Starting phenix.real_space_refine on Sat Sep 12 18:29:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7bvf_30218/09_2026/7bvf_30218.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bvf_30218/09_2026/7bvf_30218.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7bvf_30218/09_2026/7bvf_30218.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7bvf_30218/09_2026/7bvf_30218.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7bvf_30218/09_2026/7bvf_30218.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bvf_30218/09_2026/7bvf_30218.map" model { file = "/net/cci-nas-00/data/ceres_data/7bvf_30218/09_2026/7bvf_30218.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bvf_30218/09_2026/7bvf_30218.cif" } resolution = 2.97 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= -0.001 sd= 0.069 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 Ca 1 9.91 5 P 5 5.49 5 S 55 5.16 5 C 10982 2.51 5 N 2875 2.21 5 O 3015 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 85 residue(s): 0.39s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16933 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 7993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1054, 7993 Classifications: {'peptide': 1054} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 83, 'TRANS': 969} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "A" Number of atoms: 8128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1087, 8128 Classifications: {'peptide': 1087} Link IDs: {'PCIS': 2, 'PTRANS': 78, 'TRANS': 1006} Chain: "P" Number of atoms: 607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 607 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 3, 'TRANS': 76} Chain: "B" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 127 Unusual residues: {' CA': 1, '95E': 1, 'CDL': 1, 'DSL': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 41 Planarities with less than four sites: {'DSL:plan-3': 1, 'DSL:plan-4': 1} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 78 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 22 Time building chain proxies: 3.83, per 1000 atoms: 0.23 Number of scatterers: 16933 At special positions: 0 Unit cell: (132.02, 119.72, 121.36, 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) Ca 1 19.99 S 55 16.00 P 5 15.00 O 3015 8.00 N 2875 7.00 C 10982 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: 1.45 Conformation dependent library (CDL) restraints added in 755.0 milliseconds 4426 Ramachandran restraints generated. 2213 Oldfield, 0 Emsley, 2213 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4032 Finding SS restraints... Secondary structure from input PDB file: 86 helices and 22 sheets defined 42.2% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'B' and resid 24 through 40 removed outlier: 3.747A pdb=" N TRP B 28 " --> pdb=" O ARG B 24 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N VAL B 29 " --> pdb=" O GLY B 25 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ALA B 30 " --> pdb=" O THR B 26 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR B 31 " --> pdb=" O ARG B 27 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N GLY B 34 " --> pdb=" O ALA B 30 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLY B 37 " --> pdb=" O ALA B 33 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 47 removed outlier: 3.853A pdb=" N LEU B 46 " --> pdb=" O ALA B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 90 removed outlier: 4.166A pdb=" N VAL B 88 " --> pdb=" O PRO B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 141 Processing helix chain 'B' and resid 215 through 240 removed outlier: 3.994A pdb=" N ALA B 221 " --> pdb=" O LEU B 217 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU B 233 " --> pdb=" O THR B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 294 removed outlier: 3.646A pdb=" N TRP B 290 " --> pdb=" O GLY B 286 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL B 292 " --> pdb=" O LEU B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 309 removed outlier: 3.742A pdb=" N ILE B 303 " --> pdb=" O ASP B 299 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL B 309 " --> pdb=" O GLY B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 341 removed outlier: 3.535A pdb=" N LEU B 337 " --> pdb=" O TYR B 333 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU B 339 " --> pdb=" O ASN B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 351 removed outlier: 3.768A pdb=" N ARG B 351 " --> pdb=" O SER B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 369 removed outlier: 3.746A pdb=" N GLY B 358 " --> pdb=" O ASP B 354 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG B 367 " --> pdb=" O LEU B 363 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL B 369 " --> pdb=" O LEU B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 373 removed outlier: 3.511A pdb=" N LEU B 373 " --> pdb=" O LEU B 370 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 370 through 373' Processing helix chain 'B' and resid 380 through 396 removed outlier: 3.691A pdb=" N TYR B 384 " --> pdb=" O SER B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 423 removed outlier: 3.677A pdb=" N LEU B 410 " --> pdb=" O GLY B 406 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU B 413 " --> pdb=" O ALA B 409 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR B 415 " --> pdb=" O GLY B 411 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N TYR B 416 " --> pdb=" O SER B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 443 removed outlier: 4.041A pdb=" N VAL B 435 " --> pdb=" O ALA B 431 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL B 436 " --> pdb=" O ALA B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 449 removed outlier: 3.532A pdb=" N LEU B 449 " --> pdb=" O PRO B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 458 removed outlier: 3.697A pdb=" N GLY B 458 " --> pdb=" O ALA B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 471 removed outlier: 3.585A pdb=" N ARG B 464 " --> pdb=" O ARG B 460 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ILE B 465 " --> pdb=" O PRO B 461 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG B 468 " --> pdb=" O ARG B 464 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG B 471 " --> pdb=" O VAL B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 480 removed outlier: 3.719A pdb=" N VAL B 479 " --> pdb=" O THR B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 485 Processing helix chain 'B' and resid 489 through 494 Processing helix chain 'B' and resid 498 through 512 Processing helix chain 'B' and resid 517 through 520 Processing helix chain 'B' and resid 521 through 527 removed outlier: 4.209A pdb=" N TYR B 525 " --> pdb=" O GLU B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 528 through 530 No H-bonds generated for 'chain 'B' and resid 528 through 530' Processing helix chain 'B' and resid 536 through 560 removed outlier: 4.143A pdb=" N PHE B 541 " --> pdb=" O LEU B 537 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N GLY B 542 " --> pdb=" O SER B 538 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N PHE B 543 " --> pdb=" O ARG B 539 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N THR B 546 " --> pdb=" O GLY B 542 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N CYS B 549 " --> pdb=" O ILE B 545 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL B 554 " --> pdb=" O LEU B 550 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N PHE B 555 " --> pdb=" O PHE B 551 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE B 556 " --> pdb=" O THR B 552 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG B 559 " --> pdb=" O PHE B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 585 removed outlier: 3.682A pdb=" N MET B 575 " --> pdb=" O ALA B 571 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE B 578 " --> pdb=" O LEU B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 601 removed outlier: 3.779A pdb=" N HIS B 595 " --> pdb=" O TRP B 592 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LEU B 598 " --> pdb=" O HIS B 595 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N PHE B 599 " --> pdb=" O PHE B 596 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA B 600 " --> pdb=" O GLY B 597 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ALA B 601 " --> pdb=" O LEU B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 614 removed outlier: 3.576A pdb=" N ALA B 608 " --> pdb=" O ALA B 604 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU B 609 " --> pdb=" O ALA B 605 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL B 612 " --> pdb=" O ALA B 608 " (cutoff:3.500A) Processing helix chain 'B' and resid 621 through 640 removed outlier: 3.587A pdb=" N ARG B 625 " --> pdb=" O TRP B 621 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 666 removed outlier: 3.891A pdb=" N GLY B 665 " --> pdb=" O LYS B 662 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 688 removed outlier: 3.726A pdb=" N ILE B 671 " --> pdb=" O THR B 667 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE B 688 " --> pdb=" O ALA B 684 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 702 Processing helix chain 'B' and resid 705 through 728 removed outlier: 4.052A pdb=" N ILE B 709 " --> pdb=" O ALA B 705 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N MET B 722 " --> pdb=" O PHE B 718 " (cutoff:3.500A) Processing helix chain 'B' and resid 734 through 742 removed outlier: 3.564A pdb=" N VAL B 740 " --> pdb=" O GLY B 736 " (cutoff:3.500A) Processing helix chain 'B' and resid 747 through 751 removed outlier: 3.693A pdb=" N ASP B 751 " --> pdb=" O GLY B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 812 through 816 Processing helix chain 'B' and resid 974 through 978 Processing helix chain 'B' and resid 1017 through 1024 Processing helix chain 'B' and resid 1024 through 1029 Processing helix chain 'B' and resid 1030 through 1034 removed outlier: 3.863A pdb=" N ASN B1033 " --> pdb=" O ASP B1030 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY B1034 " --> pdb=" O GLY B1031 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1030 through 1034' Processing helix chain 'B' and resid 1039 through 1044 removed outlier: 3.812A pdb=" N LEU B1043 " --> pdb=" O ILE B1039 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU B1044 " --> pdb=" O THR B1040 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1039 through 1044' Processing helix chain 'A' and resid 10 through 28 removed outlier: 3.905A pdb=" N ALA A 17 " --> pdb=" O ALA A 13 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL A 18 " --> pdb=" O ARG A 14 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N SER A 20 " --> pdb=" O ALA A 16 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLY A 21 " --> pdb=" O ALA A 17 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY A 24 " --> pdb=" O SER A 20 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N CYS A 28 " --> pdb=" O GLY A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 34 removed outlier: 3.552A pdb=" N LEU A 34 " --> pdb=" O VAL A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 80 Processing helix chain 'A' and resid 130 through 134 removed outlier: 3.618A pdb=" N ALA A 133 " --> pdb=" O THR A 130 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLY A 134 " --> pdb=" O ILE A 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 130 through 134' Processing helix chain 'A' and resid 155 through 159 removed outlier: 3.669A pdb=" N GLY A 158 " --> pdb=" O ILE A 155 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ALA A 159 " --> pdb=" O PRO A 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 155 through 159' Processing helix chain 'A' and resid 205 through 229 removed outlier: 4.481A pdb=" N VAL A 211 " --> pdb=" O MET A 207 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG A 229 " --> pdb=" O ASP A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 264 removed outlier: 3.943A pdb=" N ASP A 254 " --> pdb=" O SER A 250 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ALA A 255 " --> pdb=" O ARG A 251 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA A 256 " --> pdb=" O LEU A 252 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA A 259 " --> pdb=" O ALA A 255 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR A 260 " --> pdb=" O ALA A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 288 Proline residue: A 285 - end of helix removed outlier: 3.580A pdb=" N GLY A 288 " --> pdb=" O ALA A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 299 removed outlier: 3.753A pdb=" N GLY A 298 " --> pdb=" O ARG A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 318 removed outlier: 3.937A pdb=" N GLN A 313 " --> pdb=" O SER A 309 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ALA A 316 " --> pdb=" O ALA A 312 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N VAL A 317 " --> pdb=" O GLN A 313 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER A 318 " --> pdb=" O LEU A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 325 removed outlier: 3.515A pdb=" N MET A 324 " --> pdb=" O ALA A 320 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG A 325 " --> pdb=" O GLY A 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 320 through 325' Processing helix chain 'A' and resid 326 through 347 removed outlier: 3.988A pdb=" N GLY A 332 " --> pdb=" O ALA A 328 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N CYS A 335 " --> pdb=" O ALA A 331 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL A 339 " --> pdb=" O CYS A 335 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N LEU A 344 " --> pdb=" O SER A 340 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N ARG A 345 " --> pdb=" O ARG A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 373 removed outlier: 3.875A pdb=" N ALA A 364 " --> pdb=" O ALA A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 403 removed outlier: 3.738A pdb=" N LEU A 387 " --> pdb=" O PRO A 383 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU A 390 " --> pdb=" O ALA A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 419 removed outlier: 3.697A pdb=" N ILE A 412 " --> pdb=" O ALA A 408 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE A 413 " --> pdb=" O ALA A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 421 No H-bonds generated for 'chain 'A' and resid 420 through 421' Processing helix chain 'A' and resid 422 through 428 removed outlier: 4.130A pdb=" N LEU A 426 " --> pdb=" O PRO A 423 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ILE A 427 " --> pdb=" O GLN A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 435 Processing helix chain 'A' and resid 436 through 446 removed outlier: 3.645A pdb=" N ARG A 442 " --> pdb=" O ALA A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 462 removed outlier: 3.655A pdb=" N VAL A 458 " --> pdb=" O ALA A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 465 No H-bonds generated for 'chain 'A' and resid 463 through 465' Processing helix chain 'A' and resid 466 through 471 Processing helix chain 'A' and resid 475 through 489 Processing helix chain 'A' and resid 494 through 498 Processing helix chain 'A' and resid 510 through 514 removed outlier: 3.564A pdb=" N SER A 514 " --> pdb=" O VAL A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 537 removed outlier: 3.724A pdb=" N VAL A 521 " --> pdb=" O ARG A 517 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU A 524 " --> pdb=" O ALA A 520 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL A 531 " --> pdb=" O CYS A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 563 Processing helix chain 'A' and resid 564 through 566 No H-bonds generated for 'chain 'A' and resid 564 through 566' Processing helix chain 'A' and resid 571 through 576 removed outlier: 3.774A pdb=" N PHE A 574 " --> pdb=" O ALA A 571 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ALA A 576 " --> pdb=" O GLN A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 595 removed outlier: 3.675A pdb=" N GLY A 582 " --> pdb=" O ALA A 578 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N VAL A 583 " --> pdb=" O GLY A 579 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA A 593 " --> pdb=" O ALA A 589 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG A 594 " --> pdb=" O PHE A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 618 removed outlier: 3.578A pdb=" N VAL A 607 " --> pdb=" O LEU A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 668 removed outlier: 3.939A pdb=" N MET A 649 " --> pdb=" O PRO A 645 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU A 651 " --> pdb=" O THR A 647 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU A 653 " --> pdb=" O MET A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 686 removed outlier: 3.664A pdb=" N LEU A 685 " --> pdb=" O ASN A 682 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ALA A 686 " --> pdb=" O ARG A 683 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 682 through 686' Processing helix chain 'A' and resid 689 through 712 removed outlier: 3.672A pdb=" N VAL A 693 " --> pdb=" O PRO A 689 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER A 704 " --> pdb=" O GLY A 700 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N MET A 705 " --> pdb=" O GLU A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 727 removed outlier: 3.989A pdb=" N ASN A 722 " --> pdb=" O THR A 718 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N SER A 727 " --> pdb=" O LEU A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 837 removed outlier: 3.626A pdb=" N THR A 837 " --> pdb=" O PRO A 834 " (cutoff:3.500A) Processing helix chain 'A' and resid 967 through 971 Processing helix chain 'A' and resid 981 through 985 removed outlier: 4.113A pdb=" N ALA A 984 " --> pdb=" O ILE A 981 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ALA A 985 " --> pdb=" O ALA A 982 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 981 through 985' Processing helix chain 'A' and resid 1010 through 1017 removed outlier: 3.560A pdb=" N ALA A1016 " --> pdb=" O LYS A1012 " (cutoff:3.500A) Processing helix chain 'A' and resid 1017 through 1022 removed outlier: 3.724A pdb=" N GLN A1022 " --> pdb=" O SER A1018 " (cutoff:3.500A) Processing helix chain 'A' and resid 1028 through 1032 Processing helix chain 'P' and resid 11 through 21 removed outlier: 3.636A pdb=" N GLU P 17 " --> pdb=" O ALA P 13 " (cutoff:3.500A) Processing helix chain 'P' and resid 23 through 27 Processing helix chain 'P' and resid 40 through 55 removed outlier: 3.826A pdb=" N GLU P 52 " --> pdb=" O ALA P 48 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASP P 53 " --> pdb=" O VAL P 49 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LYS P 54 " --> pdb=" O GLN P 50 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TYR P 55 " --> pdb=" O THR P 51 " (cutoff:3.500A) Processing helix chain 'P' and resid 69 through 81 Processing sheet with id=AA1, first strand: chain 'B' and resid 78 through 81 removed outlier: 3.909A pdb=" N ASP B 78 " --> pdb=" O THR B 205 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N THR B 205 " --> pdb=" O ASP B 78 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 78 through 81 removed outlier: 3.909A pdb=" N ASP B 78 " --> pdb=" O THR B 205 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N THR B 205 " --> pdb=" O ASP B 78 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 122 through 126 Processing sheet with id=AA4, first strand: chain 'B' and resid 972 through 973 removed outlier: 4.696A pdb=" N ALA B1050 " --> pdb=" O GLU B 756 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 797 through 798 removed outlier: 4.566A pdb=" N VAL B 798 " --> pdb=" O ALA B 801 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ALA B 801 " --> pdb=" O VAL B 798 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 845 through 846 removed outlier: 5.449A pdb=" N VAL B 963 " --> pdb=" O ALA B 880 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N ALA B 880 " --> pdb=" O VAL B 963 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N THR B 878 " --> pdb=" O PRO B 965 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 858 through 859 Processing sheet with id=AA8, first strand: chain 'B' and resid 863 through 864 removed outlier: 3.930A pdb=" N ALA B 945 " --> pdb=" O ALA B 903 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 984 through 986 removed outlier: 3.702A pdb=" N THR B1015 " --> pdb=" O SER B1063 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 36 through 38 Processing sheet with id=AB2, first strand: chain 'A' and resid 42 through 45 removed outlier: 3.572A pdb=" N ALA A 187 " --> pdb=" O TRP A 45 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP A 71 " --> pdb=" O ARG A 188 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA A 69 " --> pdb=" O ASP A 190 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA A 148 " --> pdb=" O LEU A 162 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 58 through 59 Processing sheet with id=AB4, first strand: chain 'A' and resid 90 through 91 removed outlier: 3.755A pdb=" N LEU A 90 " --> pdb=" O VAL A 107 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 965 through 966 removed outlier: 4.253A pdb=" N ALA A1043 " --> pdb=" O GLU A 742 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 786 through 787 Processing sheet with id=AB7, first strand: chain 'A' and resid 850 through 853 removed outlier: 3.506A pdb=" N SER A 891 " --> pdb=" O TYR A 944 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 857 through 858 Processing sheet with id=AB9, first strand: chain 'A' and resid 868 through 873 Processing sheet with id=AC1, first strand: chain 'A' and resid 879 through 880 removed outlier: 3.547A pdb=" N SER A 879 " --> pdb=" O ILE A 887 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 896 through 899 removed outlier: 3.634A pdb=" N TRP A 896 " --> pdb=" O LEU A 908 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU A 908 " --> pdb=" O TRP A 896 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 991 through 992 removed outlier: 8.409A pdb=" N ILE A1007 " --> pdb=" O PRO A 976 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LEU A 978 " --> pdb=" O ILE A1007 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 995 through 996 584 hydrogen bonds defined for protein. 1626 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: 3.19 Time building geometry restraints manager: 1.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.11 - 1.25: 2645 1.25 - 1.39: 4119 1.39 - 1.53: 9487 1.53 - 1.67: 1024 1.67 - 1.81: 96 Bond restraints: 17371 Sorted by residual: bond pdb=" C ILE A 43 " pdb=" O ILE A 43 " ideal model delta sigma weight residual 1.237 1.119 0.118 1.08e-02 8.57e+03 1.20e+02 bond pdb=" CA7 CDL A1101 " pdb=" OA8 CDL A1101 " ideal model delta sigma weight residual 1.334 1.452 -0.118 1.10e-02 8.26e+03 1.14e+02 bond pdb=" OB3 CDL A1101 " pdb=" PB2 CDL A1101 " ideal model delta sigma weight residual 1.529 1.424 0.105 1.00e-02 1.00e+04 1.10e+02 bond pdb=" CB7 CDL A1101 " pdb=" OB8 CDL A1101 " ideal model delta sigma weight residual 1.334 1.437 -0.103 1.10e-02 8.26e+03 8.71e+01 bond pdb=" CA5 CDL B1404 " pdb=" OA6 CDL B1404 " ideal model delta sigma weight residual 1.342 1.469 -0.127 1.50e-02 4.44e+03 7.14e+01 ... (remaining 17366 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.46: 23579 4.46 - 8.92: 154 8.92 - 13.38: 26 13.38 - 17.84: 3 17.84 - 22.30: 3 Bond angle restraints: 23765 Sorted by residual: angle pdb=" C51 CDL A1101 " pdb=" CB5 CDL A1101 " pdb=" OB6 CDL A1101 " ideal model delta sigma weight residual 111.33 126.56 -15.23 1.32e+00 5.72e-01 1.33e+02 angle pdb=" OB6 CDL A1101 " pdb=" CB5 CDL A1101 " pdb=" OB7 CDL A1101 " ideal model delta sigma weight residual 123.92 113.83 10.09 1.00e+00 9.92e-01 1.01e+02 angle pdb=" N PRO B 59 " pdb=" CA PRO B 59 " pdb=" C PRO B 59 " ideal model delta sigma weight residual 112.47 132.28 -19.81 2.06e+00 2.36e-01 9.25e+01 angle pdb=" C11 CDL B1404 " pdb=" CA5 CDL B1404 " pdb=" OA6 CDL B1404 " ideal model delta sigma weight residual 111.33 123.83 -12.50 1.32e+00 5.72e-01 8.94e+01 angle pdb=" O TRP A 45 " pdb=" C TRP A 45 " pdb=" N PRO A 46 " ideal model delta sigma weight residual 121.83 114.86 6.97 7.80e-01 1.64e+00 7.99e+01 ... (remaining 23760 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.30: 9738 25.30 - 50.60: 424 50.60 - 75.90: 33 75.90 - 101.20: 4 101.20 - 126.51: 1 Dihedral angle restraints: 10200 sinusoidal: 3894 harmonic: 6306 Sorted by residual: dihedral pdb=" CA TRP B 58 " pdb=" C TRP B 58 " pdb=" N PRO B 59 " pdb=" CA PRO B 59 " ideal model delta harmonic sigma weight residual -180.00 -53.49 -126.51 0 5.00e+00 4.00e-02 6.40e+02 dihedral pdb=" C PRO B 59 " pdb=" N PRO B 59 " pdb=" CA PRO B 59 " pdb=" CB PRO B 59 " ideal model delta harmonic sigma weight residual -120.70 -141.90 21.20 0 2.50e+00 1.60e-01 7.19e+01 dihedral pdb=" C THR B 732 " pdb=" N THR B 732 " pdb=" CA THR B 732 " pdb=" CB THR B 732 " ideal model delta harmonic sigma weight residual -122.00 -141.68 19.68 0 2.50e+00 1.60e-01 6.20e+01 ... (remaining 10197 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.234: 2743 0.234 - 0.468: 6 0.468 - 0.702: 1 0.702 - 0.937: 0 0.937 - 1.171: 1 Chirality restraints: 2751 Sorted by residual: chirality pdb=" CA PRO B 59 " pdb=" N PRO B 59 " pdb=" C PRO B 59 " pdb=" CB PRO B 59 " both_signs ideal model delta sigma weight residual False 2.72 1.55 1.17 2.00e-01 2.50e+01 3.43e+01 chirality pdb=" CA THR B 732 " pdb=" N THR B 732 " pdb=" C THR B 732 " pdb=" CB THR B 732 " both_signs ideal model delta sigma weight residual False 2.53 1.87 0.66 2.00e-01 2.50e+01 1.09e+01 chirality pdb=" CA TYR B 730 " pdb=" N TYR B 730 " pdb=" C TYR B 730 " pdb=" CB TYR B 730 " both_signs ideal model delta sigma weight residual False 2.51 2.92 -0.41 2.00e-01 2.50e+01 4.11e+00 ... (remaining 2748 not shown) Planarity restraints: 3018 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 56 " -0.024 2.00e-02 2.50e+03 4.76e-02 2.26e+01 pdb=" C LEU B 56 " 0.082 2.00e-02 2.50e+03 pdb=" O LEU B 56 " -0.031 2.00e-02 2.50e+03 pdb=" N ASP B 57 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 730 " 0.048 2.00e-02 2.50e+03 2.82e-02 1.59e+01 pdb=" CG TYR B 730 " -0.001 2.00e-02 2.50e+03 pdb=" CD1 TYR B 730 " -0.038 2.00e-02 2.50e+03 pdb=" CD2 TYR B 730 " -0.029 2.00e-02 2.50e+03 pdb=" CE1 TYR B 730 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR B 730 " -0.018 2.00e-02 2.50e+03 pdb=" CZ TYR B 730 " 0.014 2.00e-02 2.50e+03 pdb=" OH TYR B 730 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO B 731 " -0.016 2.00e-02 2.50e+03 3.44e-02 1.18e+01 pdb=" C PRO B 731 " 0.059 2.00e-02 2.50e+03 pdb=" O PRO B 731 " -0.023 2.00e-02 2.50e+03 pdb=" N THR B 732 " -0.020 2.00e-02 2.50e+03 ... (remaining 3015 not shown) Histogram of nonbonded interaction distances: 1.41 - 2.11: 3 2.11 - 2.81: 4875 2.81 - 3.50: 20748 3.50 - 4.20: 37585 4.20 - 4.90: 69996 Nonbonded interactions: 133207 Sorted by model distance: nonbonded pdb=" C LEU B 56 " pdb=" OD1 ASP B 57 " model vdw 1.409 3.270 nonbonded pdb=" O LEU B 56 " pdb=" OD1 ASP B 57 " model vdw 1.728 3.040 nonbonded pdb=" N ASP B 57 " pdb=" OD1 ASP B 57 " model vdw 2.075 3.120 nonbonded pdb=" OH TYR B 302 " pdb=" OD1 ASN B 318 " model vdw 2.184 3.040 nonbonded pdb=" NH1 ARG A 119 " pdb=" O LYS A 167 " model vdw 2.213 3.120 ... (remaining 133202 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: 4.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.070 Find NCS groups from input model: 0.120 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:8.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 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 : 0.007 0.127 17371 Z= 0.386 Angle : 0.979 22.302 23765 Z= 0.539 Chirality : 0.057 1.171 2751 Planarity : 0.006 0.074 3018 Dihedral : 13.597 126.506 6168 Min Nonbonded Distance : 1.409 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.18 % Allowed : 12.70 % Favored : 87.12 % Rotamer: Outliers : 0.12 % Allowed : 4.96 % Favored : 94.93 % Cbeta Deviations : 0.30 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 1.80 % 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: -4.65 (0.15), residues: 2213 helix: -2.01 (0.16), residues: 802 sheet: -3.52 (0.28), residues: 249 loop : -3.91 (0.14), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 691 TYR 0.048 0.002 TYR B 730 PHE 0.019 0.001 PHE A 954 TRP 0.025 0.002 TRP B 58 HIS 0.003 0.001 HIS B1047 Details of bonding type rmsd/Z covalent geometry : bond 0.00686 / 0.39 (17371) covalent geometry : angle 0.97949 / 0.54 (23765) hydrogen bonds : bond 0.14928 / 10.13 ( 580) hydrogen bonds : angle 5.68492 / 3.82 ( 1626) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4426 Ramachandran restraints generated. 2213 Oldfield, 0 Emsley, 2213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4426 Ramachandran restraints generated. 2213 Oldfield, 0 Emsley, 2213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 201 time to evaluate : 0.607 Fit side-chains revert: symmetry clash REVERT: B 57 ASP cc_start: 0.7581 (OUTLIER) cc_final: 0.6738 (p0) REVERT: B 124 ASP cc_start: 0.7616 (p0) cc_final: 0.7352 (p0) REVERT: A 120 ASP cc_start: 0.6813 (p0) cc_final: 0.6579 (p0) REVERT: P 14 GLU cc_start: 0.7136 (tp30) cc_final: 0.6934 (tp30) outliers start: 2 outliers final: 1 residues processed: 203 average time/residue: 0.6668 time to fit residues: 149.7818 Evaluate side-chains 162 residues out of total 1737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 160 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 ASP Chi-restraints excluded: chain B residue 59 PRO Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 5.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 7.9990 chunk 200 optimal weight: 0.0030 chunk 212 optimal weight: 7.9990 overall best weight: 1.1796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 129 ASN B 241 GLN B 296 ASN B 470 HIS B 784 ASN B 791 ASN B1077 GLN A 111 GLN A 265 HIS A 377 ASN A 441 GLN A 598 HIS A 990 GLN A1004 GLN P 5 GLN P 78 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.126488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.104723 restraints weight = 21416.988| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 1.59 r_work: 0.3066 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8898 moved from start: 0.0983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 17371 Z= 0.152 Angle : 0.663 13.042 23765 Z= 0.337 Chirality : 0.045 0.203 2751 Planarity : 0.006 0.159 3018 Dihedral : 8.261 57.650 2529 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.12 % Favored : 88.75 % Rotamer: Outliers : 1.73 % Allowed : 10.20 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 1.20 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.61 (0.16), residues: 2213 helix: -1.06 (0.18), residues: 799 sheet: -2.99 (0.30), residues: 243 loop : -3.36 (0.15), residues: 1171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 173 TYR 0.010 0.001 TYR A 626 PHE 0.012 0.001 PHE A 954 TRP 0.043 0.001 TRP B 58 HIS 0.002 0.001 HIS A 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.15 (17371) covalent geometry : angle 0.66327 / 0.34 (23765) hydrogen bonds : bond 0.04219 / 2.88 ( 580) hydrogen bonds : angle 4.38511 / 2.96 ( 1626) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4426 Ramachandran restraints generated. 2213 Oldfield, 0 Emsley, 2213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4426 Ramachandran restraints generated. 2213 Oldfield, 0 Emsley, 2213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 184 time to evaluate : 0.651 Fit side-chains REVERT: B 124 ASP cc_start: 0.8119 (p0) cc_final: 0.7861 (p0) REVERT: B 464 ARG cc_start: 0.8286 (mtm-85) cc_final: 0.7865 (ttm-80) REVERT: B 695 GLU cc_start: 0.6998 (mm-30) cc_final: 0.6761 (mm-30) REVERT: A 11 ARG cc_start: 0.7138 (mtm110) cc_final: 0.6627 (mpt180) REVERT: A 667 ARG cc_start: 0.7647 (tpp80) cc_final: 0.7165 (tpp80) outliers start: 30 outliers final: 13 residues processed: 199 average time/residue: 0.5748 time to fit residues: 128.9445 Evaluate side-chains 171 residues out of total 1737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 158 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain B residue 889 LEU Chi-restraints excluded: chain B residue 939 MET Chi-restraints excluded: chain B residue 1019 SER Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 784 ASP Chi-restraints excluded: chain A residue 908 LEU Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain P residue 55 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 53 optimal weight: 0.9990 chunk 181 optimal weight: 0.9980 chunk 116 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 127 optimal weight: 3.9990 chunk 173 optimal weight: 0.7980 chunk 57 optimal weight: 0.0670 chunk 10 optimal weight: 0.6980 chunk 187 optimal weight: 0.5980 chunk 167 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 47 GLN A 441 GLN ** A 890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 919 GLN ** A1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.130385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.108579 restraints weight = 21579.936| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 1.60 r_work: 0.3116 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 17371 Z= 0.111 Angle : 0.601 13.715 23765 Z= 0.301 Chirality : 0.043 0.200 2751 Planarity : 0.006 0.159 3018 Dihedral : 7.494 58.376 2524 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.76 % Favored : 90.10 % Rotamer: Outliers : 2.25 % Allowed : 11.87 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 1.20 % 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: -2.96 (0.17), residues: 2213 helix: -0.51 (0.19), residues: 797 sheet: -2.47 (0.31), residues: 233 loop : -3.02 (0.16), residues: 1183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 468 TYR 0.010 0.001 TYR B 425 PHE 0.008 0.001 PHE B 713 TRP 0.018 0.001 TRP B 58 HIS 0.002 0.000 HIS A 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 (17371) covalent geometry : angle 0.60099 / 0.30 (23765) hydrogen bonds : bond 0.03212 / 2.20 ( 580) hydrogen bonds : angle 3.99719 / 2.70 ( 1626) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4426 Ramachandran restraints generated. 2213 Oldfield, 0 Emsley, 2213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4426 Ramachandran restraints generated. 2213 Oldfield, 0 Emsley, 2213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 188 time to evaluate : 0.506 Fit side-chains REVERT: B 464 ARG cc_start: 0.8293 (mtm-85) cc_final: 0.7929 (ttm-80) REVERT: B 471 ARG cc_start: 0.8041 (OUTLIER) cc_final: 0.7682 (mtp180) REVERT: A 11 ARG cc_start: 0.7139 (mtm110) cc_final: 0.6618 (mpt180) REVERT: A 667 ARG cc_start: 0.7601 (tpp80) cc_final: 0.7019 (tpp80) REVERT: A 681 ARG cc_start: 0.7404 (ttp80) cc_final: 0.7001 (ttt180) outliers start: 39 outliers final: 14 residues processed: 208 average time/residue: 0.5541 time to fit residues: 130.4179 Evaluate side-chains 185 residues out of total 1737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 170 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 471 ARG Chi-restraints excluded: chain B residue 822 THR Chi-restraints excluded: chain B residue 939 MET Chi-restraints excluded: chain B residue 980 SER Chi-restraints excluded: chain B residue 1019 SER Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 47 GLN Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 749 MET Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 1056 SER Chi-restraints excluded: chain P residue 55 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 190 optimal weight: 2.9990 chunk 207 optimal weight: 0.7980 chunk 163 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 126 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 114 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 198 optimal weight: 3.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 47 GLN A 441 GLN A 890 GLN ** A1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.129133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.107202 restraints weight = 21548.421| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 1.59 r_work: 0.3092 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8852 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 17371 Z= 0.130 Angle : 0.623 13.955 23765 Z= 0.313 Chirality : 0.044 0.214 2751 Planarity : 0.006 0.161 3018 Dihedral : 7.238 59.806 2524 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.53 % Favored : 89.34 % Rotamer: Outliers : 2.42 % Allowed : 14.41 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 1.20 % 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: -2.68 (0.17), residues: 2213 helix: -0.33 (0.19), residues: 800 sheet: -2.19 (0.32), residues: 233 loop : -2.84 (0.16), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 173 TYR 0.009 0.001 TYR A 626 PHE 0.011 0.001 PHE A 954 TRP 0.016 0.001 TRP A1054 HIS 0.002 0.001 HIS A 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.13 (17371) covalent geometry : angle 0.62293 / 0.31 (23765) hydrogen bonds : bond 0.03504 / 2.40 ( 580) hydrogen bonds : angle 3.95953 / 2.68 ( 1626) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4426 Ramachandran restraints generated. 2213 Oldfield, 0 Emsley, 2213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4426 Ramachandran restraints generated. 2213 Oldfield, 0 Emsley, 2213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 178 time to evaluate : 0.609 Fit side-chains REVERT: B 89 ARG cc_start: 0.8081 (ttm-80) cc_final: 0.7826 (ttm-80) REVERT: B 464 ARG cc_start: 0.8314 (mtm-85) cc_final: 0.7937 (ttm-80) REVERT: B 471 ARG cc_start: 0.8064 (OUTLIER) cc_final: 0.7713 (mtp180) REVERT: B 695 GLU cc_start: 0.6850 (mm-30) cc_final: 0.6599 (mm-30) REVERT: A 11 ARG cc_start: 0.7154 (mtm110) cc_final: 0.6638 (mpt180) REVERT: A 85 ASN cc_start: 0.8304 (OUTLIER) cc_final: 0.8094 (p0) REVERT: A 667 ARG cc_start: 0.7625 (tpp80) cc_final: 0.7045 (tpp80) REVERT: A 681 ARG cc_start: 0.7437 (ttp80) cc_final: 0.6982 (ttt180) REVERT: A 738 ASP cc_start: 0.7352 (OUTLIER) cc_final: 0.7116 (m-30) REVERT: A 781 LEU cc_start: 0.7861 (OUTLIER) cc_final: 0.7655 (mt) outliers start: 42 outliers final: 20 residues processed: 202 average time/residue: 0.5457 time to fit residues: 124.9353 Evaluate side-chains 189 residues out of total 1737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 165 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 471 ARG Chi-restraints excluded: chain B residue 649 VAL Chi-restraints excluded: chain B residue 822 THR Chi-restraints excluded: chain B residue 939 MET Chi-restraints excluded: chain B residue 1019 SER Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 738 ASP Chi-restraints excluded: chain A residue 749 MET Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 1056 SER Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain P residue 50 GLN Chi-restraints excluded: chain P residue 55 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 32 optimal weight: 0.9990 chunk 164 optimal weight: 0.6980 chunk 208 optimal weight: 2.9990 chunk 6 optimal weight: 0.0030 chunk 73 optimal weight: 0.8980 chunk 197 optimal weight: 0.0000 chunk 122 optimal weight: 6.9990 chunk 143 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 37 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 overall best weight: 0.4194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 60 GLN B 318 ASN A 441 GLN ** A1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 78 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.132973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.111408 restraints weight = 21275.140| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 1.56 r_work: 0.3156 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.080 17371 Z= 0.103 Angle : 0.582 13.526 23765 Z= 0.291 Chirality : 0.043 0.218 2751 Planarity : 0.006 0.162 3018 Dihedral : 6.771 58.071 2524 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.86 % Favored : 91.05 % Rotamer: Outliers : 2.36 % Allowed : 14.70 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 1.20 % 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: -2.32 (0.18), residues: 2213 helix: -0.03 (0.19), residues: 802 sheet: -1.94 (0.33), residues: 227 loop : -2.64 (0.17), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 173 TYR 0.016 0.001 TYR B 425 PHE 0.007 0.001 PHE B 688 TRP 0.014 0.001 TRP A1054 HIS 0.002 0.000 HIS A 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.10 (17371) covalent geometry : angle 0.58201 / 0.29 (23765) hydrogen bonds : bond 0.02788 / 1.92 ( 580) hydrogen bonds : angle 3.75520 / 2.53 ( 1626) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4426 Ramachandran restraints generated. 2213 Oldfield, 0 Emsley, 2213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4426 Ramachandran restraints generated. 2213 Oldfield, 0 Emsley, 2213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 192 time to evaluate : 0.642 Fit side-chains REVERT: B 89 ARG cc_start: 0.8012 (ttm-80) cc_final: 0.7770 (ttm-80) REVERT: B 327 GLU cc_start: 0.7269 (pt0) cc_final: 0.6975 (pt0) REVERT: B 464 ARG cc_start: 0.8345 (mtm-85) cc_final: 0.7916 (ttm-80) REVERT: B 471 ARG cc_start: 0.8028 (OUTLIER) cc_final: 0.7689 (mtp180) REVERT: B 635 LEU cc_start: 0.8534 (tt) cc_final: 0.8287 (tp) REVERT: A 11 ARG cc_start: 0.7141 (mtm110) cc_final: 0.6640 (mpt180) REVERT: A 667 ARG cc_start: 0.7560 (tpp80) cc_final: 0.6948 (tpp80) REVERT: A 681 ARG cc_start: 0.7381 (ttp80) cc_final: 0.7047 (ttt180) outliers start: 41 outliers final: 19 residues processed: 216 average time/residue: 0.5361 time to fit residues: 131.7394 Evaluate side-chains 190 residues out of total 1737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 170 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 471 ARG Chi-restraints excluded: chain B residue 649 VAL Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 822 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 939 MET Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 749 MET Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 783 SER Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain P residue 55 TYR Chi-restraints excluded: chain P residue 78 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 77 optimal weight: 0.0000 chunk 80 optimal weight: 0.0170 chunk 126 optimal weight: 3.9990 chunk 57 optimal weight: 0.2980 chunk 145 optimal weight: 0.6980 chunk 74 optimal weight: 0.8980 chunk 113 optimal weight: 0.9990 chunk 201 optimal weight: 0.0030 chunk 18 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 overall best weight: 0.2032 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 47 GLN A 182 GLN A 441 GLN A 803 ASN ** A1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.135916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.114148 restraints weight = 21257.016| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 1.60 r_work: 0.3186 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.081 17371 Z= 0.098 Angle : 0.575 13.199 23765 Z= 0.285 Chirality : 0.042 0.221 2751 Planarity : 0.006 0.162 3018 Dihedral : 6.330 58.541 2524 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.13 % Favored : 90.78 % Rotamer: Outliers : 1.90 % Allowed : 16.08 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 1.20 % 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: -1.95 (0.18), residues: 2213 helix: 0.27 (0.20), residues: 798 sheet: -1.64 (0.35), residues: 217 loop : -2.44 (0.17), residues: 1198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 173 TYR 0.009 0.001 TYR A 293 PHE 0.007 0.001 PHE A 886 TRP 0.012 0.001 TRP A1054 HIS 0.002 0.000 HIS A 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 (17371) covalent geometry : angle 0.57501 / 0.29 (23765) hydrogen bonds : bond 0.02535 / 1.75 ( 580) hydrogen bonds : angle 3.62579 / 2.45 ( 1626) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4426 Ramachandran restraints generated. 2213 Oldfield, 0 Emsley, 2213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4426 Ramachandran restraints generated. 2213 Oldfield, 0 Emsley, 2213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 188 time to evaluate : 0.608 Fit side-chains REVERT: B 89 ARG cc_start: 0.8025 (ttm-80) cc_final: 0.7788 (ttm-80) REVERT: B 464 ARG cc_start: 0.8290 (mtm-85) cc_final: 0.7981 (ttm-80) REVERT: B 471 ARG cc_start: 0.7976 (OUTLIER) cc_final: 0.7653 (mtp180) REVERT: B 482 MET cc_start: 0.8999 (OUTLIER) cc_final: 0.8243 (mtp) REVERT: B 635 LEU cc_start: 0.8551 (tt) cc_final: 0.8287 (tp) REVERT: B 920 ASP cc_start: 0.8311 (p0) cc_final: 0.8104 (p0) REVERT: A 11 ARG cc_start: 0.7257 (mtm110) cc_final: 0.6803 (mpt180) REVERT: A 499 PHE cc_start: 0.7411 (m-80) cc_final: 0.7070 (t80) REVERT: A 667 ARG cc_start: 0.7591 (tpp80) cc_final: 0.7004 (tpp80) REVERT: A 681 ARG cc_start: 0.7492 (ttp80) cc_final: 0.7274 (ttt180) REVERT: A 738 ASP cc_start: 0.7138 (OUTLIER) cc_final: 0.6913 (m-30) outliers start: 33 outliers final: 18 residues processed: 206 average time/residue: 0.5315 time to fit residues: 124.0910 Evaluate side-chains 194 residues out of total 1737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 173 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 471 ARG Chi-restraints excluded: chain B residue 482 MET Chi-restraints excluded: chain B residue 649 VAL Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 804 MET Chi-restraints excluded: chain B residue 822 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 939 MET Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 738 ASP Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 783 SER Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain P residue 55 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 52 optimal weight: 3.9990 chunk 47 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 72 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 177 optimal weight: 0.3980 chunk 167 optimal weight: 0.6980 chunk 144 optimal weight: 0.5980 chunk 169 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 931 ASN A 47 GLN A 182 GLN A 441 GLN ** A1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 78 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.133449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.111538 restraints weight = 21222.401| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 1.59 r_work: 0.3157 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 17371 Z= 0.109 Angle : 0.598 13.541 23765 Z= 0.296 Chirality : 0.043 0.231 2751 Planarity : 0.006 0.161 3018 Dihedral : 6.250 58.232 2524 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.22 % Favored : 90.74 % Rotamer: Outliers : 2.07 % Allowed : 16.25 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 1.20 % 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: -1.79 (0.18), residues: 2213 helix: 0.39 (0.19), residues: 802 sheet: -1.50 (0.36), residues: 217 loop : -2.35 (0.17), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 173 TYR 0.014 0.001 TYR B 425 PHE 0.011 0.001 PHE A 886 TRP 0.013 0.001 TRP A1054 HIS 0.002 0.000 HIS A 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 (17371) covalent geometry : angle 0.59773 / 0.30 (23765) hydrogen bonds : bond 0.02947 / 2.03 ( 580) hydrogen bonds : angle 3.64405 / 2.46 ( 1626) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4426 Ramachandran restraints generated. 2213 Oldfield, 0 Emsley, 2213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4426 Ramachandran restraints generated. 2213 Oldfield, 0 Emsley, 2213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 175 time to evaluate : 0.672 Fit side-chains REVERT: B 464 ARG cc_start: 0.8287 (mtm-85) cc_final: 0.7968 (ttm-80) REVERT: B 471 ARG cc_start: 0.8010 (OUTLIER) cc_final: 0.7679 (mtp180) REVERT: B 482 MET cc_start: 0.8973 (OUTLIER) cc_final: 0.8192 (mtp) REVERT: B 722 MET cc_start: 0.8627 (mmt) cc_final: 0.8389 (mmt) REVERT: B 920 ASP cc_start: 0.8345 (p0) cc_final: 0.8115 (p0) REVERT: A 11 ARG cc_start: 0.7243 (mtm110) cc_final: 0.6803 (mpt180) REVERT: A 499 PHE cc_start: 0.7459 (m-80) cc_final: 0.7180 (t80) REVERT: A 667 ARG cc_start: 0.7706 (tpp80) cc_final: 0.7120 (tpp80) REVERT: A 681 ARG cc_start: 0.7483 (ttp80) cc_final: 0.7242 (ttt180) REVERT: A 738 ASP cc_start: 0.7193 (OUTLIER) cc_final: 0.6969 (m-30) outliers start: 36 outliers final: 18 residues processed: 199 average time/residue: 0.5544 time to fit residues: 125.2639 Evaluate side-chains 189 residues out of total 1737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 168 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 471 ARG Chi-restraints excluded: chain B residue 482 MET Chi-restraints excluded: chain B residue 649 VAL Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 804 MET Chi-restraints excluded: chain B residue 822 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 939 MET Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 738 ASP Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 783 SER Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain P residue 55 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 157 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 175 optimal weight: 4.9990 chunk 104 optimal weight: 4.9990 chunk 4 optimal weight: 0.5980 chunk 34 optimal weight: 4.9990 chunk 68 optimal weight: 0.7980 chunk 79 optimal weight: 0.5980 chunk 191 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 182 GLN A 441 GLN P 78 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.129007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.106747 restraints weight = 21462.559| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 1.61 r_work: 0.3091 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8885 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 17371 Z= 0.148 Angle : 0.648 16.520 23765 Z= 0.322 Chirality : 0.045 0.237 2751 Planarity : 0.006 0.160 3018 Dihedral : 6.547 53.959 2524 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.44 % Favored : 89.52 % Rotamer: Outliers : 2.42 % Allowed : 15.97 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 1.20 % 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: -1.89 (0.18), residues: 2213 helix: 0.31 (0.19), residues: 801 sheet: -1.67 (0.35), residues: 224 loop : -2.38 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 173 TYR 0.010 0.001 TYR B 648 PHE 0.013 0.001 PHE A 954 TRP 0.014 0.001 TRP B 322 HIS 0.003 0.001 HIS B1047 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.15 (17371) covalent geometry : angle 0.64754 / 0.32 (23765) hydrogen bonds : bond 0.03787 / 2.59 ( 580) hydrogen bonds : angle 3.86715 / 2.62 ( 1626) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4426 Ramachandran restraints generated. 2213 Oldfield, 0 Emsley, 2213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4426 Ramachandran restraints generated. 2213 Oldfield, 0 Emsley, 2213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 169 time to evaluate : 0.614 Fit side-chains REVERT: B 89 ARG cc_start: 0.8085 (ttm-80) cc_final: 0.7885 (ttm-80) REVERT: B 464 ARG cc_start: 0.8323 (mtm-85) cc_final: 0.7996 (ttm-80) REVERT: B 470 HIS cc_start: 0.8175 (OUTLIER) cc_final: 0.7838 (t-90) REVERT: B 471 ARG cc_start: 0.8046 (OUTLIER) cc_final: 0.7728 (mtp180) REVERT: B 482 MET cc_start: 0.8974 (OUTLIER) cc_final: 0.8178 (mtp) REVERT: B 889 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8485 (pt) REVERT: A 11 ARG cc_start: 0.7231 (mtm110) cc_final: 0.6757 (mpt180) REVERT: A 99 ASP cc_start: 0.7584 (m-30) cc_final: 0.7240 (t0) REVERT: A 102 LYS cc_start: 0.8671 (ptpp) cc_final: 0.8133 (pttm) REVERT: A 254 ASP cc_start: 0.7817 (m-30) cc_final: 0.7598 (m-30) REVERT: A 499 PHE cc_start: 0.7573 (m-80) cc_final: 0.7242 (t80) REVERT: A 667 ARG cc_start: 0.7719 (tpp80) cc_final: 0.7157 (tpp80) REVERT: A 681 ARG cc_start: 0.7458 (ttp80) cc_final: 0.7189 (ttt180) REVERT: A 781 LEU cc_start: 0.7982 (OUTLIER) cc_final: 0.7777 (mt) outliers start: 42 outliers final: 21 residues processed: 197 average time/residue: 0.5647 time to fit residues: 125.6744 Evaluate side-chains 192 residues out of total 1737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 166 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 470 HIS Chi-restraints excluded: chain B residue 471 ARG Chi-restraints excluded: chain B residue 482 MET Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 822 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 889 LEU Chi-restraints excluded: chain B residue 939 MET Chi-restraints excluded: chain B residue 1082 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 783 SER Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 969 ARG Chi-restraints excluded: chain A residue 1056 SER Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain P residue 55 TYR Chi-restraints excluded: chain P residue 78 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 54 optimal weight: 4.9990 chunk 81 optimal weight: 0.7980 chunk 40 optimal weight: 0.0980 chunk 178 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 145 optimal weight: 0.7980 chunk 208 optimal weight: 0.6980 chunk 146 optimal weight: 0.5980 chunk 175 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 47 GLN A 182 GLN A 441 GLN P 78 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.132220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.110802 restraints weight = 21123.464| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 1.52 r_work: 0.3150 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 17371 Z= 0.112 Angle : 0.602 12.912 23765 Z= 0.301 Chirality : 0.044 0.234 2751 Planarity : 0.006 0.161 3018 Dihedral : 6.356 54.405 2524 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.17 % Favored : 90.78 % Rotamer: Outliers : 1.79 % Allowed : 16.66 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 1.20 % 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: -1.69 (0.18), residues: 2213 helix: 0.50 (0.19), residues: 800 sheet: -1.46 (0.36), residues: 217 loop : -2.30 (0.17), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 173 TYR 0.014 0.001 TYR B 425 PHE 0.016 0.001 PHE A 886 TRP 0.013 0.001 TRP A1054 HIS 0.002 0.000 HIS A 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.11 (17371) covalent geometry : angle 0.60160 / 0.30 (23765) hydrogen bonds : bond 0.03032 / 2.09 ( 580) hydrogen bonds : angle 3.72605 / 2.52 ( 1626) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4426 Ramachandran restraints generated. 2213 Oldfield, 0 Emsley, 2213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4426 Ramachandran restraints generated. 2213 Oldfield, 0 Emsley, 2213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 180 time to evaluate : 0.707 Fit side-chains REVERT: B 464 ARG cc_start: 0.8288 (mtm-85) cc_final: 0.7949 (ttm-80) REVERT: B 470 HIS cc_start: 0.8099 (OUTLIER) cc_final: 0.7754 (t-90) REVERT: B 471 ARG cc_start: 0.8066 (OUTLIER) cc_final: 0.7732 (mtp180) REVERT: B 482 MET cc_start: 0.8908 (OUTLIER) cc_final: 0.8102 (mtp) REVERT: A 11 ARG cc_start: 0.7102 (mtm110) cc_final: 0.6667 (mpt180) REVERT: A 499 PHE cc_start: 0.7431 (m-80) cc_final: 0.7129 (t80) REVERT: A 667 ARG cc_start: 0.7587 (tpp80) cc_final: 0.7017 (tpp80) REVERT: A 681 ARG cc_start: 0.7407 (ttp80) cc_final: 0.7129 (ttt180) REVERT: A 781 LEU cc_start: 0.7682 (OUTLIER) cc_final: 0.7446 (mt) REVERT: P 14 GLU cc_start: 0.7328 (tp30) cc_final: 0.7056 (tp30) outliers start: 31 outliers final: 20 residues processed: 201 average time/residue: 0.5819 time to fit residues: 131.7734 Evaluate side-chains 189 residues out of total 1737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 165 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 470 HIS Chi-restraints excluded: chain B residue 471 ARG Chi-restraints excluded: chain B residue 482 MET Chi-restraints excluded: chain B residue 649 VAL Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 822 THR Chi-restraints excluded: chain B residue 939 MET Chi-restraints excluded: chain B residue 1082 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 783 SER Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 1056 SER Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain P residue 55 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 137 optimal weight: 4.9990 chunk 28 optimal weight: 0.0470 chunk 68 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 96 optimal weight: 0.0670 chunk 4 optimal weight: 2.9990 chunk 220 optimal weight: 5.9990 chunk 110 optimal weight: 0.0270 chunk 35 optimal weight: 3.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 140 HIS A 182 GLN A 441 GLN P 78 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.132307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.110182 restraints weight = 21145.388| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.59 r_work: 0.3135 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 17371 Z= 0.113 Angle : 0.603 12.871 23765 Z= 0.301 Chirality : 0.044 0.237 2751 Planarity : 0.006 0.160 3018 Dihedral : 6.252 54.014 2524 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.67 % Favored : 90.28 % Rotamer: Outliers : 1.61 % Allowed : 17.35 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 1.20 % 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 (0.18), residues: 2213 helix: 0.56 (0.19), residues: 807 sheet: -1.39 (0.36), residues: 217 loop : -2.26 (0.17), residues: 1189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 173 TYR 0.008 0.001 TYR A 276 PHE 0.009 0.001 PHE A 954 TRP 0.013 0.001 TRP A1054 HIS 0.002 0.000 HIS A 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.11 (17371) covalent geometry : angle 0.60289 / 0.30 (23765) hydrogen bonds : bond 0.03067 / 2.11 ( 580) hydrogen bonds : angle 3.69456 / 2.50 ( 1626) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4426 Ramachandran restraints generated. 2213 Oldfield, 0 Emsley, 2213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4426 Ramachandran restraints generated. 2213 Oldfield, 0 Emsley, 2213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 165 time to evaluate : 0.530 Fit side-chains REVERT: B 464 ARG cc_start: 0.8279 (mtm-85) cc_final: 0.7986 (ttm-80) REVERT: B 470 HIS cc_start: 0.8154 (OUTLIER) cc_final: 0.7803 (t-90) REVERT: B 471 ARG cc_start: 0.8023 (OUTLIER) cc_final: 0.7693 (mtp180) REVERT: B 482 MET cc_start: 0.8943 (OUTLIER) cc_final: 0.8134 (mtp) REVERT: A 11 ARG cc_start: 0.7145 (mtm110) cc_final: 0.6706 (mpt180) REVERT: A 499 PHE cc_start: 0.7397 (m-80) cc_final: 0.7146 (t80) REVERT: A 667 ARG cc_start: 0.7655 (tpp80) cc_final: 0.7072 (tpp80) REVERT: A 681 ARG cc_start: 0.7361 (ttp80) cc_final: 0.7079 (ttt180) REVERT: A 781 LEU cc_start: 0.7690 (OUTLIER) cc_final: 0.7457 (mt) outliers start: 28 outliers final: 20 residues processed: 185 average time/residue: 0.5697 time to fit residues: 119.0263 Evaluate side-chains 187 residues out of total 1737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 163 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 470 HIS Chi-restraints excluded: chain B residue 471 ARG Chi-restraints excluded: chain B residue 482 MET Chi-restraints excluded: chain B residue 649 VAL Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 822 THR Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain B residue 939 MET Chi-restraints excluded: chain B residue 1082 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 783 SER Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain P residue 55 TYR Chi-restraints excluded: chain P residue 78 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 158 optimal weight: 2.9990 chunk 86 optimal weight: 0.0670 chunk 179 optimal weight: 0.4980 chunk 91 optimal weight: 0.0970 chunk 178 optimal weight: 0.9990 chunk 122 optimal weight: 0.0070 chunk 204 optimal weight: 0.0570 chunk 130 optimal weight: 0.4980 chunk 14 optimal weight: 3.9990 chunk 203 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 overall best weight: 0.1452 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 140 HIS A 182 GLN A 441 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.132407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.110258 restraints weight = 21259.324| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 1.60 r_work: 0.3136 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.118 17371 Z= 0.150 Angle : 0.790 59.133 23765 Z= 0.434 Chirality : 0.043 0.235 2751 Planarity : 0.006 0.160 3018 Dihedral : 6.251 54.014 2524 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.76 % Favored : 90.19 % Rotamer: Outliers : 1.56 % Allowed : 17.35 % Favored : 81.10 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 1.20 % 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: -1.59 (0.18), residues: 2213 helix: 0.57 (0.19), residues: 807 sheet: -1.39 (0.36), residues: 217 loop : -2.26 (0.17), residues: 1189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 173 TYR 0.009 0.001 TYR A 276 PHE 0.009 0.001 PHE A 954 TRP 0.013 0.001 TRP A1054 HIS 0.002 0.000 HIS A 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.15 (17371) covalent geometry : angle 0.79040 / 0.43 (23765) hydrogen bonds : bond 0.03143 / 2.09 ( 580) hydrogen bonds : angle 3.69950 / 2.50 ( 1626) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4897.93 seconds wall clock time: 84 minutes 21.91 seconds (5061.91 seconds total)