Starting phenix.real_space_refine on Thu May 9 13:16:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bh9_44537/05_2024/9bh9_44537.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bh9_44537/05_2024/9bh9_44537.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bh9_44537/05_2024/9bh9_44537.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bh9_44537/05_2024/9bh9_44537.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bh9_44537/05_2024/9bh9_44537.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bh9_44537/05_2024/9bh9_44537.pdb" } resolution = 3.5 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= 0.002 sd= 0.040 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: 5 Type Number sf(0) Gaussians P 49 5.49 5 S 78 5.16 5 C 8279 2.51 5 N 2221 2.21 5 O 2528 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 594": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 720": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 13155 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 787, 6203 Classifications: {'peptide': 787} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 23, 'TRANS': 763} Chain breaks: 5 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 6203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 787, 6203 Classifications: {'peptide': 787} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 23, 'TRANS': 763} Chain breaks: 5 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "X" Number of atoms: 235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 235 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {' DC:plan2': 1, ' DG:plan': 3, ' DG:plan2': 3, ' DC:plan': 1, ' DT:plan': 1} Unresolved non-hydrogen planarities: 58 Chain: "Y" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 514 Classifications: {'DNA': 36} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 35} Unresolved non-hydrogen bonds: 256 Unresolved non-hydrogen angles: 408 Unresolved non-hydrogen dihedrals: 184 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {' DG:plan': 6, ' DG:plan2': 6, ' DC:plan2': 5, ' DA:plan2': 2, ' DC%5*END:plan2': 1, ' DC:plan': 5, ' DC%5*END:plan': 1, ' DT:plan': 10, ' DA:plan': 2} Unresolved non-hydrogen planarities: 252 Time building chain proxies: 7.33, per 1000 atoms: 0.56 Number of scatterers: 13155 At special positions: 0 Unit cell: (124.95, 149.94, 91.63, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 78 16.00 P 49 15.00 O 2528 8.00 N 2221 7.00 C 8279 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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 Time building additional restraints: 5.25 Conformation dependent library (CDL) restraints added in 2.3 seconds 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2960 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 9 sheets defined 60.5% alpha, 8.6% beta 0 base pairs and 11 stacking pairs defined. Time for finding SS restraints: 4.27 Creating SS restraints... Processing helix chain 'A' and resid 70 through 75 removed outlier: 3.831A pdb=" N GLY A 75 " --> pdb=" O ALA A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 88 Processing helix chain 'A' and resid 93 through 100 removed outlier: 3.781A pdb=" N ALA A 97 " --> pdb=" O PHE A 93 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU A 98 " --> pdb=" O GLU A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 108 Processing helix chain 'A' and resid 116 through 119 Processing helix chain 'A' and resid 120 through 121 No H-bonds generated for 'chain 'A' and resid 120 through 121' Processing helix chain 'A' and resid 122 through 136 Processing helix chain 'A' and resid 146 through 162 Processing helix chain 'A' and resid 163 through 165 No H-bonds generated for 'chain 'A' and resid 163 through 165' Processing helix chain 'A' and resid 180 through 184 Processing helix chain 'A' and resid 191 through 204 Processing helix chain 'A' and resid 206 through 210 removed outlier: 3.519A pdb=" N LEU A 210 " --> pdb=" O MET A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 223 removed outlier: 3.743A pdb=" N LEU A 221 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLY A 222 " --> pdb=" O HIS A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 246 Processing helix chain 'A' and resid 270 through 278 removed outlier: 3.536A pdb=" N VAL A 274 " --> pdb=" O ASN A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 335 removed outlier: 4.580A pdb=" N THR A 333 " --> pdb=" O LEU A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 366 Processing helix chain 'A' and resid 383 through 396 removed outlier: 3.660A pdb=" N LEU A 387 " --> pdb=" O GLU A 383 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N GLU A 389 " --> pdb=" O LYS A 385 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ASP A 392 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG A 395 " --> pdb=" O MET A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 409 Processing helix chain 'A' and resid 421 through 434 Processing helix chain 'A' and resid 444 through 447 Processing helix chain 'A' and resid 470 through 478 removed outlier: 3.622A pdb=" N GLN A 476 " --> pdb=" O LEU A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 482 removed outlier: 4.525A pdb=" N GLY A 482 " --> pdb=" O GLY A 479 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 479 through 482' Processing helix chain 'A' and resid 500 through 509 removed outlier: 4.035A pdb=" N GLY A 504 " --> pdb=" O GLU A 500 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU A 507 " --> pdb=" O LYS A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 541 removed outlier: 3.851A pdb=" N ILE A 538 " --> pdb=" O ALA A 534 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE A 539 " --> pdb=" O ILE A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 555 Processing helix chain 'A' and resid 557 through 563 removed outlier: 3.865A pdb=" N ALA A 561 " --> pdb=" O THR A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 591 removed outlier: 3.848A pdb=" N ILE A 582 " --> pdb=" O GLN A 578 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N GLU A 583 " --> pdb=" O LEU A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 622 Processing helix chain 'A' and resid 624 through 640 removed outlier: 4.336A pdb=" N ASP A 630 " --> pdb=" O ALA A 626 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA A 633 " --> pdb=" O LEU A 629 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS A 640 " --> pdb=" O GLN A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 655 Processing helix chain 'A' and resid 665 through 674 Processing helix chain 'A' and resid 677 through 686 removed outlier: 4.259A pdb=" N VAL A 683 " --> pdb=" O SER A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 700 Processing helix chain 'A' and resid 706 through 730 removed outlier: 3.982A pdb=" N ALA A 714 " --> pdb=" O HIS A 710 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N LYS A 717 " --> pdb=" O MET A 713 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG A 718 " --> pdb=" O ALA A 714 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR A 721 " --> pdb=" O LYS A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 742 removed outlier: 3.592A pdb=" N GLN A 739 " --> pdb=" O ARG A 735 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 769 removed outlier: 3.768A pdb=" N GLN A 749 " --> pdb=" O ARG A 745 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER A 750 " --> pdb=" O GLY A 746 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLY A 760 " --> pdb=" O ALA A 756 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR A 763 " --> pdb=" O ALA A 759 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL A 764 " --> pdb=" O GLY A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 782 removed outlier: 4.324A pdb=" N LEU A 777 " --> pdb=" O ASN A 773 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLN A 780 " --> pdb=" O LEU A 776 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 785 No H-bonds generated for 'chain 'A' and resid 783 through 785' Processing helix chain 'A' and resid 798 through 802 removed outlier: 4.336A pdb=" N LEU A 801 " --> pdb=" O ARG A 798 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU A 802 " --> pdb=" O VAL A 799 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 798 through 802' Processing helix chain 'A' and resid 803 through 812 removed outlier: 4.591A pdb=" N LEU A 810 " --> pdb=" O ARG A 806 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 822 Processing helix chain 'A' and resid 825 through 835 Processing helix chain 'A' and resid 849 through 860 removed outlier: 3.708A pdb=" N GLU A 855 " --> pdb=" O GLU A 851 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ARG A 856 " --> pdb=" O ALA A 852 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG A 860 " --> pdb=" O ARG A 856 " (cutoff:3.500A) Processing helix chain 'A' and resid 871 through 891 removed outlier: 4.459A pdb=" N ALA A 877 " --> pdb=" O ARG A 873 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N VAL A 880 " --> pdb=" O ALA A 876 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 75 removed outlier: 3.534A pdb=" N GLY B 75 " --> pdb=" O ALA B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 Processing helix chain 'B' and resid 93 through 101 Processing helix chain 'B' and resid 122 through 136 Processing helix chain 'B' and resid 146 through 162 Processing helix chain 'B' and resid 163 through 165 No H-bonds generated for 'chain 'B' and resid 163 through 165' Processing helix chain 'B' and resid 180 through 184 Processing helix chain 'B' and resid 191 through 204 Processing helix chain 'B' and resid 206 through 208 No H-bonds generated for 'chain 'B' and resid 206 through 208' Processing helix chain 'B' and resid 217 through 223 removed outlier: 3.685A pdb=" N LEU B 221 " --> pdb=" O LEU B 218 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLY B 222 " --> pdb=" O HIS B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 246 removed outlier: 3.522A pdb=" N LEU B 234 " --> pdb=" O LEU B 230 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N SER B 244 " --> pdb=" O ILE B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 278 Processing helix chain 'B' and resid 325 through 335 removed outlier: 4.302A pdb=" N THR B 333 " --> pdb=" O LEU B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 368 removed outlier: 3.527A pdb=" N ASN B 363 " --> pdb=" O ARG B 359 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU B 364 " --> pdb=" O GLU B 360 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N HIS B 365 " --> pdb=" O PHE B 361 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N HIS B 366 " --> pdb=" O TYR B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 397 removed outlier: 3.511A pdb=" N LEU B 387 " --> pdb=" O GLU B 383 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU B 389 " --> pdb=" O LYS B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 409 Processing helix chain 'B' and resid 421 through 434 Processing helix chain 'B' and resid 444 through 447 Processing helix chain 'B' and resid 470 through 479 removed outlier: 3.529A pdb=" N GLY B 479 " --> pdb=" O LYS B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 510 removed outlier: 3.852A pdb=" N LEU B 507 " --> pdb=" O LYS B 503 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU B 508 " --> pdb=" O GLY B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 528 through 540 removed outlier: 3.790A pdb=" N ILE B 538 " --> pdb=" O ALA B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 555 Processing helix chain 'B' and resid 557 through 564 Processing helix chain 'B' and resid 577 through 579 No H-bonds generated for 'chain 'B' and resid 577 through 579' Processing helix chain 'B' and resid 580 through 592 Processing helix chain 'B' and resid 612 through 622 Processing helix chain 'B' and resid 624 through 640 removed outlier: 3.994A pdb=" N ASP B 630 " --> pdb=" O ALA B 626 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG B 637 " --> pdb=" O ALA B 633 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS B 640 " --> pdb=" O GLN B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 647 through 655 removed outlier: 4.219A pdb=" N LEU B 653 " --> pdb=" O HIS B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 675 Processing helix chain 'B' and resid 677 through 688 removed outlier: 4.271A pdb=" N VAL B 683 " --> pdb=" O SER B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 690 through 700 Processing helix chain 'B' and resid 706 through 730 removed outlier: 4.381A pdb=" N ARG B 711 " --> pdb=" O GLU B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 742 removed outlier: 3.899A pdb=" N GLN B 739 " --> pdb=" O ARG B 735 " (cutoff:3.500A) Processing helix chain 'B' and resid 744 through 770 removed outlier: 3.671A pdb=" N GLN B 749 " --> pdb=" O ARG B 745 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA B 756 " --> pdb=" O GLN B 752 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL B 757 " --> pdb=" O GLN B 753 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY B 760 " --> pdb=" O ALA B 756 " (cutoff:3.500A) Processing helix chain 'B' and resid 773 through 782 Processing helix chain 'B' and resid 783 through 785 No H-bonds generated for 'chain 'B' and resid 783 through 785' Processing helix chain 'B' and resid 790 through 799 removed outlier: 4.141A pdb=" N ASP B 795 " --> pdb=" O GLU B 792 " (cutoff:3.500A) Processing helix chain 'B' and resid 803 through 813 Processing helix chain 'B' and resid 817 through 822 Processing helix chain 'B' and resid 825 through 835 Processing helix chain 'B' and resid 849 through 859 removed outlier: 3.674A pdb=" N VAL B 853 " --> pdb=" O GLU B 849 " (cutoff:3.500A) Processing helix chain 'B' and resid 871 through 891 removed outlier: 5.086A pdb=" N ALA B 877 " --> pdb=" O ARG B 873 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL B 880 " --> pdb=" O ALA B 876 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN B 889 " --> pdb=" O MET B 885 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 168 through 171 removed outlier: 7.106A pdb=" N ALA A 140 " --> pdb=" O ALA A 187 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N CYS A 189 " --> pdb=" O ALA A 140 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N PHE A 142 " --> pdb=" O CYS A 189 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LEU A 111 " --> pdb=" O GLY A 263 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N SER A 265 " --> pdb=" O LEU A 111 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N TYR A 113 " --> pdb=" O SER A 265 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 292 through 293 removed outlier: 6.995A pdb=" N ILE A 302 " --> pdb=" O VAL A 310 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 292 through 293 removed outlier: 6.813A pdb=" N VAL A 457 " --> pdb=" O ILE A 493 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N ILE A 495 " --> pdb=" O VAL A 457 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ILE A 459 " --> pdb=" O ILE A 495 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N VAL A 340 " --> pdb=" O LEU A 440 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N ALA A 442 " --> pdb=" O VAL A 340 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N LEU A 342 " --> pdb=" O ALA A 442 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 463 through 464 Processing sheet with id=AA5, first strand: chain 'A' and resid 595 through 598 Processing sheet with id=AA6, first strand: chain 'B' and resid 168 through 171 removed outlier: 6.341A pdb=" N LYS B 139 " --> pdb=" O GLY B 211 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N VAL B 213 " --> pdb=" O LYS B 139 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LEU B 141 " --> pdb=" O VAL B 213 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N VAL B 215 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ILE B 143 " --> pdb=" O VAL B 215 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN B 260 " --> pdb=" O GLY B 211 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LEU B 111 " --> pdb=" O GLY B 263 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N SER B 265 " --> pdb=" O LEU B 111 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N TYR B 113 " --> pdb=" O SER B 265 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ASN B 110 " --> pdb=" O GLU B 281 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N TYR B 283 " --> pdb=" O ASN B 110 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N VAL B 112 " --> pdb=" O TYR B 283 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 309 through 312 removed outlier: 6.602A pdb=" N LEU B 309 " --> pdb=" O ASP B 304 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ASP B 304 " --> pdb=" O LEU B 309 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG B 311 " --> pdb=" O ILE B 302 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LEU B 341 " --> pdb=" O ILE B 458 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL B 340 " --> pdb=" O LEU B 440 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N ALA B 442 " --> pdb=" O VAL B 340 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N LEU B 342 " --> pdb=" O ALA B 442 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ALA B 414 " --> pdb=" O ALA B 441 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 463 through 464 Processing sheet with id=AA9, first strand: chain 'B' and resid 595 through 598 621 hydrogen bonds defined for protein. 1770 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 11 stacking parallelities Total time for adding SS restraints: 4.55 Time building geometry restraints manager: 5.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 3879 1.33 - 1.45: 1835 1.45 - 1.57: 7510 1.57 - 1.69: 97 1.69 - 1.81: 124 Bond restraints: 13445 Sorted by residual: bond pdb=" C4' DT Y 39 " pdb=" O4' DT Y 39 " ideal model delta sigma weight residual 1.450 1.420 0.030 2.00e-02 2.50e+03 2.28e+00 bond pdb=" C4' DA Y 40 " pdb=" O4' DA Y 40 " ideal model delta sigma weight residual 1.450 1.422 0.028 2.00e-02 2.50e+03 2.03e+00 bond pdb=" C2' DT X 48 " pdb=" C1' DT X 48 " ideal model delta sigma weight residual 1.525 1.550 -0.025 2.00e-02 2.50e+03 1.56e+00 bond pdb=" C4' DT Y 22 " pdb=" O4' DT Y 22 " ideal model delta sigma weight residual 1.450 1.425 0.025 2.00e-02 2.50e+03 1.51e+00 bond pdb=" C3' DT X 46 " pdb=" C2' DT X 46 " ideal model delta sigma weight residual 1.525 1.549 -0.024 2.00e-02 2.50e+03 1.38e+00 ... (remaining 13440 not shown) Histogram of bond angle deviations from ideal: 99.15 - 106.12: 490 106.12 - 113.10: 7448 113.10 - 120.07: 4810 120.07 - 127.05: 5368 127.05 - 134.02: 181 Bond angle restraints: 18297 Sorted by residual: angle pdb=" O3' DT X 48 " pdb=" C3' DT X 48 " pdb=" C2' DT X 48 " ideal model delta sigma weight residual 111.50 117.10 -5.60 1.50e+00 4.44e-01 1.39e+01 angle pdb=" CA ARG A 768 " pdb=" CB ARG A 768 " pdb=" CG ARG A 768 " ideal model delta sigma weight residual 114.10 107.80 6.30 2.00e+00 2.50e-01 9.93e+00 angle pdb=" C3' DT X 48 " pdb=" O3' DT X 48 " pdb=" P DT X 49 " ideal model delta sigma weight residual 120.20 124.92 -4.72 1.50e+00 4.44e-01 9.89e+00 angle pdb=" C ASP A 169 " pdb=" N GLY A 170 " pdb=" CA GLY A 170 " ideal model delta sigma weight residual 121.05 115.67 5.38 1.85e+00 2.92e-01 8.45e+00 angle pdb=" C4' DT X 46 " pdb=" O4' DT X 46 " pdb=" C1' DT X 46 " ideal model delta sigma weight residual 109.70 105.34 4.36 1.50e+00 4.44e-01 8.45e+00 ... (remaining 18292 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.28: 7849 31.28 - 62.57: 280 62.57 - 93.85: 18 93.85 - 125.13: 0 125.13 - 156.41: 1 Dihedral angle restraints: 8148 sinusoidal: 3588 harmonic: 4560 Sorted by residual: dihedral pdb=" CA ARG B 311 " pdb=" C ARG B 311 " pdb=" N GLU B 312 " pdb=" CA GLU B 312 " ideal model delta harmonic sigma weight residual 180.00 151.54 28.46 0 5.00e+00 4.00e-02 3.24e+01 dihedral pdb=" CA HIS B 816 " pdb=" C HIS B 816 " pdb=" N THR B 817 " pdb=" CA THR B 817 " ideal model delta harmonic sigma weight residual 180.00 151.58 28.42 0 5.00e+00 4.00e-02 3.23e+01 dihedral pdb=" CA ARG A 521 " pdb=" C ARG A 521 " pdb=" N ARG A 522 " pdb=" CA ARG A 522 " ideal model delta harmonic sigma weight residual 180.00 151.75 28.25 0 5.00e+00 4.00e-02 3.19e+01 ... (remaining 8145 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1564 0.046 - 0.093: 468 0.093 - 0.139: 109 0.139 - 0.186: 10 0.186 - 0.232: 1 Chirality restraints: 2152 Sorted by residual: chirality pdb=" C3' DT X 48 " pdb=" C4' DT X 48 " pdb=" O3' DT X 48 " pdb=" C2' DT X 48 " both_signs ideal model delta sigma weight residual False -2.66 -2.43 -0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA ARG A 768 " pdb=" N ARG A 768 " pdb=" C ARG A 768 " pdb=" CB ARG A 768 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.98e-01 chirality pdb=" CA ILE A 186 " pdb=" N ILE A 186 " pdb=" C ILE A 186 " pdb=" CB ILE A 186 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.29e-01 ... (remaining 2149 not shown) Planarity restraints: 2165 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT X 49 " -0.036 2.00e-02 2.50e+03 2.67e-02 1.78e+01 pdb=" N1 DT X 49 " 0.071 2.00e-02 2.50e+03 pdb=" C2 DT X 49 " -0.027 2.00e-02 2.50e+03 pdb=" O2 DT X 49 " 0.005 2.00e-02 2.50e+03 pdb=" N3 DT X 49 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DT X 49 " -0.002 2.00e-02 2.50e+03 pdb=" O4 DT X 49 " -0.003 2.00e-02 2.50e+03 pdb=" C5 DT X 49 " -0.002 2.00e-02 2.50e+03 pdb=" C7 DT X 49 " -0.005 2.00e-02 2.50e+03 pdb=" C6 DT X 49 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG Y 38 " 0.008 2.00e-02 2.50e+03 2.01e-02 1.21e+01 pdb=" N9 DG Y 38 " -0.052 2.00e-02 2.50e+03 pdb=" C8 DG Y 38 " 0.044 2.00e-02 2.50e+03 pdb=" N7 DG Y 38 " -0.005 2.00e-02 2.50e+03 pdb=" C5 DG Y 38 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DG Y 38 " -0.003 2.00e-02 2.50e+03 pdb=" O6 DG Y 38 " -0.004 2.00e-02 2.50e+03 pdb=" N1 DG Y 38 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DG Y 38 " 0.004 2.00e-02 2.50e+03 pdb=" N2 DG Y 38 " 0.007 2.00e-02 2.50e+03 pdb=" N3 DG Y 38 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DG Y 38 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 843 " -0.241 9.50e-02 1.11e+02 1.09e-01 8.88e+00 pdb=" NE ARG B 843 " 0.022 2.00e-02 2.50e+03 pdb=" CZ ARG B 843 " -0.020 2.00e-02 2.50e+03 pdb=" NH1 ARG B 843 " 0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG B 843 " -0.001 2.00e-02 2.50e+03 ... (remaining 2162 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 4365 2.87 - 3.38: 12628 3.38 - 3.88: 20465 3.88 - 4.39: 24606 4.39 - 4.90: 40811 Nonbonded interactions: 102875 Sorted by model distance: nonbonded pdb=" OE1 GLU A 792 " pdb=" OH TYR A 811 " model vdw 2.362 2.440 nonbonded pdb=" OG1 THR A 655 " pdb=" OG SER A 722 " model vdw 2.369 2.440 nonbonded pdb=" OE1 GLN B 782 " pdb=" N2 DG Y 42 " model vdw 2.373 2.520 nonbonded pdb=" NZ LYS B 352 " pdb=" OP2 DG Y 25 " model vdw 2.379 2.520 nonbonded pdb=" OD1 ASP B 647 " pdb=" NH1 ARG B 784 " model vdw 2.394 2.520 ... (remaining 102870 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 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.970 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: 7.420 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 39.990 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13445 Z= 0.227 Angle : 0.681 7.314 18297 Z= 0.406 Chirality : 0.046 0.232 2152 Planarity : 0.009 0.109 2165 Dihedral : 15.034 156.414 5188 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 1.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 0.07 % Allowed : 0.15 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.19), residues: 1550 helix: -2.44 (0.13), residues: 832 sheet: 0.41 (0.44), residues: 120 loop : 0.21 (0.25), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 666 HIS 0.011 0.001 HIS A 366 PHE 0.019 0.001 PHE A 658 TYR 0.029 0.005 TYR A 239 ARG 0.025 0.003 ARG B 711 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 310 time to evaluate : 1.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 LEU cc_start: 0.8395 (mp) cc_final: 0.7812 (tp) REVERT: A 391 MET cc_start: 0.6625 (ttp) cc_final: 0.5895 (ttm) REVERT: B 463 ILE cc_start: 0.8574 (mm) cc_final: 0.8289 (mt) REVERT: B 550 MET cc_start: 0.7723 (mtt) cc_final: 0.7466 (mtp) REVERT: B 645 GLU cc_start: 0.6617 (pt0) cc_final: 0.5937 (tt0) REVERT: B 782 GLN cc_start: 0.7295 (tt0) cc_final: 0.7064 (tt0) REVERT: B 784 ARG cc_start: 0.8003 (mtp180) cc_final: 0.7663 (ttm110) outliers start: 1 outliers final: 1 residues processed: 311 average time/residue: 0.3225 time to fit residues: 134.8496 Evaluate side-chains 191 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 190 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 758 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 0.7980 chunk 121 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 64 optimal weight: 0.0470 chunk 125 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 chunk 93 optimal weight: 0.9980 chunk 145 optimal weight: 0.9990 overall best weight: 0.7680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 HIS A 366 HIS A 416 HIS A 710 HIS ** B 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 85 HIS ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 366 HIS B 416 HIS B 434 GLN B 548 GLN B 709 GLN B 739 GLN B 780 GLN B 888 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13445 Z= 0.223 Angle : 0.639 8.411 18297 Z= 0.340 Chirality : 0.041 0.180 2152 Planarity : 0.004 0.041 2165 Dihedral : 14.800 162.344 2180 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 1.62 % Allowed : 6.27 % Favored : 92.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.20), residues: 1550 helix: -0.68 (0.16), residues: 854 sheet: 0.63 (0.41), residues: 142 loop : 0.54 (0.27), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 661 HIS 0.006 0.001 HIS A 366 PHE 0.015 0.001 PHE B 642 TYR 0.013 0.002 TYR A 331 ARG 0.007 0.001 ARG B 522 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 220 time to evaluate : 1.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 LEU cc_start: 0.8172 (mp) cc_final: 0.7455 (tp) REVERT: A 415 PHE cc_start: 0.6909 (p90) cc_final: 0.6607 (p90) REVERT: A 808 ARG cc_start: 0.6733 (mmm160) cc_final: 0.6473 (tpt90) REVERT: B 395 ARG cc_start: 0.7797 (mtt-85) cc_final: 0.7438 (mtt-85) REVERT: B 530 SER cc_start: 0.8350 (OUTLIER) cc_final: 0.7969 (t) outliers start: 22 outliers final: 10 residues processed: 231 average time/residue: 0.3001 time to fit residues: 96.0103 Evaluate side-chains 183 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 172 time to evaluate : 1.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 484 LYS Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain B residue 85 HIS Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain B residue 517 SER Chi-restraints excluded: chain B residue 530 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 80 optimal weight: 0.6980 chunk 45 optimal weight: 0.7980 chunk 120 optimal weight: 5.9990 chunk 98 optimal weight: 0.0470 chunk 40 optimal weight: 5.9990 chunk 145 optimal weight: 0.4980 chunk 157 optimal weight: 10.0000 chunk 129 optimal weight: 1.9990 chunk 144 optimal weight: 0.6980 chunk 49 optimal weight: 0.5980 chunk 116 optimal weight: 0.3980 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 773 ASN B 73 ASN ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13445 Z= 0.171 Angle : 0.579 9.192 18297 Z= 0.303 Chirality : 0.040 0.269 2152 Planarity : 0.004 0.047 2165 Dihedral : 14.596 162.839 2178 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 1.25 % Allowed : 10.03 % Favored : 88.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.21), residues: 1550 helix: -0.02 (0.17), residues: 870 sheet: 0.81 (0.41), residues: 142 loop : 0.57 (0.27), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 661 HIS 0.007 0.001 HIS B 85 PHE 0.012 0.001 PHE A 93 TYR 0.012 0.001 TYR A 171 ARG 0.016 0.001 ARG B 884 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 181 time to evaluate : 1.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 LEU cc_start: 0.8214 (mp) cc_final: 0.7482 (tp) REVERT: A 331 TYR cc_start: 0.8241 (t80) cc_final: 0.7185 (t80) REVERT: A 391 MET cc_start: 0.6353 (OUTLIER) cc_final: 0.5854 (mtm) REVERT: A 415 PHE cc_start: 0.6910 (p90) cc_final: 0.6653 (p90) REVERT: A 464 PHE cc_start: 0.6851 (m-10) cc_final: 0.6633 (m-10) REVERT: A 808 ARG cc_start: 0.6701 (mmm160) cc_final: 0.6472 (tpt90) REVERT: B 530 SER cc_start: 0.8201 (OUTLIER) cc_final: 0.7853 (t) outliers start: 17 outliers final: 7 residues processed: 189 average time/residue: 0.2810 time to fit residues: 74.7034 Evaluate side-chains 178 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 169 time to evaluate : 1.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 HIS Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 547 SER Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain B residue 517 SER Chi-restraints excluded: chain B residue 530 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 143 optimal weight: 1.9990 chunk 109 optimal weight: 5.9990 chunk 75 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 69 optimal weight: 0.5980 chunk 97 optimal weight: 1.9990 chunk 146 optimal weight: 0.4980 chunk 154 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 138 optimal weight: 0.7980 chunk 41 optimal weight: 0.0270 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 73 ASN ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 moved from start: 0.3641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13445 Z= 0.164 Angle : 0.550 12.969 18297 Z= 0.284 Chirality : 0.039 0.245 2152 Planarity : 0.004 0.039 2165 Dihedral : 14.574 162.275 2178 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 1.62 % Allowed : 10.18 % Favored : 88.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.21), residues: 1550 helix: 0.37 (0.18), residues: 870 sheet: 0.95 (0.42), residues: 142 loop : 0.53 (0.28), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 661 HIS 0.005 0.001 HIS B 325 PHE 0.018 0.001 PHE B 181 TYR 0.027 0.001 TYR A 811 ARG 0.006 0.000 ARG A 242 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 187 time to evaluate : 1.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 LEU cc_start: 0.8265 (mp) cc_final: 0.7535 (tp) REVERT: A 415 PHE cc_start: 0.6888 (p90) cc_final: 0.6646 (p90) REVERT: A 808 ARG cc_start: 0.6897 (mmm160) cc_final: 0.6565 (tpt90) REVERT: B 197 LEU cc_start: 0.8758 (tp) cc_final: 0.8540 (tt) REVERT: B 530 SER cc_start: 0.8208 (OUTLIER) cc_final: 0.7856 (t) REVERT: B 645 GLU cc_start: 0.6917 (pt0) cc_final: 0.6075 (tt0) REVERT: B 784 ARG cc_start: 0.8437 (ttm110) cc_final: 0.7999 (ttm-80) outliers start: 22 outliers final: 13 residues processed: 199 average time/residue: 0.2801 time to fit residues: 79.0338 Evaluate side-chains 180 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 166 time to evaluate : 1.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 180 HIS Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 434 GLN Chi-restraints excluded: chain A residue 547 SER Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 517 SER Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 530 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 128 optimal weight: 0.0980 chunk 87 optimal weight: 2.9990 chunk 2 optimal weight: 7.9990 chunk 115 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 chunk 131 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 78 optimal weight: 8.9990 chunk 138 optimal weight: 0.0000 chunk 39 optimal weight: 6.9990 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 747 GLN B 73 ASN ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.3897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13445 Z= 0.171 Angle : 0.556 11.659 18297 Z= 0.285 Chirality : 0.039 0.243 2152 Planarity : 0.004 0.037 2165 Dihedral : 14.526 162.577 2178 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.84 % Allowed : 11.36 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.22), residues: 1550 helix: 0.57 (0.18), residues: 874 sheet: 0.89 (0.41), residues: 146 loop : 0.54 (0.28), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 661 HIS 0.009 0.001 HIS B 85 PHE 0.047 0.001 PHE A 87 TYR 0.010 0.001 TYR A 171 ARG 0.008 0.000 ARG B 395 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 184 time to evaluate : 1.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.7971 (tt) REVERT: A 293 LEU cc_start: 0.8238 (mp) cc_final: 0.7572 (tt) REVERT: A 415 PHE cc_start: 0.6930 (p90) cc_final: 0.6584 (p90) REVERT: A 808 ARG cc_start: 0.6857 (mmm160) cc_final: 0.6578 (tpt90) REVERT: B 197 LEU cc_start: 0.8760 (tp) cc_final: 0.8531 (tt) REVERT: B 325 HIS cc_start: 0.7999 (m90) cc_final: 0.7774 (m90) REVERT: B 530 SER cc_start: 0.8175 (OUTLIER) cc_final: 0.7780 (t) REVERT: B 645 GLU cc_start: 0.6951 (pt0) cc_final: 0.6044 (tt0) outliers start: 25 outliers final: 13 residues processed: 199 average time/residue: 0.2989 time to fit residues: 84.3520 Evaluate side-chains 181 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 166 time to evaluate : 1.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 547 SER Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 517 SER Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 776 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 0.3980 chunk 139 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 38 optimal weight: 0.0060 chunk 154 optimal weight: 0.0670 chunk 128 optimal weight: 0.0970 chunk 71 optimal weight: 9.9990 chunk 12 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 overall best weight: 0.5134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 739 GLN B 73 ASN ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.4123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13445 Z= 0.161 Angle : 0.552 12.353 18297 Z= 0.282 Chirality : 0.039 0.237 2152 Planarity : 0.004 0.045 2165 Dihedral : 14.490 162.460 2178 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.21 % Allowed : 12.32 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.22), residues: 1550 helix: 0.82 (0.18), residues: 858 sheet: 0.94 (0.41), residues: 146 loop : 0.33 (0.28), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 661 HIS 0.004 0.001 HIS B 85 PHE 0.014 0.001 PHE B 181 TYR 0.030 0.001 TYR A 331 ARG 0.009 0.000 ARG B 705 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 176 time to evaluate : 1.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8031 (tt) REVERT: A 293 LEU cc_start: 0.8190 (mp) cc_final: 0.7527 (tt) REVERT: A 415 PHE cc_start: 0.6826 (p90) cc_final: 0.6582 (p90) REVERT: A 808 ARG cc_start: 0.6878 (mmm160) cc_final: 0.6551 (tpt90) REVERT: B 197 LEU cc_start: 0.8776 (tp) cc_final: 0.8545 (tt) REVERT: B 307 MET cc_start: 0.7247 (mtp) cc_final: 0.6984 (tpt) REVERT: B 463 ILE cc_start: 0.8617 (mm) cc_final: 0.8266 (mt) REVERT: B 645 GLU cc_start: 0.6970 (pt0) cc_final: 0.6005 (tt0) REVERT: B 784 ARG cc_start: 0.8417 (ttm110) cc_final: 0.7919 (ttm-80) outliers start: 30 outliers final: 23 residues processed: 191 average time/residue: 0.2789 time to fit residues: 76.2956 Evaluate side-chains 192 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 168 time to evaluate : 1.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 180 HIS Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 385 LYS Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 547 SER Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 517 SER Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 587 MET Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 734 LEU Chi-restraints excluded: chain B residue 776 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 149 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 113 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 130 optimal weight: 0.9990 chunk 86 optimal weight: 0.7980 chunk 154 optimal weight: 0.1980 chunk 96 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 71 optimal weight: 9.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 739 GLN B 73 ASN ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.4195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13445 Z= 0.217 Angle : 0.571 10.815 18297 Z= 0.293 Chirality : 0.040 0.250 2152 Planarity : 0.004 0.053 2165 Dihedral : 14.482 162.757 2178 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.06 % Allowed : 12.83 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.21), residues: 1550 helix: 0.78 (0.18), residues: 850 sheet: 0.96 (0.42), residues: 146 loop : 0.19 (0.27), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP A 95 HIS 0.004 0.001 HIS B 416 PHE 0.039 0.002 PHE A 87 TYR 0.022 0.001 TYR A 331 ARG 0.008 0.000 ARG B 843 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 170 time to evaluate : 1.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8053 (tt) REVERT: A 293 LEU cc_start: 0.8212 (mp) cc_final: 0.7549 (tt) REVERT: A 415 PHE cc_start: 0.6900 (p90) cc_final: 0.6634 (p90) REVERT: A 808 ARG cc_start: 0.6994 (mmm160) cc_final: 0.6655 (tpt90) REVERT: B 100 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7587 (mp) REVERT: B 101 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7783 (mt) outliers start: 28 outliers final: 19 residues processed: 186 average time/residue: 0.2655 time to fit residues: 71.1404 Evaluate side-chains 184 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 162 time to evaluate : 1.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 385 LYS Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 547 SER Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain A residue 739 GLN Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain B residue 517 SER Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 776 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 0.7980 chunk 61 optimal weight: 0.5980 chunk 92 optimal weight: 0.5980 chunk 46 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 105 optimal weight: 0.8980 chunk 76 optimal weight: 8.9990 chunk 14 optimal weight: 0.0980 chunk 121 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 73 ASN ** B 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.4341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13445 Z= 0.172 Angle : 0.552 10.953 18297 Z= 0.283 Chirality : 0.039 0.231 2152 Planarity : 0.004 0.051 2165 Dihedral : 14.419 162.860 2178 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.92 % Allowed : 13.94 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.22), residues: 1550 helix: 0.92 (0.18), residues: 852 sheet: 0.95 (0.43), residues: 146 loop : 0.09 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP A 95 HIS 0.003 0.001 HIS B 416 PHE 0.038 0.001 PHE A 87 TYR 0.020 0.001 TYR A 331 ARG 0.006 0.000 ARG B 843 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 169 time to evaluate : 1.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8059 (tt) REVERT: A 293 LEU cc_start: 0.8188 (mp) cc_final: 0.7528 (tt) REVERT: A 415 PHE cc_start: 0.6869 (p90) cc_final: 0.6640 (p90) REVERT: A 808 ARG cc_start: 0.6986 (mmm160) cc_final: 0.6629 (tpt90) REVERT: B 100 LEU cc_start: 0.7988 (OUTLIER) cc_final: 0.7504 (mp) REVERT: B 392 ASP cc_start: 0.6992 (t70) cc_final: 0.6667 (t0) REVERT: B 436 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7758 (mp) REVERT: B 784 ARG cc_start: 0.8454 (ttm110) cc_final: 0.7969 (ttm-80) outliers start: 26 outliers final: 19 residues processed: 182 average time/residue: 0.2894 time to fit residues: 74.4383 Evaluate side-chains 188 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 166 time to evaluate : 1.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 385 LYS Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 547 SER Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 517 SER Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 776 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 140 optimal weight: 1.9990 chunk 147 optimal weight: 5.9990 chunk 134 optimal weight: 0.5980 chunk 143 optimal weight: 0.8980 chunk 86 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 112 optimal weight: 0.5980 chunk 44 optimal weight: 0.9990 chunk 129 optimal weight: 0.8980 chunk 135 optimal weight: 0.9990 chunk 94 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 739 GLN B 73 ASN ** B 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.4445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13445 Z= 0.186 Angle : 0.566 10.843 18297 Z= 0.288 Chirality : 0.039 0.230 2152 Planarity : 0.004 0.041 2165 Dihedral : 14.393 163.158 2178 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.99 % Allowed : 13.86 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.22), residues: 1550 helix: 0.97 (0.18), residues: 850 sheet: 0.96 (0.43), residues: 146 loop : 0.02 (0.27), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP A 95 HIS 0.003 0.001 HIS B 416 PHE 0.027 0.001 PHE A 87 TYR 0.022 0.001 TYR A 331 ARG 0.010 0.000 ARG B 843 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 167 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8068 (tt) REVERT: A 293 LEU cc_start: 0.8158 (mp) cc_final: 0.7518 (tt) REVERT: A 415 PHE cc_start: 0.6904 (p90) cc_final: 0.6646 (p90) REVERT: A 808 ARG cc_start: 0.6965 (mmm160) cc_final: 0.6636 (tpt90) REVERT: B 101 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7708 (mt) REVERT: B 392 ASP cc_start: 0.7006 (t70) cc_final: 0.6739 (t0) REVERT: B 436 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7821 (mp) REVERT: B 784 ARG cc_start: 0.8453 (ttm110) cc_final: 0.7965 (ttm-80) outliers start: 27 outliers final: 21 residues processed: 181 average time/residue: 0.2660 time to fit residues: 69.6933 Evaluate side-chains 187 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 163 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 385 LYS Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 547 SER Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain A residue 739 GLN Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 517 SER Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 776 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 151 optimal weight: 0.7980 chunk 92 optimal weight: 0.8980 chunk 72 optimal weight: 5.9990 chunk 105 optimal weight: 0.6980 chunk 159 optimal weight: 3.9990 chunk 146 optimal weight: 0.8980 chunk 126 optimal weight: 6.9990 chunk 13 optimal weight: 0.8980 chunk 98 optimal weight: 0.8980 chunk 77 optimal weight: 8.9990 chunk 100 optimal weight: 0.0070 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 73 ASN B 300 ASN ** B 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 780 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.4535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13445 Z= 0.184 Angle : 0.565 10.558 18297 Z= 0.289 Chirality : 0.039 0.223 2152 Planarity : 0.004 0.059 2165 Dihedral : 14.372 163.271 2178 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.99 % Allowed : 14.16 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.22), residues: 1550 helix: 1.00 (0.18), residues: 850 sheet: 0.83 (0.43), residues: 150 loop : 0.01 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP A 95 HIS 0.003 0.001 HIS B 416 PHE 0.029 0.001 PHE A 87 TYR 0.020 0.001 TYR A 331 ARG 0.008 0.000 ARG B 843 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 165 time to evaluate : 1.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8092 (tt) REVERT: A 293 LEU cc_start: 0.8151 (mp) cc_final: 0.7491 (tt) REVERT: A 415 PHE cc_start: 0.6889 (p90) cc_final: 0.6668 (p90) REVERT: A 509 GLN cc_start: 0.8299 (mt0) cc_final: 0.7923 (mt0) REVERT: A 808 ARG cc_start: 0.6963 (mmm160) cc_final: 0.6621 (tpt90) REVERT: B 100 LEU cc_start: 0.7960 (OUTLIER) cc_final: 0.7479 (mp) REVERT: B 101 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7707 (mt) REVERT: B 436 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7821 (mp) REVERT: B 784 ARG cc_start: 0.8441 (ttm110) cc_final: 0.7950 (ttm-80) outliers start: 27 outliers final: 18 residues processed: 181 average time/residue: 0.2585 time to fit residues: 68.3135 Evaluate side-chains 180 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 158 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 385 LYS Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 547 SER Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 517 SER Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 776 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 130 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 23 optimal weight: 6.9990 chunk 111 optimal weight: 3.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 739 GLN B 73 ASN ** B 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 780 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.181370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.135872 restraints weight = 16125.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.134816 restraints weight = 17741.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.136047 restraints weight = 16918.181| |-----------------------------------------------------------------------------| r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.4573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13445 Z= 0.202 Angle : 0.571 10.226 18297 Z= 0.291 Chirality : 0.040 0.218 2152 Planarity : 0.004 0.056 2165 Dihedral : 14.381 163.647 2178 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.99 % Allowed : 14.09 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.22), residues: 1550 helix: 0.95 (0.18), residues: 850 sheet: 0.83 (0.43), residues: 150 loop : -0.00 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP A 95 HIS 0.004 0.001 HIS B 416 PHE 0.028 0.001 PHE A 87 TYR 0.018 0.001 TYR A 331 ARG 0.007 0.000 ARG B 395 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2598.38 seconds wall clock time: 48 minutes 27.45 seconds (2907.45 seconds total)