Starting phenix.real_space_refine on Sun Jul 5 01:19:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ggq_51339/07_2026/9ggq_51339.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ggq_51339/07_2026/9ggq_51339.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ggq_51339/07_2026/9ggq_51339.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ggq_51339/07_2026/9ggq_51339.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ggq_51339/07_2026/9ggq_51339.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ggq_51339/07_2026/9ggq_51339.map" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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 P 84 5.49 5 Mg 4 5.21 5 S 87 5.16 5 C 15189 2.51 5 N 4374 2.21 5 O 4888 1.98 5 F 2 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24628 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 6512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 835, 6512 Classifications: {'peptide': 835} Link IDs: {'PTRANS': 28, 'TRANS': 806} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PTR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 6121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 6121 Classifications: {'peptide': 776} Link IDs: {'PTRANS': 28, 'TRANS': 747} Chain breaks: 1 Chain: "C" Number of atoms: 4090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 518, 4090 Classifications: {'peptide': 518} Link IDs: {'PTRANS': 21, 'TRANS': 496} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PTR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 6121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 6121 Classifications: {'peptide': 776} Link IDs: {'PTRANS': 28, 'TRANS': 747} Chain breaks: 1 Chain: "E" Number of atoms: 373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 373 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "H" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 444 Classifications: {'DNA': 22} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 21} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "G" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 414 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "F" Number of atoms: 483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 483 Classifications: {'DNA': 24} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 23} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'MFX': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'MFX': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Time building chain proxies: 4.86, per 1000 atoms: 0.20 Number of scatterers: 24628 At special positions: 0 Unit cell: (157.38, 147.06, 174.58, 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) S 87 16.00 P 84 15.00 Mg 4 11.99 F 2 9.00 O 4888 8.00 N 4374 7.00 C 15189 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.01 Conformation dependent library (CDL) restraints added in 829.6 milliseconds 5774 Ramachandran restraints generated. 2887 Oldfield, 0 Emsley, 2887 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5390 Finding SS restraints... Secondary structure from input PDB file: 109 helices and 33 sheets defined 44.2% alpha, 16.2% beta 36 base pairs and 71 stacking pairs defined. Time for finding SS restraints: 2.80 Creating SS restraints... Processing helix chain 'A' and resid 13 through 32 Processing helix chain 'A' and resid 42 through 56 removed outlier: 3.535A pdb=" N GLY A 56 " --> pdb=" O MET A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 77 Processing helix chain 'A' and resid 81 through 92 removed outlier: 4.016A pdb=" N VAL A 85 " --> pdb=" O GLY A 81 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N MET A 92 " --> pdb=" O THR A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 133 Processing helix chain 'A' and resid 164 through 170 Processing helix chain 'A' and resid 186 through 201 Processing helix chain 'A' and resid 204 through 209 Processing helix chain 'A' and resid 226 through 235 removed outlier: 3.596A pdb=" N GLU A 230 " --> pdb=" O ARG A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 283 removed outlier: 3.534A pdb=" N LEU A 273 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 324 Processing helix chain 'A' and resid 346 through 386 removed outlier: 3.652A pdb=" N ILE A 379 " --> pdb=" O ASP A 375 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA A 386 " --> pdb=" O ALA A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 400 removed outlier: 3.578A pdb=" N HIS A 399 " --> pdb=" O GLU A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 411 Processing helix chain 'A' and resid 420 through 427 removed outlier: 3.717A pdb=" N ALA A 427 " --> pdb=" O MET A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 460 Processing helix chain 'A' and resid 461 through 466 removed outlier: 6.533A pdb=" N GLN A 464 " --> pdb=" O LEU A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 493 removed outlier: 3.530A pdb=" N HIS A 471 " --> pdb=" O THR A 467 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU A 472 " --> pdb=" O GLY A 468 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LYS A 473 " --> pdb=" O LEU A 469 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N LEU A 474 " --> pdb=" O GLU A 470 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N LEU A 475 " --> pdb=" O HIS A 471 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP A 476 " --> pdb=" O GLU A 472 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE A 491 " --> pdb=" O GLU A 487 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU A 492 " --> pdb=" O LEU A 488 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLY A 493 " --> pdb=" O LEU A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 514 removed outlier: 4.014A pdb=" N MET A 499 " --> pdb=" O ALA A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 557 No H-bonds generated for 'chain 'A' and resid 555 through 557' Processing helix chain 'A' and resid 620 through 622 No H-bonds generated for 'chain 'A' and resid 620 through 622' Processing helix chain 'A' and resid 661 through 664 Processing helix chain 'A' and resid 709 through 711 No H-bonds generated for 'chain 'A' and resid 709 through 711' Processing helix chain 'A' and resid 757 through 761 removed outlier: 3.767A pdb=" N GLU A 760 " --> pdb=" O ALA A 757 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYR A 761 " --> pdb=" O VAL A 758 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 757 through 761' Processing helix chain 'B' and resid 10 through 22 removed outlier: 3.854A pdb=" N ARG B 22 " --> pdb=" O ALA B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 28 Processing helix chain 'B' and resid 33 through 53 removed outlier: 3.771A pdb=" N VAL B 40 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ALA B 53 " --> pdb=" O ASP B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 96 Processing helix chain 'B' and resid 120 through 126 Processing helix chain 'B' and resid 183 through 198 removed outlier: 3.808A pdb=" N LEU B 187 " --> pdb=" O GLU B 183 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG B 190 " --> pdb=" O ILE B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 230 Processing helix chain 'B' and resid 279 through 300 Processing helix chain 'B' and resid 301 through 306 removed outlier: 3.602A pdb=" N ALA B 306 " --> pdb=" O TYR B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 316 removed outlier: 3.647A pdb=" N ALA B 315 " --> pdb=" O THR B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 364 removed outlier: 4.150A pdb=" N SER B 347 " --> pdb=" O SER B 343 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU B 356 " --> pdb=" O GLN B 352 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ALA B 358 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N GLU B 359 " --> pdb=" O GLU B 355 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TYR B 360 " --> pdb=" O LEU B 356 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU B 361 " --> pdb=" O LEU B 357 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU B 362 " --> pdb=" O ALA B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 384 removed outlier: 3.526A pdb=" N LYS B 369 " --> pdb=" O PRO B 365 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ILE B 370 " --> pdb=" O THR B 366 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL B 371 " --> pdb=" O ASP B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 418 removed outlier: 3.707A pdb=" N SER B 418 " --> pdb=" O PRO B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 435 Processing helix chain 'B' and resid 457 through 463 Processing helix chain 'B' and resid 464 through 475 Processing helix chain 'B' and resid 500 through 518 removed outlier: 3.777A pdb=" N SER B 504 " --> pdb=" O ASP B 500 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N HIS B 505 " --> pdb=" O VAL B 501 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE B 506 " --> pdb=" O ASP B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 525 removed outlier: 3.759A pdb=" N VAL B 522 " --> pdb=" O MET B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 560 Processing helix chain 'B' and resid 576 through 597 Processing helix chain 'B' and resid 602 through 609 Processing helix chain 'B' and resid 610 through 612 No H-bonds generated for 'chain 'B' and resid 610 through 612' Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 624 through 640 removed outlier: 3.704A pdb=" N ARG B 628 " --> pdb=" O GLN B 624 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 658 Processing helix chain 'B' and resid 678 through 683 removed outlier: 3.722A pdb=" N ILE B 682 " --> pdb=" O ASP B 678 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR B 683 " --> pdb=" O HIS B 679 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 678 through 683' Processing helix chain 'B' and resid 684 through 696 removed outlier: 4.047A pdb=" N LYS B 696 " --> pdb=" O THR B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 718 through 731 Processing helix chain 'B' and resid 741 through 745 removed outlier: 3.515A pdb=" N GLU B 744 " --> pdb=" O GLY B 741 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N MET B 745 " --> pdb=" O LEU B 742 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 741 through 745' Processing helix chain 'B' and resid 746 through 755 Processing helix chain 'B' and resid 771 through 782 removed outlier: 4.119A pdb=" N GLN B 775 " --> pdb=" O ILE B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 785 through 796 Processing helix chain 'B' and resid 797 through 802 removed outlier: 3.631A pdb=" N ASN B 801 " --> pdb=" O LEU B 797 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE B 802 " --> pdb=" O LYS B 798 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 797 through 802' Processing helix chain 'C' and resid 13 through 32 Processing helix chain 'C' and resid 42 through 55 Processing helix chain 'C' and resid 66 through 77 Processing helix chain 'C' and resid 82 through 92 removed outlier: 3.610A pdb=" N MET C 92 " --> pdb=" O THR C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 133 Processing helix chain 'C' and resid 164 through 170 Processing helix chain 'C' and resid 186 through 201 Processing helix chain 'C' and resid 204 through 209 Processing helix chain 'C' and resid 226 through 235 Processing helix chain 'C' and resid 269 through 283 removed outlier: 3.766A pdb=" N GLU C 283 " --> pdb=" O GLU C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 324 removed outlier: 3.900A pdb=" N VAL C 316 " --> pdb=" O VAL C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 387 removed outlier: 3.538A pdb=" N ILE C 350 " --> pdb=" O ASN C 346 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ASP C 375 " --> pdb=" O ARG C 371 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG C 376 " --> pdb=" O LYS C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 389 through 400 Processing helix chain 'C' and resid 402 through 411 Processing helix chain 'C' and resid 420 through 427 removed outlier: 3.776A pdb=" N ALA C 427 " --> pdb=" O MET C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 460 Processing helix chain 'C' and resid 461 through 468 removed outlier: 6.428A pdb=" N GLN C 464 " --> pdb=" O LEU C 461 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N THR C 467 " --> pdb=" O GLN C 464 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N GLY C 468 " --> pdb=" O LYS C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 493 removed outlier: 4.131A pdb=" N LEU C 474 " --> pdb=" O GLU C 470 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N LEU C 475 " --> pdb=" O HIS C 471 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE C 491 " --> pdb=" O GLU C 487 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU C 492 " --> pdb=" O LEU C 488 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLY C 493 " --> pdb=" O LEU C 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 514 removed outlier: 3.667A pdb=" N VAL C 501 " --> pdb=" O ARG C 497 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE C 502 " --> pdb=" O LEU C 498 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 22 removed outlier: 4.103A pdb=" N ARG D 22 " --> pdb=" O ALA D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 28 removed outlier: 3.542A pdb=" N ILE D 27 " --> pdb=" O PRO D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 51 removed outlier: 3.722A pdb=" N VAL D 40 " --> pdb=" O LEU D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 54 No H-bonds generated for 'chain 'D' and resid 52 through 54' Processing helix chain 'D' and resid 89 through 97 Processing helix chain 'D' and resid 120 through 126 Processing helix chain 'D' and resid 184 through 198 removed outlier: 3.632A pdb=" N ARG D 190 " --> pdb=" O ILE D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 230 Processing helix chain 'D' and resid 279 through 301 removed outlier: 3.685A pdb=" N ALA D 283 " --> pdb=" O GLY D 279 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLY D 284 " --> pdb=" O THR D 280 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N PHE D 285 " --> pdb=" O HIS D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 306 Processing helix chain 'D' and resid 311 through 316 removed outlier: 3.671A pdb=" N ALA D 315 " --> pdb=" O THR D 311 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG D 316 " --> pdb=" O GLY D 312 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 311 through 316' Processing helix chain 'D' and resid 344 through 362 removed outlier: 3.931A pdb=" N ALA D 348 " --> pdb=" O GLU D 344 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN D 352 " --> pdb=" O ALA D 348 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ALA D 358 " --> pdb=" O ASN D 354 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLU D 359 " --> pdb=" O GLU D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 364 through 384 removed outlier: 3.662A pdb=" N ALA D 368 " --> pdb=" O ASN D 364 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA D 384 " --> pdb=" O ARG D 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 418 removed outlier: 3.714A pdb=" N SER D 418 " --> pdb=" O PRO D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 435 removed outlier: 3.663A pdb=" N GLN D 434 " --> pdb=" O GLY D 430 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY D 435 " --> pdb=" O SER D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 457 through 463 Processing helix chain 'D' and resid 464 through 475 Processing helix chain 'D' and resid 500 through 518 Processing helix chain 'D' and resid 518 through 524 removed outlier: 3.798A pdb=" N VAL D 522 " --> pdb=" O MET D 518 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 560 Processing helix chain 'D' and resid 576 through 597 Processing helix chain 'D' and resid 602 through 608 removed outlier: 3.935A pdb=" N GLU D 608 " --> pdb=" O ALA D 604 " (cutoff:3.500A) Processing helix chain 'D' and resid 609 through 611 No H-bonds generated for 'chain 'D' and resid 609 through 611' Processing helix chain 'D' and resid 616 through 622 Processing helix chain 'D' and resid 624 through 640 removed outlier: 3.514A pdb=" N ARG D 628 " --> pdb=" O GLN D 624 " (cutoff:3.500A) Processing helix chain 'D' and resid 678 through 684 Processing helix chain 'D' and resid 686 through 698 removed outlier: 3.813A pdb=" N LYS D 696 " --> pdb=" O THR D 692 " (cutoff:3.500A) Processing helix chain 'D' and resid 718 through 731 removed outlier: 3.608A pdb=" N SER D 730 " --> pdb=" O LEU D 726 " (cutoff:3.500A) Processing helix chain 'D' and resid 741 through 745 removed outlier: 3.583A pdb=" N MET D 745 " --> pdb=" O LEU D 742 " (cutoff:3.500A) Processing helix chain 'D' and resid 746 through 755 Processing helix chain 'D' and resid 771 through 782 removed outlier: 3.970A pdb=" N GLN D 775 " --> pdb=" O ILE D 771 " (cutoff:3.500A) Processing helix chain 'D' and resid 785 through 797 Processing helix chain 'D' and resid 797 through 802 Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 12 removed outlier: 6.624A pdb=" N THR A 9 " --> pdb=" O ARG B 764 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N THR B 766 " --> pdb=" O THR A 9 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N VAL A 11 " --> pdb=" O THR B 766 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N VAL B 527 " --> pdb=" O VAL B 765 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ILE B 493 " --> pdb=" O TYR B 528 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N ALA B 530 " --> pdb=" O ILE B 493 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N ILE B 495 " --> pdb=" O ALA B 530 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N LEU B 420 " --> pdb=" O ILE B 494 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N MET B 496 " --> pdb=" O LEU B 420 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N LEU B 422 " --> pdb=" O MET B 496 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLU B 419 " --> pdb=" O ALA B 442 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N LEU B 444 " --> pdb=" O GLU B 419 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N TYR B 421 " --> pdb=" O LEU B 444 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 64 through 65 Processing sheet with id=AA3, first strand: chain 'A' and resid 145 through 147 Processing sheet with id=AA4, first strand: chain 'A' and resid 171 through 174 removed outlier: 3.501A pdb=" N GLY A 173 " --> pdb=" O THR A 180 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 327 through 333 removed outlier: 4.573A pdb=" N TYR A 241 " --> pdb=" O ASN A 224 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 245 through 250 removed outlier: 6.773A pdb=" N ARG A 245 " --> pdb=" O HIS A 262 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N GLU A 257 " --> pdb=" O VAL A 307 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL A 307 " --> pdb=" O GLU A 257 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N VAL A 304 " --> pdb=" O LEU A 292 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N LEU A 292 " --> pdb=" O VAL A 304 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N GLU A 306 " --> pdb=" O SER A 290 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 335 through 338 Processing sheet with id=AA8, first strand: chain 'A' and resid 415 through 416 Processing sheet with id=AA9, first strand: chain 'A' and resid 578 through 585 removed outlier: 3.955A pdb=" N ARG A 580 " --> pdb=" O LEU A 543 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU A 543 " --> pdb=" O ARG A 580 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS A 550 " --> pdb=" O THR A 542 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER A 544 " --> pdb=" O TYR A 548 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N TYR A 548 " --> pdb=" O SER A 544 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG A 617 " --> pdb=" O VAL A 549 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 599 through 603 removed outlier: 3.840A pdb=" N ALA A 633 " --> pdb=" O PHE A 593 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 682 through 688 removed outlier: 4.172A pdb=" N THR A 654 " --> pdb=" O THR A 650 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 703 through 707 removed outlier: 3.946A pdb=" N SER A 734 " --> pdb=" O PHE A 697 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 752 through 753 removed outlier: 3.569A pdb=" N GLY A 753 " --> pdb=" O VAL A 822 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL A 822 " --> pdb=" O GLY A 753 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 802 through 808 removed outlier: 4.644A pdb=" N LEU A 804 " --> pdb=" O MET A 797 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N MET A 797 " --> pdb=" O LEU A 804 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ARG A 806 " --> pdb=" O ILE A 795 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ILE A 795 " --> pdb=" O ARG A 806 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE A 798 " --> pdb=" O GLY A 835 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 149 through 150 removed outlier: 6.546A pdb=" N ARG B 142 " --> pdb=" O VAL B 156 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N VAL B 156 " --> pdb=" O ARG B 142 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 149 through 150 removed outlier: 3.922A pdb=" N ILE B 134 " --> pdb=" O HIS B 141 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS B 129 " --> pdb=" O TRP B 170 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N THR B 165 " --> pdb=" O ASP B 73 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL B 69 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASP B 207 " --> pdb=" O LYS B 212 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 241 through 247 removed outlier: 3.675A pdb=" N PHE B 241 " --> pdb=" O LEU B 256 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ASN B 265 " --> pdb=" O ALA B 321 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N VAL B 323 " --> pdb=" O ASN B 265 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N TYR B 267 " --> pdb=" O VAL B 323 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N VAL B 325 " --> pdb=" O TYR B 267 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N PHE B 269 " --> pdb=" O VAL B 325 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N CYS B 268 " --> pdb=" O GLN B 275 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 542 through 546 removed outlier: 3.592A pdb=" N GLN B 542 " --> pdb=" O LYS B 539 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 565 through 566 Processing sheet with id=AC2, first strand: chain 'B' and resid 645 through 653 removed outlier: 3.539A pdb=" N VAL B 664 " --> pdb=" O TYR B 675 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 8 through 12 removed outlier: 6.451A pdb=" N THR C 9 " --> pdb=" O ARG D 764 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N THR D 766 " --> pdb=" O THR C 9 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N VAL C 11 " --> pdb=" O THR D 766 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N VAL D 527 " --> pdb=" O VAL D 765 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ILE D 493 " --> pdb=" O TYR D 528 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N ALA D 530 " --> pdb=" O ILE D 493 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ILE D 495 " --> pdb=" O ALA D 530 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LEU D 420 " --> pdb=" O ILE D 494 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N MET D 496 " --> pdb=" O LEU D 420 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N LEU D 422 " --> pdb=" O MET D 496 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N GLU D 419 " --> pdb=" O ALA D 442 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N LEU D 444 " --> pdb=" O GLU D 419 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N TYR D 421 " --> pdb=" O LEU D 444 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 64 through 65 Processing sheet with id=AC5, first strand: chain 'C' and resid 145 through 147 Processing sheet with id=AC6, first strand: chain 'C' and resid 171 through 174 Processing sheet with id=AC7, first strand: chain 'C' and resid 327 through 333 removed outlier: 4.463A pdb=" N TYR C 241 " --> pdb=" O ASN C 224 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 245 through 250 removed outlier: 6.768A pdb=" N ARG C 245 " --> pdb=" O HIS C 262 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N GLU C 257 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL C 307 " --> pdb=" O GLU C 257 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ALA C 291 " --> pdb=" O GLU C 306 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 335 through 338 Processing sheet with id=AD1, first strand: chain 'C' and resid 415 through 416 Processing sheet with id=AD2, first strand: chain 'D' and resid 149 through 158 removed outlier: 6.995A pdb=" N ILE D 144 " --> pdb=" O GLN D 151 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ARG D 142 " --> pdb=" O PRO D 153 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N ALA D 155 " --> pdb=" O ILE D 140 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N ILE D 140 " --> pdb=" O ALA D 155 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N LYS D 129 " --> pdb=" O TRP D 170 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLN D 135 " --> pdb=" O GLY D 164 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N PHE D 169 " --> pdb=" O VAL D 69 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N VAL D 69 " --> pdb=" O PHE D 169 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N SER D 68 " --> pdb=" O HIS D 64 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR D 62 " --> pdb=" O SER D 70 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ILE D 59 " --> pdb=" O ARG D 204 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N ARG D 206 " --> pdb=" O ILE D 59 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N VAL D 61 " --> pdb=" O ARG D 206 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 241 through 246 removed outlier: 3.702A pdb=" N PHE D 241 " --> pdb=" O LEU D 256 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL D 252 " --> pdb=" O THR D 245 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ASN D 265 " --> pdb=" O ALA D 321 " (cutoff:3.500A) removed outlier: 8.229A pdb=" N VAL D 323 " --> pdb=" O ASN D 265 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N TYR D 267 " --> pdb=" O VAL D 323 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N VAL D 325 " --> pdb=" O TYR D 267 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N PHE D 269 " --> pdb=" O VAL D 325 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N CYS D 268 " --> pdb=" O GLN D 275 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 542 through 546 removed outlier: 3.552A pdb=" N GLN D 542 " --> pdb=" O LYS D 539 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 566 through 567 removed outlier: 3.644A pdb=" N HIS D 567 " --> pdb=" O PHE D 706 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N PHE D 706 " --> pdb=" O HIS D 567 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 648 through 653 removed outlier: 3.756A pdb=" N VAL D 664 " --> pdb=" O TYR D 675 " (cutoff:3.500A) 1041 hydrogen bonds defined for protein. 2952 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 86 hydrogen bonds 172 hydrogen bond angles 0 basepair planarities 36 basepair parallelities 71 stacking parallelities Total time for adding SS restraints: 4.94 Time building geometry restraints manager: 2.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6381 1.33 - 1.45: 4492 1.45 - 1.57: 13996 1.57 - 1.69: 164 1.69 - 1.81: 159 Bond restraints: 25192 Sorted by residual: bond pdb=" OH PTR A 122 " pdb=" P PTR A 122 " ideal model delta sigma weight residual 1.769 1.611 0.158 2.00e-02 2.50e+03 6.23e+01 bond pdb=" OH PTR C 122 " pdb=" P PTR C 122 " ideal model delta sigma weight residual 1.769 1.612 0.157 2.00e-02 2.50e+03 6.14e+01 bond pdb=" C3' DC H 11 " pdb=" C2' DC H 11 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.72e+00 bond pdb=" C20 MFX H 201 " pdb=" O03 MFX H 201 " ideal model delta sigma weight residual 1.242 1.303 -0.061 2.00e-02 2.50e+03 9.31e+00 bond pdb=" C1' DT H 3 " pdb=" N1 DT H 3 " ideal model delta sigma weight residual 1.468 1.511 -0.043 1.40e-02 5.10e+03 9.31e+00 ... (remaining 25187 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.30: 34086 2.30 - 4.59: 299 4.59 - 6.89: 22 6.89 - 9.18: 4 9.18 - 11.48: 2 Bond angle restraints: 34413 Sorted by residual: angle pdb=" C ALA C 220 " pdb=" CA ALA C 220 " pdb=" CB ALA C 220 " ideal model delta sigma weight residual 116.63 110.48 6.15 1.16e+00 7.43e-01 2.81e+01 angle pdb=" C ALA A 220 " pdb=" CA ALA A 220 " pdb=" CB ALA A 220 " ideal model delta sigma weight residual 116.63 110.52 6.11 1.16e+00 7.43e-01 2.77e+01 angle pdb=" O4' DC F 8 " pdb=" C4' DC F 8 " pdb=" C3' DC F 8 " ideal model delta sigma weight residual 106.00 103.12 2.88 6.00e-01 2.78e+00 2.30e+01 angle pdb=" O4' DT F 17 " pdb=" C4' DT F 17 " pdb=" C3' DT F 17 " ideal model delta sigma weight residual 106.00 103.13 2.87 6.00e-01 2.78e+00 2.28e+01 angle pdb=" O4' DT F 16 " pdb=" C4' DT F 16 " pdb=" C3' DT F 16 " ideal model delta sigma weight residual 106.00 103.26 2.74 6.00e-01 2.78e+00 2.08e+01 ... (remaining 34408 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.99: 14786 34.99 - 69.98: 456 69.98 - 104.98: 13 104.98 - 139.97: 3 139.97 - 174.96: 4 Dihedral angle restraints: 15262 sinusoidal: 6886 harmonic: 8376 Sorted by residual: dihedral pdb=" C08 MFX F 201 " pdb=" N MFX F 201 " pdb=" C06 MFX F 201 " pdb=" C12 MFX F 201 " ideal model delta sinusoidal sigma weight residual 290.45 146.30 144.15 1 3.00e+01 1.11e-03 1.93e+01 dihedral pdb=" C08 MFX H 201 " pdb=" N MFX H 201 " pdb=" C06 MFX H 201 " pdb=" C12 MFX H 201 " ideal model delta sinusoidal sigma weight residual 290.45 148.03 142.42 1 3.00e+01 1.11e-03 1.91e+01 dihedral pdb=" C02 MFX H 201 " pdb=" C10 MFX H 201 " pdb=" N02 MFX H 201 " pdb=" C07 MFX H 201 " ideal model delta sinusoidal sigma weight residual 65.19 -60.75 125.94 1 3.00e+01 1.11e-03 1.69e+01 ... (remaining 15259 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 2404 0.030 - 0.061: 940 0.061 - 0.091: 303 0.091 - 0.121: 214 0.121 - 0.152: 25 Chirality restraints: 3886 Sorted by residual: chirality pdb=" CA ILE C 163 " pdb=" N ILE C 163 " pdb=" C ILE C 163 " pdb=" CB ILE C 163 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.76e-01 chirality pdb=" CA ILE A 163 " pdb=" N ILE A 163 " pdb=" C ILE A 163 " pdb=" CB ILE A 163 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.47e-01 chirality pdb=" CA ILE B 663 " pdb=" N ILE B 663 " pdb=" C ILE B 663 " pdb=" CB ILE B 663 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.78e-01 ... (remaining 3883 not shown) Planarity restraints: 4200 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" N MFX F 201 " -0.048 2.00e-02 2.50e+03 1.10e-01 4.84e+02 pdb=" C06 MFX F 201 " -0.284 2.00e-02 2.50e+03 pdb=" C11 MFX F 201 " 0.017 2.00e-02 2.50e+03 pdb=" C12 MFX F 201 " -0.001 2.00e-02 2.50e+03 pdb=" C13 MFX F 201 " 0.063 2.00e-02 2.50e+03 pdb=" C14 MFX F 201 " -0.018 2.00e-02 2.50e+03 pdb=" C15 MFX F 201 " -0.018 2.00e-02 2.50e+03 pdb=" C16 MFX F 201 " 0.009 2.00e-02 2.50e+03 pdb=" C17 MFX F 201 " -0.041 2.00e-02 2.50e+03 pdb=" C18 MFX F 201 " 0.026 2.00e-02 2.50e+03 pdb=" C19 MFX F 201 " 0.008 2.00e-02 2.50e+03 pdb=" C20 MFX F 201 " 0.097 2.00e-02 2.50e+03 pdb=" F MFX F 201 " -0.063 2.00e-02 2.50e+03 pdb=" N01 MFX F 201 " -0.047 2.00e-02 2.50e+03 pdb=" O01 MFX F 201 " 0.296 2.00e-02 2.50e+03 pdb=" O02 MFX F 201 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N MFX H 201 " 0.043 2.00e-02 2.50e+03 9.22e-02 3.40e+02 pdb=" C06 MFX H 201 " 0.235 2.00e-02 2.50e+03 pdb=" C11 MFX H 201 " -0.014 2.00e-02 2.50e+03 pdb=" C12 MFX H 201 " 0.012 2.00e-02 2.50e+03 pdb=" C13 MFX H 201 " -0.048 2.00e-02 2.50e+03 pdb=" C14 MFX H 201 " 0.028 2.00e-02 2.50e+03 pdb=" C15 MFX H 201 " 0.018 2.00e-02 2.50e+03 pdb=" C16 MFX H 201 " -0.012 2.00e-02 2.50e+03 pdb=" C17 MFX H 201 " 0.048 2.00e-02 2.50e+03 pdb=" C18 MFX H 201 " -0.027 2.00e-02 2.50e+03 pdb=" C19 MFX H 201 " -0.000 2.00e-02 2.50e+03 pdb=" C20 MFX H 201 " -0.109 2.00e-02 2.50e+03 pdb=" F MFX H 201 " 0.031 2.00e-02 2.50e+03 pdb=" N01 MFX H 201 " 0.024 2.00e-02 2.50e+03 pdb=" O01 MFX H 201 " -0.242 2.00e-02 2.50e+03 pdb=" O02 MFX H 201 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG F 9 " 0.025 2.00e-02 2.50e+03 1.04e-02 3.22e+00 pdb=" N9 DG F 9 " -0.024 2.00e-02 2.50e+03 pdb=" C8 DG F 9 " -0.004 2.00e-02 2.50e+03 pdb=" N7 DG F 9 " 0.000 2.00e-02 2.50e+03 pdb=" C5 DG F 9 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DG F 9 " 0.004 2.00e-02 2.50e+03 pdb=" O6 DG F 9 " 0.006 2.00e-02 2.50e+03 pdb=" N1 DG F 9 " 0.002 2.00e-02 2.50e+03 pdb=" C2 DG F 9 " -0.001 2.00e-02 2.50e+03 pdb=" N2 DG F 9 " -0.001 2.00e-02 2.50e+03 pdb=" N3 DG F 9 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DG F 9 " -0.003 2.00e-02 2.50e+03 ... (remaining 4197 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 90 2.46 - 3.07: 15507 3.07 - 3.68: 34070 3.68 - 4.29: 50213 4.29 - 4.90: 85503 Nonbonded interactions: 185383 Sorted by model distance: nonbonded pdb="MG MG C 901 " pdb=" O03 MFX H 201 " model vdw 1.848 2.170 nonbonded pdb="MG MG C 901 " pdb=" O02 MFX H 201 " model vdw 1.858 2.170 nonbonded pdb="MG MG C 901 " pdb=" O HOH H 301 " model vdw 1.875 2.170 nonbonded pdb="MG MG A 901 " pdb=" O03 MFX F 201 " model vdw 1.876 2.170 nonbonded pdb="MG MG C 901 " pdb=" O HOH H 303 " model vdw 1.877 2.170 ... (remaining 185378 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'D' } 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: 13.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.530 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 23.290 Find NCS groups from input model: 0.320 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:7.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 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 0.183 25194 Z= 0.302 Angle : 0.537 11.476 34413 Z= 0.367 Chirality : 0.042 0.152 3886 Planarity : 0.004 0.110 4200 Dihedral : 14.798 174.962 9872 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.37 % Allowed : 5.05 % Favored : 94.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.16), residues: 2887 helix: 2.21 (0.16), residues: 1086 sheet: 0.16 (0.23), residues: 540 loop : -1.71 (0.15), residues: 1261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 709 TYR 0.013 0.001 TYR A 266 PHE 0.010 0.001 PHE B 285 TRP 0.010 0.001 TRP D 725 HIS 0.004 0.001 HIS D 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.25 (25192) covalent geometry : angle 0.53728 / 0.37 (34413) hydrogen bonds : bond 0.19624 / 13.12 ( 1125) hydrogen bonds : angle 5.96192 / 4.19 ( 3124) Misc. bond : bond 0.18307 / 9.19 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5774 Ramachandran restraints generated. 2887 Oldfield, 0 Emsley, 2887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5774 Ramachandran restraints generated. 2887 Oldfield, 0 Emsley, 2887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 217 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 625 LEU cc_start: 0.7666 (mt) cc_final: 0.7278 (pp) REVERT: A 648 MET cc_start: 0.8597 (mtp) cc_final: 0.8351 (mpp) REVERT: A 696 LEU cc_start: 0.8154 (mt) cc_final: 0.7695 (tt) REVERT: A 797 MET cc_start: 0.8950 (mtp) cc_final: 0.8696 (mpp) REVERT: B 95 MET cc_start: 0.6974 (mmm) cc_final: 0.6690 (mpm) REVERT: B 145 TYR cc_start: 0.7674 (m-80) cc_final: 0.7033 (m-80) REVERT: B 166 MET cc_start: 0.7307 (tmm) cc_final: 0.6612 (tmm) REVERT: B 193 GLU cc_start: 0.9232 (mt-10) cc_final: 0.8915 (tm-30) REVERT: C 284 LYS cc_start: 0.8819 (mttp) cc_final: 0.8556 (tppt) REVERT: C 286 VAL cc_start: 0.9092 (p) cc_final: 0.8786 (m) REVERT: D 41 PHE cc_start: 0.9248 (m-10) cc_final: 0.8888 (m-80) REVERT: D 145 TYR cc_start: 0.8707 (m-80) cc_final: 0.8370 (m-80) REVERT: D 187 LEU cc_start: 0.9560 (mt) cc_final: 0.9173 (pt) REVERT: D 482 GLU cc_start: 0.8448 (tt0) cc_final: 0.8120 (tp30) REVERT: D 781 MET cc_start: 0.8906 (mmt) cc_final: 0.8568 (mmt) REVERT: D 802 ILE cc_start: 0.7611 (mt) cc_final: 0.7163 (pt) outliers start: 9 outliers final: 4 residues processed: 225 average time/residue: 0.6325 time to fit residues: 162.8610 Evaluate side-chains 142 residues out of total 2438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 138 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 707 ILE Chi-restraints excluded: chain D residue 666 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 587 HIS B 643 HIS B 721 GLN B 801 ASN D 569 ASN D 638 ASN D 646 GLN D 658 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.110388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.060159 restraints weight = 55186.086| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 2.47 r_work: 0.2818 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2713 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8933 moved from start: 0.1079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 25194 Z= 0.190 Angle : 0.612 9.421 34413 Z= 0.332 Chirality : 0.046 0.213 3886 Planarity : 0.005 0.050 4200 Dihedral : 16.845 168.358 4233 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.64 % Allowed : 8.04 % Favored : 90.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.16), residues: 2887 helix: 1.99 (0.16), residues: 1150 sheet: 0.31 (0.24), residues: 511 loop : -1.66 (0.15), residues: 1226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 309 TYR 0.014 0.001 TYR A 266 PHE 0.028 0.002 PHE B 169 TRP 0.007 0.001 TRP D 170 HIS 0.005 0.001 HIS C 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.19 (25192) covalent geometry : angle 0.61172 / 0.33 (34413) hydrogen bonds : bond 0.07043 / 4.63 ( 1125) hydrogen bonds : angle 4.87697 / 3.40 ( 3124) Misc. bond : bond 0.00370 / 0.19 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5774 Ramachandran restraints generated. 2887 Oldfield, 0 Emsley, 2887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5774 Ramachandran restraints generated. 2887 Oldfield, 0 Emsley, 2887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 2438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 143 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 625 LEU cc_start: 0.7609 (mt) cc_final: 0.7221 (pp) REVERT: A 696 LEU cc_start: 0.7984 (mt) cc_final: 0.7718 (tt) REVERT: A 797 MET cc_start: 0.9269 (mtp) cc_final: 0.8879 (tmm) REVERT: B 71 VAL cc_start: 0.8625 (t) cc_final: 0.8366 (m) REVERT: B 145 TYR cc_start: 0.7699 (m-80) cc_final: 0.6990 (m-80) REVERT: B 169 PHE cc_start: 0.8762 (p90) cc_final: 0.8536 (p90) REVERT: B 643 HIS cc_start: 0.8162 (m-70) cc_final: 0.7852 (m90) REVERT: D 72 GLN cc_start: 0.9271 (tt0) cc_final: 0.9020 (tp40) REVERT: D 187 LEU cc_start: 0.9568 (mt) cc_final: 0.9195 (pt) REVERT: D 264 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.8403 (tt0) REVERT: D 482 GLU cc_start: 0.8818 (tt0) cc_final: 0.8153 (tp30) REVERT: D 781 MET cc_start: 0.9068 (mmt) cc_final: 0.8857 (mmt) REVERT: D 802 ILE cc_start: 0.7088 (mt) cc_final: 0.6796 (pt) outliers start: 40 outliers final: 13 residues processed: 171 average time/residue: 0.5522 time to fit residues: 109.7559 Evaluate side-chains 144 residues out of total 2438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 130 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 825 ILE Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 707 ILE Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain D residue 39 MET Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 264 GLU Chi-restraints excluded: chain D residue 362 LEU Chi-restraints excluded: chain D residue 666 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 206 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 151 optimal weight: 20.0000 chunk 260 optimal weight: 2.9990 chunk 248 optimal weight: 3.9990 chunk 81 optimal weight: 0.0570 chunk 179 optimal weight: 0.5980 chunk 186 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 148 optimal weight: 6.9990 overall best weight: 1.7304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 589 HIS B 354 ASN B 643 HIS B 801 ASN D 646 GLN D 658 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.110553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.060623 restraints weight = 55124.171| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 2.45 r_work: 0.2825 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8931 moved from start: 0.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 25194 Z= 0.167 Angle : 0.568 9.135 34413 Z= 0.309 Chirality : 0.044 0.193 3886 Planarity : 0.004 0.038 4200 Dihedral : 16.681 170.588 4231 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.72 % Allowed : 9.06 % Favored : 89.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.15), residues: 2887 helix: 2.05 (0.15), residues: 1151 sheet: 0.49 (0.23), residues: 520 loop : -1.71 (0.15), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 291 TYR 0.013 0.001 TYR A 266 PHE 0.025 0.001 PHE B 169 TRP 0.006 0.001 TRP B 629 HIS 0.004 0.001 HIS C 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.17 (25192) covalent geometry : angle 0.56751 / 0.31 (34413) hydrogen bonds : bond 0.06487 / 4.23 ( 1125) hydrogen bonds : angle 4.62846 / 3.22 ( 3124) Misc. bond : bond 0.00328 / 0.17 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5774 Ramachandran restraints generated. 2887 Oldfield, 0 Emsley, 2887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5774 Ramachandran restraints generated. 2887 Oldfield, 0 Emsley, 2887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 2438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 131 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 648 MET cc_start: 0.8247 (mtm) cc_final: 0.7853 (mpp) REVERT: A 696 LEU cc_start: 0.8008 (mt) cc_final: 0.7680 (tt) REVERT: A 797 MET cc_start: 0.9319 (mtp) cc_final: 0.8906 (tmm) REVERT: B 169 PHE cc_start: 0.8742 (p90) cc_final: 0.8503 (p90) REVERT: B 781 MET cc_start: 0.9032 (OUTLIER) cc_final: 0.7916 (mmm) REVERT: D 72 GLN cc_start: 0.9232 (tt0) cc_final: 0.9007 (tp40) REVERT: D 187 LEU cc_start: 0.9564 (mt) cc_final: 0.9199 (pt) REVERT: D 264 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.8340 (tt0) REVERT: D 482 GLU cc_start: 0.8793 (tt0) cc_final: 0.8183 (tp30) REVERT: D 781 MET cc_start: 0.9062 (mmt) cc_final: 0.8806 (mmt) outliers start: 42 outliers final: 20 residues processed: 163 average time/residue: 0.5348 time to fit residues: 102.0796 Evaluate side-chains 145 residues out of total 2438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 123 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 423 MET Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 789 VAL Chi-restraints excluded: chain A residue 825 ILE Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 707 ILE Chi-restraints excluded: chain B residue 781 MET Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 390 ILE Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain D residue 39 MET Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 264 GLU Chi-restraints excluded: chain D residue 646 GLN Chi-restraints excluded: chain D residue 666 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 226 optimal weight: 10.0000 chunk 79 optimal weight: 7.9990 chunk 215 optimal weight: 10.0000 chunk 36 optimal weight: 1.9990 chunk 238 optimal weight: 0.5980 chunk 282 optimal weight: 3.9990 chunk 212 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 190 optimal weight: 0.9990 chunk 173 optimal weight: 0.0870 chunk 113 optimal weight: 1.9990 overall best weight: 1.1364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 589 HIS C 413 ASN D 658 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.111142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.061355 restraints weight = 54991.600| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 2.47 r_work: 0.2846 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2742 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8924 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25194 Z= 0.133 Angle : 0.536 8.921 34413 Z= 0.292 Chirality : 0.043 0.193 3886 Planarity : 0.004 0.050 4200 Dihedral : 16.668 170.222 4231 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.56 % Allowed : 9.68 % Favored : 88.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.16), residues: 2887 helix: 2.16 (0.15), residues: 1154 sheet: 0.55 (0.23), residues: 515 loop : -1.68 (0.15), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 826 TYR 0.012 0.001 TYR A 266 PHE 0.021 0.001 PHE B 169 TRP 0.006 0.001 TRP B 629 HIS 0.003 0.001 HIS C 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (25192) covalent geometry : angle 0.53602 / 0.29 (34413) hydrogen bonds : bond 0.05679 / 3.71 ( 1125) hydrogen bonds : angle 4.41824 / 3.06 ( 3124) Misc. bond : bond 0.00021 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5774 Ramachandran restraints generated. 2887 Oldfield, 0 Emsley, 2887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5774 Ramachandran restraints generated. 2887 Oldfield, 0 Emsley, 2887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 2438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 129 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 797 MET cc_start: 0.9304 (mtp) cc_final: 0.8894 (tmm) REVERT: B 206 ARG cc_start: 0.8526 (OUTLIER) cc_final: 0.8294 (pmm-80) REVERT: D 72 GLN cc_start: 0.9247 (tt0) cc_final: 0.9019 (tp40) REVERT: D 264 GLU cc_start: 0.8692 (OUTLIER) cc_final: 0.8430 (tt0) REVERT: D 482 GLU cc_start: 0.8805 (tt0) cc_final: 0.8211 (tp30) REVERT: D 781 MET cc_start: 0.9000 (mmt) cc_final: 0.8745 (mmt) outliers start: 38 outliers final: 21 residues processed: 158 average time/residue: 0.5714 time to fit residues: 105.0054 Evaluate side-chains 148 residues out of total 2438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 125 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 423 MET Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 789 VAL Chi-restraints excluded: chain A residue 825 ILE Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 206 ARG Chi-restraints excluded: chain B residue 461 MET Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain B residue 707 ILE Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 390 ILE Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain D residue 39 MET Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 264 GLU Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain D residue 362 LEU Chi-restraints excluded: chain D residue 666 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 134 optimal weight: 0.4980 chunk 69 optimal weight: 20.0000 chunk 27 optimal weight: 3.9990 chunk 99 optimal weight: 8.9990 chunk 72 optimal weight: 6.9990 chunk 152 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 chunk 291 optimal weight: 20.0000 chunk 46 optimal weight: 2.9990 chunk 92 optimal weight: 20.0000 chunk 85 optimal weight: 1.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 652 ASN C 413 ASN D 646 GLN D 658 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.110103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.060094 restraints weight = 54852.828| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 2.43 r_work: 0.2810 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2705 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8938 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 25194 Z= 0.186 Angle : 0.574 9.078 34413 Z= 0.312 Chirality : 0.045 0.199 3886 Planarity : 0.004 0.041 4200 Dihedral : 16.673 169.720 4231 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.05 % Allowed : 10.38 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.15), residues: 2887 helix: 2.07 (0.15), residues: 1157 sheet: 0.48 (0.23), residues: 525 loop : -1.70 (0.15), residues: 1205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 291 TYR 0.012 0.001 TYR C 21 PHE 0.019 0.001 PHE A 706 TRP 0.008 0.001 TRP D 725 HIS 0.004 0.001 HIS C 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.19 (25192) covalent geometry : angle 0.57438 / 0.31 (34413) hydrogen bonds : bond 0.06678 / 4.34 ( 1125) hydrogen bonds : angle 4.39124 / 3.04 ( 3124) Misc. bond : bond 0.00034 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5774 Ramachandran restraints generated. 2887 Oldfield, 0 Emsley, 2887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5774 Ramachandran restraints generated. 2887 Oldfield, 0 Emsley, 2887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 132 time to evaluate : 0.765 Fit side-chains revert: symmetry clash REVERT: A 648 MET cc_start: 0.8012 (mtm) cc_final: 0.7751 (mpp) REVERT: A 686 ASP cc_start: 0.8208 (t0) cc_final: 0.7499 (p0) REVERT: A 797 MET cc_start: 0.9301 (mtp) cc_final: 0.8869 (tmm) REVERT: B 206 ARG cc_start: 0.8521 (OUTLIER) cc_final: 0.8310 (pmm-80) REVERT: D 41 PHE cc_start: 0.9205 (m-10) cc_final: 0.8754 (m-80) REVERT: D 72 GLN cc_start: 0.9235 (tt0) cc_final: 0.8992 (tp40) REVERT: D 222 ILE cc_start: 0.7492 (mp) cc_final: 0.7282 (mm) REVERT: D 264 GLU cc_start: 0.8721 (OUTLIER) cc_final: 0.8413 (tt0) REVERT: D 482 GLU cc_start: 0.8784 (tt0) cc_final: 0.8173 (tp30) REVERT: D 686 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.8050 (pm20) REVERT: D 781 MET cc_start: 0.9038 (mmt) cc_final: 0.8738 (mmt) outliers start: 50 outliers final: 26 residues processed: 173 average time/residue: 0.5291 time to fit residues: 106.8980 Evaluate side-chains 154 residues out of total 2438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 125 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 423 MET Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 789 VAL Chi-restraints excluded: chain A residue 825 ILE Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 206 ARG Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 707 ILE Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 390 ILE Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 39 MET Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 264 GLU Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain D residue 362 LEU Chi-restraints excluded: chain D residue 646 GLN Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 686 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 107 optimal weight: 2.9990 chunk 135 optimal weight: 2.9990 chunk 214 optimal weight: 2.9990 chunk 212 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 13 optimal weight: 0.3980 chunk 235 optimal weight: 1.9990 chunk 193 optimal weight: 0.9990 chunk 281 optimal weight: 6.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 652 ASN C 413 ASN D 658 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.110503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.060566 restraints weight = 54889.658| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 2.44 r_work: 0.2825 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2720 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8933 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 25194 Z= 0.162 Angle : 0.560 9.066 34413 Z= 0.303 Chirality : 0.044 0.198 3886 Planarity : 0.004 0.062 4200 Dihedral : 16.683 170.284 4231 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.80 % Allowed : 10.91 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.16), residues: 2887 helix: 2.12 (0.15), residues: 1155 sheet: 0.50 (0.23), residues: 519 loop : -1.70 (0.15), residues: 1213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 291 TYR 0.011 0.001 TYR A 266 PHE 0.029 0.001 PHE B 169 TRP 0.017 0.001 TRP D 647 HIS 0.004 0.001 HIS C 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (25192) covalent geometry : angle 0.55995 / 0.30 (34413) hydrogen bonds : bond 0.06176 / 4.02 ( 1125) hydrogen bonds : angle 4.30839 / 2.98 ( 3124) Misc. bond : bond 0.00029 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5774 Ramachandran restraints generated. 2887 Oldfield, 0 Emsley, 2887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5774 Ramachandran restraints generated. 2887 Oldfield, 0 Emsley, 2887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 2438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 128 time to evaluate : 0.975 Fit side-chains revert: symmetry clash REVERT: A 648 MET cc_start: 0.8028 (mtm) cc_final: 0.7687 (mpp) REVERT: A 686 ASP cc_start: 0.8218 (t0) cc_final: 0.7452 (p0) REVERT: A 797 MET cc_start: 0.9289 (mtp) cc_final: 0.8873 (tmm) REVERT: B 206 ARG cc_start: 0.8510 (OUTLIER) cc_final: 0.8305 (pmm-80) REVERT: B 781 MET cc_start: 0.8993 (OUTLIER) cc_final: 0.7906 (mmm) REVERT: D 41 PHE cc_start: 0.9231 (m-10) cc_final: 0.8803 (m-80) REVERT: D 72 GLN cc_start: 0.9216 (tt0) cc_final: 0.8971 (tp-100) REVERT: D 264 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.8407 (tt0) REVERT: D 482 GLU cc_start: 0.8774 (tt0) cc_final: 0.8177 (tp30) REVERT: D 686 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.8011 (pm20) REVERT: D 781 MET cc_start: 0.9016 (mmt) cc_final: 0.8720 (mmt) outliers start: 44 outliers final: 26 residues processed: 162 average time/residue: 0.6245 time to fit residues: 117.7529 Evaluate side-chains 156 residues out of total 2438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 126 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 423 MET Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 695 MET Chi-restraints excluded: chain A residue 789 VAL Chi-restraints excluded: chain A residue 825 ILE Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 206 ARG Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 707 ILE Chi-restraints excluded: chain B residue 781 MET Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 390 ILE Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 264 GLU Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain D residue 362 LEU Chi-restraints excluded: chain D residue 616 THR Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 686 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 254 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 chunk 252 optimal weight: 0.9990 chunk 260 optimal weight: 2.9990 chunk 108 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 161 optimal weight: 2.9990 chunk 293 optimal weight: 7.9990 chunk 171 optimal weight: 2.9990 chunk 183 optimal weight: 0.8980 chunk 64 optimal weight: 20.0000 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 652 ASN C 413 ASN D 646 GLN D 658 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.111232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.062855 restraints weight = 55004.427| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 2.73 r_work: 0.2830 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8894 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 25194 Z= 0.125 Angle : 0.532 9.130 34413 Z= 0.288 Chirality : 0.043 0.195 3886 Planarity : 0.004 0.036 4200 Dihedral : 16.676 170.431 4231 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.68 % Allowed : 11.16 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.16), residues: 2887 helix: 2.24 (0.15), residues: 1156 sheet: 0.57 (0.23), residues: 516 loop : -1.65 (0.15), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG B 291 TYR 0.011 0.001 TYR A 266 PHE 0.017 0.001 PHE D 285 TRP 0.008 0.001 TRP D 647 HIS 0.003 0.001 HIS C 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (25192) covalent geometry : angle 0.53224 / 0.29 (34413) hydrogen bonds : bond 0.05390 / 3.51 ( 1125) hydrogen bonds : angle 4.19024 / 2.89 ( 3124) Misc. bond : bond 0.00024 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5774 Ramachandran restraints generated. 2887 Oldfield, 0 Emsley, 2887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5774 Ramachandran restraints generated. 2887 Oldfield, 0 Emsley, 2887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 2438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 128 time to evaluate : 1.002 Fit side-chains revert: symmetry clash REVERT: A 648 MET cc_start: 0.7903 (mtm) cc_final: 0.7651 (mpp) REVERT: A 686 ASP cc_start: 0.8176 (t0) cc_final: 0.7462 (p0) REVERT: A 797 MET cc_start: 0.9308 (mtp) cc_final: 0.8888 (tmm) REVERT: D 41 PHE cc_start: 0.9231 (m-10) cc_final: 0.8823 (m-80) REVERT: D 72 GLN cc_start: 0.9207 (tt0) cc_final: 0.8958 (tp-100) REVERT: D 187 LEU cc_start: 0.9383 (mm) cc_final: 0.8963 (pt) REVERT: D 264 GLU cc_start: 0.8696 (OUTLIER) cc_final: 0.8378 (tt0) REVERT: D 482 GLU cc_start: 0.8815 (tt0) cc_final: 0.8192 (tp30) REVERT: D 686 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.7941 (pm20) REVERT: D 781 MET cc_start: 0.8989 (mmt) cc_final: 0.8680 (mmt) outliers start: 41 outliers final: 28 residues processed: 162 average time/residue: 0.6204 time to fit residues: 117.0484 Evaluate side-chains 153 residues out of total 2438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 123 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 423 MET Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 789 VAL Chi-restraints excluded: chain A residue 825 ILE Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 707 ILE Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 390 ILE Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 264 GLU Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain D residue 289 MET Chi-restraints excluded: chain D residue 362 LEU Chi-restraints excluded: chain D residue 616 THR Chi-restraints excluded: chain D residue 646 GLN Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 686 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 84 optimal weight: 0.4980 chunk 24 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 99 optimal weight: 7.9990 chunk 223 optimal weight: 5.9990 chunk 272 optimal weight: 4.9990 chunk 208 optimal weight: 0.0980 chunk 46 optimal weight: 1.9990 chunk 55 optimal weight: 10.0000 chunk 170 optimal weight: 3.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 652 ASN C 413 ASN D 646 GLN D 658 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.110901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.062493 restraints weight = 55222.587| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 2.69 r_work: 0.2825 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8906 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 25194 Z= 0.141 Angle : 0.551 12.407 34413 Z= 0.295 Chirality : 0.044 0.501 3886 Planarity : 0.004 0.061 4200 Dihedral : 16.668 170.231 4231 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.64 % Allowed : 11.57 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.16), residues: 2887 helix: 2.23 (0.15), residues: 1156 sheet: 0.56 (0.23), residues: 516 loop : -1.65 (0.15), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 227 TYR 0.021 0.001 TYR A 548 PHE 0.036 0.001 PHE B 169 TRP 0.018 0.001 TRP D 647 HIS 0.003 0.001 HIS C 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (25192) covalent geometry : angle 0.55148 / 0.30 (34413) hydrogen bonds : bond 0.05613 / 3.65 ( 1125) hydrogen bonds : angle 4.19863 / 2.90 ( 3124) Misc. bond : bond 0.00025 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5774 Ramachandran restraints generated. 2887 Oldfield, 0 Emsley, 2887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5774 Ramachandran restraints generated. 2887 Oldfield, 0 Emsley, 2887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 2438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 125 time to evaluate : 0.969 Fit side-chains REVERT: A 538 ASP cc_start: 0.9074 (OUTLIER) cc_final: 0.8777 (p0) REVERT: A 650 THR cc_start: 0.8597 (p) cc_final: 0.8294 (t) REVERT: A 686 ASP cc_start: 0.8212 (t0) cc_final: 0.7452 (p0) REVERT: A 797 MET cc_start: 0.9295 (mtp) cc_final: 0.8894 (tmm) REVERT: B 169 PHE cc_start: 0.8798 (p90) cc_final: 0.8460 (p90) REVERT: D 41 PHE cc_start: 0.9228 (m-10) cc_final: 0.8833 (m-80) REVERT: D 72 GLN cc_start: 0.9202 (tt0) cc_final: 0.8942 (tp40) REVERT: D 264 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.8378 (tt0) REVERT: D 482 GLU cc_start: 0.8796 (tt0) cc_final: 0.8175 (tp30) REVERT: D 686 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8017 (pm20) REVERT: D 781 MET cc_start: 0.8998 (mmt) cc_final: 0.8685 (mmt) outliers start: 40 outliers final: 27 residues processed: 156 average time/residue: 0.6123 time to fit residues: 111.3191 Evaluate side-chains 154 residues out of total 2438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 124 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 423 MET Chi-restraints excluded: chain A residue 538 ASP Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 695 MET Chi-restraints excluded: chain A residue 789 VAL Chi-restraints excluded: chain A residue 825 ILE Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 707 ILE Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 390 ILE Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 264 GLU Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain D residue 289 MET Chi-restraints excluded: chain D residue 362 LEU Chi-restraints excluded: chain D residue 616 THR Chi-restraints excluded: chain D residue 646 GLN Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 686 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 50 optimal weight: 0.0670 chunk 44 optimal weight: 5.9990 chunk 235 optimal weight: 1.9990 chunk 40 optimal weight: 0.4980 chunk 196 optimal weight: 1.9990 chunk 164 optimal weight: 0.5980 chunk 172 optimal weight: 0.9990 chunk 240 optimal weight: 4.9990 chunk 228 optimal weight: 20.0000 chunk 68 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.8322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 652 ASN C 413 ASN D 646 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.111587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.063389 restraints weight = 55247.711| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 2.75 r_work: 0.2845 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8894 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 25194 Z= 0.116 Angle : 0.532 10.790 34413 Z= 0.285 Chirality : 0.043 0.289 3886 Planarity : 0.004 0.062 4200 Dihedral : 16.662 170.574 4231 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.48 % Allowed : 11.81 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.16), residues: 2887 helix: 2.32 (0.15), residues: 1155 sheet: 0.61 (0.23), residues: 516 loop : -1.62 (0.16), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG B 291 TYR 0.010 0.001 TYR C 21 PHE 0.036 0.001 PHE B 169 TRP 0.021 0.001 TRP D 647 HIS 0.004 0.001 HIS D 643 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.12 (25192) covalent geometry : angle 0.53219 / 0.29 (34413) hydrogen bonds : bond 0.05008 / 3.26 ( 1125) hydrogen bonds : angle 4.12235 / 2.85 ( 3124) Misc. bond : bond 0.00018 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5774 Ramachandran restraints generated. 2887 Oldfield, 0 Emsley, 2887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5774 Ramachandran restraints generated. 2887 Oldfield, 0 Emsley, 2887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 2438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 125 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 538 ASP cc_start: 0.9073 (OUTLIER) cc_final: 0.8775 (p0) REVERT: A 648 MET cc_start: 0.7864 (mtm) cc_final: 0.7609 (mpt) REVERT: A 650 THR cc_start: 0.8571 (p) cc_final: 0.8240 (t) REVERT: A 686 ASP cc_start: 0.8106 (t0) cc_final: 0.7407 (p0) REVERT: A 797 MET cc_start: 0.9295 (mtp) cc_final: 0.8892 (tmm) REVERT: B 169 PHE cc_start: 0.8789 (p90) cc_final: 0.8445 (p90) REVERT: B 531 GLN cc_start: 0.9376 (OUTLIER) cc_final: 0.8635 (mm110) REVERT: B 707 ILE cc_start: 0.8466 (OUTLIER) cc_final: 0.8122 (tp) REVERT: D 41 PHE cc_start: 0.9207 (m-10) cc_final: 0.8788 (m-80) REVERT: D 72 GLN cc_start: 0.9191 (tt0) cc_final: 0.8915 (tp40) REVERT: D 264 GLU cc_start: 0.8693 (OUTLIER) cc_final: 0.8338 (tt0) REVERT: D 482 GLU cc_start: 0.8808 (tt0) cc_final: 0.8189 (tp30) REVERT: D 686 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.8046 (pm20) REVERT: D 781 MET cc_start: 0.8976 (mmt) cc_final: 0.8712 (mmt) outliers start: 36 outliers final: 25 residues processed: 155 average time/residue: 0.6377 time to fit residues: 115.3233 Evaluate side-chains 151 residues out of total 2438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 121 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 423 MET Chi-restraints excluded: chain A residue 538 ASP Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 667 ARG Chi-restraints excluded: chain A residue 695 MET Chi-restraints excluded: chain A residue 789 VAL Chi-restraints excluded: chain A residue 825 ILE Chi-restraints excluded: chain B residue 39 MET Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 531 GLN Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 707 ILE Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 264 GLU Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain D residue 362 LEU Chi-restraints excluded: chain D residue 616 THR Chi-restraints excluded: chain D residue 646 GLN Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 686 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 194 optimal weight: 0.8980 chunk 220 optimal weight: 9.9990 chunk 26 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 69 optimal weight: 20.0000 chunk 186 optimal weight: 0.0770 chunk 206 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 chunk 209 optimal weight: 2.9990 chunk 74 optimal weight: 30.0000 chunk 131 optimal weight: 1.9990 overall best weight: 1.3942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 652 ASN C 413 ASN D 646 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.110956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.061302 restraints weight = 55119.646| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 2.42 r_work: 0.2849 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 25194 Z= 0.146 Angle : 0.553 11.180 34413 Z= 0.296 Chirality : 0.043 0.274 3886 Planarity : 0.004 0.066 4200 Dihedral : 16.650 170.418 4231 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.35 % Allowed : 12.14 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.16), residues: 2887 helix: 2.23 (0.15), residues: 1156 sheet: 0.56 (0.23), residues: 526 loop : -1.62 (0.16), residues: 1205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG B 291 TYR 0.011 0.001 TYR C 21 PHE 0.035 0.001 PHE B 169 TRP 0.022 0.001 TRP D 647 HIS 0.003 0.001 HIS D 643 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 (25192) covalent geometry : angle 0.55255 / 0.30 (34413) hydrogen bonds : bond 0.05555 / 3.62 ( 1125) hydrogen bonds : angle 4.14912 / 2.87 ( 3124) Misc. bond : bond 0.00027 / 0.01 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5774 Ramachandran restraints generated. 2887 Oldfield, 0 Emsley, 2887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5774 Ramachandran restraints generated. 2887 Oldfield, 0 Emsley, 2887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 2438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 123 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 538 ASP cc_start: 0.9083 (OUTLIER) cc_final: 0.8776 (p0) REVERT: A 648 MET cc_start: 0.7984 (mtm) cc_final: 0.7775 (mpt) REVERT: A 650 THR cc_start: 0.8596 (p) cc_final: 0.8262 (t) REVERT: A 686 ASP cc_start: 0.8132 (t0) cc_final: 0.7435 (p0) REVERT: A 797 MET cc_start: 0.9251 (mtp) cc_final: 0.8893 (tmm) REVERT: B 531 GLN cc_start: 0.9394 (OUTLIER) cc_final: 0.8638 (mm110) REVERT: D 41 PHE cc_start: 0.9222 (m-10) cc_final: 0.8781 (m-80) REVERT: D 72 GLN cc_start: 0.9188 (tt0) cc_final: 0.8916 (tp-100) REVERT: D 264 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.8286 (tt0) REVERT: D 482 GLU cc_start: 0.8776 (tt0) cc_final: 0.8173 (tp30) REVERT: D 686 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8088 (pm20) REVERT: D 781 MET cc_start: 0.8995 (mmt) cc_final: 0.8679 (mmt) outliers start: 33 outliers final: 26 residues processed: 149 average time/residue: 0.6568 time to fit residues: 113.7765 Evaluate side-chains 153 residues out of total 2438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 123 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 423 MET Chi-restraints excluded: chain A residue 538 ASP Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 667 ARG Chi-restraints excluded: chain A residue 695 MET Chi-restraints excluded: chain A residue 789 VAL Chi-restraints excluded: chain A residue 825 ILE Chi-restraints excluded: chain B residue 39 MET Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 531 GLN Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 707 ILE Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 390 ILE Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 264 GLU Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain D residue 362 LEU Chi-restraints excluded: chain D residue 616 THR Chi-restraints excluded: chain D residue 646 GLN Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 686 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 208 optimal weight: 3.9990 chunk 165 optimal weight: 2.9990 chunk 199 optimal weight: 0.9980 chunk 281 optimal weight: 6.9990 chunk 95 optimal weight: 0.6980 chunk 167 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 259 optimal weight: 1.9990 chunk 248 optimal weight: 3.9990 chunk 96 optimal weight: 7.9990 chunk 264 optimal weight: 6.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 652 ASN C 413 ASN D 646 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.111240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.062739 restraints weight = 55295.294| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 2.72 r_work: 0.2830 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8900 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 25194 Z= 0.137 Angle : 0.548 11.541 34413 Z= 0.293 Chirality : 0.043 0.261 3886 Planarity : 0.004 0.065 4200 Dihedral : 16.649 170.671 4231 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.35 % Allowed : 12.10 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.16), residues: 2887 helix: 2.25 (0.15), residues: 1156 sheet: 0.61 (0.23), residues: 519 loop : -1.62 (0.15), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 227 TYR 0.012 0.001 TYR A 548 PHE 0.038 0.001 PHE B 169 TRP 0.008 0.001 TRP D 647 HIS 0.003 0.001 HIS C 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 (25192) covalent geometry : angle 0.54753 / 0.29 (34413) hydrogen bonds : bond 0.05437 / 3.54 ( 1125) hydrogen bonds : angle 4.13616 / 2.86 ( 3124) Misc. bond : bond 0.00028 / 0.01 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12435.29 seconds wall clock time: 211 minutes 20.22 seconds (12680.22 seconds total)