Starting phenix.real_space_refine on Sat Jul 4 10:25:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nnp_49585/07_2026/9nnp_49585.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nnp_49585/07_2026/9nnp_49585.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9nnp_49585/07_2026/9nnp_49585.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nnp_49585/07_2026/9nnp_49585.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9nnp_49585/07_2026/9nnp_49585.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nnp_49585/07_2026/9nnp_49585.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.018 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 7 5.49 5 S 81 5.16 5 C 12387 2.51 5 N 3475 2.21 5 O 3546 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19498 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 6344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 797, 6344 Classifications: {'peptide': 797} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 767} Chain breaks: 1 Chain: "B" Number of atoms: 7361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 963, 7361 Classifications: {'peptide': 963} Link IDs: {'PCIS': 4, 'PTRANS': 61, 'TRANS': 897} Chain breaks: 1 Chain: "C" Number of atoms: 5648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 5648 Classifications: {'peptide': 750} Link IDs: {'PCIS': 4, 'PTRANS': 56, 'TRANS': 689} Chain: "D" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 143 Classifications: {'DNA': 7} Link IDs: {'rna3p': 6} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 13274 SG CYS B 988 79.652 78.465 102.501 1.00107.15 S ATOM 13540 SG CYS B1023 77.610 80.550 105.025 1.00103.85 S ATOM 13576 SG CYS B1028 76.254 79.977 101.479 1.00 98.59 S ATOM 11414 SG CYS B 680 32.962 82.378 102.204 1.00 97.19 S ATOM 11458 SG CYS B 754 31.649 78.891 100.211 1.00 92.58 S ATOM 11470 SG CYS B 756 34.728 79.302 100.807 1.00107.57 S Time building chain proxies: 4.25, per 1000 atoms: 0.22 Number of scatterers: 19498 At special positions: 0 Unit cell: (124.12, 110.21, 220.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 81 16.00 P 7 15.00 O 3546 8.00 N 3475 7.00 C 12387 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.47 Conformation dependent library (CDL) restraints added in 837.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B1101 " pdb="ZN ZN B1101 " - pdb=" NE2 HIS B 993 " pdb="ZN ZN B1101 " - pdb=" SG CYS B1028 " pdb="ZN ZN B1101 " - pdb=" SG CYS B1023 " pdb="ZN ZN B1101 " - pdb=" SG CYS B 988 " pdb=" ZN B1102 " pdb="ZN ZN B1102 " - pdb=" SG CYS B 754 " pdb="ZN ZN B1102 " - pdb=" SG CYS B 756 " pdb="ZN ZN B1102 " - pdb=" SG CYS B 680 " Number of angles added : 3 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4676 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 20 sheets defined 47.8% alpha, 14.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 45 through 57 Processing helix chain 'A' and resid 67 through 76 removed outlier: 4.057A pdb=" N PHE A 71 " --> pdb=" O HIS A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 114 removed outlier: 3.839A pdb=" N CYS A 106 " --> pdb=" O GLY A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 137 Processing helix chain 'A' and resid 144 through 150 Processing helix chain 'A' and resid 153 through 158 removed outlier: 3.584A pdb=" N ALA A 158 " --> pdb=" O HIS A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 185 Processing helix chain 'A' and resid 185 through 199 Processing helix chain 'A' and resid 209 through 220 Processing helix chain 'A' and resid 226 through 228 No H-bonds generated for 'chain 'A' and resid 226 through 228' Processing helix chain 'A' and resid 229 through 234 Processing helix chain 'A' and resid 238 through 242 Processing helix chain 'A' and resid 256 through 273 removed outlier: 4.222A pdb=" N THR A 260 " --> pdb=" O ARG A 256 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL A 262 " --> pdb=" O LEU A 258 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL A 263 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N TYR A 273 " --> pdb=" O ILE A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 280 Processing helix chain 'A' and resid 316 through 324 Processing helix chain 'A' and resid 324 through 332 Processing helix chain 'A' and resid 348 through 361 Processing helix chain 'A' and resid 365 through 373 removed outlier: 3.777A pdb=" N MET A 369 " --> pdb=" O THR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 376 No H-bonds generated for 'chain 'A' and resid 374 through 376' Processing helix chain 'A' and resid 378 through 384 Processing helix chain 'A' and resid 397 through 415 removed outlier: 3.555A pdb=" N VAL A 401 " --> pdb=" O SER A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 443 Processing helix chain 'A' and resid 449 through 457 Processing helix chain 'A' and resid 464 through 470 removed outlier: 4.046A pdb=" N GLN A 468 " --> pdb=" O SER A 465 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN A 470 " --> pdb=" O SER A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 526 Processing helix chain 'A' and resid 527 through 533 removed outlier: 3.724A pdb=" N GLN A 533 " --> pdb=" O PHE A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 552 Processing helix chain 'A' and resid 555 through 561 Processing helix chain 'A' and resid 567 through 585 removed outlier: 3.775A pdb=" N THR A 571 " --> pdb=" O ALA A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 651 Processing helix chain 'A' and resid 658 through 684 Processing helix chain 'A' and resid 685 through 690 Processing helix chain 'A' and resid 736 through 747 Processing helix chain 'A' and resid 749 through 759 removed outlier: 3.701A pdb=" N ALA A 753 " --> pdb=" O THR A 749 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA A 759 " --> pdb=" O LEU A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 816 removed outlier: 3.760A pdb=" N GLY A 815 " --> pdb=" O ARG A 812 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 840 Processing helix chain 'A' and resid 844 through 846 No H-bonds generated for 'chain 'A' and resid 844 through 846' Processing helix chain 'A' and resid 864 through 874 removed outlier: 3.757A pdb=" N HIS A 868 " --> pdb=" O VAL A 864 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG A 874 " --> pdb=" O LEU A 870 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 39 Processing helix chain 'B' and resid 66 through 76 removed outlier: 3.676A pdb=" N GLU B 72 " --> pdb=" O GLN B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 133 Processing helix chain 'B' and resid 138 through 146 removed outlier: 3.615A pdb=" N ILE B 142 " --> pdb=" O GLN B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 153 Processing helix chain 'B' and resid 156 through 167 Processing helix chain 'B' and resid 185 through 194 Processing helix chain 'B' and resid 198 through 209 removed outlier: 3.527A pdb=" N LEU B 202 " --> pdb=" O GLY B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 221 removed outlier: 3.508A pdb=" N ARG B 219 " --> pdb=" O ALA B 215 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR B 221 " --> pdb=" O TYR B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 236 removed outlier: 3.510A pdb=" N PHE B 231 " --> pdb=" O SER B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 251 removed outlier: 4.082A pdb=" N THR B 246 " --> pdb=" O LEU B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 257 removed outlier: 3.731A pdb=" N ARG B 255 " --> pdb=" O LEU B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 263 removed outlier: 3.848A pdb=" N ALA B 261 " --> pdb=" O GLY B 258 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N THR B 262 " --> pdb=" O ALA B 259 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR B 263 " --> pdb=" O GLY B 260 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 258 through 263' Processing helix chain 'B' and resid 264 through 274 removed outlier: 3.848A pdb=" N THR B 274 " --> pdb=" O ASP B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 304 through 308 removed outlier: 3.669A pdb=" N ALA B 307 " --> pdb=" O SER B 304 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG B 308 " --> pdb=" O GLN B 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 304 through 308' Processing helix chain 'B' and resid 309 through 314 Processing helix chain 'B' and resid 314 through 343 removed outlier: 3.702A pdb=" N GLU B 329 " --> pdb=" O ALA B 325 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA B 332 " --> pdb=" O ARG B 328 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N CYS B 343 " --> pdb=" O HIS B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 363 Processing helix chain 'B' and resid 364 through 375 Processing helix chain 'B' and resid 392 through 400 Processing helix chain 'B' and resid 400 through 408 Processing helix chain 'B' and resid 409 through 418 removed outlier: 3.772A pdb=" N VAL B 418 " --> pdb=" O VAL B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 437 removed outlier: 3.858A pdb=" N LYS B 431 " --> pdb=" O GLY B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 472 Processing helix chain 'B' and resid 473 through 475 No H-bonds generated for 'chain 'B' and resid 473 through 475' Processing helix chain 'B' and resid 500 through 509 Processing helix chain 'B' and resid 520 through 525 Processing helix chain 'B' and resid 554 through 560 removed outlier: 3.539A pdb=" N ILE B 558 " --> pdb=" O ASP B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 561 through 563 No H-bonds generated for 'chain 'B' and resid 561 through 563' Processing helix chain 'B' and resid 565 through 576 Processing helix chain 'B' and resid 579 through 592 Processing helix chain 'B' and resid 603 through 608 removed outlier: 3.734A pdb=" N MET B 608 " --> pdb=" O ALA B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 661 removed outlier: 3.528A pdb=" N ARG B 651 " --> pdb=" O GLY B 647 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA B 655 " --> pdb=" O ARG B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 776 through 793 removed outlier: 4.075A pdb=" N MET B 780 " --> pdb=" O GLY B 776 " (cutoff:3.500A) Processing helix chain 'B' and resid 795 through 802 Processing helix chain 'B' and resid 812 through 816 removed outlier: 4.230A pdb=" N VAL B 815 " --> pdb=" O ASP B 812 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N TYR B 816 " --> pdb=" O THR B 813 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 812 through 816' Processing helix chain 'B' and resid 852 through 859 Processing helix chain 'B' and resid 860 through 862 No H-bonds generated for 'chain 'B' and resid 860 through 862' Processing helix chain 'B' and resid 893 through 908 Processing helix chain 'B' and resid 912 through 919 Processing helix chain 'B' and resid 927 through 949 removed outlier: 4.626A pdb=" N GLY B 939 " --> pdb=" O SER B 935 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N ARG B 940 " --> pdb=" O GLU B 936 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE B 941 " --> pdb=" O LEU B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 953 through 957 removed outlier: 3.539A pdb=" N TYR B 956 " --> pdb=" O ALA B 953 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 65 Processing helix chain 'C' and resid 70 through 81 removed outlier: 3.769A pdb=" N ALA C 77 " --> pdb=" O ALA C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 93 Processing helix chain 'C' and resid 94 through 113 removed outlier: 3.607A pdb=" N TRP C 98 " --> pdb=" O ASN C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 172 removed outlier: 3.708A pdb=" N LEU C 165 " --> pdb=" O ASP C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 188 Processing helix chain 'C' and resid 189 through 194 removed outlier: 3.933A pdb=" N SER C 193 " --> pdb=" O PRO C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 229 removed outlier: 4.141A pdb=" N LEU C 229 " --> pdb=" O ALA C 225 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 225 through 229' Processing helix chain 'C' and resid 267 through 283 removed outlier: 3.632A pdb=" N LEU C 271 " --> pdb=" O SER C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 301 removed outlier: 3.907A pdb=" N GLU C 301 " --> pdb=" O PRO C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 344 Processing helix chain 'C' and resid 352 through 356 removed outlier: 4.017A pdb=" N VAL C 355 " --> pdb=" O GLY C 352 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL C 356 " --> pdb=" O ALA C 353 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 352 through 356' Processing helix chain 'C' and resid 361 through 373 removed outlier: 3.537A pdb=" N VAL C 365 " --> pdb=" O ALA C 361 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU C 373 " --> pdb=" O ALA C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 383 Processing helix chain 'C' and resid 412 through 426 removed outlier: 3.706A pdb=" N GLN C 416 " --> pdb=" O GLY C 412 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASP C 423 " --> pdb=" O ALA C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 427 through 429 No H-bonds generated for 'chain 'C' and resid 427 through 429' Processing helix chain 'C' and resid 434 through 448 removed outlier: 3.720A pdb=" N LEU C 438 " --> pdb=" O GLY C 434 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 469 Proline residue: C 463 - end of helix Processing helix chain 'C' and resid 469 through 492 removed outlier: 3.554A pdb=" N ARG C 473 " --> pdb=" O CYS C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 542 removed outlier: 3.555A pdb=" N ILE C 524 " --> pdb=" O ALA C 520 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLU C 525 " --> pdb=" O SER C 521 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ASP C 526 " --> pdb=" O GLY C 522 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASN C 542 " --> pdb=" O VAL C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 588 through 609 removed outlier: 3.978A pdb=" N THR C 592 " --> pdb=" O GLY C 588 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N THR C 593 " --> pdb=" O PRO C 589 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA C 594 " --> pdb=" O ALA C 590 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR C 609 " --> pdb=" O VAL C 605 " (cutoff:3.500A) Processing helix chain 'C' and resid 610 through 612 No H-bonds generated for 'chain 'C' and resid 610 through 612' Processing helix chain 'C' and resid 615 through 636 Processing helix chain 'C' and resid 642 through 647 removed outlier: 4.062A pdb=" N TRP C 646 " --> pdb=" O ASP C 642 " (cutoff:3.500A) Processing helix chain 'C' and resid 660 through 666 removed outlier: 3.675A pdb=" N GLY C 666 " --> pdb=" O ALA C 663 " (cutoff:3.500A) Processing helix chain 'C' and resid 667 through 672 removed outlier: 3.532A pdb=" N ASP C 671 " --> pdb=" O ALA C 668 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ALA C 672 " --> pdb=" O LEU C 669 " (cutoff:3.500A) Processing helix chain 'C' and resid 695 through 697 No H-bonds generated for 'chain 'C' and resid 695 through 697' Processing helix chain 'C' and resid 707 through 731 removed outlier: 3.611A pdb=" N HIS C 711 " --> pdb=" O ASP C 707 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU C 718 " --> pdb=" O GLU C 714 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY C 725 " --> pdb=" O LEU C 721 " (cutoff:3.500A) Processing helix chain 'C' and resid 740 through 745 Processing sheet with id=AA1, first strand: chain 'A' and resid 117 through 120 removed outlier: 6.351A pdb=" N VAL A 117 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N ASP A 249 " --> pdb=" O VAL A 117 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N THR A 119 " --> pdb=" O ASP A 249 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ILE A 246 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N VAL A 289 " --> pdb=" O ILE A 246 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ILE A 248 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ALA A 91 " --> pdb=" O LEU A 286 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N CYS A 288 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N TYR A 93 " --> pdb=" O CYS A 288 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N GLY A 290 " --> pdb=" O TYR A 93 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ILE A 95 " --> pdb=" O GLY A 290 " (cutoff:3.500A) removed outlier: 9.050A pdb=" N ALA A 338 " --> pdb=" O VAL A 92 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU A 94 " --> pdb=" O ALA A 338 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N PHE A 340 " --> pdb=" O LEU A 94 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N THR A 96 " --> pdb=" O PHE A 340 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 297 through 303 removed outlier: 4.754A pdb=" N SER A 297 " --> pdb=" O SER A 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 807 through 809 removed outlier: 6.001A pdb=" N ARG A 393 " --> pdb=" O MET A 808 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N THR A 392 " --> pdb=" O ALA A 822 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 476 through 480 removed outlier: 6.986A pdb=" N MET A 794 " --> pdb=" O SER A 432 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N PHE A 783 " --> pdb=" O MET A 794 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ILE A 796 " --> pdb=" O SER A 781 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N SER A 781 " --> pdb=" O ILE A 796 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ALA A 798 " --> pdb=" O ASN A 779 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ASN A 779 " --> pdb=" O ALA A 798 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 700 through 703 removed outlier: 5.729A pdb=" N LEU A 728 " --> pdb=" O ARG A 767 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ARG A 767 " --> pdb=" O LEU A 728 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY A 730 " --> pdb=" O VAL A 765 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL A 764 " --> pdb=" O VAL A 776 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 700 through 703 Processing sheet with id=AA7, first strand: chain 'A' and resid 515 through 516 removed outlier: 3.565A pdb=" N GLY A 515 " --> pdb=" O PHE A 693 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 49 through 56 removed outlier: 6.964A pdb=" N LEU B 23 " --> pdb=" O PHE B 51 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N TYR B 53 " --> pdb=" O THR B 21 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N THR B 21 " --> pdb=" O TYR B 53 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ALA B 55 " --> pdb=" O GLU B 19 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N GLU B 19 " --> pdb=" O ALA B 55 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N VAL B 18 " --> pdb=" O ARG B 90 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N THR B 92 " --> pdb=" O VAL B 18 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N VAL B 20 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N CYS B 94 " --> pdb=" O VAL B 20 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ALA B 22 " --> pdb=" O CYS B 94 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N LEU B 96 " --> pdb=" O ALA B 22 " (cutoff:3.500A) removed outlier: 9.404A pdb=" N TYR B 24 " --> pdb=" O LEU B 96 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N PHE B 89 " --> pdb=" O ARG B 117 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ARG B 117 " --> pdb=" O PHE B 89 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL B 91 " --> pdb=" O VAL B 115 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N VAL B 115 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N PHE B 93 " --> pdb=" O MET B 113 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 421 through 426 removed outlier: 6.525A pdb=" N ARG B 421 " --> pdb=" O HIS B 885 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL B 773 " --> pdb=" O LEU B 884 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N SER B 886 " --> pdb=" O VAL B 773 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 453 through 456 removed outlier: 5.650A pdb=" N VAL B 535 " --> pdb=" O ILE B 615 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 624 through 632 removed outlier: 5.587A pdb=" N GLY B 761 " --> pdb=" O SER B 678 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N PHE B 675 " --> pdb=" O VAL B 843 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 829 through 830 Processing sheet with id=AB4, first strand: chain 'B' and resid 960 through 966 removed outlier: 6.697A pdb=" N LEU B 972 " --> pdb=" O ALA B 964 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N SER B 966 " --> pdb=" O TRP B 970 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N TRP B 970 " --> pdb=" O SER B 966 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N THR B1003 " --> pdb=" O LEU B 975 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL B1017 " --> pdb=" O THR B1038 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N THR B1038 " --> pdb=" O VAL B1017 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N LEU B1019 " --> pdb=" O LEU B1036 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 46 through 56 removed outlier: 8.319A pdb=" N TYR C 30 " --> pdb=" O TRP C 22 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N TRP C 22 " --> pdb=" O TYR C 30 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N HIS C 32 " --> pdb=" O ALA C 20 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ALA C 20 " --> pdb=" O HIS C 32 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N LEU C 34 " --> pdb=" O LEU C 18 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N LEU C 18 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N TYR C 36 " --> pdb=" O ILE C 16 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ILE C 16 " --> pdb=" O TYR C 36 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL C 38 " --> pdb=" O SER C 14 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 221 through 223 removed outlier: 3.630A pdb=" N SER C 196 " --> pdb=" O ASN C 157 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ALA C 150 " --> pdb=" O VAL C 260 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N ALA C 262 " --> pdb=" O ALA C 150 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N LEU C 152 " --> pdb=" O ALA C 262 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N PHE C 259 " --> pdb=" O PHE C 321 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N VAL C 323 " --> pdb=" O PHE C 259 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N SER C 261 " --> pdb=" O VAL C 323 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 230 through 237 Processing sheet with id=AB8, first strand: chain 'C' and resid 295 through 296 Processing sheet with id=AB9, first strand: chain 'C' and resid 398 through 400 removed outlier: 3.716A pdb=" N THR C 578 " --> pdb=" O ASN C 573 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 496 through 501 removed outlier: 5.453A pdb=" N VAL C 498 " --> pdb=" O VAL C 509 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N VAL C 509 " --> pdb=" O VAL C 498 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLY C 556 " --> pdb=" O ARG C 407 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N CYS C 409 " --> pdb=" O LEU C 554 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N LEU C 554 " --> pdb=" O CYS C 409 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 648 through 650 906 hydrogen bonds defined for protein. 2583 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: 3.74 Time building geometry restraints manager: 1.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6233 1.34 - 1.46: 2993 1.46 - 1.57: 10639 1.57 - 1.69: 14 1.69 - 1.81: 111 Bond restraints: 19990 Sorted by residual: bond pdb=" C3' DT D 12 " pdb=" C2' DT D 12 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.79e+00 bond pdb=" CA ASN C 511 " pdb=" CB ASN C 511 " ideal model delta sigma weight residual 1.527 1.582 -0.055 2.48e-02 1.63e+03 4.92e+00 bond pdb=" C3' DA D 13 " pdb=" C2' DA D 13 " ideal model delta sigma weight residual 1.516 1.530 -0.014 8.00e-03 1.56e+04 2.94e+00 bond pdb=" C1' DT D 12 " pdb=" N1 DT D 12 " ideal model delta sigma weight residual 1.468 1.490 -0.022 1.40e-02 5.10e+03 2.52e+00 bond pdb=" C2' DT D 12 " pdb=" C1' DT D 12 " ideal model delta sigma weight residual 1.518 1.534 -0.016 1.00e-02 1.00e+04 2.41e+00 ... (remaining 19985 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.03: 27160 3.03 - 6.07: 112 6.07 - 9.10: 11 9.10 - 12.13: 0 12.13 - 15.17: 1 Bond angle restraints: 27284 Sorted by residual: angle pdb=" CA LEU A 545 " pdb=" CB LEU A 545 " pdb=" CG LEU A 545 " ideal model delta sigma weight residual 116.30 131.47 -15.17 3.50e+00 8.16e-02 1.88e+01 angle pdb=" N GLY B 834 " pdb=" CA GLY B 834 " pdb=" C GLY B 834 " ideal model delta sigma weight residual 112.34 120.70 -8.36 2.04e+00 2.40e-01 1.68e+01 angle pdb=" N3 DT D 12 " pdb=" C4 DT D 12 " pdb=" O4 DT D 12 " ideal model delta sigma weight residual 119.90 122.36 -2.46 6.00e-01 2.78e+00 1.68e+01 angle pdb=" N3 DT D 8 " pdb=" C4 DT D 8 " pdb=" O4 DT D 8 " ideal model delta sigma weight residual 119.90 122.35 -2.45 6.00e-01 2.78e+00 1.66e+01 angle pdb=" O4 DT D 12 " pdb=" C4 DT D 12 " pdb=" C5 DT D 12 " ideal model delta sigma weight residual 124.90 122.32 2.58 7.00e-01 2.04e+00 1.36e+01 ... (remaining 27279 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 10242 17.88 - 35.76: 1213 35.76 - 53.64: 350 53.64 - 71.52: 57 71.52 - 89.40: 19 Dihedral angle restraints: 11881 sinusoidal: 4618 harmonic: 7263 Sorted by residual: dihedral pdb=" CA PRO C 396 " pdb=" C PRO C 396 " pdb=" N PRO C 397 " pdb=" CA PRO C 397 " ideal model delta harmonic sigma weight residual 180.00 -140.05 -39.95 0 5.00e+00 4.00e-02 6.38e+01 dihedral pdb=" CA ILE B 277 " pdb=" C ILE B 277 " pdb=" N PRO B 278 " pdb=" CA PRO B 278 " ideal model delta harmonic sigma weight residual -180.00 -154.65 -25.35 0 5.00e+00 4.00e-02 2.57e+01 dihedral pdb=" CA PRO B 493 " pdb=" C PRO B 493 " pdb=" N PRO B 494 " pdb=" CA PRO B 494 " ideal model delta harmonic sigma weight residual -180.00 -155.89 -24.11 0 5.00e+00 4.00e-02 2.32e+01 ... (remaining 11878 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 2073 0.033 - 0.066: 700 0.066 - 0.100: 181 0.100 - 0.133: 116 0.133 - 0.166: 7 Chirality restraints: 3077 Sorted by residual: chirality pdb=" CA PRO C 397 " pdb=" N PRO C 397 " pdb=" C PRO C 397 " pdb=" CB PRO C 397 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 6.89e-01 chirality pdb=" CB ILE C 390 " pdb=" CA ILE C 390 " pdb=" CG1 ILE C 390 " pdb=" CG2 ILE C 390 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.66e-01 chirality pdb=" CA ASN C 511 " pdb=" N ASN C 511 " pdb=" C ASN C 511 " pdb=" CB ASN C 511 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.59e-01 ... (remaining 3074 not shown) Planarity restraints: 3547 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO C 396 " -0.051 5.00e-02 4.00e+02 7.75e-02 9.61e+00 pdb=" N PRO C 397 " 0.134 5.00e-02 4.00e+02 pdb=" CA PRO C 397 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO C 397 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 834 " 0.043 5.00e-02 4.00e+02 6.52e-02 6.80e+00 pdb=" N PRO B 835 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO B 835 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 835 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 395 " 0.042 5.00e-02 4.00e+02 6.34e-02 6.44e+00 pdb=" N PRO C 396 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO C 396 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 396 " 0.035 5.00e-02 4.00e+02 ... (remaining 3544 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 519 2.71 - 3.26: 18058 3.26 - 3.81: 29910 3.81 - 4.35: 37059 4.35 - 4.90: 65367 Nonbonded interactions: 150913 Sorted by model distance: nonbonded pdb=" OG1 THR B 274 " pdb=" OH TYR B 318 " model vdw 2.165 3.040 nonbonded pdb=" OG SER C 66 " pdb=" OD1 ASP C 68 " model vdw 2.169 3.040 nonbonded pdb=" OD1 ASP C 630 " pdb=" OH TYR C 739 " model vdw 2.184 3.040 nonbonded pdb=" OE2 GLU B 239 " pdb=" OG SER B 304 " model vdw 2.197 3.040 nonbonded pdb=" NH1 ARG B 763 " pdb=" O ARG B 823 " model vdw 2.220 3.120 ... (remaining 150908 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: 4.880 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: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 20.000 Find NCS groups from input model: 0.140 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: 0.000 Load rotamer database and sin/cos tables:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 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 : 0.002 0.055 19997 Z= 0.127 Angle : 0.550 15.166 27287 Z= 0.300 Chirality : 0.040 0.166 3077 Planarity : 0.005 0.078 3547 Dihedral : 16.824 89.405 7205 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.72 % Favored : 95.00 % Rotamer: Outliers : 1.75 % Allowed : 21.13 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.84 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.17), residues: 2500 helix: 1.08 (0.16), residues: 1074 sheet: -0.28 (0.25), residues: 411 loop : -1.67 (0.19), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 676 TYR 0.016 0.001 TYR B 450 PHE 0.022 0.001 PHE A 149 TRP 0.008 0.001 TRP C 453 HIS 0.003 0.000 HIS C 710 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.13 (19990) covalent geometry : angle 0.54999 / 0.30 (27284) hydrogen bonds : bond 0.15162 / 10.00 ( 901) hydrogen bonds : angle 5.63351 / 3.92 ( 2583) metal coordination : bond 0.00261 / 0.15 ( 7) metal coordination : angle 0.37875 / 0.22 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 185 time to evaluate : 0.612 Fit side-chains REVERT: A 185 TYR cc_start: 0.9023 (OUTLIER) cc_final: 0.7933 (t80) REVERT: A 306 LYS cc_start: 0.7652 (mmtp) cc_final: 0.6681 (tptp) REVERT: A 517 PHE cc_start: 0.5745 (m-80) cc_final: 0.5516 (m-80) REVERT: A 701 ILE cc_start: 0.7373 (mt) cc_final: 0.7012 (tt) REVERT: B 40 ASN cc_start: 0.8461 (t0) cc_final: 0.7868 (t0) REVERT: B 73 GLU cc_start: 0.7275 (tp30) cc_final: 0.6795 (mt-10) REVERT: B 141 HIS cc_start: 0.7161 (m90) cc_final: 0.6795 (m-70) REVERT: B 284 ASP cc_start: 0.6858 (p0) cc_final: 0.6641 (t70) REVERT: B 335 LYS cc_start: 0.8205 (mttp) cc_final: 0.7876 (mttt) REVERT: B 341 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.7961 (ttp-170) REVERT: B 633 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7656 (mt) REVERT: C 1 MET cc_start: 0.2301 (OUTLIER) cc_final: 0.1381 (ttp) REVERT: C 83 THR cc_start: 0.8656 (m) cc_final: 0.8119 (p) REVERT: C 123 ARG cc_start: 0.7590 (mtp-110) cc_final: 0.7235 (mtp-110) REVERT: C 256 TYR cc_start: 0.8930 (p90) cc_final: 0.8564 (p90) REVERT: C 375 PRO cc_start: 0.5706 (Cg_endo) cc_final: 0.5432 (Cg_exo) outliers start: 35 outliers final: 30 residues processed: 207 average time/residue: 0.1708 time to fit residues: 51.3016 Evaluate side-chains 215 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 181 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 185 TYR Chi-restraints excluded: chain A residue 207 ASN Chi-restraints excluded: chain A residue 316 ASN Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 768 ASP Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 823 ILE Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 341 ARG Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 566 GLU Chi-restraints excluded: chain B residue 590 ILE Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 793 LEU Chi-restraints excluded: chain B residue 1031 ASN Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 542 ASN Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 657 ASP Chi-restraints excluded: chain C residue 719 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 216 optimal weight: 0.4980 chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 10.0000 chunk 247 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 32 HIS C 542 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.162251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.138575 restraints weight = 23175.230| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 1.35 r_work: 0.3152 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.0649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 19997 Z= 0.168 Angle : 0.566 8.620 27287 Z= 0.293 Chirality : 0.043 0.161 3077 Planarity : 0.005 0.063 3547 Dihedral : 7.699 74.586 2928 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.88 % Favored : 94.84 % Rotamer: Outliers : 2.45 % Allowed : 19.53 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.84 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.17), residues: 2500 helix: 1.18 (0.16), residues: 1077 sheet: -0.24 (0.25), residues: 411 loop : -1.73 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 676 TYR 0.020 0.002 TYR C 212 PHE 0.033 0.002 PHE A 149 TRP 0.011 0.001 TRP C 507 HIS 0.005 0.001 HIS C 279 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.17 (19990) covalent geometry : angle 0.56558 / 0.29 (27284) hydrogen bonds : bond 0.04702 / 3.11 ( 901) hydrogen bonds : angle 4.61759 / 3.25 ( 2583) metal coordination : bond 0.00116 / 0.06 ( 7) metal coordination : angle 0.31713 / 0.20 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 188 time to evaluate : 0.655 Fit side-chains revert: symmetry clash REVERT: A 185 TYR cc_start: 0.8912 (OUTLIER) cc_final: 0.8115 (t80) REVERT: A 306 LYS cc_start: 0.7542 (mmtp) cc_final: 0.6728 (tptp) REVERT: A 517 PHE cc_start: 0.6859 (m-80) cc_final: 0.6589 (m-80) REVERT: A 676 ARG cc_start: 0.7310 (mtp-110) cc_final: 0.7082 (mtp-110) REVERT: A 701 ILE cc_start: 0.7898 (mt) cc_final: 0.7620 (tt) REVERT: A 852 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8732 (pp) REVERT: A 858 ARG cc_start: 0.8513 (ttm110) cc_final: 0.8310 (ttm170) REVERT: B 40 ASN cc_start: 0.8594 (t0) cc_final: 0.8130 (t0) REVERT: B 67 GLU cc_start: 0.8312 (tt0) cc_final: 0.7980 (tt0) REVERT: B 73 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.7077 (mt-10) REVERT: B 84 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.7654 (mt) REVERT: B 141 HIS cc_start: 0.7444 (m90) cc_final: 0.7204 (m-70) REVERT: B 335 LYS cc_start: 0.8655 (mttp) cc_final: 0.8308 (mttt) REVERT: C 123 ARG cc_start: 0.8014 (mtp-110) cc_final: 0.7759 (mtp-110) REVERT: C 213 GLN cc_start: 0.8093 (tp-100) cc_final: 0.7559 (tt0) REVERT: C 256 TYR cc_start: 0.8847 (p90) cc_final: 0.8514 (p90) REVERT: C 375 PRO cc_start: 0.6245 (Cg_endo) cc_final: 0.5987 (Cg_exo) REVERT: C 433 HIS cc_start: 0.6505 (OUTLIER) cc_final: 0.5517 (t-90) REVERT: C 566 GLN cc_start: 0.8252 (tp40) cc_final: 0.8004 (tp40) outliers start: 49 outliers final: 25 residues processed: 229 average time/residue: 0.1644 time to fit residues: 55.3518 Evaluate side-chains 209 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 179 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 185 TYR Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 590 ILE Chi-restraints excluded: chain B residue 637 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 193 SER Chi-restraints excluded: chain C residue 395 ASP Chi-restraints excluded: chain C residue 433 HIS Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 656 SER Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 719 ILE Chi-restraints excluded: chain C residue 722 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 249 optimal weight: 0.9980 chunk 169 optimal weight: 5.9990 chunk 121 optimal weight: 2.9990 chunk 179 optimal weight: 8.9990 chunk 232 optimal weight: 0.7980 chunk 154 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 56 optimal weight: 0.4980 chunk 214 optimal weight: 0.9980 chunk 156 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 576 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.156615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.122954 restraints weight = 23648.794| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.51 r_work: 0.2955 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.0867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 19997 Z= 0.146 Angle : 0.536 8.831 27287 Z= 0.276 Chirality : 0.042 0.168 3077 Planarity : 0.005 0.065 3547 Dihedral : 7.149 74.689 2882 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.96 % Favored : 94.72 % Rotamer: Outliers : 2.85 % Allowed : 19.68 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.84 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.17), residues: 2500 helix: 1.20 (0.16), residues: 1090 sheet: -0.24 (0.25), residues: 409 loop : -1.72 (0.19), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 200 TYR 0.018 0.001 TYR C 212 PHE 0.029 0.001 PHE A 149 TRP 0.011 0.001 TRP C 507 HIS 0.005 0.001 HIS C 279 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (19990) covalent geometry : angle 0.53619 / 0.28 (27284) hydrogen bonds : bond 0.04297 / 2.84 ( 901) hydrogen bonds : angle 4.40628 / 3.11 ( 2583) metal coordination : bond 0.00142 / 0.07 ( 7) metal coordination : angle 0.58165 / 0.38 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 185 time to evaluate : 0.760 Fit side-chains revert: symmetry clash REVERT: A 185 TYR cc_start: 0.8950 (OUTLIER) cc_final: 0.8027 (t80) REVERT: A 306 LYS cc_start: 0.7661 (mmtp) cc_final: 0.6553 (tptp) REVERT: A 517 PHE cc_start: 0.6105 (m-80) cc_final: 0.5735 (m-80) REVERT: A 701 ILE cc_start: 0.7556 (mt) cc_final: 0.7225 (tt) REVERT: A 852 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8679 (pp) REVERT: A 858 ARG cc_start: 0.8320 (ttm110) cc_final: 0.8082 (ttm110) REVERT: B 40 ASN cc_start: 0.8458 (t0) cc_final: 0.7946 (t0) REVERT: B 67 GLU cc_start: 0.8177 (tt0) cc_final: 0.7873 (tt0) REVERT: B 73 GLU cc_start: 0.7275 (OUTLIER) cc_final: 0.6921 (mt-10) REVERT: B 84 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.7540 (mt) REVERT: B 141 HIS cc_start: 0.7315 (m90) cc_final: 0.7032 (m-70) REVERT: B 334 GLU cc_start: 0.7930 (tm-30) cc_final: 0.7615 (tm-30) REVERT: B 335 LYS cc_start: 0.8424 (mttp) cc_final: 0.7715 (mttt) REVERT: C 83 THR cc_start: 0.8755 (m) cc_final: 0.8277 (p) REVERT: C 123 ARG cc_start: 0.7874 (mtp-110) cc_final: 0.7481 (mtp-110) REVERT: C 256 TYR cc_start: 0.8912 (p90) cc_final: 0.8539 (p90) REVERT: C 375 PRO cc_start: 0.5867 (Cg_endo) cc_final: 0.5627 (Cg_exo) REVERT: C 433 HIS cc_start: 0.6418 (OUTLIER) cc_final: 0.5383 (t-90) REVERT: C 566 GLN cc_start: 0.8216 (tp40) cc_final: 0.7944 (tp40) REVERT: C 631 ARG cc_start: 0.8268 (tpp-160) cc_final: 0.7732 (mmp80) outliers start: 57 outliers final: 28 residues processed: 229 average time/residue: 0.1676 time to fit residues: 56.5313 Evaluate side-chains 204 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 171 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 185 TYR Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 823 ILE Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain B residue 590 ILE Chi-restraints excluded: chain B residue 637 VAL Chi-restraints excluded: chain B residue 793 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 433 HIS Chi-restraints excluded: chain C residue 542 ASN Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 656 SER Chi-restraints excluded: chain C residue 719 ILE Chi-restraints excluded: chain C residue 722 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 177 optimal weight: 4.9990 chunk 195 optimal weight: 0.6980 chunk 141 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 159 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 201 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 244 optimal weight: 0.0270 overall best weight: 1.7444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 155 HIS B 576 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.154590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.125511 restraints weight = 23488.429| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.03 r_work: 0.2965 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.1181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 19997 Z= 0.209 Angle : 0.594 8.964 27287 Z= 0.305 Chirality : 0.044 0.167 3077 Planarity : 0.005 0.066 3547 Dihedral : 7.280 75.320 2881 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.60 % Favored : 94.08 % Rotamer: Outliers : 3.81 % Allowed : 19.73 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.84 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.17), residues: 2500 helix: 1.06 (0.16), residues: 1083 sheet: -0.44 (0.25), residues: 399 loop : -1.79 (0.18), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 699 TYR 0.017 0.002 TYR B 78 PHE 0.034 0.002 PHE A 149 TRP 0.016 0.002 TRP C 507 HIS 0.007 0.001 HIS C 279 Details of bonding type rmsd/Z covalent geometry : bond 0.00521 / 0.21 (19990) covalent geometry : angle 0.59447 / 0.31 (27284) hydrogen bonds : bond 0.04923 / 3.26 ( 901) hydrogen bonds : angle 4.49740 / 3.18 ( 2583) metal coordination : bond 0.00291 / 0.16 ( 7) metal coordination : angle 0.69008 / 0.45 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 175 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 185 TYR cc_start: 0.9066 (OUTLIER) cc_final: 0.8194 (t80) REVERT: A 306 LYS cc_start: 0.7602 (mmtp) cc_final: 0.6653 (tptp) REVERT: A 517 PHE cc_start: 0.6558 (m-80) cc_final: 0.6189 (m-80) REVERT: A 701 ILE cc_start: 0.7672 (mt) cc_final: 0.7314 (tt) REVERT: A 852 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8709 (pp) REVERT: A 858 ARG cc_start: 0.8352 (ttm110) cc_final: 0.8113 (ttm110) REVERT: B 40 ASN cc_start: 0.8468 (t0) cc_final: 0.7975 (t0) REVERT: B 67 GLU cc_start: 0.8178 (tt0) cc_final: 0.7827 (tt0) REVERT: B 73 GLU cc_start: 0.7476 (OUTLIER) cc_final: 0.7013 (mt-10) REVERT: B 84 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.7537 (mt) REVERT: B 141 HIS cc_start: 0.7310 (m90) cc_final: 0.7027 (m-70) REVERT: B 334 GLU cc_start: 0.7994 (tm-30) cc_final: 0.7645 (tm-30) REVERT: B 335 LYS cc_start: 0.8519 (mttp) cc_final: 0.7842 (mttt) REVERT: C 83 THR cc_start: 0.8811 (m) cc_final: 0.8343 (p) REVERT: C 123 ARG cc_start: 0.7932 (mtp-110) cc_final: 0.7490 (mtp-110) REVERT: C 256 TYR cc_start: 0.8941 (p90) cc_final: 0.8597 (p90) REVERT: C 433 HIS cc_start: 0.6482 (OUTLIER) cc_final: 0.5472 (t-90) REVERT: C 566 GLN cc_start: 0.8278 (tp40) cc_final: 0.7932 (tp40) REVERT: C 631 ARG cc_start: 0.8311 (tpp-160) cc_final: 0.7796 (mmp80) REVERT: C 718 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7317 (mm-30) outliers start: 76 outliers final: 48 residues processed: 239 average time/residue: 0.1668 time to fit residues: 59.0592 Evaluate side-chains 223 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 169 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ARG Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 185 TYR Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 342 ASN Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 823 ILE Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 343 CYS Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 590 ILE Chi-restraints excluded: chain B residue 637 VAL Chi-restraints excluded: chain B residue 773 VAL Chi-restraints excluded: chain B residue 777 SER Chi-restraints excluded: chain B residue 793 LEU Chi-restraints excluded: chain B residue 904 LEU Chi-restraints excluded: chain B residue 947 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 433 HIS Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 656 SER Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 718 GLU Chi-restraints excluded: chain C residue 719 ILE Chi-restraints excluded: chain C residue 722 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 10 optimal weight: 0.3980 chunk 215 optimal weight: 0.9980 chunk 198 optimal weight: 0.9980 chunk 229 optimal weight: 3.9990 chunk 92 optimal weight: 0.0670 chunk 91 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 180 optimal weight: 0.8980 chunk 232 optimal weight: 1.9990 chunk 125 optimal weight: 3.9990 chunk 231 optimal weight: 3.9990 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 576 HIS C 392 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.157114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.125866 restraints weight = 23400.386| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.14 r_work: 0.2961 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.1185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19997 Z= 0.118 Angle : 0.515 8.776 27287 Z= 0.266 Chirality : 0.041 0.162 3077 Planarity : 0.005 0.067 3547 Dihedral : 7.146 74.994 2881 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.64 % Favored : 95.04 % Rotamer: Outliers : 2.80 % Allowed : 20.98 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.84 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.17), residues: 2500 helix: 1.29 (0.16), residues: 1086 sheet: -0.40 (0.25), residues: 411 loop : -1.66 (0.19), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 676 TYR 0.015 0.001 TYR C 212 PHE 0.026 0.001 PHE A 149 TRP 0.010 0.001 TRP C 98 HIS 0.008 0.001 HIS B 576 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (19990) covalent geometry : angle 0.51503 / 0.27 (27284) hydrogen bonds : bond 0.03806 / 2.51 ( 901) hydrogen bonds : angle 4.29784 / 3.03 ( 2583) metal coordination : bond 0.00181 / 0.10 ( 7) metal coordination : angle 0.92180 / 0.61 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 180 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 185 TYR cc_start: 0.9013 (OUTLIER) cc_final: 0.8152 (t80) REVERT: A 306 LYS cc_start: 0.7649 (mmtp) cc_final: 0.6845 (ttpt) REVERT: A 308 ARG cc_start: 0.6799 (mmm-85) cc_final: 0.5496 (tpp80) REVERT: A 517 PHE cc_start: 0.6133 (m-80) cc_final: 0.5704 (m-80) REVERT: A 545 LEU cc_start: 0.4758 (mm) cc_final: 0.4122 (mt) REVERT: A 701 ILE cc_start: 0.7554 (mt) cc_final: 0.7183 (tt) REVERT: A 773 MET cc_start: 0.7855 (mmm) cc_final: 0.7439 (mmt) REVERT: A 852 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8680 (pp) REVERT: A 858 ARG cc_start: 0.8535 (ttm110) cc_final: 0.8291 (ttm110) REVERT: B 67 GLU cc_start: 0.8296 (tt0) cc_final: 0.8000 (tt0) REVERT: B 73 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.7007 (mt-10) REVERT: B 84 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.7534 (mt) REVERT: B 141 HIS cc_start: 0.7303 (m90) cc_final: 0.6984 (m-70) REVERT: B 334 GLU cc_start: 0.8088 (tm-30) cc_final: 0.7718 (tm-30) REVERT: B 335 LYS cc_start: 0.8491 (mttp) cc_final: 0.7829 (mttt) REVERT: C 8 TRP cc_start: 0.8605 (m100) cc_final: 0.8221 (m100) REVERT: C 83 THR cc_start: 0.8887 (m) cc_final: 0.8430 (p) REVERT: C 123 ARG cc_start: 0.7859 (mtp-110) cc_final: 0.7516 (mtp180) REVERT: C 256 TYR cc_start: 0.8978 (p90) cc_final: 0.8583 (p90) REVERT: C 433 HIS cc_start: 0.6481 (OUTLIER) cc_final: 0.5524 (t-90) REVERT: C 545 ARG cc_start: 0.8544 (mtp180) cc_final: 0.8271 (mtt-85) REVERT: C 566 GLN cc_start: 0.8390 (tp40) cc_final: 0.8134 (tp40) REVERT: C 718 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7639 (mm-30) outliers start: 56 outliers final: 38 residues processed: 223 average time/residue: 0.1745 time to fit residues: 56.7056 Evaluate side-chains 214 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 170 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 86 ARG Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 185 TYR Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 342 ASN Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 823 ILE Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 590 ILE Chi-restraints excluded: chain B residue 637 VAL Chi-restraints excluded: chain B residue 773 VAL Chi-restraints excluded: chain B residue 777 SER Chi-restraints excluded: chain B residue 793 LEU Chi-restraints excluded: chain B residue 804 TYR Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 249 ARG Chi-restraints excluded: chain C residue 433 HIS Chi-restraints excluded: chain C residue 542 ASN Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 656 SER Chi-restraints excluded: chain C residue 718 GLU Chi-restraints excluded: chain C residue 722 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 247 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 210 optimal weight: 0.6980 chunk 4 optimal weight: 4.9990 chunk 61 optimal weight: 9.9990 chunk 190 optimal weight: 2.9990 chunk 146 optimal weight: 4.9990 chunk 65 optimal weight: 0.5980 chunk 63 optimal weight: 3.9990 chunk 194 optimal weight: 0.8980 chunk 170 optimal weight: 20.0000 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 576 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.161891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.140802 restraints weight = 23068.353| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 1.19 r_work: 0.3299 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 19997 Z= 0.157 Angle : 0.540 8.914 27287 Z= 0.277 Chirality : 0.042 0.159 3077 Planarity : 0.005 0.066 3547 Dihedral : 7.158 74.944 2879 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.00 % Favored : 94.68 % Rotamer: Outliers : 3.41 % Allowed : 20.43 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.84 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.17), residues: 2500 helix: 1.26 (0.16), residues: 1085 sheet: -0.42 (0.25), residues: 399 loop : -1.70 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 676 TYR 0.014 0.001 TYR C 212 PHE 0.030 0.001 PHE A 149 TRP 0.012 0.001 TRP C 507 HIS 0.005 0.001 HIS C 279 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.16 (19990) covalent geometry : angle 0.54004 / 0.28 (27284) hydrogen bonds : bond 0.04164 / 2.75 ( 901) hydrogen bonds : angle 4.31309 / 3.04 ( 2583) metal coordination : bond 0.00250 / 0.14 ( 7) metal coordination : angle 0.69374 / 0.46 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 178 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 185 TYR cc_start: 0.8948 (OUTLIER) cc_final: 0.8250 (t80) REVERT: A 430 PHE cc_start: 0.8284 (m-80) cc_final: 0.8081 (m-80) REVERT: A 852 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8777 (pp) REVERT: A 858 ARG cc_start: 0.8093 (ttm110) cc_final: 0.7888 (ttm110) REVERT: A 870 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8773 (tt) REVERT: B 67 GLU cc_start: 0.8121 (tt0) cc_final: 0.7846 (tt0) REVERT: B 73 GLU cc_start: 0.7353 (OUTLIER) cc_final: 0.7130 (mt-10) REVERT: B 75 ARG cc_start: 0.8151 (OUTLIER) cc_final: 0.7945 (ttp-170) REVERT: B 84 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.7664 (mt) REVERT: B 335 LYS cc_start: 0.8629 (mttp) cc_final: 0.8039 (mttt) REVERT: C 83 THR cc_start: 0.8785 (m) cc_final: 0.8394 (p) REVERT: C 123 ARG cc_start: 0.7763 (mtp-110) cc_final: 0.7519 (mtp-110) REVERT: C 256 TYR cc_start: 0.8726 (p90) cc_final: 0.8392 (p90) REVERT: C 433 HIS cc_start: 0.6403 (OUTLIER) cc_final: 0.5558 (t-90) REVERT: C 545 ARG cc_start: 0.7952 (mtp180) cc_final: 0.7751 (mtt-85) REVERT: C 718 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7321 (mm-30) outliers start: 68 outliers final: 46 residues processed: 235 average time/residue: 0.1616 time to fit residues: 56.3975 Evaluate side-chains 224 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 170 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ARG Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 185 TYR Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 342 ASN Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 75 ARG Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 343 CYS Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 590 ILE Chi-restraints excluded: chain B residue 637 VAL Chi-restraints excluded: chain B residue 773 VAL Chi-restraints excluded: chain B residue 777 SER Chi-restraints excluded: chain B residue 793 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 249 ARG Chi-restraints excluded: chain C residue 433 HIS Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 656 SER Chi-restraints excluded: chain C residue 718 GLU Chi-restraints excluded: chain C residue 722 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 179 optimal weight: 7.9990 chunk 22 optimal weight: 2.9990 chunk 66 optimal weight: 8.9990 chunk 105 optimal weight: 0.0270 chunk 156 optimal weight: 0.7980 chunk 95 optimal weight: 0.6980 chunk 83 optimal weight: 0.3980 chunk 204 optimal weight: 0.9990 chunk 223 optimal weight: 1.9990 chunk 120 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 576 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.165036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.143402 restraints weight = 23132.318| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 1.20 r_work: 0.3360 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 19997 Z= 0.106 Angle : 0.503 8.830 27287 Z= 0.259 Chirality : 0.040 0.149 3077 Planarity : 0.005 0.066 3547 Dihedral : 7.054 74.622 2879 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.32 % Favored : 95.36 % Rotamer: Outliers : 2.65 % Allowed : 21.13 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.84 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.17), residues: 2500 helix: 1.42 (0.16), residues: 1086 sheet: -0.36 (0.25), residues: 411 loop : -1.59 (0.19), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 308 TYR 0.015 0.001 TYR C 212 PHE 0.026 0.001 PHE A 149 TRP 0.021 0.001 TRP C 8 HIS 0.003 0.001 HIS C 710 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (19990) covalent geometry : angle 0.50340 / 0.26 (27284) hydrogen bonds : bond 0.03428 / 2.26 ( 901) hydrogen bonds : angle 4.17418 / 2.93 ( 2583) metal coordination : bond 0.00182 / 0.10 ( 7) metal coordination : angle 1.01157 / 0.66 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 184 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 545 LEU cc_start: 0.5785 (mm) cc_final: 0.5276 (mt) REVERT: A 858 ARG cc_start: 0.8020 (ttm110) cc_final: 0.7817 (ttm110) REVERT: B 73 GLU cc_start: 0.7217 (OUTLIER) cc_final: 0.6908 (mt-10) REVERT: B 75 ARG cc_start: 0.8086 (OUTLIER) cc_final: 0.7879 (ttp-170) REVERT: B 84 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.7624 (mt) REVERT: B 335 LYS cc_start: 0.8604 (mttp) cc_final: 0.8311 (mptt) REVERT: B 973 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7778 (mt) REVERT: C 83 THR cc_start: 0.8769 (m) cc_final: 0.8402 (p) REVERT: C 123 ARG cc_start: 0.7729 (mtp-110) cc_final: 0.7429 (mtp-110) REVERT: C 256 TYR cc_start: 0.8676 (p90) cc_final: 0.8339 (p90) REVERT: C 433 HIS cc_start: 0.6392 (OUTLIER) cc_final: 0.5606 (t-90) REVERT: C 545 ARG cc_start: 0.7893 (mtp180) cc_final: 0.7690 (mtt-85) REVERT: C 718 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7308 (mm-30) outliers start: 53 outliers final: 40 residues processed: 229 average time/residue: 0.1649 time to fit residues: 56.0750 Evaluate side-chains 222 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 176 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 86 ARG Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 342 ASN Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 823 ILE Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 75 ARG Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 343 CYS Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 590 ILE Chi-restraints excluded: chain B residue 637 VAL Chi-restraints excluded: chain B residue 773 VAL Chi-restraints excluded: chain B residue 777 SER Chi-restraints excluded: chain B residue 793 LEU Chi-restraints excluded: chain B residue 959 VAL Chi-restraints excluded: chain B residue 973 LEU Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 433 HIS Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 656 SER Chi-restraints excluded: chain C residue 718 GLU Chi-restraints excluded: chain C residue 719 ILE Chi-restraints excluded: chain C residue 722 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 214 optimal weight: 7.9990 chunk 167 optimal weight: 0.8980 chunk 141 optimal weight: 0.6980 chunk 194 optimal weight: 2.9990 chunk 224 optimal weight: 0.0060 chunk 201 optimal weight: 3.9990 chunk 181 optimal weight: 2.9990 chunk 110 optimal weight: 0.8980 chunk 211 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 128 optimal weight: 0.7980 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 576 HIS B1031 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.165142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.143588 restraints weight = 22957.189| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 1.20 r_work: 0.3247 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19997 Z= 0.112 Angle : 0.510 8.883 27287 Z= 0.261 Chirality : 0.041 0.150 3077 Planarity : 0.005 0.066 3547 Dihedral : 6.857 74.604 2875 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.52 % Favored : 95.16 % Rotamer: Outliers : 2.90 % Allowed : 21.23 % Favored : 75.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.84 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.17), residues: 2500 helix: 1.46 (0.16), residues: 1085 sheet: -0.34 (0.25), residues: 411 loop : -1.58 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1032 TYR 0.012 0.001 TYR B 318 PHE 0.028 0.001 PHE A 149 TRP 0.015 0.001 TRP C 8 HIS 0.004 0.001 HIS C 279 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 (19990) covalent geometry : angle 0.51041 / 0.26 (27284) hydrogen bonds : bond 0.03473 / 2.30 ( 901) hydrogen bonds : angle 4.14430 / 2.91 ( 2583) metal coordination : bond 0.00244 / 0.14 ( 7) metal coordination : angle 0.86067 / 0.57 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 176 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 185 TYR cc_start: 0.8838 (OUTLIER) cc_final: 0.8032 (t80) REVERT: A 306 LYS cc_start: 0.7060 (tttm) cc_final: 0.6248 (tptp) REVERT: A 545 LEU cc_start: 0.5648 (mm) cc_final: 0.5068 (mt) REVERT: A 858 ARG cc_start: 0.7971 (ttm110) cc_final: 0.7744 (ttm110) REVERT: A 870 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8682 (tt) REVERT: B 73 GLU cc_start: 0.7057 (OUTLIER) cc_final: 0.6832 (mt-10) REVERT: B 75 ARG cc_start: 0.8014 (OUTLIER) cc_final: 0.7748 (ttp-170) REVERT: B 84 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.7564 (mt) REVERT: B 335 LYS cc_start: 0.8461 (mttp) cc_final: 0.7896 (mttt) REVERT: B 973 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7561 (mt) REVERT: C 83 THR cc_start: 0.8753 (m) cc_final: 0.8360 (p) REVERT: C 123 ARG cc_start: 0.7720 (mtp-110) cc_final: 0.7386 (mtp-110) REVERT: C 256 TYR cc_start: 0.8725 (p90) cc_final: 0.8361 (p90) REVERT: C 433 HIS cc_start: 0.6356 (OUTLIER) cc_final: 0.5493 (t-90) REVERT: C 545 ARG cc_start: 0.8009 (mtp180) cc_final: 0.7787 (mtt-85) REVERT: C 718 GLU cc_start: 0.7430 (OUTLIER) cc_final: 0.6923 (mm-30) outliers start: 58 outliers final: 47 residues processed: 226 average time/residue: 0.1599 time to fit residues: 53.9333 Evaluate side-chains 227 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 172 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 86 ARG Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 185 TYR Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 342 ASN Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 823 ILE Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 75 ARG Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 343 CYS Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 590 ILE Chi-restraints excluded: chain B residue 637 VAL Chi-restraints excluded: chain B residue 773 VAL Chi-restraints excluded: chain B residue 777 SER Chi-restraints excluded: chain B residue 793 LEU Chi-restraints excluded: chain B residue 959 VAL Chi-restraints excluded: chain B residue 973 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1031 ASN Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 433 HIS Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 656 SER Chi-restraints excluded: chain C residue 718 GLU Chi-restraints excluded: chain C residue 719 ILE Chi-restraints excluded: chain C residue 722 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 167 optimal weight: 1.9990 chunk 87 optimal weight: 0.0970 chunk 204 optimal weight: 0.6980 chunk 80 optimal weight: 2.9990 chunk 172 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 229 optimal weight: 0.7980 chunk 202 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 chunk 34 optimal weight: 0.4980 chunk 241 optimal weight: 0.6980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 576 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.166783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.143273 restraints weight = 22921.919| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 1.28 r_work: 0.3181 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 19997 Z= 0.105 Angle : 0.508 8.889 27287 Z= 0.260 Chirality : 0.040 0.147 3077 Planarity : 0.005 0.066 3547 Dihedral : 6.838 74.459 2875 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.36 % Favored : 95.32 % Rotamer: Outliers : 2.75 % Allowed : 21.18 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.84 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.17), residues: 2500 helix: 1.52 (0.16), residues: 1086 sheet: -0.31 (0.25), residues: 410 loop : -1.55 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B1032 TYR 0.011 0.001 TYR C 212 PHE 0.026 0.001 PHE A 149 TRP 0.015 0.001 TRP C 8 HIS 0.003 0.001 HIS C 710 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.10 (19990) covalent geometry : angle 0.50781 / 0.26 (27284) hydrogen bonds : bond 0.03342 / 2.21 ( 901) hydrogen bonds : angle 4.11404 / 2.89 ( 2583) metal coordination : bond 0.00232 / 0.13 ( 7) metal coordination : angle 1.01029 / 0.67 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 171 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 185 TYR cc_start: 0.8868 (OUTLIER) cc_final: 0.8037 (t80) REVERT: A 306 LYS cc_start: 0.7135 (tttm) cc_final: 0.6178 (tptp) REVERT: A 545 LEU cc_start: 0.5084 (mm) cc_final: 0.4465 (mt) REVERT: A 858 ARG cc_start: 0.8490 (ttm110) cc_final: 0.8257 (ttm110) REVERT: B 73 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.6916 (mt-10) REVERT: B 75 ARG cc_start: 0.8286 (OUTLIER) cc_final: 0.8021 (ttp-170) REVERT: B 84 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.7597 (mt) REVERT: B 334 GLU cc_start: 0.8259 (tm-30) cc_final: 0.7885 (mm-30) REVERT: B 335 LYS cc_start: 0.8634 (mttp) cc_final: 0.8296 (mttt) REVERT: B 973 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7708 (mt) REVERT: C 83 THR cc_start: 0.8855 (m) cc_final: 0.8444 (p) REVERT: C 123 ARG cc_start: 0.7886 (mtp-110) cc_final: 0.7519 (mtp-110) REVERT: C 256 TYR cc_start: 0.8842 (p90) cc_final: 0.8420 (p90) REVERT: C 433 HIS cc_start: 0.6489 (OUTLIER) cc_final: 0.5553 (t-90) REVERT: C 545 ARG cc_start: 0.8417 (mtp180) cc_final: 0.8188 (mtt-85) REVERT: C 718 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7398 (mm-30) outliers start: 55 outliers final: 44 residues processed: 218 average time/residue: 0.1523 time to fit residues: 49.0375 Evaluate side-chains 215 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 164 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 86 ARG Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 185 TYR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 342 ASN Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 754 GLU Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 823 ILE Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 75 ARG Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 343 CYS Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 590 ILE Chi-restraints excluded: chain B residue 637 VAL Chi-restraints excluded: chain B residue 773 VAL Chi-restraints excluded: chain B residue 777 SER Chi-restraints excluded: chain B residue 793 LEU Chi-restraints excluded: chain B residue 959 VAL Chi-restraints excluded: chain B residue 973 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 249 ARG Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 433 HIS Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 656 SER Chi-restraints excluded: chain C residue 718 GLU Chi-restraints excluded: chain C residue 719 ILE Chi-restraints excluded: chain C residue 722 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 18 optimal weight: 6.9990 chunk 75 optimal weight: 3.9990 chunk 156 optimal weight: 0.8980 chunk 19 optimal weight: 0.4980 chunk 29 optimal weight: 0.7980 chunk 184 optimal weight: 0.5980 chunk 72 optimal weight: 2.9990 chunk 150 optimal weight: 1.9990 chunk 108 optimal weight: 0.9990 chunk 14 optimal weight: 0.4980 chunk 211 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 576 HIS 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 = 0.156415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.126411 restraints weight = 23418.412| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.01 r_work: 0.3036 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19997 Z= 0.110 Angle : 0.509 8.954 27287 Z= 0.260 Chirality : 0.041 0.149 3077 Planarity : 0.005 0.065 3547 Dihedral : 6.785 74.168 2874 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.36 % Favored : 95.32 % Rotamer: Outliers : 2.80 % Allowed : 21.13 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.84 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.17), residues: 2500 helix: 1.57 (0.16), residues: 1085 sheet: -0.33 (0.25), residues: 427 loop : -1.56 (0.19), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 325 TYR 0.012 0.001 TYR B 318 PHE 0.027 0.001 PHE A 149 TRP 0.017 0.001 TRP C 8 HIS 0.003 0.001 HIS C 279 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 (19990) covalent geometry : angle 0.50859 / 0.26 (27284) hydrogen bonds : bond 0.03346 / 2.21 ( 901) hydrogen bonds : angle 4.08300 / 2.87 ( 2583) metal coordination : bond 0.00213 / 0.12 ( 7) metal coordination : angle 0.80603 / 0.54 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 172 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 185 TYR cc_start: 0.8863 (OUTLIER) cc_final: 0.7991 (t80) REVERT: A 306 LYS cc_start: 0.7218 (tttm) cc_final: 0.6197 (tptp) REVERT: A 545 LEU cc_start: 0.4850 (mm) cc_final: 0.4275 (mt) REVERT: A 858 ARG cc_start: 0.8305 (ttm110) cc_final: 0.8037 (ttm110) REVERT: B 73 GLU cc_start: 0.7244 (OUTLIER) cc_final: 0.6767 (mt-10) REVERT: B 75 ARG cc_start: 0.8214 (OUTLIER) cc_final: 0.7930 (ttp-170) REVERT: B 84 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.7500 (mt) REVERT: B 334 GLU cc_start: 0.7978 (tm-30) cc_final: 0.7626 (mm-30) REVERT: B 335 LYS cc_start: 0.8406 (mttp) cc_final: 0.8057 (mttt) REVERT: B 973 LEU cc_start: 0.7941 (OUTLIER) cc_final: 0.7484 (mt) REVERT: C 83 THR cc_start: 0.8833 (m) cc_final: 0.8398 (p) REVERT: C 123 ARG cc_start: 0.7760 (mtp-110) cc_final: 0.7388 (mtp-110) REVERT: C 256 TYR cc_start: 0.8874 (p90) cc_final: 0.8460 (p90) REVERT: C 433 HIS cc_start: 0.6408 (OUTLIER) cc_final: 0.5461 (t-90) REVERT: C 545 ARG cc_start: 0.8373 (mtp180) cc_final: 0.8107 (mtt-85) REVERT: C 718 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7155 (mm-30) outliers start: 56 outliers final: 47 residues processed: 221 average time/residue: 0.1650 time to fit residues: 54.0071 Evaluate side-chains 224 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 170 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 86 ARG Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 185 TYR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 342 ASN Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 754 GLU Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 823 ILE Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 75 ARG Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 343 CYS Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 590 ILE Chi-restraints excluded: chain B residue 637 VAL Chi-restraints excluded: chain B residue 773 VAL Chi-restraints excluded: chain B residue 777 SER Chi-restraints excluded: chain B residue 793 LEU Chi-restraints excluded: chain B residue 959 VAL Chi-restraints excluded: chain B residue 973 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 403 VAL Chi-restraints excluded: chain C residue 433 HIS Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 656 SER Chi-restraints excluded: chain C residue 718 GLU Chi-restraints excluded: chain C residue 719 ILE Chi-restraints excluded: chain C residue 722 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 31 optimal weight: 0.0170 chunk 84 optimal weight: 0.9990 chunk 127 optimal weight: 0.5980 chunk 218 optimal weight: 3.9990 chunk 247 optimal weight: 0.9980 chunk 220 optimal weight: 0.0970 chunk 22 optimal weight: 0.9990 chunk 165 optimal weight: 3.9990 chunk 90 optimal weight: 5.9990 chunk 213 optimal weight: 2.9990 chunk 190 optimal weight: 3.9990 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 576 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.160231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.131301 restraints weight = 23299.542| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 1.95 r_work: 0.3121 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 19997 Z= 0.105 Angle : 0.505 8.983 27287 Z= 0.258 Chirality : 0.040 0.147 3077 Planarity : 0.005 0.066 3547 Dihedral : 6.754 73.944 2874 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.36 % Favored : 95.32 % Rotamer: Outliers : 2.85 % Allowed : 21.18 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.84 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.17), residues: 2500 helix: 1.61 (0.16), residues: 1085 sheet: -0.29 (0.25), residues: 427 loop : -1.53 (0.20), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 325 TYR 0.011 0.001 TYR C 212 PHE 0.026 0.001 PHE A 149 TRP 0.014 0.001 TRP C 8 HIS 0.003 0.000 HIS C 279 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.10 (19990) covalent geometry : angle 0.50504 / 0.26 (27284) hydrogen bonds : bond 0.03217 / 2.13 ( 901) hydrogen bonds : angle 4.05289 / 2.84 ( 2583) metal coordination : bond 0.00191 / 0.11 ( 7) metal coordination : angle 0.71142 / 0.45 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4688.84 seconds wall clock time: 80 minutes 55.62 seconds (4855.62 seconds total)