Starting phenix.real_space_refine on Sun Sep 13 11:14:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9tz3_56458/09_2026/9tz3_56458.cif Found real_map, /net/cci-nas-00/data/ceres_data/9tz3_56458/09_2026/9tz3_56458.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9tz3_56458/09_2026/9tz3_56458.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9tz3_56458/09_2026/9tz3_56458.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9tz3_56458/09_2026/9tz3_56458.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9tz3_56458/09_2026/9tz3_56458.map" } resolution = 3.66 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.010 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 4 5.49 5 Mg 2 5.21 5 S 124 5.16 5 C 14150 2.51 5 N 3871 2.21 5 O 4165 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22318 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 6583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 813, 6583 Classifications: {'peptide': 813} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 773} Chain breaks: 1 Chain: "B" Number of atoms: 9481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1192, 9481 Classifications: {'peptide': 1192} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 55, 'TRANS': 1134} Chain breaks: 6 Chain: "C" Number of atoms: 2812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2812 Classifications: {'peptide': 341} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 334} Chain: "D" Number of atoms: 2621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2621 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 10, 'TRANS': 310} Chain breaks: 1 Chain: "E" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 644 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "F" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 103 Classifications: {'peptide': 13} Link IDs: {'PTRANS': 1, 'TRANS': 11} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 44 Unusual residues: {' MG': 1, 'GDP': 1, 'MYR': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MYR:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 16283 SG CYS C 137 45.032 129.306 31.857 1.00 78.95 S ATOM 16307 SG CYS C 140 47.312 131.720 34.613 1.00 69.03 S ATOM 18921 SG CYS D 43 47.176 127.698 32.279 1.00 75.05 S ATOM 18942 SG CYS D 46 45.309 128.461 34.182 1.00 65.44 S ATOM 19018 SG CYS D 55 53.313 134.411 21.710 1.00 86.71 S ATOM 19038 SG CYS D 58 53.381 137.166 21.953 1.00 86.42 S ATOM 22171 SG CYS F 18 49.659 134.953 21.477 1.00 99.86 S ATOM 22197 SG CYS F 21 51.551 135.130 18.687 1.00103.42 S Time building chain proxies: 4.70, per 1000 atoms: 0.21 Number of scatterers: 22318 At special positions: 0 Unit cell: (103.675, 181.25, 229.825, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 124 16.00 P 4 15.00 Mg 2 11.99 O 4165 8.00 N 3871 7.00 C 14150 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.62 Conformation dependent library (CDL) restraints added in 1.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 600 " pdb="ZN ZN C 600 " - pdb=" SG CYS D 46 " pdb="ZN ZN C 600 " - pdb=" SG CYS C 137 " pdb="ZN ZN C 600 " - pdb=" SG CYS D 43 " pdb="ZN ZN C 600 " - pdb=" SG CYS C 140 " pdb=" ZN F 601 " pdb="ZN ZN F 601 " - pdb=" SG CYS D 58 " pdb="ZN ZN F 601 " - pdb=" SG CYS F 18 " pdb="ZN ZN F 601 " - pdb=" SG CYS F 21 " pdb="ZN ZN F 601 " - pdb=" SG CYS D 55 " Number of angles added : 12 5464 Ramachandran restraints generated. 2732 Oldfield, 0 Emsley, 2732 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5264 Finding SS restraints... Secondary structure from input PDB file: 111 helices and 23 sheets defined 52.0% alpha, 12.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 34 through 41 removed outlier: 3.820A pdb=" N VAL A 38 " --> pdb=" O SER A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 47 removed outlier: 3.690A pdb=" N LYS A 45 " --> pdb=" O PRO A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 100 No H-bonds generated for 'chain 'A' and resid 98 through 100' Processing helix chain 'A' and resid 170 through 184 Processing helix chain 'A' and resid 190 through 205 removed outlier: 4.236A pdb=" N LEU A 196 " --> pdb=" O TRP A 192 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N PHE A 198 " --> pdb=" O ASP A 194 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N ARG A 199 " --> pdb=" O ARG A 195 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU A 200 " --> pdb=" O LEU A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 242 removed outlier: 4.325A pdb=" N ASP A 241 " --> pdb=" O LYS A 238 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLU A 242 " --> pdb=" O ASP A 239 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 238 through 242' Processing helix chain 'A' and resid 268 through 273 Processing helix chain 'A' and resid 280 through 286 removed outlier: 3.631A pdb=" N ASP A 283 " --> pdb=" O GLY A 280 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N HIS A 284 " --> pdb=" O PRO A 281 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU A 286 " --> pdb=" O ASP A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 300 Processing helix chain 'A' and resid 309 through 319 removed outlier: 3.512A pdb=" N PHE A 319 " --> pdb=" O LEU A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 326 removed outlier: 3.757A pdb=" N ASN A 325 " --> pdb=" O TYR A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 334 removed outlier: 3.604A pdb=" N PHE A 333 " --> pdb=" O LEU A 330 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU A 334 " --> pdb=" O THR A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 351 Processing helix chain 'A' and resid 364 through 368 removed outlier: 3.539A pdb=" N SER A 368 " --> pdb=" O GLU A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 385 removed outlier: 3.557A pdb=" N ARG A 377 " --> pdb=" O ASN A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 402 Processing helix chain 'A' and resid 403 through 406 Processing helix chain 'A' and resid 407 through 413 removed outlier: 3.593A pdb=" N ILE A 411 " --> pdb=" O ASN A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 484 removed outlier: 3.513A pdb=" N CYS A 484 " --> pdb=" O ILE A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 502 removed outlier: 4.112A pdb=" N VAL A 499 " --> pdb=" O TRP A 495 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLU A 500 " --> pdb=" O TYR A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 510 Processing helix chain 'A' and resid 510 through 529 removed outlier: 3.754A pdb=" N HIS A 514 " --> pdb=" O ASP A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 560 Processing helix chain 'A' and resid 565 through 578 Processing helix chain 'A' and resid 641 through 660 removed outlier: 3.962A pdb=" N LEU A 646 " --> pdb=" O ARG A 642 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE A 647 " --> pdb=" O GLN A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 697 Processing helix chain 'A' and resid 699 through 708 removed outlier: 3.853A pdb=" N LYS A 706 " --> pdb=" O ASN A 702 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N TYR A 707 " --> pdb=" O PHE A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 717 removed outlier: 3.711A pdb=" N GLY A 716 " --> pdb=" O GLY A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 740 removed outlier: 3.664A pdb=" N VAL A 734 " --> pdb=" O ALA A 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 780 through 787 removed outlier: 3.838A pdb=" N VAL A 784 " --> pdb=" O ASN A 780 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N MET A 787 " --> pdb=" O MET A 783 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 809 removed outlier: 3.994A pdb=" N GLN A 796 " --> pdb=" O SER A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 812 through 821 Processing helix chain 'A' and resid 834 through 836 No H-bonds generated for 'chain 'A' and resid 834 through 836' Processing helix chain 'A' and resid 837 through 847 removed outlier: 3.545A pdb=" N LYS A 841 " --> pdb=" O LYS A 837 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL A 842 " --> pdb=" O THR A 838 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LYS A 845 " --> pdb=" O LYS A 841 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N PHE A 846 " --> pdb=" O VAL A 842 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG A 847 " --> pdb=" O GLN A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 868 removed outlier: 3.831A pdb=" N HIS A 857 " --> pdb=" O GLU A 853 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 21 removed outlier: 3.605A pdb=" N SER B 18 " --> pdb=" O SER B 15 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N TYR B 19 " --> pdb=" O VAL B 16 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER B 21 " --> pdb=" O SER B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 78 Processing helix chain 'B' and resid 110 through 114 removed outlier: 3.511A pdb=" N ILE B 114 " --> pdb=" O LEU B 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 110 through 114' Processing helix chain 'B' and resid 121 through 142 removed outlier: 3.663A pdb=" N LEU B 133 " --> pdb=" O ALA B 129 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER B 142 " --> pdb=" O GLN B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 187 Processing helix chain 'B' and resid 238 through 252 removed outlier: 3.985A pdb=" N PHE B 242 " --> pdb=" O ALA B 238 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N SER B 243 " --> pdb=" O MET B 239 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N PHE B 252 " --> pdb=" O ILE B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 270 Processing helix chain 'B' and resid 274 through 279 Processing helix chain 'B' and resid 283 through 294 Processing helix chain 'B' and resid 297 through 301 removed outlier: 3.618A pdb=" N ARG B 301 " --> pdb=" O PRO B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 311 Processing helix chain 'B' and resid 318 through 323 removed outlier: 3.599A pdb=" N PHE B 323 " --> pdb=" O ILE B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 329 removed outlier: 3.543A pdb=" N ALA B 329 " --> pdb=" O GLN B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 349 removed outlier: 3.947A pdb=" N ILE B 343 " --> pdb=" O ALA B 339 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU B 344 " --> pdb=" O ASP B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 358 Processing helix chain 'B' and resid 374 through 385 removed outlier: 3.575A pdb=" N LEU B 378 " --> pdb=" O GLY B 374 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SER B 380 " --> pdb=" O VAL B 376 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL B 381 " --> pdb=" O ILE B 377 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N CYS B 385 " --> pdb=" O VAL B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 405 Processing helix chain 'B' and resid 410 through 418 Processing helix chain 'B' and resid 418 through 426 removed outlier: 3.645A pdb=" N PHE B 425 " --> pdb=" O TYR B 421 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER B 426 " --> pdb=" O LEU B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 445 removed outlier: 3.813A pdb=" N ARG B 434 " --> pdb=" O VAL B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 448 No H-bonds generated for 'chain 'B' and resid 446 through 448' Processing helix chain 'B' and resid 457 through 462 removed outlier: 3.520A pdb=" N GLU B 461 " --> pdb=" O ASN B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 471 removed outlier: 3.889A pdb=" N ALA B 471 " --> pdb=" O ALA B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 485 removed outlier: 3.839A pdb=" N ARG B 479 " --> pdb=" O ALA B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 506 removed outlier: 4.193A pdb=" N LEU B 489 " --> pdb=" O ASN B 485 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA B 490 " --> pdb=" O ILE B 486 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASN B 506 " --> pdb=" O LEU B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 546 removed outlier: 4.110A pdb=" N LYS B 540 " --> pdb=" O MET B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 560 removed outlier: 3.934A pdb=" N LYS B 553 " --> pdb=" O GLU B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 569 removed outlier: 4.059A pdb=" N VAL B 566 " --> pdb=" O THR B 562 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY B 569 " --> pdb=" O CYS B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 576 removed outlier: 3.904A pdb=" N ASN B 574 " --> pdb=" O ARG B 570 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASP B 575 " --> pdb=" O GLN B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 582 Processing helix chain 'B' and resid 583 through 587 removed outlier: 3.583A pdb=" N ASN B 586 " --> pdb=" O THR B 583 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASP B 587 " --> pdb=" O PHE B 584 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 583 through 587' Processing helix chain 'B' and resid 590 through 609 removed outlier: 3.974A pdb=" N ARG B 594 " --> pdb=" O ASP B 590 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE B 598 " --> pdb=" O ARG B 594 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N VAL B 602 " --> pdb=" O PHE B 598 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N GLY B 603 " --> pdb=" O ASP B 599 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N VAL B 604 " --> pdb=" O SER B 600 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TYR B 607 " --> pdb=" O GLY B 603 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY B 609 " --> pdb=" O ALA B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 623 Proline residue: B 618 - end of helix Processing helix chain 'B' and resid 624 through 626 No H-bonds generated for 'chain 'B' and resid 624 through 626' Processing helix chain 'B' and resid 628 through 646 removed outlier: 3.720A pdb=" N ILE B 632 " --> pdb=" O GLU B 628 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 661 removed outlier: 3.819A pdb=" N TYR B 654 " --> pdb=" O LYS B 650 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASP B 659 " --> pdb=" O GLU B 655 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA B 661 " --> pdb=" O ALA B 657 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 666 removed outlier: 3.739A pdb=" N CYS B 665 " --> pdb=" O PRO B 662 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 686 removed outlier: 3.505A pdb=" N ARG B 672 " --> pdb=" O ASN B 668 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 700 removed outlier: 4.597A pdb=" N MET B 696 " --> pdb=" O TYR B 692 " (cutoff:3.500A) Proline residue: B 697 - end of helix Processing helix chain 'B' and resid 701 through 703 No H-bonds generated for 'chain 'B' and resid 701 through 703' Processing helix chain 'B' and resid 712 through 719 removed outlier: 3.856A pdb=" N LEU B 716 " --> pdb=" O ARG B 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 725 through 734 removed outlier: 3.523A pdb=" N ARG B 734 " --> pdb=" O ASP B 730 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 753 removed outlier: 4.188A pdb=" N LEU B 741 " --> pdb=" O ASP B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 764 through 778 Processing helix chain 'B' and resid 780 through 790 removed outlier: 3.931A pdb=" N GLU B 784 " --> pdb=" O THR B 780 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASP B 785 " --> pdb=" O GLU B 781 " (cutoff:3.500A) Processing helix chain 'B' and resid 790 through 801 Processing helix chain 'B' and resid 802 through 804 No H-bonds generated for 'chain 'B' and resid 802 through 804' Processing helix chain 'B' and resid 821 through 825 Processing helix chain 'B' and resid 938 through 967 removed outlier: 3.726A pdb=" N ASN B 967 " --> pdb=" O GLN B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 1023 through 1027 removed outlier: 3.733A pdb=" N GLU B1026 " --> pdb=" O GLN B1023 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N GLY B1027 " --> pdb=" O LYS B1024 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1023 through 1027' Processing helix chain 'B' and resid 1249 through 1253 removed outlier: 3.925A pdb=" N GLY B1252 " --> pdb=" O PRO B1249 " (cutoff:3.500A) Processing helix chain 'B' and resid 1272 through 1276 removed outlier: 3.577A pdb=" N SER B1276 " --> pdb=" O PRO B1273 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 127 removed outlier: 4.175A pdb=" N ARG C 115 " --> pdb=" O ASN C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 170 removed outlier: 3.551A pdb=" N THR C 141 " --> pdb=" O CYS C 137 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLN C 160 " --> pdb=" O GLU C 156 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU C 170 " --> pdb=" O LEU C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 216 removed outlier: 3.992A pdb=" N GLN C 179 " --> pdb=" O ASP C 175 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU C 180 " --> pdb=" O ASP C 176 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N GLN C 181 " --> pdb=" O SER C 177 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N MET C 182 " --> pdb=" O GLU C 178 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLU C 183 " --> pdb=" O GLN C 179 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP C 200 " --> pdb=" O GLN C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 265 removed outlier: 4.412A pdb=" N ARG C 221 " --> pdb=" O ALA C 217 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLU C 235 " --> pdb=" O ARG C 231 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N PHE C 236 " --> pdb=" O GLU C 232 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS C 248 " --> pdb=" O ASP C 244 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER C 249 " --> pdb=" O ASP C 245 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS C 265 " --> pdb=" O LEU C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 322 removed outlier: 3.696A pdb=" N ILE C 303 " --> pdb=" O GLU C 299 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY C 308 " --> pdb=" O ASN C 304 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLN C 309 " --> pdb=" O ALA C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 384 removed outlier: 3.689A pdb=" N ASP C 366 " --> pdb=" O ASP C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 446 removed outlier: 3.837A pdb=" N TRP C 425 " --> pdb=" O SER C 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 62 Processing helix chain 'D' and resid 74 through 100 removed outlier: 3.964A pdb=" N SER D 87 " --> pdb=" O SER D 83 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LYS D 88 " --> pdb=" O ARG D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 128 Processing helix chain 'D' and resid 130 through 152 Processing helix chain 'D' and resid 152 through 165 removed outlier: 4.492A pdb=" N GLN D 156 " --> pdb=" O TYR D 152 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ARG D 157 " --> pdb=" O SER D 153 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLU D 160 " --> pdb=" O GLN D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 205 removed outlier: 3.730A pdb=" N ARG D 170 " --> pdb=" O GLN D 166 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER D 196 " --> pdb=" O ASN D 192 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N HIS D 197 " --> pdb=" O LEU D 193 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE D 205 " --> pdb=" O LEU D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 277 No H-bonds generated for 'chain 'D' and resid 275 through 277' Processing helix chain 'D' and resid 278 through 287 removed outlier: 3.585A pdb=" N LYS D 287 " --> pdb=" O VAL D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 297 removed outlier: 3.929A pdb=" N SER D 297 " --> pdb=" O MET D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 322 Processing helix chain 'D' and resid 340 through 362 removed outlier: 3.725A pdb=" N GLN D 362 " --> pdb=" O LEU D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 369 removed outlier: 3.680A pdb=" N LEU D 369 " --> pdb=" O LEU D 366 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 383 Processing helix chain 'D' and resid 398 through 402 removed outlier: 4.154A pdb=" N LEU D 401 " --> pdb=" O ARG D 398 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU D 402 " --> pdb=" O ALA D 399 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 398 through 402' Processing helix chain 'E' and resid 7 through 24 removed outlier: 3.548A pdb=" N GLN E 13 " --> pdb=" O ASN E 9 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP E 19 " --> pdb=" O SER E 15 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG E 20 " --> pdb=" O ARG E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 44 removed outlier: 3.583A pdb=" N SER E 32 " --> pdb=" O GLU E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 78 removed outlier: 3.602A pdb=" N LEU E 69 " --> pdb=" O MET E 65 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 232 through 234 removed outlier: 7.050A pdb=" N HIS A 8 " --> pdb=" O GLY A 232 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N VAL A 234 " --> pdb=" O HIS A 8 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ILE A 10 " --> pdb=" O VAL A 234 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 85 through 96 removed outlier: 11.927A pdb=" N TRP A 87 " --> pdb=" O GLU A 27 " (cutoff:3.500A) removed outlier: 12.567A pdb=" N GLU A 27 " --> pdb=" O TRP A 87 " (cutoff:3.500A) removed outlier: 9.585A pdb=" N GLU A 89 " --> pdb=" O SER A 25 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N SER A 25 " --> pdb=" O GLU A 89 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N LEU A 91 " --> pdb=" O ILE A 23 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ILE A 23 " --> pdb=" O LEU A 91 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LEU A 93 " --> pdb=" O LEU A 21 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N LEU A 21 " --> pdb=" O LEU A 93 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N VAL A 95 " --> pdb=" O VAL A 19 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N ILE A 23 " --> pdb=" O GLU A 220 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N GLU A 220 " --> pdb=" O ILE A 23 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N SER A 25 " --> pdb=" O MET A 218 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL A 219 " --> pdb=" O HIS A 141 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 68 through 69 removed outlier: 3.645A pdb=" N TYR A 58 " --> pdb=" O TRP A 111 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR A 109 " --> pdb=" O THR A 60 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 74 through 75 removed outlier: 3.645A pdb=" N TYR A 58 " --> pdb=" O TRP A 111 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR A 109 " --> pdb=" O THR A 60 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 229 through 230 removed outlier: 7.275A pdb=" N CYS A 223 " --> pdb=" O ILE B 819 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 591 through 592 removed outlier: 6.597A pdb=" N LYS A 624 " --> pdb=" O ARG A 602 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ILE A 604 " --> pdb=" O PHE A 622 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N PHE A 622 " --> pdb=" O ILE A 604 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR A 610 " --> pdb=" O GLN A 620 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 591 through 592 removed outlier: 6.597A pdb=" N LYS A 624 " --> pdb=" O ARG A 602 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ILE A 604 " --> pdb=" O PHE A 622 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N PHE A 622 " --> pdb=" O ILE A 604 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 688 through 689 removed outlier: 3.516A pdb=" N PHE A 758 " --> pdb=" O LEU A 750 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 27 through 34 removed outlier: 6.721A pdb=" N ARG B 42 " --> pdb=" O ASP B 29 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N SER B 31 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N VAL B 40 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS B 89 " --> pdb=" O PHE B 102 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 108 through 109 Processing sheet with id=AB2, first strand: chain 'B' and resid 175 through 176 removed outlier: 6.197A pdb=" N LEU B 175 " --> pdb=" O VAL B 203 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 984 through 989 removed outlier: 6.889A pdb=" N VAL B1356 " --> pdb=" O VAL B 986 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N HIS B 988 " --> pdb=" O VAL B1354 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N VAL B1354 " --> pdb=" O HIS B 988 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N PHE B1344 " --> pdb=" O PHE B1338 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N PHE B1338 " --> pdb=" O PHE B1344 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 996 through 1001 removed outlier: 6.965A pdb=" N CYS B1011 " --> pdb=" O ASN B 997 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ILE B 999 " --> pdb=" O ALA B1009 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ALA B1009 " --> pdb=" O ILE B 999 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N VAL B1001 " --> pdb=" O LEU B1007 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N LEU B1007 " --> pdb=" O VAL B1001 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE B1008 " --> pdb=" O TRP B1020 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU B1036 " --> pdb=" O ILE B1019 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 1045 through 1050 removed outlier: 4.136A pdb=" N THR B1047 " --> pdb=" O ALA B1060 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ALA B1065 " --> pdb=" O SER B1061 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VAL B1066 " --> pdb=" O SER B1087 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N SER B1087 " --> pdb=" O VAL B1066 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LEU B1068 " --> pdb=" O LEU B1085 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N HIS B1083 " --> pdb=" O GLY B1070 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 1098 through 1101 removed outlier: 4.027A pdb=" N ASP B1100 " --> pdb=" O ALA B1115 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N SER B1120 " --> pdb=" O THR B1116 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N TRP B1133 " --> pdb=" O GLY B1123 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ASP B1125 " --> pdb=" O ASN B1131 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N ASN B1131 " --> pdb=" O ASP B1125 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 1144 through 1149 removed outlier: 3.856A pdb=" N SER B1146 " --> pdb=" O GLY B1159 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N THR B1164 " --> pdb=" O THR B1160 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N CYS B1167 " --> pdb=" O SER B1177 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N SER B1177 " --> pdb=" O CYS B1167 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ASP B1169 " --> pdb=" O PRO B1175 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 1187 through 1192 removed outlier: 6.738A pdb=" N ALA B1203 " --> pdb=" O ARG B1188 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LEU B1190 " --> pdb=" O ILE B1201 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ILE B1201 " --> pdb=" O LEU B1190 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N MET B1192 " --> pdb=" O TRP B1199 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N TRP B1199 " --> pdb=" O MET B1192 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLU B1209 " --> pdb=" O VAL B1204 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL B1210 " --> pdb=" O LEU B1224 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N PHE B1222 " --> pdb=" O MET B1212 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ASP B1214 " --> pdb=" O ARG B1220 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ARG B1220 " --> pdb=" O ASP B1214 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ARG B1221 " --> pdb=" O GLU B1299 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N VAL B1301 " --> pdb=" O ARG B1221 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N THR B1223 " --> pdb=" O VAL B1301 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N GLU B1303 " --> pdb=" O THR B1223 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N TRP B1225 " --> pdb=" O GLU B1303 " (cutoff:3.500A) removed outlier: 8.715A pdb=" N GLN B1305 " --> pdb=" O TRP B1225 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 1187 through 1192 removed outlier: 6.738A pdb=" N ALA B1203 " --> pdb=" O ARG B1188 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LEU B1190 " --> pdb=" O ILE B1201 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ILE B1201 " --> pdb=" O LEU B1190 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N MET B1192 " --> pdb=" O TRP B1199 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N TRP B1199 " --> pdb=" O MET B1192 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLU B1209 " --> pdb=" O VAL B1204 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL B1210 " --> pdb=" O LEU B1224 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N PHE B1222 " --> pdb=" O MET B1212 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ASP B1214 " --> pdb=" O ARG B1220 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ARG B1220 " --> pdb=" O ASP B1214 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ARG B1221 " --> pdb=" O GLU B1299 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N VAL B1301 " --> pdb=" O ARG B1221 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N THR B1223 " --> pdb=" O VAL B1301 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N GLU B1303 " --> pdb=" O THR B1223 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N TRP B1225 " --> pdb=" O GLU B1303 " (cutoff:3.500A) removed outlier: 8.715A pdb=" N GLN B1305 " --> pdb=" O TRP B1225 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 1242 through 1248 removed outlier: 3.515A pdb=" N ALA B1259 " --> pdb=" O GLY B1244 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 277 through 279 Processing sheet with id=AC3, first strand: chain 'C' and resid 328 through 331 removed outlier: 3.728A pdb=" N TYR C 338 " --> pdb=" O VAL C 331 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LEU C 349 " --> pdb=" O LEU C 339 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 395 through 397 Processing sheet with id=AC5, first strand: chain 'D' and resid 210 through 211 1049 hydrogen bonds defined for protein. 3018 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: 4.46 Time building geometry restraints manager: 2.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5988 1.33 - 1.45: 3933 1.45 - 1.57: 12643 1.57 - 1.70: 7 1.70 - 1.82: 194 Bond restraints: 22765 Sorted by residual: bond pdb=" N GLY B 2 " pdb=" CA GLY B 2 " ideal model delta sigma weight residual 1.451 1.214 0.237 1.60e-02 3.91e+03 2.19e+02 bond pdb=" C1 MYR B1401 " pdb=" C2 MYR B1401 " ideal model delta sigma weight residual 1.544 1.597 -0.053 2.00e-02 2.50e+03 6.89e+00 bond pdb=" N LEU B 5 " pdb=" CA LEU B 5 " ideal model delta sigma weight residual 1.465 1.489 -0.024 1.22e-02 6.72e+03 3.85e+00 bond pdb=" N GLN D 166 " pdb=" CA GLN D 166 " ideal model delta sigma weight residual 1.456 1.478 -0.022 1.23e-02 6.61e+03 3.23e+00 bond pdb=" CB GLN A 645 " pdb=" CG GLN A 645 " ideal model delta sigma weight residual 1.520 1.567 -0.047 3.00e-02 1.11e+03 2.45e+00 ... (remaining 22760 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.47: 30445 2.47 - 4.94: 266 4.94 - 7.40: 36 7.40 - 9.87: 5 9.87 - 12.34: 3 Bond angle restraints: 30755 Sorted by residual: angle pdb=" N VAL A 266 " pdb=" CA VAL A 266 " pdb=" C VAL A 266 " ideal model delta sigma weight residual 112.29 108.00 4.29 9.40e-01 1.13e+00 2.08e+01 angle pdb=" C SER B1074 " pdb=" N LYS B1075 " pdb=" CA LYS B1075 " ideal model delta sigma weight residual 122.46 128.78 -6.32 1.41e+00 5.03e-01 2.01e+01 angle pdb=" C GLU B 254 " pdb=" N GLY B 255 " pdb=" CA GLY B 255 " ideal model delta sigma weight residual 121.70 129.06 -7.36 1.80e+00 3.09e-01 1.67e+01 angle pdb=" C ILE A 760 " pdb=" N ASP A 761 " pdb=" CA ASP A 761 " ideal model delta sigma weight residual 121.54 129.14 -7.60 1.91e+00 2.74e-01 1.58e+01 angle pdb=" C LEU B 5 " pdb=" CA LEU B 5 " pdb=" CB LEU B 5 " ideal model delta sigma weight residual 117.23 112.11 5.12 1.36e+00 5.41e-01 1.42e+01 ... (remaining 30750 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.47: 13334 27.47 - 54.93: 513 54.93 - 82.40: 45 82.40 - 109.86: 15 109.86 - 137.33: 1 Dihedral angle restraints: 13908 sinusoidal: 5804 harmonic: 8104 Sorted by residual: dihedral pdb=" O2B GDP B1402 " pdb=" O3A GDP B1402 " pdb=" PB GDP B1402 " pdb=" PA GDP B1402 " ideal model delta sinusoidal sigma weight residual -180.00 -42.67 -137.33 1 2.00e+01 2.50e-03 4.16e+01 dihedral pdb=" CA PHE B 259 " pdb=" C PHE B 259 " pdb=" N ASP B 260 " pdb=" CA ASP B 260 " ideal model delta harmonic sigma weight residual 180.00 155.80 24.20 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" O5' GDP B1402 " pdb=" O3A GDP B1402 " pdb=" PA GDP B1402 " pdb=" PB GDP B1402 " ideal model delta sinusoidal sigma weight residual -179.98 -92.45 -87.53 1 2.00e+01 2.50e-03 2.30e+01 ... (remaining 13905 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 3201 0.089 - 0.179: 204 0.179 - 0.268: 2 0.268 - 0.358: 0 0.358 - 0.447: 1 Chirality restraints: 3408 Sorted by residual: chirality pdb=" CB VAL B 834 " pdb=" CA VAL B 834 " pdb=" CG1 VAL B 834 " pdb=" CG2 VAL B 834 " both_signs ideal model delta sigma weight residual False -2.63 -2.18 -0.45 2.00e-01 2.50e+01 5.01e+00 chirality pdb=" CA ILE D 263 " pdb=" N ILE D 263 " pdb=" C ILE D 263 " pdb=" CB ILE D 263 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.55e-01 chirality pdb=" CA ASP A 761 " pdb=" N ASP A 761 " pdb=" C ASP A 761 " pdb=" CB ASP A 761 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.39e-01 ... (remaining 3405 not shown) Planarity restraints: 3938 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 661 " 0.049 5.00e-02 4.00e+02 7.32e-02 8.58e+00 pdb=" N PRO B 662 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO B 662 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 662 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET B 696 " 0.044 5.00e-02 4.00e+02 6.64e-02 7.05e+00 pdb=" N PRO B 697 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO B 697 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 697 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 464 " 0.039 5.00e-02 4.00e+02 5.84e-02 5.45e+00 pdb=" N PRO B 465 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO B 465 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 465 " 0.033 5.00e-02 4.00e+02 ... (remaining 3935 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 25 2.63 - 3.20: 17357 3.20 - 3.77: 31812 3.77 - 4.33: 43378 4.33 - 4.90: 72809 Nonbonded interactions: 165381 Sorted by model distance: nonbonded pdb=" OD1 ASP A 761 " pdb="MG MG A 901 " model vdw 2.065 2.170 nonbonded pdb=" O2A ADP A 900 " pdb=" O2B ADP A 900 " model vdw 2.139 3.040 nonbonded pdb=" ND2 ASN B 153 " pdb="MG MG B1403 " model vdw 2.247 2.250 nonbonded pdb=" CG ASP A 761 " pdb="MG MG A 901 " model vdw 2.299 2.400 nonbonded pdb=" OD2 ASP B 166 " pdb="MG MG B1403 " model vdw 2.344 2.170 ... (remaining 165376 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 5.940 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: 0.030 Extract box with map and model: 0.530 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 22.800 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 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 : 0.003 0.237 22774 Z= 0.195 Angle : 0.855 48.163 30767 Z= 0.357 Chirality : 0.044 0.447 3408 Planarity : 0.005 0.073 3938 Dihedral : 14.432 137.327 8644 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 0.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.49 % Allowed : 6.86 % Favored : 92.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.14), residues: 2732 helix: -0.63 (0.12), residues: 1272 sheet: -0.58 (0.29), residues: 303 loop : -1.09 (0.16), residues: 1157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 799 TYR 0.027 0.001 TYR A 803 PHE 0.014 0.001 PHE A 798 TRP 0.019 0.001 TRP B 127 HIS 0.006 0.001 HIS C 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.18 (22765) covalent geometry : angle 0.61436 / 0.34 (30755) hydrogen bonds : bond 0.17660 / 11.25 ( 1032) hydrogen bonds : angle 5.93182 / 4.04 ( 3018) metal coordination : bond 0.02572 / 1.25 ( 8) metal coordination : angle 30.08765 / 16.32 ( 12) Misc. bond : bond 0.10530 / 5.54 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5464 Ramachandran restraints generated. 2732 Oldfield, 0 Emsley, 2732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5464 Ramachandran restraints generated. 2732 Oldfield, 0 Emsley, 2732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 2464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 555 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ASP cc_start: 0.7800 (t0) cc_final: 0.7584 (t0) REVERT: A 355 TRP cc_start: 0.6920 (m100) cc_final: 0.6154 (m-10) REVERT: B 333 LYS cc_start: 0.8071 (mttt) cc_final: 0.7857 (mmmt) REVERT: B 708 ILE cc_start: 0.9200 (pt) cc_final: 0.8981 (mt) REVERT: B 731 TYR cc_start: 0.7542 (t80) cc_final: 0.6797 (t80) REVERT: B 1093 LYS cc_start: 0.8069 (mmtt) cc_final: 0.7579 (ttpp) REVERT: B 1192 MET cc_start: 0.9074 (mmt) cc_final: 0.8635 (mmt) REVERT: B 1326 VAL cc_start: 0.8205 (t) cc_final: 0.7914 (p) REVERT: B 1353 ILE cc_start: 0.9226 (mm) cc_final: 0.9003 (mt) REVERT: C 177 SER cc_start: 0.8630 (p) cc_final: 0.8235 (m) REVERT: C 333 TYR cc_start: 0.7537 (OUTLIER) cc_final: 0.6839 (t80) REVERT: C 394 TYR cc_start: 0.8106 (m-80) cc_final: 0.7896 (m-80) REVERT: C 436 LEU cc_start: 0.8691 (mt) cc_final: 0.8302 (mt) REVERT: D 168 HIS cc_start: 0.5975 (m170) cc_final: 0.5741 (m170) outliers start: 12 outliers final: 11 residues processed: 564 average time/residue: 0.1857 time to fit residues: 154.1179 Evaluate side-chains 310 residues out of total 2464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 298 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 580 HIS Chi-restraints excluded: chain B residue 1179 HIS Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 333 TYR Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 313 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 0.0980 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 7.9990 chunk 111 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 8 HIS A 560 GLN A 574 GLN A 649 GLN B 58 GLN B 153 ASN ** B 744 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1063 ASN B1243 HIS ** B1339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 424 GLN ** D 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.149473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.104865 restraints weight = 36394.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.102600 restraints weight = 25793.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.103430 restraints weight = 23286.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.103969 restraints weight = 21334.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.104104 restraints weight = 18992.432| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 22774 Z= 0.127 Angle : 0.597 18.656 30767 Z= 0.290 Chirality : 0.041 0.181 3408 Planarity : 0.004 0.047 3938 Dihedral : 6.492 129.097 3048 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.87 % Allowed : 12.01 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.15), residues: 2732 helix: 1.00 (0.14), residues: 1295 sheet: -0.02 (0.30), residues: 297 loop : -0.93 (0.17), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B1275 TYR 0.027 0.001 TYR A 803 PHE 0.031 0.001 PHE B1338 TRP 0.021 0.001 TRP B1168 HIS 0.005 0.001 HIS C 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (22765) covalent geometry : angle 0.56323 / 0.29 (30755) hydrogen bonds : bond 0.04292 / 2.77 ( 1032) hydrogen bonds : angle 4.07523 / 2.77 ( 3018) metal coordination : bond 0.01817 / 0.97 ( 8) metal coordination : angle 10.02067 / 5.38 ( 12) Misc. bond : bond 0.00244 / 0.13 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5464 Ramachandran restraints generated. 2732 Oldfield, 0 Emsley, 2732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5464 Ramachandran restraints generated. 2732 Oldfield, 0 Emsley, 2732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 326 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 355 TRP cc_start: 0.7120 (m100) cc_final: 0.5867 (m100) REVERT: A 617 MET cc_start: 0.7129 (mmt) cc_final: 0.6583 (mmt) REVERT: A 852 ASP cc_start: 0.8349 (m-30) cc_final: 0.7835 (t0) REVERT: B 333 LYS cc_start: 0.8268 (mttt) cc_final: 0.7924 (mmmt) REVERT: B 696 MET cc_start: 0.9115 (mmt) cc_final: 0.8858 (mmt) REVERT: B 708 ILE cc_start: 0.9290 (pt) cc_final: 0.9086 (mt) REVERT: B 948 ILE cc_start: 0.8339 (mm) cc_final: 0.8043 (tt) REVERT: B 1056 TYR cc_start: 0.7018 (m-80) cc_final: 0.6645 (m-80) REVERT: B 1093 LYS cc_start: 0.8194 (mmtt) cc_final: 0.7680 (ttpp) REVERT: B 1192 MET cc_start: 0.9251 (mmt) cc_final: 0.8843 (mmt) REVERT: B 1326 VAL cc_start: 0.8676 (t) cc_final: 0.8297 (p) REVERT: C 177 SER cc_start: 0.8915 (p) cc_final: 0.8459 (m) REVERT: C 300 TRP cc_start: 0.6477 (m-90) cc_final: 0.6202 (m-90) REVERT: C 333 TYR cc_start: 0.7829 (OUTLIER) cc_final: 0.6611 (t80) outliers start: 46 outliers final: 30 residues processed: 358 average time/residue: 0.1561 time to fit residues: 87.8959 Evaluate side-chains 302 residues out of total 2464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 271 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LYS Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 754 THR Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 580 HIS Chi-restraints excluded: chain B residue 600 SER Chi-restraints excluded: chain B residue 753 ASN Chi-restraints excluded: chain B residue 1062 ASP Chi-restraints excluded: chain B residue 1179 HIS Chi-restraints excluded: chain B residue 1255 ILE Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 288 PHE Chi-restraints excluded: chain C residue 333 TYR Chi-restraints excluded: chain C residue 447 PHE Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 128 CYS Chi-restraints excluded: chain D residue 150 LYS Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 70 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 62 optimal weight: 4.9990 chunk 93 optimal weight: 0.8980 chunk 244 optimal weight: 3.9990 chunk 16 optimal weight: 10.0000 chunk 110 optimal weight: 0.8980 chunk 221 optimal weight: 0.3980 chunk 140 optimal weight: 1.9990 chunk 174 optimal weight: 6.9990 chunk 198 optimal weight: 7.9990 chunk 44 optimal weight: 0.6980 chunk 38 optimal weight: 0.0770 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 744 HIS ** B1339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 147 GLN ** D 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.149145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.105981 restraints weight = 36041.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.103750 restraints weight = 25925.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.104382 restraints weight = 25269.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.105002 restraints weight = 22141.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.105050 restraints weight = 19941.819| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 22774 Z= 0.109 Angle : 0.539 13.548 30767 Z= 0.263 Chirality : 0.040 0.162 3408 Planarity : 0.003 0.038 3938 Dihedral : 6.012 126.316 3041 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.39 % Allowed : 12.05 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.16), residues: 2732 helix: 1.68 (0.15), residues: 1290 sheet: 0.09 (0.30), residues: 291 loop : -0.80 (0.17), residues: 1151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1275 TYR 0.025 0.001 TYR A 803 PHE 0.019 0.001 PHE C 419 TRP 0.022 0.001 TRP B1168 HIS 0.007 0.001 HIS C 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (22765) covalent geometry : angle 0.52120 / 0.26 (30755) hydrogen bonds : bond 0.03671 / 2.38 ( 1032) hydrogen bonds : angle 3.76067 / 2.55 ( 3018) metal coordination : bond 0.01763 / 0.85 ( 8) metal coordination : angle 6.97562 / 3.62 ( 12) Misc. bond : bond 0.00015 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5464 Ramachandran restraints generated. 2732 Oldfield, 0 Emsley, 2732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5464 Ramachandran restraints generated. 2732 Oldfield, 0 Emsley, 2732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 301 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 355 TRP cc_start: 0.7159 (m100) cc_final: 0.6289 (m-10) REVERT: A 617 MET cc_start: 0.7179 (mmt) cc_final: 0.6634 (mmt) REVERT: A 852 ASP cc_start: 0.8325 (m-30) cc_final: 0.7850 (t0) REVERT: B 333 LYS cc_start: 0.8325 (mttt) cc_final: 0.7972 (mmmt) REVERT: B 507 MET cc_start: 0.2699 (mpp) cc_final: 0.1976 (mtt) REVERT: B 531 GLN cc_start: 0.8423 (OUTLIER) cc_final: 0.7844 (mp10) REVERT: B 696 MET cc_start: 0.9093 (mmt) cc_final: 0.8869 (mmt) REVERT: B 708 ILE cc_start: 0.9276 (pt) cc_final: 0.9037 (mt) REVERT: B 731 TYR cc_start: 0.7872 (OUTLIER) cc_final: 0.7082 (t80) REVERT: B 948 ILE cc_start: 0.8343 (mm) cc_final: 0.8089 (tp) REVERT: B 1056 TYR cc_start: 0.7048 (m-80) cc_final: 0.6646 (m-80) REVERT: B 1093 LYS cc_start: 0.8205 (mmtt) cc_final: 0.7710 (ttpp) REVERT: B 1192 MET cc_start: 0.9217 (mmt) cc_final: 0.8767 (mmt) REVERT: B 1326 VAL cc_start: 0.8639 (t) cc_final: 0.8290 (p) REVERT: B 1338 PHE cc_start: 0.8720 (p90) cc_final: 0.8334 (p90) REVERT: C 177 SER cc_start: 0.8875 (p) cc_final: 0.8427 (m) REVERT: C 300 TRP cc_start: 0.6486 (m-90) cc_final: 0.6200 (m-90) REVERT: C 333 TYR cc_start: 0.7865 (OUTLIER) cc_final: 0.6582 (t80) REVERT: C 394 TYR cc_start: 0.8457 (m-80) cc_final: 0.8215 (m-80) REVERT: D 276 TYR cc_start: 0.6777 (m-80) cc_final: 0.6518 (m-80) REVERT: F 19 GLN cc_start: 0.7822 (OUTLIER) cc_final: 0.7438 (pt0) outliers start: 59 outliers final: 36 residues processed: 339 average time/residue: 0.1486 time to fit residues: 80.1940 Evaluate side-chains 315 residues out of total 2464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 275 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 754 THR Chi-restraints excluded: chain A residue 820 PHE Chi-restraints excluded: chain A residue 868 HIS Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 340 ASP Chi-restraints excluded: chain B residue 531 GLN Chi-restraints excluded: chain B residue 580 HIS Chi-restraints excluded: chain B residue 600 SER Chi-restraints excluded: chain B residue 731 TYR Chi-restraints excluded: chain B residue 942 THR Chi-restraints excluded: chain B residue 1012 SER Chi-restraints excluded: chain B residue 1062 ASP Chi-restraints excluded: chain B residue 1068 LEU Chi-restraints excluded: chain B residue 1143 LEU Chi-restraints excluded: chain B residue 1179 HIS Chi-restraints excluded: chain B residue 1222 PHE Chi-restraints excluded: chain B residue 1255 ILE Chi-restraints excluded: chain B residue 1269 ASP Chi-restraints excluded: chain B residue 1335 VAL Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 333 TYR Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 150 LYS Chi-restraints excluded: chain D residue 269 SER Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain F residue 19 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 189 optimal weight: 2.9990 chunk 265 optimal weight: 10.0000 chunk 197 optimal weight: 0.0270 chunk 261 optimal weight: 0.9990 chunk 88 optimal weight: 0.9980 chunk 97 optimal weight: 0.7980 chunk 72 optimal weight: 4.9990 chunk 257 optimal weight: 4.9990 chunk 234 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 173 optimal weight: 0.3980 overall best weight: 0.6440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 777 GLN B1052 GLN B1063 ASN B1193 HIS ** B1339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 ASN D 368 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.148913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.104900 restraints weight = 36174.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.102925 restraints weight = 26388.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.103404 restraints weight = 23901.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.104008 restraints weight = 22456.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.104036 restraints weight = 20107.573| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 22774 Z= 0.106 Angle : 0.529 11.293 30767 Z= 0.258 Chirality : 0.040 0.193 3408 Planarity : 0.003 0.060 3938 Dihedral : 5.933 124.201 3041 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.68 % Allowed : 12.70 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.16), residues: 2732 helix: 1.95 (0.15), residues: 1297 sheet: 0.18 (0.30), residues: 288 loop : -0.66 (0.17), residues: 1147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B1275 TYR 0.026 0.001 TYR B 731 PHE 0.016 0.001 PHE B1344 TRP 0.017 0.001 TRP B1168 HIS 0.006 0.001 HIS B1193 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (22765) covalent geometry : angle 0.51293 / 0.26 (30755) hydrogen bonds : bond 0.03500 / 2.27 ( 1032) hydrogen bonds : angle 3.59947 / 2.44 ( 3018) metal coordination : bond 0.01577 / 0.76 ( 8) metal coordination : angle 6.56284 / 3.42 ( 12) Misc. bond : bond 0.00019 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5464 Ramachandran restraints generated. 2732 Oldfield, 0 Emsley, 2732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5464 Ramachandran restraints generated. 2732 Oldfield, 0 Emsley, 2732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 273 time to evaluate : 0.884 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: A 16 ASP cc_start: 0.7980 (t0) cc_final: 0.7659 (t0) REVERT: A 355 TRP cc_start: 0.7201 (m100) cc_final: 0.5924 (m100) REVERT: A 617 MET cc_start: 0.7263 (mmt) cc_final: 0.6672 (mmt) REVERT: A 852 ASP cc_start: 0.8303 (m-30) cc_final: 0.7853 (t0) REVERT: B 333 LYS cc_start: 0.8333 (mttt) cc_final: 0.7972 (mmmt) REVERT: B 507 MET cc_start: 0.2832 (mpp) cc_final: 0.2110 (mtm) REVERT: B 696 MET cc_start: 0.9090 (mmt) cc_final: 0.8872 (mmt) REVERT: B 708 ILE cc_start: 0.9281 (pt) cc_final: 0.9047 (mt) REVERT: B 948 ILE cc_start: 0.8346 (mm) cc_final: 0.7956 (tt) REVERT: B 1056 TYR cc_start: 0.7008 (m-80) cc_final: 0.6625 (m-80) REVERT: B 1093 LYS cc_start: 0.8221 (mmtt) cc_final: 0.7732 (ttpp) REVERT: B 1192 MET cc_start: 0.9208 (mmt) cc_final: 0.8731 (mmt) REVERT: B 1326 VAL cc_start: 0.8661 (t) cc_final: 0.8307 (p) REVERT: B 1338 PHE cc_start: 0.8874 (p90) cc_final: 0.8546 (p90) REVERT: C 177 SER cc_start: 0.8889 (p) cc_final: 0.8457 (m) REVERT: C 266 LYS cc_start: 0.8750 (mmmt) cc_final: 0.8484 (mtmm) REVERT: C 290 LEU cc_start: 0.8311 (tt) cc_final: 0.8014 (tp) REVERT: C 333 TYR cc_start: 0.7960 (OUTLIER) cc_final: 0.6668 (t80) REVERT: D 276 TYR cc_start: 0.6875 (m-80) cc_final: 0.6627 (m-80) REVERT: D 294 MET cc_start: 0.4967 (tpp) cc_final: 0.4760 (tpt) REVERT: D 368 GLN cc_start: 0.7107 (OUTLIER) cc_final: 0.6780 (pt0) outliers start: 66 outliers final: 51 residues processed: 321 average time/residue: 0.1479 time to fit residues: 75.5747 Evaluate side-chains 318 residues out of total 2464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 265 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LYS Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 754 THR Chi-restraints excluded: chain A residue 820 PHE Chi-restraints excluded: chain A residue 868 HIS Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 340 ASP Chi-restraints excluded: chain B residue 580 HIS Chi-restraints excluded: chain B residue 600 SER Chi-restraints excluded: chain B residue 658 SER Chi-restraints excluded: chain B residue 773 LYS Chi-restraints excluded: chain B residue 777 GLN Chi-restraints excluded: chain B residue 942 THR Chi-restraints excluded: chain B residue 947 LEU Chi-restraints excluded: chain B residue 1012 SER Chi-restraints excluded: chain B residue 1062 ASP Chi-restraints excluded: chain B residue 1083 HIS Chi-restraints excluded: chain B residue 1143 LEU Chi-restraints excluded: chain B residue 1164 THR Chi-restraints excluded: chain B residue 1179 HIS Chi-restraints excluded: chain B residue 1222 PHE Chi-restraints excluded: chain B residue 1255 ILE Chi-restraints excluded: chain B residue 1335 VAL Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 333 TYR Chi-restraints excluded: chain C residue 447 PHE Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain D residue 150 LYS Chi-restraints excluded: chain D residue 203 SER Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 269 SER Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 368 GLN Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 70 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 142 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 216 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 120 optimal weight: 0.2980 chunk 105 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 45 HIS B 777 GLN ** B1339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 ASN D 368 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.145885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.097835 restraints weight = 36267.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.097972 restraints weight = 23939.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.098082 restraints weight = 20004.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.098961 restraints weight = 18740.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.099079 restraints weight = 17414.513| |-----------------------------------------------------------------------------| r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 22774 Z= 0.177 Angle : 0.564 10.963 30767 Z= 0.278 Chirality : 0.042 0.209 3408 Planarity : 0.003 0.036 3938 Dihedral : 6.088 122.241 3041 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.00 % Allowed : 13.35 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.16), residues: 2732 helix: 1.95 (0.15), residues: 1309 sheet: 0.05 (0.29), residues: 302 loop : -0.70 (0.18), residues: 1121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1275 TYR 0.036 0.002 TYR C 328 PHE 0.020 0.002 PHE B 496 TRP 0.023 0.001 TRP D 267 HIS 0.006 0.001 HIS C 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.18 (22765) covalent geometry : angle 0.55068 / 0.28 (30755) hydrogen bonds : bond 0.04114 / 2.67 ( 1032) hydrogen bonds : angle 3.67581 / 2.50 ( 3018) metal coordination : bond 0.01300 / 0.64 ( 8) metal coordination : angle 6.11902 / 3.19 ( 12) Misc. bond : bond 0.00035 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5464 Ramachandran restraints generated. 2732 Oldfield, 0 Emsley, 2732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5464 Ramachandran restraints generated. 2732 Oldfield, 0 Emsley, 2732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 276 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: A 355 TRP cc_start: 0.7337 (m100) cc_final: 0.6106 (m100) REVERT: A 617 MET cc_start: 0.7293 (mmt) cc_final: 0.6690 (mmt) REVERT: A 852 ASP cc_start: 0.8306 (m-30) cc_final: 0.7883 (t0) REVERT: B 333 LYS cc_start: 0.8420 (mttt) cc_final: 0.8013 (mmmt) REVERT: B 507 MET cc_start: 0.2952 (mpp) cc_final: 0.2384 (mtt) REVERT: B 708 ILE cc_start: 0.9279 (pt) cc_final: 0.9058 (mt) REVERT: B 948 ILE cc_start: 0.8348 (mm) cc_final: 0.7961 (tt) REVERT: B 965 MET cc_start: 0.7515 (mmm) cc_final: 0.7287 (mmm) REVERT: B 1056 TYR cc_start: 0.7045 (m-80) cc_final: 0.6635 (m-80) REVERT: B 1093 LYS cc_start: 0.8320 (mmtt) cc_final: 0.7804 (ttpp) REVERT: B 1136 LYS cc_start: 0.8694 (OUTLIER) cc_final: 0.8076 (ttpp) REVERT: B 1192 MET cc_start: 0.9238 (mmt) cc_final: 0.8677 (mmt) REVERT: B 1197 GLN cc_start: 0.8076 (mp10) cc_final: 0.7693 (pt0) REVERT: B 1268 TRP cc_start: 0.6913 (OUTLIER) cc_final: 0.6240 (m-10) REVERT: B 1326 VAL cc_start: 0.8810 (t) cc_final: 0.8507 (p) REVERT: B 1338 PHE cc_start: 0.8984 (p90) cc_final: 0.8745 (p90) REVERT: C 177 SER cc_start: 0.8932 (p) cc_final: 0.8509 (m) REVERT: C 300 TRP cc_start: 0.6367 (m-90) cc_final: 0.5899 (m-90) REVERT: C 333 TYR cc_start: 0.7945 (OUTLIER) cc_final: 0.6662 (t80) REVERT: D 276 TYR cc_start: 0.7089 (m-80) cc_final: 0.6746 (m-80) REVERT: D 373 HIS cc_start: 0.7669 (m90) cc_final: 0.7459 (m90) outliers start: 74 outliers final: 52 residues processed: 329 average time/residue: 0.1507 time to fit residues: 78.9387 Evaluate side-chains 317 residues out of total 2464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 262 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 754 THR Chi-restraints excluded: chain A residue 867 VAL Chi-restraints excluded: chain A residue 868 HIS Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 340 ASP Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain B residue 580 HIS Chi-restraints excluded: chain B residue 600 SER Chi-restraints excluded: chain B residue 658 SER Chi-restraints excluded: chain B residue 714 LEU Chi-restraints excluded: chain B residue 942 THR Chi-restraints excluded: chain B residue 944 LEU Chi-restraints excluded: chain B residue 947 LEU Chi-restraints excluded: chain B residue 1012 SER Chi-restraints excluded: chain B residue 1062 ASP Chi-restraints excluded: chain B residue 1068 LEU Chi-restraints excluded: chain B residue 1083 HIS Chi-restraints excluded: chain B residue 1117 VAL Chi-restraints excluded: chain B residue 1136 LYS Chi-restraints excluded: chain B residue 1143 LEU Chi-restraints excluded: chain B residue 1164 THR Chi-restraints excluded: chain B residue 1179 HIS Chi-restraints excluded: chain B residue 1255 ILE Chi-restraints excluded: chain B residue 1268 TRP Chi-restraints excluded: chain B residue 1335 VAL Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 333 TYR Chi-restraints excluded: chain C residue 447 PHE Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 203 SER Chi-restraints excluded: chain D residue 208 ILE Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 269 SER Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 58 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 206 optimal weight: 10.0000 chunk 155 optimal weight: 0.7980 chunk 156 optimal weight: 0.0010 chunk 6 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 139 optimal weight: 0.9980 chunk 221 optimal weight: 8.9990 chunk 149 optimal weight: 3.9990 chunk 185 optimal weight: 6.9990 chunk 179 optimal weight: 3.9990 chunk 93 optimal weight: 0.9980 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1152 HIS ** B1153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.146933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.102126 restraints weight = 35983.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.100452 restraints weight = 25694.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.100896 restraints weight = 22973.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.101400 restraints weight = 22399.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.101639 restraints weight = 19363.106| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 22774 Z= 0.127 Angle : 0.539 12.428 30767 Z= 0.265 Chirality : 0.041 0.182 3408 Planarity : 0.003 0.037 3938 Dihedral : 5.969 121.106 3041 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.76 % Allowed : 13.96 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.16), residues: 2732 helix: 2.07 (0.15), residues: 1316 sheet: 0.03 (0.29), residues: 302 loop : -0.64 (0.18), residues: 1114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1275 TYR 0.045 0.001 TYR C 328 PHE 0.016 0.001 PHE B1344 TRP 0.017 0.001 TRP D 267 HIS 0.008 0.001 HIS C 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (22765) covalent geometry : angle 0.52730 / 0.26 (30755) hydrogen bonds : bond 0.03729 / 2.40 ( 1032) hydrogen bonds : angle 3.55427 / 2.42 ( 3018) metal coordination : bond 0.01265 / 0.61 ( 8) metal coordination : angle 5.62020 / 2.92 ( 12) Misc. bond : bond 0.00028 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5464 Ramachandran restraints generated. 2732 Oldfield, 0 Emsley, 2732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5464 Ramachandran restraints generated. 2732 Oldfield, 0 Emsley, 2732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 276 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ASP cc_start: 0.7997 (t0) cc_final: 0.7657 (t0) REVERT: A 355 TRP cc_start: 0.7333 (m100) cc_final: 0.6080 (m100) REVERT: A 617 MET cc_start: 0.7285 (mmt) cc_final: 0.6716 (mmt) REVERT: A 852 ASP cc_start: 0.8263 (m-30) cc_final: 0.7877 (t0) REVERT: B 333 LYS cc_start: 0.8395 (mttt) cc_final: 0.8001 (mmmt) REVERT: B 507 MET cc_start: 0.2857 (mpp) cc_final: 0.2346 (mtt) REVERT: B 708 ILE cc_start: 0.9260 (pt) cc_final: 0.9024 (mt) REVERT: B 948 ILE cc_start: 0.8387 (mm) cc_final: 0.8022 (tt) REVERT: B 1056 TYR cc_start: 0.7036 (m-80) cc_final: 0.6535 (m-80) REVERT: B 1093 LYS cc_start: 0.8321 (mmtt) cc_final: 0.7810 (ttpp) REVERT: B 1136 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.7998 (ttpp) REVERT: B 1192 MET cc_start: 0.9196 (mmt) cc_final: 0.8655 (mmt) REVERT: B 1268 TRP cc_start: 0.6954 (OUTLIER) cc_final: 0.6424 (m-10) REVERT: B 1326 VAL cc_start: 0.8765 (t) cc_final: 0.8462 (p) REVERT: B 1338 PHE cc_start: 0.8973 (p90) cc_final: 0.8750 (p90) REVERT: C 177 SER cc_start: 0.8940 (p) cc_final: 0.8525 (m) REVERT: C 266 LYS cc_start: 0.8720 (mmmt) cc_final: 0.8486 (mtmm) REVERT: C 300 TRP cc_start: 0.6394 (m-90) cc_final: 0.6077 (m-90) REVERT: C 333 TYR cc_start: 0.8035 (OUTLIER) cc_final: 0.6750 (t80) REVERT: D 276 TYR cc_start: 0.7196 (m-80) cc_final: 0.6859 (m-80) outliers start: 68 outliers final: 52 residues processed: 326 average time/residue: 0.1440 time to fit residues: 75.0423 Evaluate side-chains 317 residues out of total 2464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 262 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 133 TYR Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 754 THR Chi-restraints excluded: chain A residue 867 VAL Chi-restraints excluded: chain A residue 868 HIS Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 340 ASP Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain B residue 580 HIS Chi-restraints excluded: chain B residue 600 SER Chi-restraints excluded: chain B residue 942 THR Chi-restraints excluded: chain B residue 944 LEU Chi-restraints excluded: chain B residue 947 LEU Chi-restraints excluded: chain B residue 1012 SER Chi-restraints excluded: chain B residue 1062 ASP Chi-restraints excluded: chain B residue 1068 LEU Chi-restraints excluded: chain B residue 1083 HIS Chi-restraints excluded: chain B residue 1117 VAL Chi-restraints excluded: chain B residue 1136 LYS Chi-restraints excluded: chain B residue 1143 LEU Chi-restraints excluded: chain B residue 1164 THR Chi-restraints excluded: chain B residue 1179 HIS Chi-restraints excluded: chain B residue 1195 LEU Chi-restraints excluded: chain B residue 1222 PHE Chi-restraints excluded: chain B residue 1255 ILE Chi-restraints excluded: chain B residue 1268 TRP Chi-restraints excluded: chain B residue 1335 VAL Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 333 TYR Chi-restraints excluded: chain C residue 447 PHE Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain D residue 203 SER Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 269 SER Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain E residue 15 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 3 optimal weight: 6.9990 chunk 138 optimal weight: 3.9990 chunk 181 optimal weight: 0.6980 chunk 156 optimal weight: 10.0000 chunk 45 optimal weight: 0.9990 chunk 163 optimal weight: 8.9990 chunk 211 optimal weight: 0.8980 chunk 182 optimal weight: 2.9990 chunk 248 optimal weight: 3.9990 chunk 246 optimal weight: 0.9990 chunk 266 optimal weight: 0.9980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B1329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 168 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.146945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.101489 restraints weight = 35939.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.100759 restraints weight = 26887.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.100761 restraints weight = 23480.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.100887 restraints weight = 23613.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.101418 restraints weight = 20977.954| |-----------------------------------------------------------------------------| r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.3258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22774 Z= 0.123 Angle : 0.533 9.502 30767 Z= 0.263 Chirality : 0.041 0.188 3408 Planarity : 0.003 0.036 3938 Dihedral : 5.877 119.475 3041 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.33 % Favored : 96.63 % Rotamer: Outliers : 2.72 % Allowed : 14.94 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.16), residues: 2732 helix: 2.15 (0.15), residues: 1314 sheet: 0.04 (0.29), residues: 312 loop : -0.61 (0.18), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B1040 TYR 0.057 0.001 TYR C 328 PHE 0.021 0.001 PHE D 395 TRP 0.037 0.001 TRP D 267 HIS 0.005 0.001 HIS C 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.12 (22765) covalent geometry : angle 0.52299 / 0.26 (30755) hydrogen bonds : bond 0.03627 / 2.34 ( 1032) hydrogen bonds : angle 3.51078 / 2.39 ( 3018) metal coordination : bond 0.01200 / 0.58 ( 8) metal coordination : angle 5.34715 / 2.76 ( 12) Misc. bond : bond 0.00018 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5464 Ramachandran restraints generated. 2732 Oldfield, 0 Emsley, 2732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5464 Ramachandran restraints generated. 2732 Oldfield, 0 Emsley, 2732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 266 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ASP cc_start: 0.8042 (t0) cc_final: 0.7701 (t0) REVERT: A 187 MET cc_start: 0.6817 (tpp) cc_final: 0.6411 (ttm) REVERT: A 355 TRP cc_start: 0.7329 (m100) cc_final: 0.6027 (m100) REVERT: A 617 MET cc_start: 0.7295 (mmt) cc_final: 0.6712 (mmt) REVERT: A 852 ASP cc_start: 0.8304 (m-30) cc_final: 0.7846 (t0) REVERT: B 333 LYS cc_start: 0.8457 (mttt) cc_final: 0.7981 (mmmt) REVERT: B 507 MET cc_start: 0.3106 (mpp) cc_final: 0.2710 (mtt) REVERT: B 708 ILE cc_start: 0.9259 (pt) cc_final: 0.9045 (mt) REVERT: B 948 ILE cc_start: 0.8329 (mm) cc_final: 0.7963 (tt) REVERT: B 1056 TYR cc_start: 0.7160 (m-80) cc_final: 0.6656 (m-80) REVERT: B 1093 LYS cc_start: 0.8354 (mmtt) cc_final: 0.7856 (ttpp) REVERT: B 1192 MET cc_start: 0.9228 (mmt) cc_final: 0.8650 (mmt) REVERT: B 1268 TRP cc_start: 0.6774 (OUTLIER) cc_final: 0.6495 (m-10) REVERT: B 1326 VAL cc_start: 0.8824 (t) cc_final: 0.8523 (p) REVERT: B 1338 PHE cc_start: 0.9060 (p90) cc_final: 0.8792 (p90) REVERT: C 177 SER cc_start: 0.8993 (p) cc_final: 0.8560 (m) REVERT: C 266 LYS cc_start: 0.8813 (mmmt) cc_final: 0.8541 (mtmm) REVERT: C 290 LEU cc_start: 0.7877 (tp) cc_final: 0.7535 (tp) REVERT: C 300 TRP cc_start: 0.6585 (m-90) cc_final: 0.6251 (m-90) REVERT: C 333 TYR cc_start: 0.8016 (OUTLIER) cc_final: 0.6785 (t80) REVERT: D 276 TYR cc_start: 0.7229 (m-80) cc_final: 0.6865 (m-80) REVERT: D 294 MET cc_start: 0.4858 (tpp) cc_final: 0.4636 (tpt) outliers start: 67 outliers final: 59 residues processed: 312 average time/residue: 0.1456 time to fit residues: 72.5775 Evaluate side-chains 317 residues out of total 2464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 256 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 133 TYR Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 754 THR Chi-restraints excluded: chain A residue 802 CYS Chi-restraints excluded: chain A residue 867 VAL Chi-restraints excluded: chain A residue 868 HIS Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 340 ASP Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain B residue 580 HIS Chi-restraints excluded: chain B residue 600 SER Chi-restraints excluded: chain B residue 658 SER Chi-restraints excluded: chain B residue 942 THR Chi-restraints excluded: chain B residue 944 LEU Chi-restraints excluded: chain B residue 947 LEU Chi-restraints excluded: chain B residue 1012 SER Chi-restraints excluded: chain B residue 1025 MET Chi-restraints excluded: chain B residue 1062 ASP Chi-restraints excluded: chain B residue 1068 LEU Chi-restraints excluded: chain B residue 1083 HIS Chi-restraints excluded: chain B residue 1117 VAL Chi-restraints excluded: chain B residue 1143 LEU Chi-restraints excluded: chain B residue 1164 THR Chi-restraints excluded: chain B residue 1179 HIS Chi-restraints excluded: chain B residue 1187 ILE Chi-restraints excluded: chain B residue 1195 LEU Chi-restraints excluded: chain B residue 1222 PHE Chi-restraints excluded: chain B residue 1255 ILE Chi-restraints excluded: chain B residue 1268 TRP Chi-restraints excluded: chain B residue 1335 VAL Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 333 TYR Chi-restraints excluded: chain C residue 422 GLU Chi-restraints excluded: chain C residue 447 PHE Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 203 SER Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 269 SER Chi-restraints excluded: chain E residue 15 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 53 optimal weight: 0.0670 chunk 158 optimal weight: 9.9990 chunk 176 optimal weight: 3.9990 chunk 145 optimal weight: 2.9990 chunk 215 optimal weight: 9.9990 chunk 164 optimal weight: 5.9990 chunk 237 optimal weight: 6.9990 chunk 22 optimal weight: 6.9990 chunk 242 optimal weight: 1.9990 chunk 206 optimal weight: 8.9990 chunk 202 optimal weight: 0.9980 overall best weight: 2.0124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 715 ASN D 168 HIS D 197 HIS D 363 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.143954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.096258 restraints weight = 36163.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.096066 restraints weight = 23713.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.096245 restraints weight = 18482.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.096877 restraints weight = 18385.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.096940 restraints weight = 17396.737| |-----------------------------------------------------------------------------| r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 22774 Z= 0.216 Angle : 0.611 10.207 30767 Z= 0.303 Chirality : 0.043 0.174 3408 Planarity : 0.004 0.037 3938 Dihedral : 6.108 118.386 3039 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.92 % Favored : 96.05 % Rotamer: Outliers : 3.00 % Allowed : 15.06 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.16), residues: 2732 helix: 2.01 (0.15), residues: 1308 sheet: -0.02 (0.29), residues: 304 loop : -0.76 (0.18), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B1040 TYR 0.026 0.002 TYR C 328 PHE 0.021 0.002 PHE B 496 TRP 0.048 0.002 TRP D 267 HIS 0.014 0.001 HIS C 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00534 / 0.22 (22765) covalent geometry : angle 0.60131 / 0.30 (30755) hydrogen bonds : bond 0.04466 / 2.91 ( 1032) hydrogen bonds : angle 3.69135 / 2.52 ( 3018) metal coordination : bond 0.01000 / 0.50 ( 8) metal coordination : angle 5.54030 / 2.87 ( 12) Misc. bond : bond 0.00029 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5464 Ramachandran restraints generated. 2732 Oldfield, 0 Emsley, 2732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5464 Ramachandran restraints generated. 2732 Oldfield, 0 Emsley, 2732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 266 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 TRP cc_start: 0.7553 (m100) cc_final: 0.6157 (m100) REVERT: A 187 MET cc_start: 0.6860 (tpp) cc_final: 0.6483 (ttm) REVERT: A 355 TRP cc_start: 0.7419 (m100) cc_final: 0.6252 (m100) REVERT: A 852 ASP cc_start: 0.8280 (m-30) cc_final: 0.7883 (t0) REVERT: B 333 LYS cc_start: 0.8504 (mttt) cc_final: 0.8068 (mmmt) REVERT: B 507 MET cc_start: 0.3244 (mpp) cc_final: 0.2764 (mtt) REVERT: B 708 ILE cc_start: 0.9249 (pt) cc_final: 0.9037 (mt) REVERT: B 948 ILE cc_start: 0.8391 (mm) cc_final: 0.8043 (tt) REVERT: B 1093 LYS cc_start: 0.8381 (mmtt) cc_final: 0.7907 (ttpp) REVERT: B 1136 LYS cc_start: 0.8745 (OUTLIER) cc_final: 0.8125 (ttpp) REVERT: B 1192 MET cc_start: 0.9199 (mmt) cc_final: 0.8552 (mmt) REVERT: B 1197 GLN cc_start: 0.8113 (mp10) cc_final: 0.7684 (pt0) REVERT: B 1268 TRP cc_start: 0.6898 (OUTLIER) cc_final: 0.6686 (m-10) REVERT: B 1326 VAL cc_start: 0.8884 (t) cc_final: 0.8627 (p) REVERT: B 1338 PHE cc_start: 0.9138 (p90) cc_final: 0.8910 (p90) REVERT: C 177 SER cc_start: 0.9090 (p) cc_final: 0.8606 (m) REVERT: C 300 TRP cc_start: 0.6659 (m-90) cc_final: 0.6431 (m-90) REVERT: C 333 TYR cc_start: 0.8120 (OUTLIER) cc_final: 0.7002 (t80) REVERT: D 276 TYR cc_start: 0.7529 (m-80) cc_final: 0.7141 (m-80) REVERT: E 70 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8423 (tt) REVERT: F 19 GLN cc_start: 0.7961 (pt0) cc_final: 0.7701 (pt0) outliers start: 74 outliers final: 60 residues processed: 320 average time/residue: 0.1550 time to fit residues: 79.2464 Evaluate side-chains 319 residues out of total 2464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 255 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 133 TYR Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 565 ASN Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 754 THR Chi-restraints excluded: chain A residue 802 CYS Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 867 VAL Chi-restraints excluded: chain A residue 868 HIS Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 340 ASP Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain B residue 580 HIS Chi-restraints excluded: chain B residue 600 SER Chi-restraints excluded: chain B residue 658 SER Chi-restraints excluded: chain B residue 942 THR Chi-restraints excluded: chain B residue 944 LEU Chi-restraints excluded: chain B residue 1012 SER Chi-restraints excluded: chain B residue 1025 MET Chi-restraints excluded: chain B residue 1062 ASP Chi-restraints excluded: chain B residue 1068 LEU Chi-restraints excluded: chain B residue 1083 HIS Chi-restraints excluded: chain B residue 1117 VAL Chi-restraints excluded: chain B residue 1136 LYS Chi-restraints excluded: chain B residue 1143 LEU Chi-restraints excluded: chain B residue 1164 THR Chi-restraints excluded: chain B residue 1179 HIS Chi-restraints excluded: chain B residue 1187 ILE Chi-restraints excluded: chain B residue 1255 ILE Chi-restraints excluded: chain B residue 1268 TRP Chi-restraints excluded: chain B residue 1335 VAL Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 333 TYR Chi-restraints excluded: chain C residue 422 GLU Chi-restraints excluded: chain C residue 447 PHE Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 203 SER Chi-restraints excluded: chain D residue 208 ILE Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 269 SER Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 70 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 100 optimal weight: 1.9990 chunk 204 optimal weight: 1.9990 chunk 161 optimal weight: 7.9990 chunk 192 optimal weight: 3.9990 chunk 150 optimal weight: 5.9990 chunk 214 optimal weight: 3.9990 chunk 158 optimal weight: 9.9990 chunk 60 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 120 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.145065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.101734 restraints weight = 35961.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.099071 restraints weight = 27641.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.099494 restraints weight = 26515.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.100141 restraints weight = 23973.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.100241 restraints weight = 21123.112| |-----------------------------------------------------------------------------| r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.3517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 22774 Z= 0.156 Angle : 0.570 10.775 30767 Z= 0.281 Chirality : 0.042 0.169 3408 Planarity : 0.003 0.039 3938 Dihedral : 6.062 119.235 3039 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.55 % Favored : 96.41 % Rotamer: Outliers : 2.80 % Allowed : 15.75 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.16), residues: 2732 helix: 2.10 (0.15), residues: 1307 sheet: -0.01 (0.29), residues: 304 loop : -0.72 (0.18), residues: 1121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1040 TYR 0.046 0.002 TYR C 328 PHE 0.019 0.001 PHE C 390 TRP 0.040 0.002 TRP D 267 HIS 0.010 0.001 HIS C 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.16 (22765) covalent geometry : angle 0.56133 / 0.28 (30755) hydrogen bonds : bond 0.04046 / 2.62 ( 1032) hydrogen bonds : angle 3.59916 / 2.46 ( 3018) metal coordination : bond 0.00990 / 0.48 ( 8) metal coordination : angle 5.16061 / 2.69 ( 12) Misc. bond : bond 0.00018 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5464 Ramachandran restraints generated. 2732 Oldfield, 0 Emsley, 2732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5464 Ramachandran restraints generated. 2732 Oldfield, 0 Emsley, 2732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 266 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 TRP cc_start: 0.7567 (m100) cc_final: 0.6202 (m100) REVERT: A 187 MET cc_start: 0.6897 (tpp) cc_final: 0.6525 (ttm) REVERT: A 355 TRP cc_start: 0.7410 (m100) cc_final: 0.6166 (m100) REVERT: A 617 MET cc_start: 0.7338 (mmt) cc_final: 0.6747 (mmt) REVERT: A 852 ASP cc_start: 0.8234 (m-30) cc_final: 0.7903 (t0) REVERT: B 333 LYS cc_start: 0.8468 (mttt) cc_final: 0.8048 (mmmt) REVERT: B 708 ILE cc_start: 0.9237 (pt) cc_final: 0.9006 (mt) REVERT: B 948 ILE cc_start: 0.8468 (mm) cc_final: 0.8144 (tt) REVERT: B 1093 LYS cc_start: 0.8398 (mmtt) cc_final: 0.7920 (ttpp) REVERT: B 1136 LYS cc_start: 0.8665 (OUTLIER) cc_final: 0.8025 (ttpp) REVERT: B 1192 MET cc_start: 0.9142 (mmt) cc_final: 0.8490 (mmt) REVERT: B 1197 GLN cc_start: 0.8037 (mp10) cc_final: 0.7637 (pt0) REVERT: B 1268 TRP cc_start: 0.6994 (OUTLIER) cc_final: 0.6648 (m-10) REVERT: B 1326 VAL cc_start: 0.8793 (t) cc_final: 0.8534 (p) REVERT: B 1338 PHE cc_start: 0.9069 (p90) cc_final: 0.8869 (p90) REVERT: C 177 SER cc_start: 0.9086 (p) cc_final: 0.8605 (m) REVERT: C 266 LYS cc_start: 0.8717 (mmmt) cc_final: 0.8496 (mtmm) REVERT: C 333 TYR cc_start: 0.8177 (OUTLIER) cc_final: 0.7202 (t80) REVERT: D 276 TYR cc_start: 0.7605 (m-80) cc_final: 0.7277 (m-80) REVERT: E 67 GLN cc_start: 0.8048 (mm-40) cc_final: 0.7729 (mt0) outliers start: 69 outliers final: 59 residues processed: 312 average time/residue: 0.1487 time to fit residues: 75.1964 Evaluate side-chains 330 residues out of total 2464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 268 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 133 TYR Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 565 ASN Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 754 THR Chi-restraints excluded: chain A residue 802 CYS Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 867 VAL Chi-restraints excluded: chain A residue 868 HIS Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 340 ASP Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain B residue 580 HIS Chi-restraints excluded: chain B residue 600 SER Chi-restraints excluded: chain B residue 658 SER Chi-restraints excluded: chain B residue 942 THR Chi-restraints excluded: chain B residue 1008 PHE Chi-restraints excluded: chain B residue 1012 SER Chi-restraints excluded: chain B residue 1025 MET Chi-restraints excluded: chain B residue 1062 ASP Chi-restraints excluded: chain B residue 1068 LEU Chi-restraints excluded: chain B residue 1083 HIS Chi-restraints excluded: chain B residue 1117 VAL Chi-restraints excluded: chain B residue 1136 LYS Chi-restraints excluded: chain B residue 1143 LEU Chi-restraints excluded: chain B residue 1164 THR Chi-restraints excluded: chain B residue 1179 HIS Chi-restraints excluded: chain B residue 1187 ILE Chi-restraints excluded: chain B residue 1255 ILE Chi-restraints excluded: chain B residue 1268 TRP Chi-restraints excluded: chain B residue 1335 VAL Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 333 TYR Chi-restraints excluded: chain C residue 422 GLU Chi-restraints excluded: chain C residue 447 PHE Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 150 LYS Chi-restraints excluded: chain D residue 197 HIS Chi-restraints excluded: chain D residue 203 SER Chi-restraints excluded: chain D residue 208 ILE Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 269 SER Chi-restraints excluded: chain E residue 15 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 243 optimal weight: 0.8980 chunk 265 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 181 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 3 optimal weight: 3.9990 chunk 269 optimal weight: 0.9980 chunk 271 optimal weight: 0.9990 chunk 167 optimal weight: 5.9990 chunk 184 optimal weight: 4.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 301 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.145908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.108971 restraints weight = 35895.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.106062 restraints weight = 38415.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.107353 restraints weight = 35885.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.109239 restraints weight = 23096.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.109426 restraints weight = 18909.430| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.3579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22774 Z= 0.125 Angle : 0.563 11.440 30767 Z= 0.274 Chirality : 0.041 0.173 3408 Planarity : 0.003 0.037 3938 Dihedral : 5.925 117.862 3037 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.59 % Favored : 96.38 % Rotamer: Outliers : 2.27 % Allowed : 16.31 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.16), residues: 2732 helix: 2.20 (0.15), residues: 1308 sheet: 0.00 (0.29), residues: 304 loop : -0.67 (0.18), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1040 TYR 0.036 0.001 TYR C 328 PHE 0.021 0.001 PHE B1344 TRP 0.038 0.002 TRP D 267 HIS 0.008 0.001 HIS C 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.12 (22765) covalent geometry : angle 0.55394 / 0.27 (30755) hydrogen bonds : bond 0.03737 / 2.42 ( 1032) hydrogen bonds : angle 3.50403 / 2.40 ( 3018) metal coordination : bond 0.01043 / 0.50 ( 8) metal coordination : angle 5.07703 / 2.62 ( 12) Misc. bond : bond 0.00007 / 0.00 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5464 Ramachandran restraints generated. 2732 Oldfield, 0 Emsley, 2732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5464 Ramachandran restraints generated. 2732 Oldfield, 0 Emsley, 2732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 272 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ASP cc_start: 0.7939 (t0) cc_final: 0.7662 (t0) REVERT: A 187 MET cc_start: 0.6849 (tpp) cc_final: 0.6585 (ttm) REVERT: A 355 TRP cc_start: 0.7391 (m100) cc_final: 0.6153 (m100) REVERT: A 617 MET cc_start: 0.7313 (mmt) cc_final: 0.6741 (mmt) REVERT: A 797 GLU cc_start: 0.7253 (tm-30) cc_final: 0.7036 (tm-30) REVERT: A 852 ASP cc_start: 0.8225 (m-30) cc_final: 0.7916 (t0) REVERT: B 333 LYS cc_start: 0.8440 (mttt) cc_final: 0.7937 (mmmt) REVERT: B 708 ILE cc_start: 0.9244 (pt) cc_final: 0.9002 (mt) REVERT: B 948 ILE cc_start: 0.8498 (mm) cc_final: 0.8195 (tt) REVERT: B 1093 LYS cc_start: 0.8396 (mmtt) cc_final: 0.7928 (ttpp) REVERT: B 1136 LYS cc_start: 0.8571 (OUTLIER) cc_final: 0.7921 (ttpp) REVERT: B 1192 MET cc_start: 0.9104 (mmt) cc_final: 0.8455 (mmt) REVERT: B 1268 TRP cc_start: 0.7031 (OUTLIER) cc_final: 0.6569 (m-10) REVERT: B 1326 VAL cc_start: 0.8708 (t) cc_final: 0.8459 (p) REVERT: C 177 SER cc_start: 0.9070 (p) cc_final: 0.8587 (m) REVERT: C 333 TYR cc_start: 0.8137 (OUTLIER) cc_final: 0.7347 (t80) REVERT: D 267 TRP cc_start: 0.7186 (p90) cc_final: 0.6928 (p90) REVERT: D 276 TYR cc_start: 0.7573 (m-80) cc_final: 0.7279 (m-80) REVERT: E 67 GLN cc_start: 0.8081 (mm-40) cc_final: 0.7802 (mt0) outliers start: 56 outliers final: 53 residues processed: 310 average time/residue: 0.1532 time to fit residues: 76.2834 Evaluate side-chains 320 residues out of total 2464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 264 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 133 TYR Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 565 ASN Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 754 THR Chi-restraints excluded: chain A residue 802 CYS Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 867 VAL Chi-restraints excluded: chain A residue 868 HIS Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 340 ASP Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain B residue 580 HIS Chi-restraints excluded: chain B residue 600 SER Chi-restraints excluded: chain B residue 658 SER Chi-restraints excluded: chain B residue 942 THR Chi-restraints excluded: chain B residue 1012 SER Chi-restraints excluded: chain B residue 1025 MET Chi-restraints excluded: chain B residue 1062 ASP Chi-restraints excluded: chain B residue 1068 LEU Chi-restraints excluded: chain B residue 1083 HIS Chi-restraints excluded: chain B residue 1117 VAL Chi-restraints excluded: chain B residue 1136 LYS Chi-restraints excluded: chain B residue 1143 LEU Chi-restraints excluded: chain B residue 1164 THR Chi-restraints excluded: chain B residue 1179 HIS Chi-restraints excluded: chain B residue 1187 ILE Chi-restraints excluded: chain B residue 1255 ILE Chi-restraints excluded: chain B residue 1268 TRP Chi-restraints excluded: chain B residue 1335 VAL Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 333 TYR Chi-restraints excluded: chain C residue 422 GLU Chi-restraints excluded: chain C residue 447 PHE Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 150 LYS Chi-restraints excluded: chain D residue 203 SER Chi-restraints excluded: chain D residue 208 ILE Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 269 SER Chi-restraints excluded: chain E residue 15 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 22 optimal weight: 0.9990 chunk 252 optimal weight: 6.9990 chunk 219 optimal weight: 1.9990 chunk 186 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 218 optimal weight: 6.9990 chunk 114 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 180 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B1329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 336 HIS D 168 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.144490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.098742 restraints weight = 36098.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.098334 restraints weight = 23191.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.097850 restraints weight = 19486.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.098375 restraints weight = 18857.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.098567 restraints weight = 17526.883| |-----------------------------------------------------------------------------| r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.3682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 22774 Z= 0.176 Angle : 0.598 11.552 30767 Z= 0.295 Chirality : 0.042 0.167 3408 Planarity : 0.003 0.040 3938 Dihedral : 6.042 117.275 3037 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.14 % Favored : 95.83 % Rotamer: Outliers : 2.72 % Allowed : 16.07 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.16), residues: 2732 helix: 2.11 (0.15), residues: 1307 sheet: -0.15 (0.29), residues: 298 loop : -0.72 (0.18), residues: 1127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG C 327 TYR 0.026 0.002 TYR C 328 PHE 0.028 0.002 PHE B1338 TRP 0.034 0.002 TRP D 267 HIS 0.009 0.001 HIS C 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.18 (22765) covalent geometry : angle 0.58952 / 0.29 (30755) hydrogen bonds : bond 0.04184 / 2.72 ( 1032) hydrogen bonds : angle 3.61973 / 2.49 ( 3018) metal coordination : bond 0.00926 / 0.46 ( 8) metal coordination : angle 5.17028 / 2.66 ( 12) Misc. bond : bond 0.00009 / 0.00 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4529.42 seconds wall clock time: 78 minutes 45.00 seconds (4725.00 seconds total)