Starting phenix.real_space_refine on Sat Mar 16 00:00:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t2v_40989/03_2024/8t2v_40989_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t2v_40989/03_2024/8t2v_40989.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t2v_40989/03_2024/8t2v_40989.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t2v_40989/03_2024/8t2v_40989.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t2v_40989/03_2024/8t2v_40989_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t2v_40989/03_2024/8t2v_40989_updated.pdb" } resolution = 3.4 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= 0.015 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: 6 Type Number sf(0) Gaussians Ca 7 9.91 5 Mg 1 5.21 5 S 101 5.16 5 C 8225 2.51 5 N 2209 2.21 5 O 2591 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 252": "OE1" <-> "OE2" Residue "A PHE 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 305": "OD1" <-> "OD2" Residue "A PHE 419": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 642": "OE1" <-> "OE2" Residue "A TYR 814": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 960": "OE1" <-> "OE2" Residue "B GLU 65": "OE1" <-> "OE2" Residue "B ASP 127": "OD1" <-> "OD2" Residue "B TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 370": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 378": "OE1" <-> "OE2" Residue "B GLU 400": "OE1" <-> "OE2" Residue "B ASP 596": "OD1" <-> "OD2" Residue "B GLU 616": "OE1" <-> "OE2" Residue "B TYR 657": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 672": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 13134 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 7247 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 946, 7239 Classifications: {'peptide': 946} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 59, 'TRANS': 882} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 946, 7239 Classifications: {'peptide': 946} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 59, 'TRANS': 882} Chain breaks: 2 bond proxies already assigned to first conformer: 7403 Chain: "B" Number of atoms: 5502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 718, 5502 Classifications: {'peptide': 718} Link IDs: {'PCIS': 3, 'PTRANS': 32, 'TRANS': 682} Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 3, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 61 Unusual residues: {' CA': 5, 'NAG': 4} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 79 Unusual residues: {' CA': 2, ' MG': 1, 'CLR': 2, 'NAG': 1} Classifications: {'undetermined': 6, 'water': 6} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 10.60, per 1000 atoms: 0.81 Number of scatterers: 13134 At special positions: 0 Unit cell: (103.68, 166.32, 133.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 7 19.99 S 101 16.00 Mg 1 11.99 O 2591 8.00 N 2209 7.00 C 8225 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS A 56 " - pdb=" SG CYS A 65 " distance=2.04 Simple disulfide: pdb=" SG CYS A 107 " - pdb=" SG CYS A 130 " distance=2.11 Simple disulfide: pdb=" SG CYS A 146 " - pdb=" SG CYS A 167 " distance=2.07 Simple disulfide: pdb=" SG CYS A 473 " - pdb=" SG CYS A 484 " distance=2.06 Simple disulfide: pdb=" SG CYS A 490 " - pdb=" SG CYS A 545 " distance=2.05 Simple disulfide: pdb=" SG CYS A 602 " - pdb=" SG CYS A 608 " distance=2.06 Simple disulfide: pdb=" SG CYS A 674 " - pdb=" SG CYS A 687 " distance=2.05 Simple disulfide: pdb=" SG CYS A 826 " - pdb=" SG CYS A 890 " distance=2.06 Simple disulfide: pdb=" SG CYS A 880 " - pdb=" SG CYS A 885 " distance=2.04 Simple disulfide: pdb=" SG CYS B 5 " - pdb=" SG CYS B 23 " distance=2.02 Simple disulfide: pdb=" SG CYS B 13 " - pdb=" SG CYS B 435 " distance=2.06 Simple disulfide: pdb=" SG CYS B 16 " - pdb=" SG CYS B 38 " distance=2.07 Simple disulfide: pdb=" SG CYS B 26 " - pdb=" SG CYS B 49 " distance=2.07 Simple disulfide: pdb=" SG CYS B 177 " - pdb=" SG CYS B 184 " distance=2.02 Simple disulfide: pdb=" SG CYS B 232 " - pdb=" SG CYS B 273 " distance=2.12 Simple disulfide: pdb=" SG CYS B 374 " - pdb=" SG CYS B 386 " distance=2.07 Simple disulfide: pdb=" SG CYS B 406 " - pdb=" SG CYS B 433 " distance=2.04 Simple disulfide: pdb=" SG CYS B 437 " - pdb=" SG CYS B 457 " distance=2.06 Simple disulfide: pdb=" SG CYS B 448 " - pdb=" SG CYS B 460 " distance=2.06 Simple disulfide: pdb=" SG CYS B 460 " - pdb=" SG CYS B 471 " distance=2.06 Simple disulfide: pdb=" SG CYS B 462 " - pdb=" SG CYS B 471 " distance=2.05 Simple disulfide: pdb=" SG CYS B 473 " - pdb=" SG CYS B 503 " distance=2.06 Simple disulfide: pdb=" SG CYS B 486 " - pdb=" SG CYS B 501 " distance=2.05 Simple disulfide: pdb=" SG CYS B 495 " - pdb=" SG CYS B 506 " distance=2.04 Simple disulfide: pdb=" SG CYS B 508 " - pdb=" SG CYS B 521 " distance=2.07 Simple disulfide: pdb=" SG CYS B 523 " - pdb=" SG CYS B 544 " distance=2.05 Simple disulfide: pdb=" SG CYS B 528 " - pdb=" SG CYS B 542 " distance=2.05 Simple disulfide: pdb=" SG CYS B 536 " - pdb=" SG CYS B 547 " distance=2.04 Simple disulfide: pdb=" SG CYS B 549 " - pdb=" SG CYS B 558 " distance=2.05 Simple disulfide: pdb=" SG CYS B 560 " - pdb=" SG CYS B 583 " distance=2.06 Simple disulfide: pdb=" SG CYS B 567 " - pdb=" SG CYS B 581 " distance=2.05 Simple disulfide: pdb=" SG CYS B 575 " - pdb=" SG CYS B 586 " distance=2.02 Simple disulfide: pdb=" SG CYS B 588 " - pdb=" SG CYS B 598 " distance=2.08 Simple disulfide: pdb=" SG CYS B 601 " - pdb=" SG CYS B 604 " distance=2.05 Simple disulfide: pdb=" SG CYS B 608 " - pdb=" SG CYS B 655 " distance=2.08 Simple disulfide: pdb=" SG CYS B 614 " - pdb=" SG CYS B 635 " distance=2.06 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 631 " distance=2.06 Simple disulfide: pdb=" SG CYS B 663 " - pdb=" SG CYS B 687 " distance=2.07 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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=0, symmetry=0 Links applied BETA1-3 " BMA F 3 " - " BMA F 4 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " BETA1-6 " BMA F 3 " - " BMA F 5 " " BMA H 3 " - " BMA H 4 " NAG-ASN " NAG A1105 " - " ASN A 249 " " NAG A1106 " - " ASN A 680 " " NAG A1107 " - " ASN A 570 " " NAG A1108 " - " ASN A 15 " " NAG B 801 " - " ASN B 654 " " NAG C 1 " - " ASN A 931 " " NAG D 1 " - " ASN B 559 " " NAG E 1 " - " ASN B 320 " " NAG F 1 " - " ASN B 371 " " NAG G 1 " - " ASN B 99 " " NAG H 1 " - " ASN B 452 " Time building additional restraints: 5.56 Conformation dependent library (CDL) restraints added in 3.9 seconds 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3048 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 30 helices and 23 sheets defined 12.6% alpha, 25.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.45 Creating SS restraints... Processing helix chain 'A' and resid 152 through 157 Processing helix chain 'A' and resid 188 through 191 No H-bonds generated for 'chain 'A' and resid 188 through 191' Processing helix chain 'A' and resid 200 through 206 Processing helix chain 'A' and resid 260 through 263 No H-bonds generated for 'chain 'A' and resid 260 through 263' Processing helix chain 'A' and resid 516 through 518 No H-bonds generated for 'chain 'A' and resid 516 through 518' 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 911 through 915 Processing helix chain 'A' and resid 966 through 990 Processing helix chain 'B' and resid 13 through 19 Processing helix chain 'B' and resid 41 through 47 removed outlier: 3.823A pdb=" N ASP B 47 " --> pdb=" O ASN B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 79 No H-bonds generated for 'chain 'B' and resid 77 through 79' Processing helix chain 'B' and resid 122 through 130 removed outlier: 4.363A pdb=" N ASP B 126 " --> pdb=" O SER B 123 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU B 128 " --> pdb=" O LYS B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 141 Processing helix chain 'B' and resid 170 through 173 Processing helix chain 'B' and resid 200 through 206 removed outlier: 3.845A pdb=" N ASN B 204 " --> pdb=" O VAL B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 231 Processing helix chain 'B' and resid 233 through 236 No H-bonds generated for 'chain 'B' and resid 233 through 236' Processing helix chain 'B' and resid 260 through 263 Processing helix chain 'B' and resid 282 through 285 removed outlier: 4.532A pdb=" N THR B 285 " --> pdb=" O SER B 282 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 282 through 285' Processing helix chain 'B' and resid 292 through 301 Processing helix chain 'B' and resid 312 through 322 removed outlier: 4.502A pdb=" N ASN B 316 " --> pdb=" O GLU B 312 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LEU B 317 " --> pdb=" O ASN B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 351 Processing helix chain 'B' and resid 436 through 440 Processing helix chain 'B' and resid 446 through 448 No H-bonds generated for 'chain 'B' and resid 446 through 448' Processing helix chain 'B' and resid 494 through 497 Processing helix chain 'B' and resid 536 through 538 No H-bonds generated for 'chain 'B' and resid 536 through 538' Processing helix chain 'B' and resid 574 through 577 Processing helix chain 'B' and resid 607 through 609 No H-bonds generated for 'chain 'B' and resid 607 through 609' Processing helix chain 'B' and resid 612 through 620 removed outlier: 3.722A pdb=" N CYS B 617 " --> pdb=" O GLU B 613 " (cutoff:3.500A) Processing helix chain 'B' and resid 694 through 717 Processing sheet with id= A, first strand: chain 'A' and resid 9 through 12 removed outlier: 4.704A pdb=" N VAL A 425 " --> pdb=" O ASP A 434 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N ILE A 436 " --> pdb=" O GLY A 423 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N GLY A 423 " --> pdb=" O ILE A 436 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N GLY A 438 " --> pdb=" O LEU A 421 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N LEU A 421 " --> pdb=" O GLY A 438 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 52 through 56 removed outlier: 4.069A pdb=" N SER A 22 " --> pdb=" O GLY A 38 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 76 through 79 Processing sheet with id= D, first strand: chain 'A' and resid 96 through 100 removed outlier: 3.838A pdb=" N SER A 96 " --> pdb=" O CYS A 107 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 173 through 175 Processing sheet with id= F, first strand: chain 'A' and resid 235 through 242 removed outlier: 5.798A pdb=" N GLY A 256 " --> pdb=" O GLY A 236 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N SER A 238 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VAL A 254 " --> pdb=" O SER A 238 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N ALA A 240 " --> pdb=" O GLU A 252 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N GLU A 252 " --> pdb=" O ALA A 240 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 306 through 310 Processing sheet with id= H, first strand: chain 'A' and resid 360 through 362 removed outlier: 3.734A pdb=" N GLN A 405 " --> pdb=" O VAL A 391 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 393 through 395 removed outlier: 4.517A pdb=" N LEU A 393 " --> pdb=" O ARG A 400 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 585 through 588 Processing sheet with id= K, first strand: chain 'A' and resid 530 through 536 Processing sheet with id= L, first strand: chain 'A' and resid 612 through 619 removed outlier: 4.104A pdb=" N ARG A 661 " --> pdb=" O LEU A 704 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 736 through 741 removed outlier: 5.661A pdb=" N LEU A 649 " --> pdb=" O GLU A 688 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N GLU A 688 " --> pdb=" O LEU A 649 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N VAL A 651 " --> pdb=" O LEU A 686 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N LEU A 686 " --> pdb=" O VAL A 651 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'A' and resid 748 through 755 removed outlier: 7.141A pdb=" N PHE A 908 " --> pdb=" O ILE A 815 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N ILE A 815 " --> pdb=" O PHE A 908 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'A' and resid 758 through 760 removed outlier: 9.311A pdb=" N LEU A 759 " --> pdb=" O TRP A 952 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N GLN A 954 " --> pdb=" O LEU A 759 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N PHE A 922 " --> pdb=" O LEU A 955 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N GLN A 925 " --> pdb=" O PRO A 804 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 87 through 92 removed outlier: 6.128A pdb=" N ILE B 426 " --> pdb=" O ILE B 88 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N LEU B 90 " --> pdb=" O ILE B 426 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N GLN B 428 " --> pdb=" O LEU B 90 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N LEU B 92 " --> pdb=" O GLN B 428 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N THR B 430 " --> pdb=" O LEU B 92 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 97 through 105 Processing sheet with id= R, first strand: chain 'B' and resid 328 through 332 removed outlier: 6.870A pdb=" N LEU B 306 " --> pdb=" O THR B 329 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N GLY B 331 " --> pdb=" O LEU B 306 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N PHE B 308 " --> pdb=" O GLY B 331 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ALA B 155 " --> pdb=" O HIS B 192 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N HIS B 192 " --> pdb=" O ALA B 155 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'B' and resid 454 through 456 Processing sheet with id= T, first strand: chain 'B' and resid 500 through 502 Processing sheet with id= U, first strand: chain 'B' and resid 541 through 543 Processing sheet with id= V, first strand: chain 'B' and resid 580 through 582 Processing sheet with id= W, first strand: chain 'B' and resid 638 through 640 removed outlier: 3.523A pdb=" N ILE B 678 " --> pdb=" O TYR B 670 " (cutoff:3.500A) 393 hydrogen bonds defined for protein. 1040 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.29 Time building geometry restraints manager: 6.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 2227 1.30 - 1.44: 3331 1.44 - 1.57: 7712 1.57 - 1.71: 1 1.71 - 1.85: 128 Bond restraints: 13399 Sorted by residual: bond pdb=" C GLY A 423 " pdb=" O GLY A 423 " ideal model delta sigma weight residual 1.233 1.186 0.047 7.00e-03 2.04e+04 4.49e+01 bond pdb=" C PRO A 433 " pdb=" O PRO A 433 " ideal model delta sigma weight residual 1.233 1.159 0.074 1.16e-02 7.43e+03 4.03e+01 bond pdb=" C SER A 420 " pdb=" O SER A 420 " ideal model delta sigma weight residual 1.235 1.165 0.070 1.14e-02 7.69e+03 3.81e+01 bond pdb=" CA SER B 211 " pdb=" CB SER B 211 " ideal model delta sigma weight residual 1.534 1.458 0.076 1.34e-02 5.57e+03 3.25e+01 bond pdb=" N GLY A 641 " pdb=" CA GLY A 641 " ideal model delta sigma weight residual 1.442 1.483 -0.041 7.70e-03 1.69e+04 2.85e+01 ... (remaining 13394 not shown) Histogram of bond angle deviations from ideal: 94.52 - 102.65: 98 102.65 - 110.79: 3856 110.79 - 118.92: 8229 118.92 - 127.06: 5891 127.06 - 135.19: 150 Bond angle restraints: 18224 Sorted by residual: angle pdb=" C PRO A 403 " pdb=" CA PRO A 403 " pdb=" CB PRO A 403 " ideal model delta sigma weight residual 111.56 102.38 9.18 1.09e+00 8.42e-01 7.09e+01 angle pdb=" CA GLY A 387 " pdb=" C GLY A 387 " pdb=" O GLY A 387 " ideal model delta sigma weight residual 122.22 116.88 5.34 6.50e-01 2.37e+00 6.76e+01 angle pdb=" CA GLY B 555 " pdb=" C GLY B 555 " pdb=" O GLY B 555 " ideal model delta sigma weight residual 122.22 117.90 4.32 6.50e-01 2.37e+00 4.41e+01 angle pdb=" N PRO A 403 " pdb=" CA PRO A 403 " pdb=" CB PRO A 403 " ideal model delta sigma weight residual 103.30 108.50 -5.20 8.00e-01 1.56e+00 4.22e+01 angle pdb=" CA GLY B 518 " pdb=" C GLY B 518 " pdb=" O GLY B 518 " ideal model delta sigma weight residual 122.22 118.22 4.00 6.50e-01 2.37e+00 3.80e+01 ... (remaining 18219 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.38: 7726 24.38 - 48.75: 632 48.75 - 73.12: 138 73.12 - 97.50: 61 97.50 - 121.87: 19 Dihedral angle restraints: 8576 sinusoidal: 3814 harmonic: 4762 Sorted by residual: dihedral pdb=" CB CYS B 16 " pdb=" SG CYS B 16 " pdb=" SG CYS B 38 " pdb=" CB CYS B 38 " ideal model delta sinusoidal sigma weight residual -86.00 -176.18 90.18 1 1.00e+01 1.00e-02 9.63e+01 dihedral pdb=" CB CYS B 549 " pdb=" SG CYS B 549 " pdb=" SG CYS B 558 " pdb=" CB CYS B 558 " ideal model delta sinusoidal sigma weight residual 93.00 -179.32 -87.68 1 1.00e+01 1.00e-02 9.21e+01 dihedral pdb=" CB CYS B 601 " pdb=" SG CYS B 601 " pdb=" SG CYS B 604 " pdb=" CB CYS B 604 " ideal model delta sinusoidal sigma weight residual -86.00 -164.75 78.75 1 1.00e+01 1.00e-02 7.73e+01 ... (remaining 8573 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.147: 1863 0.147 - 0.293: 238 0.293 - 0.440: 3 0.440 - 0.587: 1 0.587 - 0.733: 1 Chirality restraints: 2106 Sorted by residual: chirality pdb=" C1 BMA F 3 " pdb=" O4 NAG F 2 " pdb=" C2 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-02 2.50e+03 7.23e+01 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-02 2.50e+03 6.88e+01 chirality pdb=" C1 BMA E 3 " pdb=" O4 NAG E 2 " pdb=" C2 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-02 2.50e+03 5.74e+01 ... (remaining 2103 not shown) Planarity restraints: 2365 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 1 " 0.145 2.00e-02 2.50e+03 1.25e-01 1.96e+02 pdb=" C7 NAG C 1 " -0.097 2.00e-02 2.50e+03 pdb=" C8 NAG C 1 " 0.127 2.00e-02 2.50e+03 pdb=" N2 NAG C 1 " -0.178 2.00e-02 2.50e+03 pdb=" O7 NAG C 1 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 308 " -0.077 2.00e-02 2.50e+03 4.86e-02 4.13e+01 pdb=" CG PHE B 308 " 0.081 2.00e-02 2.50e+03 pdb=" CD1 PHE B 308 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 PHE B 308 " 0.042 2.00e-02 2.50e+03 pdb=" CE1 PHE B 308 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE B 308 " -0.027 2.00e-02 2.50e+03 pdb=" CZ PHE B 308 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1106 " 0.064 2.00e-02 2.50e+03 5.44e-02 3.70e+01 pdb=" C7 NAG A1106 " -0.032 2.00e-02 2.50e+03 pdb=" C8 NAG A1106 " 0.053 2.00e-02 2.50e+03 pdb=" N2 NAG A1106 " -0.082 2.00e-02 2.50e+03 pdb=" O7 NAG A1106 " -0.003 2.00e-02 2.50e+03 ... (remaining 2362 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.38: 75 2.38 - 3.01: 7286 3.01 - 3.64: 19745 3.64 - 4.27: 28742 4.27 - 4.90: 46990 Nonbonded interactions: 102838 Sorted by model distance: nonbonded pdb=" OE1 GLU B 220 " pdb="CA CA B 805 " model vdw 1.751 2.510 nonbonded pdb=" OE1 GLU A 243 " pdb="CA CA A1102 " model vdw 1.789 2.510 nonbonded pdb=" OE2 GLU A 252 " pdb="CA CA A1102 " model vdw 1.794 2.510 nonbonded pdb=" OE2 GLU A 642 " pdb="CA CA A1109 " model vdw 1.822 2.510 nonbonded pdb="MG MG B 804 " pdb=" O HOH B 902 " model vdw 1.906 2.170 ... (remaining 102833 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'G' } 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=0.00 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: 1.600 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: 0.010 Extract box with map and model: 6.200 Check model and map are aligned: 0.220 Set scattering table: 0.120 Process input model: 43.480 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 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 : 0.016 0.080 13399 Z= 1.044 Angle : 1.929 11.241 18224 Z= 1.328 Chirality : 0.095 0.733 2106 Planarity : 0.009 0.152 2354 Dihedral : 20.167 121.873 5414 Min Nonbonded Distance : 1.751 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.97 % Allowed : 9.06 % Favored : 89.98 % Rotamer: Outliers : 5.50 % Allowed : 17.48 % Favored : 77.03 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 6.19 % Cis-general : 0.06 % 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: -1.99 (0.20), residues: 1657 helix: -0.68 (0.37), residues: 162 sheet: -0.46 (0.23), residues: 478 loop : -1.94 (0.19), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.008 TRP A 100 HIS 0.018 0.003 HIS A 112 PHE 0.081 0.010 PHE B 308 TYR 0.064 0.010 TYR A 288 ARG 0.020 0.002 ARG A 320 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 51 time to evaluate : 1.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ASP cc_start: 0.9255 (OUTLIER) cc_final: 0.9002 (m-30) REVERT: A 400 ARG cc_start: 0.1721 (OUTLIER) cc_final: 0.0346 (tpt170) REVERT: A 402 ARG cc_start: 0.3222 (OUTLIER) cc_final: 0.2560 (mtm-85) REVERT: A 549 MET cc_start: 0.8201 (mmm) cc_final: 0.7715 (mmm) REVERT: A 779 LYS cc_start: 0.8961 (OUTLIER) cc_final: 0.8344 (tppt) REVERT: A 924 LEU cc_start: 0.9707 (OUTLIER) cc_final: 0.9478 (tp) REVERT: B 534 GLU cc_start: 0.6569 (OUTLIER) cc_final: 0.5473 (mp0) outliers start: 78 outliers final: 38 residues processed: 124 average time/residue: 0.2612 time to fit residues: 47.5757 Evaluate side-chains 89 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 45 time to evaluate : 1.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 292 SER Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 400 ARG Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 402 ARG Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 587 HIS Chi-restraints excluded: chain A residue 628 ASP Chi-restraints excluded: chain A residue 679 GLU Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 692 PRO Chi-restraints excluded: chain A residue 779 LYS Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain A residue 950 GLN Chi-restraints excluded: chain A residue 955 LEU Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain B residue 46 LYS Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 376 ASN Chi-restraints excluded: chain B residue 475 GLU Chi-restraints excluded: chain B residue 534 GLU Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 636 ARG Chi-restraints excluded: chain B residue 642 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 0.7980 chunk 125 optimal weight: 0.7980 chunk 69 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 chunk 84 optimal weight: 9.9990 chunk 66 optimal weight: 5.9990 chunk 129 optimal weight: 0.9980 chunk 50 optimal weight: 6.9990 chunk 78 optimal weight: 6.9990 chunk 96 optimal weight: 5.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 376 ASN ** B 668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 13399 Z= 0.252 Angle : 0.744 16.890 18224 Z= 0.359 Chirality : 0.049 0.400 2106 Planarity : 0.005 0.141 2354 Dihedral : 15.505 108.468 2499 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.86 % Favored : 93.72 % Rotamer: Outliers : 2.68 % Allowed : 18.39 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.19 % Cis-general : 0.06 % 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: -1.25 (0.21), residues: 1657 helix: 0.59 (0.43), residues: 163 sheet: -0.29 (0.22), residues: 546 loop : -1.44 (0.20), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 776 HIS 0.005 0.001 HIS B 539 PHE 0.011 0.001 PHE B 248 TYR 0.019 0.001 TYR A 288 ARG 0.004 0.001 ARG B 216 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 47 time to evaluate : 1.400 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 400 ARG cc_start: 0.1482 (OUTLIER) cc_final: -0.0027 (mmt90) REVERT: A 549 MET cc_start: 0.7949 (mmm) cc_final: 0.7572 (mmm) REVERT: B 534 GLU cc_start: 0.6073 (OUTLIER) cc_final: 0.4853 (mp0) REVERT: B 636 ARG cc_start: 0.8392 (OUTLIER) cc_final: 0.8141 (mmp-170) outliers start: 38 outliers final: 24 residues processed: 83 average time/residue: 0.2217 time to fit residues: 28.9059 Evaluate side-chains 73 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 46 time to evaluate : 1.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 400 ARG Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 587 HIS Chi-restraints excluded: chain A residue 628 ASP Chi-restraints excluded: chain A residue 749 GLU Chi-restraints excluded: chain A residue 779 LYS Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 462 CYS Chi-restraints excluded: chain B residue 475 GLU Chi-restraints excluded: chain B residue 525 ASP Chi-restraints excluded: chain B residue 534 GLU Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 636 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 83 optimal weight: 10.0000 chunk 46 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 102 optimal weight: 9.9990 chunk 41 optimal weight: 0.0970 chunk 150 optimal weight: 0.3980 chunk 162 optimal weight: 4.9990 chunk 133 optimal weight: 0.9980 chunk 148 optimal weight: 30.0000 chunk 51 optimal weight: 8.9990 chunk 120 optimal weight: 0.0670 overall best weight: 1.1118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 HIS ** B 668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 13399 Z= 0.204 Angle : 0.672 11.047 18224 Z= 0.323 Chirality : 0.047 0.391 2106 Planarity : 0.005 0.134 2354 Dihedral : 12.676 99.237 2446 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.70 % Favored : 93.12 % Rotamer: Outliers : 2.11 % Allowed : 20.16 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.19 % Cis-general : 0.06 % 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: -0.89 (0.21), residues: 1657 helix: 0.92 (0.43), residues: 162 sheet: -0.06 (0.22), residues: 552 loop : -1.21 (0.21), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 839 HIS 0.004 0.001 HIS A 546 PHE 0.012 0.001 PHE B 248 TYR 0.013 0.001 TYR A 288 ARG 0.005 0.000 ARG B 633 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 45 time to evaluate : 1.513 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 288 TYR cc_start: 0.9091 (OUTLIER) cc_final: 0.7962 (t80) REVERT: A 400 ARG cc_start: 0.1572 (OUTLIER) cc_final: -0.0057 (mmt90) REVERT: A 549 MET cc_start: 0.7895 (mmm) cc_final: 0.7576 (mmm) REVERT: A 924 LEU cc_start: 0.9384 (tp) cc_final: 0.9039 (pp) REVERT: B 142 MET cc_start: 0.8979 (OUTLIER) cc_final: 0.8713 (tpt) REVERT: B 357 LEU cc_start: 0.9154 (mt) cc_final: 0.8916 (mt) REVERT: B 534 GLU cc_start: 0.5866 (OUTLIER) cc_final: 0.3759 (mp0) REVERT: B 636 ARG cc_start: 0.8468 (OUTLIER) cc_final: 0.8081 (mmp-170) outliers start: 30 outliers final: 21 residues processed: 72 average time/residue: 0.2499 time to fit residues: 28.3159 Evaluate side-chains 70 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 44 time to evaluate : 1.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 400 ARG Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 587 HIS Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 628 ASP Chi-restraints excluded: chain A residue 749 GLU Chi-restraints excluded: chain A residue 779 LYS Chi-restraints excluded: chain A residue 839 TRP Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 462 CYS Chi-restraints excluded: chain B residue 475 GLU Chi-restraints excluded: chain B residue 534 GLU Chi-restraints excluded: chain B residue 550 ASP Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 636 ARG Chi-restraints excluded: chain B residue 642 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 148 optimal weight: 20.0000 chunk 112 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 71 optimal weight: 0.9990 chunk 100 optimal weight: 0.7980 chunk 150 optimal weight: 8.9990 chunk 159 optimal weight: 6.9990 chunk 78 optimal weight: 9.9990 chunk 142 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 13399 Z= 0.256 Angle : 0.673 17.043 18224 Z= 0.322 Chirality : 0.046 0.392 2106 Planarity : 0.005 0.130 2354 Dihedral : 11.588 91.929 2440 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.94 % Favored : 92.87 % Rotamer: Outliers : 3.24 % Allowed : 20.58 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.19 % Cis-general : 0.06 % 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 (0.21), residues: 1657 helix: 1.01 (0.42), residues: 162 sheet: -0.01 (0.22), residues: 569 loop : -1.20 (0.21), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 929 HIS 0.003 0.001 HIS B 280 PHE 0.012 0.001 PHE A 289 TYR 0.012 0.001 TYR A 288 ARG 0.007 0.000 ARG B 530 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 43 time to evaluate : 1.456 Fit side-chains revert: symmetry clash REVERT: A 288 TYR cc_start: 0.9181 (OUTLIER) cc_final: 0.7307 (t80) REVERT: A 400 ARG cc_start: 0.1720 (OUTLIER) cc_final: -0.0071 (mmm-85) REVERT: A 549 MET cc_start: 0.7811 (mmm) cc_final: 0.7582 (mmm) REVERT: A 924 LEU cc_start: 0.9409 (tp) cc_final: 0.9035 (pp) REVERT: A 987 MET cc_start: 0.4463 (ptp) cc_final: 0.4180 (pmm) REVERT: B 142 MET cc_start: 0.9043 (OUTLIER) cc_final: 0.8784 (tpt) REVERT: B 568 MET cc_start: 0.9292 (tpt) cc_final: 0.9090 (tpt) REVERT: B 590 GLN cc_start: 0.7805 (OUTLIER) cc_final: 0.7497 (tm-30) REVERT: B 636 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.8176 (mmp-170) outliers start: 46 outliers final: 27 residues processed: 84 average time/residue: 0.2313 time to fit residues: 30.7535 Evaluate side-chains 75 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 43 time to evaluate : 1.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 400 ARG Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 587 HIS Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 628 ASP Chi-restraints excluded: chain A residue 779 LYS Chi-restraints excluded: chain A residue 839 TRP Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 462 CYS Chi-restraints excluded: chain B residue 475 GLU Chi-restraints excluded: chain B residue 506 CYS Chi-restraints excluded: chain B residue 525 ASP Chi-restraints excluded: chain B residue 550 ASP Chi-restraints excluded: chain B residue 590 GLN Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 636 ARG Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 655 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 132 optimal weight: 0.0980 chunk 90 optimal weight: 9.9990 chunk 2 optimal weight: 4.9990 chunk 118 optimal weight: 5.9990 chunk 65 optimal weight: 7.9990 chunk 136 optimal weight: 7.9990 chunk 110 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 81 optimal weight: 0.0980 chunk 143 optimal weight: 0.0170 chunk 40 optimal weight: 0.7980 overall best weight: 0.3418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 443 ASN ** A 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.087 13399 Z= 0.167 Angle : 0.642 13.729 18224 Z= 0.304 Chirality : 0.046 0.377 2106 Planarity : 0.005 0.126 2354 Dihedral : 10.553 88.550 2437 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.10 % Favored : 93.72 % Rotamer: Outliers : 2.47 % Allowed : 20.86 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.19 % Cis-general : 0.06 % 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: -0.65 (0.21), residues: 1657 helix: 1.03 (0.43), residues: 163 sheet: 0.23 (0.22), residues: 561 loop : -1.13 (0.21), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 929 HIS 0.020 0.001 HIS A 787 PHE 0.009 0.001 PHE B 248 TYR 0.013 0.001 TYR A 288 ARG 0.003 0.000 ARG A 90 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 46 time to evaluate : 1.394 Fit side-chains revert: symmetry clash REVERT: A 288 TYR cc_start: 0.9044 (OUTLIER) cc_final: 0.7803 (t80) REVERT: A 400 ARG cc_start: 0.0951 (OUTLIER) cc_final: 0.0091 (mmt90) REVERT: A 549 MET cc_start: 0.7851 (mmm) cc_final: 0.7563 (mmm) REVERT: A 693 MET cc_start: 0.8930 (ppp) cc_final: 0.8645 (ppp) REVERT: A 924 LEU cc_start: 0.9476 (tp) cc_final: 0.9117 (pp) REVERT: B 357 LEU cc_start: 0.9079 (mt) cc_final: 0.8849 (mt) REVERT: B 409 GLU cc_start: 0.9690 (OUTLIER) cc_final: 0.9476 (tp30) REVERT: B 636 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.8103 (mmp-170) outliers start: 35 outliers final: 23 residues processed: 76 average time/residue: 0.2386 time to fit residues: 28.5641 Evaluate side-chains 70 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 43 time to evaluate : 1.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 400 ARG Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 587 HIS Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 628 ASP Chi-restraints excluded: chain A residue 779 LYS Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 409 GLU Chi-restraints excluded: chain B residue 462 CYS Chi-restraints excluded: chain B residue 475 GLU Chi-restraints excluded: chain B residue 506 CYS Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 636 ARG Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 655 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 53 optimal weight: 0.9980 chunk 143 optimal weight: 0.9990 chunk 31 optimal weight: 0.0670 chunk 93 optimal weight: 50.0000 chunk 39 optimal weight: 3.9990 chunk 159 optimal weight: 20.0000 chunk 132 optimal weight: 9.9990 chunk 73 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 83 optimal weight: 10.0000 overall best weight: 2.0124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 GLN ** B 668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 13399 Z= 0.263 Angle : 0.667 13.467 18224 Z= 0.319 Chirality : 0.046 0.381 2106 Planarity : 0.005 0.124 2354 Dihedral : 10.089 87.907 2436 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.58 % Favored : 93.30 % Rotamer: Outliers : 2.89 % Allowed : 20.58 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.19 % Cis-general : 0.06 % 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 (0.21), residues: 1657 helix: 1.15 (0.42), residues: 164 sheet: 0.19 (0.22), residues: 568 loop : -1.08 (0.21), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 929 HIS 0.003 0.001 HIS B 280 PHE 0.012 0.001 PHE A 289 TYR 0.012 0.001 TYR A 288 ARG 0.009 0.000 ARG B 530 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 44 time to evaluate : 1.602 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 400 ARG cc_start: 0.1801 (OUTLIER) cc_final: -0.0008 (mmm-85) REVERT: A 549 MET cc_start: 0.7756 (mmm) cc_final: 0.7535 (mmm) REVERT: A 693 MET cc_start: 0.8934 (ppp) cc_final: 0.8638 (ppp) REVERT: A 924 LEU cc_start: 0.9489 (tp) cc_final: 0.9151 (pp) REVERT: A 987 MET cc_start: 0.4113 (ptp) cc_final: 0.3893 (pmm) REVERT: B 142 MET cc_start: 0.9027 (OUTLIER) cc_final: 0.8756 (tpt) REVERT: B 568 MET cc_start: 0.9328 (tpp) cc_final: 0.8964 (tpt) REVERT: B 636 ARG cc_start: 0.8558 (OUTLIER) cc_final: 0.8259 (mmp-170) outliers start: 41 outliers final: 27 residues processed: 80 average time/residue: 0.2539 time to fit residues: 31.1867 Evaluate side-chains 74 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 44 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 400 ARG Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 587 HIS Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 628 ASP Chi-restraints excluded: chain A residue 779 LYS Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 957 ARG Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 462 CYS Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 475 GLU Chi-restraints excluded: chain B residue 506 CYS Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 636 ARG Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 655 CYS Chi-restraints excluded: chain B residue 661 ASP Chi-restraints excluded: chain B residue 687 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 153 optimal weight: 10.0000 chunk 17 optimal weight: 1.9990 chunk 90 optimal weight: 6.9990 chunk 116 optimal weight: 2.9990 chunk 134 optimal weight: 4.9990 chunk 89 optimal weight: 20.0000 chunk 159 optimal weight: 6.9990 chunk 99 optimal weight: 0.8980 chunk 96 optimal weight: 4.9990 chunk 73 optimal weight: 0.7980 chunk 98 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 13399 Z= 0.250 Angle : 0.661 12.496 18224 Z= 0.315 Chirality : 0.045 0.374 2106 Planarity : 0.005 0.121 2354 Dihedral : 9.529 87.276 2436 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.76 % Favored : 93.12 % Rotamer: Outliers : 3.52 % Allowed : 20.65 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.19 % Cis-general : 0.06 % 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: -0.61 (0.21), residues: 1657 helix: 1.14 (0.43), residues: 164 sheet: 0.17 (0.22), residues: 568 loop : -1.08 (0.21), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 929 HIS 0.003 0.001 HIS A 587 PHE 0.012 0.001 PHE A 289 TYR 0.011 0.001 TYR A 288 ARG 0.006 0.000 ARG A 402 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 46 time to evaluate : 1.391 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 288 TYR cc_start: 0.9213 (OUTLIER) cc_final: 0.7191 (t80) REVERT: A 400 ARG cc_start: 0.1984 (OUTLIER) cc_final: 0.0024 (mmm-85) REVERT: A 549 MET cc_start: 0.7829 (mmm) cc_final: 0.7622 (mmm) REVERT: A 693 MET cc_start: 0.8912 (ppp) cc_final: 0.8599 (ppp) REVERT: A 880 CYS cc_start: 0.7195 (OUTLIER) cc_final: 0.6986 (p) REVERT: A 902 MET cc_start: 0.8257 (tpp) cc_final: 0.7851 (tpt) REVERT: A 924 LEU cc_start: 0.9503 (tp) cc_final: 0.9158 (pp) REVERT: B 142 MET cc_start: 0.9050 (OUTLIER) cc_final: 0.8788 (tpt) REVERT: B 636 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.8195 (mmp-170) outliers start: 50 outliers final: 38 residues processed: 90 average time/residue: 0.2450 time to fit residues: 34.4150 Evaluate side-chains 87 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 44 time to evaluate : 1.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 400 ARG Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 587 HIS Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 628 ASP Chi-restraints excluded: chain A residue 779 LYS Chi-restraints excluded: chain A residue 839 TRP Chi-restraints excluded: chain A residue 880 CYS Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 957 ARG Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 361 ASP Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 462 CYS Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 475 GLU Chi-restraints excluded: chain B residue 506 CYS Chi-restraints excluded: chain B residue 531 TYR Chi-restraints excluded: chain B residue 550 ASP Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 636 ARG Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 655 CYS Chi-restraints excluded: chain B residue 661 ASP Chi-restraints excluded: chain B residue 687 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 63 optimal weight: 9.9990 chunk 94 optimal weight: 7.9990 chunk 47 optimal weight: 0.0980 chunk 31 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 101 optimal weight: 5.9990 chunk 108 optimal weight: 9.9990 chunk 78 optimal weight: 7.9990 chunk 14 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 144 optimal weight: 7.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 13399 Z= 0.228 Angle : 0.664 16.929 18224 Z= 0.314 Chirality : 0.045 0.367 2106 Planarity : 0.005 0.119 2354 Dihedral : 9.160 86.209 2436 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.40 % Favored : 93.48 % Rotamer: Outliers : 3.17 % Allowed : 21.35 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.19 % Cis-general : 0.06 % 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: -0.61 (0.21), residues: 1657 helix: 1.07 (0.43), residues: 164 sheet: 0.19 (0.22), residues: 569 loop : -1.07 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 929 HIS 0.003 0.001 HIS A 587 PHE 0.011 0.001 PHE B 248 TYR 0.011 0.001 TYR A 288 ARG 0.005 0.000 ARG B 530 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 45 time to evaluate : 1.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 TYR cc_start: 0.9190 (OUTLIER) cc_final: 0.7162 (t80) REVERT: A 400 ARG cc_start: 0.2052 (OUTLIER) cc_final: 0.0153 (mmm-85) REVERT: A 549 MET cc_start: 0.7819 (mmm) cc_final: 0.7608 (mmm) REVERT: A 693 MET cc_start: 0.8939 (ppp) cc_final: 0.8631 (ppp) REVERT: A 880 CYS cc_start: 0.7196 (OUTLIER) cc_final: 0.6969 (p) REVERT: A 924 LEU cc_start: 0.9545 (tp) cc_final: 0.9201 (pp) REVERT: B 142 MET cc_start: 0.9038 (OUTLIER) cc_final: 0.8769 (tpt) REVERT: B 636 ARG cc_start: 0.8521 (OUTLIER) cc_final: 0.8190 (mmp-170) outliers start: 45 outliers final: 36 residues processed: 86 average time/residue: 0.2450 time to fit residues: 32.0504 Evaluate side-chains 85 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 44 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 400 ARG Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 587 HIS Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 628 ASP Chi-restraints excluded: chain A residue 779 LYS Chi-restraints excluded: chain A residue 839 TRP Chi-restraints excluded: chain A residue 880 CYS Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 957 ARG Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 72 LYS Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 462 CYS Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 475 GLU Chi-restraints excluded: chain B residue 506 CYS Chi-restraints excluded: chain B residue 525 ASP Chi-restraints excluded: chain B residue 531 TYR Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 636 ARG Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 655 CYS Chi-restraints excluded: chain B residue 661 ASP Chi-restraints excluded: chain B residue 687 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 152 optimal weight: 3.9990 chunk 139 optimal weight: 9.9990 chunk 148 optimal weight: 20.0000 chunk 89 optimal weight: 20.0000 chunk 64 optimal weight: 9.9990 chunk 116 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 133 optimal weight: 4.9990 chunk 140 optimal weight: 3.9990 chunk 147 optimal weight: 0.9990 chunk 97 optimal weight: 0.0770 overall best weight: 2.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 13399 Z= 0.278 Angle : 0.677 15.427 18224 Z= 0.323 Chirality : 0.045 0.369 2106 Planarity : 0.005 0.118 2354 Dihedral : 9.042 85.797 2436 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.88 % Favored : 93.00 % Rotamer: Outliers : 3.38 % Allowed : 21.21 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.19 % Cis-general : 0.06 % 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: -0.66 (0.21), residues: 1657 helix: 1.02 (0.43), residues: 164 sheet: 0.13 (0.22), residues: 570 loop : -1.08 (0.21), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 929 HIS 0.005 0.001 HIS B 509 PHE 0.013 0.001 PHE A 289 TYR 0.011 0.001 TYR A 448 ARG 0.007 0.000 ARG B 530 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 44 time to evaluate : 1.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 TYR cc_start: 0.9264 (OUTLIER) cc_final: 0.7277 (t80) REVERT: A 400 ARG cc_start: 0.2082 (OUTLIER) cc_final: 0.0073 (mmm-85) REVERT: A 549 MET cc_start: 0.7727 (mmm) cc_final: 0.7518 (mmm) REVERT: A 693 MET cc_start: 0.8927 (ppp) cc_final: 0.8622 (ppp) REVERT: A 807 SER cc_start: 0.7512 (OUTLIER) cc_final: 0.7307 (p) REVERT: A 902 MET cc_start: 0.8241 (tpp) cc_final: 0.7875 (tpt) REVERT: A 924 LEU cc_start: 0.9550 (tp) cc_final: 0.9190 (pp) REVERT: B 142 MET cc_start: 0.9072 (OUTLIER) cc_final: 0.8816 (tpt) REVERT: B 636 ARG cc_start: 0.8571 (OUTLIER) cc_final: 0.8230 (mmp-170) outliers start: 48 outliers final: 40 residues processed: 87 average time/residue: 0.2508 time to fit residues: 33.8154 Evaluate side-chains 89 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 44 time to evaluate : 1.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 400 ARG Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 587 HIS Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 628 ASP Chi-restraints excluded: chain A residue 779 LYS Chi-restraints excluded: chain A residue 807 SER Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 839 TRP Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 957 ARG Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain B residue 72 LYS Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 361 ASP Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 462 CYS Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 475 GLU Chi-restraints excluded: chain B residue 506 CYS Chi-restraints excluded: chain B residue 525 ASP Chi-restraints excluded: chain B residue 531 TYR Chi-restraints excluded: chain B residue 550 ASP Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 636 ARG Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 655 CYS Chi-restraints excluded: chain B residue 661 ASP Chi-restraints excluded: chain B residue 687 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 156 optimal weight: 7.9990 chunk 95 optimal weight: 0.9980 chunk 74 optimal weight: 7.9990 chunk 108 optimal weight: 7.9990 chunk 164 optimal weight: 10.0000 chunk 151 optimal weight: 9.9990 chunk 130 optimal weight: 0.8980 chunk 13 optimal weight: 0.4980 chunk 101 optimal weight: 0.0570 chunk 80 optimal weight: 0.0670 chunk 103 optimal weight: 5.9990 overall best weight: 0.5036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 13399 Z= 0.169 Angle : 0.648 15.525 18224 Z= 0.305 Chirality : 0.045 0.354 2106 Planarity : 0.005 0.115 2354 Dihedral : 8.736 83.967 2436 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.92 % Favored : 93.90 % Rotamer: Outliers : 2.61 % Allowed : 21.85 % Favored : 75.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.19 % Cis-general : 0.06 % 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: -0.54 (0.21), residues: 1657 helix: 0.92 (0.42), residues: 169 sheet: 0.31 (0.22), residues: 564 loop : -1.04 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 929 HIS 0.003 0.001 HIS A 587 PHE 0.009 0.001 PHE A 356 TYR 0.012 0.001 TYR A 288 ARG 0.002 0.000 ARG A 724 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 43 time to evaluate : 1.578 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 288 TYR cc_start: 0.9131 (OUTLIER) cc_final: 0.7140 (t80) REVERT: A 400 ARG cc_start: 0.1404 (OUTLIER) cc_final: 0.0224 (mmt90) REVERT: A 549 MET cc_start: 0.7762 (mmm) cc_final: 0.7516 (mmm) REVERT: A 693 MET cc_start: 0.8938 (ppp) cc_final: 0.8619 (ppp) REVERT: A 807 SER cc_start: 0.7477 (OUTLIER) cc_final: 0.7276 (p) REVERT: A 902 MET cc_start: 0.8167 (tpp) cc_final: 0.7796 (tpt) REVERT: A 924 LEU cc_start: 0.9528 (tp) cc_final: 0.9152 (pp) REVERT: A 987 MET cc_start: 0.4721 (ptp) cc_final: 0.4492 (pmm) REVERT: B 636 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.8160 (mmp-170) outliers start: 37 outliers final: 28 residues processed: 77 average time/residue: 0.2554 time to fit residues: 30.4900 Evaluate side-chains 75 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 43 time to evaluate : 1.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 400 ARG Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 587 HIS Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 628 ASP Chi-restraints excluded: chain A residue 779 LYS Chi-restraints excluded: chain A residue 807 SER Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 839 TRP Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 462 CYS Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 475 GLU Chi-restraints excluded: chain B residue 506 CYS Chi-restraints excluded: chain B residue 531 TYR Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 636 ARG Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 655 CYS Chi-restraints excluded: chain B residue 687 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 chunk 54 optimal weight: 0.0020 chunk 134 optimal weight: 8.9990 chunk 16 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 overall best weight: 1.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.073285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.047542 restraints weight = 93103.824| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 5.85 r_work: 0.2769 rms_B_bonded: 5.53 restraints_weight: 2.0000 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2750 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2750 r_free = 0.2750 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2750 r_free = 0.2750 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2750 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 13399 Z= 0.258 Angle : 0.667 15.169 18224 Z= 0.317 Chirality : 0.045 0.363 2106 Planarity : 0.005 0.114 2354 Dihedral : 8.697 83.021 2436 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.40 % Favored : 93.48 % Rotamer: Outliers : 2.89 % Allowed : 21.78 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.19 % Cis-general : 0.06 % 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: -0.58 (0.21), residues: 1657 helix: 1.04 (0.43), residues: 164 sheet: 0.20 (0.22), residues: 568 loop : -1.04 (0.21), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 929 HIS 0.003 0.001 HIS B 280 PHE 0.012 0.001 PHE A 289 TYR 0.011 0.001 TYR A 448 ARG 0.009 0.000 ARG B 530 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2945.62 seconds wall clock time: 53 minutes 45.09 seconds (3225.09 seconds total)