Starting phenix.real_space_refine on Sun Dec 10 02:52:15 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t2v_40989/12_2023/8t2v_40989_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t2v_40989/12_2023/8t2v_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_40989/12_2023/8t2v_40989.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t2v_40989/12_2023/8t2v_40989.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t2v_40989/12_2023/8t2v_40989_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t2v_40989/12_2023/8t2v_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-1.21rc1-5172/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: 6 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: 6 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: 6 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: 6 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: 10.83, per 1000 atoms: 0.82 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 3.6 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: 3.42 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: 4.68 Time building geometry restraints manager: 6.01 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 - 21.63: 7496 21.63 - 43.25: 753 43.25 - 64.88: 150 64.88 - 86.50: 31 86.50 - 108.13: 13 Dihedral angle restraints: 8443 sinusoidal: 3681 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 8440 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: 2.060 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: 6.370 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 44.350 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.790 ------------------------------------------------------------------------------- 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 : 17.642 108.126 5281 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 : 1.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 78 outliers final: 38 residues processed: 124 average time/residue: 0.2724 time to fit residues: 49.4733 Evaluate side-chains 83 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 45 time to evaluate : 1.466 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 1 residues processed: 38 average time/residue: 0.1408 time to fit residues: 11.1712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 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: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 0.8363 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 13399 Z= 0.254 Angle : 0.739 17.905 18224 Z= 0.358 Chirality : 0.047 0.407 2106 Planarity : 0.005 0.139 2354 Dihedral : 9.983 96.444 2278 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.68 % Favored : 93.90 % Rotamer: Outliers : 1.34 % Allowed : 17.97 % Favored : 80.69 % 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: -1.23 (0.21), residues: 1657 helix: 0.59 (0.43), residues: 163 sheet: -0.27 (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 262 HIS 0.005 0.001 HIS B 539 PHE 0.011 0.001 PHE B 248 TYR 0.020 0.001 TYR A 288 ARG 0.007 0.001 ARG B 636 *********************** 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 66 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 47 time to evaluate : 1.586 Fit side-chains outliers start: 19 outliers final: 10 residues processed: 64 average time/residue: 0.2153 time to fit residues: 23.0169 Evaluate side-chains 56 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 46 time to evaluate : 1.524 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1181 time to fit residues: 4.3417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 83 optimal weight: 7.9990 chunk 46 optimal weight: 0.0980 chunk 124 optimal weight: 3.9990 chunk 102 optimal weight: 9.9990 chunk 41 optimal weight: 0.0970 chunk 150 optimal weight: 7.9990 chunk 162 optimal weight: 5.9990 chunk 133 optimal weight: 2.9990 chunk 148 optimal weight: 20.0000 chunk 51 optimal weight: 9.9990 chunk 120 optimal weight: 0.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.8375 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 13399 Z= 0.239 Angle : 0.686 11.998 18224 Z= 0.332 Chirality : 0.047 0.394 2106 Planarity : 0.005 0.134 2354 Dihedral : 9.268 94.965 2278 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.88 % Favored : 92.87 % Rotamer: Outliers : 1.13 % Allowed : 19.38 % Favored : 79.49 % 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: -0.97 (0.21), residues: 1657 helix: 0.84 (0.43), residues: 163 sheet: -0.12 (0.22), residues: 547 loop : -1.25 (0.21), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 929 HIS 0.006 0.001 HIS A 787 PHE 0.013 0.001 PHE A 289 TYR 0.012 0.001 TYR A 448 ARG 0.005 0.000 ARG B 530 *********************** 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 60 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 44 time to evaluate : 1.419 Fit side-chains outliers start: 16 outliers final: 8 residues processed: 57 average time/residue: 0.2307 time to fit residues: 21.9531 Evaluate side-chains 52 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 44 time to evaluate : 1.595 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1410 time to fit residues: 4.2077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 148 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 77 optimal weight: 20.0000 chunk 16 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 150 optimal weight: 8.9990 chunk 159 optimal weight: 20.0000 chunk 78 optimal weight: 10.0000 chunk 142 optimal weight: 8.9990 chunk 42 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 376 ASN B 438 GLN ** B 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.085 13399 Z= 0.431 Angle : 0.776 17.768 18224 Z= 0.381 Chirality : 0.048 0.400 2106 Planarity : 0.006 0.132 2354 Dihedral : 8.954 95.209 2278 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.39 % Favored : 91.43 % Rotamer: Outliers : 1.55 % Allowed : 20.58 % Favored : 77.87 % 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: -1.22 (0.21), residues: 1657 helix: 0.77 (0.42), residues: 161 sheet: -0.36 (0.22), residues: 557 loop : -1.39 (0.21), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 260 HIS 0.006 0.001 HIS B 280 PHE 0.025 0.002 PHE A 289 TYR 0.020 0.002 TYR A 237 ARG 0.014 0.001 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 67 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 45 time to evaluate : 1.508 Fit side-chains outliers start: 22 outliers final: 13 residues processed: 61 average time/residue: 0.2087 time to fit residues: 21.9886 Evaluate side-chains 57 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 44 time to evaluate : 1.505 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1215 time to fit residues: 4.9410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 132 optimal weight: 0.0050 chunk 90 optimal weight: 7.9990 chunk 2 optimal weight: 0.8980 chunk 118 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 136 optimal weight: 5.9990 chunk 110 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 81 optimal weight: 0.0040 chunk 143 optimal weight: 0.0370 chunk 40 optimal weight: 0.5980 overall best weight: 0.3084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 438 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: 0.8357 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 13399 Z= 0.175 Angle : 0.671 14.810 18224 Z= 0.318 Chirality : 0.046 0.376 2106 Planarity : 0.005 0.126 2354 Dihedral : 8.310 92.624 2278 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.46 % Favored : 93.36 % Rotamer: Outliers : 0.99 % Allowed : 21.49 % Favored : 77.52 % 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: -0.84 (0.21), residues: 1657 helix: 0.89 (0.42), residues: 162 sheet: 0.05 (0.22), residues: 559 loop : -1.22 (0.21), residues: 936 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 0.011 0.001 PHE B 248 TYR 0.013 0.001 TYR A 288 ARG 0.004 0.000 ARG B 636 *********************** 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 59 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 45 time to evaluate : 1.746 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 5 residues processed: 58 average time/residue: 0.2279 time to fit residues: 22.4967 Evaluate side-chains 47 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 42 time to evaluate : 1.458 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1278 time to fit residues: 3.3784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 53 optimal weight: 6.9990 chunk 143 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 93 optimal weight: 50.0000 chunk 39 optimal weight: 1.9990 chunk 159 optimal weight: 20.0000 chunk 132 optimal weight: 6.9990 chunk 73 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 83 optimal weight: 20.0000 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 438 GLN B 449 ASN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 13399 Z= 0.395 Angle : 0.741 14.069 18224 Z= 0.359 Chirality : 0.047 0.391 2106 Planarity : 0.006 0.125 2354 Dihedral : 8.212 92.586 2278 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 15.07 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.15 % Favored : 91.73 % Rotamer: Outliers : 0.99 % Allowed : 22.41 % Favored : 76.60 % 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: -1.04 (0.21), residues: 1657 helix: 0.94 (0.42), residues: 162 sheet: -0.19 (0.22), residues: 569 loop : -1.34 (0.21), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 113 HIS 0.005 0.001 HIS B 509 PHE 0.019 0.002 PHE A 289 TYR 0.014 0.002 TYR A 448 ARG 0.015 0.001 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 55 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 41 time to evaluate : 1.537 Fit side-chains outliers start: 14 outliers final: 5 residues processed: 53 average time/residue: 0.2148 time to fit residues: 19.5695 Evaluate side-chains 46 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 41 time to evaluate : 1.526 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1187 time to fit residues: 3.1775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 90 optimal weight: 0.9990 chunk 116 optimal weight: 0.9980 chunk 134 optimal weight: 4.9990 chunk 89 optimal weight: 0.0980 chunk 159 optimal weight: 6.9990 chunk 99 optimal weight: 0.3980 chunk 96 optimal weight: 2.9990 chunk 73 optimal weight: 6.9990 chunk 98 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.8376 moved from start: 0.2140 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= 0.188 Angle : 0.662 13.210 18224 Z= 0.315 Chirality : 0.045 0.370 2106 Planarity : 0.005 0.121 2354 Dihedral : 7.715 90.524 2278 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.22 % Favored : 93.66 % Rotamer: Outliers : 0.56 % Allowed : 22.48 % Favored : 76.96 % 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: 1.00 (0.43), residues: 162 sheet: 0.04 (0.22), residues: 561 loop : -1.23 (0.21), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 929 HIS 0.002 0.001 HIS B 539 PHE 0.011 0.001 PHE B 248 TYR 0.010 0.001 TYR A 288 ARG 0.004 0.000 ARG B 636 *********************** 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 53 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 45 time to evaluate : 1.621 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 51 average time/residue: 0.2517 time to fit residues: 21.9043 Evaluate side-chains 48 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 43 time to evaluate : 1.636 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1330 time to fit residues: 3.2785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 63 optimal weight: 10.0000 chunk 94 optimal weight: 0.0270 chunk 47 optimal weight: 0.1980 chunk 31 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 chunk 108 optimal weight: 9.9990 chunk 78 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 125 optimal weight: 0.9990 chunk 144 optimal weight: 10.0000 overall best weight: 0.6442 ------------------------------------------------------------------------------- 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 438 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: 0.8361 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 13399 Z= 0.177 Angle : 0.655 12.692 18224 Z= 0.310 Chirality : 0.045 0.365 2106 Planarity : 0.005 0.118 2354 Dihedral : 7.254 86.967 2278 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.40 % Favored : 93.48 % Rotamer: Outliers : 0.56 % Allowed : 22.69 % Favored : 76.74 % 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: -0.69 (0.21), residues: 1657 helix: 0.97 (0.42), residues: 165 sheet: 0.14 (0.22), residues: 567 loop : -1.12 (0.21), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 929 HIS 0.002 0.001 HIS B 539 PHE 0.010 0.001 PHE B 248 TYR 0.016 0.001 TYR B 318 ARG 0.003 0.000 ARG B 636 *********************** 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 52 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 44 time to evaluate : 1.556 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 52 average time/residue: 0.2316 time to fit residues: 20.4188 Evaluate side-chains 44 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 41 time to evaluate : 1.543 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2206 time to fit residues: 3.0404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 148 optimal weight: 20.0000 chunk 89 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 116 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 133 optimal weight: 0.9990 chunk 140 optimal weight: 9.9990 chunk 147 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 483 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: 0.8373 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 13399 Z= 0.199 Angle : 0.675 13.153 18224 Z= 0.316 Chirality : 0.045 0.366 2106 Planarity : 0.005 0.113 2354 Dihedral : 7.134 85.573 2278 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.52 % Favored : 93.36 % Rotamer: Outliers : 0.14 % Allowed : 23.33 % 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: -0.66 (0.21), residues: 1657 helix: 0.99 (0.43), residues: 165 sheet: 0.18 (0.22), residues: 563 loop : -1.11 (0.21), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 929 HIS 0.002 0.001 HIS B 539 PHE 0.011 0.001 PHE B 248 TYR 0.015 0.001 TYR B 318 ARG 0.005 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 44 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 42 time to evaluate : 1.509 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 43 average time/residue: 0.2303 time to fit residues: 17.0000 Evaluate side-chains 41 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 1.511 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 7.9990 chunk 74 optimal weight: 9.9990 chunk 108 optimal weight: 6.9990 chunk 164 optimal weight: 20.0000 chunk 151 optimal weight: 8.9990 chunk 130 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 101 optimal weight: 8.9990 chunk 80 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 overall best weight: 2.4784 ------------------------------------------------------------------------------- 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 ** 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: 0.8409 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 13399 Z= 0.306 Angle : 0.712 14.603 18224 Z= 0.340 Chirality : 0.046 0.369 2106 Planarity : 0.005 0.116 2354 Dihedral : 7.223 85.414 2278 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.55 % Favored : 92.33 % Rotamer: Outliers : 0.28 % Allowed : 23.04 % 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: -0.79 (0.21), residues: 1657 helix: 0.88 (0.42), residues: 170 sheet: 0.06 (0.22), residues: 564 loop : -1.18 (0.21), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 113 HIS 0.004 0.001 HIS B 280 PHE 0.015 0.002 PHE A 289 TYR 0.011 0.001 TYR A 448 ARG 0.012 0.000 ARG B 530 ********************** 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 48 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 44 time to evaluate : 1.634 Fit side-chains outliers start: 4 outliers final: 0 residues processed: 46 average time/residue: 0.2378 time to fit residues: 19.0124 Evaluate side-chains 43 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 1.643 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 120 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 131 optimal weight: 0.0870 chunk 54 optimal weight: 8.9990 chunk 134 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 115 optimal weight: 0.5980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 319 GLN ** 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 = 0.3811 r_free = 0.3811 target = 0.074562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.048594 restraints weight = 93954.816| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 5.90 r_work: 0.2829 rms_B_bonded: 5.45 restraints_weight: 2.0000 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2819 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2819 r_free = 0.2819 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2819 r_free = 0.2819 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2819 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 13399 Z= 0.175 Angle : 0.681 12.689 18224 Z= 0.320 Chirality : 0.045 0.355 2106 Planarity : 0.005 0.109 2354 Dihedral : 6.978 83.866 2278 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.22 % Favored : 93.66 % Rotamer: Outliers : 0.14 % Allowed : 23.40 % Favored : 76.46 % 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: -0.67 (0.21), residues: 1657 helix: 0.79 (0.42), residues: 169 sheet: 0.23 (0.22), residues: 557 loop : -1.12 (0.21), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 238 HIS 0.001 0.001 HIS A 658 PHE 0.010 0.001 PHE A 356 TYR 0.014 0.001 TYR B 318 ARG 0.003 0.000 ARG B 636 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2921.27 seconds wall clock time: 53 minutes 52.94 seconds (3232.94 seconds total)