Starting phenix.real_space_refine on Fri Mar 6 05:05:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6yj6_10817/03_2026/6yj6_10817_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6yj6_10817/03_2026/6yj6_10817.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6yj6_10817/03_2026/6yj6_10817_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6yj6_10817/03_2026/6yj6_10817_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6yj6_10817/03_2026/6yj6_10817.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6yj6_10817/03_2026/6yj6_10817.map" } resolution = 3.1 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1963 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 50 5.16 5 C 8677 2.51 5 N 2279 2.21 5 O 2519 1.98 5 H 13353 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26878 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 13550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 819, 13550 Classifications: {'peptide': 819} Link IDs: {'PTRANS': 16, 'TRANS': 802} Chain breaks: 3 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 7927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 7927 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 32, 'TRANS': 453} Chain breaks: 2 Chain: "B" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 110 Classifications: {'peptide': 22} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'TRANS': 21} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'UNK:plan-1': 22} Unresolved non-hydrogen planarities: 22 Chain: "C" Number of atoms: 5291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 5291 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 22, 'TRANS': 307} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 4.25, per 1000 atoms: 0.16 Number of scatterers: 26878 At special positions: 0 Unit cell: (118.674, 140.535, 117.633, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 50 16.00 O 2519 8.00 N 2279 7.00 C 8677 6.00 H 13353 1.00 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: 2.05 Conformation dependent library (CDL) restraints added in 809.0 milliseconds 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3188 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 7 sheets defined 56.7% alpha, 8.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 131 through 140 removed outlier: 4.186A pdb=" N GLU A 137 " --> pdb=" O SER A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 158 removed outlier: 3.713A pdb=" N PHE A 151 " --> pdb=" O ALA A 147 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS A 156 " --> pdb=" O ASN A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 176 removed outlier: 3.534A pdb=" N TYR A 165 " --> pdb=" O ASN A 161 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TYR A 172 " --> pdb=" O LEU A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 190 removed outlier: 3.853A pdb=" N ASN A 183 " --> pdb=" O ASN A 179 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N HIS A 190 " --> pdb=" O PHE A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 209 removed outlier: 3.659A pdb=" N LYS A 200 " --> pdb=" O TRP A 196 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE A 201 " --> pdb=" O GLU A 197 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU A 205 " --> pdb=" O ILE A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 226 removed outlier: 3.710A pdb=" N TYR A 217 " --> pdb=" O ARG A 213 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N CYS A 218 " --> pdb=" O GLN A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 244 removed outlier: 3.583A pdb=" N LYS A 242 " --> pdb=" O MET A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 259 removed outlier: 3.695A pdb=" N ALA A 249 " --> pdb=" O GLN A 245 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ARG A 255 " --> pdb=" O ASP A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 277 removed outlier: 3.661A pdb=" N ILE A 272 " --> pdb=" O ARG A 268 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU A 273 " --> pdb=" O GLU A 269 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR A 274 " --> pdb=" O LEU A 270 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL A 275 " --> pdb=" O ALA A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 304 removed outlier: 3.586A pdb=" N GLU A 285 " --> pdb=" O GLU A 281 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU A 286 " --> pdb=" O ASP A 282 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS A 289 " --> pdb=" O GLU A 285 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL A 290 " --> pdb=" O LEU A 286 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA A 293 " --> pdb=" O LYS A 289 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU A 296 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 348 removed outlier: 3.564A pdb=" N ALA A 348 " --> pdb=" O LYS A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 371 removed outlier: 3.674A pdb=" N PHE A 367 " --> pdb=" O LEU A 363 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU A 368 " --> pdb=" O ALA A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 388 removed outlier: 3.582A pdb=" N THR A 380 " --> pdb=" O ASP A 376 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE A 388 " --> pdb=" O CYS A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 399 Processing helix chain 'A' and resid 407 through 413 removed outlier: 3.677A pdb=" N ARG A 410 " --> pdb=" O ASP A 407 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N PHE A 411 " --> pdb=" O ASN A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 419 Processing helix chain 'A' and resid 431 through 445 removed outlier: 4.081A pdb=" N ARG A 437 " --> pdb=" O ASP A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 456 Processing helix chain 'A' and resid 457 through 460 removed outlier: 3.814A pdb=" N ASP A 460 " --> pdb=" O CYS A 457 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 457 through 460' Processing helix chain 'A' and resid 466 through 480 removed outlier: 3.573A pdb=" N PHE A 471 " --> pdb=" O ALA A 467 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU A 472 " --> pdb=" O ASP A 468 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA A 476 " --> pdb=" O GLU A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 491 removed outlier: 4.073A pdb=" N ILE A 487 " --> pdb=" O TYR A 483 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ASP A 488 " --> pdb=" O LYS A 484 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N PHE A 489 " --> pdb=" O GLU A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 496 Processing helix chain 'A' and resid 501 through 515 Proline residue: A 507 - end of helix removed outlier: 3.571A pdb=" N ARG A 510 " --> pdb=" O LYS A 506 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N CYS A 511 " --> pdb=" O PRO A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 529 removed outlier: 4.366A pdb=" N GLU A 523 " --> pdb=" O GLU A 519 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N PHE A 524 " --> pdb=" O THR A 520 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA A 528 " --> pdb=" O PHE A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 549 removed outlier: 3.700A pdb=" N TYR A 546 " --> pdb=" O LEU A 542 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR A 547 " --> pdb=" O ALA A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 571 removed outlier: 3.595A pdb=" N PHE A 555 " --> pdb=" O ASP A 551 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N HIS A 557 " --> pdb=" O GLU A 553 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASP A 561 " --> pdb=" O HIS A 557 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLN A 569 " --> pdb=" O MET A 565 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASP A 571 " --> pdb=" O LYS A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 637 removed outlier: 4.213A pdb=" N ARG A 617 " --> pdb=" O ALA A 613 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE A 618 " --> pdb=" O GLU A 614 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU A 619 " --> pdb=" O ARG A 615 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG A 620 " --> pdb=" O GLU A 616 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ARG A 623 " --> pdb=" O GLU A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 665 removed outlier: 3.658A pdb=" N SER A 651 " --> pdb=" O ALA A 647 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR A 656 " --> pdb=" O ILE A 652 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N LEU A 660 " --> pdb=" O THR A 656 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N ILE A 663 " --> pdb=" O GLU A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 668 No H-bonds generated for 'chain 'A' and resid 666 through 668' Processing helix chain 'A' and resid 676 through 684 removed outlier: 3.718A pdb=" N ILE A 682 " --> pdb=" O LYS A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 687 No H-bonds generated for 'chain 'A' and resid 685 through 687' Processing helix chain 'A' and resid 691 through 701 removed outlier: 3.789A pdb=" N GLN A 696 " --> pdb=" O GLU A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 735 through 749 Processing helix chain 'A' and resid 751 through 763 removed outlier: 3.786A pdb=" N GLY A 755 " --> pdb=" O SER A 751 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N SER A 757 " --> pdb=" O GLU A 753 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL A 758 " --> pdb=" O ASP A 754 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL A 759 " --> pdb=" O GLY A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 774 through 787 Processing helix chain 'A' and resid 791 through 806 removed outlier: 4.153A pdb=" N LEU A 795 " --> pdb=" O ASP A 791 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA A 796 " --> pdb=" O GLU A 792 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N GLU A 797 " --> pdb=" O GLU A 793 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLN A 805 " --> pdb=" O GLY A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 820 removed outlier: 3.515A pdb=" N LEU A 813 " --> pdb=" O ASN A 809 " (cutoff:3.500A) Processing helix chain 'A' and resid 823 through 831 removed outlier: 3.995A pdb=" N ILE A 829 " --> pdb=" O SER A 825 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 852 removed outlier: 3.633A pdb=" N LEU A 840 " --> pdb=" O GLN A 836 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP A 847 " --> pdb=" O LEU A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 876 through 887 Processing helix chain 'A' and resid 890 through 903 removed outlier: 3.807A pdb=" N LEU A 895 " --> pdb=" O PHE A 891 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR A 897 " --> pdb=" O SER A 893 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ARG A 900 " --> pdb=" O GLN A 896 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 924 removed outlier: 3.528A pdb=" N ASN A 912 " --> pdb=" O ASP A 908 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET A 924 " --> pdb=" O ILE A 920 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 953 removed outlier: 4.335A pdb=" N PHE A 933 " --> pdb=" O ALA A 929 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG A 940 " --> pdb=" O PHE A 936 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N TYR A 941 " --> pdb=" O HIS A 937 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR A 945 " --> pdb=" O TYR A 941 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TYR A 953 " --> pdb=" O ARG A 949 " (cutoff:3.500A) Processing helix chain 'A' and resid 956 through 972 removed outlier: 3.502A pdb=" N GLU A 960 " --> pdb=" O LEU A 956 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ASP A 962 " --> pdb=" O LYS A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 974 through 988 removed outlier: 4.125A pdb=" N GLU A 980 " --> pdb=" O SER A 976 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG A 984 " --> pdb=" O GLU A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 1009 removed outlier: 3.524A pdb=" N ILE A1004 " --> pdb=" O TYR A1000 " (cutoff:3.500A) Processing helix chain 'A' and resid 1011 through 1022 removed outlier: 4.367A pdb=" N HIS A1017 " --> pdb=" O GLU A1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 59 removed outlier: 3.517A pdb=" N GLN B 53 " --> pdb=" O HIS B 49 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N CYS B 59 " --> pdb=" O ALA B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 70 removed outlier: 3.821A pdb=" N GLU B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA B 68 " --> pdb=" O LYS B 64 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE B 69 " --> pdb=" O VAL B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 130 removed outlier: 4.242A pdb=" N ASN B 130 " --> pdb=" O SER B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 140 removed outlier: 3.965A pdb=" N LYS B 138 " --> pdb=" O LYS B 134 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU B 140 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 181 Processing helix chain 'B' and resid 187 through 196 removed outlier: 4.317A pdb=" N SER B 193 " --> pdb=" O ASN B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 212 removed outlier: 4.191A pdb=" N ASN B 211 " --> pdb=" O ASN B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 299 removed outlier: 3.507A pdb=" N TYR B 291 " --> pdb=" O GLU B 287 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYS B 298 " --> pdb=" O GLU B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 309 Processing helix chain 'B' and resid 310 through 329 removed outlier: 3.722A pdb=" N GLU B 317 " --> pdb=" O GLU B 313 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ILE B 321 " --> pdb=" O GLU B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 338 Processing helix chain 'B' and resid 348 through 353 Processing helix chain 'B' and resid 375 through 383 removed outlier: 3.982A pdb=" N SER B 379 " --> pdb=" O PRO B 376 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N VAL B 380 " --> pdb=" O ARG B 377 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N GLU B 381 " --> pdb=" O SER B 378 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N TYR B 382 " --> pdb=" O SER B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 406 removed outlier: 3.834A pdb=" N ASN B 405 " --> pdb=" O ILE B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 445 removed outlier: 3.776A pdb=" N ILE B 445 " --> pdb=" O ILE B 441 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 441 through 445' Processing helix chain 'B' and resid 447 through 455 Processing helix chain 'B' and resid 471 through 491 removed outlier: 3.625A pdb=" N LEU B 475 " --> pdb=" O LYS B 471 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE B 478 " --> pdb=" O ASP B 474 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE B 481 " --> pdb=" O LYS B 477 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN B 491 " --> pdb=" O GLY B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 506 removed outlier: 3.558A pdb=" N LEU B 501 " --> pdb=" O ASN B 497 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE B 504 " --> pdb=" O LYS B 500 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N LYS B 505 " --> pdb=" O LEU B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 585 removed outlier: 3.585A pdb=" N ASN B 579 " --> pdb=" O ALA B 575 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N MET B 582 " --> pdb=" O GLU B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 1008 through 1015 removed outlier: 3.548A pdb=" N UNK B1014 " --> pdb=" O UNK B1010 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N UNK B1015 " --> pdb=" O UNK B1011 " (cutoff:3.500A) Processing helix chain 'B' and resid 1018 through 1026 removed outlier: 3.526A pdb=" N UNK B1023 " --> pdb=" O UNK B1019 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 52 Processing helix chain 'C' and resid 66 through 81 Proline residue: C 75 - end of helix Processing helix chain 'C' and resid 88 through 91 Processing helix chain 'C' and resid 107 through 115 removed outlier: 3.541A pdb=" N LEU C 111 " --> pdb=" O GLY C 107 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS C 113 " --> pdb=" O GLU C 109 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N PHE C 114 " --> pdb=" O ILE C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 158 removed outlier: 3.586A pdb=" N MET C 141 " --> pdb=" O GLN C 137 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N TRP C 147 " --> pdb=" O PHE C 143 " (cutoff:3.500A) Proline residue: C 148 - end of helix removed outlier: 3.748A pdb=" N LYS C 156 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU C 157 " --> pdb=" O ARG C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 182 removed outlier: 3.554A pdb=" N GLY C 177 " --> pdb=" O LYS C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 234 removed outlier: 3.500A pdb=" N ASP C 233 " --> pdb=" O PRO C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 260 removed outlier: 3.701A pdb=" N VAL C 260 " --> pdb=" O PHE C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 354 Processing sheet with id=AA1, first strand: chain 'B' and resid 29 through 30 removed outlier: 3.550A pdb=" N ARG C 334 " --> pdb=" O ILE C 331 " (cutoff:3.500A) removed outlier: 12.487A pdb=" N THR C 293 " --> pdb=" O TYR C 421 " (cutoff:3.500A) removed outlier: 9.234A pdb=" N ILE C 423 " --> pdb=" O THR C 293 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N TYR C 295 " --> pdb=" O ILE C 423 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N GLU C 425 " --> pdb=" O TYR C 295 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N SER B 152 " --> pdb=" O ILE B 116 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N LYS B 118 " --> pdb=" O PRO B 150 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N THR B 120 " --> pdb=" O VAL B 148 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N VAL B 148 " --> pdb=" O THR B 120 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LYS B 159 " --> pdb=" O LYS B 106 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYS B 106 " --> pdb=" O LYS B 159 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 29 through 30 removed outlier: 3.550A pdb=" N ARG C 334 " --> pdb=" O ILE C 331 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N SER B 38 " --> pdb=" O ASP B 155 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N THR B 157 " --> pdb=" O SER B 38 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N GLU B 40 " --> pdb=" O THR B 157 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N LYS B 159 " --> pdb=" O GLU B 40 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LYS B 159 " --> pdb=" O LYS B 106 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYS B 106 " --> pdb=" O LYS B 159 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 264 through 266 Processing sheet with id=AA4, first strand: chain 'B' and resid 271 through 272 Processing sheet with id=AA5, first strand: chain 'B' and resid 387 through 388 Processing sheet with id=AA6, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AA7, first strand: chain 'C' and resid 84 through 86 removed outlier: 6.408A pdb=" N ALA C 61 " --> pdb=" O TYR C 85 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL C 167 " --> pdb=" O PHE C 62 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N THR C 5 " --> pdb=" O ILE C 164 " (cutoff:3.500A) removed outlier: 8.372A pdb=" N LEU C 166 " --> pdb=" O THR C 5 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N TYR C 7 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N THR C 168 " --> pdb=" O TYR C 7 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ALA C 9 " --> pdb=" O THR C 168 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE C 8 " --> pdb=" O ASP C 205 " (cutoff:3.500A) 567 hydrogen bonds defined for protein. 1602 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.44 Time building geometry restraints manager: 2.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 13337 1.03 - 1.22: 21 1.22 - 1.42: 5848 1.42 - 1.61: 7885 1.61 - 1.81: 84 Bond restraints: 27175 Sorted by residual: bond pdb=" CA LYS C 359 " pdb=" C LYS C 359 " ideal model delta sigma weight residual 1.524 1.422 0.102 1.30e-02 5.92e+03 6.17e+01 bond pdb=" N HIS C 357 " pdb=" CA HIS C 357 " ideal model delta sigma weight residual 1.468 1.410 0.058 1.24e-02 6.50e+03 2.21e+01 bond pdb=" CA HIS C 357 " pdb=" CB HIS C 357 " ideal model delta sigma weight residual 1.530 1.482 0.048 1.24e-02 6.50e+03 1.50e+01 bond pdb=" NZ LYS C 359 " pdb=" HZ2 LYS C 359 " ideal model delta sigma weight residual 0.890 0.961 -0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" NZ LYS C 358 " pdb=" HZ3 LYS C 358 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.24e+01 ... (remaining 27170 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 48406 2.36 - 4.72: 613 4.72 - 7.08: 59 7.08 - 9.45: 3 9.45 - 11.81: 2 Bond angle restraints: 49083 Sorted by residual: angle pdb=" N LYS C 359 " pdb=" CA LYS C 359 " pdb=" C LYS C 359 " ideal model delta sigma weight residual 109.25 98.38 10.87 1.53e+00 4.27e-01 5.04e+01 angle pdb=" N LYS C 358 " pdb=" CA LYS C 358 " pdb=" C LYS C 358 " ideal model delta sigma weight residual 110.80 122.61 -11.81 2.13e+00 2.20e-01 3.07e+01 angle pdb=" N ALA A 859 " pdb=" CA ALA A 859 " pdb=" CB ALA A 859 " ideal model delta sigma weight residual 114.17 108.66 5.51 1.14e+00 7.69e-01 2.34e+01 angle pdb=" N VAL A 765 " pdb=" CA VAL A 765 " pdb=" CB VAL A 765 " ideal model delta sigma weight residual 112.21 107.06 5.15 1.10e+00 8.26e-01 2.19e+01 angle pdb=" N HIS C 357 " pdb=" CA HIS C 357 " pdb=" CB HIS C 357 " ideal model delta sigma weight residual 110.39 103.25 7.14 1.54e+00 4.22e-01 2.15e+01 ... (remaining 49078 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.94: 11527 13.94 - 27.87: 908 27.87 - 41.81: 256 41.81 - 55.75: 59 55.75 - 69.69: 20 Dihedral angle restraints: 12770 sinusoidal: 6894 harmonic: 5876 Sorted by residual: dihedral pdb=" CA ARG A 141 " pdb=" C ARG A 141 " pdb=" N ASN A 142 " pdb=" CA ASN A 142 " ideal model delta harmonic sigma weight residual -180.00 -145.34 -34.66 0 5.00e+00 4.00e-02 4.81e+01 dihedral pdb=" CA GLU B 76 " pdb=" C GLU B 76 " pdb=" N SER B 77 " pdb=" CA SER B 77 " ideal model delta harmonic sigma weight residual 180.00 146.17 33.83 0 5.00e+00 4.00e-02 4.58e+01 dihedral pdb=" CA GLU C 192 " pdb=" C GLU C 192 " pdb=" N ASN C 193 " pdb=" CA ASN C 193 " ideal model delta harmonic sigma weight residual -180.00 -153.80 -26.20 0 5.00e+00 4.00e-02 2.75e+01 ... (remaining 12767 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.126: 2003 0.126 - 0.253: 33 0.253 - 0.379: 0 0.379 - 0.506: 0 0.506 - 0.632: 1 Chirality restraints: 2037 Sorted by residual: chirality pdb=" CA LYS C 358 " pdb=" N LYS C 358 " pdb=" C LYS C 358 " pdb=" CB LYS C 358 " both_signs ideal model delta sigma weight residual False 2.51 1.88 0.63 2.00e-01 2.50e+01 1.00e+01 chirality pdb=" CA ILE A 388 " pdb=" N ILE A 388 " pdb=" C ILE A 388 " pdb=" CB ILE A 388 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.19 2.00e-01 2.50e+01 9.37e-01 chirality pdb=" CG LEU A 441 " pdb=" CB LEU A 441 " pdb=" CD1 LEU A 441 " pdb=" CD2 LEU A 441 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 8.41e-01 ... (remaining 2034 not shown) Planarity restraints: 3948 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL C 356 " 0.018 2.00e-02 2.50e+03 3.85e-02 1.49e+01 pdb=" C VAL C 356 " -0.067 2.00e-02 2.50e+03 pdb=" O VAL C 356 " 0.026 2.00e-02 2.50e+03 pdb=" N HIS C 357 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 141 " -0.015 2.00e-02 2.50e+03 3.06e-02 9.38e+00 pdb=" C ARG A 141 " 0.053 2.00e-02 2.50e+03 pdb=" O ARG A 141 " -0.020 2.00e-02 2.50e+03 pdb=" N ASN A 142 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 358 " -0.011 2.00e-02 2.50e+03 2.27e-02 5.16e+00 pdb=" C LYS C 358 " 0.039 2.00e-02 2.50e+03 pdb=" O LYS C 358 " -0.015 2.00e-02 2.50e+03 pdb=" N LYS C 359 " -0.013 2.00e-02 2.50e+03 ... (remaining 3945 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.24: 2541 2.24 - 2.83: 60823 2.83 - 3.42: 67698 3.42 - 4.01: 94205 4.01 - 4.60: 148397 Nonbonded interactions: 373664 Sorted by model distance: nonbonded pdb=" OE1 GLU C 87 " pdb=" HE1 TRP C 123 " model vdw 1.651 2.450 nonbonded pdb=" O ASP A 276 " pdb=" H THR C 360 " model vdw 1.674 2.450 nonbonded pdb=" H ASN B 267 " pdb=" O GLN B 586 " model vdw 1.681 2.450 nonbonded pdb=" O LYS A 993 " pdb="HD22 ASN B 86 " model vdw 1.712 2.450 nonbonded pdb=" HE ARG A 967 " pdb=" O SER B 164 " model vdw 1.712 2.450 ... (remaining 373659 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.130 Extract box with map and model: 0.300 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 23.690 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.102 13822 Z= 0.327 Angle : 0.847 11.807 18677 Z= 0.477 Chirality : 0.049 0.632 2037 Planarity : 0.005 0.046 2394 Dihedral : 9.596 69.687 5209 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.15 % Favored : 94.73 % Rotamer: Outliers : 0.07 % Allowed : 2.77 % Favored : 97.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -4.59 (0.17), residues: 1613 helix: -3.86 (0.11), residues: 803 sheet: -2.03 (0.46), residues: 107 loop : -1.96 (0.23), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.002 ARG B 366 TYR 0.035 0.003 TYR B 97 PHE 0.023 0.003 PHE A 219 TRP 0.016 0.002 TRP A 387 HIS 0.018 0.003 HIS B 336 Details of bonding type rmsd covalent geometry : bond 0.00786 (13822) covalent geometry : angle 0.84726 (18677) hydrogen bonds : bond 0.30273 ( 550) hydrogen bonds : angle 9.65162 ( 1602) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 360 is missing expected H atoms. Skipping. Evaluate side-chains 258 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 257 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 ASP cc_start: 0.8046 (t0) cc_final: 0.7325 (m-30) REVERT: A 537 ASP cc_start: 0.7697 (m-30) cc_final: 0.7457 (m-30) REVERT: A 550 ASN cc_start: 0.7873 (m110) cc_final: 0.7585 (t0) REVERT: A 551 ASP cc_start: 0.7456 (t70) cc_final: 0.6836 (t0) REVERT: A 553 GLU cc_start: 0.7651 (mp0) cc_final: 0.7345 (mp0) REVERT: A 634 LYS cc_start: 0.8287 (mtpm) cc_final: 0.8029 (pttt) REVERT: A 652 ILE cc_start: 0.8564 (tt) cc_final: 0.8336 (pt) REVERT: A 684 ARG cc_start: 0.6718 (mtm180) cc_final: 0.6393 (mtp85) REVERT: A 698 GLU cc_start: 0.6311 (mp0) cc_final: 0.5954 (mp0) REVERT: B 58 MET cc_start: 0.7655 (mtt) cc_final: 0.7436 (mtt) REVERT: B 585 ASP cc_start: 0.7534 (m-30) cc_final: 0.7222 (m-30) REVERT: C 56 ASN cc_start: 0.6609 (p0) cc_final: 0.6366 (p0) outliers start: 1 outliers final: 1 residues processed: 258 average time/residue: 0.3439 time to fit residues: 119.9852 Evaluate side-chains 127 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 126 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 360 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 98 optimal weight: 0.4980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 ASN A 175 GLN A 294 ASN A 361 ASN A 408 ASN A 770 GLN A 997 HIS A1011 ASN B 129 ASN B 131 ASN B 144 ASN B 449 ASN B 464 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.135637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.109007 restraints weight = 50362.749| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.32 r_work: 0.3238 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13822 Z= 0.154 Angle : 0.599 6.356 18677 Z= 0.324 Chirality : 0.041 0.171 2037 Planarity : 0.004 0.044 2394 Dihedral : 5.500 30.961 1820 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 0.74 % Allowed : 6.70 % Favored : 92.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.88 (0.19), residues: 1613 helix: -1.96 (0.15), residues: 835 sheet: -1.67 (0.45), residues: 116 loop : -1.66 (0.24), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 949 TYR 0.019 0.001 TYR B 436 PHE 0.012 0.001 PHE A 839 TRP 0.010 0.001 TRP B 365 HIS 0.010 0.002 HIS B 336 Details of bonding type rmsd covalent geometry : bond 0.00350 (13822) covalent geometry : angle 0.59913 (18677) hydrogen bonds : bond 0.05305 ( 550) hydrogen bonds : angle 4.96341 ( 1602) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 360 is missing expected H atoms. Skipping. Evaluate side-chains 161 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 150 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 ASP cc_start: 0.8566 (t0) cc_final: 0.7556 (m-30) REVERT: A 255 ARG cc_start: 0.7589 (ptm160) cc_final: 0.7263 (mtm-85) REVERT: A 281 GLU cc_start: 0.8351 (mp0) cc_final: 0.8119 (mp0) REVERT: A 551 ASP cc_start: 0.7672 (t70) cc_final: 0.7343 (p0) REVERT: A 634 LYS cc_start: 0.8388 (mtpm) cc_final: 0.7844 (ttpp) REVERT: A 652 ILE cc_start: 0.8708 (tt) cc_final: 0.8464 (pt) REVERT: A 684 ARG cc_start: 0.6631 (mtm180) cc_final: 0.6248 (mtp85) REVERT: B 58 MET cc_start: 0.8210 (mtt) cc_final: 0.7846 (mtt) REVERT: B 129 ASN cc_start: 0.7747 (OUTLIER) cc_final: 0.7505 (t0) REVERT: B 215 ASP cc_start: 0.7031 (t70) cc_final: 0.6684 (t0) REVERT: B 585 ASP cc_start: 0.7924 (m-30) cc_final: 0.7600 (m-30) outliers start: 11 outliers final: 6 residues processed: 160 average time/residue: 0.2505 time to fit residues: 60.5652 Evaluate side-chains 125 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 118 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 360 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 98 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 148 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 121 optimal weight: 1.9990 chunk 122 optimal weight: 0.4980 chunk 41 optimal weight: 6.9990 chunk 151 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 129 ASN B 131 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.133010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.105788 restraints weight = 50863.469| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.35 r_work: 0.3188 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13822 Z= 0.146 Angle : 0.543 6.003 18677 Z= 0.291 Chirality : 0.039 0.153 2037 Planarity : 0.004 0.034 2394 Dihedral : 5.122 27.098 1820 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 0.81 % Allowed : 7.51 % Favored : 91.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.99 (0.20), residues: 1613 helix: -1.03 (0.17), residues: 830 sheet: -1.51 (0.43), residues: 125 loop : -1.49 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 949 TYR 0.016 0.001 TYR B 436 PHE 0.015 0.001 PHE A 695 TRP 0.008 0.001 TRP B 365 HIS 0.007 0.001 HIS B 336 Details of bonding type rmsd covalent geometry : bond 0.00343 (13822) covalent geometry : angle 0.54302 (18677) hydrogen bonds : bond 0.04445 ( 550) hydrogen bonds : angle 4.40108 ( 1602) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 360 is missing expected H atoms. Skipping. Evaluate side-chains 137 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 125 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 ASP cc_start: 0.8577 (t0) cc_final: 0.7488 (m-30) REVERT: A 255 ARG cc_start: 0.7572 (ptm160) cc_final: 0.7318 (mtm-85) REVERT: A 362 ILE cc_start: 0.8033 (OUTLIER) cc_final: 0.7712 (mp) REVERT: A 551 ASP cc_start: 0.7706 (t70) cc_final: 0.7258 (p0) REVERT: A 634 LYS cc_start: 0.8368 (mtpm) cc_final: 0.7866 (ttpp) REVERT: A 652 ILE cc_start: 0.8753 (tt) cc_final: 0.8499 (pt) REVERT: A 684 ARG cc_start: 0.6638 (mtm180) cc_final: 0.6291 (mtp85) REVERT: A 943 TYR cc_start: 0.7914 (m-10) cc_final: 0.7632 (m-10) REVERT: A 1013 GLU cc_start: 0.8332 (mp0) cc_final: 0.8128 (mp0) REVERT: B 129 ASN cc_start: 0.7652 (OUTLIER) cc_final: 0.7369 (t0) REVERT: B 215 ASP cc_start: 0.7060 (t70) cc_final: 0.6811 (t0) REVERT: C 56 ASN cc_start: 0.7472 (p0) cc_final: 0.7238 (p0) outliers start: 12 outliers final: 8 residues processed: 135 average time/residue: 0.2432 time to fit residues: 50.0788 Evaluate side-chains 123 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 113 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 927 LEU Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 328 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 1 optimal weight: 6.9990 chunk 34 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 154 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 chunk 131 optimal weight: 1.9990 chunk 148 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 GLN B 49 HIS B 131 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.131464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.103988 restraints weight = 51039.971| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.36 r_work: 0.3164 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 13822 Z= 0.149 Angle : 0.530 6.667 18677 Z= 0.284 Chirality : 0.039 0.146 2037 Planarity : 0.003 0.035 2394 Dihedral : 4.924 23.983 1819 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 0.88 % Allowed : 7.85 % Favored : 91.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.20), residues: 1613 helix: -0.61 (0.18), residues: 827 sheet: -1.43 (0.42), residues: 125 loop : -1.43 (0.24), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 949 TYR 0.014 0.001 TYR B 436 PHE 0.014 0.001 PHE A 769 TRP 0.008 0.001 TRP B 365 HIS 0.006 0.001 HIS B 336 Details of bonding type rmsd covalent geometry : bond 0.00352 (13822) covalent geometry : angle 0.52994 (18677) hydrogen bonds : bond 0.03915 ( 550) hydrogen bonds : angle 4.17423 ( 1602) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 360 is missing expected H atoms. Skipping. Evaluate side-chains 138 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 125 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 ASP cc_start: 0.8563 (t0) cc_final: 0.7406 (m-30) REVERT: A 255 ARG cc_start: 0.7525 (ptm160) cc_final: 0.7287 (mtm-85) REVERT: A 634 LYS cc_start: 0.8357 (mtpm) cc_final: 0.7844 (ttpp) REVERT: A 684 ARG cc_start: 0.6703 (mtm180) cc_final: 0.6269 (mtp85) REVERT: A 943 TYR cc_start: 0.8185 (m-10) cc_final: 0.7834 (m-10) REVERT: A 1016 ASP cc_start: 0.7934 (m-30) cc_final: 0.7590 (m-30) REVERT: B 187 GLU cc_start: 0.8157 (tp30) cc_final: 0.7816 (tt0) REVERT: B 215 ASP cc_start: 0.6962 (t70) cc_final: 0.6724 (t0) REVERT: C 56 ASN cc_start: 0.7425 (p0) cc_final: 0.7165 (p0) outliers start: 13 outliers final: 9 residues processed: 135 average time/residue: 0.2601 time to fit residues: 52.7333 Evaluate side-chains 123 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 114 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 GLN Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 927 LEU Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 141 MET Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 360 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 155 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 162 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 138 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 chunk 160 optimal weight: 3.9990 chunk 158 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 156 optimal weight: 0.5980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 669 ASN ** A 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.128058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.100297 restraints weight = 51883.380| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.37 r_work: 0.3111 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.3500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 13822 Z= 0.197 Angle : 0.558 7.778 18677 Z= 0.298 Chirality : 0.041 0.151 2037 Planarity : 0.004 0.052 2394 Dihedral : 4.923 24.742 1819 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 0.74 % Allowed : 8.73 % Favored : 90.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.20), residues: 1613 helix: -0.52 (0.18), residues: 838 sheet: -1.37 (0.42), residues: 125 loop : -1.39 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 622 TYR 0.017 0.001 TYR B 97 PHE 0.017 0.001 PHE A 253 TRP 0.008 0.001 TRP B 435 HIS 0.007 0.001 HIS B 336 Details of bonding type rmsd covalent geometry : bond 0.00477 (13822) covalent geometry : angle 0.55826 (18677) hydrogen bonds : bond 0.04044 ( 550) hydrogen bonds : angle 4.13860 ( 1602) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 360 is missing expected H atoms. Skipping. Evaluate side-chains 139 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 128 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 ASP cc_start: 0.8551 (t0) cc_final: 0.7330 (m-30) REVERT: A 255 ARG cc_start: 0.7706 (ptm160) cc_final: 0.7248 (ptp-170) REVERT: A 634 LYS cc_start: 0.8440 (mtpm) cc_final: 0.7866 (ttpp) REVERT: A 684 ARG cc_start: 0.6813 (mtm180) cc_final: 0.6356 (mtp85) REVERT: A 861 ILE cc_start: 0.8153 (mm) cc_final: 0.7922 (mm) REVERT: A 1016 ASP cc_start: 0.7912 (m-30) cc_final: 0.7596 (m-30) REVERT: B 215 ASP cc_start: 0.6986 (t70) cc_final: 0.6719 (t0) REVERT: C 56 ASN cc_start: 0.7462 (p0) cc_final: 0.7175 (p0) outliers start: 11 outliers final: 8 residues processed: 135 average time/residue: 0.2673 time to fit residues: 53.5832 Evaluate side-chains 119 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 111 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 927 LEU Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 360 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 144 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 36 optimal weight: 0.9990 chunk 114 optimal weight: 0.9990 chunk 140 optimal weight: 5.9990 chunk 128 optimal weight: 0.6980 chunk 32 optimal weight: 0.4980 chunk 61 optimal weight: 1.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 405 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.129421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.101517 restraints weight = 51914.514| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.39 r_work: 0.3131 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.3717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13822 Z= 0.135 Angle : 0.505 5.486 18677 Z= 0.269 Chirality : 0.039 0.144 2037 Planarity : 0.003 0.038 2394 Dihedral : 4.704 22.331 1819 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 0.81 % Allowed : 9.00 % Favored : 90.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.21), residues: 1613 helix: -0.19 (0.18), residues: 840 sheet: -1.36 (0.42), residues: 125 loop : -1.24 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 949 TYR 0.015 0.001 TYR B 436 PHE 0.014 0.001 PHE A 769 TRP 0.007 0.001 TRP B 365 HIS 0.005 0.001 HIS B 336 Details of bonding type rmsd covalent geometry : bond 0.00316 (13822) covalent geometry : angle 0.50459 (18677) hydrogen bonds : bond 0.03512 ( 550) hydrogen bonds : angle 3.92917 ( 1602) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 360 is missing expected H atoms. Skipping. Evaluate side-chains 134 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 122 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 ASP cc_start: 0.8547 (t0) cc_final: 0.7297 (m-30) REVERT: A 255 ARG cc_start: 0.7517 (ptm160) cc_final: 0.7132 (mtm-85) REVERT: A 278 ASP cc_start: 0.8330 (OUTLIER) cc_final: 0.8062 (t0) REVERT: A 281 GLU cc_start: 0.8115 (mp0) cc_final: 0.7828 (mp0) REVERT: A 634 LYS cc_start: 0.8360 (mtpm) cc_final: 0.7810 (ttpp) REVERT: A 684 ARG cc_start: 0.6803 (mtm180) cc_final: 0.6333 (mtp85) REVERT: A 1016 ASP cc_start: 0.7923 (m-30) cc_final: 0.7604 (m-30) REVERT: B 215 ASP cc_start: 0.7229 (t70) cc_final: 0.6978 (t0) REVERT: C 56 ASN cc_start: 0.7434 (p0) cc_final: 0.7142 (p0) outliers start: 12 outliers final: 8 residues processed: 131 average time/residue: 0.2299 time to fit residues: 46.5778 Evaluate side-chains 120 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 111 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 766 ASN Chi-restraints excluded: chain A residue 927 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 360 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 69 optimal weight: 1.9990 chunk 122 optimal weight: 0.3980 chunk 73 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 137 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 128 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 chunk 116 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 357 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.129069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.101285 restraints weight = 51649.612| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.37 r_work: 0.3128 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.3880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13822 Z= 0.140 Angle : 0.505 5.425 18677 Z= 0.269 Chirality : 0.039 0.145 2037 Planarity : 0.003 0.036 2394 Dihedral : 4.606 22.325 1819 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 0.74 % Allowed : 9.61 % Favored : 89.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.21), residues: 1613 helix: -0.06 (0.18), residues: 848 sheet: -1.37 (0.42), residues: 125 loop : -1.19 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 622 TYR 0.013 0.001 TYR B 436 PHE 0.013 0.001 PHE A 769 TRP 0.007 0.001 TRP B 365 HIS 0.005 0.001 HIS B 336 Details of bonding type rmsd covalent geometry : bond 0.00334 (13822) covalent geometry : angle 0.50460 (18677) hydrogen bonds : bond 0.03506 ( 550) hydrogen bonds : angle 3.87365 ( 1602) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 360 is missing expected H atoms. Skipping. Evaluate side-chains 132 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 121 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 ASP cc_start: 0.8597 (t0) cc_final: 0.7341 (m-30) REVERT: A 255 ARG cc_start: 0.7523 (ptm160) cc_final: 0.7042 (mtm-85) REVERT: A 278 ASP cc_start: 0.8389 (OUTLIER) cc_final: 0.8150 (t0) REVERT: A 281 GLU cc_start: 0.8108 (mp0) cc_final: 0.7823 (mp0) REVERT: A 551 ASP cc_start: 0.7264 (t0) cc_final: 0.6838 (p0) REVERT: A 634 LYS cc_start: 0.8211 (mtpm) cc_final: 0.7652 (ttpp) REVERT: A 638 PHE cc_start: 0.5773 (t80) cc_final: 0.5568 (t80) REVERT: A 684 ARG cc_start: 0.6833 (mtm180) cc_final: 0.6319 (mtp85) REVERT: A 1016 ASP cc_start: 0.7932 (m-30) cc_final: 0.7596 (m-30) REVERT: B 215 ASP cc_start: 0.7206 (t70) cc_final: 0.7002 (t0) REVERT: C 56 ASN cc_start: 0.7421 (p0) cc_final: 0.7106 (p0) outliers start: 11 outliers final: 8 residues processed: 129 average time/residue: 0.2251 time to fit residues: 44.5836 Evaluate side-chains 120 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 111 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 927 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 571 GLU Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 360 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 116 optimal weight: 0.0370 chunk 100 optimal weight: 0.0470 chunk 15 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 113 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 124 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 160 optimal weight: 3.9990 chunk 123 optimal weight: 0.9980 overall best weight: 0.5356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.130086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.102216 restraints weight = 51878.947| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.39 r_work: 0.3148 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.3975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 13822 Z= 0.105 Angle : 0.481 5.347 18677 Z= 0.256 Chirality : 0.038 0.140 2037 Planarity : 0.003 0.036 2394 Dihedral : 4.448 20.480 1819 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.61 % Allowed : 9.95 % Favored : 89.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.21), residues: 1613 helix: 0.21 (0.18), residues: 847 sheet: -1.33 (0.43), residues: 125 loop : -1.07 (0.25), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 35 TYR 0.013 0.001 TYR B 436 PHE 0.019 0.001 PHE A 695 TRP 0.007 0.001 TRP B 365 HIS 0.003 0.001 HIS B 336 Details of bonding type rmsd covalent geometry : bond 0.00244 (13822) covalent geometry : angle 0.48100 (18677) hydrogen bonds : bond 0.03204 ( 550) hydrogen bonds : angle 3.75507 ( 1602) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 360 is missing expected H atoms. Skipping. Evaluate side-chains 128 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 119 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 ASP cc_start: 0.8581 (t0) cc_final: 0.7323 (m-30) REVERT: A 255 ARG cc_start: 0.7513 (ptm160) cc_final: 0.7041 (mtm-85) REVERT: A 278 ASP cc_start: 0.8356 (OUTLIER) cc_final: 0.8139 (t0) REVERT: A 281 GLU cc_start: 0.8162 (mp0) cc_final: 0.7904 (mp0) REVERT: A 551 ASP cc_start: 0.7209 (t0) cc_final: 0.6849 (p0) REVERT: A 634 LYS cc_start: 0.8149 (mtpm) cc_final: 0.7641 (ttpp) REVERT: A 1016 ASP cc_start: 0.7964 (m-30) cc_final: 0.7635 (m-30) REVERT: C 56 ASN cc_start: 0.7376 (p0) cc_final: 0.7028 (p0) outliers start: 9 outliers final: 7 residues processed: 125 average time/residue: 0.2312 time to fit residues: 45.0270 Evaluate side-chains 124 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 116 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 927 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 571 GLU Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 360 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 155 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 84 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 160 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 138 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 117 optimal weight: 0.2980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.129975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.102099 restraints weight = 51840.169| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.39 r_work: 0.3157 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.4076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13822 Z= 0.119 Angle : 0.485 5.188 18677 Z= 0.258 Chirality : 0.038 0.146 2037 Planarity : 0.003 0.036 2394 Dihedral : 4.394 20.439 1819 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 0.54 % Allowed : 10.08 % Favored : 89.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.64 (0.21), residues: 1613 helix: 0.29 (0.18), residues: 855 sheet: -1.28 (0.43), residues: 125 loop : -1.12 (0.24), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 684 TYR 0.012 0.001 TYR B 436 PHE 0.019 0.001 PHE A 695 TRP 0.007 0.001 TRP B 365 HIS 0.004 0.001 HIS B 336 Details of bonding type rmsd covalent geometry : bond 0.00281 (13822) covalent geometry : angle 0.48546 (18677) hydrogen bonds : bond 0.03246 ( 550) hydrogen bonds : angle 3.72941 ( 1602) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 360 is missing expected H atoms. Skipping. Evaluate side-chains 130 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 122 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 ASP cc_start: 0.8597 (t0) cc_final: 0.8341 (t0) REVERT: A 255 ARG cc_start: 0.7512 (ptm160) cc_final: 0.7022 (mtm-85) REVERT: A 281 GLU cc_start: 0.8130 (mp0) cc_final: 0.7860 (mp0) REVERT: A 551 ASP cc_start: 0.7196 (t0) cc_final: 0.6849 (p0) REVERT: A 634 LYS cc_start: 0.8152 (mtpm) cc_final: 0.7647 (ttpp) REVERT: A 668 LYS cc_start: 0.7392 (tptt) cc_final: 0.6881 (tttp) REVERT: A 1016 ASP cc_start: 0.7957 (m-30) cc_final: 0.7618 (m-30) REVERT: C 56 ASN cc_start: 0.7372 (p0) cc_final: 0.7012 (p0) REVERT: C 132 LYS cc_start: 0.9004 (mmmm) cc_final: 0.8133 (tptp) outliers start: 8 outliers final: 7 residues processed: 128 average time/residue: 0.2534 time to fit residues: 48.9573 Evaluate side-chains 126 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 119 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 927 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 571 GLU Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 360 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 40 optimal weight: 0.0670 chunk 128 optimal weight: 1.9990 chunk 163 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 111 optimal weight: 0.9990 chunk 147 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 143 optimal weight: 0.6980 chunk 22 optimal weight: 0.0980 overall best weight: 0.5720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.130744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.102853 restraints weight = 51605.277| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.39 r_work: 0.3170 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.4170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 13822 Z= 0.106 Angle : 0.474 5.126 18677 Z= 0.251 Chirality : 0.038 0.138 2037 Planarity : 0.003 0.035 2394 Dihedral : 4.288 20.525 1819 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.54 % Allowed : 10.15 % Favored : 89.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.21), residues: 1613 helix: 0.47 (0.19), residues: 854 sheet: -1.23 (0.44), residues: 125 loop : -1.05 (0.25), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 684 TYR 0.013 0.001 TYR B 436 PHE 0.018 0.001 PHE A 695 TRP 0.007 0.001 TRP A 230 HIS 0.004 0.001 HIS B 336 Details of bonding type rmsd covalent geometry : bond 0.00250 (13822) covalent geometry : angle 0.47374 (18677) hydrogen bonds : bond 0.03101 ( 550) hydrogen bonds : angle 3.67212 ( 1602) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 360 is missing expected H atoms. Skipping. Evaluate side-chains 136 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 128 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 ARG cc_start: 0.7512 (ptm160) cc_final: 0.7021 (mtm-85) REVERT: A 281 GLU cc_start: 0.8142 (mp0) cc_final: 0.7744 (mp0) REVERT: A 551 ASP cc_start: 0.7188 (t0) cc_final: 0.6887 (p0) REVERT: A 634 LYS cc_start: 0.8091 (mtpm) cc_final: 0.7595 (ttpp) REVERT: A 668 LYS cc_start: 0.7317 (tptt) cc_final: 0.6834 (tttp) REVERT: A 1016 ASP cc_start: 0.7966 (m-30) cc_final: 0.7617 (m-30) REVERT: C 56 ASN cc_start: 0.7339 (p0) cc_final: 0.6973 (p0) REVERT: C 132 LYS cc_start: 0.9009 (mmmm) cc_final: 0.8140 (tptp) outliers start: 8 outliers final: 8 residues processed: 134 average time/residue: 0.2813 time to fit residues: 55.3970 Evaluate side-chains 127 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 119 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 927 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 571 GLU Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 360 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 147 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 130 optimal weight: 10.0000 chunk 113 optimal weight: 1.9990 chunk 152 optimal weight: 0.5980 chunk 117 optimal weight: 0.4980 chunk 75 optimal weight: 0.7980 chunk 153 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.130000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.102090 restraints weight = 51696.389| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.38 r_work: 0.3158 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.4257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 13822 Z= 0.125 Angle : 0.485 5.144 18677 Z= 0.257 Chirality : 0.038 0.143 2037 Planarity : 0.003 0.034 2394 Dihedral : 4.294 20.519 1819 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 0.54 % Allowed : 10.22 % Favored : 89.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.21), residues: 1613 helix: 0.48 (0.18), residues: 854 sheet: -1.23 (0.44), residues: 125 loop : -1.06 (0.25), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 684 TYR 0.012 0.001 TYR B 436 PHE 0.018 0.001 PHE A 695 TRP 0.007 0.001 TRP B 365 HIS 0.005 0.001 HIS B 336 Details of bonding type rmsd covalent geometry : bond 0.00296 (13822) covalent geometry : angle 0.48487 (18677) hydrogen bonds : bond 0.03227 ( 550) hydrogen bonds : angle 3.70193 ( 1602) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7322.00 seconds wall clock time: 124 minutes 34.62 seconds (7474.62 seconds total)