Starting phenix.real_space_refine on Fri Aug 7 17:25:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rx7_54360/08_2026/9rx7_54360.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rx7_54360/08_2026/9rx7_54360.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9rx7_54360/08_2026/9rx7_54360.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rx7_54360/08_2026/9rx7_54360.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9rx7_54360/08_2026/9rx7_54360.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rx7_54360/08_2026/9rx7_54360.map" } resolution = 3.33 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= 0.021 sd= 0.040 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 2 5.49 5 Mg 1 5.21 5 S 125 5.16 5 C 14092 2.51 5 N 3855 2.21 5 O 4134 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22211 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 6554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 811, 6554 Classifications: {'peptide': 811} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 771} Chain breaks: 2 Chain: "B" Number of atoms: 9653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1212, 9653 Classifications: {'peptide': 1212} Link IDs: {'PCIS': 2, 'PTRANS': 56, 'TRANS': 1153} Chain breaks: 6 Chain: "C" Number of atoms: 2773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2773 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 6, 'TRANS': 330} Chain breaks: 1 Chain: "D" Number of atoms: 2417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2417 Classifications: {'peptide': 295} Link IDs: {'PTRANS': 9, 'TRANS': 285} Chain breaks: 3 Chain: "I" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 72 Classifications: {'peptide': 9} Link IDs: {'PTRANS': 1, 'TRANS': 7} Chain: "L" Number of atoms: 696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 696 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {' MG': 1, 'MYR': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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: "D" 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 16426 SG CYS C 137 46.685 132.021 30.503 1.00192.59 S ATOM 16450 SG CYS C 140 48.897 132.938 33.181 1.00174.14 S ATOM 19018 SG CYS D 43 49.205 129.077 31.174 1.00184.99 S ATOM 19039 SG CYS D 46 47.470 129.698 32.606 1.00178.69 S ATOM 19115 SG CYS D 55 56.784 135.135 19.817 1.00180.82 S ATOM 19135 SG CYS D 58 56.113 137.707 20.159 1.00188.96 S ATOM 21421 SG CYS I 18 53.170 136.082 19.404 1.00175.69 S ATOM 21447 SG CYS I 21 55.236 136.857 18.617 1.00189.69 S Time building chain proxies: 4.63, per 1000 atoms: 0.21 Number of scatterers: 22211 At special positions: 0 Unit cell: (103.2, 183.18, 232.2, 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 125 16.00 P 2 15.00 Mg 1 11.99 O 4134 8.00 N 3855 7.00 C 14092 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 693 " - pdb=" SG CYS C 165 " distance=2.03 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: 1.60 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 501 " pdb="ZN ZN C 501 " - pdb=" SG CYS D 46 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 140 " pdb="ZN ZN C 501 " - pdb=" SG CYS D 43 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 137 " pdb=" ZN D 501 " pdb="ZN ZN D 501 " - pdb=" SG CYS D 55 " pdb="ZN ZN D 501 " - pdb=" SG CYS I 18 " pdb="ZN ZN D 501 " - pdb=" SG CYS D 58 " pdb="ZN ZN D 501 " - pdb=" SG CYS I 21 " Number of angles added : 12 5428 Ramachandran restraints generated. 2714 Oldfield, 0 Emsley, 2714 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5242 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 17 sheets defined 54.3% alpha, 11.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 34 through 39 removed outlier: 3.903A pdb=" N VAL A 38 " --> pdb=" O SER A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 47 removed outlier: 3.563A pdb=" N SER A 47 " --> pdb=" O LEU A 44 " (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 173 through 178 removed outlier: 4.083A pdb=" N LEU A 178 " --> pdb=" O ARG A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 184 Processing helix chain 'A' and resid 193 through 201 removed outlier: 3.918A pdb=" N THR A 197 " --> pdb=" O LEU A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 212 Processing helix chain 'A' and resid 264 through 275 removed outlier: 3.624A pdb=" N SER A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 283 Processing helix chain 'A' and resid 289 through 301 removed outlier: 3.505A pdb=" N ASN A 297 " --> pdb=" O ARG A 293 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE A 298 " --> pdb=" O ASP A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 319 removed outlier: 4.155A pdb=" N LEU A 315 " --> pdb=" O GLU A 311 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE A 319 " --> pdb=" O LEU A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 327 removed outlier: 3.760A pdb=" N THR A 324 " --> pdb=" O TYR A 321 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ASN A 325 " --> pdb=" O TYR A 322 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N GLU A 327 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 335 removed outlier: 4.237A pdb=" N LYS A 332 " --> pdb=" O LYS A 328 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS A 335 " --> pdb=" O THR A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 353 removed outlier: 3.908A pdb=" N GLY A 353 " --> pdb=" O LEU A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 364 removed outlier: 3.847A pdb=" N LEU A 364 " --> pdb=" O VAL A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 368 Processing helix chain 'A' and resid 373 through 383 Processing helix chain 'A' and resid 396 through 402 Processing helix chain 'A' and resid 403 through 406 Processing helix chain 'A' and resid 408 through 413 Processing helix chain 'A' and resid 475 through 484 Processing helix chain 'A' and resid 486 through 501 removed outlier: 3.708A pdb=" N VAL A 499 " --> pdb=" O TRP A 495 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLU A 500 " --> pdb=" O TYR A 496 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N CYS A 501 " --> pdb=" O VAL A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 510 Processing helix chain 'A' and resid 510 through 530 Processing helix chain 'A' and resid 532 through 561 Processing helix chain 'A' and resid 565 through 578 removed outlier: 3.835A pdb=" N GLY A 578 " --> pdb=" O GLN A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 584 Processing helix chain 'A' and resid 641 through 661 removed outlier: 3.573A pdb=" N GLN A 649 " --> pdb=" O GLN A 645 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU A 661 " --> pdb=" O LEU A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 697 removed outlier: 3.951A pdb=" N ASP A 695 " --> pdb=" O ALA A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 708 Processing helix chain 'A' and resid 713 through 717 removed outlier: 3.618A pdb=" N GLY A 716 " --> pdb=" O GLY A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 740 removed outlier: 3.757A pdb=" N GLY A 731 " --> pdb=" O LYS A 727 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR A 732 " --> pdb=" O SER A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 780 through 788 removed outlier: 4.108A pdb=" N VAL A 784 " --> pdb=" O ASN A 780 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU A 785 " --> pdb=" O LYS A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 810 removed outlier: 4.024A pdb=" N GLN A 796 " --> pdb=" O SER A 792 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR A 803 " --> pdb=" O ARG A 799 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N HIS A 808 " --> pdb=" O THR A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 812 through 822 removed outlier: 3.703A pdb=" N ILE A 816 " --> pdb=" O TYR A 812 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU A 822 " --> pdb=" O ASN A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 823 through 825 No H-bonds generated for 'chain 'A' and resid 823 through 825' Processing helix chain 'A' and resid 828 through 833 removed outlier: 3.609A pdb=" N LEU A 833 " --> pdb=" O PRO A 829 " (cutoff:3.500A) Processing helix chain 'A' and resid 837 through 844 Processing helix chain 'A' and resid 851 through 871 removed outlier: 3.591A pdb=" N ALA A 855 " --> pdb=" O SER A 851 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N VAL A 856 " --> pdb=" O ASP A 852 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU A 870 " --> pdb=" O SER A 866 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 20 removed outlier: 3.613A pdb=" N TYR B 19 " --> pdb=" O SER B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 78 removed outlier: 3.660A pdb=" N LYS B 68 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN B 69 " --> pdb=" O THR B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 81 No H-bonds generated for 'chain 'B' and resid 79 through 81' Processing helix chain 'B' and resid 109 through 115 removed outlier: 4.346A pdb=" N SER B 115 " --> pdb=" O TYR B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 143 Processing helix chain 'B' and resid 150 through 154 removed outlier: 4.082A pdb=" N VAL B 154 " --> pdb=" O THR B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 187 Processing helix chain 'B' and resid 198 through 202 Processing helix chain 'B' and resid 204 through 215 removed outlier: 3.573A pdb=" N MET B 215 " --> pdb=" O GLU B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 253 removed outlier: 4.160A pdb=" N ILE B 241 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N PHE B 242 " --> pdb=" O ALA B 238 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N SER B 243 " --> pdb=" O MET B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 269 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: 3.766A pdb=" N LYS B 300 " --> pdb=" O GLU B 297 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG B 301 " --> pdb=" O PRO B 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 297 through 301' Processing helix chain 'B' and resid 303 through 311 Processing helix chain 'B' and resid 317 through 323 removed outlier: 4.275A pdb=" N TYR B 321 " --> pdb=" O PRO B 317 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR B 322 " --> pdb=" O GLU B 318 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N PHE B 323 " --> pdb=" O ILE B 319 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 317 through 323' Processing helix chain 'B' and resid 323 through 329 removed outlier: 3.538A pdb=" N ALA B 329 " --> pdb=" O GLN B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 349 removed outlier: 3.504A pdb=" N ARG B 342 " --> pdb=" O SER B 338 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE B 343 " --> pdb=" O ALA B 339 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU B 344 " --> pdb=" O ASP B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 357 removed outlier: 3.828A pdb=" N ILE B 353 " --> pdb=" O ASP B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 384 Processing helix chain 'B' and resid 391 through 405 removed outlier: 3.526A pdb=" N LYS B 395 " --> pdb=" O TYR B 391 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU B 400 " --> pdb=" O LEU B 396 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU B 403 " --> pdb=" O LEU B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 418 Processing helix chain 'B' and resid 418 through 425 Processing helix chain 'B' and resid 426 through 428 No H-bonds generated for 'chain 'B' and resid 426 through 428' Processing helix chain 'B' and resid 430 through 445 removed outlier: 3.916A pdb=" N LEU B 438 " --> pdb=" O ARG B 434 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG B 439 " --> pdb=" O ALA B 435 " (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 467 removed outlier: 3.678A pdb=" N GLU B 461 " --> pdb=" O ASN B 457 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N LEU B 464 " --> pdb=" O PRO B 460 " (cutoff:3.500A) Proline residue: B 465 - end of helix Processing helix chain 'B' and resid 468 through 473 removed outlier: 3.796A pdb=" N ALA B 471 " --> pdb=" O ALA B 468 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLN B 472 " --> pdb=" O HIS B 469 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP B 473 " --> pdb=" O LEU B 470 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 468 through 473' Processing helix chain 'B' and resid 475 through 485 removed outlier: 3.812A pdb=" N ARG B 479 " --> pdb=" O ALA B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 510 removed outlier: 4.251A pdb=" N LEU B 489 " --> pdb=" O ASN B 485 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA B 490 " --> pdb=" O ILE B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 545 removed outlier: 3.824A pdb=" N LYS B 540 " --> pdb=" O MET B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 560 removed outlier: 4.427A pdb=" N LYS B 553 " --> pdb=" O GLU B 549 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU B 558 " --> pdb=" O GLN B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 569 removed outlier: 3.507A pdb=" N VAL B 566 " --> pdb=" O THR B 562 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY B 569 " --> pdb=" O CYS B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 576 Processing helix chain 'B' and resid 576 through 582 Processing helix chain 'B' and resid 583 through 587 removed outlier: 3.569A pdb=" N ASP B 587 " --> pdb=" O PHE B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 600 Processing helix chain 'B' and resid 601 through 609 removed outlier: 4.122A pdb=" N TYR B 607 " --> pdb=" O GLY B 603 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY B 609 " --> pdb=" O ALA B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 624 Proline residue: B 618 - end of helix Processing helix chain 'B' and resid 628 through 646 removed outlier: 3.733A pdb=" N ILE B 632 " --> pdb=" O GLU B 628 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 661 removed outlier: 3.838A pdb=" N TYR B 654 " --> pdb=" O LYS B 650 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU B 655 " --> pdb=" O PRO B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 666 removed outlier: 3.984A pdb=" N CYS B 665 " --> pdb=" O PRO B 662 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N HIS B 666 " --> pdb=" O PHE B 663 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 662 through 666' Processing helix chain 'B' and resid 668 through 686 removed outlier: 3.548A pdb=" N ARG B 672 " --> pdb=" O ASN B 668 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE B 686 " --> pdb=" O VAL B 682 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 695 removed outlier: 3.635A pdb=" N VAL B 691 " --> pdb=" O SER B 687 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N TYR B 692 " --> pdb=" O THR B 688 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N CYS B 693 " --> pdb=" O ALA B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 695 through 700 removed outlier: 3.608A pdb=" N LEU B 699 " --> pdb=" O LEU B 695 " (cutoff:3.500A) 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 717 removed outlier: 4.103A pdb=" N LEU B 716 " --> pdb=" O ARG B 712 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU B 717 " --> pdb=" O LYS B 713 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 712 through 717' Processing helix chain 'B' and resid 725 through 734 removed outlier: 3.769A pdb=" N ARG B 734 " --> pdb=" O ASP B 730 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 753 Processing helix chain 'B' and resid 764 through 777 Processing helix chain 'B' and resid 780 through 789 removed outlier: 3.622A pdb=" N LEU B 788 " --> pdb=" O GLU B 784 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ALA B 789 " --> pdb=" O ASP B 785 " (cutoff:3.500A) Processing helix chain 'B' and resid 790 through 801 removed outlier: 3.938A pdb=" N LYS B 799 " --> pdb=" O MET B 795 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LYS B 801 " --> pdb=" O SER B 797 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 809 removed outlier: 3.676A pdb=" N GLN B 807 " --> pdb=" O ASN B 803 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N HIS B 809 " --> pdb=" O VAL B 805 " (cutoff:3.500A) Processing helix chain 'B' and resid 821 through 825 Processing helix chain 'B' and resid 940 through 962 removed outlier: 3.689A pdb=" N LEU B 944 " --> pdb=" O CYS B 940 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N GLN B 946 " --> pdb=" O THR B 942 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU B 947 " --> pdb=" O GLU B 943 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN B 954 " --> pdb=" O GLN B 950 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N CYS B 955 " --> pdb=" O LYS B 951 " (cutoff:3.500A) Processing helix chain 'B' and resid 963 through 965 No H-bonds generated for 'chain 'B' and resid 963 through 965' Processing helix chain 'B' and resid 1022 through 1027 Processing helix chain 'B' and resid 1138 through 1142 removed outlier: 3.737A pdb=" N SER B1141 " --> pdb=" O ASP B1138 " (cutoff:3.500A) Processing helix chain 'B' and resid 1272 through 1276 Processing helix chain 'C' and resid 111 through 127 removed outlier: 3.640A pdb=" N ARG C 115 " --> pdb=" O ASN C 111 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N GLY C 120 " --> pdb=" O LEU C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 172 removed outlier: 3.723A pdb=" N THR C 143 " --> pdb=" O GLU C 139 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LEU C 148 " --> pdb=" O LEU C 144 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASP C 149 " --> pdb=" O LEU C 145 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE C 168 " --> pdb=" O ARG C 164 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU C 169 " --> pdb=" O CYS C 165 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLU C 170 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLN C 171 " --> pdb=" O GLU C 167 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N MET C 172 " --> pdb=" O ILE C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 178 removed outlier: 3.709A pdb=" N GLU C 178 " --> pdb=" O ASP C 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 175 through 178' Processing helix chain 'C' and resid 179 through 189 removed outlier: 4.004A pdb=" N LEU C 189 " --> pdb=" O LYS C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 215 removed outlier: 3.509A pdb=" N GLU C 197 " --> pdb=" O ARG C 193 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE C 207 " --> pdb=" O LYS C 203 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLU C 213 " --> pdb=" O ALA C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 265 removed outlier: 3.767A pdb=" N LEU C 222 " --> pdb=" O GLU C 218 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASP C 245 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LYS C 248 " --> pdb=" O ASP C 244 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N MET C 254 " --> pdb=" O VAL C 250 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ARG C 255 " --> pdb=" O GLU C 251 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N TYR C 256 " --> pdb=" O ASN C 252 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA C 257 " --> pdb=" O GLN C 253 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS C 263 " --> pdb=" O THR C 259 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU C 264 " --> pdb=" O GLN C 260 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS C 265 " --> pdb=" O LEU C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 274 Processing helix chain 'C' and resid 304 through 322 removed outlier: 4.284A pdb=" N GLY C 308 " --> pdb=" O ASN C 304 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLN C 309 " --> pdb=" O ALA C 305 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR C 310 " --> pdb=" O ALA C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 336 Processing helix chain 'C' and resid 357 through 361 removed outlier: 4.160A pdb=" N PHE C 360 " --> pdb=" O LEU C 357 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N TRP C 361 " --> pdb=" O ARG C 358 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 357 through 361' Processing helix chain 'C' and resid 365 through 384 removed outlier: 4.263A pdb=" N MET C 369 " --> pdb=" O PHE C 365 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL C 370 " --> pdb=" O ASP C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 446 removed outlier: 3.875A pdb=" N TRP C 438 " --> pdb=" O THR C 434 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N VAL C 443 " --> pdb=" O GLY C 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 62 removed outlier: 3.501A pdb=" N GLN D 60 " --> pdb=" O ALA D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 100 removed outlier: 3.551A pdb=" N LEU D 85 " --> pdb=" O ARG D 81 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER D 87 " --> pdb=" O SER D 83 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU D 90 " --> pdb=" O LYS D 86 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU D 95 " --> pdb=" O GLU D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 132 removed outlier: 4.225A pdb=" N THR D 106 " --> pdb=" O GLY D 102 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N TRP D 111 " --> pdb=" O ASP D 107 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLU D 121 " --> pdb=" O LYS D 117 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLN D 122 " --> pdb=" O MET D 118 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU D 123 " --> pdb=" O ARG D 119 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU D 132 " --> pdb=" O CYS D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 146 removed outlier: 4.100A pdb=" N GLY D 140 " --> pdb=" O LYS D 136 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU D 141 " --> pdb=" O ASN D 137 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU D 142 " --> pdb=" O SER D 138 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR D 144 " --> pdb=" O GLY D 140 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LYS D 145 " --> pdb=" O LEU D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 187 removed outlier: 3.536A pdb=" N ARG D 154 " --> pdb=" O LYS D 150 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU D 160 " --> pdb=" O GLN D 156 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ILE D 165 " --> pdb=" O LYS D 161 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ILE D 181 " --> pdb=" O GLU D 177 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ASP D 182 " --> pdb=" O LYS D 178 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU D 183 " --> pdb=" O LYS D 179 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG D 184 " --> pdb=" O THR D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 205 removed outlier: 3.553A pdb=" N ARG D 195 " --> pdb=" O ALA D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 281 removed outlier: 3.978A pdb=" N ALA D 278 " --> pdb=" O ASP D 275 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N TYR D 279 " --> pdb=" O TYR D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 321 removed outlier: 3.922A pdb=" N ILE D 303 " --> pdb=" O PRO D 299 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N SER D 304 " --> pdb=" O ALA D 300 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N HIS D 319 " --> pdb=" O ASN D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 335 removed outlier: 3.517A pdb=" N GLU D 333 " --> pdb=" O CYS D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 360 removed outlier: 3.615A pdb=" N ASN D 352 " --> pdb=" O VAL D 348 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA D 353 " --> pdb=" O LYS D 349 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE D 360 " --> pdb=" O LEU D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 363 No H-bonds generated for 'chain 'D' and resid 361 through 363' Processing helix chain 'D' and resid 365 through 369 removed outlier: 3.675A pdb=" N GLN D 368 " --> pdb=" O ASN D 365 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU D 369 " --> pdb=" O LEU D 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 365 through 369' Processing helix chain 'D' and resid 373 through 383 Processing helix chain 'L' and resid 6 through 24 removed outlier: 3.730A pdb=" N LEU L 10 " --> pdb=" O GLY L 6 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ASP L 19 " --> pdb=" O SER L 15 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ARG L 20 " --> pdb=" O ARG L 16 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU L 21 " --> pdb=" O ARG L 17 " (cutoff:3.500A) Processing helix chain 'L' and resid 26 through 44 removed outlier: 3.609A pdb=" N SER L 32 " --> pdb=" O GLU L 28 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU L 43 " --> pdb=" O ALA L 39 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA L 44 " --> pdb=" O TYR L 40 " (cutoff:3.500A) Processing helix chain 'L' and resid 51 through 79 removed outlier: 3.543A pdb=" N SER L 56 " --> pdb=" O GLN L 52 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU L 57 " --> pdb=" O ALA L 53 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLN L 60 " --> pdb=" O SER L 56 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ARG L 61 " --> pdb=" O LEU L 57 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASP L 62 " --> pdb=" O GLU L 58 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU L 70 " --> pdb=" O LYS L 66 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG L 74 " --> pdb=" O LEU L 70 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 10 removed outlier: 4.771A pdb=" N VAL A 224 " --> pdb=" O TYR A 231 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 68 through 69 Processing sheet with id=AA3, first strand: chain 'A' and resid 68 through 69 removed outlier: 4.076A pdb=" N TYR A 58 " --> pdb=" O TRP A 111 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N ALA A 104 " --> pdb=" O SER A 128 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N SER A 128 " --> pdb=" O ALA A 104 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL A 106 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N THR A 126 " --> pdb=" O VAL A 106 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LEU A 108 " --> pdb=" O GLY A 124 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N GLY A 124 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ILE A 110 " --> pdb=" O VAL A 122 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N THR A 126 " --> pdb=" O LYS A 144 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N LYS A 144 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 10.668A pdb=" N SER A 128 " --> pdb=" O ASP A 142 " (cutoff:3.500A) removed outlier: 11.110A pdb=" N ASP A 142 " --> pdb=" O SER A 128 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N MET A 215 " --> pdb=" O VAL A 145 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N TYR A 216 " --> pdb=" O LEU A 26 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N LEU A 26 " --> pdb=" O TYR A 216 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N MET A 218 " --> pdb=" O GLY A 24 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N VAL A 19 " --> pdb=" O LEU A 93 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N SER A 25 " --> pdb=" O TRP A 87 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N TRP A 87 " --> pdb=" O SER A 25 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N GLU A 27 " --> pdb=" O TRP A 85 " (cutoff:3.500A) removed outlier: 9.221A pdb=" N TRP A 85 " --> pdb=" O GLU A 27 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 591 through 592 removed outlier: 3.547A pdb=" N ILE A 591 " --> pdb=" O ILE A 601 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LYS A 624 " --> pdb=" O ARG A 602 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ILE A 604 " --> pdb=" O PHE A 622 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N PHE A 622 " --> pdb=" O ILE A 604 " (cutoff:3.500A) removed outlier: 10.266A pdb=" N GLN A 620 " --> pdb=" O PRO A 606 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 688 through 689 Processing sheet with id=AA6, first strand: chain 'B' and resid 31 through 34 removed outlier: 6.208A pdb=" N SER B 31 " --> pdb=" O ARG B 42 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N ARG B 42 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL B 52 " --> pdb=" O ALA B 41 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS B 89 " --> pdb=" O PHE B 102 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 984 through 989 removed outlier: 5.737A pdb=" N LEU B 985 " --> pdb=" O LYS B1358 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N LYS B1358 " --> pdb=" O LEU B 985 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA B 987 " --> pdb=" O VAL B1356 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL B1356 " --> pdb=" O ALA B 987 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ASP B1334 " --> pdb=" O ALA B1348 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 996 through 1001 removed outlier: 4.144A pdb=" N ARG B 998 " --> pdb=" O CYS B1011 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU B1036 " --> pdb=" O ILE B1019 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 1045 through 1051 removed outlier: 3.900A pdb=" N THR B1047 " --> pdb=" O ALA B1060 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ALA B1065 " --> pdb=" O SER B1061 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN B1086 " --> pdb=" O LEU B1068 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 1100 through 1105 removed outlier: 4.096A pdb=" N ASP B1100 " --> pdb=" O ALA B1115 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR B1114 " --> pdb=" O VAL B1122 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU B1121 " --> pdb=" O LEU B1135 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 1146 through 1149 removed outlier: 3.971A pdb=" N SER B1146 " --> pdb=" O GLY B1159 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N MET B1165 " --> pdb=" O SER B1178 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N SER B1178 " --> pdb=" O MET B1165 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N CYS B1167 " --> pdb=" O ILE B1176 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU B1174 " --> pdb=" O ASP B1169 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 1187 through 1192 removed outlier: 4.066A pdb=" N ARG B1189 " --> pdb=" O ALA B1203 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLU B1209 " --> pdb=" O VAL B1204 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ASP B1214 " --> pdb=" O ARG B1220 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N ARG B1220 " --> pdb=" O ASP B1214 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLU B1299 " --> pdb=" O ARG B1221 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLU B1303 " --> pdb=" O TRP B1225 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 1242 through 1249 Processing sheet with id=AB5, first strand: chain 'C' and resid 276 through 279 removed outlier: 3.639A pdb=" N PHE C 282 " --> pdb=" O SER C 279 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 328 through 331 removed outlier: 3.519A pdb=" N TYR C 338 " --> pdb=" O VAL C 331 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU C 349 " --> pdb=" O LEU C 339 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 396 through 397 removed outlier: 3.532A pdb=" N TYR C 413 " --> pdb=" O ILE C 403 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 208 through 209 removed outlier: 3.694A pdb=" N ILE D 261 " --> pdb=" O LEU D 270 " (cutoff:3.500A) 995 hydrogen bonds defined for protein. 2883 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: 4.30 Time building geometry restraints manager: 2.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7304 1.34 - 1.46: 4966 1.46 - 1.58: 10188 1.58 - 1.71: 3 1.71 - 1.83: 196 Bond restraints: 22657 Sorted by residual: bond pdb=" C LEU A 167 " pdb=" N SER A 168 " ideal model delta sigma weight residual 1.331 1.379 -0.048 1.32e-02 5.74e+03 1.33e+01 bond pdb=" CA SER A 168 " pdb=" CB SER A 168 " ideal model delta sigma weight residual 1.525 1.557 -0.032 1.36e-02 5.41e+03 5.69e+00 bond pdb=" CA PHE B 331 " pdb=" C PHE B 331 " ideal model delta sigma weight residual 1.522 1.491 0.032 1.37e-02 5.33e+03 5.30e+00 bond pdb=" CA GLU B 711 " pdb=" C GLU B 711 " ideal model delta sigma weight residual 1.522 1.549 -0.027 1.43e-02 4.89e+03 3.62e+00 bond pdb=" C PRO B 761 " pdb=" N PRO B 762 " ideal model delta sigma weight residual 1.330 1.353 -0.023 1.25e-02 6.40e+03 3.24e+00 ... (remaining 22652 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.67: 30244 2.67 - 5.34: 299 5.34 - 8.01: 47 8.01 - 10.69: 5 10.69 - 13.36: 3 Bond angle restraints: 30598 Sorted by residual: angle pdb=" N THR A 179 " pdb=" CA THR A 179 " pdb=" C THR A 179 " ideal model delta sigma weight residual 111.07 116.77 -5.70 1.07e+00 8.73e-01 2.84e+01 angle pdb=" C ARG A 162 " pdb=" N THR A 163 " pdb=" CA THR A 163 " ideal model delta sigma weight residual 121.31 128.73 -7.42 1.49e+00 4.50e-01 2.48e+01 angle pdb=" C MET B 964 " pdb=" N MET B 965 " pdb=" CA MET B 965 " ideal model delta sigma weight residual 120.82 128.02 -7.20 1.50e+00 4.44e-01 2.31e+01 angle pdb=" C MET A 203 " pdb=" N ILE A 204 " pdb=" CA ILE A 204 " ideal model delta sigma weight residual 121.97 130.07 -8.10 1.80e+00 3.09e-01 2.03e+01 angle pdb=" C ALA A 181 " pdb=" N HIS A 182 " pdb=" CA HIS A 182 " ideal model delta sigma weight residual 120.28 126.15 -5.87 1.34e+00 5.57e-01 1.92e+01 ... (remaining 30593 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 12174 17.96 - 35.92: 1263 35.92 - 53.88: 297 53.88 - 71.84: 72 71.84 - 89.80: 30 Dihedral angle restraints: 13836 sinusoidal: 5769 harmonic: 8067 Sorted by residual: dihedral pdb=" CA LEU A 167 " pdb=" C LEU A 167 " pdb=" N SER A 168 " pdb=" CA SER A 168 " ideal model delta harmonic sigma weight residual 180.00 156.85 23.15 0 5.00e+00 4.00e-02 2.14e+01 dihedral pdb=" CA LEU A 178 " pdb=" C LEU A 178 " pdb=" N THR A 179 " pdb=" CA THR A 179 " ideal model delta harmonic sigma weight residual -180.00 -157.61 -22.39 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" CA ILE B 707 " pdb=" C ILE B 707 " pdb=" N ILE B 708 " pdb=" CA ILE B 708 " ideal model delta harmonic sigma weight residual 180.00 -158.70 -21.30 0 5.00e+00 4.00e-02 1.81e+01 ... (remaining 13833 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 2933 0.065 - 0.129: 417 0.129 - 0.194: 30 0.194 - 0.258: 2 0.258 - 0.323: 3 Chirality restraints: 3385 Sorted by residual: chirality pdb=" CG LEU A 529 " pdb=" CB LEU A 529 " pdb=" CD1 LEU A 529 " pdb=" CD2 LEU A 529 " both_signs ideal model delta sigma weight residual False -2.59 -2.27 -0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" CG LEU C 212 " pdb=" CB LEU C 212 " pdb=" CD1 LEU C 212 " pdb=" CD2 LEU C 212 " both_signs ideal model delta sigma weight residual False -2.59 -2.86 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" CB ILE B 937 " pdb=" CA ILE B 937 " pdb=" CG1 ILE B 937 " pdb=" CG2 ILE B 937 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.86e+00 ... (remaining 3382 not shown) Planarity restraints: 3926 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 167 " 0.037 2.00e-02 2.50e+03 7.29e-02 5.32e+01 pdb=" C LEU A 167 " -0.126 2.00e-02 2.50e+03 pdb=" O LEU A 167 " 0.049 2.00e-02 2.50e+03 pdb=" N SER A 168 " 0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 154 " -0.013 2.00e-02 2.50e+03 2.55e-02 6.51e+00 pdb=" C VAL B 154 " 0.044 2.00e-02 2.50e+03 pdb=" O VAL B 154 " -0.017 2.00e-02 2.50e+03 pdb=" N MET B 155 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B1172 " 0.008 2.00e-02 2.50e+03 1.86e-02 6.03e+00 pdb=" CG PHE B1172 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE B1172 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE B1172 " 0.024 2.00e-02 2.50e+03 pdb=" CE1 PHE B1172 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B1172 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE B1172 " -0.001 2.00e-02 2.50e+03 ... (remaining 3923 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 210 2.64 - 3.20: 18321 3.20 - 3.77: 33122 3.77 - 4.33: 43073 4.33 - 4.90: 71522 Nonbonded interactions: 166248 Sorted by model distance: nonbonded pdb=" OD2 ASP B 166 " pdb="MG MG B1402 " model vdw 2.072 2.170 nonbonded pdb=" O1A GDP B1401 " pdb="MG MG B1402 " model vdw 2.103 2.170 nonbonded pdb=" O2B GDP B1401 " pdb="MG MG B1402 " model vdw 2.185 2.170 nonbonded pdb=" N CYS D 55 " pdb="ZN ZN D 501 " model vdw 2.204 2.310 nonbonded pdb=" OD1 ASN D 352 " pdb=" OG1 THR D 374 " model vdw 2.213 3.040 ... (remaining 166243 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.540 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 22.660 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: 0.000 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 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 : 0.004 0.132 22667 Z= 0.198 Angle : 0.970 59.891 30612 Z= 0.427 Chirality : 0.045 0.323 3385 Planarity : 0.005 0.073 3926 Dihedral : 15.979 89.803 8591 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.02 % Favored : 95.80 % Rotamer: Outliers : 0.16 % Allowed : 13.62 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.14), residues: 2714 helix: -0.94 (0.12), residues: 1264 sheet: 0.35 (0.31), residues: 258 loop : -1.42 (0.17), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 952 TYR 0.025 0.001 TYR A 803 PHE 0.039 0.001 PHE B1172 TRP 0.013 0.001 TRP B 670 HIS 0.005 0.001 HIS C 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.18 (22657) covalent geometry : angle 0.71971 / 0.41 (30598) SS BOND : bond 0.00074 / 0.04 ( 1) SS BOND : angle 0.34789 / 0.20 ( 2) hydrogen bonds : bond 0.20043 / 13.03 ( 993) hydrogen bonds : angle 6.43904 / 4.40 ( 2883) metal coordination : bond 0.07316 / 5.94 ( 8) metal coordination : angle 32.82572 / 16.28 ( 12) Misc. bond : bond 0.09815 / 5.17 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5428 Ramachandran restraints generated. 2714 Oldfield, 0 Emsley, 2714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5428 Ramachandran restraints generated. 2714 Oldfield, 0 Emsley, 2714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 2452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 107 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 SER cc_start: 0.8832 (m) cc_final: 0.8606 (p) REVERT: A 358 MET cc_start: 0.9021 (ptm) cc_final: 0.8722 (ptp) REVERT: A 516 MET cc_start: 0.9074 (tmm) cc_final: 0.8815 (tmm) REVERT: A 556 MET cc_start: 0.9403 (mmm) cc_final: 0.8965 (tpp) REVERT: A 722 MET cc_start: 0.9297 (tpp) cc_final: 0.8925 (tmm) REVERT: A 859 MET cc_start: 0.9422 (tpt) cc_final: 0.9138 (ttm) REVERT: B 964 MET cc_start: 0.8463 (ppp) cc_final: 0.8115 (tmm) REVERT: B 1101 MET cc_start: 0.7783 (mtp) cc_final: 0.7425 (mtp) REVERT: B 1165 MET cc_start: 0.7693 (mtm) cc_final: 0.7332 (ppp) REVERT: C 182 MET cc_start: 0.9073 (tpp) cc_final: 0.8848 (tpp) REVERT: C 377 GLN cc_start: 0.7219 (OUTLIER) cc_final: 0.6885 (mm-40) REVERT: C 394 TYR cc_start: 0.6392 (m-80) cc_final: 0.6038 (m-10) REVERT: L 4 MET cc_start: 0.9061 (tpt) cc_final: 0.8807 (tpp) REVERT: L 58 GLU cc_start: 0.9169 (tt0) cc_final: 0.8535 (tp30) outliers start: 4 outliers final: 1 residues processed: 111 average time/residue: 0.1873 time to fit residues: 32.1523 Evaluate side-chains 87 residues out of total 2452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 85 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain C residue 377 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 10.0000 chunk 111 optimal weight: 9.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 186 HIS A 370 HIS A 491 ASN A 526 GLN ** B 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 HIS B1103 HIS B1328 HIS ** D 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 352 ASN D 363 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.047272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.031561 restraints weight = 200235.544| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 6.23 r_work: 0.2810 rms_B_bonded: 5.98 restraints_weight: 2.0000 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 22667 Z= 0.230 Angle : 0.673 28.410 30612 Z= 0.325 Chirality : 0.041 0.161 3385 Planarity : 0.004 0.048 3926 Dihedral : 4.719 38.164 3005 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.83 % Favored : 95.98 % Rotamer: Outliers : 1.71 % Allowed : 14.36 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.16), residues: 2714 helix: 0.85 (0.14), residues: 1297 sheet: 0.47 (0.32), residues: 250 loop : -1.08 (0.18), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 193 TYR 0.027 0.001 TYR B 692 PHE 0.018 0.001 PHE A 214 TRP 0.019 0.001 TRP C 442 HIS 0.008 0.001 HIS B 424 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.23 (22657) covalent geometry : angle 0.60991 / 0.32 (30598) SS BOND : bond 0.00408 / 0.21 ( 1) SS BOND : angle 0.64879 / 0.35 ( 2) hydrogen bonds : bond 0.04860 / 3.20 ( 993) hydrogen bonds : angle 4.72567 / 3.25 ( 2883) metal coordination : bond 0.02040 / 0.95 ( 8) metal coordination : angle 14.40387 / 6.86 ( 12) Misc. bond : bond 0.00006 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5428 Ramachandran restraints generated. 2714 Oldfield, 0 Emsley, 2714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5428 Ramachandran restraints generated. 2714 Oldfield, 0 Emsley, 2714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 2452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 87 time to evaluate : 0.907 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 165 SER cc_start: 0.9079 (m) cc_final: 0.8874 (p) REVERT: A 358 MET cc_start: 0.9094 (ptm) cc_final: 0.8763 (ptp) REVERT: A 516 MET cc_start: 0.9501 (tmm) cc_final: 0.9236 (tmm) REVERT: A 556 MET cc_start: 0.9531 (mmm) cc_final: 0.9106 (tpp) REVERT: A 654 MET cc_start: 0.9705 (mtm) cc_final: 0.9454 (ptt) REVERT: A 722 MET cc_start: 0.9450 (tpp) cc_final: 0.9101 (tmm) REVERT: A 859 MET cc_start: 0.9654 (tpt) cc_final: 0.9313 (ttm) REVERT: B 155 MET cc_start: 0.8849 (mmm) cc_final: 0.8291 (mmt) REVERT: B 941 LYS cc_start: 0.5079 (OUTLIER) cc_final: 0.2178 (mttp) REVERT: B 964 MET cc_start: 0.8472 (ppp) cc_final: 0.8055 (tmm) REVERT: B 1165 MET cc_start: 0.7834 (mtm) cc_final: 0.7572 (ppp) REVERT: C 145 LEU cc_start: 0.9592 (OUTLIER) cc_final: 0.9247 (tt) REVERT: C 377 GLN cc_start: 0.6928 (OUTLIER) cc_final: 0.6645 (mm-40) REVERT: C 394 TYR cc_start: 0.6788 (m-80) cc_final: 0.6515 (m-80) REVERT: D 189 ARG cc_start: 0.8991 (OUTLIER) cc_final: 0.8712 (mtm110) REVERT: L 45 MET cc_start: 0.9327 (mtt) cc_final: 0.9103 (mtp) REVERT: L 58 GLU cc_start: 0.9610 (tt0) cc_final: 0.9144 (tp30) REVERT: L 67 GLN cc_start: 0.9600 (mm-40) cc_final: 0.9278 (mm-40) outliers start: 42 outliers final: 14 residues processed: 124 average time/residue: 0.1468 time to fit residues: 29.6094 Evaluate side-chains 103 residues out of total 2452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 85 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 395 TYR Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 69 GLN Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 580 HIS Chi-restraints excluded: chain B residue 941 LYS Chi-restraints excluded: chain B residue 955 CYS Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 377 GLN Chi-restraints excluded: chain D residue 55 CYS Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 189 ARG Chi-restraints excluded: chain D residue 352 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 267 optimal weight: 5.9990 chunk 240 optimal weight: 1.9990 chunk 98 optimal weight: 0.0070 chunk 219 optimal weight: 50.0000 chunk 149 optimal weight: 0.3980 chunk 116 optimal weight: 0.0770 chunk 12 optimal weight: 1.9990 chunk 140 optimal weight: 0.6980 chunk 30 optimal weight: 5.9990 chunk 120 optimal weight: 0.8980 chunk 17 optimal weight: 6.9990 overall best weight: 0.4156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 32 GLN A 386 GLN A 808 HIS ** B 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1103 HIS D 373 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.047681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.032948 restraints weight = 219477.027| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 5.43 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 22667 Z= 0.092 Angle : 0.510 14.503 30612 Z= 0.253 Chirality : 0.039 0.175 3385 Planarity : 0.003 0.046 3926 Dihedral : 4.356 38.033 3005 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.39 % Favored : 96.46 % Rotamer: Outliers : 1.31 % Allowed : 14.31 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.16), residues: 2714 helix: 1.37 (0.15), residues: 1299 sheet: 0.48 (0.32), residues: 248 loop : -0.97 (0.18), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 20 TYR 0.019 0.001 TYR A 803 PHE 0.011 0.001 PHE D 360 TRP 0.025 0.001 TRP C 442 HIS 0.004 0.001 HIS B 988 Details of bonding type rmsd/Z covalent geometry : bond 0.00181 / 0.09 (22657) covalent geometry : angle 0.48548 / 0.25 (30598) SS BOND : bond 0.00080 / 0.04 ( 1) SS BOND : angle 0.07753 / 0.04 ( 2) hydrogen bonds : bond 0.03888 / 2.57 ( 993) hydrogen bonds : angle 4.16452 / 2.88 ( 2883) metal coordination : bond 0.01212 / 0.53 ( 8) metal coordination : angle 7.87757 / 3.60 ( 12) Misc. bond : bond 0.00002 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5428 Ramachandran restraints generated. 2714 Oldfield, 0 Emsley, 2714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5428 Ramachandran restraints generated. 2714 Oldfield, 0 Emsley, 2714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 2452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 86 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 MET cc_start: 0.8636 (mpp) cc_final: 0.8368 (mpp) REVERT: A 358 MET cc_start: 0.8585 (ptm) cc_final: 0.8248 (ptp) REVERT: A 394 MET cc_start: 0.9026 (mmm) cc_final: 0.8752 (mmm) REVERT: A 516 MET cc_start: 0.9133 (tmm) cc_final: 0.8877 (tmm) REVERT: A 556 MET cc_start: 0.9403 (mmm) cc_final: 0.8955 (tpp) REVERT: A 617 MET cc_start: 0.9660 (mpp) cc_final: 0.9381 (mpp) REVERT: A 722 MET cc_start: 0.9286 (tpp) cc_final: 0.9044 (tmm) REVERT: A 859 MET cc_start: 0.9421 (tpt) cc_final: 0.9193 (ttm) REVERT: B 155 MET cc_start: 0.8627 (mmm) cc_final: 0.8099 (mmt) REVERT: B 941 LYS cc_start: 0.3059 (OUTLIER) cc_final: 0.2172 (mttp) REVERT: B 964 MET cc_start: 0.8365 (ppp) cc_final: 0.7879 (tmm) REVERT: B 1101 MET cc_start: 0.7516 (mtp) cc_final: 0.6843 (ptm) REVERT: C 145 LEU cc_start: 0.9520 (OUTLIER) cc_final: 0.9166 (tt) REVERT: C 394 TYR cc_start: 0.6365 (m-80) cc_final: 0.6052 (m-80) REVERT: L 58 GLU cc_start: 0.9170 (tt0) cc_final: 0.8660 (tp30) REVERT: L 67 GLN cc_start: 0.9301 (mm-40) cc_final: 0.8967 (mm-40) outliers start: 32 outliers final: 12 residues processed: 115 average time/residue: 0.1409 time to fit residues: 27.1706 Evaluate side-chains 96 residues out of total 2452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 395 TYR Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 580 HIS Chi-restraints excluded: chain B residue 708 ILE Chi-restraints excluded: chain B residue 941 LYS Chi-restraints excluded: chain B residue 955 CYS Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 278 HIS Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 412 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 16 optimal weight: 9.9990 chunk 88 optimal weight: 10.0000 chunk 178 optimal weight: 40.0000 chunk 181 optimal weight: 5.9990 chunk 109 optimal weight: 1.9990 chunk 264 optimal weight: 10.0000 chunk 218 optimal weight: 10.0000 chunk 135 optimal weight: 5.9990 chunk 177 optimal weight: 40.0000 chunk 259 optimal weight: 5.9990 chunk 91 optimal weight: 8.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 748 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 967 ASN ** B1193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 108 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.046672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.031460 restraints weight = 201372.902| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 5.83 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 22667 Z= 0.303 Angle : 0.685 12.283 30612 Z= 0.345 Chirality : 0.043 0.190 3385 Planarity : 0.004 0.048 3926 Dihedral : 4.498 38.420 3000 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.35 % Favored : 95.50 % Rotamer: Outliers : 1.79 % Allowed : 15.05 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.16), residues: 2714 helix: 1.51 (0.14), residues: 1301 sheet: 0.28 (0.32), residues: 255 loop : -0.99 (0.19), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 193 TYR 0.018 0.002 TYR A 858 PHE 0.021 0.002 PHE A 214 TRP 0.012 0.001 TRP A 339 HIS 0.008 0.001 HIS B 424 Details of bonding type rmsd/Z covalent geometry : bond 0.00647 / 0.30 (22657) covalent geometry : angle 0.66974 / 0.34 (30598) SS BOND : bond 0.00437 / 0.23 ( 1) SS BOND : angle 0.88019 / 0.48 ( 2) hydrogen bonds : bond 0.04768 / 3.16 ( 993) hydrogen bonds : angle 4.60028 / 3.19 ( 2883) metal coordination : bond 0.02981 / 2.33 ( 8) metal coordination : angle 7.19929 / 4.11 ( 12) Misc. bond : bond 0.00024 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5428 Ramachandran restraints generated. 2714 Oldfield, 0 Emsley, 2714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5428 Ramachandran restraints generated. 2714 Oldfield, 0 Emsley, 2714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 2452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 84 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 ARG cc_start: 0.8926 (OUTLIER) cc_final: 0.8661 (mmp-170) REVERT: A 187 MET cc_start: 0.8656 (mpp) cc_final: 0.8350 (mpp) REVERT: A 358 MET cc_start: 0.8869 (ptm) cc_final: 0.8462 (ptm) REVERT: A 516 MET cc_start: 0.9324 (tmm) cc_final: 0.9059 (tmm) REVERT: A 556 MET cc_start: 0.9552 (mmm) cc_final: 0.9057 (tpp) REVERT: A 654 MET cc_start: 0.9363 (OUTLIER) cc_final: 0.9092 (ptt) REVERT: A 682 MET cc_start: 0.8768 (tmm) cc_final: 0.8284 (tmm) REVERT: A 722 MET cc_start: 0.9418 (tpp) cc_final: 0.9177 (tmm) REVERT: A 859 MET cc_start: 0.9534 (tpt) cc_final: 0.9238 (ttm) REVERT: B 155 MET cc_start: 0.8684 (mmm) cc_final: 0.7913 (mmt) REVERT: B 941 LYS cc_start: 0.3182 (OUTLIER) cc_final: 0.1672 (mttp) REVERT: B 964 MET cc_start: 0.8569 (ppp) cc_final: 0.8088 (tmm) REVERT: B 1101 MET cc_start: 0.7238 (mtp) cc_final: 0.6591 (ptm) REVERT: C 394 TYR cc_start: 0.6517 (m-80) cc_final: 0.6217 (m-80) REVERT: L 45 MET cc_start: 0.8733 (mtt) cc_final: 0.7768 (mtp) REVERT: L 67 GLN cc_start: 0.9277 (mm-40) cc_final: 0.8961 (mm-40) outliers start: 44 outliers final: 23 residues processed: 126 average time/residue: 0.1413 time to fit residues: 29.1205 Evaluate side-chains 106 residues out of total 2452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 80 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 183 ARG Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 395 TYR Chi-restraints excluded: chain A residue 654 MET Chi-restraints excluded: chain A residue 679 HIS Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 69 GLN Chi-restraints excluded: chain B residue 108 ASP Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 580 HIS Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 719 VAL Chi-restraints excluded: chain B residue 939 THR Chi-restraints excluded: chain B residue 941 LYS Chi-restraints excluded: chain B residue 955 CYS Chi-restraints excluded: chain B residue 1335 VAL Chi-restraints excluded: chain C residue 278 HIS Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 77 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 27 optimal weight: 8.9990 chunk 57 optimal weight: 8.9990 chunk 232 optimal weight: 10.0000 chunk 253 optimal weight: 50.0000 chunk 66 optimal weight: 9.9990 chunk 99 optimal weight: 0.2980 chunk 260 optimal weight: 30.0000 chunk 85 optimal weight: 0.0770 chunk 230 optimal weight: 10.0000 chunk 4 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 overall best weight: 3.2342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 649 GLN ** D 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 158 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.046656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.032292 restraints weight = 226589.504| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 6.17 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 22667 Z= 0.173 Angle : 0.551 8.533 30612 Z= 0.279 Chirality : 0.040 0.161 3385 Planarity : 0.003 0.043 3926 Dihedral : 4.363 38.546 3000 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.91 % Favored : 95.95 % Rotamer: Outliers : 1.55 % Allowed : 15.58 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.17), residues: 2714 helix: 1.74 (0.15), residues: 1298 sheet: 0.29 (0.32), residues: 253 loop : -0.91 (0.19), residues: 1163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 221 TYR 0.018 0.001 TYR A 803 PHE 0.016 0.001 PHE B1172 TRP 0.011 0.001 TRP C 442 HIS 0.005 0.001 HIS B 424 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.17 (22657) covalent geometry : angle 0.54052 / 0.28 (30598) SS BOND : bond 0.00290 / 0.15 ( 1) SS BOND : angle 0.25721 / 0.14 ( 2) hydrogen bonds : bond 0.04122 / 2.74 ( 993) hydrogen bonds : angle 4.29870 / 2.99 ( 2883) metal coordination : bond 0.01394 / 0.98 ( 8) metal coordination : angle 5.33919 / 2.93 ( 12) Misc. bond : bond 0.00013 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5428 Ramachandran restraints generated. 2714 Oldfield, 0 Emsley, 2714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5428 Ramachandran restraints generated. 2714 Oldfield, 0 Emsley, 2714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 2452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 82 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 MET cc_start: 0.8689 (mpp) cc_final: 0.8477 (mpp) REVERT: A 358 MET cc_start: 0.8819 (ptm) cc_final: 0.8525 (ptp) REVERT: A 516 MET cc_start: 0.9308 (tmm) cc_final: 0.9045 (tmm) REVERT: A 556 MET cc_start: 0.9581 (mmm) cc_final: 0.9083 (tpp) REVERT: A 654 MET cc_start: 0.9413 (ptp) cc_final: 0.9133 (ptt) REVERT: A 682 MET cc_start: 0.8764 (tmm) cc_final: 0.8359 (tmm) REVERT: A 722 MET cc_start: 0.9435 (tpp) cc_final: 0.9187 (tmm) REVERT: A 859 MET cc_start: 0.9533 (tpt) cc_final: 0.9245 (ttm) REVERT: B 155 MET cc_start: 0.8614 (mmm) cc_final: 0.7763 (mmm) REVERT: B 941 LYS cc_start: 0.3030 (OUTLIER) cc_final: 0.1951 (mttm) REVERT: B 1101 MET cc_start: 0.7508 (mtp) cc_final: 0.6774 (ptm) REVERT: C 394 TYR cc_start: 0.6232 (m-80) cc_final: 0.5934 (m-80) REVERT: L 67 GLN cc_start: 0.9299 (mm-40) cc_final: 0.8942 (mm-40) outliers start: 38 outliers final: 24 residues processed: 118 average time/residue: 0.1301 time to fit residues: 25.8863 Evaluate side-chains 105 residues out of total 2452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 80 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 395 TYR Chi-restraints excluded: chain A residue 679 HIS Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 580 HIS Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 719 VAL Chi-restraints excluded: chain B residue 939 THR Chi-restraints excluded: chain B residue 941 LYS Chi-restraints excluded: chain B residue 955 CYS Chi-restraints excluded: chain B residue 1335 VAL Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 278 HIS Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain L residue 40 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 260 optimal weight: 7.9990 chunk 42 optimal weight: 10.0000 chunk 70 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 62.1719 > 50:) chunk 231 optimal weight: 30.0000 chunk 126 optimal weight: 0.0370 chunk 269 optimal weight: 5.9990 chunk 128 optimal weight: 3.9990 chunk 150 optimal weight: 0.9990 chunk 65 optimal weight: 0.0670 chunk 158 optimal weight: 4.9990 chunk 194 optimal weight: 8.9990 overall best weight: 2.0202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 297 ASN D 60 GLN L 54 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.046775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.032082 restraints weight = 224869.921| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 5.32 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 22667 Z= 0.119 Angle : 0.516 9.621 30612 Z= 0.259 Chirality : 0.039 0.157 3385 Planarity : 0.003 0.043 3926 Dihedral : 4.202 37.003 3000 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.94 % Favored : 95.91 % Rotamer: Outliers : 1.59 % Allowed : 15.78 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.17), residues: 2714 helix: 1.93 (0.15), residues: 1299 sheet: 0.30 (0.32), residues: 261 loop : -0.79 (0.19), residues: 1154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 221 TYR 0.019 0.001 TYR A 803 PHE 0.012 0.001 PHE B1172 TRP 0.011 0.001 TRP C 442 HIS 0.004 0.001 HIS B 424 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (22657) covalent geometry : angle 0.50777 / 0.26 (30598) SS BOND : bond 0.00288 / 0.15 ( 1) SS BOND : angle 0.67193 / 0.36 ( 2) hydrogen bonds : bond 0.03702 / 2.46 ( 993) hydrogen bonds : angle 4.07892 / 2.83 ( 2883) metal coordination : bond 0.00915 / 0.58 ( 8) metal coordination : angle 4.65321 / 2.45 ( 12) Misc. bond : bond 0.00007 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5428 Ramachandran restraints generated. 2714 Oldfield, 0 Emsley, 2714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5428 Ramachandran restraints generated. 2714 Oldfield, 0 Emsley, 2714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 2452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 81 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 126 THR cc_start: 0.9263 (OUTLIER) cc_final: 0.8972 (p) REVERT: A 183 ARG cc_start: 0.8792 (OUTLIER) cc_final: 0.8546 (mmp-170) REVERT: A 187 MET cc_start: 0.8753 (mpp) cc_final: 0.8481 (mpp) REVERT: A 358 MET cc_start: 0.8719 (ptm) cc_final: 0.8424 (ptp) REVERT: A 394 MET cc_start: 0.9000 (mmm) cc_final: 0.8785 (mmm) REVERT: A 516 MET cc_start: 0.9203 (tmm) cc_final: 0.8957 (tmm) REVERT: A 556 MET cc_start: 0.9456 (mmm) cc_final: 0.8953 (tpp) REVERT: A 579 ASP cc_start: 0.9313 (OUTLIER) cc_final: 0.8901 (p0) REVERT: A 583 MET cc_start: 0.8808 (ptt) cc_final: 0.8347 (ptt) REVERT: A 654 MET cc_start: 0.9364 (ptp) cc_final: 0.9077 (ptt) REVERT: A 682 MET cc_start: 0.8646 (tmm) cc_final: 0.8306 (tmm) REVERT: A 722 MET cc_start: 0.9297 (tpp) cc_final: 0.8978 (tmm) REVERT: A 859 MET cc_start: 0.9444 (tpt) cc_final: 0.9210 (ttm) REVERT: B 155 MET cc_start: 0.8610 (mmm) cc_final: 0.7854 (mmm) REVERT: B 941 LYS cc_start: 0.3110 (OUTLIER) cc_final: 0.2514 (mttm) REVERT: B 964 MET cc_start: 0.8403 (ptm) cc_final: 0.7744 (tmm) REVERT: B 1101 MET cc_start: 0.7513 (mtp) cc_final: 0.6763 (ptm) REVERT: B 1170 MET cc_start: 0.8132 (mmm) cc_final: 0.7772 (mpp) REVERT: C 145 LEU cc_start: 0.9522 (OUTLIER) cc_final: 0.9251 (tt) REVERT: C 394 TYR cc_start: 0.6417 (m-80) cc_final: 0.6123 (m-80) REVERT: L 67 GLN cc_start: 0.9300 (mm-40) cc_final: 0.8953 (mm-40) outliers start: 39 outliers final: 23 residues processed: 118 average time/residue: 0.1276 time to fit residues: 25.5730 Evaluate side-chains 107 residues out of total 2452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 79 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 183 ARG Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 395 TYR Chi-restraints excluded: chain A residue 579 ASP Chi-restraints excluded: chain A residue 637 HIS Chi-restraints excluded: chain A residue 679 HIS Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 425 PHE Chi-restraints excluded: chain B residue 580 HIS Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 719 VAL Chi-restraints excluded: chain B residue 941 LYS Chi-restraints excluded: chain B residue 955 CYS Chi-restraints excluded: chain B residue 1335 VAL Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain L residue 40 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 157 optimal weight: 6.9990 chunk 158 optimal weight: 3.9990 chunk 56 optimal weight: 10.0000 chunk 162 optimal weight: 4.9990 chunk 82 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 92 optimal weight: 1.9990 chunk 183 optimal weight: 2.9990 chunk 231 optimal weight: 30.0000 chunk 188 optimal weight: 30.0000 chunk 24 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 988 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1193 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 = 0.3619 r_free = 0.3619 target = 0.046572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.032013 restraints weight = 225409.658| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 5.30 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 22667 Z= 0.179 Angle : 0.561 9.585 30612 Z= 0.281 Chirality : 0.040 0.233 3385 Planarity : 0.003 0.044 3926 Dihedral : 4.227 37.408 3000 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.24 % Favored : 95.58 % Rotamer: Outliers : 1.79 % Allowed : 15.95 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.17), residues: 2714 helix: 1.88 (0.15), residues: 1300 sheet: 0.29 (0.31), residues: 261 loop : -0.81 (0.19), residues: 1153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 193 TYR 0.017 0.001 TYR A 803 PHE 0.018 0.001 PHE B1172 TRP 0.010 0.001 TRP C 442 HIS 0.006 0.001 HIS B 424 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.18 (22657) covalent geometry : angle 0.55222 / 0.28 (30598) SS BOND : bond 0.00258 / 0.14 ( 1) SS BOND : angle 0.56857 / 0.31 ( 2) hydrogen bonds : bond 0.03916 / 2.60 ( 993) hydrogen bonds : angle 4.19124 / 2.92 ( 2883) metal coordination : bond 0.01149 / 0.75 ( 8) metal coordination : angle 4.88660 / 2.70 ( 12) Misc. bond : bond 0.00012 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5428 Ramachandran restraints generated. 2714 Oldfield, 0 Emsley, 2714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5428 Ramachandran restraints generated. 2714 Oldfield, 0 Emsley, 2714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 2452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 80 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 THR cc_start: 0.9277 (OUTLIER) cc_final: 0.8958 (p) REVERT: A 187 MET cc_start: 0.8785 (mpp) cc_final: 0.8565 (mpp) REVERT: A 358 MET cc_start: 0.8793 (ptm) cc_final: 0.8513 (ptm) REVERT: A 394 MET cc_start: 0.9045 (mmm) cc_final: 0.8817 (mmm) REVERT: A 516 MET cc_start: 0.9198 (tmm) cc_final: 0.8975 (tmm) REVERT: A 538 MET cc_start: 0.9318 (ttp) cc_final: 0.9054 (mtp) REVERT: A 556 MET cc_start: 0.9449 (mmm) cc_final: 0.8945 (tpp) REVERT: A 654 MET cc_start: 0.9368 (ptp) cc_final: 0.9087 (ptt) REVERT: A 682 MET cc_start: 0.8637 (tmm) cc_final: 0.8330 (tmm) REVERT: A 722 MET cc_start: 0.9295 (tpp) cc_final: 0.8977 (tmm) REVERT: A 859 MET cc_start: 0.9440 (tpt) cc_final: 0.9236 (ttm) REVERT: B 155 MET cc_start: 0.8630 (mmm) cc_final: 0.7917 (mmt) REVERT: B 941 LYS cc_start: 0.3045 (OUTLIER) cc_final: 0.1810 (mttp) REVERT: B 964 MET cc_start: 0.8383 (ptm) cc_final: 0.7465 (tmm) REVERT: B 1101 MET cc_start: 0.7538 (mtp) cc_final: 0.6726 (ptm) REVERT: B 1170 MET cc_start: 0.8106 (mmm) cc_final: 0.7743 (mpp) REVERT: C 394 TYR cc_start: 0.6444 (m-80) cc_final: 0.6148 (m-80) REVERT: C 432 MET cc_start: 0.6281 (mtt) cc_final: 0.6065 (mtp) outliers start: 44 outliers final: 30 residues processed: 120 average time/residue: 0.1338 time to fit residues: 26.8815 Evaluate side-chains 109 residues out of total 2452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 77 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 61 CYS Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 395 TYR Chi-restraints excluded: chain A residue 637 HIS Chi-restraints excluded: chain A residue 679 HIS Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 425 PHE Chi-restraints excluded: chain B residue 580 HIS Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 719 VAL Chi-restraints excluded: chain B residue 779 MET Chi-restraints excluded: chain B residue 939 THR Chi-restraints excluded: chain B residue 941 LYS Chi-restraints excluded: chain B residue 1335 VAL Chi-restraints excluded: chain C residue 140 CYS Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 278 HIS Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 267 TRP Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain L residue 40 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 113 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 259 optimal weight: 9.9990 chunk 137 optimal weight: 2.9990 chunk 30 optimal weight: 7.9990 chunk 173 optimal weight: 30.0000 chunk 149 optimal weight: 0.0010 chunk 258 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 192 optimal weight: 9.9990 chunk 228 optimal weight: 10.0000 overall best weight: 3.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B1193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 258 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.046607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.032021 restraints weight = 222904.854| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 5.28 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 22667 Z= 0.179 Angle : 0.571 12.024 30612 Z= 0.287 Chirality : 0.040 0.208 3385 Planarity : 0.003 0.044 3926 Dihedral : 4.253 40.696 3000 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.46 % Favored : 95.36 % Rotamer: Outliers : 1.67 % Allowed : 16.44 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.17), residues: 2714 helix: 1.82 (0.15), residues: 1308 sheet: 0.12 (0.32), residues: 267 loop : -0.81 (0.19), residues: 1139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 193 TYR 0.018 0.001 TYR A 803 PHE 0.018 0.001 PHE B1172 TRP 0.010 0.001 TRP C 442 HIS 0.010 0.001 HIS B 744 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.18 (22657) covalent geometry : angle 0.56299 / 0.29 (30598) SS BOND : bond 0.00251 / 0.13 ( 1) SS BOND : angle 0.48397 / 0.27 ( 2) hydrogen bonds : bond 0.03986 / 2.65 ( 993) hydrogen bonds : angle 4.23650 / 2.97 ( 2883) metal coordination : bond 0.01127 / 0.74 ( 8) metal coordination : angle 4.77610 / 2.68 ( 12) Misc. bond : bond 0.00013 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5428 Ramachandran restraints generated. 2714 Oldfield, 0 Emsley, 2714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5428 Ramachandran restraints generated. 2714 Oldfield, 0 Emsley, 2714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 2452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 77 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 THR cc_start: 0.9272 (OUTLIER) cc_final: 0.8963 (p) REVERT: A 358 MET cc_start: 0.8794 (ptm) cc_final: 0.8567 (ptm) REVERT: A 394 MET cc_start: 0.9063 (mmm) cc_final: 0.8820 (mmm) REVERT: A 516 MET cc_start: 0.9205 (tmm) cc_final: 0.8986 (tmm) REVERT: A 538 MET cc_start: 0.9327 (ttp) cc_final: 0.9064 (mtp) REVERT: A 556 MET cc_start: 0.9450 (mmm) cc_final: 0.8945 (tpp) REVERT: A 654 MET cc_start: 0.9360 (ptp) cc_final: 0.9097 (ptt) REVERT: A 682 MET cc_start: 0.8643 (tmm) cc_final: 0.8345 (tmm) REVERT: B 106 VAL cc_start: 0.9145 (OUTLIER) cc_final: 0.8794 (p) REVERT: B 155 MET cc_start: 0.8618 (mmm) cc_final: 0.7872 (mmm) REVERT: B 941 LYS cc_start: 0.3078 (OUTLIER) cc_final: 0.2091 (mttm) REVERT: B 1101 MET cc_start: 0.7539 (mtp) cc_final: 0.6712 (ptm) REVERT: B 1170 MET cc_start: 0.8083 (mmm) cc_final: 0.7717 (mpp) REVERT: C 394 TYR cc_start: 0.6392 (m-80) cc_final: 0.6119 (m-80) REVERT: L 1 MET cc_start: 0.8593 (mtp) cc_final: 0.8345 (mtp) outliers start: 41 outliers final: 32 residues processed: 115 average time/residue: 0.1281 time to fit residues: 24.9610 Evaluate side-chains 112 residues out of total 2452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 77 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 61 CYS Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 395 TYR Chi-restraints excluded: chain A residue 637 HIS Chi-restraints excluded: chain A residue 679 HIS Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 69 GLN Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 425 PHE Chi-restraints excluded: chain B residue 580 HIS Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 719 VAL Chi-restraints excluded: chain B residue 779 MET Chi-restraints excluded: chain B residue 939 THR Chi-restraints excluded: chain B residue 941 LYS Chi-restraints excluded: chain B residue 1335 VAL Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 182 ASP Chi-restraints excluded: chain D residue 267 TRP Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain L residue 40 TYR Chi-restraints excluded: chain L residue 50 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 136 optimal weight: 0.8980 chunk 239 optimal weight: 7.9990 chunk 156 optimal weight: 4.9990 chunk 258 optimal weight: 20.0000 chunk 184 optimal weight: 40.0000 chunk 32 optimal weight: 0.8980 chunk 223 optimal weight: 0.2980 chunk 187 optimal weight: 20.0000 chunk 250 optimal weight: 6.9990 chunk 81 optimal weight: 0.3980 chunk 89 optimal weight: 9.9990 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 709 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.046878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.032628 restraints weight = 224093.862| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 6.37 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 22667 Z= 0.103 Angle : 0.531 11.566 30612 Z= 0.265 Chirality : 0.039 0.263 3385 Planarity : 0.003 0.043 3926 Dihedral : 4.132 39.880 3000 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.83 % Favored : 95.98 % Rotamer: Outliers : 1.26 % Allowed : 16.88 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.17), residues: 2714 helix: 2.01 (0.15), residues: 1303 sheet: 0.20 (0.32), residues: 267 loop : -0.69 (0.19), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 221 TYR 0.020 0.001 TYR A 803 PHE 0.015 0.001 PHE B1172 TRP 0.011 0.001 TRP C 442 HIS 0.003 0.001 HIS A 808 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 (22657) covalent geometry : angle 0.52495 / 0.26 (30598) SS BOND : bond 0.00117 / 0.06 ( 1) SS BOND : angle 0.29612 / 0.17 ( 2) hydrogen bonds : bond 0.03568 / 2.37 ( 993) hydrogen bonds : angle 4.03620 / 2.83 ( 2883) metal coordination : bond 0.00721 / 0.42 ( 8) metal coordination : angle 4.15272 / 2.18 ( 12) Misc. bond : bond 0.00003 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5428 Ramachandran restraints generated. 2714 Oldfield, 0 Emsley, 2714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5428 Ramachandran restraints generated. 2714 Oldfield, 0 Emsley, 2714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 2452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 78 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 126 THR cc_start: 0.9175 (OUTLIER) cc_final: 0.8969 (p) REVERT: A 358 MET cc_start: 0.8827 (ptm) cc_final: 0.8623 (ptm) REVERT: A 394 MET cc_start: 0.9111 (mmm) cc_final: 0.8847 (mmm) REVERT: A 516 MET cc_start: 0.9363 (tmm) cc_final: 0.9097 (tmm) REVERT: A 556 MET cc_start: 0.9559 (mmm) cc_final: 0.9073 (tpp) REVERT: A 654 MET cc_start: 0.9437 (ptp) cc_final: 0.9165 (ptt) REVERT: A 682 MET cc_start: 0.8720 (tmm) cc_final: 0.8380 (tmm) REVERT: B 106 VAL cc_start: 0.9168 (OUTLIER) cc_final: 0.8920 (p) REVERT: B 155 MET cc_start: 0.8551 (mmm) cc_final: 0.7912 (mmt) REVERT: B 941 LYS cc_start: 0.3030 (OUTLIER) cc_final: 0.2359 (tttp) REVERT: B 964 MET cc_start: 0.8439 (ptm) cc_final: 0.7552 (tmm) REVERT: B 1101 MET cc_start: 0.7377 (mtp) cc_final: 0.6620 (ptm) REVERT: C 394 TYR cc_start: 0.6259 (m-80) cc_final: 0.5990 (m-80) outliers start: 31 outliers final: 26 residues processed: 106 average time/residue: 0.1268 time to fit residues: 23.0053 Evaluate side-chains 107 residues out of total 2452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 78 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 395 TYR Chi-restraints excluded: chain A residue 679 HIS Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 425 PHE Chi-restraints excluded: chain B residue 580 HIS Chi-restraints excluded: chain B residue 660 ILE Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 719 VAL Chi-restraints excluded: chain B residue 779 MET Chi-restraints excluded: chain B residue 939 THR Chi-restraints excluded: chain B residue 941 LYS Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain C residue 140 CYS Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain L residue 40 TYR Chi-restraints excluded: chain L residue 50 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 161 optimal weight: 4.9990 chunk 243 optimal weight: 2.9990 chunk 175 optimal weight: 20.0000 chunk 89 optimal weight: 9.9990 chunk 198 optimal weight: 30.0000 chunk 120 optimal weight: 3.9990 chunk 79 optimal weight: 0.6980 chunk 148 optimal weight: 3.9990 chunk 189 optimal weight: 30.0000 chunk 197 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 709 GLN ** B1193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.046576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.032137 restraints weight = 227928.760| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 6.50 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 22667 Z= 0.168 Angle : 0.576 10.370 30612 Z= 0.288 Chirality : 0.040 0.226 3385 Planarity : 0.003 0.044 3926 Dihedral : 4.190 43.930 3000 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.42 % Favored : 95.39 % Rotamer: Outliers : 1.59 % Allowed : 16.64 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.17), residues: 2714 helix: 1.94 (0.15), residues: 1304 sheet: 0.19 (0.32), residues: 267 loop : -0.75 (0.19), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 193 TYR 0.026 0.001 TYR A 803 PHE 0.013 0.001 PHE B1172 TRP 0.010 0.001 TRP C 442 HIS 0.006 0.001 HIS B 746 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.17 (22657) covalent geometry : angle 0.56844 / 0.29 (30598) SS BOND : bond 0.00263 / 0.14 ( 1) SS BOND : angle 0.44356 / 0.25 ( 2) hydrogen bonds : bond 0.03860 / 2.56 ( 993) hydrogen bonds : angle 4.17712 / 2.93 ( 2883) metal coordination : bond 0.01059 / 0.71 ( 8) metal coordination : angle 4.63260 / 2.61 ( 12) Misc. bond : bond 0.00011 / 0.01 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5428 Ramachandran restraints generated. 2714 Oldfield, 0 Emsley, 2714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5428 Ramachandran restraints generated. 2714 Oldfield, 0 Emsley, 2714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 2452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 78 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 126 THR cc_start: 0.9226 (OUTLIER) cc_final: 0.8958 (p) REVERT: A 358 MET cc_start: 0.8891 (ptm) cc_final: 0.8652 (ptm) REVERT: A 394 MET cc_start: 0.9119 (mmm) cc_final: 0.8867 (mmm) REVERT: A 516 MET cc_start: 0.9381 (tmm) cc_final: 0.9121 (tmm) REVERT: A 538 MET cc_start: 0.9414 (ttp) cc_final: 0.9112 (mtp) REVERT: A 556 MET cc_start: 0.9591 (mmm) cc_final: 0.9105 (tpp) REVERT: A 654 MET cc_start: 0.9449 (ptp) cc_final: 0.9192 (ptt) REVERT: A 682 MET cc_start: 0.8746 (tmm) cc_final: 0.8410 (tmm) REVERT: B 106 VAL cc_start: 0.9144 (OUTLIER) cc_final: 0.8810 (p) REVERT: B 155 MET cc_start: 0.8551 (mmm) cc_final: 0.7865 (mmm) REVERT: B 941 LYS cc_start: 0.3113 (OUTLIER) cc_final: 0.2066 (mttm) REVERT: B 964 MET cc_start: 0.8473 (ptm) cc_final: 0.7758 (tmm) REVERT: B 1101 MET cc_start: 0.7310 (mtp) cc_final: 0.6624 (ptm) REVERT: B 1170 MET cc_start: 0.7972 (mmm) cc_final: 0.7706 (mpp) REVERT: C 145 LEU cc_start: 0.9491 (OUTLIER) cc_final: 0.9209 (tt) REVERT: C 394 TYR cc_start: 0.6439 (m-80) cc_final: 0.6162 (m-80) outliers start: 39 outliers final: 29 residues processed: 113 average time/residue: 0.1379 time to fit residues: 26.7971 Evaluate side-chains 111 residues out of total 2452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 78 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 395 TYR Chi-restraints excluded: chain A residue 637 HIS Chi-restraints excluded: chain A residue 679 HIS Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 425 PHE Chi-restraints excluded: chain B residue 660 ILE Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 719 VAL Chi-restraints excluded: chain B residue 779 MET Chi-restraints excluded: chain B residue 939 THR Chi-restraints excluded: chain B residue 941 LYS Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain C residue 140 CYS Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 267 TRP Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain L residue 40 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 224 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 198 optimal weight: 20.0000 chunk 104 optimal weight: 9.9990 chunk 124 optimal weight: 0.6980 chunk 219 optimal weight: 40.0000 chunk 127 optimal weight: 4.9990 chunk 194 optimal weight: 8.9990 chunk 10 optimal weight: 4.9990 chunk 146 optimal weight: 4.9990 chunk 154 optimal weight: 7.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B1193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 298 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.046241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.031627 restraints weight = 230165.054| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 5.36 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 22667 Z= 0.196 Angle : 0.604 9.956 30612 Z= 0.303 Chirality : 0.040 0.219 3385 Planarity : 0.003 0.043 3926 Dihedral : 4.357 52.777 3000 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.27 % Favored : 95.54 % Rotamer: Outliers : 1.39 % Allowed : 16.84 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.17), residues: 2714 helix: 1.85 (0.15), residues: 1295 sheet: 0.19 (0.32), residues: 266 loop : -0.79 (0.19), residues: 1153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 193 TYR 0.023 0.001 TYR A 803 PHE 0.017 0.001 PHE A 762 TRP 0.012 0.001 TRP B1357 HIS 0.005 0.001 HIS B 424 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.20 (22657) covalent geometry : angle 0.59676 / 0.30 (30598) SS BOND : bond 0.00371 / 0.20 ( 1) SS BOND : angle 0.33668 / 0.18 ( 2) hydrogen bonds : bond 0.04134 / 2.75 ( 993) hydrogen bonds : angle 4.31928 / 3.04 ( 2883) metal coordination : bond 0.01185 / 0.82 ( 8) metal coordination : angle 4.77528 / 2.80 ( 12) Misc. bond : bond 0.00016 / 0.01 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5612.73 seconds wall clock time: 96 minutes 53.65 seconds (5813.65 seconds total)