Starting phenix.real_space_refine on Wed Aug 27 02:07:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6mdo_9102/08_2025/6mdo_9102_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6mdo_9102/08_2025/6mdo_9102.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6mdo_9102/08_2025/6mdo_9102.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6mdo_9102/08_2025/6mdo_9102.map" model { file = "/net/cci-nas-00/data/ceres_data/6mdo_9102/08_2025/6mdo_9102_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6mdo_9102/08_2025/6mdo_9102_trim.cif" } resolution = 3.9 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 31 5.49 5 S 125 5.16 5 C 14171 2.51 5 N 3917 2.21 5 O 4271 1.98 5 H 22858 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Residue "A ARG 388": not complete - not flipped Time to flip 56 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 45373 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 8082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 8082 Classifications: {'peptide': 511} Link IDs: {'PTRANS': 22, 'TRANS': 488} Chain breaks: 1 Chain: "B" Number of atoms: 8203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 519, 8203 Classifications: {'peptide': 519} Link IDs: {'PTRANS': 23, 'TRANS': 495} Chain breaks: 1 Chain: "C" Number of atoms: 8244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 8244 Classifications: {'peptide': 521} Link IDs: {'PTRANS': 23, 'TRANS': 497} Chain breaks: 1 Chain: "D" Number of atoms: 8308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 8308 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 23, 'TRANS': 501} Chain breaks: 1 Chain: "E" Number of atoms: 8059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 509, 8059 Classifications: {'peptide': 509} Link IDs: {'PTRANS': 20, 'TRANS': 488} Chain breaks: 2 Chain: "F" Number of atoms: 3874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 3874 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 12, 'TRANS': 228} Chain: "H" Number of atoms: 270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 270 Classifications: {'peptide': 17} Link IDs: {'TRANS': 16} Chain: "A" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.63, per 1000 atoms: 0.19 Number of scatterers: 45373 At special positions: 0 Unit cell: (148.03, 131, 117.9, 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) S 125 16.00 P 31 15.00 O 4271 8.00 N 3917 7.00 C 14171 6.00 H 22858 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.45 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 715.3 nanoseconds 5634 Ramachandran restraints generated. 2817 Oldfield, 0 Emsley, 2817 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5260 Finding SS restraints... Secondary structure from input PDB file: 128 helices and 14 sheets defined 53.4% alpha, 7.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.39 Creating SS restraints... Processing helix chain 'A' and resid 223 through 234 Processing helix chain 'A' and resid 241 through 249 removed outlier: 3.772A pdb=" N VAL A 245 " --> pdb=" O PRO A 241 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N GLN A 247 " --> pdb=" O GLU A 243 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N MET A 248 " --> pdb=" O ILE A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 277 removed outlier: 3.616A pdb=" N ARG A 271 " --> pdb=" O THR A 267 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN A 272 " --> pdb=" O LEU A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 317 removed outlier: 4.335A pdb=" N SER A 298 " --> pdb=" O TYR A 294 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLU A 299 " --> pdb=" O VAL A 295 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N ALA A 309 " --> pdb=" O LEU A 305 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU A 310 " --> pdb=" O PHE A 306 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU A 311 " --> pdb=" O ALA A 307 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N GLU A 312 " --> pdb=" O ASP A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 359 removed outlier: 3.802A pdb=" N GLN A 353 " --> pdb=" O THR A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 418 removed outlier: 4.654A pdb=" N ARG A 413 " --> pdb=" O ILE A 409 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N MET A 414 " --> pdb=" O HIS A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 432 removed outlier: 3.906A pdb=" N VAL A 431 " --> pdb=" O LYS A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 455 removed outlier: 3.869A pdb=" N GLU A 442 " --> pdb=" O GLY A 438 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLY A 443 " --> pdb=" O ALA A 439 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ALA A 452 " --> pdb=" O ALA A 448 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N MET A 453 " --> pdb=" O GLN A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 486 Processing helix chain 'A' and resid 498 through 503 removed outlier: 4.176A pdb=" N TYR A 502 " --> pdb=" O ASP A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 531 removed outlier: 3.754A pdb=" N THR A 515 " --> pdb=" O GLY A 511 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLN A 526 " --> pdb=" O GLU A 522 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLN A 527 " --> pdb=" O LEU A 523 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR A 528 " --> pdb=" O LEU A 524 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS A 529 " --> pdb=" O VAL A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 559 Processing helix chain 'A' and resid 569 through 574 Processing helix chain 'A' and resid 577 through 594 removed outlier: 3.807A pdb=" N CYS A 582 " --> pdb=" O GLU A 578 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLN A 583 " --> pdb=" O THR A 579 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS A 587 " --> pdb=" O GLN A 583 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYS A 594 " --> pdb=" O ASP A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 609 removed outlier: 3.508A pdb=" N LEU A 608 " --> pdb=" O ASP A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 631 removed outlier: 3.729A pdb=" N LEU A 623 " --> pdb=" O SER A 619 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU A 629 " --> pdb=" O ALA A 625 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 655 Processing helix chain 'A' and resid 672 through 684 removed outlier: 3.908A pdb=" N GLU A 678 " --> pdb=" O GLU A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 698 removed outlier: 3.556A pdb=" N ILE A 694 " --> pdb=" O GLU A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 719 removed outlier: 3.802A pdb=" N GLN A 719 " --> pdb=" O GLU A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 734 removed outlier: 4.709A pdb=" N VAL A 726 " --> pdb=" O PRO A 722 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N ARG A 727 " --> pdb=" O GLU A 723 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 240 removed outlier: 5.533A pdb=" N SER B 237 " --> pdb=" O ARG B 233 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N ARG B 238 " --> pdb=" O ALA B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 249 Processing helix chain 'B' and resid 266 through 277 Processing helix chain 'B' and resid 296 through 316 removed outlier: 4.103A pdb=" N ILE B 302 " --> pdb=" O SER B 298 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU B 305 " --> pdb=" O ASN B 301 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N PHE B 306 " --> pdb=" O ILE B 302 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ASP B 308 " --> pdb=" O LYS B 304 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ALA B 309 " --> pdb=" O LEU B 305 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU B 311 " --> pdb=" O ALA B 307 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLU B 312 " --> pdb=" O ASP B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 334 removed outlier: 4.232A pdb=" N ILE B 333 " --> pdb=" O GLU B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 359 removed outlier: 3.910A pdb=" N ASP B 359 " --> pdb=" O LEU B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 379 removed outlier: 3.879A pdb=" N LEU B 378 " --> pdb=" O ARG B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 385 Processing helix chain 'B' and resid 399 through 417 removed outlier: 3.805A pdb=" N LEU B 407 " --> pdb=" O ARG B 403 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ARG B 413 " --> pdb=" O ILE B 409 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N MET B 414 " --> pdb=" O HIS B 410 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N HIS B 417 " --> pdb=" O ARG B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 433 Processing helix chain 'B' and resid 437 through 455 removed outlier: 3.987A pdb=" N GLU B 442 " --> pdb=" O GLY B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 486 Processing helix chain 'B' and resid 498 through 502 removed outlier: 3.644A pdb=" N SER B 501 " --> pdb=" O ASP B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 511 through 530 removed outlier: 4.076A pdb=" N THR B 515 " --> pdb=" O GLY B 511 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU B 518 " --> pdb=" O VAL B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 560 Processing helix chain 'B' and resid 569 through 573 Processing helix chain 'B' and resid 577 through 593 removed outlier: 3.707A pdb=" N ALA B 584 " --> pdb=" O ALA B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 609 Processing helix chain 'B' and resid 619 through 630 Processing helix chain 'B' and resid 649 through 655 Processing helix chain 'B' and resid 673 through 684 Processing helix chain 'B' and resid 687 through 698 Processing helix chain 'B' and resid 706 through 719 removed outlier: 3.677A pdb=" N MET B 712 " --> pdb=" O LYS B 708 " (cutoff:3.500A) Processing helix chain 'B' and resid 721 through 735 removed outlier: 4.362A pdb=" N VAL B 726 " --> pdb=" O PRO B 722 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ARG B 727 " --> pdb=" O GLU B 723 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 236 removed outlier: 3.674A pdb=" N ALA C 236 " --> pdb=" O ARG C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 249 removed outlier: 3.648A pdb=" N VAL C 245 " --> pdb=" O PRO C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 277 Processing helix chain 'C' and resid 296 through 307 removed outlier: 3.820A pdb=" N ILE C 302 " --> pdb=" O SER C 298 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG C 303 " --> pdb=" O GLU C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 317 Processing helix chain 'C' and resid 329 through 334 removed outlier: 4.230A pdb=" N ILE C 333 " --> pdb=" O GLU C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 359 removed outlier: 3.951A pdb=" N VAL C 351 " --> pdb=" O HIS C 347 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N SER C 356 " --> pdb=" O ASN C 352 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASP C 359 " --> pdb=" O LEU C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 385 Processing helix chain 'C' and resid 399 through 417 removed outlier: 4.173A pdb=" N ARG C 413 " --> pdb=" O ILE C 409 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N MET C 414 " --> pdb=" O HIS C 410 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N HIS C 417 " --> pdb=" O ARG C 413 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 433 removed outlier: 3.727A pdb=" N LEU C 429 " --> pdb=" O ASP C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 457 removed outlier: 3.562A pdb=" N GLY C 443 " --> pdb=" O ALA C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 486 Processing helix chain 'C' and resid 497 through 503 removed outlier: 4.080A pdb=" N SER C 501 " --> pdb=" O GLU C 497 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N TYR C 502 " --> pdb=" O ASP C 498 " (cutoff:3.500A) Processing helix chain 'C' and resid 511 through 531 removed outlier: 3.710A pdb=" N THR C 515 " --> pdb=" O GLY C 511 " (cutoff:3.500A) Processing helix chain 'C' and resid 549 through 561 removed outlier: 3.760A pdb=" N ALA C 557 " --> pdb=" O ALA C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 577 through 593 Processing helix chain 'C' and resid 604 through 609 Processing helix chain 'C' and resid 619 through 631 removed outlier: 3.605A pdb=" N LEU C 623 " --> pdb=" O SER C 619 " (cutoff:3.500A) Processing helix chain 'C' and resid 649 through 655 Processing helix chain 'C' and resid 672 through 684 Processing helix chain 'C' and resid 687 through 699 removed outlier: 4.199A pdb=" N THR C 693 " --> pdb=" O LYS C 689 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE C 694 " --> pdb=" O GLU C 690 " (cutoff:3.500A) Processing helix chain 'C' and resid 706 through 719 removed outlier: 3.787A pdb=" N MET C 712 " --> pdb=" O LYS C 708 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLU C 715 " --> pdb=" O LEU C 711 " (cutoff:3.500A) Processing helix chain 'C' and resid 721 through 738 removed outlier: 4.605A pdb=" N VAL C 726 " --> pdb=" O PRO C 722 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N ARG C 727 " --> pdb=" O GLU C 723 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N GLU C 735 " --> pdb=" O ALA C 731 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLU C 736 " --> pdb=" O LEU C 732 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 235 Processing helix chain 'D' and resid 235 through 240 Processing helix chain 'D' and resid 241 through 248 removed outlier: 4.466A pdb=" N VAL D 245 " --> pdb=" O PRO D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 276 removed outlier: 3.628A pdb=" N LEU D 269 " --> pdb=" O GLY D 265 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N GLY D 274 " --> pdb=" O ALA D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 291 removed outlier: 4.303A pdb=" N ILE D 290 " --> pdb=" O GLY D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 316 removed outlier: 3.619A pdb=" N ILE D 302 " --> pdb=" O SER D 298 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LYS D 304 " --> pdb=" O ALA D 300 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU D 305 " --> pdb=" O ASN D 301 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N ASP D 308 " --> pdb=" O LYS D 304 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ALA D 309 " --> pdb=" O LEU D 305 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN D 313 " --> pdb=" O ALA D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 334 removed outlier: 4.431A pdb=" N ILE D 333 " --> pdb=" O GLU D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 348 removed outlier: 3.980A pdb=" N ASP D 348 " --> pdb=" O GLY D 345 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 345 through 348' Processing helix chain 'D' and resid 349 through 359 removed outlier: 4.134A pdb=" N GLN D 353 " --> pdb=" O THR D 349 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASP D 359 " --> pdb=" O LEU D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 384 Processing helix chain 'D' and resid 401 through 417 removed outlier: 3.623A pdb=" N GLN D 405 " --> pdb=" O LYS D 401 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N HIS D 410 " --> pdb=" O ILE D 406 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N ARG D 413 " --> pdb=" O ILE D 409 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N MET D 414 " --> pdb=" O HIS D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 433 Processing helix chain 'D' and resid 438 through 458 removed outlier: 4.163A pdb=" N LEU D 444 " --> pdb=" O GLU D 440 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N VAL D 445 " --> pdb=" O LEU D 441 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ARG D 455 " --> pdb=" O THR D 451 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N HIS D 456 " --> pdb=" O ALA D 452 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE D 458 " --> pdb=" O ASN D 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 481 through 489 Processing helix chain 'D' and resid 511 through 531 removed outlier: 4.000A pdb=" N THR D 515 " --> pdb=" O GLY D 511 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLN D 526 " --> pdb=" O GLU D 522 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLN D 527 " --> pdb=" O LEU D 523 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N THR D 528 " --> pdb=" O LEU D 524 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS D 529 " --> pdb=" O VAL D 525 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 561 removed outlier: 3.695A pdb=" N ALA D 554 " --> pdb=" O THR D 550 " (cutoff:3.500A) Processing helix chain 'D' and resid 577 through 595 removed outlier: 3.820A pdb=" N MET D 585 " --> pdb=" O LYS D 581 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS D 594 " --> pdb=" O ASP D 590 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N SER D 595 " --> pdb=" O ASP D 591 " (cutoff:3.500A) Processing helix chain 'D' and resid 604 through 609 Processing helix chain 'D' and resid 619 through 631 removed outlier: 4.133A pdb=" N LEU D 623 " --> pdb=" O SER D 619 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LYS D 631 " --> pdb=" O LEU D 627 " (cutoff:3.500A) Processing helix chain 'D' and resid 634 through 638 removed outlier: 4.193A pdb=" N GLY D 637 " --> pdb=" O PRO D 634 " (cutoff:3.500A) Processing helix chain 'D' and resid 651 through 656 removed outlier: 3.569A pdb=" N MET D 655 " --> pdb=" O VAL D 651 " (cutoff:3.500A) Processing helix chain 'D' and resid 656 through 661 removed outlier: 3.860A pdb=" N ALA D 660 " --> pdb=" O GLU D 656 " (cutoff:3.500A) Processing helix chain 'D' and resid 672 through 684 Processing helix chain 'D' and resid 687 through 699 removed outlier: 5.026A pdb=" N GLN D 697 " --> pdb=" O THR D 693 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL D 698 " --> pdb=" O ILE D 694 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N LYS D 699 " --> pdb=" O ALA D 695 " (cutoff:3.500A) Processing helix chain 'D' and resid 706 through 720 removed outlier: 4.313A pdb=" N MET D 712 " --> pdb=" O LYS D 708 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N MET D 720 " --> pdb=" O MET D 716 " (cutoff:3.500A) Processing helix chain 'D' and resid 721 through 737 removed outlier: 4.399A pdb=" N VAL D 726 " --> pdb=" O PRO D 722 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ARG D 727 " --> pdb=" O GLU D 723 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU D 735 " --> pdb=" O ALA D 731 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 236 removed outlier: 3.904A pdb=" N PHE E 227 " --> pdb=" O LEU E 223 " (cutoff:3.500A) Processing helix chain 'E' and resid 265 through 278 removed outlier: 4.021A pdb=" N ASN E 278 " --> pdb=" O GLY E 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 291 removed outlier: 4.495A pdb=" N ILE E 290 " --> pdb=" O GLY E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 296 through 317 removed outlier: 4.561A pdb=" N ILE E 302 " --> pdb=" O SER E 298 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ARG E 303 " --> pdb=" O GLU E 299 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LEU E 305 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ASP E 308 " --> pdb=" O LYS E 304 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA E 309 " --> pdb=" O LEU E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 329 through 334 removed outlier: 3.806A pdb=" N ILE E 333 " --> pdb=" O GLU E 329 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 359 Processing helix chain 'E' and resid 376 through 384 removed outlier: 4.766A pdb=" N GLU E 381 " --> pdb=" O ASP E 377 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N ALA E 382 " --> pdb=" O LEU E 378 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU E 383 " --> pdb=" O ILE E 379 " (cutoff:3.500A) Processing helix chain 'E' and resid 399 through 411 Processing helix chain 'E' and resid 411 through 416 Processing helix chain 'E' and resid 425 through 433 removed outlier: 4.518A pdb=" N VAL E 431 " --> pdb=" O LYS E 427 " (cutoff:3.500A) Processing helix chain 'E' and resid 437 through 455 removed outlier: 3.754A pdb=" N LEU E 441 " --> pdb=" O SER E 437 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU E 442 " --> pdb=" O GLY E 438 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA E 452 " --> pdb=" O ALA E 448 " (cutoff:3.500A) Processing helix chain 'E' and resid 479 through 489 removed outlier: 3.879A pdb=" N SER E 483 " --> pdb=" O ASP E 479 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ILE E 488 " --> pdb=" O LEU E 484 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LYS E 489 " --> pdb=" O GLU E 485 " (cutoff:3.500A) Processing helix chain 'E' and resid 511 through 531 removed outlier: 4.106A pdb=" N THR E 515 " --> pdb=" O GLY E 511 " (cutoff:3.500A) Processing helix chain 'E' and resid 548 through 561 removed outlier: 3.601A pdb=" N LEU E 552 " --> pdb=" O GLY E 548 " (cutoff:3.500A) Processing helix chain 'E' and resid 577 through 584 Processing helix chain 'E' and resid 584 through 595 removed outlier: 3.741A pdb=" N ILE E 588 " --> pdb=" O ALA E 584 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N SER E 595 " --> pdb=" O ASP E 591 " (cutoff:3.500A) Processing helix chain 'E' and resid 604 through 609 Processing helix chain 'E' and resid 619 through 632 removed outlier: 3.539A pdb=" N LEU E 623 " --> pdb=" O SER E 619 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N LEU E 629 " --> pdb=" O ALA E 625 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU E 630 " --> pdb=" O LEU E 626 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS E 631 " --> pdb=" O LEU E 627 " (cutoff:3.500A) Processing helix chain 'E' and resid 649 through 655 Processing helix chain 'E' and resid 672 through 684 Processing helix chain 'E' and resid 687 through 699 removed outlier: 3.745A pdb=" N GLN E 696 " --> pdb=" O THR E 692 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLN E 697 " --> pdb=" O THR E 693 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N LYS E 699 " --> pdb=" O ALA E 695 " (cutoff:3.500A) Processing helix chain 'E' and resid 706 through 719 removed outlier: 3.638A pdb=" N GLU E 715 " --> pdb=" O LEU E 711 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN E 719 " --> pdb=" O GLU E 715 " (cutoff:3.500A) Processing helix chain 'E' and resid 725 through 734 removed outlier: 4.011A pdb=" N ALA E 731 " --> pdb=" O ARG E 727 " (cutoff:3.500A) Processing helix chain 'F' and resid 499 through 503 removed outlier: 4.105A pdb=" N ILE F 503 " --> pdb=" O TYR F 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 499 through 503' Processing helix chain 'F' and resid 511 through 530 removed outlier: 3.772A pdb=" N THR F 515 " --> pdb=" O GLY F 511 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU F 524 " --> pdb=" O ASP F 520 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LYS F 529 " --> pdb=" O VAL F 525 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN F 530 " --> pdb=" O GLN F 526 " (cutoff:3.500A) Processing helix chain 'F' and resid 549 through 560 Processing helix chain 'F' and resid 577 through 595 removed outlier: 3.828A pdb=" N GLN F 583 " --> pdb=" O THR F 579 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ASP F 591 " --> pdb=" O LYS F 587 " (cutoff:3.500A) Processing helix chain 'F' and resid 604 through 609 Processing helix chain 'F' and resid 619 through 631 removed outlier: 3.635A pdb=" N LEU F 623 " --> pdb=" O SER F 619 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LYS F 631 " --> pdb=" O LEU F 627 " (cutoff:3.500A) Processing helix chain 'F' and resid 649 through 655 Processing helix chain 'F' and resid 672 through 684 Processing helix chain 'F' and resid 687 through 696 removed outlier: 3.920A pdb=" N THR F 693 " --> pdb=" O LYS F 689 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ILE F 694 " --> pdb=" O GLU F 690 " (cutoff:3.500A) Processing helix chain 'F' and resid 706 through 720 removed outlier: 4.078A pdb=" N GLU F 715 " --> pdb=" O LEU F 711 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N MET F 716 " --> pdb=" O MET F 712 " (cutoff:3.500A) Processing helix chain 'F' and resid 724 through 736 removed outlier: 3.556A pdb=" N LEU F 730 " --> pdb=" O VAL F 726 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA F 731 " --> pdb=" O ARG F 727 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 283 through 285 removed outlier: 3.609A pdb=" N LYS A 283 " --> pdb=" O ILE A 324 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU A 368 " --> pdb=" O HIS A 323 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR A 373 " --> pdb=" O LEU A 258 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N VAL A 391 " --> pdb=" O GLY A 255 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 564 through 568 removed outlier: 6.258A pdb=" N PHE A 564 " --> pdb=" O CYS A 599 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N VAL A 601 " --> pdb=" O PHE A 564 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LYS A 566 " --> pdb=" O VAL A 601 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N THR A 663 " --> pdb=" O SER A 538 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU A 540 " --> pdb=" O THR A 663 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 280 through 285 removed outlier: 5.417A pdb=" N ILE B 324 " --> pdb=" O GLU B 281 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N ILE B 370 " --> pdb=" O HIS B 323 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ILE B 325 " --> pdb=" O ILE B 370 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N MET B 372 " --> pdb=" O ILE B 325 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N PHE B 327 " --> pdb=" O MET B 372 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N VAL B 391 " --> pdb=" O GLY B 255 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 564 through 568 removed outlier: 6.485A pdb=" N PHE B 564 " --> pdb=" O CYS B 599 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N VAL B 601 " --> pdb=" O PHE B 564 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N LYS B 566 " --> pdb=" O VAL B 601 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL B 539 " --> pdb=" O GLY B 644 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N THR B 646 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N LEU B 541 " --> pdb=" O THR B 646 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU B 540 " --> pdb=" O THR B 663 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 670 through 672 Processing sheet with id=AA6, first strand: chain 'C' and resid 283 through 284 removed outlier: 7.203A pdb=" N HIS C 323 " --> pdb=" O LEU C 368 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N ILE C 370 " --> pdb=" O HIS C 323 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ILE C 325 " --> pdb=" O ILE C 370 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N MET C 372 " --> pdb=" O ILE C 325 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LEU C 258 " --> pdb=" O THR C 373 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N MET C 393 " --> pdb=" O LEU C 257 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 597 through 601 removed outlier: 6.612A pdb=" N SER C 598 " --> pdb=" O LEU C 641 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N ILE C 643 " --> pdb=" O SER C 598 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N VAL C 600 " --> pdb=" O ILE C 643 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N THR C 645 " --> pdb=" O VAL C 600 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 255 through 259 removed outlier: 3.701A pdb=" N LEU D 368 " --> pdb=" O HIS D 323 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LYS D 283 " --> pdb=" O ILE D 326 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 565 through 568 removed outlier: 6.529A pdb=" N SER D 598 " --> pdb=" O LEU D 641 " (cutoff:3.500A) removed outlier: 8.372A pdb=" N ILE D 643 " --> pdb=" O SER D 598 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N VAL D 600 " --> pdb=" O ILE D 643 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N THR D 645 " --> pdb=" O VAL D 600 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N VAL D 602 " --> pdb=" O THR D 645 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 611 through 612 removed outlier: 3.601A pdb=" N VAL D 612 " --> pdb=" O ARG D 617 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG D 617 " --> pdb=" O VAL D 612 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'E' and resid 372 through 373 removed outlier: 6.581A pdb=" N LEU E 258 " --> pdb=" O THR E 373 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 283 through 285 removed outlier: 6.695A pdb=" N LYS E 283 " --> pdb=" O ILE E 326 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 565 through 568 removed outlier: 3.554A pdb=" N LYS E 566 " --> pdb=" O CYS E 599 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N VAL E 539 " --> pdb=" O ILE E 642 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR E 646 " --> pdb=" O LEU E 541 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 564 through 568 removed outlier: 4.177A pdb=" N CYS F 599 " --> pdb=" O PHE F 564 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N LYS F 566 " --> pdb=" O CYS F 599 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL F 601 " --> pdb=" O LYS F 566 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU F 641 " --> pdb=" O SER F 598 " (cutoff:3.500A) 940 hydrogen bonds defined for protein. 2772 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: 11.11 Time building geometry restraints manager: 5.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 22825 1.02 - 1.22: 45 1.22 - 1.42: 8880 1.42 - 1.62: 13756 1.62 - 1.82: 217 Bond restraints: 45723 Sorted by residual: bond pdb=" C4 ATP B 802 " pdb=" N9 ATP B 802 " ideal model delta sigma weight residual 1.374 1.300 0.074 1.00e-02 1.00e+04 5.41e+01 bond pdb=" C4 ATP F 801 " pdb=" C5 ATP F 801 " ideal model delta sigma weight residual 1.388 1.459 -0.071 1.00e-02 1.00e+04 5.10e+01 bond pdb=" C4 ATP E 801 " pdb=" C5 ATP E 801 " ideal model delta sigma weight residual 1.388 1.459 -0.071 1.00e-02 1.00e+04 5.01e+01 bond pdb=" C4 ATP D 801 " pdb=" C5 ATP D 801 " ideal model delta sigma weight residual 1.388 1.458 -0.070 1.00e-02 1.00e+04 4.86e+01 bond pdb=" C4 ATP C 802 " pdb=" C5 ATP C 802 " ideal model delta sigma weight residual 1.388 1.456 -0.068 1.00e-02 1.00e+04 4.60e+01 ... (remaining 45718 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.76: 82996 6.76 - 13.52: 125 13.52 - 20.28: 9 20.28 - 27.04: 41 27.04 - 33.80: 8 Bond angle restraints: 83179 Sorted by residual: angle pdb=" PB ATP A 801 " pdb=" O3B ATP A 801 " pdb=" PG ATP A 801 " ideal model delta sigma weight residual 139.87 113.53 26.34 1.00e+00 1.00e+00 6.94e+02 angle pdb=" PB ATP C 801 " pdb=" O3B ATP C 801 " pdb=" PG ATP C 801 " ideal model delta sigma weight residual 139.87 114.01 25.86 1.00e+00 1.00e+00 6.69e+02 angle pdb=" PA ATP A 801 " pdb=" O3A ATP A 801 " pdb=" PB ATP A 801 " ideal model delta sigma weight residual 136.83 111.28 25.55 1.00e+00 1.00e+00 6.53e+02 angle pdb=" PB ATP D 802 " pdb=" O3B ATP D 802 " pdb=" PG ATP D 802 " ideal model delta sigma weight residual 139.87 114.48 25.39 1.00e+00 1.00e+00 6.45e+02 angle pdb=" PB ATP B 802 " pdb=" O3B ATP B 802 " pdb=" PG ATP B 802 " ideal model delta sigma weight residual 139.87 114.85 25.02 1.00e+00 1.00e+00 6.26e+02 ... (remaining 83174 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 36.00: 20653 36.00 - 72.00: 561 72.00 - 107.99: 25 107.99 - 143.99: 5 143.99 - 179.99: 2 Dihedral angle restraints: 21246 sinusoidal: 12276 harmonic: 8970 Sorted by residual: dihedral pdb=" CA PRO D 613 " pdb=" C PRO D 613 " pdb=" N ILE D 614 " pdb=" CA ILE D 614 " ideal model delta harmonic sigma weight residual 180.00 101.34 78.66 0 5.00e+00 4.00e-02 2.47e+02 dihedral pdb=" CD ARG A 388 " pdb=" NE ARG A 388 " pdb=" CZ ARG A 388 " pdb=" NH1 ARG A 388 " ideal model delta sinusoidal sigma weight residual 0.00 179.99 -179.99 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" CA ASN C 214 " pdb=" C ASN C 214 " pdb=" N PHE C 215 " pdb=" CA PHE C 215 " ideal model delta harmonic sigma weight residual 180.00 134.43 45.57 0 5.00e+00 4.00e-02 8.31e+01 ... (remaining 21243 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.561: 3522 0.561 - 1.122: 0 1.122 - 1.684: 0 1.684 - 2.245: 6 2.245 - 2.806: 1 Chirality restraints: 3529 Sorted by residual: chirality pdb=" CG LEU B 420 " pdb=" CB LEU B 420 " pdb=" CD1 LEU B 420 " pdb=" CD2 LEU B 420 " both_signs ideal model delta sigma weight residual False -2.59 0.22 -2.81 2.00e-01 2.50e+01 1.97e+02 chirality pdb=" CG LEU C 484 " pdb=" CB LEU C 484 " pdb=" CD1 LEU C 484 " pdb=" CD2 LEU C 484 " both_signs ideal model delta sigma weight residual False -2.59 -0.64 -1.95 2.00e-01 2.50e+01 9.49e+01 chirality pdb=" CG LEU E 713 " pdb=" CB LEU E 713 " pdb=" CD1 LEU E 713 " pdb=" CD2 LEU E 713 " both_signs ideal model delta sigma weight residual False -2.59 -0.65 -1.94 2.00e-01 2.50e+01 9.37e+01 ... (remaining 3526 not shown) Planarity restraints: 6639 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO D 241 " 0.017 2.00e-02 2.50e+03 3.39e-02 1.15e+01 pdb=" C PRO D 241 " -0.059 2.00e-02 2.50e+03 pdb=" O PRO D 241 " 0.022 2.00e-02 2.50e+03 pdb=" N PRO D 242 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 671 " 0.017 2.00e-02 2.50e+03 3.34e-02 1.11e+01 pdb=" C ALA B 671 " -0.058 2.00e-02 2.50e+03 pdb=" O ALA B 671 " 0.022 2.00e-02 2.50e+03 pdb=" N THR B 672 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS F 549 " -0.016 2.00e-02 2.50e+03 3.27e-02 1.07e+01 pdb=" C LYS F 549 " 0.057 2.00e-02 2.50e+03 pdb=" O LYS F 549 " -0.021 2.00e-02 2.50e+03 pdb=" N THR F 550 " -0.019 2.00e-02 2.50e+03 ... (remaining 6636 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 3814 2.21 - 2.81: 100942 2.81 - 3.40: 117238 3.40 - 4.00: 155767 4.00 - 4.60: 241788 Nonbonded interactions: 619549 Sorted by model distance: nonbonded pdb=" O LEU D 355 " pdb="HH12 ARG D 388 " model vdw 1.610 2.450 nonbonded pdb="HH21 ARG A 385 " pdb=" O1B ATP B 801 " model vdw 1.625 2.450 nonbonded pdb=" OE1 GLU A 390 " pdb="HH12 ARG B 446 " model vdw 1.627 2.450 nonbonded pdb=" H GLY B 222 " pdb=" OE1 GLN B 405 " model vdw 1.627 2.450 nonbonded pdb=" O GLU A 243 " pdb="HE22 GLN A 247 " model vdw 1.634 2.450 ... (remaining 619544 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 215 through 240 or resid 250 through 457 or resid 459 thro \ ugh 547 or (resid 548 and (name N or name CA or name C or name O or name HA2 or \ name HA3)) or resid 549 through 801)) selection = (chain 'B' and (resid 215 through 240 or resid 250 through 263 or (resid 264 and \ (name N or name CA or name C or name O or name CB or name SG or name HA or name \ HB2 or name HB3 or name HG )) or resid 265 through 387 or (resid 388 and (name \ N or name CA or name C or name O or name CB or name CG or name CD or name NE or \ name CZ or name NH1 or name NH2 or name H or name HA or name HB2 or name HB3 or \ name HG2 or name HG3 or name HD2 or name HD3 or name HE or name HH11 or name HH1 \ 2 or name HH21)) or resid 389 through 457 or resid 459 or resid 477 through 547 \ or (resid 548 and (name N or name CA or name C or name O or name HA2 or name HA3 \ )) or resid 549 through 801)) selection = (chain 'C' and (resid 215 through 240 or resid 250 through 263 or (resid 264 and \ (name N or name CA or name C or name O or name CB or name SG or name HA or name \ HB2 or name HB3 or name HG )) or resid 265 through 387 or (resid 388 and (name \ N or name CA or name C or name O or name CB or name CG or name CD or name NE or \ name CZ or name NH1 or name NH2 or name H or name HA or name HB2 or name HB3 or \ name HG2 or name HG3 or name HD2 or name HD3 or name HE or name HH11 or name HH1 \ 2 or name HH21)) or resid 389 through 457 or resid 470 or resid 477 through 547 \ or (resid 548 and (name N or name CA or name C or name O or name HA2 or name HA3 \ )) or resid 549 through 801)) selection = (chain 'D' and (resid 215 through 240 or resid 250 through 263 or (resid 264 and \ (name N or name CA or name C or name O or name CB or name SG or name HA or name \ HB2 or name HB3 or name HG )) or resid 265 through 387 or (resid 388 and (name \ N or name CA or name C or name O or name CB or name CG or name CD or name NE or \ name CZ or name NH1 or name NH2 or name H or name HA or name HB2 or name HB3 or \ name HG2 or name HG3 or name HD2 or name HD3 or name HE or name HH11 or name HH1 \ 2 or name HH21)) or resid 389 through 457 or resid 470 or resid 477 through 801) \ ) selection = (chain 'E' and (resid 215 through 263 or (resid 264 and (name N or name CA or na \ me C or name O or name CB or name SG or name HA or name HB2 or name HB3 or name \ HG )) or resid 265 through 387 or (resid 388 and (name N or name CA or name C or \ name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or na \ me NH2 or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 or n \ ame HD2 or name HD3 or name HE or name HH11 or name HH12 or name HH21)) or resid \ 389 through 457 or resid 470 or resid 477 through 547 or (resid 548 and (name N \ or name CA or name C or name O or name HA2 or name HA3)) or resid 549 through 8 \ 01)) } 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 group one per residue 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: 0.780 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: 0.290 Extract box with map and model: 0.620 Check model and map are aligned: 0.150 Set scattering table: 0.120 Process input model: 43.670 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 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 : 0.015 0.138 22865 Z= 0.654 Angle : 1.436 26.338 30876 Z= 0.933 Chirality : 0.115 2.806 3529 Planarity : 0.007 0.067 3934 Dihedral : 14.298 179.987 9033 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.04 % Allowed : 0.32 % Favored : 99.65 % Rotamer: Outliers : 0.16 % Allowed : 7.33 % Favored : 92.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.44 % Twisted General : 0.59 % 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 aren not related in a simple way. whole: -3.28 (0.13), residues: 2817 helix: -2.41 (0.12), residues: 1276 sheet: -1.69 (0.22), residues: 337 loop : -1.85 (0.14), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.002 ARG C 233 TYR 0.036 0.004 TYR F 593 PHE 0.028 0.004 PHE D 240 TRP 0.026 0.004 TRP B 213 HIS 0.016 0.003 HIS C 347 Details of bonding type rmsd covalent geometry : bond 0.01462 (22865) covalent geometry : angle 1.43571 (30876) hydrogen bonds : bond 0.11405 ( 940) hydrogen bonds : angle 6.87534 ( 2772) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5634 Ramachandran restraints generated. 2817 Oldfield, 0 Emsley, 2817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5634 Ramachandran restraints generated. 2817 Oldfield, 0 Emsley, 2817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 14 is missing expected H atoms. Skipping. Evaluate side-chains 231 residues out of total 2427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 227 time to evaluate : 1.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 481 LEU cc_start: 0.7829 (OUTLIER) cc_final: 0.7626 (tm) outliers start: 4 outliers final: 1 residues processed: 231 average time/residue: 0.4387 time to fit residues: 151.6673 Evaluate side-chains 163 residues out of total 2427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 161 time to evaluate : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain D residue 477 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 0.9980 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 GLN A 496 GLN A 620 ASN A 669 ASN B 365 ASN B 454 ASN B 505 ASN B 659 ASN B 696 GLN B 719 GLN C 272 GLN C 374 ASN C 620 ASN C 696 GLN D 449 GLN D 697 GLN E 435 ASN E 486 ASN E 696 GLN E 719 GLN F 675 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.035922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2631 r_free = 0.2631 target = 0.028214 restraints weight = 544385.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2682 r_free = 0.2682 target = 0.029709 restraints weight = 273727.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.030897 restraints weight = 169090.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.031749 restraints weight = 115363.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.032344 restraints weight = 84029.554| |-----------------------------------------------------------------------------| r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22865 Z= 0.161 Angle : 0.719 11.668 30876 Z= 0.376 Chirality : 0.080 1.819 3529 Planarity : 0.005 0.045 3934 Dihedral : 12.767 177.321 3357 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.15 % Allowed : 10.80 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 aren not related in a simple way. whole: -2.32 (0.14), residues: 2817 helix: -1.37 (0.13), residues: 1291 sheet: -1.16 (0.23), residues: 335 loop : -1.68 (0.16), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 403 TYR 0.013 0.002 TYR D 502 PHE 0.017 0.001 PHE C 215 TRP 0.011 0.001 TRP C 510 HIS 0.006 0.001 HIS C 410 Details of bonding type rmsd covalent geometry : bond 0.00335 (22865) covalent geometry : angle 0.71925 (30876) hydrogen bonds : bond 0.04830 ( 940) hydrogen bonds : angle 5.91664 ( 2772) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5634 Ramachandran restraints generated. 2817 Oldfield, 0 Emsley, 2817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5634 Ramachandran restraints generated. 2817 Oldfield, 0 Emsley, 2817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 14 is missing expected H atoms. Skipping. Evaluate side-chains 206 residues out of total 2427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 178 time to evaluate : 1.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 657 MET cc_start: 0.9406 (ttm) cc_final: 0.9157 (ttm) REVERT: A 724 TYR cc_start: 0.9511 (m-80) cc_final: 0.8667 (m-80) REVERT: B 578 GLU cc_start: 0.9275 (pm20) cc_final: 0.8731 (pm20) REVERT: B 712 MET cc_start: 0.8767 (tpp) cc_final: 0.8543 (tpp) REVERT: B 720 MET cc_start: 0.8858 (tpp) cc_final: 0.8625 (tpp) REVERT: C 275 LYS cc_start: 0.9323 (tptt) cc_final: 0.8957 (tppt) REVERT: C 289 GLU cc_start: 0.9562 (tt0) cc_final: 0.9359 (mm-30) REVERT: C 372 MET cc_start: 0.8918 (ptp) cc_final: 0.8268 (mpp) REVERT: C 414 MET cc_start: 0.9309 (ttm) cc_final: 0.8657 (mtt) REVERT: C 568 CYS cc_start: 0.9622 (t) cc_final: 0.9049 (p) REVERT: C 585 MET cc_start: 0.9599 (ptp) cc_final: 0.9182 (ptp) REVERT: C 712 MET cc_start: 0.9621 (mtt) cc_final: 0.9320 (tpp) REVERT: C 716 MET cc_start: 0.9646 (mtp) cc_final: 0.9254 (mtp) REVERT: E 585 MET cc_start: 0.9506 (OUTLIER) cc_final: 0.9155 (mtp) REVERT: F 720 MET cc_start: 0.9530 (mtp) cc_final: 0.9315 (mtp) REVERT: H 6 ASP cc_start: 0.9225 (m-30) cc_final: 0.8823 (m-30) outliers start: 28 outliers final: 16 residues processed: 197 average time/residue: 0.4032 time to fit residues: 120.1111 Evaluate side-chains 179 residues out of total 2427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 162 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 GLU Chi-restraints excluded: chain A residue 669 ASN Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 347 HIS Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 724 TYR Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 347 HIS Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 477 ARG Chi-restraints excluded: chain D residue 484 LEU Chi-restraints excluded: chain E residue 585 MET Chi-restraints excluded: chain E residue 655 MET Chi-restraints excluded: chain E residue 724 TYR Chi-restraints excluded: chain F residue 588 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 35 optimal weight: 2.9990 chunk 105 optimal weight: 0.0270 chunk 255 optimal weight: 4.9990 chunk 221 optimal weight: 9.9990 chunk 97 optimal weight: 6.9990 chunk 76 optimal weight: 5.9990 chunk 112 optimal weight: 5.9990 chunk 158 optimal weight: 10.0000 chunk 189 optimal weight: 0.0980 chunk 249 optimal weight: 7.9990 chunk 64 optimal weight: 6.9990 overall best weight: 2.8244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 418 GLN ** E 675 GLN ** 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 = 0.2859 r_free = 0.2859 target = 0.034031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2575 r_free = 0.2575 target = 0.026279 restraints weight = 573345.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2630 r_free = 0.2630 target = 0.027778 restraints weight = 286938.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.028868 restraints weight = 173980.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.029656 restraints weight = 118246.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.030231 restraints weight = 86509.339| |-----------------------------------------------------------------------------| r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22865 Z= 0.166 Angle : 0.660 10.864 30876 Z= 0.345 Chirality : 0.079 1.796 3529 Planarity : 0.004 0.041 3934 Dihedral : 11.814 177.633 3355 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.15 % Allowed : 11.62 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: -1.78 (0.14), residues: 2817 helix: -0.77 (0.13), residues: 1280 sheet: -0.91 (0.24), residues: 331 loop : -1.61 (0.16), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 725 TYR 0.013 0.001 TYR D 502 PHE 0.013 0.001 PHE D 227 TRP 0.007 0.001 TRP F 704 HIS 0.005 0.001 HIS D 347 Details of bonding type rmsd covalent geometry : bond 0.00338 (22865) covalent geometry : angle 0.65991 (30876) hydrogen bonds : bond 0.04129 ( 940) hydrogen bonds : angle 5.57665 ( 2772) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5634 Ramachandran restraints generated. 2817 Oldfield, 0 Emsley, 2817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5634 Ramachandran restraints generated. 2817 Oldfield, 0 Emsley, 2817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 14 is missing expected H atoms. Skipping. Evaluate side-chains 196 residues out of total 2427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 168 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 657 MET cc_start: 0.9742 (ttm) cc_final: 0.9195 (tpp) REVERT: B 712 MET cc_start: 0.8926 (tpp) cc_final: 0.8720 (tpp) REVERT: B 720 MET cc_start: 0.8919 (tpp) cc_final: 0.8591 (tpp) REVERT: C 275 LYS cc_start: 0.9336 (tptt) cc_final: 0.8952 (tppt) REVERT: C 372 MET cc_start: 0.8941 (ptp) cc_final: 0.8336 (mpp) REVERT: C 414 MET cc_start: 0.9439 (ttm) cc_final: 0.9128 (mtp) REVERT: C 585 MET cc_start: 0.9526 (ptp) cc_final: 0.9246 (ptp) REVERT: C 712 MET cc_start: 0.9681 (mtt) cc_final: 0.9168 (tpp) REVERT: C 716 MET cc_start: 0.9689 (mtp) cc_final: 0.9071 (mtp) REVERT: D 340 MET cc_start: 0.7716 (mmp) cc_final: 0.6948 (tpp) REVERT: E 585 MET cc_start: 0.9617 (OUTLIER) cc_final: 0.9282 (mtp) REVERT: E 656 GLU cc_start: 0.9595 (tt0) cc_final: 0.9141 (tm-30) REVERT: E 716 MET cc_start: 0.9200 (mtp) cc_final: 0.8909 (mtp) REVERT: F 607 ARG cc_start: 0.9386 (mmp80) cc_final: 0.8924 (mmp80) REVERT: H 6 ASP cc_start: 0.9316 (m-30) cc_final: 0.8834 (m-30) outliers start: 28 outliers final: 15 residues processed: 187 average time/residue: 0.3881 time to fit residues: 109.3550 Evaluate side-chains 172 residues out of total 2427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 156 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 GLU Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 347 HIS Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 724 TYR Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain D residue 213 TRP Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 477 ARG Chi-restraints excluded: chain D residue 484 LEU Chi-restraints excluded: chain D residue 568 CYS Chi-restraints excluded: chain E residue 585 MET Chi-restraints excluded: chain E residue 655 MET Chi-restraints excluded: chain E residue 718 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 193 optimal weight: 5.9990 chunk 198 optimal weight: 10.0000 chunk 21 optimal weight: 0.9980 chunk 103 optimal weight: 5.9990 chunk 146 optimal weight: 10.0000 chunk 93 optimal weight: 9.9990 chunk 52 optimal weight: 9.9990 chunk 109 optimal weight: 4.9990 chunk 86 optimal weight: 0.7980 chunk 80 optimal weight: 6.9990 chunk 90 optimal weight: 3.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 685 ASN F 561 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.033581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2557 r_free = 0.2557 target = 0.025869 restraints weight = 574969.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2612 r_free = 0.2612 target = 0.027334 restraints weight = 290234.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2650 r_free = 0.2650 target = 0.028383 restraints weight = 177392.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.029165 restraints weight = 121041.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.029684 restraints weight = 88918.068| |-----------------------------------------------------------------------------| r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 22865 Z= 0.169 Angle : 0.632 11.158 30876 Z= 0.329 Chirality : 0.079 1.783 3529 Planarity : 0.004 0.080 3934 Dihedral : 11.513 178.504 3355 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.28 % Allowed : 12.28 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.56 (0.14), residues: 2817 helix: -0.49 (0.14), residues: 1278 sheet: -0.92 (0.24), residues: 343 loop : -1.58 (0.16), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 734 TYR 0.010 0.001 TYR A 502 PHE 0.013 0.001 PHE B 589 TRP 0.007 0.001 TRP F 704 HIS 0.004 0.001 HIS E 323 Details of bonding type rmsd covalent geometry : bond 0.00341 (22865) covalent geometry : angle 0.63229 (30876) hydrogen bonds : bond 0.03837 ( 940) hydrogen bonds : angle 5.45333 ( 2772) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5634 Ramachandran restraints generated. 2817 Oldfield, 0 Emsley, 2817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5634 Ramachandran restraints generated. 2817 Oldfield, 0 Emsley, 2817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 14 is missing expected H atoms. Skipping. Evaluate side-chains 191 residues out of total 2427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 160 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 291 LEU cc_start: 0.9380 (OUTLIER) cc_final: 0.9172 (mp) REVERT: A 657 MET cc_start: 0.9750 (ttm) cc_final: 0.9240 (tpp) REVERT: B 372 MET cc_start: 0.9112 (mtm) cc_final: 0.8864 (mtm) REVERT: B 720 MET cc_start: 0.9000 (tpp) cc_final: 0.8740 (tpp) REVERT: C 372 MET cc_start: 0.9035 (ptp) cc_final: 0.8504 (mpp) REVERT: C 414 MET cc_start: 0.9398 (ttm) cc_final: 0.9101 (mtp) REVERT: C 585 MET cc_start: 0.9502 (ptp) cc_final: 0.9229 (ptp) REVERT: C 712 MET cc_start: 0.9685 (mtt) cc_final: 0.9174 (tpp) REVERT: C 716 MET cc_start: 0.9586 (mtp) cc_final: 0.9053 (mtp) REVERT: D 340 MET cc_start: 0.7668 (mmp) cc_final: 0.7108 (tpp) REVERT: E 585 MET cc_start: 0.9642 (OUTLIER) cc_final: 0.9297 (mtp) REVERT: E 657 MET cc_start: 0.9181 (mmm) cc_final: 0.8580 (mmm) REVERT: E 716 MET cc_start: 0.9162 (mtp) cc_final: 0.8942 (mtp) REVERT: H 6 ASP cc_start: 0.9333 (m-30) cc_final: 0.8845 (m-30) outliers start: 31 outliers final: 23 residues processed: 181 average time/residue: 0.3850 time to fit residues: 107.7229 Evaluate side-chains 174 residues out of total 2427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 149 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 432 GLU Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain B residue 347 HIS Chi-restraints excluded: chain B residue 538 SER Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 724 TYR Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 347 HIS Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain D residue 246 GLU Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 333 ILE Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 477 ARG Chi-restraints excluded: chain D residue 484 LEU Chi-restraints excluded: chain D residue 568 CYS Chi-restraints excluded: chain E residue 585 MET Chi-restraints excluded: chain E residue 655 MET Chi-restraints excluded: chain E residue 718 LEU Chi-restraints excluded: chain F residue 626 LEU Chi-restraints excluded: chain F residue 657 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 156 optimal weight: 9.9990 chunk 182 optimal weight: 10.0000 chunk 247 optimal weight: 4.9990 chunk 169 optimal weight: 9.9990 chunk 251 optimal weight: 10.0000 chunk 158 optimal weight: 6.9990 chunk 176 optimal weight: 0.0570 chunk 249 optimal weight: 9.9990 chunk 209 optimal weight: 1.9990 chunk 72 optimal weight: 9.9990 chunk 225 optimal weight: 1.9990 overall best weight: 3.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 418 GLN F 527 GLN F 561 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.033542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2574 r_free = 0.2574 target = 0.026341 restraints weight = 572154.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2628 r_free = 0.2628 target = 0.027731 restraints weight = 291260.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.028802 restraints weight = 181496.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.029541 restraints weight = 124657.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.030098 restraints weight = 92387.786| |-----------------------------------------------------------------------------| r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.3432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22865 Z= 0.163 Angle : 0.613 11.271 30876 Z= 0.318 Chirality : 0.079 1.769 3529 Planarity : 0.004 0.045 3934 Dihedral : 11.213 178.726 3355 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.28 % Allowed : 13.06 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.32 (0.14), residues: 2817 helix: -0.23 (0.14), residues: 1283 sheet: -0.77 (0.25), residues: 341 loop : -1.54 (0.16), residues: 1193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 734 TYR 0.010 0.001 TYR A 611 PHE 0.013 0.001 PHE D 227 TRP 0.008 0.001 TRP C 213 HIS 0.004 0.001 HIS E 323 Details of bonding type rmsd covalent geometry : bond 0.00326 (22865) covalent geometry : angle 0.61330 (30876) hydrogen bonds : bond 0.03516 ( 940) hydrogen bonds : angle 5.23627 ( 2772) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5634 Ramachandran restraints generated. 2817 Oldfield, 0 Emsley, 2817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5634 Ramachandran restraints generated. 2817 Oldfield, 0 Emsley, 2817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 14 is missing expected H atoms. Skipping. Evaluate side-chains 186 residues out of total 2427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 155 time to evaluate : 1.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 291 LEU cc_start: 0.9340 (OUTLIER) cc_final: 0.9130 (mp) REVERT: A 657 MET cc_start: 0.9780 (ttm) cc_final: 0.9284 (tpp) REVERT: B 372 MET cc_start: 0.9143 (mtm) cc_final: 0.8782 (mtm) REVERT: B 502 TYR cc_start: 0.8943 (m-80) cc_final: 0.8631 (m-80) REVERT: B 578 GLU cc_start: 0.9453 (pm20) cc_final: 0.9126 (pm20) REVERT: B 585 MET cc_start: 0.9416 (mmp) cc_final: 0.9209 (mmp) REVERT: C 275 LYS cc_start: 0.9336 (tptt) cc_final: 0.8962 (tppt) REVERT: C 372 MET cc_start: 0.9191 (ptp) cc_final: 0.8722 (mpp) REVERT: C 585 MET cc_start: 0.9503 (ptp) cc_final: 0.9225 (ptp) REVERT: C 712 MET cc_start: 0.9677 (mtt) cc_final: 0.9141 (tpp) REVERT: C 716 MET cc_start: 0.9566 (mtp) cc_final: 0.9024 (mtp) REVERT: D 276 MET cc_start: 0.8370 (ttm) cc_final: 0.8159 (ttp) REVERT: D 340 MET cc_start: 0.7597 (mmp) cc_final: 0.7094 (tpp) REVERT: E 585 MET cc_start: 0.9676 (OUTLIER) cc_final: 0.9465 (mtp) REVERT: E 657 MET cc_start: 0.9195 (mmm) cc_final: 0.8639 (mmm) REVERT: E 712 MET cc_start: 0.8856 (tpp) cc_final: 0.8648 (tpp) REVERT: E 716 MET cc_start: 0.9193 (mtp) cc_final: 0.8821 (mtp) REVERT: F 657 MET cc_start: 0.9644 (OUTLIER) cc_final: 0.9378 (ppp) REVERT: H 6 ASP cc_start: 0.9223 (m-30) cc_final: 0.8722 (m-30) outliers start: 31 outliers final: 22 residues processed: 176 average time/residue: 0.3721 time to fit residues: 100.3177 Evaluate side-chains 171 residues out of total 2427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 146 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 432 GLU Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 347 HIS Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 724 TYR Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 347 HIS Chi-restraints excluded: chain D residue 246 GLU Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 477 ARG Chi-restraints excluded: chain D residue 484 LEU Chi-restraints excluded: chain D residue 568 CYS Chi-restraints excluded: chain E residue 585 MET Chi-restraints excluded: chain E residue 641 LEU Chi-restraints excluded: chain E residue 655 MET Chi-restraints excluded: chain E residue 718 LEU Chi-restraints excluded: chain F residue 527 GLN Chi-restraints excluded: chain F residue 626 LEU Chi-restraints excluded: chain F residue 657 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 231 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 204 optimal weight: 9.9990 chunk 72 optimal weight: 7.9990 chunk 237 optimal weight: 1.9990 chunk 138 optimal weight: 6.9990 chunk 78 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 207 optimal weight: 5.9990 chunk 249 optimal weight: 0.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 418 GLN F 561 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.032964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2555 r_free = 0.2555 target = 0.025799 restraints weight = 566362.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2606 r_free = 0.2606 target = 0.027157 restraints weight = 283660.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.028198 restraints weight = 175139.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.028994 restraints weight = 120708.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.029559 restraints weight = 88594.472| |-----------------------------------------------------------------------------| r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.3719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 22865 Z= 0.182 Angle : 0.613 10.942 30876 Z= 0.318 Chirality : 0.079 1.761 3529 Planarity : 0.004 0.045 3934 Dihedral : 11.151 179.220 3355 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.24 % Allowed : 13.84 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.26 (0.15), residues: 2817 helix: -0.12 (0.14), residues: 1296 sheet: -0.78 (0.25), residues: 345 loop : -1.60 (0.16), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 734 TYR 0.009 0.001 TYR A 611 PHE 0.012 0.001 PHE D 227 TRP 0.010 0.001 TRP B 213 HIS 0.004 0.001 HIS E 323 Details of bonding type rmsd covalent geometry : bond 0.00359 (22865) covalent geometry : angle 0.61328 (30876) hydrogen bonds : bond 0.03499 ( 940) hydrogen bonds : angle 5.24503 ( 2772) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5634 Ramachandran restraints generated. 2817 Oldfield, 0 Emsley, 2817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5634 Ramachandran restraints generated. 2817 Oldfield, 0 Emsley, 2817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 14 is missing expected H atoms. Skipping. Evaluate side-chains 178 residues out of total 2427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 148 time to evaluate : 1.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 657 MET cc_start: 0.9780 (ttm) cc_final: 0.9335 (tpp) REVERT: A 724 TYR cc_start: 0.9631 (m-80) cc_final: 0.8892 (m-80) REVERT: B 372 MET cc_start: 0.9125 (mtm) cc_final: 0.8590 (mtm) REVERT: B 453 MET cc_start: 0.9631 (mmm) cc_final: 0.9143 (ttm) REVERT: B 502 TYR cc_start: 0.9010 (m-80) cc_final: 0.8700 (m-80) REVERT: B 578 GLU cc_start: 0.9479 (pm20) cc_final: 0.9164 (pm20) REVERT: B 657 MET cc_start: 0.9330 (ppp) cc_final: 0.9125 (ppp) REVERT: C 275 LYS cc_start: 0.9357 (tptt) cc_final: 0.9009 (tppt) REVERT: C 372 MET cc_start: 0.9205 (ptp) cc_final: 0.8787 (mpp) REVERT: C 585 MET cc_start: 0.9506 (ptp) cc_final: 0.9210 (ptp) REVERT: C 712 MET cc_start: 0.9679 (mtt) cc_final: 0.9184 (tpp) REVERT: C 716 MET cc_start: 0.9568 (mtp) cc_final: 0.8968 (mtp) REVERT: D 340 MET cc_start: 0.7585 (mmp) cc_final: 0.7120 (tpp) REVERT: E 657 MET cc_start: 0.9261 (mmm) cc_final: 0.8849 (mmm) REVERT: E 712 MET cc_start: 0.8904 (tpp) cc_final: 0.8654 (tpp) REVERT: E 716 MET cc_start: 0.9200 (mtp) cc_final: 0.8786 (mtp) REVERT: F 657 MET cc_start: 0.9661 (OUTLIER) cc_final: 0.9398 (ppp) REVERT: H 6 ASP cc_start: 0.9252 (m-30) cc_final: 0.8683 (m-30) outliers start: 30 outliers final: 24 residues processed: 167 average time/residue: 0.3349 time to fit residues: 87.5603 Evaluate side-chains 168 residues out of total 2427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 143 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 GLU Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 724 TYR Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 347 HIS Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain C residue 720 MET Chi-restraints excluded: chain D residue 246 GLU Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 477 ARG Chi-restraints excluded: chain D residue 484 LEU Chi-restraints excluded: chain D residue 568 CYS Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 585 MET Chi-restraints excluded: chain E residue 641 LEU Chi-restraints excluded: chain E residue 655 MET Chi-restraints excluded: chain E residue 718 LEU Chi-restraints excluded: chain F residue 626 LEU Chi-restraints excluded: chain F residue 657 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 53 optimal weight: 8.9990 chunk 222 optimal weight: 10.0000 chunk 115 optimal weight: 0.2980 chunk 103 optimal weight: 7.9990 chunk 273 optimal weight: 9.9990 chunk 6 optimal weight: 8.9990 chunk 248 optimal weight: 3.9990 chunk 123 optimal weight: 10.0000 chunk 177 optimal weight: 10.0000 chunk 131 optimal weight: 7.9990 chunk 119 optimal weight: 0.6980 overall best weight: 4.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 GLN A 366 ASN D 418 GLN E 495 ASN F 561 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.031952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2538 r_free = 0.2538 target = 0.025056 restraints weight = 571798.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2584 r_free = 0.2584 target = 0.026297 restraints weight = 287844.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2626 r_free = 0.2626 target = 0.027313 restraints weight = 180234.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2656 r_free = 0.2656 target = 0.028053 restraints weight = 125538.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.028598 restraints weight = 92684.895| |-----------------------------------------------------------------------------| r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.4063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 22865 Z= 0.197 Angle : 0.624 10.973 30876 Z= 0.324 Chirality : 0.079 1.757 3529 Planarity : 0.004 0.048 3934 Dihedral : 11.134 179.994 3355 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 1.19 % Allowed : 14.34 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.28 (0.15), residues: 2817 helix: -0.11 (0.14), residues: 1308 sheet: -0.69 (0.25), residues: 343 loop : -1.69 (0.16), residues: 1166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 734 TYR 0.012 0.001 TYR C 724 PHE 0.013 0.001 PHE D 227 TRP 0.010 0.001 TRP C 213 HIS 0.005 0.001 HIS E 323 Details of bonding type rmsd covalent geometry : bond 0.00387 (22865) covalent geometry : angle 0.62434 (30876) hydrogen bonds : bond 0.03409 ( 940) hydrogen bonds : angle 5.24605 ( 2772) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5634 Ramachandran restraints generated. 2817 Oldfield, 0 Emsley, 2817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5634 Ramachandran restraints generated. 2817 Oldfield, 0 Emsley, 2817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 14 is missing expected H atoms. Skipping. Evaluate side-chains 177 residues out of total 2427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 148 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 657 MET cc_start: 0.9771 (ttm) cc_final: 0.9392 (tpp) REVERT: B 372 MET cc_start: 0.9140 (mtm) cc_final: 0.8616 (mtm) REVERT: B 502 TYR cc_start: 0.9079 (m-80) cc_final: 0.8775 (m-80) REVERT: B 578 GLU cc_start: 0.9472 (pm20) cc_final: 0.9223 (pm20) REVERT: B 657 MET cc_start: 0.9390 (ppp) cc_final: 0.9181 (ppp) REVERT: C 275 LYS cc_start: 0.9350 (tptt) cc_final: 0.8975 (tppt) REVERT: C 372 MET cc_start: 0.9146 (ptp) cc_final: 0.8875 (mpp) REVERT: C 712 MET cc_start: 0.9664 (mtt) cc_final: 0.9209 (tpp) REVERT: C 716 MET cc_start: 0.9545 (mtp) cc_final: 0.8966 (mtp) REVERT: D 340 MET cc_start: 0.7612 (mmp) cc_final: 0.7201 (tpp) REVERT: E 657 MET cc_start: 0.9276 (mmm) cc_final: 0.8911 (mmm) REVERT: E 712 MET cc_start: 0.8974 (tpp) cc_final: 0.8686 (tpp) REVERT: E 716 MET cc_start: 0.9198 (mtp) cc_final: 0.8809 (mtp) REVERT: F 657 MET cc_start: 0.9677 (OUTLIER) cc_final: 0.9416 (ppp) outliers start: 29 outliers final: 24 residues processed: 168 average time/residue: 0.3381 time to fit residues: 88.7287 Evaluate side-chains 170 residues out of total 2427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 145 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 GLU Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 676 LEU Chi-restraints excluded: chain B residue 724 TYR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 347 HIS Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain D residue 246 GLU Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 477 ARG Chi-restraints excluded: chain D residue 484 LEU Chi-restraints excluded: chain D residue 568 CYS Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 585 MET Chi-restraints excluded: chain E residue 641 LEU Chi-restraints excluded: chain E residue 655 MET Chi-restraints excluded: chain E residue 718 LEU Chi-restraints excluded: chain F residue 527 GLN Chi-restraints excluded: chain F residue 626 LEU Chi-restraints excluded: chain F residue 657 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 237 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 115 optimal weight: 20.0000 chunk 22 optimal weight: 7.9990 chunk 187 optimal weight: 4.9990 chunk 44 optimal weight: 10.0000 chunk 137 optimal weight: 0.4980 chunk 41 optimal weight: 7.9990 chunk 241 optimal weight: 5.9990 chunk 243 optimal weight: 7.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 561 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.032716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2557 r_free = 0.2557 target = 0.025760 restraints weight = 570022.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2611 r_free = 0.2611 target = 0.027157 restraints weight = 284331.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.028181 restraints weight = 172988.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2682 r_free = 0.2682 target = 0.028934 restraints weight = 118688.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.029454 restraints weight = 87392.665| |-----------------------------------------------------------------------------| r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.4180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22865 Z= 0.124 Angle : 0.596 10.960 30876 Z= 0.301 Chirality : 0.079 1.745 3529 Planarity : 0.004 0.046 3934 Dihedral : 10.922 179.421 3355 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 1.03 % Allowed : 15.00 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.97 (0.15), residues: 2817 helix: 0.16 (0.14), residues: 1315 sheet: -0.59 (0.26), residues: 346 loop : -1.55 (0.17), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 734 TYR 0.009 0.001 TYR D 502 PHE 0.014 0.001 PHE E 327 TRP 0.008 0.001 TRP B 213 HIS 0.004 0.001 HIS E 323 Details of bonding type rmsd covalent geometry : bond 0.00258 (22865) covalent geometry : angle 0.59631 (30876) hydrogen bonds : bond 0.03196 ( 940) hydrogen bonds : angle 5.01998 ( 2772) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5634 Ramachandran restraints generated. 2817 Oldfield, 0 Emsley, 2817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5634 Ramachandran restraints generated. 2817 Oldfield, 0 Emsley, 2817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 14 is missing expected H atoms. Skipping. Evaluate side-chains 177 residues out of total 2427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 152 time to evaluate : 1.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 585 MET cc_start: 0.9599 (ptp) cc_final: 0.9303 (ptp) REVERT: A 657 MET cc_start: 0.9741 (ttm) cc_final: 0.9386 (tpp) REVERT: A 712 MET cc_start: 0.9481 (tpp) cc_final: 0.8888 (tpp) REVERT: A 716 MET cc_start: 0.9307 (mtp) cc_final: 0.8992 (mtm) REVERT: B 502 TYR cc_start: 0.9067 (m-80) cc_final: 0.8780 (m-80) REVERT: B 578 GLU cc_start: 0.9408 (pm20) cc_final: 0.9152 (pm20) REVERT: B 657 MET cc_start: 0.9308 (ppp) cc_final: 0.9037 (ppp) REVERT: C 275 LYS cc_start: 0.9347 (tptt) cc_final: 0.8977 (tppt) REVERT: C 372 MET cc_start: 0.9202 (ptp) cc_final: 0.8940 (mpp) REVERT: C 585 MET cc_start: 0.9565 (ptp) cc_final: 0.9300 (ptp) REVERT: C 712 MET cc_start: 0.9626 (mtt) cc_final: 0.9362 (tpp) REVERT: C 716 MET cc_start: 0.9507 (mtp) cc_final: 0.9109 (mtp) REVERT: D 340 MET cc_start: 0.7578 (mmp) cc_final: 0.7178 (tpp) REVERT: D 372 MET cc_start: 0.8451 (mtt) cc_final: 0.7992 (mpp) REVERT: E 657 MET cc_start: 0.9239 (mmm) cc_final: 0.8868 (mmm) REVERT: E 712 MET cc_start: 0.8954 (tpp) cc_final: 0.8635 (tpp) REVERT: E 716 MET cc_start: 0.9169 (mtp) cc_final: 0.8736 (mtp) REVERT: F 657 MET cc_start: 0.9670 (OUTLIER) cc_final: 0.9397 (ppp) REVERT: H 6 ASP cc_start: 0.9249 (m-30) cc_final: 0.8648 (m-30) outliers start: 25 outliers final: 20 residues processed: 167 average time/residue: 0.3717 time to fit residues: 95.6809 Evaluate side-chains 165 residues out of total 2427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 144 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 GLU Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 724 TYR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 347 HIS Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain C residue 720 MET Chi-restraints excluded: chain D residue 246 GLU Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 477 ARG Chi-restraints excluded: chain D residue 484 LEU Chi-restraints excluded: chain D residue 568 CYS Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 641 LEU Chi-restraints excluded: chain E residue 655 MET Chi-restraints excluded: chain F residue 626 LEU Chi-restraints excluded: chain F residue 657 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 99 optimal weight: 3.9990 chunk 202 optimal weight: 6.9990 chunk 28 optimal weight: 0.0970 chunk 224 optimal weight: 0.9980 chunk 108 optimal weight: 0.9990 chunk 227 optimal weight: 9.9990 chunk 272 optimal weight: 9.9990 chunk 60 optimal weight: 8.9990 chunk 230 optimal weight: 9.9990 chunk 184 optimal weight: 0.5980 chunk 215 optimal weight: 7.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 561 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.032985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2573 r_free = 0.2573 target = 0.026080 restraints weight = 569028.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2625 r_free = 0.2625 target = 0.027480 restraints weight = 282552.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.028482 restraints weight = 171631.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.029250 restraints weight = 118495.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.029770 restraints weight = 86703.599| |-----------------------------------------------------------------------------| r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.4319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 22865 Z= 0.110 Angle : 0.599 10.917 30876 Z= 0.298 Chirality : 0.079 1.739 3529 Planarity : 0.004 0.043 3934 Dihedral : 10.678 179.522 3355 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 0.78 % Allowed : 15.29 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.76 (0.15), residues: 2817 helix: 0.35 (0.14), residues: 1321 sheet: -0.48 (0.26), residues: 346 loop : -1.47 (0.17), residues: 1150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 734 TYR 0.009 0.001 TYR A 294 PHE 0.017 0.001 PHE E 327 TRP 0.007 0.001 TRP B 213 HIS 0.003 0.001 HIS C 410 Details of bonding type rmsd covalent geometry : bond 0.00240 (22865) covalent geometry : angle 0.59886 (30876) hydrogen bonds : bond 0.03119 ( 940) hydrogen bonds : angle 4.86826 ( 2772) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5634 Ramachandran restraints generated. 2817 Oldfield, 0 Emsley, 2817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5634 Ramachandran restraints generated. 2817 Oldfield, 0 Emsley, 2817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 14 is missing expected H atoms. Skipping. Evaluate side-chains 166 residues out of total 2427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 147 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 585 MET cc_start: 0.9572 (ptp) cc_final: 0.9291 (ptp) REVERT: A 657 MET cc_start: 0.9746 (ttm) cc_final: 0.9406 (tpp) REVERT: A 712 MET cc_start: 0.9439 (tpp) cc_final: 0.8818 (tpp) REVERT: B 372 MET cc_start: 0.8863 (mtm) cc_final: 0.8534 (mtm) REVERT: B 502 TYR cc_start: 0.9076 (m-80) cc_final: 0.8780 (m-80) REVERT: B 578 GLU cc_start: 0.9406 (pm20) cc_final: 0.9128 (pm20) REVERT: B 657 MET cc_start: 0.9290 (ppp) cc_final: 0.9017 (ppp) REVERT: C 275 LYS cc_start: 0.9379 (tptt) cc_final: 0.9083 (tppt) REVERT: C 372 MET cc_start: 0.9271 (ptp) cc_final: 0.9047 (mpp) REVERT: C 712 MET cc_start: 0.9638 (mtt) cc_final: 0.9360 (tpp) REVERT: C 716 MET cc_start: 0.9518 (mtp) cc_final: 0.9124 (mtp) REVERT: D 340 MET cc_start: 0.7568 (mmp) cc_final: 0.7112 (tpp) REVERT: D 372 MET cc_start: 0.8540 (mtt) cc_final: 0.8003 (mpp) REVERT: E 657 MET cc_start: 0.9241 (mmm) cc_final: 0.8866 (mmm) REVERT: E 712 MET cc_start: 0.8979 (tpp) cc_final: 0.8656 (tpp) REVERT: E 716 MET cc_start: 0.9146 (mtp) cc_final: 0.8691 (mtp) REVERT: F 657 MET cc_start: 0.9651 (ptm) cc_final: 0.9389 (ppp) REVERT: H 6 ASP cc_start: 0.9218 (m-30) cc_final: 0.8580 (m-30) outliers start: 19 outliers final: 16 residues processed: 160 average time/residue: 0.3785 time to fit residues: 94.4624 Evaluate side-chains 161 residues out of total 2427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 145 time to evaluate : 1.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 GLU Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 347 HIS Chi-restraints excluded: chain D residue 246 GLU Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 477 ARG Chi-restraints excluded: chain D residue 484 LEU Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 641 LEU Chi-restraints excluded: chain E residue 655 MET Chi-restraints excluded: chain F residue 626 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 14 optimal weight: 4.9990 chunk 129 optimal weight: 0.5980 chunk 157 optimal weight: 10.0000 chunk 153 optimal weight: 8.9990 chunk 174 optimal weight: 5.9990 chunk 44 optimal weight: 9.9990 chunk 124 optimal weight: 6.9990 chunk 146 optimal weight: 8.9990 chunk 118 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 33 optimal weight: 0.3980 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 272 GLN F 561 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.031739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2529 r_free = 0.2529 target = 0.024697 restraints weight = 597935.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2587 r_free = 0.2587 target = 0.026117 restraints weight = 293550.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2625 r_free = 0.2625 target = 0.027100 restraints weight = 175588.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.027866 restraints weight = 119612.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.028420 restraints weight = 86309.119| |-----------------------------------------------------------------------------| r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.4437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22865 Z= 0.122 Angle : 0.598 10.889 30876 Z= 0.299 Chirality : 0.078 1.728 3529 Planarity : 0.004 0.045 3934 Dihedral : 10.555 179.665 3355 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 0.66 % Allowed : 15.53 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.72 (0.15), residues: 2817 helix: 0.39 (0.14), residues: 1329 sheet: -0.43 (0.26), residues: 346 loop : -1.47 (0.17), residues: 1142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 734 TYR 0.007 0.001 TYR D 502 PHE 0.016 0.001 PHE E 327 TRP 0.006 0.001 TRP B 213 HIS 0.003 0.001 HIS E 323 Details of bonding type rmsd covalent geometry : bond 0.00259 (22865) covalent geometry : angle 0.59801 (30876) hydrogen bonds : bond 0.03083 ( 940) hydrogen bonds : angle 4.86023 ( 2772) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5634 Ramachandran restraints generated. 2817 Oldfield, 0 Emsley, 2817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5634 Ramachandran restraints generated. 2817 Oldfield, 0 Emsley, 2817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 14 is missing expected H atoms. Skipping. Evaluate side-chains 161 residues out of total 2427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 145 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 585 MET cc_start: 0.9547 (ptp) cc_final: 0.9278 (ptp) REVERT: A 657 MET cc_start: 0.9723 (ttm) cc_final: 0.9343 (tmm) REVERT: A 712 MET cc_start: 0.9473 (tpp) cc_final: 0.8866 (tpp) REVERT: B 372 MET cc_start: 0.8937 (mtm) cc_final: 0.8584 (mtm) REVERT: B 502 TYR cc_start: 0.9134 (m-80) cc_final: 0.8848 (m-80) REVERT: B 657 MET cc_start: 0.9369 (ppp) cc_final: 0.9101 (ppp) REVERT: C 275 LYS cc_start: 0.9358 (tptt) cc_final: 0.8982 (tppt) REVERT: C 712 MET cc_start: 0.9632 (mtt) cc_final: 0.9360 (tpp) REVERT: C 716 MET cc_start: 0.9529 (mtp) cc_final: 0.9148 (mtp) REVERT: D 340 MET cc_start: 0.7559 (mmp) cc_final: 0.7104 (tpp) REVERT: D 372 MET cc_start: 0.8523 (mtt) cc_final: 0.8012 (mpp) REVERT: E 657 MET cc_start: 0.9233 (mmm) cc_final: 0.8866 (mmm) REVERT: E 712 MET cc_start: 0.8991 (tpp) cc_final: 0.8666 (tpp) REVERT: E 716 MET cc_start: 0.9209 (mtp) cc_final: 0.8772 (mtp) REVERT: F 657 MET cc_start: 0.9657 (ptm) cc_final: 0.9396 (ppp) REVERT: H 6 ASP cc_start: 0.9261 (m-30) cc_final: 0.8735 (m-30) outliers start: 16 outliers final: 15 residues processed: 156 average time/residue: 0.3342 time to fit residues: 81.4173 Evaluate side-chains 157 residues out of total 2427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 142 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 GLU Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 347 HIS Chi-restraints excluded: chain D residue 246 GLU Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 477 ARG Chi-restraints excluded: chain D residue 484 LEU Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 641 LEU Chi-restraints excluded: chain E residue 655 MET Chi-restraints excluded: chain F residue 626 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 254 optimal weight: 0.5980 chunk 217 optimal weight: 0.9990 chunk 55 optimal weight: 10.0000 chunk 224 optimal weight: 0.9980 chunk 109 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 209 optimal weight: 9.9990 chunk 115 optimal weight: 20.0000 chunk 47 optimal weight: 0.8980 chunk 45 optimal weight: 10.0000 chunk 268 optimal weight: 8.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 496 GLN F 561 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.032005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2538 r_free = 0.2538 target = 0.024876 restraints weight = 593307.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2596 r_free = 0.2596 target = 0.026303 restraints weight = 290864.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2637 r_free = 0.2637 target = 0.027343 restraints weight = 174175.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.028098 restraints weight = 117331.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.028624 restraints weight = 85011.215| |-----------------------------------------------------------------------------| r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.4540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 22865 Z= 0.114 Angle : 0.601 10.912 30876 Z= 0.299 Chirality : 0.078 1.738 3529 Planarity : 0.004 0.043 3934 Dihedral : 10.430 179.688 3355 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 0.74 % Allowed : 15.41 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.63 (0.15), residues: 2817 helix: 0.47 (0.14), residues: 1324 sheet: -0.38 (0.26), residues: 345 loop : -1.43 (0.18), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 734 TYR 0.007 0.001 TYR D 502 PHE 0.014 0.001 PHE E 327 TRP 0.006 0.001 TRP B 213 HIS 0.006 0.001 HIS B 347 Details of bonding type rmsd covalent geometry : bond 0.00247 (22865) covalent geometry : angle 0.60130 (30876) hydrogen bonds : bond 0.03023 ( 940) hydrogen bonds : angle 4.78996 ( 2772) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5295.79 seconds wall clock time: 91 minutes 44.78 seconds (5504.78 seconds total)