Starting phenix.real_space_refine on Mon Sep 30 07:01:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ggq_51339/09_2024/9ggq_51339.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ggq_51339/09_2024/9ggq_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ggq_51339/09_2024/9ggq_51339.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ggq_51339/09_2024/9ggq_51339.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ggq_51339/09_2024/9ggq_51339.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ggq_51339/09_2024/9ggq_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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 15.82, per 1000 atoms: 0.64 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: 6.27 Conformation dependent library (CDL) restraints added in 2.9 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: 7.84 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: 10.52 Time building geometry restraints manager: 7.14 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: 7.500 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: 0.020 Extract box with map and model: 0.990 Check model and map are aligned: 0.170 Set scattering table: 0.240 Process input model: 61.460 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.380 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 9 poor density : 217 time to evaluate : 2.587 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: 1.3817 time to fit residues: 356.2910 Evaluate side-chains 142 residues out of total 2438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 138 time to evaluate : 2.616 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 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 fitting. rotamer outliers: 33 poor density : 154 time to evaluate : 2.823 Fit side-chains REVERT: A 417 LEU cc_start: 0.8971 (mt) cc_final: 0.8692 (mm) REVERT: A 625 LEU cc_start: 0.7682 (mt) cc_final: 0.7297 (pp) REVERT: A 696 LEU cc_start: 0.8153 (mt) cc_final: 0.7845 (tt) REVERT: A 795 ILE cc_start: 0.9440 (pt) cc_final: 0.9234 (mm) REVERT: B 145 TYR cc_start: 0.7639 (m-80) cc_final: 0.7091 (m-80) REVERT: B 169 PHE cc_start: 0.8727 (p90) cc_final: 0.8480 (p90) REVERT: B 193 GLU cc_start: 0.9189 (mt-10) cc_final: 0.8910 (tm-30) REVERT: B 707 ILE cc_start: 0.8745 (OUTLIER) cc_final: 0.8369 (tp) REVERT: C 201 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7851 (tp30) REVERT: D 41 PHE cc_start: 0.9262 (m-10) cc_final: 0.8884 (m-80) REVERT: D 72 GLN cc_start: 0.9245 (tt0) cc_final: 0.8998 (tp40) REVERT: D 482 GLU cc_start: 0.8432 (tt0) cc_final: 0.8129 (tp30) REVERT: D 781 MET cc_start: 0.8688 (mmt) cc_final: 0.8437 (mmt) REVERT: D 802 ILE cc_start: 0.7371 (mt) cc_final: 0.7081 (pt) outliers start: 33 outliers final: 6 residues processed: 178 average time/residue: 1.2952 time to fit residues: 268.7955 Evaluate side-chains 142 residues out of total 2438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 134 time to evaluate : 2.632 ------------------------------------------------------------------------------- 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 201 GLU 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 148 optimal weight: 7.9990 chunk 83 optimal weight: 0.8980 chunk 222 optimal weight: 1.9990 chunk 182 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 268 optimal weight: 0.7980 chunk 289 optimal weight: 2.9990 chunk 239 optimal weight: 7.9990 chunk 266 optimal weight: 0.9990 chunk 91 optimal weight: 20.0000 chunk 215 optimal weight: 4.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 C 413 ASN D 569 ASN D 646 GLN D 658 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25192 Z= 0.185 Angle : 0.517 8.828 34413 Z= 0.277 Chirality : 0.042 0.232 3886 Planarity : 0.004 0.034 4200 Dihedral : 16.425 172.810 4231 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.60 % Allowed : 9.52 % Favored : 88.88 % 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: 0.68 (0.16), residues: 2887 helix: 2.29 (0.16), residues: 1155 sheet: 0.56 (0.23), residues: 529 loop : -1.52 (0.16), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 725 HIS 0.003 0.001 HIS C 378 PHE 0.024 0.001 PHE B 169 TYR 0.012 0.001 TYR A 266 ARG 0.008 0.000 ARG A 826 *********************** 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 180 residues out of total 2438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 141 time to evaluate : 2.579 Fit side-chains revert: symmetry clash REVERT: A 417 LEU cc_start: 0.8949 (mt) cc_final: 0.8662 (mm) REVERT: A 686 ASP cc_start: 0.8400 (t0) cc_final: 0.7769 (p0) REVERT: B 169 PHE cc_start: 0.8768 (p90) cc_final: 0.8317 (p90) REVERT: B 193 GLU cc_start: 0.9178 (mt-10) cc_final: 0.8909 (tm-30) REVERT: C 201 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7880 (tp30) REVERT: C 504 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7630 (mp0) REVERT: D 41 PHE cc_start: 0.9270 (m-10) cc_final: 0.8905 (m-80) REVERT: D 187 LEU cc_start: 0.9454 (mm) cc_final: 0.9118 (pt) REVERT: D 222 ILE cc_start: 0.7573 (mp) cc_final: 0.7357 (mm) REVERT: D 482 GLU cc_start: 0.8437 (tt0) cc_final: 0.8132 (tp30) outliers start: 39 outliers final: 18 residues processed: 172 average time/residue: 1.2959 time to fit residues: 259.1275 Evaluate side-chains 144 residues out of total 2438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 124 time to evaluate : 2.557 ------------------------------------------------------------------------------- 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 400 LEU Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain C residue 201 GLU 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 39 MET Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 270 THR 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 265 optimal weight: 10.0000 chunk 201 optimal weight: 6.9990 chunk 139 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 128 optimal weight: 5.9990 chunk 180 optimal weight: 3.9990 chunk 269 optimal weight: 4.9990 chunk 285 optimal weight: 0.9990 chunk 140 optimal weight: 2.9990 chunk 255 optimal weight: 0.9980 chunk 76 optimal weight: 8.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 652 ASN B 801 ASN D 646 GLN D 658 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1581 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= 0.343 Angle : 0.592 9.269 34413 Z= 0.318 Chirality : 0.044 0.157 3886 Planarity : 0.004 0.047 4200 Dihedral : 16.524 172.786 4229 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.05 % Allowed : 9.60 % Favored : 88.35 % 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: 0.47 (0.16), residues: 2887 helix: 2.09 (0.15), residues: 1157 sheet: 0.55 (0.23), residues: 514 loop : -1.65 (0.15), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 725 HIS 0.006 0.001 HIS C 378 PHE 0.022 0.002 PHE B 169 TYR 0.013 0.001 TYR A 266 ARG 0.010 0.001 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 180 residues out of total 2438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 130 time to evaluate : 2.666 Fit side-chains revert: symmetry clash REVERT: A 648 MET cc_start: 0.8204 (mtm) cc_final: 0.7793 (mpp) REVERT: A 686 ASP cc_start: 0.8410 (t0) cc_final: 0.7741 (p0) REVERT: B 193 GLU cc_start: 0.9164 (mt-10) cc_final: 0.8901 (tm-30) REVERT: B 353 MET cc_start: 0.9059 (OUTLIER) cc_final: 0.8811 (tpp) REVERT: C 504 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7664 (mp0) REVERT: D 41 PHE cc_start: 0.9271 (m-10) cc_final: 0.8893 (m-80) REVERT: D 187 LEU cc_start: 0.9447 (mm) cc_final: 0.9076 (pt) REVERT: D 222 ILE cc_start: 0.7650 (mp) cc_final: 0.7429 (mm) REVERT: D 264 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.8166 (tt0) REVERT: D 482 GLU cc_start: 0.8449 (tt0) cc_final: 0.8116 (tp30) REVERT: D 686 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.8023 (pm20) REVERT: D 712 ARG cc_start: 0.8811 (mtm110) cc_final: 0.8496 (mtm110) outliers start: 50 outliers final: 19 residues processed: 171 average time/residue: 1.3447 time to fit residues: 268.1306 Evaluate side-chains 149 residues out of total 2438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 126 time to evaluate : 2.629 ------------------------------------------------------------------------------- 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 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 646 GLN 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 237 optimal weight: 5.9990 chunk 161 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 212 optimal weight: 8.9990 chunk 117 optimal weight: 4.9990 chunk 243 optimal weight: 2.9990 chunk 197 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 145 optimal weight: 5.9990 chunk 255 optimal weight: 3.9990 chunk 71 optimal weight: 20.0000 overall best weight: 2.7788 ------------------------------------------------------------------------------- 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 C 413 ASN D 646 GLN D 658 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 25192 Z= 0.390 Angle : 0.615 9.279 34413 Z= 0.331 Chirality : 0.045 0.182 3886 Planarity : 0.005 0.044 4200 Dihedral : 16.582 172.032 4229 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 1.80 % Allowed : 10.42 % Favored : 87.78 % 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: 0.26 (0.15), residues: 2887 helix: 1.93 (0.15), residues: 1146 sheet: 0.40 (0.23), residues: 518 loop : -1.75 (0.15), residues: 1223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 725 HIS 0.005 0.001 HIS C 378 PHE 0.037 0.002 PHE B 169 TYR 0.017 0.001 TYR A 548 ARG 0.010 0.001 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 173 residues out of total 2438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 129 time to evaluate : 2.634 Fit side-chains revert: symmetry clash REVERT: A 686 ASP cc_start: 0.8379 (t0) cc_final: 0.7684 (p0) REVERT: A 796 MET cc_start: 0.8812 (OUTLIER) cc_final: 0.8264 (mpp) REVERT: B 169 PHE cc_start: 0.8753 (p90) cc_final: 0.8356 (p90) REVERT: B 353 MET cc_start: 0.9054 (OUTLIER) cc_final: 0.8827 (tpp) REVERT: B 597 MET cc_start: 0.8962 (ptm) cc_final: 0.8749 (ptt) REVERT: C 504 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7693 (mp0) REVERT: D 187 LEU cc_start: 0.9456 (mm) cc_final: 0.9115 (pt) REVERT: D 222 ILE cc_start: 0.7670 (mp) cc_final: 0.7444 (mm) REVERT: D 482 GLU cc_start: 0.8455 (tt0) cc_final: 0.8109 (tp30) REVERT: D 686 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.8051 (pm20) outliers start: 44 outliers final: 22 residues processed: 164 average time/residue: 1.3288 time to fit residues: 253.3852 Evaluate side-chains 151 residues out of total 2438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 125 time to evaluate : 2.613 ------------------------------------------------------------------------------- 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 789 VAL Chi-restraints excluded: chain A residue 796 MET Chi-restraints excluded: chain A residue 825 ILE Chi-restraints excluded: chain B residue 39 MET 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 95 optimal weight: 40.0000 chunk 256 optimal weight: 0.0040 chunk 56 optimal weight: 5.9990 chunk 167 optimal weight: 0.9980 chunk 70 optimal weight: 9.9990 chunk 285 optimal weight: 1.9990 chunk 236 optimal weight: 0.0970 chunk 132 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 94 optimal weight: 5.9990 chunk 149 optimal weight: 2.9990 overall best weight: 0.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 652 ASN D 658 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25192 Z= 0.163 Angle : 0.523 8.852 34413 Z= 0.277 Chirality : 0.041 0.147 3886 Planarity : 0.004 0.049 4200 Dihedral : 16.462 171.854 4229 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.35 % Allowed : 11.36 % 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 (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: 0.55 (0.16), residues: 2887 helix: 2.26 (0.16), residues: 1144 sheet: 0.51 (0.23), residues: 516 loop : -1.63 (0.15), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 629 HIS 0.003 0.000 HIS D 643 PHE 0.031 0.001 PHE B 169 TYR 0.009 0.001 TYR A 266 ARG 0.010 0.000 ARG B 291 *********************** 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 164 residues out of total 2438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 131 time to evaluate : 2.758 Fit side-chains revert: symmetry clash REVERT: A 345 MET cc_start: 0.9281 (OUTLIER) cc_final: 0.8916 (mtp) REVERT: A 648 MET cc_start: 0.8177 (mtm) cc_final: 0.7880 (mpp) REVERT: A 686 ASP cc_start: 0.8266 (t0) cc_final: 0.7728 (p0) REVERT: A 796 MET cc_start: 0.8772 (mtp) cc_final: 0.8219 (mpp) REVERT: B 169 PHE cc_start: 0.8760 (p90) cc_final: 0.8334 (p90) REVERT: B 353 MET cc_start: 0.9039 (OUTLIER) cc_final: 0.8822 (tpp) REVERT: B 597 MET cc_start: 0.8900 (ptm) cc_final: 0.8678 (ptt) REVERT: B 707 ILE cc_start: 0.8689 (OUTLIER) cc_final: 0.8313 (tp) REVERT: C 504 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7650 (mp0) REVERT: D 41 PHE cc_start: 0.9262 (m-10) cc_final: 0.8865 (m-80) REVERT: D 222 ILE cc_start: 0.7589 (mp) cc_final: 0.7386 (mm) REVERT: D 482 GLU cc_start: 0.8450 (tt0) cc_final: 0.8131 (tp30) REVERT: D 686 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.8050 (pm20) REVERT: D 712 ARG cc_start: 0.8759 (mtm110) cc_final: 0.8402 (mtm110) outliers start: 33 outliers final: 18 residues processed: 157 average time/residue: 1.3482 time to fit residues: 245.9126 Evaluate side-chains 146 residues out of total 2438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 123 time to evaluate : 2.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 MET 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 130 LEU Chi-restraints excluded: chain B residue 303 SER 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 275 optimal weight: 9.9990 chunk 32 optimal weight: 1.9990 chunk 162 optimal weight: 1.9990 chunk 208 optimal weight: 0.5980 chunk 161 optimal weight: 2.9990 chunk 240 optimal weight: 5.9990 chunk 159 optimal weight: 0.4980 chunk 284 optimal weight: 2.9990 chunk 177 optimal weight: 0.6980 chunk 173 optimal weight: 0.0370 chunk 131 optimal weight: 0.9990 overall best weight: 0.5660 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 25192 Z= 0.139 Angle : 0.499 8.373 34413 Z= 0.264 Chirality : 0.040 0.144 3886 Planarity : 0.004 0.045 4200 Dihedral : 16.381 171.587 4229 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.19 % Allowed : 11.77 % Favored : 87.04 % 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: 0.83 (0.16), residues: 2887 helix: 2.47 (0.16), residues: 1146 sheet: 0.66 (0.23), residues: 552 loop : -1.53 (0.16), residues: 1189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 629 HIS 0.002 0.000 HIS D 141 PHE 0.029 0.001 PHE B 169 TYR 0.016 0.001 TYR A 548 ARG 0.013 0.000 ARG C 227 *********************** 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 172 residues out of total 2438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 143 time to evaluate : 2.643 Fit side-chains revert: symmetry clash REVERT: A 625 LEU cc_start: 0.7749 (mt) cc_final: 0.7258 (pp) REVERT: A 630 ARG cc_start: 0.8559 (ptm-80) cc_final: 0.8325 (mtm110) REVERT: A 648 MET cc_start: 0.8210 (mtm) cc_final: 0.7801 (mpt) REVERT: A 686 ASP cc_start: 0.8200 (t0) cc_final: 0.7716 (p0) REVERT: A 796 MET cc_start: 0.8747 (mtp) cc_final: 0.8214 (mpp) REVERT: C 504 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7648 (mp0) REVERT: D 41 PHE cc_start: 0.9184 (m-10) cc_final: 0.8636 (m-80) REVERT: D 482 GLU cc_start: 0.8449 (tt0) cc_final: 0.8143 (tp30) REVERT: D 712 ARG cc_start: 0.8769 (mtm110) cc_final: 0.8429 (mtm110) outliers start: 29 outliers final: 17 residues processed: 168 average time/residue: 1.4153 time to fit residues: 275.1216 Evaluate side-chains 147 residues out of total 2438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 129 time to evaluate : 2.635 ------------------------------------------------------------------------------- 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 789 VAL Chi-restraints excluded: chain B residue 39 MET 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 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 616 THR Chi-restraints excluded: chain D residue 666 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 175 optimal weight: 0.5980 chunk 113 optimal weight: 0.0770 chunk 169 optimal weight: 0.9990 chunk 85 optimal weight: 7.9990 chunk 55 optimal weight: 20.0000 chunk 180 optimal weight: 2.9990 chunk 193 optimal weight: 3.9990 chunk 140 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 223 optimal weight: 0.0010 chunk 258 optimal weight: 0.7980 overall best weight: 0.4744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 801 ASN D 141 HIS D 658 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2084 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= 0.133 Angle : 0.499 9.551 34413 Z= 0.261 Chirality : 0.040 0.151 3886 Planarity : 0.004 0.056 4200 Dihedral : 16.318 172.419 4229 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.15 % Allowed : 12.10 % Favored : 86.75 % 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: 0.96 (0.16), residues: 2887 helix: 2.53 (0.16), residues: 1157 sheet: 0.75 (0.23), residues: 550 loop : -1.46 (0.16), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 629 HIS 0.002 0.000 HIS A 357 PHE 0.017 0.001 PHE D 285 TYR 0.008 0.001 TYR A 266 ARG 0.015 0.000 ARG A 826 *********************** 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 166 residues out of total 2438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 138 time to evaluate : 2.948 Fit side-chains REVERT: A 538 ASP cc_start: 0.9117 (OUTLIER) cc_final: 0.8829 (p0) REVERT: A 625 LEU cc_start: 0.7793 (mt) cc_final: 0.7299 (pp) REVERT: A 630 ARG cc_start: 0.8550 (ptm-80) cc_final: 0.8332 (mtm110) REVERT: A 648 MET cc_start: 0.8187 (mtm) cc_final: 0.7777 (mpt) REVERT: A 686 ASP cc_start: 0.8190 (t0) cc_final: 0.7734 (p0) REVERT: A 722 ARG cc_start: 0.8235 (ttm170) cc_final: 0.7721 (pmt170) REVERT: A 796 MET cc_start: 0.8700 (mtp) cc_final: 0.8190 (mpp) REVERT: B 34 THR cc_start: 0.9282 (m) cc_final: 0.9046 (p) REVERT: B 169 PHE cc_start: 0.8756 (p90) cc_final: 0.8429 (p90) REVERT: C 405 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.8376 (mp0) REVERT: C 504 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7667 (mp0) REVERT: D 41 PHE cc_start: 0.9218 (m-10) cc_final: 0.8648 (m-80) REVERT: D 72 GLN cc_start: 0.9196 (tt0) cc_final: 0.8924 (tp-100) REVERT: D 187 LEU cc_start: 0.9411 (mm) cc_final: 0.9026 (pt) REVERT: D 206 ARG cc_start: 0.8896 (mtm-85) cc_final: 0.8636 (mtm-85) REVERT: D 482 GLU cc_start: 0.8419 (tt0) cc_final: 0.8116 (tp30) REVERT: D 686 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.7954 (pm20) REVERT: D 712 ARG cc_start: 0.8751 (mtm110) cc_final: 0.8417 (mtm110) outliers start: 28 outliers final: 18 residues processed: 162 average time/residue: 1.3800 time to fit residues: 260.6688 Evaluate side-chains 155 residues out of total 2438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 133 time to evaluate : 2.711 ------------------------------------------------------------------------------- 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 726 LEU Chi-restraints excluded: chain A residue 789 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 554 GLN Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 390 ILE Chi-restraints excluded: chain C residue 405 GLU 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 289 MET 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 272 optimal weight: 2.9990 chunk 248 optimal weight: 2.9990 chunk 264 optimal weight: 8.9990 chunk 159 optimal weight: 0.9980 chunk 115 optimal weight: 9.9990 chunk 208 optimal weight: 1.9990 chunk 81 optimal weight: 10.0000 chunk 239 optimal weight: 0.0470 chunk 250 optimal weight: 0.6980 chunk 173 optimal weight: 1.9990 chunk 280 optimal weight: 2.9990 overall best weight: 1.1482 ------------------------------------------------------------------------------- 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 658 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25192 Z= 0.192 Angle : 0.532 9.938 34413 Z= 0.279 Chirality : 0.042 0.257 3886 Planarity : 0.004 0.057 4200 Dihedral : 16.344 173.016 4228 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.19 % Allowed : 12.31 % 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 (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: 2.46 (0.16), residues: 1155 sheet: 0.74 (0.23), residues: 543 loop : -1.51 (0.16), residues: 1189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 725 HIS 0.003 0.001 HIS C 378 PHE 0.016 0.001 PHE D 285 TYR 0.013 0.001 TYR A 548 ARG 0.015 0.000 ARG B 291 *********************** 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 163 residues out of total 2438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 134 time to evaluate : 2.658 Fit side-chains REVERT: A 538 ASP cc_start: 0.9124 (OUTLIER) cc_final: 0.8839 (p0) REVERT: A 630 ARG cc_start: 0.8567 (ptm-80) cc_final: 0.8354 (mtm110) REVERT: A 648 MET cc_start: 0.8221 (mtm) cc_final: 0.7774 (mpt) REVERT: A 665 ARG cc_start: 0.8061 (tmm-80) cc_final: 0.7846 (ttp80) REVERT: A 686 ASP cc_start: 0.8195 (t0) cc_final: 0.7709 (p0) REVERT: A 796 MET cc_start: 0.8701 (mtp) cc_final: 0.8188 (mpp) REVERT: B 34 THR cc_start: 0.9285 (m) cc_final: 0.9046 (p) REVERT: B 169 PHE cc_start: 0.8761 (p90) cc_final: 0.8434 (p90) REVERT: C 504 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7661 (mp0) REVERT: D 41 PHE cc_start: 0.9239 (m-10) cc_final: 0.8711 (m-80) REVERT: D 72 GLN cc_start: 0.9186 (tt0) cc_final: 0.8914 (tp-100) REVERT: D 187 LEU cc_start: 0.9331 (mm) cc_final: 0.9013 (pt) REVERT: D 206 ARG cc_start: 0.8864 (mtm-85) cc_final: 0.8587 (mtm-85) REVERT: D 482 GLU cc_start: 0.8431 (tt0) cc_final: 0.8119 (tp30) REVERT: D 686 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7987 (pm20) outliers start: 29 outliers final: 19 residues processed: 159 average time/residue: 1.3216 time to fit residues: 244.8176 Evaluate side-chains 153 residues out of total 2438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 131 time to evaluate : 2.819 ------------------------------------------------------------------------------- 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 726 LEU Chi-restraints excluded: chain A residue 789 VAL Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 554 GLN Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 316 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 71 VAL Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain D residue 289 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 171 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 194 optimal weight: 0.7980 chunk 293 optimal weight: 2.9990 chunk 270 optimal weight: 0.9990 chunk 234 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 180 optimal weight: 0.1980 chunk 143 optimal weight: 0.9980 chunk 185 optimal weight: 2.9990 chunk 249 optimal weight: 0.0030 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 801 ASN C 413 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 25192 Z= 0.138 Angle : 0.510 10.731 34413 Z= 0.265 Chirality : 0.041 0.248 3886 Planarity : 0.004 0.062 4200 Dihedral : 16.293 172.771 4228 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.03 % Allowed : 12.59 % Favored : 86.38 % 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: 0.97 (0.16), residues: 2887 helix: 2.50 (0.16), residues: 1158 sheet: 0.80 (0.23), residues: 550 loop : -1.44 (0.16), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 629 HIS 0.004 0.000 HIS B 643 PHE 0.019 0.001 PHE A 697 TYR 0.009 0.001 TYR C 21 ARG 0.017 0.000 ARG B 291 ********************** 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 161 residues out of total 2438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 136 time to evaluate : 2.841 Fit side-chains REVERT: A 538 ASP cc_start: 0.9142 (OUTLIER) cc_final: 0.8876 (p0) REVERT: A 625 LEU cc_start: 0.7872 (mt) cc_final: 0.7368 (pp) REVERT: A 648 MET cc_start: 0.8190 (mtm) cc_final: 0.7744 (mpt) REVERT: A 650 THR cc_start: 0.8359 (p) cc_final: 0.8087 (t) REVERT: A 665 ARG cc_start: 0.8088 (tmm-80) cc_final: 0.7877 (ttp80) REVERT: A 686 ASP cc_start: 0.8244 (t0) cc_final: 0.7787 (p0) REVERT: A 722 ARG cc_start: 0.8284 (ttm170) cc_final: 0.7739 (pmt170) REVERT: A 796 MET cc_start: 0.8666 (mtp) cc_final: 0.8156 (mpm) REVERT: B 34 THR cc_start: 0.9266 (m) cc_final: 0.9032 (p) REVERT: C 405 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.8373 (mp0) REVERT: C 504 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7622 (mp0) REVERT: D 41 PHE cc_start: 0.9235 (m-10) cc_final: 0.8686 (m-80) REVERT: D 72 GLN cc_start: 0.9172 (tt0) cc_final: 0.8884 (tp40) REVERT: D 187 LEU cc_start: 0.9312 (mm) cc_final: 0.9027 (pt) REVERT: D 206 ARG cc_start: 0.8897 (mtm-85) cc_final: 0.8640 (mtm-85) REVERT: D 298 ASP cc_start: 0.8579 (t0) cc_final: 0.8026 (p0) REVERT: D 482 GLU cc_start: 0.8423 (tt0) cc_final: 0.8115 (tp30) REVERT: D 686 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.7958 (pm20) outliers start: 25 outliers final: 18 residues processed: 158 average time/residue: 1.3400 time to fit residues: 247.2915 Evaluate side-chains 155 residues out of total 2438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 133 time to evaluate : 2.459 ------------------------------------------------------------------------------- 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 726 LEU Chi-restraints excluded: chain A residue 789 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 554 GLN Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 390 ILE Chi-restraints excluded: chain C residue 405 GLU 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 71 VAL Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain D residue 289 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 71 optimal weight: 5.9990 chunk 215 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 234 optimal weight: 1.9990 chunk 98 optimal weight: 20.0000 chunk 240 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 43 optimal weight: 0.6980 chunk 205 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.111330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.061485 restraints weight = 55219.647| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 2.47 r_work: 0.2846 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25192 Z= 0.209 Angle : 0.542 10.241 34413 Z= 0.285 Chirality : 0.042 0.224 3886 Planarity : 0.004 0.060 4200 Dihedral : 16.337 173.174 4228 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.07 % Allowed : 12.59 % Favored : 86.34 % 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: 2.43 (0.16), residues: 1155 sheet: 0.76 (0.23), residues: 543 loop : -1.50 (0.16), residues: 1189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 629 HIS 0.003 0.001 HIS C 378 PHE 0.017 0.001 PHE B 285 TYR 0.012 0.001 TYR A 266 ARG 0.016 0.000 ARG B 291 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7812.86 seconds wall clock time: 137 minutes 30.24 seconds (8250.24 seconds total)