Starting phenix.real_space_refine on Sun Jan 26 09:59:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ggq_51339/01_2025/9ggq_51339.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ggq_51339/01_2025/9ggq_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9ggq_51339/01_2025/9ggq_51339.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ggq_51339/01_2025/9ggq_51339.map" model { file = "/net/cci-nas-00/data/ceres_data/9ggq_51339/01_2025/9ggq_51339.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ggq_51339/01_2025/9ggq_51339.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: 16.72, per 1000 atoms: 0.68 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: 5.96 Conformation dependent library (CDL) restraints added in 3.5 seconds 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: 9.51 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: 11.41 Time building geometry restraints manager: 6.82 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=" 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=" C20 MFX F 201 " pdb=" O03 MFX F 201 " ideal model delta sigma weight residual 1.242 1.303 -0.061 2.00e-02 2.50e+03 9.27e+00 bond pdb=" C11 MFX F 201 " pdb=" N01 MFX F 201 " ideal model delta sigma weight residual 1.374 1.430 -0.056 2.00e-02 2.50e+03 7.93e+00 ... (remaining 25187 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.30: 34162 2.30 - 4.59: 223 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=" OH PTR C 122 " pdb=" P PTR C 122 " pdb=" O2P PTR C 122 " ideal model delta sigma weight residual 99.92 111.40 -11.48 3.00e+00 1.11e-01 1.46e+01 angle pdb=" CA ALA C 220 " pdb=" C ALA C 220 " pdb=" N ALA C 221 " ideal model delta sigma weight residual 119.63 116.56 3.07 8.10e-01 1.52e+00 1.43e+01 angle pdb=" CA ALA A 220 " pdb=" C ALA A 220 " pdb=" N ALA A 221 " ideal model delta sigma weight residual 119.63 116.58 3.05 8.10e-01 1.52e+00 1.42e+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: 2456 0.030 - 0.061: 936 0.061 - 0.091: 272 0.091 - 0.121: 201 0.121 - 0.152: 21 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: 10.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.930 Check model and map are aligned: 0.170 Set scattering table: 0.230 Process input model: 65.380 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.100 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:12.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.158 25192 Z= 0.207 Angle : 0.502 11.476 34413 Z= 0.271 Chirality : 0.041 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.010 0.001 TRP D 725 HIS 0.004 0.001 HIS D 281 PHE 0.010 0.001 PHE B 285 TYR 0.013 0.001 TYR A 266 ARG 0.003 0.000 ARG D 709 *********************** 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 : 2.608 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: 1.5304 time to fit residues: 394.4537 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 : 2.679 ------------------------------------------------------------------------------- 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 249 optimal weight: 3.9990 chunk 223 optimal weight: 0.0010 chunk 124 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 150 optimal weight: 0.0040 chunk 119 optimal weight: 0.0060 chunk 231 optimal weight: 7.9990 chunk 89 optimal weight: 20.0000 chunk 140 optimal weight: 0.0980 chunk 172 optimal weight: 1.9990 chunk 267 optimal weight: 8.9990 overall best weight: 0.4216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 587 HIS ** B 643 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 721 GLN B 801 ASN D 638 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 = 0.3960 r_free = 0.3960 target = 0.113144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.064103 restraints weight = 55255.309| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 2.47 r_work: 0.2902 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 25192 Z= 0.143 Angle : 0.517 9.296 34413 Z= 0.276 Chirality : 0.041 0.202 3886 Planarity : 0.004 0.048 4200 Dihedral : 16.539 173.039 4233 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.35 % Allowed : 8.12 % Favored : 90.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.16), residues: 2887 helix: 2.24 (0.16), residues: 1144 sheet: 0.44 (0.23), residues: 552 loop : -1.54 (0.16), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 629 HIS 0.003 0.000 HIS B 64 PHE 0.034 0.001 PHE B 169 TYR 0.010 0.001 TYR C 266 ARG 0.012 0.000 ARG D 599 *********************** 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 187 residues out of total 2438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 154 time to evaluate : 2.581 Fit side-chains REVERT: A 417 LEU cc_start: 0.9022 (mt) cc_final: 0.8751 (mm) REVERT: A 625 LEU cc_start: 0.7620 (mt) cc_final: 0.7254 (pp) REVERT: A 696 LEU cc_start: 0.7945 (mt) cc_final: 0.7681 (tt) REVERT: A 797 MET cc_start: 0.9278 (mtp) cc_final: 0.8925 (mpp) REVERT: B 145 TYR cc_start: 0.7621 (m-80) cc_final: 0.7097 (m-80) REVERT: B 169 PHE cc_start: 0.8765 (p90) cc_final: 0.8509 (p90) REVERT: B 193 GLU cc_start: 0.9281 (mt-10) cc_final: 0.8916 (tm-30) REVERT: B 707 ILE cc_start: 0.8521 (OUTLIER) cc_final: 0.8174 (tp) REVERT: D 41 PHE cc_start: 0.9242 (m-10) cc_final: 0.8881 (m-80) REVERT: D 72 GLN cc_start: 0.9252 (tt0) cc_final: 0.9010 (tp40) REVERT: D 482 GLU cc_start: 0.8778 (tt0) cc_final: 0.8198 (tp30) REVERT: D 802 ILE cc_start: 0.7162 (mt) cc_final: 0.6873 (pt) outliers start: 33 outliers final: 6 residues processed: 178 average time/residue: 1.3891 time to fit residues: 286.4780 Evaluate side-chains 140 residues out of total 2438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 133 time to evaluate : 2.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 707 ILE Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain D residue 39 MET 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 231 optimal weight: 10.0000 chunk 94 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 271 optimal weight: 4.9990 chunk 138 optimal weight: 0.9980 chunk 149 optimal weight: 4.9990 chunk 93 optimal weight: 7.9990 chunk 257 optimal weight: 0.5980 chunk 219 optimal weight: 3.9990 chunk 195 optimal weight: 0.8980 chunk 223 optimal weight: 10.0000 overall best weight: 2.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 589 HIS A 652 ASN ** B 643 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 801 ASN C 413 ASN D 569 ASN D 646 GLN D 658 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.109910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.059579 restraints weight = 54667.999| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 2.47 r_work: 0.2803 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2698 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 25192 Z= 0.331 Angle : 0.592 9.334 34413 Z= 0.318 Chirality : 0.044 0.224 3886 Planarity : 0.004 0.037 4200 Dihedral : 16.537 172.897 4231 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.64 % Allowed : 9.64 % Favored : 88.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.16), residues: 2887 helix: 2.05 (0.15), residues: 1158 sheet: 0.48 (0.23), residues: 529 loop : -1.63 (0.16), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 725 HIS 0.006 0.001 HIS C 378 PHE 0.024 0.002 PHE B 169 TYR 0.014 0.001 TYR A 266 ARG 0.008 0.001 ARG B 291 *********************** 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: 40 poor density : 133 time to evaluate : 2.659 Fit side-chains revert: symmetry clash REVERT: A 648 MET cc_start: 0.8127 (mtm) cc_final: 0.7886 (mpp) REVERT: A 797 MET cc_start: 0.9284 (mtp) cc_final: 0.8907 (mpp) REVERT: B 169 PHE cc_start: 0.8820 (p90) cc_final: 0.8596 (p90) REVERT: B 193 GLU cc_start: 0.9256 (mt-10) cc_final: 0.8907 (tm-30) REVERT: D 187 LEU cc_start: 0.9394 (mm) cc_final: 0.9104 (pt) REVERT: D 222 ILE cc_start: 0.7475 (mp) cc_final: 0.7262 (mm) REVERT: D 264 GLU cc_start: 0.8753 (OUTLIER) cc_final: 0.8477 (tt0) REVERT: D 482 GLU cc_start: 0.8790 (tt0) cc_final: 0.8180 (tp30) outliers start: 40 outliers final: 18 residues processed: 165 average time/residue: 1.4039 time to fit residues: 270.1707 Evaluate side-chains 141 residues out of total 2438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 122 time to evaluate : 2.766 ------------------------------------------------------------------------------- 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 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 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 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 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 24 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 chunk 64 optimal weight: 20.0000 chunk 106 optimal weight: 3.9990 chunk 164 optimal weight: 0.5980 chunk 250 optimal weight: 2.9990 chunk 201 optimal weight: 6.9990 chunk 169 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 188 optimal weight: 4.9990 chunk 160 optimal weight: 4.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 589 HIS A 652 ASN B 801 ASN D 646 GLN D 658 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.110366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.060266 restraints weight = 55185.941| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 2.44 r_work: 0.2817 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2712 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 25192 Z= 0.270 Angle : 0.559 9.289 34413 Z= 0.300 Chirality : 0.043 0.153 3886 Planarity : 0.004 0.044 4200 Dihedral : 16.514 172.458 4231 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.89 % Allowed : 9.97 % Favored : 88.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.16), residues: 2887 helix: 2.07 (0.15), residues: 1155 sheet: 0.52 (0.23), residues: 514 loop : -1.67 (0.15), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 725 HIS 0.004 0.001 HIS C 378 PHE 0.021 0.001 PHE B 169 TYR 0.013 0.001 TYR A 266 ARG 0.009 0.000 ARG B 291 *********************** 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 178 residues out of total 2438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 132 time to evaluate : 2.332 Fit side-chains revert: symmetry clash REVERT: A 686 ASP cc_start: 0.8194 (t0) cc_final: 0.7439 (p0) REVERT: A 796 MET cc_start: 0.8765 (OUTLIER) cc_final: 0.7878 (mmt) REVERT: A 797 MET cc_start: 0.9258 (mtp) cc_final: 0.8854 (tmm) REVERT: B 169 PHE cc_start: 0.8819 (p90) cc_final: 0.8389 (p90) REVERT: B 193 GLU cc_start: 0.9257 (mt-10) cc_final: 0.8907 (tm-30) REVERT: B 206 ARG cc_start: 0.8558 (OUTLIER) cc_final: 0.8356 (pmm150) REVERT: B 353 MET cc_start: 0.8851 (OUTLIER) cc_final: 0.8602 (tpp) REVERT: C 504 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.8358 (mp0) REVERT: D 41 PHE cc_start: 0.9242 (m-10) cc_final: 0.8892 (m-80) REVERT: D 222 ILE cc_start: 0.7463 (mp) cc_final: 0.7242 (mm) REVERT: D 264 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.8431 (tt0) REVERT: D 482 GLU cc_start: 0.8785 (tt0) cc_final: 0.8203 (tp30) REVERT: D 686 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.8041 (pm20) outliers start: 46 outliers final: 19 residues processed: 170 average time/residue: 1.5173 time to fit residues: 298.8008 Evaluate side-chains 152 residues out of total 2438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 127 time to evaluate : 2.917 ------------------------------------------------------------------------------- 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 631 ILE Chi-restraints excluded: chain A residue 789 VAL Chi-restraints excluded: chain A residue 796 MET 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 353 MET Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 707 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 C residue 504 GLU 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 666 VAL Chi-restraints excluded: chain D residue 686 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 27 optimal weight: 0.9990 chunk 218 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 129 optimal weight: 0.8980 chunk 242 optimal weight: 7.9990 chunk 140 optimal weight: 0.0870 chunk 4 optimal weight: 0.9980 chunk 272 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 263 optimal weight: 2.9990 chunk 256 optimal weight: 0.0270 overall best weight: 0.5816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 413 ASN D 646 GLN D 658 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.112566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.063278 restraints weight = 55401.520| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 2.48 r_work: 0.2894 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 25192 Z= 0.139 Angle : 0.494 8.553 34413 Z= 0.263 Chirality : 0.041 0.147 3886 Planarity : 0.003 0.038 4200 Dihedral : 16.423 171.979 4231 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.60 % Allowed : 10.38 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.16), residues: 2887 helix: 2.32 (0.16), residues: 1155 sheet: 0.59 (0.24), residues: 510 loop : -1.56 (0.16), residues: 1222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 647 HIS 0.002 0.000 HIS A 357 PHE 0.019 0.001 PHE B 169 TYR 0.008 0.001 TYR A 266 ARG 0.010 0.000 ARG B 291 *********************** 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 170 residues out of total 2438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 131 time to evaluate : 2.510 Fit side-chains revert: symmetry clash REVERT: A 625 LEU cc_start: 0.7723 (mt) cc_final: 0.7232 (pp) REVERT: A 648 MET cc_start: 0.7835 (mtm) cc_final: 0.7593 (mpt) REVERT: A 686 ASP cc_start: 0.8239 (t0) cc_final: 0.7581 (p0) REVERT: A 796 MET cc_start: 0.8763 (mtp) cc_final: 0.7975 (mpp) REVERT: A 797 MET cc_start: 0.9246 (mtp) cc_final: 0.8999 (tmt) REVERT: B 169 PHE cc_start: 0.8814 (p90) cc_final: 0.8323 (p90) REVERT: B 353 MET cc_start: 0.8838 (OUTLIER) cc_final: 0.8607 (tpp) REVERT: C 504 GLU cc_start: 0.8630 (OUTLIER) cc_final: 0.8326 (mp0) REVERT: D 41 PHE cc_start: 0.9197 (m-10) cc_final: 0.8739 (m-80) REVERT: D 482 GLU cc_start: 0.8793 (tt0) cc_final: 0.8222 (tp30) outliers start: 39 outliers final: 18 residues processed: 163 average time/residue: 1.4125 time to fit residues: 267.3371 Evaluate side-chains 147 residues out of total 2438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 127 time to evaluate : 2.816 ------------------------------------------------------------------------------- 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 789 VAL Chi-restraints excluded: chain A residue 825 ILE Chi-restraints excluded: chain B residue 39 MET Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain B residue 666 VAL 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 390 ILE Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 504 GLU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 62 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 244 optimal weight: 0.0770 chunk 284 optimal weight: 2.9990 chunk 294 optimal weight: 3.9990 chunk 82 optimal weight: 30.0000 chunk 189 optimal weight: 0.9980 chunk 159 optimal weight: 1.9990 chunk 175 optimal weight: 0.9980 chunk 149 optimal weight: 0.9980 chunk 281 optimal weight: 3.9990 chunk 264 optimal weight: 0.0170 chunk 93 optimal weight: 7.9990 overall best weight: 0.6176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 801 ASN D 646 GLN D 658 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.112750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.064826 restraints weight = 55435.380| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 2.77 r_work: 0.2872 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 25192 Z= 0.139 Angle : 0.488 8.230 34413 Z= 0.259 Chirality : 0.040 0.146 3886 Planarity : 0.003 0.048 4200 Dihedral : 16.365 172.025 4229 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.39 % Allowed : 10.99 % Favored : 87.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.16), residues: 2887 helix: 2.45 (0.16), residues: 1157 sheet: 0.70 (0.23), residues: 551 loop : -1.50 (0.16), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 647 HIS 0.002 0.000 HIS C 378 PHE 0.019 0.001 PHE A 706 TYR 0.016 0.001 TYR A 548 ARG 0.011 0.000 ARG A 826 *********************** 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 170 residues out of total 2438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 136 time to evaluate : 2.700 Fit side-chains revert: symmetry clash REVERT: A 625 LEU cc_start: 0.7709 (mt) cc_final: 0.7213 (pp) REVERT: A 648 MET cc_start: 0.7749 (mtm) cc_final: 0.7506 (mpp) REVERT: A 686 ASP cc_start: 0.8102 (t0) cc_final: 0.7451 (p0) REVERT: A 796 MET cc_start: 0.8761 (mtp) cc_final: 0.7999 (mpp) REVERT: A 797 MET cc_start: 0.9235 (mtp) cc_final: 0.8999 (tmt) REVERT: B 95 MET cc_start: 0.7029 (tpp) cc_final: 0.6148 (tpp) REVERT: B 169 PHE cc_start: 0.8799 (p90) cc_final: 0.8340 (p90) REVERT: B 597 MET cc_start: 0.8629 (ptm) cc_final: 0.8412 (ptt) REVERT: C 504 GLU cc_start: 0.8630 (OUTLIER) cc_final: 0.8342 (mp0) REVERT: D 41 PHE cc_start: 0.9201 (m-10) cc_final: 0.8734 (m-80) REVERT: D 482 GLU cc_start: 0.8872 (tt0) cc_final: 0.8236 (tp30) REVERT: D 686 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.7979 (pm20) outliers start: 34 outliers final: 18 residues processed: 164 average time/residue: 1.4254 time to fit residues: 271.2538 Evaluate side-chains 145 residues out of total 2438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 125 time to evaluate : 2.619 ------------------------------------------------------------------------------- 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 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 666 VAL Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 346 ASN Chi-restraints excluded: chain C residue 390 ILE Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 504 GLU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 62 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 197 optimal weight: 1.9990 chunk 237 optimal weight: 2.9990 chunk 279 optimal weight: 20.0000 chunk 83 optimal weight: 4.9990 chunk 170 optimal weight: 3.9990 chunk 73 optimal weight: 20.0000 chunk 107 optimal weight: 0.0050 chunk 64 optimal weight: 20.0000 chunk 25 optimal weight: 0.7980 chunk 194 optimal weight: 0.0000 chunk 28 optimal weight: 6.9990 overall best weight: 1.1602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 801 ASN C 413 ASN D 141 HIS D 646 GLN D 658 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.111648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.062026 restraints weight = 55469.483| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 2.47 r_work: 0.2860 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.1843 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: