Starting phenix.real_space_refine on Sat Jul 4 02:48:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7bvc_30216/07_2026/7bvc_30216.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bvc_30216/07_2026/7bvc_30216.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7bvc_30216/07_2026/7bvc_30216.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bvc_30216/07_2026/7bvc_30216.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7bvc_30216/07_2026/7bvc_30216.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7bvc_30216/07_2026/7bvc_30216.cif" model { file = "/net/cci-nas-00/data/ceres_data/7bvc_30216/07_2026/7bvc_30216.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bvc_30216/07_2026/7bvc_30216.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.070 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 2 9.91 5 P 7 5.49 5 S 60 5.16 5 C 11110 2.51 5 N 2914 2.21 5 O 3113 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 76 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17206 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 8147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1078, 8147 Classifications: {'peptide': 1078} Link IDs: {'PCIS': 2, 'PTRANS': 77, 'TRANS': 998} Chain: "B" Number of atoms: 8105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8105 Classifications: {'peptide': 1063} Link IDs: {'PCIS': 1, 'PTRANS': 76, 'TRANS': 985} Chain: "P" Number of atoms: 673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 673 Classifications: {'peptide': 90} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 85} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 141 Unusual residues: {' CA': 1, 'CDL': 1, 'F8L': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'F8L:plan-1': 1, 'F8L:plan-2': 1, 'F8L:plan-10': 1} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 140 Unusual residues: {' CA': 1, '95E': 1, 'CDL': 1, 'PNS': 1, 'PO4': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Time building chain proxies: 4.25, per 1000 atoms: 0.25 Number of scatterers: 17206 At special positions: 0 Unit cell: (123.82, 134.48, 123.82, 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 2 19.99 S 60 16.00 P 7 15.00 O 3113 8.00 N 2914 7.00 C 11110 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 85 " - pdb=" SG CYS B 145 " distance=2.78 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: 1.65 Conformation dependent library (CDL) restraints added in 754.2 milliseconds 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4060 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 21 sheets defined 40.3% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 5 through 15 removed outlier: 3.817A pdb=" N LEU A 10 " --> pdb=" O ARG A 6 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N VAL A 13 " --> pdb=" O ARG A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 128 removed outlier: 3.642A pdb=" N SER A 128 " --> pdb=" O GLU A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 220 removed outlier: 3.547A pdb=" N LEU A 206 " --> pdb=" O MET A 202 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N CYS A 208 " --> pdb=" O LEU A 204 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N VAL A 209 " --> pdb=" O GLY A 205 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE A 210 " --> pdb=" O LEU A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 251 removed outlier: 3.735A pdb=" N THR A 241 " --> pdb=" O TRP A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 272 removed outlier: 3.697A pdb=" N ASN A 265 " --> pdb=" O ASP A 261 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N MET A 266 " --> pdb=" O ASP A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 287 removed outlier: 3.793A pdb=" N GLY A 286 " --> pdb=" O ARG A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 303 removed outlier: 3.692A pdb=" N SER A 297 " --> pdb=" O ASP A 293 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL A 298 " --> pdb=" O TRP A 294 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N HIS A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 313 Processing helix chain 'A' and resid 314 through 316 No H-bonds generated for 'chain 'A' and resid 314 through 316' Processing helix chain 'A' and resid 317 through 330 Processing helix chain 'A' and resid 331 through 336 removed outlier: 3.531A pdb=" N GLY A 336 " --> pdb=" O LEU A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 342 removed outlier: 3.761A pdb=" N ALA A 340 " --> pdb=" O GLY A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 358 removed outlier: 3.610A pdb=" N MET A 346 " --> pdb=" O ASN A 342 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU A 347 " --> pdb=" O ARG A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 386 removed outlier: 3.720A pdb=" N PHE A 372 " --> pdb=" O PRO A 368 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE A 375 " --> pdb=" O ALA A 371 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N MET A 379 " --> pdb=" O ILE A 375 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU A 380 " --> pdb=" O THR A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 405 removed outlier: 3.716A pdb=" N ILE A 397 " --> pdb=" O ALA A 393 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL A 398 " --> pdb=" O ALA A 394 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR A 405 " --> pdb=" O MET A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 413 removed outlier: 3.684A pdb=" N LEU A 411 " --> pdb=" O PRO A 408 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE A 412 " --> pdb=" O GLN A 409 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA A 413 " --> pdb=" O GLY A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 429 removed outlier: 3.648A pdb=" N GLY A 420 " --> pdb=" O PRO A 416 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N ARG A 422 " --> pdb=" O LEU A 418 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N ALA A 423 " --> pdb=" O VAL A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 432 No H-bonds generated for 'chain 'A' and resid 430 through 432' Processing helix chain 'A' and resid 437 through 449 Proline residue: A 443 - end of helix removed outlier: 3.740A pdb=" N VAL A 448 " --> pdb=" O LEU A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 456 removed outlier: 3.575A pdb=" N PHE A 456 " --> pdb=" O PHE A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 475 Processing helix chain 'A' and resid 484 through 491 Processing helix chain 'A' and resid 501 through 523 removed outlier: 3.502A pdb=" N LEU A 509 " --> pdb=" O ALA A 505 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N MET A 518 " --> pdb=" O PHE A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 548 removed outlier: 3.702A pdb=" N LEU A 534 " --> pdb=" O VAL A 530 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N TRP A 535 " --> pdb=" O SER A 531 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG A 536 " --> pdb=" O GLY A 532 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR A 541 " --> pdb=" O LEU A 537 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU A 548 " --> pdb=" O GLY A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 561 removed outlier: 3.674A pdb=" N PHE A 559 " --> pdb=" O ALA A 556 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA A 561 " --> pdb=" O GLN A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 581 removed outlier: 3.846A pdb=" N GLY A 567 " --> pdb=" O ALA A 563 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA A 568 " --> pdb=" O GLY A 564 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLY A 571 " --> pdb=" O GLY A 567 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL A 572 " --> pdb=" O ALA A 568 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA A 578 " --> pdb=" O ALA A 574 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ARG A 579 " --> pdb=" O PHE A 575 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL A 580 " --> pdb=" O ALA A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 603 removed outlier: 3.974A pdb=" N LEU A 588 " --> pdb=" O SER A 584 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA A 589 " --> pdb=" O ARG A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 651 removed outlier: 4.026A pdb=" N ILE A 634 " --> pdb=" O PRO A 630 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N PHE A 635 " --> pdb=" O VAL A 631 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LEU A 636 " --> pdb=" O THR A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 676 through 696 removed outlier: 4.258A pdb=" N MET A 690 " --> pdb=" O GLU A 686 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA A 693 " --> pdb=" O SER A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 713 Processing helix chain 'A' and resid 814 through 818 removed outlier: 4.303A pdb=" N GLY A 817 " --> pdb=" O LEU A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 953 through 957 removed outlier: 3.947A pdb=" N LEU A 957 " --> pdb=" O ALA A 953 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 953 through 957' Processing helix chain 'A' and resid 996 through 1008 removed outlier: 3.519A pdb=" N VAL A1002 " --> pdb=" O LYS A 998 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N ASN A1005 " --> pdb=" O VAL A1001 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N GLN A1006 " --> pdb=" O VAL A1002 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 32 removed outlier: 3.594A pdb=" N ILE B 25 " --> pdb=" O LYS B 21 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N TRP B 28 " --> pdb=" O ARG B 24 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR B 31 " --> pdb=" O ARG B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 40 Processing helix chain 'B' and resid 108 through 113 Processing helix chain 'B' and resid 137 through 141 Processing helix chain 'B' and resid 219 through 225 Processing helix chain 'B' and resid 230 through 245 Processing helix chain 'B' and resid 246 through 248 No H-bonds generated for 'chain 'B' and resid 246 through 248' Processing helix chain 'B' and resid 263 through 280 removed outlier: 4.200A pdb=" N GLY B 267 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL B 268 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE B 275 " --> pdb=" O GLY B 271 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TRP B 276 " --> pdb=" O GLY B 272 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N VAL B 278 " --> pdb=" O ALA B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 295 removed outlier: 3.698A pdb=" N THR B 295 " --> pdb=" O GLN B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 300 Processing helix chain 'B' and resid 307 through 311 removed outlier: 3.810A pdb=" N GLY B 310 " --> pdb=" O ARG B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 327 removed outlier: 3.688A pdb=" N LEU B 323 " --> pdb=" O TYR B 319 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU B 325 " --> pdb=" O ASN B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 340 Processing helix chain 'B' and resid 341 through 354 Processing helix chain 'B' and resid 356 through 360 removed outlier: 3.789A pdb=" N GLY B 360 " --> pdb=" O PRO B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 382 removed outlier: 3.749A pdb=" N MET B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 412 removed outlier: 3.823A pdb=" N ILE B 394 " --> pdb=" O PRO B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 429 removed outlier: 3.871A pdb=" N ILE B 421 " --> pdb=" O ALA B 417 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR B 422 " --> pdb=" O ALA B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 437 removed outlier: 3.875A pdb=" N LEU B 435 " --> pdb=" O PRO B 432 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ILE B 436 " --> pdb=" O THR B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 444 removed outlier: 3.615A pdb=" N GLY B 444 " --> pdb=" O ALA B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 456 removed outlier: 3.696A pdb=" N ILE B 451 " --> pdb=" O PRO B 447 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG B 454 " --> pdb=" O ARG B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 473 Proline residue: B 467 - end of helix Processing helix chain 'B' and resid 475 through 480 Processing helix chain 'B' and resid 484 through 498 Processing helix chain 'B' and resid 503 through 507 Processing helix chain 'B' and resid 508 through 513 Processing helix chain 'B' and resid 526 through 546 removed outlier: 4.201A pdb=" N THR B 532 " --> pdb=" O ALA B 528 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N CYS B 535 " --> pdb=" O PHE B 531 " (cutoff:3.500A) Proline residue: B 538 - end of helix removed outlier: 3.696A pdb=" N ARG B 545 " --> pdb=" O PHE B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 553 through 571 removed outlier: 3.591A pdb=" N LEU B 560 " --> pdb=" O PRO B 556 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N MET B 561 " --> pdb=" O ALA B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 584 removed outlier: 3.957A pdb=" N LEU B 584 " --> pdb=" O HIS B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 600 removed outlier: 3.738A pdb=" N GLY B 590 " --> pdb=" O ALA B 586 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA B 594 " --> pdb=" O GLY B 590 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU B 595 " --> pdb=" O ALA B 591 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL B 598 " --> pdb=" O ALA B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 626 removed outlier: 3.640A pdb=" N ARG B 611 " --> pdb=" O SER B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 676 removed outlier: 4.077A pdb=" N ILE B 657 " --> pdb=" O GLN B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 681 through 687 removed outlier: 3.655A pdb=" N ARG B 685 " --> pdb=" O ARG B 681 " (cutoff:3.500A) Processing helix chain 'B' and resid 689 through 713 removed outlier: 4.037A pdb=" N VAL B 693 " --> pdb=" O ALA B 689 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N MET B 698 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLY B 709 " --> pdb=" O SER B 705 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N VAL B 710 " --> pdb=" O MET B 706 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL B 711 " --> pdb=" O ALA B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 721 through 726 Processing helix chain 'B' and resid 727 through 729 No H-bonds generated for 'chain 'B' and resid 727 through 729' Processing helix chain 'B' and resid 732 through 735 removed outlier: 3.568A pdb=" N ASP B 735 " --> pdb=" O GLY B 732 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 732 through 735' Processing helix chain 'B' and resid 793 through 797 removed outlier: 3.716A pdb=" N TRP B 796 " --> pdb=" O ASP B 793 " (cutoff:3.500A) Processing helix chain 'B' and resid 850 through 855 Processing helix chain 'B' and resid 958 through 962 Processing helix chain 'B' and resid 1001 through 1008 removed outlier: 3.979A pdb=" N GLN B1007 " --> pdb=" O TYR B1003 " (cutoff:3.500A) Processing helix chain 'B' and resid 1014 through 1018 removed outlier: 3.993A pdb=" N GLY B1018 " --> pdb=" O GLY B1015 " (cutoff:3.500A) Processing helix chain 'B' and resid 1023 through 1027 Processing helix chain 'P' and resid 4 through 20 removed outlier: 3.566A pdb=" N ALA P 10 " --> pdb=" O GLU P 6 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU P 14 " --> pdb=" O ALA P 10 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE P 15 " --> pdb=" O GLY P 11 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU P 18 " --> pdb=" O GLU P 14 " (cutoff:3.500A) Processing helix chain 'P' and resid 40 through 53 removed outlier: 4.012A pdb=" N GLU P 46 " --> pdb=" O LEU P 42 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU P 52 " --> pdb=" O ALA P 48 " (cutoff:3.500A) Processing helix chain 'P' and resid 69 through 84 Processing sheet with id=AA1, first strand: chain 'A' and resid 193 through 194 Processing sheet with id=AA2, first strand: chain 'A' and resid 37 through 40 removed outlier: 3.878A pdb=" N ALA A 64 " --> pdb=" O ASP A 185 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 102 through 103 removed outlier: 3.993A pdb=" N VAL A 111 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N ALA A 119 " --> pdb=" O VAL A 111 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 951 through 952 Processing sheet with id=AA5, first strand: chain 'A' and resid 826 through 827 removed outlier: 3.702A pdb=" N MET A 826 " --> pdb=" O PHE A 942 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 838 through 839 Processing sheet with id=AA7, first strand: chain 'A' and resid 838 through 839 removed outlier: 3.619A pdb=" N VAL A 928 " --> pdb=" O LYS A 879 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 855 through 857 Processing sheet with id=AA9, first strand: chain 'A' and resid 865 through 866 removed outlier: 3.703A pdb=" N TYR A 865 " --> pdb=" O ASN A 873 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 977 through 978 removed outlier: 3.733A pdb=" N TYR A 991 " --> pdb=" O PRO A 962 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 216 through 218 removed outlier: 3.870A pdb=" N GLY B1065 " --> pdb=" O THR B 53 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 191 through 192 Processing sheet with id=AB4, first strand: chain 'B' and resid 147 through 149 Processing sheet with id=AB5, first strand: chain 'B' and resid 97 through 100 removed outlier: 7.386A pdb=" N VAL B 116 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N GLY B 100 " --> pdb=" O MET B 114 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N MET B 114 " --> pdb=" O GLY B 100 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N VAL B 125 " --> pdb=" O ALA B 133 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N ALA B 133 " --> pdb=" O VAL B 125 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VAL B 127 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N VAL B 131 " --> pdb=" O VAL B 127 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 157 through 159 Processing sheet with id=AB7, first strand: chain 'B' and resid 956 through 957 Processing sheet with id=AB8, first strand: chain 'B' and resid 826 through 827 removed outlier: 3.723A pdb=" N ALA B 826 " --> pdb=" O VAL B 947 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 837 through 840 Processing sheet with id=AC1, first strand: chain 'B' and resid 837 through 840 removed outlier: 4.006A pdb=" N ALA B 929 " --> pdb=" O ALA B 888 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR B 889 " --> pdb=" O VAL B 897 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 968 through 970 Processing sheet with id=AC3, first strand: chain 'B' and resid 986 through 987 594 hydrogen bonds defined for protein. 1662 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: 3.27 Time building geometry restraints manager: 2.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.26: 2745 1.26 - 1.40: 4172 1.40 - 1.54: 10174 1.54 - 1.68: 440 1.68 - 1.82: 102 Bond restraints: 17633 Sorted by residual: bond pdb=" OA3 CDL B1204 " pdb=" PA1 CDL B1204 " ideal model delta sigma weight residual 1.529 1.416 0.113 1.00e-02 1.00e+04 1.27e+02 bond pdb=" C55 F8L A1102 " pdb=" C57 F8L A1102 " ideal model delta sigma weight residual 1.545 1.325 0.220 2.00e-02 2.50e+03 1.20e+02 bond pdb=" CA7 CDL B1204 " pdb=" OA8 CDL B1204 " ideal model delta sigma weight residual 1.334 1.446 -0.112 1.10e-02 8.26e+03 1.04e+02 bond pdb=" OB3 CDL B1204 " pdb=" PB2 CDL B1204 " ideal model delta sigma weight residual 1.529 1.430 0.099 1.00e-02 1.00e+04 9.71e+01 bond pdb=" C55 F8L A1102 " pdb=" O56 F8L A1102 " ideal model delta sigma weight residual 1.401 1.596 -0.195 2.00e-02 2.50e+03 9.55e+01 ... (remaining 17628 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.40: 23923 4.40 - 8.80: 144 8.80 - 13.20: 26 13.20 - 17.59: 12 17.59 - 21.99: 2 Bond angle restraints: 24107 Sorted by residual: angle pdb=" CB GLN B 713 " pdb=" CG GLN B 713 " pdb=" CD GLN B 713 " ideal model delta sigma weight residual 112.60 90.61 21.99 1.70e+00 3.46e-01 1.67e+02 angle pdb=" C11 CDL A1101 " pdb=" CA5 CDL A1101 " pdb=" OA6 CDL A1101 " ideal model delta sigma weight residual 111.33 126.01 -14.68 1.32e+00 5.72e-01 1.23e+02 angle pdb=" C11 CDL B1204 " pdb=" CA5 CDL B1204 " pdb=" OA6 CDL B1204 " ideal model delta sigma weight residual 111.33 125.39 -14.06 1.32e+00 5.72e-01 1.13e+02 angle pdb=" CB3 CDL B1204 " pdb=" CB4 CDL B1204 " pdb=" CB6 CDL B1204 " ideal model delta sigma weight residual 111.75 90.95 20.80 1.98e+00 2.56e-01 1.11e+02 angle pdb=" C51 CDL A1101 " pdb=" CB5 CDL A1101 " pdb=" OB6 CDL A1101 " ideal model delta sigma weight residual 111.33 124.94 -13.61 1.32e+00 5.72e-01 1.06e+02 ... (remaining 24102 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.29: 9699 21.29 - 42.58: 589 42.58 - 63.87: 105 63.87 - 85.16: 12 85.16 - 106.45: 7 Dihedral angle restraints: 10412 sinusoidal: 4063 harmonic: 6349 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 73.55 106.45 0 5.00e+00 4.00e-02 4.53e+02 dihedral pdb=" CA TYR A 698 " pdb=" C TYR A 698 " pdb=" N PRO A 699 " pdb=" CA PRO A 699 " ideal model delta harmonic sigma weight residual 0.00 42.66 -42.66 0 5.00e+00 4.00e-02 7.28e+01 dihedral pdb=" CB CYS B 85 " pdb=" SG CYS B 85 " pdb=" SG CYS B 145 " pdb=" CB CYS B 145 " ideal model delta sinusoidal sigma weight residual -86.00 -22.88 -63.12 1 1.00e+01 1.00e-02 5.26e+01 ... (remaining 10409 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 2652 0.101 - 0.203: 100 0.203 - 0.304: 7 0.304 - 0.405: 0 0.405 - 0.507: 1 Chirality restraints: 2760 Sorted by residual: chirality pdb=" CA THR B 716 " pdb=" N THR B 716 " pdb=" C THR B 716 " pdb=" CB THR B 716 " both_signs ideal model delta sigma weight residual False 2.53 2.02 0.51 2.00e-01 2.50e+01 6.42e+00 chirality pdb=" CA ARG A 697 " pdb=" N ARG A 697 " pdb=" C ARG A 697 " pdb=" CB ARG A 697 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" C10 95E B1203 " pdb=" C11 95E B1203 " pdb=" C13 95E B1203 " pdb=" N9 95E B1203 " both_signs ideal model delta sigma weight residual False 2.35 2.62 -0.28 2.00e-01 2.50e+01 1.89e+00 ... (remaining 2757 not shown) Planarity restraints: 3082 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 698 " 0.048 2.00e-02 2.50e+03 2.58e-02 1.33e+01 pdb=" CG TYR A 698 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR A 698 " -0.033 2.00e-02 2.50e+03 pdb=" CD2 TYR A 698 " -0.019 2.00e-02 2.50e+03 pdb=" CE1 TYR A 698 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR A 698 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR A 698 " 0.020 2.00e-02 2.50e+03 pdb=" OH TYR A 698 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 699 " -0.017 2.00e-02 2.50e+03 3.63e-02 1.32e+01 pdb=" C PRO A 699 " 0.063 2.00e-02 2.50e+03 pdb=" O PRO A 699 " -0.024 2.00e-02 2.50e+03 pdb=" N VAL A 700 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO B 715 " -0.017 2.00e-02 2.50e+03 3.54e-02 1.26e+01 pdb=" C PRO B 715 " 0.061 2.00e-02 2.50e+03 pdb=" O PRO B 715 " -0.024 2.00e-02 2.50e+03 pdb=" N THR B 716 " -0.021 2.00e-02 2.50e+03 ... (remaining 3079 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 364 2.69 - 3.24: 16189 3.24 - 3.79: 24905 3.79 - 4.35: 34550 4.35 - 4.90: 59096 Nonbonded interactions: 135104 Sorted by model distance: nonbonded pdb=" O27 PNS B1201 " pdb=" O33 PNS B1201 " model vdw 2.134 3.040 nonbonded pdb=" OG1 THR B 576 " pdb=" O1 PO4 B1202 " model vdw 2.208 3.040 nonbonded pdb=" N TRP A 864 " pdb=" O GLN A 876 " model vdw 2.232 3.120 nonbonded pdb=" OE2 GLU B 781 " pdb=" OH TYR B 816 " model vdw 2.237 3.040 nonbonded pdb=" O SER B1070 " pdb=" OG SER B1070 " model vdw 2.250 3.040 ... (remaining 135099 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: 4.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.410 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 17.000 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 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 : 0.009 0.754 17634 Z= 0.494 Angle : 0.949 21.992 24109 Z= 0.511 Chirality : 0.047 0.507 2760 Planarity : 0.005 0.052 3082 Dihedral : 14.089 106.454 6349 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.27 % Favored : 91.69 % Rotamer: Outliers : 0.17 % Allowed : 3.14 % Favored : 96.69 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 1.25 % 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: -4.30 (0.15), residues: 2225 helix: -2.20 (0.15), residues: 857 sheet: -2.36 (0.32), residues: 225 loop : -3.58 (0.14), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 697 TYR 0.048 0.002 TYR A 698 PHE 0.011 0.001 PHE B 99 TRP 0.034 0.001 TRP A 864 HIS 0.003 0.001 HIS B1069 Details of bonding type rmsd/Z covalent geometry : bond 0.00681 / 0.40 (17633) covalent geometry : angle 0.93966 / 0.51 (24107) SS BOND : bond 0.75381 / 39.67 ( 1) SS BOND : angle 14.70631 / 8.62 ( 2) hydrogen bonds : bond 0.15847 / 10.57 ( 588) hydrogen bonds : angle 6.05631 / 4.25 ( 1662) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 267 time to evaluate : 0.628 Fit side-chains revert: symmetry clash REVERT: A 7 ILE cc_start: 0.8011 (mt) cc_final: 0.7645 (mm) REVERT: A 72 ARG cc_start: 0.8021 (ttm110) cc_final: 0.7811 (ttm-80) REVERT: A 225 ARG cc_start: 0.5667 (ttt-90) cc_final: 0.5391 (ttt-90) REVERT: A 495 SER cc_start: 0.8675 (t) cc_final: 0.8423 (p) REVERT: A 577 PHE cc_start: 0.8044 (m-80) cc_final: 0.7672 (m-10) REVERT: A 622 LYS cc_start: 0.8640 (ptpp) cc_final: 0.8272 (pttp) REVERT: A 648 TRP cc_start: 0.7862 (t60) cc_final: 0.7488 (t60) REVERT: A 699 PRO cc_start: 0.9249 (OUTLIER) cc_final: 0.9034 (Cg_endo) REVERT: A 837 LYS cc_start: 0.7238 (pptt) cc_final: 0.6554 (ptpt) REVERT: A 879 LYS cc_start: 0.8459 (mttt) cc_final: 0.8062 (mttp) REVERT: A 906 LYS cc_start: 0.8005 (mttm) cc_final: 0.7682 (mtmm) REVERT: B 24 ARG cc_start: 0.7514 (ttp80) cc_final: 0.7263 (ttp-170) REVERT: B 28 TRP cc_start: 0.7762 (m100) cc_final: 0.7373 (m100) REVERT: B 146 GLN cc_start: 0.7390 (mt0) cc_final: 0.7063 (mt0) REVERT: B 174 LYS cc_start: 0.8284 (mmtp) cc_final: 0.7737 (pttm) REVERT: B 227 LEU cc_start: 0.8063 (mp) cc_final: 0.7795 (tp) REVERT: B 428 LEU cc_start: 0.8822 (tt) cc_final: 0.8609 (tp) REVERT: B 781 GLU cc_start: 0.7938 (mt-10) cc_final: 0.7696 (mt-10) REVERT: B 801 LYS cc_start: 0.8618 (mmtt) cc_final: 0.8023 (mmmt) REVERT: B 821 LYS cc_start: 0.7819 (mmtp) cc_final: 0.7052 (pttp) outliers start: 3 outliers final: 3 residues processed: 270 average time/residue: 0.7422 time to fit residues: 219.1318 Evaluate side-chains 168 residues out of total 1754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 164 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 699 PRO Chi-restraints excluded: chain B residue 145 CYS Chi-restraints excluded: chain B residue 273 MET Chi-restraints excluded: chain B residue 713 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 216 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.5980 chunk 200 optimal weight: 0.0040 chunk 212 optimal weight: 0.9990 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 135 HIS A 177 GLN A 361 ASN A 482 GLN A 667 ASN A 741 GLN A 760 ASN A 832 ASN ** A 904 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 938 GLN B 291 GLN B 393 GLN B 610 ASN B 653 GLN B 956 GLN B 959 GLN B1013 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.135042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.109829 restraints weight = 22152.821| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 1.87 r_work: 0.3215 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.1240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17634 Z= 0.115 Angle : 0.588 7.993 24109 Z= 0.297 Chirality : 0.043 0.148 2760 Planarity : 0.005 0.054 3082 Dihedral : 10.343 106.215 2642 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.36 % Favored : 91.55 % Rotamer: Outliers : 1.65 % Allowed : 10.33 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.62 % 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: -3.32 (0.16), residues: 2225 helix: -1.23 (0.17), residues: 853 sheet: -2.04 (0.31), residues: 240 loop : -3.10 (0.15), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 89 TYR 0.012 0.001 TYR A 110 PHE 0.016 0.001 PHE A 620 TRP 0.026 0.001 TRP A 864 HIS 0.003 0.001 HIS B 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (17633) covalent geometry : angle 0.58840 / 0.30 (24107) SS BOND : bond 0.00224 / 0.12 ( 1) SS BOND : angle 0.10649 / 0.06 ( 2) hydrogen bonds : bond 0.03703 / 2.49 ( 588) hydrogen bonds : angle 4.50601 / 3.19 ( 1662) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 181 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 ILE cc_start: 0.7925 (mt) cc_final: 0.7665 (mm) REVERT: A 72 ARG cc_start: 0.8425 (ttm110) cc_final: 0.8162 (ttm-80) REVERT: A 577 PHE cc_start: 0.8335 (m-80) cc_final: 0.7935 (m-10) REVERT: A 622 LYS cc_start: 0.8823 (ptpp) cc_final: 0.8495 (pttp) REVERT: A 648 TRP cc_start: 0.8169 (t60) cc_final: 0.7585 (t-100) REVERT: A 837 LYS cc_start: 0.7324 (pptt) cc_final: 0.6772 (ptpt) REVERT: A 879 LYS cc_start: 0.8543 (mttt) cc_final: 0.8230 (mttp) REVERT: A 906 LYS cc_start: 0.8382 (mttm) cc_final: 0.8092 (mtmm) REVERT: A 1052 GLN cc_start: 0.8301 (tt0) cc_final: 0.7783 (tm-30) REVERT: A 1065 THR cc_start: 0.8344 (p) cc_final: 0.7990 (t) REVERT: B 24 ARG cc_start: 0.8090 (ttp80) cc_final: 0.7706 (ttp-170) REVERT: B 146 GLN cc_start: 0.7394 (mt0) cc_final: 0.7075 (mt0) REVERT: B 174 LYS cc_start: 0.8343 (mmtp) cc_final: 0.7883 (ptmm) REVERT: B 202 GLN cc_start: 0.8041 (mm-40) cc_final: 0.7640 (mm-40) REVERT: B 227 LEU cc_start: 0.8352 (mp) cc_final: 0.7999 (tp) REVERT: B 543 MET cc_start: 0.8744 (mtp) cc_final: 0.8508 (mtt) REVERT: B 821 LYS cc_start: 0.7842 (mmtp) cc_final: 0.7053 (pttp) REVERT: B 854 ARG cc_start: 0.5551 (OUTLIER) cc_final: 0.5344 (mtp85) outliers start: 29 outliers final: 8 residues processed: 202 average time/residue: 0.6787 time to fit residues: 151.0571 Evaluate side-chains 169 residues out of total 1754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 160 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 702 THR Chi-restraints excluded: chain A residue 736 GLN Chi-restraints excluded: chain A residue 856 THR Chi-restraints excluded: chain A residue 1047 ILE Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 854 ARG Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain P residue 62 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 131 optimal weight: 6.9990 chunk 114 optimal weight: 0.0070 chunk 27 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 215 optimal weight: 0.9980 chunk 164 optimal weight: 4.9990 chunk 137 optimal weight: 0.3980 chunk 41 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 904 GLN ** B1069 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.135757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.110374 restraints weight = 22267.508| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.92 r_work: 0.3217 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 17634 Z= 0.106 Angle : 0.557 7.667 24109 Z= 0.281 Chirality : 0.042 0.153 2760 Planarity : 0.005 0.104 3082 Dihedral : 9.661 115.718 2632 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.64 % Favored : 92.31 % Rotamer: Outliers : 1.71 % Allowed : 11.98 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.62 % 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: -2.65 (0.17), residues: 2225 helix: -0.65 (0.18), residues: 863 sheet: -1.71 (0.33), residues: 223 loop : -2.74 (0.16), residues: 1139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 668 TYR 0.012 0.001 TYR B 288 PHE 0.014 0.001 PHE A 620 TRP 0.024 0.001 TRP A 864 HIS 0.003 0.001 HIS A 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (17633) covalent geometry : angle 0.55735 / 0.28 (24107) SS BOND : bond 0.00313 / 0.16 ( 1) SS BOND : angle 1.02964 / 0.56 ( 2) hydrogen bonds : bond 0.03177 / 2.14 ( 588) hydrogen bonds : angle 4.15921 / 2.93 ( 1662) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 174 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7964 (pt) REVERT: A 105 ASN cc_start: 0.7355 (t0) cc_final: 0.6939 (t0) REVERT: A 577 PHE cc_start: 0.8325 (m-80) cc_final: 0.7905 (m-10) REVERT: A 622 LYS cc_start: 0.8752 (ptpp) cc_final: 0.8419 (pttp) REVERT: A 648 TRP cc_start: 0.8154 (t60) cc_final: 0.7546 (t-100) REVERT: A 837 LYS cc_start: 0.7077 (pptt) cc_final: 0.6203 (ptmt) REVERT: A 879 LYS cc_start: 0.8417 (mttt) cc_final: 0.8116 (mttp) REVERT: A 906 LYS cc_start: 0.8350 (mttm) cc_final: 0.8055 (mtmm) REVERT: A 1052 GLN cc_start: 0.8269 (tt0) cc_final: 0.7733 (tm-30) REVERT: A 1065 THR cc_start: 0.8340 (p) cc_final: 0.8009 (t) REVERT: B 24 ARG cc_start: 0.8047 (ttp80) cc_final: 0.7703 (ttp-170) REVERT: B 114 MET cc_start: 0.8902 (ttm) cc_final: 0.8653 (ttp) REVERT: B 121 THR cc_start: 0.7836 (p) cc_final: 0.7428 (t) REVERT: B 146 GLN cc_start: 0.7464 (mt0) cc_final: 0.7062 (mt0) REVERT: B 174 LYS cc_start: 0.8368 (mmtp) cc_final: 0.7876 (ptmm) REVERT: B 227 LEU cc_start: 0.8369 (mp) cc_final: 0.7977 (tp) REVERT: B 543 MET cc_start: 0.8690 (mtp) cc_final: 0.8394 (mtt) REVERT: B 821 LYS cc_start: 0.7731 (mmtp) cc_final: 0.6847 (pttp) REVERT: B 1056 GLU cc_start: 0.7322 (tp30) cc_final: 0.7053 (tm-30) outliers start: 30 outliers final: 14 residues processed: 195 average time/residue: 0.6345 time to fit residues: 137.3648 Evaluate side-chains 169 residues out of total 1754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 154 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 702 THR Chi-restraints excluded: chain A residue 736 GLN Chi-restraints excluded: chain A residue 856 THR Chi-restraints excluded: chain A residue 1047 ILE Chi-restraints excluded: chain A residue 1067 VAL Chi-restraints excluded: chain A residue 1079 LEU Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 681 ARG Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 1047 SER Chi-restraints excluded: chain P residue 62 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 213 optimal weight: 0.1980 chunk 185 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 156 optimal weight: 0.8980 chunk 168 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 202 optimal weight: 1.9990 chunk 162 optimal weight: 1.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 502 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.131653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.106302 restraints weight = 22352.583| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 1.88 r_work: 0.3160 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17634 Z= 0.160 Angle : 0.609 7.677 24109 Z= 0.308 Chirality : 0.045 0.164 2760 Planarity : 0.005 0.107 3082 Dihedral : 9.370 107.808 2632 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.58 % Favored : 91.37 % Rotamer: Outliers : 2.80 % Allowed : 12.66 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.62 % 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: -2.46 (0.17), residues: 2225 helix: -0.52 (0.18), residues: 869 sheet: -1.56 (0.30), residues: 272 loop : -2.64 (0.17), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 72 TYR 0.013 0.001 TYR B 288 PHE 0.013 0.001 PHE A 610 TRP 0.021 0.001 TRP A 864 HIS 0.004 0.001 HIS B 673 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.16 (17633) covalent geometry : angle 0.60900 / 0.31 (24107) SS BOND : bond 0.00434 / 0.23 ( 1) SS BOND : angle 1.40386 / 0.77 ( 2) hydrogen bonds : bond 0.04040 / 2.71 ( 588) hydrogen bonds : angle 4.25611 / 2.98 ( 1662) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 161 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.8028 (pt) REVERT: A 105 ASN cc_start: 0.7739 (t0) cc_final: 0.7248 (t0) REVERT: A 577 PHE cc_start: 0.8389 (m-80) cc_final: 0.7994 (m-10) REVERT: A 622 LYS cc_start: 0.8751 (ptpp) cc_final: 0.8432 (pttp) REVERT: A 648 TRP cc_start: 0.8178 (t60) cc_final: 0.7607 (t-100) REVERT: A 837 LYS cc_start: 0.7279 (pptt) cc_final: 0.6447 (ptmt) REVERT: A 879 LYS cc_start: 0.8494 (mttt) cc_final: 0.8191 (mttp) REVERT: A 906 LYS cc_start: 0.8469 (mttm) cc_final: 0.8168 (mtmm) REVERT: A 982 ARG cc_start: 0.8146 (OUTLIER) cc_final: 0.7195 (ttp-170) REVERT: A 1052 GLN cc_start: 0.8278 (tt0) cc_final: 0.7770 (tm-30) REVERT: B 24 ARG cc_start: 0.8037 (ttp80) cc_final: 0.7528 (ttp-170) REVERT: B 28 TRP cc_start: 0.8269 (m100) cc_final: 0.7733 (m100) REVERT: B 121 THR cc_start: 0.7880 (p) cc_final: 0.7504 (t) REVERT: B 146 GLN cc_start: 0.7437 (mt0) cc_final: 0.7034 (mt0) REVERT: B 174 LYS cc_start: 0.8433 (mmtp) cc_final: 0.7896 (ptmm) REVERT: B 202 GLN cc_start: 0.8166 (mm-40) cc_final: 0.7699 (mm-40) REVERT: B 227 LEU cc_start: 0.8421 (mp) cc_final: 0.8022 (tp) REVERT: B 543 MET cc_start: 0.8724 (mtp) cc_final: 0.8482 (mtt) REVERT: B 676 ARG cc_start: 0.8240 (mtp85) cc_final: 0.7943 (mtt-85) REVERT: B 821 LYS cc_start: 0.7785 (mmtp) cc_final: 0.6933 (pttp) REVERT: B 1069 HIS cc_start: 0.7913 (m-70) cc_final: 0.7684 (m170) outliers start: 49 outliers final: 24 residues processed: 196 average time/residue: 0.7183 time to fit residues: 155.3555 Evaluate side-chains 176 residues out of total 1754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 150 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 160 ASP Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 702 THR Chi-restraints excluded: chain A residue 833 LYS Chi-restraints excluded: chain A residue 856 THR Chi-restraints excluded: chain A residue 982 ARG Chi-restraints excluded: chain A residue 1047 ILE Chi-restraints excluded: chain A residue 1067 VAL Chi-restraints excluded: chain A residue 1079 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 681 ARG Chi-restraints excluded: chain B residue 841 SER Chi-restraints excluded: chain B residue 875 ASN Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 1047 SER Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 55 TYR Chi-restraints excluded: chain P residue 62 GLU Chi-restraints excluded: chain P residue 69 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 109 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 96 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 149 optimal weight: 0.0670 chunk 116 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 chunk 187 optimal weight: 0.8980 chunk 193 optimal weight: 2.9990 chunk 197 optimal weight: 0.2980 chunk 150 optimal weight: 0.5980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.135448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.110115 restraints weight = 22096.570| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 1.88 r_work: 0.3214 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 17634 Z= 0.099 Angle : 0.543 7.923 24109 Z= 0.274 Chirality : 0.042 0.138 2760 Planarity : 0.005 0.090 3082 Dihedral : 8.687 101.263 2632 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.74 % Favored : 93.21 % Rotamer: Outliers : 2.28 % Allowed : 13.98 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.62 % 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: -2.09 (0.17), residues: 2225 helix: -0.20 (0.19), residues: 872 sheet: -1.51 (0.31), residues: 269 loop : -2.41 (0.17), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 676 TYR 0.012 0.001 TYR B 288 PHE 0.010 0.001 PHE A 620 TRP 0.024 0.001 TRP A 864 HIS 0.002 0.001 HIS B 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.10 (17633) covalent geometry : angle 0.54290 / 0.27 (24107) SS BOND : bond 0.00159 / 0.08 ( 1) SS BOND : angle 0.75295 / 0.41 ( 2) hydrogen bonds : bond 0.02978 / 2.01 ( 588) hydrogen bonds : angle 4.02248 / 2.82 ( 1662) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 164 time to evaluate : 0.651 Fit side-chains revert: symmetry clash REVERT: A 10 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7998 (pt) REVERT: A 72 ARG cc_start: 0.7575 (mtp85) cc_final: 0.7221 (mmp80) REVERT: A 105 ASN cc_start: 0.7344 (t0) cc_final: 0.6950 (t0) REVERT: A 577 PHE cc_start: 0.8318 (m-80) cc_final: 0.7927 (m-10) REVERT: A 622 LYS cc_start: 0.8657 (ptpp) cc_final: 0.8343 (pttp) REVERT: A 648 TRP cc_start: 0.8136 (t60) cc_final: 0.7573 (t-100) REVERT: A 837 LYS cc_start: 0.7140 (pptt) cc_final: 0.6217 (ptmt) REVERT: A 848 ARG cc_start: 0.7012 (OUTLIER) cc_final: 0.5780 (mpt180) REVERT: A 864 TRP cc_start: 0.7176 (t-100) cc_final: 0.6741 (t-100) REVERT: A 879 LYS cc_start: 0.8340 (mttt) cc_final: 0.8040 (mttp) REVERT: A 906 LYS cc_start: 0.8393 (mttm) cc_final: 0.8111 (mtmm) REVERT: A 960 GLN cc_start: 0.8471 (tp40) cc_final: 0.8257 (mm-40) REVERT: A 1052 GLN cc_start: 0.8221 (tt0) cc_final: 0.7723 (tm-30) REVERT: B 24 ARG cc_start: 0.7951 (ttp80) cc_final: 0.7632 (ttp-170) REVERT: B 121 THR cc_start: 0.7859 (p) cc_final: 0.7475 (t) REVERT: B 146 GLN cc_start: 0.7410 (mt0) cc_final: 0.6947 (mt0) REVERT: B 149 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.7967 (mt-10) REVERT: B 174 LYS cc_start: 0.8399 (mmtp) cc_final: 0.7853 (pttt) REVERT: B 202 GLN cc_start: 0.8172 (mm-40) cc_final: 0.7734 (mm-40) REVERT: B 227 LEU cc_start: 0.8371 (mp) cc_final: 0.7991 (tp) REVERT: B 273 MET cc_start: 0.8691 (tpp) cc_final: 0.8401 (mmt) REVERT: B 543 MET cc_start: 0.8638 (mtp) cc_final: 0.8399 (mtt) REVERT: B 676 ARG cc_start: 0.8140 (mtp85) cc_final: 0.7852 (mtt-85) REVERT: B 801 LYS cc_start: 0.8834 (mmtt) cc_final: 0.8265 (mmpt) REVERT: B 821 LYS cc_start: 0.7696 (mmtp) cc_final: 0.6838 (pttp) REVERT: B 935 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.6565 (mt-10) outliers start: 40 outliers final: 21 residues processed: 195 average time/residue: 0.7228 time to fit residues: 155.9057 Evaluate side-chains 178 residues out of total 1754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 153 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 702 THR Chi-restraints excluded: chain A residue 736 GLN Chi-restraints excluded: chain A residue 833 LYS Chi-restraints excluded: chain A residue 848 ARG Chi-restraints excluded: chain A residue 856 THR Chi-restraints excluded: chain A residue 994 ILE Chi-restraints excluded: chain A residue 1047 ILE Chi-restraints excluded: chain A residue 1067 VAL Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 681 ARG Chi-restraints excluded: chain B residue 841 SER Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 930 VAL Chi-restraints excluded: chain B residue 935 GLU Chi-restraints excluded: chain B residue 1047 SER Chi-restraints excluded: chain P residue 55 TYR Chi-restraints excluded: chain P residue 62 GLU Chi-restraints excluded: chain P residue 69 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 66 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 69 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 74 optimal weight: 0.0570 chunk 185 optimal weight: 2.9990 chunk 127 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 875 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.135023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.109665 restraints weight = 22198.072| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.89 r_work: 0.3207 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17634 Z= 0.109 Angle : 0.550 7.794 24109 Z= 0.276 Chirality : 0.042 0.136 2760 Planarity : 0.005 0.081 3082 Dihedral : 8.331 90.721 2632 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.82 % Favored : 92.13 % Rotamer: Outliers : 2.05 % Allowed : 14.38 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.62 % 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: -1.86 (0.17), residues: 2225 helix: -0.01 (0.19), residues: 868 sheet: -1.22 (0.31), residues: 259 loop : -2.30 (0.17), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 668 TYR 0.012 0.001 TYR B 288 PHE 0.014 0.001 PHE A 872 TRP 0.019 0.001 TRP A 864 HIS 0.002 0.001 HIS B 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 (17633) covalent geometry : angle 0.54955 / 0.28 (24107) SS BOND : bond 0.00201 / 0.11 ( 1) SS BOND : angle 0.79970 / 0.43 ( 2) hydrogen bonds : bond 0.03141 / 2.12 ( 588) hydrogen bonds : angle 3.98199 / 2.80 ( 1662) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 161 time to evaluate : 0.716 Fit side-chains revert: symmetry clash REVERT: A 10 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7953 (pt) REVERT: A 105 ASN cc_start: 0.7402 (t0) cc_final: 0.6961 (t0) REVERT: A 577 PHE cc_start: 0.8318 (m-80) cc_final: 0.7901 (m-10) REVERT: A 622 LYS cc_start: 0.8631 (ptpp) cc_final: 0.8292 (pttp) REVERT: A 648 TRP cc_start: 0.8157 (t60) cc_final: 0.7564 (t-100) REVERT: A 837 LYS cc_start: 0.7164 (pptt) cc_final: 0.6169 (ptmt) REVERT: A 848 ARG cc_start: 0.7002 (OUTLIER) cc_final: 0.5781 (mpt180) REVERT: A 864 TRP cc_start: 0.7078 (t-100) cc_final: 0.6556 (t-100) REVERT: A 879 LYS cc_start: 0.8283 (mttt) cc_final: 0.7981 (mttp) REVERT: A 906 LYS cc_start: 0.8371 (mttm) cc_final: 0.8086 (mtmm) REVERT: A 960 GLN cc_start: 0.8484 (tp40) cc_final: 0.8271 (mm-40) REVERT: A 1052 GLN cc_start: 0.8241 (tt0) cc_final: 0.7720 (tm-30) REVERT: B 24 ARG cc_start: 0.7930 (ttp80) cc_final: 0.7543 (ttp-170) REVERT: B 121 THR cc_start: 0.7971 (p) cc_final: 0.7589 (t) REVERT: B 146 GLN cc_start: 0.7393 (mt0) cc_final: 0.6900 (mt0) REVERT: B 149 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7977 (mt-10) REVERT: B 174 LYS cc_start: 0.8406 (mmtp) cc_final: 0.7843 (pttt) REVERT: B 227 LEU cc_start: 0.8367 (mp) cc_final: 0.7952 (tp) REVERT: B 273 MET cc_start: 0.8705 (tpp) cc_final: 0.8403 (mmt) REVERT: B 543 MET cc_start: 0.8636 (mtp) cc_final: 0.8400 (mtt) REVERT: B 801 LYS cc_start: 0.8825 (mmtt) cc_final: 0.8281 (mmpt) REVERT: B 821 LYS cc_start: 0.7677 (mmtp) cc_final: 0.6798 (pttp) REVERT: B 935 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.6623 (mt-10) outliers start: 36 outliers final: 21 residues processed: 188 average time/residue: 0.6755 time to fit residues: 140.7300 Evaluate side-chains 174 residues out of total 1754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 149 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 160 ASP Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 682 MET Chi-restraints excluded: chain A residue 702 THR Chi-restraints excluded: chain A residue 736 GLN Chi-restraints excluded: chain A residue 833 LYS Chi-restraints excluded: chain A residue 848 ARG Chi-restraints excluded: chain A residue 856 THR Chi-restraints excluded: chain A residue 994 ILE Chi-restraints excluded: chain A residue 1047 ILE Chi-restraints excluded: chain A residue 1079 LEU Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 681 ARG Chi-restraints excluded: chain B residue 841 SER Chi-restraints excluded: chain B residue 875 ASN Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 935 GLU Chi-restraints excluded: chain B residue 1047 SER Chi-restraints excluded: chain P residue 55 TYR Chi-restraints excluded: chain P residue 62 GLU Chi-restraints excluded: chain P residue 69 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 113 optimal weight: 0.0050 chunk 36 optimal weight: 1.9990 chunk 163 optimal weight: 3.9990 chunk 216 optimal weight: 0.0570 chunk 194 optimal weight: 10.0000 chunk 118 optimal weight: 0.9990 chunk 81 optimal weight: 0.0050 chunk 39 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 221 optimal weight: 7.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 904 GLN B 875 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.136445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.111212 restraints weight = 22182.045| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 1.88 r_work: 0.3233 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 17634 Z= 0.096 Angle : 0.534 7.712 24109 Z= 0.268 Chirality : 0.041 0.134 2760 Planarity : 0.004 0.073 3082 Dihedral : 8.067 82.864 2632 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.83 % Favored : 93.12 % Rotamer: Outliers : 2.11 % Allowed : 14.77 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.62 % 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: -1.68 (0.18), residues: 2225 helix: 0.14 (0.19), residues: 870 sheet: -1.14 (0.32), residues: 249 loop : -2.20 (0.17), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 337 TYR 0.011 0.001 TYR B 288 PHE 0.012 0.001 PHE A 872 TRP 0.022 0.001 TRP A 864 HIS 0.003 0.001 HIS B 673 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 (17633) covalent geometry : angle 0.53396 / 0.27 (24107) SS BOND : bond 0.00125 / 0.07 ( 1) SS BOND : angle 0.58946 / 0.32 ( 2) hydrogen bonds : bond 0.02827 / 1.91 ( 588) hydrogen bonds : angle 3.90269 / 2.74 ( 1662) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 160 time to evaluate : 0.684 Fit side-chains revert: symmetry clash REVERT: A 10 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.8015 (pt) REVERT: A 105 ASN cc_start: 0.7258 (t0) cc_final: 0.6855 (t0) REVERT: A 577 PHE cc_start: 0.8313 (m-80) cc_final: 0.7951 (m-10) REVERT: A 622 LYS cc_start: 0.8643 (ptpp) cc_final: 0.8297 (pttp) REVERT: A 648 TRP cc_start: 0.8156 (t60) cc_final: 0.7563 (t-100) REVERT: A 690 MET cc_start: 0.8813 (OUTLIER) cc_final: 0.7006 (mmm) REVERT: A 837 LYS cc_start: 0.7110 (pptt) cc_final: 0.6140 (ptmt) REVERT: A 848 ARG cc_start: 0.7007 (OUTLIER) cc_final: 0.5809 (mpt180) REVERT: A 864 TRP cc_start: 0.7156 (OUTLIER) cc_final: 0.6734 (t-100) REVERT: A 879 LYS cc_start: 0.8236 (mttt) cc_final: 0.7957 (mttp) REVERT: A 906 LYS cc_start: 0.8385 (mttm) cc_final: 0.8097 (mtmm) REVERT: A 960 GLN cc_start: 0.8469 (tp40) cc_final: 0.8263 (mm-40) REVERT: A 1052 GLN cc_start: 0.8189 (tt0) cc_final: 0.7723 (tm-30) REVERT: B 24 ARG cc_start: 0.7939 (ttp80) cc_final: 0.7603 (ttp-170) REVERT: B 121 THR cc_start: 0.8014 (p) cc_final: 0.7622 (t) REVERT: B 146 GLN cc_start: 0.7376 (mt0) cc_final: 0.6918 (mt0) REVERT: B 149 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7912 (mt-10) REVERT: B 174 LYS cc_start: 0.8394 (mmtp) cc_final: 0.7856 (pttt) REVERT: B 202 GLN cc_start: 0.8162 (mm-40) cc_final: 0.7615 (mm-40) REVERT: B 227 LEU cc_start: 0.8353 (mp) cc_final: 0.7970 (tp) REVERT: B 273 MET cc_start: 0.8703 (tpp) cc_final: 0.8421 (mmt) REVERT: B 543 MET cc_start: 0.8614 (mtp) cc_final: 0.8389 (mtt) REVERT: B 676 ARG cc_start: 0.8098 (mtp85) cc_final: 0.7860 (mtt90) REVERT: B 801 LYS cc_start: 0.8836 (mmtt) cc_final: 0.8308 (mmpt) REVERT: B 821 LYS cc_start: 0.7677 (mmtp) cc_final: 0.6776 (pttp) REVERT: B 935 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.6729 (mt-10) REVERT: P 18 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7467 (mp0) outliers start: 37 outliers final: 19 residues processed: 186 average time/residue: 0.6595 time to fit residues: 135.2673 Evaluate side-chains 179 residues out of total 1754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 153 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 160 ASP Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 682 MET Chi-restraints excluded: chain A residue 690 MET Chi-restraints excluded: chain A residue 702 THR Chi-restraints excluded: chain A residue 736 GLN Chi-restraints excluded: chain A residue 833 LYS Chi-restraints excluded: chain A residue 848 ARG Chi-restraints excluded: chain A residue 856 THR Chi-restraints excluded: chain A residue 864 TRP Chi-restraints excluded: chain A residue 994 ILE Chi-restraints excluded: chain A residue 1047 ILE Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 681 ARG Chi-restraints excluded: chain B residue 841 SER Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 935 GLU Chi-restraints excluded: chain P residue 18 GLU Chi-restraints excluded: chain P residue 55 TYR Chi-restraints excluded: chain P residue 69 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 10 optimal weight: 5.9990 chunk 126 optimal weight: 0.7980 chunk 141 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 218 optimal weight: 0.5980 chunk 146 optimal weight: 3.9990 chunk 120 optimal weight: 5.9990 chunk 215 optimal weight: 0.9980 chunk 212 optimal weight: 4.9990 chunk 167 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 875 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.133003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.107491 restraints weight = 22260.961| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 1.90 r_work: 0.3161 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17634 Z= 0.147 Angle : 0.583 7.884 24109 Z= 0.293 Chirality : 0.044 0.157 2760 Planarity : 0.005 0.070 3082 Dihedral : 8.204 76.887 2632 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.18 % Favored : 91.78 % Rotamer: Outliers : 2.28 % Allowed : 14.72 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.62 % 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: -1.76 (0.17), residues: 2225 helix: -0.01 (0.19), residues: 873 sheet: -1.20 (0.32), residues: 261 loop : -2.17 (0.17), residues: 1091 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 337 TYR 0.011 0.001 TYR A 110 PHE 0.014 0.001 PHE A 610 TRP 0.018 0.001 TRP A 864 HIS 0.003 0.001 HIS B 673 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.15 (17633) covalent geometry : angle 0.58329 / 0.29 (24107) SS BOND : bond 0.00293 / 0.15 ( 1) SS BOND : angle 1.04692 / 0.57 ( 2) hydrogen bonds : bond 0.03656 / 2.46 ( 588) hydrogen bonds : angle 4.04990 / 2.83 ( 1662) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 153 time to evaluate : 0.635 Fit side-chains revert: symmetry clash REVERT: A 10 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7989 (pt) REVERT: A 105 ASN cc_start: 0.7628 (t0) cc_final: 0.7148 (t0) REVERT: A 577 PHE cc_start: 0.8331 (m-80) cc_final: 0.7923 (m-10) REVERT: A 622 LYS cc_start: 0.8646 (ptpp) cc_final: 0.8317 (pttp) REVERT: A 648 TRP cc_start: 0.8168 (t60) cc_final: 0.7567 (t-100) REVERT: A 837 LYS cc_start: 0.7273 (pptt) cc_final: 0.6258 (ptmt) REVERT: A 848 ARG cc_start: 0.6986 (OUTLIER) cc_final: 0.5738 (mpt180) REVERT: A 864 TRP cc_start: 0.7095 (OUTLIER) cc_final: 0.6731 (t-100) REVERT: A 879 LYS cc_start: 0.8281 (mttt) cc_final: 0.7984 (mttp) REVERT: A 906 LYS cc_start: 0.8424 (mttm) cc_final: 0.8111 (mtmm) REVERT: A 1052 GLN cc_start: 0.8246 (tt0) cc_final: 0.7732 (tm-30) REVERT: B 24 ARG cc_start: 0.7904 (ttp80) cc_final: 0.7538 (ttp-170) REVERT: B 121 THR cc_start: 0.8009 (p) cc_final: 0.7601 (t) REVERT: B 146 GLN cc_start: 0.7399 (mt0) cc_final: 0.6957 (mt0) REVERT: B 149 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.8040 (mt-10) REVERT: B 174 LYS cc_start: 0.8389 (mmtp) cc_final: 0.7769 (pttt) REVERT: B 202 GLN cc_start: 0.8233 (mm-40) cc_final: 0.7687 (mm-40) REVERT: B 227 LEU cc_start: 0.8388 (mp) cc_final: 0.8000 (tp) REVERT: B 273 MET cc_start: 0.8729 (tpp) cc_final: 0.8425 (mmt) REVERT: B 543 MET cc_start: 0.8662 (mtp) cc_final: 0.8435 (mtt) REVERT: B 676 ARG cc_start: 0.8224 (mtp85) cc_final: 0.7997 (mtt-85) REVERT: B 801 LYS cc_start: 0.8816 (mmtt) cc_final: 0.8225 (mmpt) REVERT: B 821 LYS cc_start: 0.7714 (mmtp) cc_final: 0.6816 (pttp) REVERT: B 935 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.6791 (mt-10) REVERT: P 18 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7503 (mp0) outliers start: 40 outliers final: 22 residues processed: 180 average time/residue: 0.7096 time to fit residues: 140.5502 Evaluate side-chains 177 residues out of total 1754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 149 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 160 ASP Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 682 MET Chi-restraints excluded: chain A residue 702 THR Chi-restraints excluded: chain A residue 736 GLN Chi-restraints excluded: chain A residue 833 LYS Chi-restraints excluded: chain A residue 848 ARG Chi-restraints excluded: chain A residue 856 THR Chi-restraints excluded: chain A residue 864 TRP Chi-restraints excluded: chain A residue 994 ILE Chi-restraints excluded: chain A residue 1047 ILE Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 681 ARG Chi-restraints excluded: chain B residue 841 SER Chi-restraints excluded: chain B residue 875 ASN Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 935 GLU Chi-restraints excluded: chain B residue 1047 SER Chi-restraints excluded: chain P residue 18 GLU Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 55 TYR Chi-restraints excluded: chain P residue 69 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 95 optimal weight: 0.8980 chunk 124 optimal weight: 0.6980 chunk 75 optimal weight: 0.0570 chunk 58 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 154 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 82 optimal weight: 0.8980 chunk 134 optimal weight: 0.8980 chunk 74 optimal weight: 0.9980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.135141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.109788 restraints weight = 22300.956| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.89 r_work: 0.3208 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17634 Z= 0.106 Angle : 0.555 8.061 24109 Z= 0.278 Chirality : 0.042 0.149 2760 Planarity : 0.005 0.068 3082 Dihedral : 7.956 69.520 2632 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.92 % Favored : 93.03 % Rotamer: Outliers : 1.83 % Allowed : 15.29 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.62 % 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: -1.58 (0.18), residues: 2225 helix: 0.18 (0.19), residues: 871 sheet: -1.15 (0.32), residues: 261 loop : -2.09 (0.17), residues: 1093 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 337 TYR 0.014 0.001 TYR A 891 PHE 0.013 0.001 PHE A 872 TRP 0.019 0.001 TRP A 864 HIS 0.003 0.001 HIS A 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (17633) covalent geometry : angle 0.55544 / 0.28 (24107) SS BOND : bond 0.00157 / 0.08 ( 1) SS BOND : angle 0.72427 / 0.39 ( 2) hydrogen bonds : bond 0.03059 / 2.07 ( 588) hydrogen bonds : angle 3.95530 / 2.77 ( 1662) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 156 time to evaluate : 0.681 Fit side-chains revert: symmetry clash REVERT: A 10 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7963 (pt) REVERT: A 105 ASN cc_start: 0.7378 (t0) cc_final: 0.6943 (t0) REVERT: A 577 PHE cc_start: 0.8312 (m-80) cc_final: 0.7898 (m-10) REVERT: A 622 LYS cc_start: 0.8628 (ptpp) cc_final: 0.8282 (pttp) REVERT: A 648 TRP cc_start: 0.8146 (t60) cc_final: 0.7542 (t-100) REVERT: A 837 LYS cc_start: 0.7160 (pptt) cc_final: 0.6167 (ptmt) REVERT: A 848 ARG cc_start: 0.6977 (OUTLIER) cc_final: 0.5774 (mpt180) REVERT: A 864 TRP cc_start: 0.7085 (OUTLIER) cc_final: 0.6623 (t-100) REVERT: A 879 LYS cc_start: 0.8242 (mttt) cc_final: 0.7953 (mttp) REVERT: A 906 LYS cc_start: 0.8414 (mttm) cc_final: 0.8095 (mtmm) REVERT: A 960 GLN cc_start: 0.8470 (tp40) cc_final: 0.8261 (mm-40) REVERT: A 1052 GLN cc_start: 0.8200 (tt0) cc_final: 0.7718 (tm-30) REVERT: B 24 ARG cc_start: 0.7882 (ttp80) cc_final: 0.7546 (ttp-170) REVERT: B 121 THR cc_start: 0.8003 (p) cc_final: 0.7602 (t) REVERT: B 146 GLN cc_start: 0.7372 (mt0) cc_final: 0.6933 (mt0) REVERT: B 149 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7989 (mt-10) REVERT: B 174 LYS cc_start: 0.8381 (mmtp) cc_final: 0.7846 (pttt) REVERT: B 202 GLN cc_start: 0.8261 (mm-40) cc_final: 0.7722 (mm-40) REVERT: B 227 LEU cc_start: 0.8364 (mp) cc_final: 0.7984 (tp) REVERT: B 273 MET cc_start: 0.8714 (tpp) cc_final: 0.8427 (mmt) REVERT: B 543 MET cc_start: 0.8639 (mtp) cc_final: 0.8376 (mtt) REVERT: B 676 ARG cc_start: 0.8140 (mtp85) cc_final: 0.7924 (mtt-85) REVERT: B 801 LYS cc_start: 0.8823 (mmtt) cc_final: 0.8248 (mmpt) REVERT: B 821 LYS cc_start: 0.7674 (mmtp) cc_final: 0.6763 (pttp) REVERT: B 935 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.6781 (mt-10) outliers start: 32 outliers final: 20 residues processed: 179 average time/residue: 0.7111 time to fit residues: 140.7012 Evaluate side-chains 180 residues out of total 1754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 155 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 160 ASP Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 702 THR Chi-restraints excluded: chain A residue 736 GLN Chi-restraints excluded: chain A residue 833 LYS Chi-restraints excluded: chain A residue 848 ARG Chi-restraints excluded: chain A residue 856 THR Chi-restraints excluded: chain A residue 864 TRP Chi-restraints excluded: chain A residue 994 ILE Chi-restraints excluded: chain A residue 1047 ILE Chi-restraints excluded: chain A residue 1079 LEU Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 681 ARG Chi-restraints excluded: chain B residue 841 SER Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 935 GLU Chi-restraints excluded: chain B residue 1047 SER Chi-restraints excluded: chain P residue 55 TYR Chi-restraints excluded: chain P residue 69 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.3514 > 50: distance: 12 - 13: 3.185 distance: 12 - 18: 3.804 distance: 14 - 15: 11.077 distance: 14 - 19: 13.787 distance: 16 - 17: 4.987 distance: 17 - 18: 5.771 distance: 19 - 20: 6.444 distance: 20 - 21: 3.689 distance: 20 - 23: 3.674 distance: 21 - 30: 4.768 distance: 24 - 25: 3.700 distance: 25 - 26: 7.999 distance: 27 - 28: 15.351 distance: 27 - 29: 10.915 distance: 30 - 31: 5.767 distance: 31 - 32: 3.902 distance: 31 - 34: 3.799 distance: 32 - 33: 3.105 distance: 32 - 35: 4.567 distance: 33 - 230: 6.815 distance: 36 - 39: 3.383 distance: 37 - 43: 3.594 distance: 39 - 40: 11.350 distance: 40 - 42: 6.667 distance: 43 - 44: 3.463 distance: 43 - 220: 5.284 distance: 44 - 45: 5.258 distance: 44 - 47: 3.203 distance: 45 - 46: 5.781 distance: 45 - 51: 4.027 distance: 46 - 217: 3.733 distance: 47 - 48: 5.727 distance: 48 - 49: 5.056 distance: 48 - 50: 7.801 distance: 51 - 52: 4.364 distance: 52 - 53: 3.244 distance: 53 - 54: 7.053 distance: 55 - 56: 3.996 distance: 55 - 57: 12.559 distance: 58 - 59: 3.838 distance: 59 - 60: 4.494 distance: 60 - 61: 3.183 distance: 60 - 65: 7.270 distance: 62 - 63: 9.110 distance: 62 - 64: 9.633 distance: 65 - 66: 8.121 distance: 66 - 67: 4.947 distance: 66 - 69: 7.446 distance: 67 - 68: 5.788 distance: 67 - 73: 6.686 distance: 69 - 70: 12.277 distance: 69 - 71: 15.809 distance: 70 - 72: 6.054 distance: 73 - 74: 7.487 distance: 73 - 79: 7.661 distance: 74 - 75: 5.528 distance: 74 - 77: 14.369 distance: 75 - 76: 36.934 distance: 75 - 80: 14.866 distance: 77 - 78: 10.271 distance: 78 - 79: 9.367 distance: 80 - 81: 14.130 distance: 81 - 82: 17.431 distance: 81 - 84: 6.977 distance: 82 - 83: 17.038 distance: 82 - 86: 8.207 distance: 84 - 85: 28.180