 1000 atoms: 0.64 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: 2.14 Conformation dependent library (CDL) restraints added in 925.5 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: 0.89 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: 2.36 Time building geometry restraints manager: 2.37 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 - 34.49: 5006 34.49 - 68.97: 148 68.97 - 103.46: 9 103.46 - 137.94: 2 137.94 - 172.43: 3 Dihedral angle restraints: 5168 sinusoidal: 2244 harmonic: 2924 Sorted by residual: dihedral pdb=" C6 IHP B 901 " pdb=" C1 IHP B 901 " pdb=" C2 IHP B 901 " pdb=" O12 IHP B 901 " ideal model delta sinusoidal sigma weight residual 61.05 -126.52 -172.43 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" O12 IHP B 901 " pdb=" C2 IHP B 901 " pdb=" C3 IHP B 901 " pdb=" O13 IHP B 901 " ideal model delta sinusoidal sigma weight residual 64.08 -106.98 171.06 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" C4 IHP B 901 " pdb=" C2 IHP B 901 " pdb=" C3 IHP B 901 " pdb=" O12 IHP B 901 " ideal model delta sinusoidal sigma weight residual 60.90 -130.41 -168.69 1 3.00e+01 1.11e-03 2.11e+01 ... (remaining 5165 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: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.100 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 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 8327 Z= 0.620 Angle : 0.992 13.675 11256 Z= 0.626 Chirality : 0.247 4.945 1216 Planarity : 0.006 0.073 1423 Dihedral : 16.580 172.427 3274 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.013 0.002 TRP C 38 HIS 0.011 0.001 HIS B 514 PHE 0.019 0.002 PHE B 300 TYR 0.010 0.002 TYR A 110 ARG 0.003 0.000 ARG C 79 *********************** 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 : 0.964 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: 0.7272 (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: 0.2494 time to fit residues: 51.7023 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 : 0.896 ------------------------------------------------------------------------------- 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 81 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 40 optimal weight: 0.0010 chunk 25 optimal weight: 0.3980 chunk 49 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 88 optimal weight: 0.9990 overall best weight: 0.8590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.148814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.121251 restraints weight = 9615.670| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.83 r_work: 0.3198 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 8327 Z= 0.202 Angle : 0.629 12.984 11256 Z= 0.316 Chirality : 0.044 0.301 1216 Planarity : 0.005 0.058 1423 Dihedral : 11.528 59.388 1235 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.27 % Allowed : 8.33 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.76 (0.22), residues: 972 helix: -2.74 (0.16), residues: 626 sheet: -0.66 (0.54), residues: 69 loop : -1.74 (0.35), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 430 HIS 0.007 0.001 HIS B 514 PHE 0.014 0.001 PHE B 300 TYR 0.013 0.001 TYR A 50 ARG 0.003 0.000 ARG B 134 *********************** 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 157 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 146 time to evaluate : 1.023 Fit side-chains revert: symmetry clash REVERT: A 38 ASP cc_start: 0.7772 (m-30) cc_final: 0.7408 (m-30) REVERT: A 94 ASN cc_start: 0.8633 (m-40) cc_final: 0.8379 (m-40) REVERT: B 273 MET cc_start: 0.7520 (ttp) cc_final: 0.7246 (ttt) REVERT: B 452 MET cc_start: 0.8154 (mmt) cc_final: 0.7869 (mtt) REVERT: B 571 ASN cc_start: 0.8312 (m110) cc_final: 0.7272 (p0) REVERT: B 776 ASP cc_start: 0.8012 (p0) cc_final: 0.7554 (p0) REVERT: B 819 GLU cc_start: 0.8320 (tp30) cc_final: 0.8082 (mp0) outliers start: 11 outliers final: 7 residues processed: 154 average time/residue: 0.2349 time to fit residues: 48.3506 Evaluate side-chains 136 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 129 time to evaluate : 0.950 ------------------------------------------------------------------------------- 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 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 5 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 1 optimal weight: 0.1980 chunk 89 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 70 optimal weight: 7.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 52 ASN A 69 GLN ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3695 r_free = 0.3695 target = 0.145360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.118325 restraints weight = 9730.830| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 1.97 r_work: 0.3165 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 8327 Z= 0.301 Angle : 0.632 12.122 11256 Z= 0.314 Chirality : 0.047 0.333 1216 Planarity : 0.005 0.055 1423 Dihedral : 11.427 58.882 1231 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.08 % Allowed : 9.72 % Favored : 88.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.25), residues: 972 helix: -1.65 (0.19), residues: 629 sheet: -0.31 (0.56), residues: 69 loop : -1.43 (0.37), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 430 HIS 0.004 0.001 HIS A 95 PHE 0.015 0.002 PHE B 300 TYR 0.020 0.002 TYR B 206 ARG 0.004 0.000 ARG C 79 *********************** 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 157 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 139 time to evaluate : 1.073 Fit side-chains revert: symmetry clash REVERT: A 38 ASP cc_start: 0.7813 (m-30) cc_final: 0.7429 (m-30) REVERT: B 235 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8396 (mp) REVERT: B 273 MET cc_start: 0.7423 (ttp) cc_final: 0.7200 (ttt) REVERT: B 452 MET cc_start: 0.8253 (mmt) cc_final: 0.7834 (mtt) REVERT: B 571 ASN cc_start: 0.8422 (m110) cc_final: 0.7491 (p0) REVERT: B 776 ASP cc_start: 0.7966 (p0) cc_final: 0.7521 (p0) outliers start: 18 outliers final: 11 residues processed: 151 average time/residue: 0.2355 time to fit residues: 47.6295 Evaluate side-chains 141 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 129 time to evaluate : 0.887 ------------------------------------------------------------------------------- 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 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 431 MET Chi-restraints excluded: chain B residue 466 SER Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain B residue 789 THR 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 93 optimal weight: 0.6980 chunk 94 optimal weight: 0.5980 chunk 22 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 95 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3733 r_free = 0.3733 target = 0.148536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.120770 restraints weight = 9532.580| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.77 r_work: 0.3235 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 8327 Z= 0.187 Angle : 0.555 9.691 11256 Z= 0.277 Chirality : 0.043 0.284 1216 Planarity : 0.004 0.054 1423 Dihedral : 11.034 59.777 1231 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.62 % Allowed : 11.00 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.26), residues: 972 helix: -1.04 (0.20), residues: 632 sheet: -0.07 (0.56), residues: 70 loop : -1.14 (0.39), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 430 HIS 0.002 0.001 HIS A 95 PHE 0.011 0.001 PHE B 300 TYR 0.009 0.001 TYR B 154 ARG 0.002 0.000 ARG C 79 *********************** 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 153 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 139 time to evaluate : 0.954 Fit side-chains REVERT: A 38 ASP cc_start: 0.7817 (m-30) cc_final: 0.7461 (m-30) REVERT: B 235 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8269 (mp) REVERT: B 452 MET cc_start: 0.8245 (mmt) cc_final: 0.7905 (mtt) REVERT: B 571 ASN cc_start: 0.8403 (m110) cc_final: 0.7572 (p0) REVERT: B 776 ASP cc_start: 0.7933 (p0) cc_final: 0.7512 (p0) outliers start: 14 outliers final: 9 residues processed: 148 average time/residue: 0.2194 time to fit residues: 44.1019 Evaluate side-chains 145 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 135 time to evaluate : 0.955 ------------------------------------------------------------------------------- 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 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 C residue 74 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 68 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 49 optimal weight: 0.2980 chunk 95 optimal weight: 4.9990 chunk 92 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 64 optimal weight: 0.0870 overall best weight: 0.8562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.148490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.120979 restraints weight = 9673.064| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.81 r_work: 0.3185 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 8327 Z= 0.191 Angle : 0.551 9.066 11256 Z= 0.274 Chirality : 0.043 0.258 1216 Planarity : 0.004 0.053 1423 Dihedral : 10.862 59.668 1231 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.74 % Allowed : 12.04 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.27), residues: 972 helix: -0.59 (0.20), residues: 630 sheet: 0.05 (0.58), residues: 70 loop : -1.07 (0.39), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 430 HIS 0.003 0.001 HIS A 95 PHE 0.011 0.001 PHE B 300 TYR 0.010 0.001 TYR A 110 ARG 0.002 0.000 ARG C 79 *********************** 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 153 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 138 time to evaluate : 0.912 Fit side-chains REVERT: A 38 ASP cc_start: 0.7816 (m-30) cc_final: 0.7458 (m-30) REVERT: B 235 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8291 (mp) REVERT: B 452 MET cc_start: 0.8260 (mmt) cc_final: 0.7897 (mtt) REVERT: B 464 MET cc_start: 0.8502 (tpp) cc_final: 0.8185 (tpp) REVERT: B 531 ARG cc_start: 0.7221 (mtt180) cc_final: 0.7000 (mmt180) REVERT: B 571 ASN cc_start: 0.8370 (m110) cc_final: 0.7527 (p0) REVERT: B 695 VAL cc_start: 0.9356 (p) cc_final: 0.9150 (t) REVERT: B 776 ASP cc_start: 0.7987 (p0) cc_final: 0.7597 (p0) outliers start: 15 outliers final: 13 residues processed: 148 average time/residue: 0.2359 time to fit residues: 46.6181 Evaluate side-chains 143 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 129 time to evaluate : 0.967 ------------------------------------------------------------------------------- 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 126 LYS 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 25 optimal weight: 0.1980 chunk 44 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.148981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.121607 restraints weight = 9655.488| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 1.81 r_work: 0.3230 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 8327 Z= 0.174 Angle : 0.534 8.619 11256 Z= 0.267 Chirality : 0.042 0.239 1216 Planarity : 0.004 0.053 1423 Dihedral : 10.669 59.016 1231 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.62 % Allowed : 13.08 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.27), residues: 972 helix: -0.23 (0.20), residues: 629 sheet: 0.22 (0.58), residues: 70 loop : -0.93 (0.40), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 430 HIS 0.002 0.001 HIS A 95 PHE 0.011 0.001 PHE B 300 TYR 0.010 0.001 TYR B 247 ARG 0.002 0.000 ARG B 697 *********************** 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: 14 poor density : 136 time to evaluate : 0.876 Fit side-chains REVERT: A 38 ASP cc_start: 0.7844 (m-30) cc_final: 0.7499 (m-30) REVERT: B 158 TYR cc_start: 0.8921 (m-80) cc_final: 0.8721 (m-80) REVERT: B 235 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8317 (mp) REVERT: B 452 MET cc_start: 0.8280 (mmt) cc_final: 0.7957 (mtt) REVERT: B 464 MET cc_start: 0.8526 (tpp) cc_final: 0.8247 (tpp) REVERT: B 531 ARG cc_start: 0.7297 (mtt180) cc_final: 0.7086 (mmt180) REVERT: B 570 ASP cc_start: 0.8321 (m-30) cc_final: 0.8101 (m-30) REVERT: B 571 ASN cc_start: 0.8367 (m110) cc_final: 0.7573 (p0) REVERT: B 695 VAL cc_start: 0.9382 (p) cc_final: 0.9160 (t) REVERT: B 776 ASP cc_start: 0.7915 (p0) cc_final: 0.7541 (p0) outliers start: 14 outliers final: 13 residues processed: 144 average time/residue: 0.2217 time to fit residues: 42.8669 Evaluate side-chains 145 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 131 time to evaluate : 0.938 ------------------------------------------------------------------------------- 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 126 LYS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 58 optimal weight: 0.0770 chunk 38 optimal weight: 0.9980 chunk 39 optimal weight: 0.3980 chunk 25 optimal weight: 2.9990 chunk 80 optimal weight: 0.6980 chunk 87 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 3 optimal weight: 0.0870 chunk 32 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 48 optimal weight: 0.6980 overall best weight: 0.3916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.150568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.123562 restraints weight = 9626.322| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 1.82 r_work: 0.3231 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 8327 Z= 0.133 Angle : 0.501 7.989 11256 Z= 0.252 Chirality : 0.041 0.224 1216 Planarity : 0.004 0.053 1423 Dihedral : 10.319 59.232 1231 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.62 % Allowed : 13.31 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.27), residues: 972 helix: 0.21 (0.21), residues: 631 sheet: 0.33 (0.58), residues: 70 loop : -0.91 (0.39), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 430 HIS 0.002 0.000 HIS A 95 PHE 0.009 0.001 PHE B 300 TYR 0.010 0.001 TYR B 206 ARG 0.002 0.000 ARG B 797 *********************** 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 156 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 142 time to evaluate : 0.892 Fit side-chains REVERT: A 38 ASP cc_start: 0.7844 (m-30) cc_final: 0.7485 (m-30) REVERT: B 158 TYR cc_start: 0.8852 (m-80) cc_final: 0.8608 (m-80) REVERT: B 166 MET cc_start: 0.8196 (tpt) cc_final: 0.7961 (tpt) REVERT: B 452 MET cc_start: 0.8186 (mmt) cc_final: 0.7911 (mtt) REVERT: B 464 MET cc_start: 0.8457 (tpp) cc_final: 0.8179 (tpp) REVERT: B 477 GLU cc_start: 0.6929 (mp0) cc_final: 0.6648 (pm20) REVERT: B 571 ASN cc_start: 0.8346 (m110) cc_final: 0.7502 (p0) REVERT: B 776 ASP cc_start: 0.7857 (p0) cc_final: 0.7496 (p0) outliers start: 14 outliers final: 6 residues processed: 153 average time/residue: 0.2361 time to fit residues: 48.1881 Evaluate side-chains 140 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 134 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 274 LEU Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 466 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 42 optimal weight: 1.9990 chunk 61 optimal weight: 0.4980 chunk 56 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 8 optimal weight: 0.0970 chunk 59 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3746 r_free = 0.3746 target = 0.149853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.122472 restraints weight = 9697.761| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 1.85 r_work: 0.3227 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 8327 Z= 0.154 Angle : 0.529 10.434 11256 Z= 0.261 Chirality : 0.041 0.231 1216 Planarity : 0.004 0.053 1423 Dihedral : 10.276 59.372 1231 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.81 % Allowed : 14.35 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.27), residues: 972 helix: 0.39 (0.21), residues: 631 sheet: 0.33 (0.58), residues: 70 loop : -0.85 (0.39), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 430 HIS 0.002 0.001 HIS A 95 PHE 0.010 0.001 PHE B 300 TYR 0.010 0.001 TYR B 206 ARG 0.002 0.000 ARG B 148 *********************** 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 143 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 136 time to evaluate : 0.968 Fit side-chains REVERT: A 38 ASP cc_start: 0.7874 (m-30) cc_final: 0.7512 (m-30) REVERT: B 158 TYR cc_start: 0.8829 (m-80) cc_final: 0.8619 (m-80) REVERT: B 366 LYS cc_start: 0.6640 (ptmt) cc_final: 0.6289 (ptmm) REVERT: B 452 MET cc_start: 0.8212 (mmt) cc_final: 0.7915 (mtt) REVERT: B 464 MET cc_start: 0.8466 (tpp) cc_final: 0.8222 (tpp) REVERT: B 571 ASN cc_start: 0.8324 (m110) cc_final: 0.7477 (p0) REVERT: B 776 ASP cc_start: 0.7804 (p0) cc_final: 0.7446 (p0) outliers start: 7 outliers final: 6 residues processed: 140 average time/residue: 0.2078 time to fit residues: 39.7357 Evaluate side-chains 137 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 131 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 126 LYS Chi-restraints excluded: chain B residue 274 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 7 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 95 optimal weight: 4.9990 chunk 50 optimal weight: 0.0970 chunk 25 optimal weight: 0.0470 chunk 12 optimal weight: 0.9990 chunk 13 optimal weight: 7.9990 chunk 1 optimal weight: 0.8980 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3744 r_free = 0.3744 target = 0.149470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.122170 restraints weight = 9760.012| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 1.85 r_work: 0.3223 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 8327 Z= 0.159 Angle : 0.530 10.250 11256 Z= 0.262 Chirality : 0.041 0.231 1216 Planarity : 0.004 0.053 1423 Dihedral : 10.197 59.664 1231 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.27 % Allowed : 13.89 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.27), residues: 972 helix: 0.55 (0.21), residues: 631 sheet: 0.20 (0.58), residues: 71 loop : -0.78 (0.40), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 430 HIS 0.002 0.001 HIS A 95 PHE 0.010 0.001 PHE B 300 TYR 0.009 0.001 TYR B 206 ARG 0.002 0.000 ARG B 148 *********************** 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 143 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 132 time to evaluate : 0.989 Fit side-chains REVERT: A 38 ASP cc_start: 0.7878 (m-30) cc_final: 0.7521 (m-30) REVERT: B 158 TYR cc_start: 0.8846 (m-80) cc_final: 0.8626 (m-80) REVERT: B 366 LYS cc_start: 0.6632 (ptmt) cc_final: 0.6289 (ptmm) REVERT: B 452 MET cc_start: 0.8258 (mmt) cc_final: 0.7946 (mtt) REVERT: B 464 MET cc_start: 0.8477 (tpp) cc_final: 0.8251 (tpp) REVERT: B 571 ASN cc_start: 0.8323 (m110) cc_final: 0.7458 (p0) REVERT: B 776 ASP cc_start: 0.7807 (p0) cc_final: 0.7449 (p0) outliers start: 11 outliers final: 9 residues processed: 141 average time/residue: 0.2234 time to fit residues: 42.6508 Evaluate side-chains 139 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 130 time to evaluate : 0.969 ------------------------------------------------------------------------------- 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 274 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 43 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 90 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3730 r_free = 0.3730 target = 0.148368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.121012 restraints weight = 9621.767| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 1.84 r_work: 0.3218 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 8327 Z= 0.178 Angle : 0.531 8.218 11256 Z= 0.264 Chirality : 0.042 0.237 1216 Planarity : 0.004 0.052 1423 Dihedral : 10.201 59.587 1231 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.04 % Allowed : 14.12 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.27), residues: 972 helix: 0.59 (0.21), residues: 632 sheet: 0.14 (0.58), residues: 70 loop : -0.83 (0.39), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 430 HIS 0.002 0.001 HIS A 95 PHE 0.011 0.001 PHE B 300 TYR 0.011 0.001 TYR B 154 ARG 0.002 0.000 ARG B 148 ********************** 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 138 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 129 time to evaluate : 1.016 Fit side-chains REVERT: A 38 ASP cc_start: 0.7874 (m-30) cc_final: 0.7500 (m-30) REVERT: B 158 TYR cc_start: 0.8833 (m-80) cc_final: 0.8620 (m-80) REVERT: B 366 LYS cc_start: 0.6592 (ptmt) cc_final: 0.6253 (ptmm) REVERT: B 452 MET cc_start: 0.8229 (mmt) cc_final: 0.7913 (mtt) REVERT: B 464 MET cc_start: 0.8495 (tpp) cc_final: 0.8255 (tpp) REVERT: B 571 ASN cc_start: 0.8302 (m110) cc_final: 0.7428 (p0) REVERT: B 776 ASP cc_start: 0.7809 (p0) cc_final: 0.7442 (p0) outliers start: 9 outliers final: 8 residues processed: 136 average time/residue: 0.2239 time to fit residues: 41.1707 Evaluate side-chains 136 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 128 time to evaluate : 1.053 ------------------------------------------------------------------------------- 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 274 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 11 optimal weight: 9.9990 chunk 23 optimal weight: 0.5980 chunk 46 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 17 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 693 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.148910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.121959 restraints weight = 9768.554| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.79 r_work: 0.3203 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 8327 Z= 0.186 Angle : 0.531 8.333 11256 Z= 0.266 Chirality : 0.043 0.242 1216 Planarity : 0.004 0.052 1423 Dihedral : 10.209 59.492 1231 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.04 % Allowed : 14.12 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.27), residues: 972 helix: 0.61 (0.21), residues: 630 sheet: 0.08 (0.57), residues: 71 loop : -0.73 (0.40), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 430 HIS 0.002 0.001 HIS B 212 PHE 0.011 0.001 PHE B 300 TYR 0.011 0.001 TYR B 154 ARG 0.002 0.000 ARG B 148 =============================================================================== Job complete usr+sys time: 4635.46 seconds wall clock time: 82 minutes 46.42 seconds (4966.42 seconds total)