Starting phenix.real_space_refine on Sun Jan 19 01:26:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bh9_44537/01_2025/9bh9_44537.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bh9_44537/01_2025/9bh9_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/cci-nas-00/data/ceres_data/9bh9_44537/01_2025/9bh9_44537.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bh9_44537/01_2025/9bh9_44537.map" model { file = "/net/cci-nas-00/data/ceres_data/9bh9_44537/01_2025/9bh9_44537.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bh9_44537/01_2025/9bh9_44537.cif" } 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. Time to flip 3 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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: 8.45, per 1000 atoms: 0.64 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.11 Conformation dependent library (CDL) restraints added in 1.6 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: 4.94 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: 4.79 Time building geometry restraints manager: 3.62 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: 0.00 - 1.46: 17451 1.46 - 2.93: 737 2.93 - 4.39: 91 4.39 - 5.85: 15 5.85 - 7.31: 3 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 3.040 nonbonded pdb=" OG1 THR A 655 " pdb=" OG SER A 722 " model vdw 2.369 3.040 nonbonded pdb=" OE1 GLN B 782 " pdb=" N2 DG Y 42 " model vdw 2.373 3.120 nonbonded pdb=" NZ LYS B 352 " pdb=" OP2 DG Y 25 " model vdw 2.379 3.120 nonbonded pdb=" OD1 ASP B 647 " pdb=" NH1 ARG B 784 " model vdw 2.394 3.120 ... (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 Time spend for trying shortcut: 0.00 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: 2.840 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: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 34.900 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.050 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.730 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 1 poor density : 310 time to evaluate : 1.335 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: 0.3268 time to fit residues: 137.1384 Evaluate side-chains 191 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 190 time to evaluate : 1.314 ------------------------------------------------------------------------------- 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: 0.9980 chunk 121 optimal weight: 4.9990 chunk 67 optimal weight: 0.5980 chunk 41 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 64 optimal weight: 0.7980 chunk 125 optimal weight: 0.6980 chunk 48 optimal weight: 0.8980 chunk 76 optimal weight: 9.9990 chunk 93 optimal weight: 0.8980 chunk 145 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 A 816 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 888 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.184601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.140981 restraints weight = 16356.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.139331 restraints weight = 20737.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.140430 restraints weight = 19665.204| |-----------------------------------------------------------------------------| r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13445 Z= 0.216 Angle : 0.643 8.210 18297 Z= 0.341 Chirality : 0.041 0.174 2152 Planarity : 0.004 0.044 2165 Dihedral : 14.849 162.237 2180 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Rotamer: Outliers : 1.47 % Allowed : 6.78 % Favored : 91.74 % 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: -0.42 (0.20), residues: 1550 helix: -0.65 (0.16), residues: 860 sheet: 0.52 (0.40), residues: 142 loop : 0.51 (0.27), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 661 HIS 0.006 0.001 HIS A 366 PHE 0.015 0.001 PHE B 658 TYR 0.013 0.002 TYR A 667 ARG 0.008 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 237 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 217 time to evaluate : 1.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 264 MET cc_start: 0.6977 (OUTLIER) cc_final: 0.6748 (mtm) REVERT: A 293 LEU cc_start: 0.8122 (mp) cc_final: 0.7733 (tp) REVERT: B 530 SER cc_start: 0.8334 (OUTLIER) cc_final: 0.8068 (t) outliers start: 20 outliers final: 10 residues processed: 227 average time/residue: 0.3036 time to fit residues: 95.5436 Evaluate side-chains 173 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 161 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 264 MET 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 132 optimal weight: 0.7980 chunk 91 optimal weight: 0.4980 chunk 61 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 56 optimal weight: 0.7980 chunk 33 optimal weight: 5.9990 chunk 149 optimal weight: 0.9990 chunk 124 optimal weight: 7.9990 chunk 141 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.181494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.137852 restraints weight = 16406.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.136370 restraints weight = 17649.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.137544 restraints weight = 17661.178| |-----------------------------------------------------------------------------| r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13445 Z= 0.210 Angle : 0.607 9.256 18297 Z= 0.316 Chirality : 0.040 0.235 2152 Planarity : 0.004 0.044 2165 Dihedral : 14.746 162.410 2178 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 1.33 % Allowed : 10.62 % Favored : 88.05 % 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: 0.11 (0.21), residues: 1550 helix: -0.05 (0.17), residues: 858 sheet: 0.73 (0.41), residues: 142 loop : 0.44 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 661 HIS 0.013 0.001 HIS B 85 PHE 0.042 0.002 PHE A 87 TYR 0.012 0.001 TYR A 171 ARG 0.008 0.000 ARG B 843 *********************** 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 195 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 177 time to evaluate : 1.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 LEU cc_start: 0.8219 (mp) cc_final: 0.7791 (tp) REVERT: A 331 TYR cc_start: 0.7775 (t80) cc_final: 0.6836 (t80) REVERT: A 391 MET cc_start: 0.6542 (OUTLIER) cc_final: 0.6030 (mtm) REVERT: A 655 THR cc_start: 0.8788 (OUTLIER) cc_final: 0.8507 (m) REVERT: B 197 LEU cc_start: 0.8912 (tp) cc_final: 0.8672 (tt) REVERT: B 530 SER cc_start: 0.8260 (OUTLIER) cc_final: 0.7988 (t) REVERT: B 784 ARG cc_start: 0.8280 (ttm110) cc_final: 0.7939 (ttm-80) outliers start: 18 outliers final: 8 residues processed: 188 average time/residue: 0.3002 time to fit residues: 78.8543 Evaluate side-chains 171 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 160 time to evaluate : 1.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 A residue 655 THR Chi-restraints excluded: chain B residue 240 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 Chi-restraints excluded: chain B residue 590 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 21 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 115 optimal weight: 0.3980 chunk 101 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 0.2980 chunk 107 optimal weight: 20.0000 chunk 57 optimal weight: 0.3980 chunk 18 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 816 HIS B 73 ASN B 85 HIS ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 780 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.186682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.141264 restraints weight = 16466.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.140208 restraints weight = 22643.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.142329 restraints weight = 19939.148| |-----------------------------------------------------------------------------| r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.3675 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= 0.176 Angle : 0.562 9.215 18297 Z= 0.293 Chirality : 0.040 0.238 2152 Planarity : 0.004 0.042 2165 Dihedral : 14.618 162.519 2178 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 1.99 % Allowed : 10.91 % Favored : 87.09 % 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: 0.49 (0.21), residues: 1550 helix: 0.38 (0.18), residues: 854 sheet: 0.81 (0.41), residues: 146 loop : 0.37 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 661 HIS 0.005 0.001 HIS A 417 PHE 0.015 0.001 PHE B 181 TYR 0.012 0.001 TYR A 171 ARG 0.006 0.001 ARG B 808 *********************** 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 214 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 187 time to evaluate : 1.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8067 (tt) REVERT: A 293 LEU cc_start: 0.8127 (mp) cc_final: 0.7764 (tp) REVERT: A 469 LEU cc_start: 0.8337 (tp) cc_final: 0.8063 (tp) REVERT: A 655 THR cc_start: 0.8797 (OUTLIER) cc_final: 0.8528 (m) outliers start: 27 outliers final: 14 residues processed: 203 average time/residue: 0.2917 time to fit residues: 83.0671 Evaluate side-chains 180 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 164 time to evaluate : 1.326 ------------------------------------------------------------------------------- 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 180 HIS 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 484 LYS 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 655 THR 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 590 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 25 optimal weight: 5.9990 chunk 91 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 149 optimal weight: 7.9990 chunk 83 optimal weight: 7.9990 chunk 66 optimal weight: 0.0070 chunk 74 optimal weight: 6.9990 chunk 135 optimal weight: 0.2980 chunk 19 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 overall best weight: 1.0604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 73 ASN B 85 HIS ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.180081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.135107 restraints weight = 16427.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.132551 restraints weight = 19101.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.133494 restraints weight = 20600.972| |-----------------------------------------------------------------------------| r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.3888 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= 0.227 Angle : 0.590 9.982 18297 Z= 0.304 Chirality : 0.041 0.247 2152 Planarity : 0.004 0.041 2165 Dihedral : 14.592 163.141 2178 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.92 % Allowed : 12.83 % Favored : 85.25 % 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: 0.56 (0.21), residues: 1550 helix: 0.46 (0.18), residues: 856 sheet: 0.74 (0.42), residues: 146 loop : 0.40 (0.28), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 666 HIS 0.006 0.001 HIS A 338 PHE 0.042 0.002 PHE A 87 TYR 0.011 0.001 TYR A 171 ARG 0.006 0.000 ARG A 808 *********************** 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 192 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 166 time to evaluate : 1.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 LEU cc_start: 0.8186 (mp) cc_final: 0.7795 (tt) REVERT: A 655 THR cc_start: 0.8721 (OUTLIER) cc_final: 0.8423 (m) REVERT: B 396 ARG cc_start: 0.7661 (ptt-90) cc_final: 0.7105 (ptt-90) REVERT: B 436 LEU cc_start: 0.7883 (mp) cc_final: 0.7649 (mp) outliers start: 26 outliers final: 15 residues processed: 182 average time/residue: 0.2847 time to fit residues: 73.4888 Evaluate side-chains 180 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 164 time to evaluate : 1.500 ------------------------------------------------------------------------------- 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 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 655 THR 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 385 LYS Chi-restraints excluded: chain B residue 517 SER Chi-restraints excluded: chain B residue 587 MET Chi-restraints excluded: chain B residue 590 LEU 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 134 optimal weight: 1.9990 chunk 95 optimal weight: 0.2980 chunk 54 optimal weight: 1.9990 chunk 116 optimal weight: 0.9980 chunk 15 optimal weight: 0.2980 chunk 105 optimal weight: 0.9980 chunk 81 optimal weight: 0.0980 chunk 133 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 chunk 67 optimal weight: 0.6980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 73 ASN B 85 HIS ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.182124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.136862 restraints weight = 16377.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.135795 restraints weight = 18648.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.136585 restraints weight = 18604.317| |-----------------------------------------------------------------------------| r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.4089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 13445 Z= 0.163 Angle : 0.560 9.051 18297 Z= 0.288 Chirality : 0.039 0.225 2152 Planarity : 0.004 0.070 2165 Dihedral : 14.501 163.263 2178 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.70 % Allowed : 13.50 % Favored : 84.81 % 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: 0.76 (0.21), residues: 1550 helix: 0.71 (0.18), residues: 856 sheet: 0.76 (0.42), residues: 146 loop : 0.34 (0.27), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP A 95 HIS 0.004 0.001 HIS A 417 PHE 0.012 0.001 PHE B 181 TYR 0.010 0.001 TYR A 331 ARG 0.008 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 193 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 170 time to evaluate : 1.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8054 (tt) REVERT: A 293 LEU cc_start: 0.8090 (mp) cc_final: 0.7760 (tt) REVERT: A 655 THR cc_start: 0.8763 (OUTLIER) cc_final: 0.8516 (m) REVERT: B 392 ASP cc_start: 0.6458 (t70) cc_final: 0.6017 (t0) REVERT: B 396 ARG cc_start: 0.7411 (ptt-90) cc_final: 0.6996 (ptt90) REVERT: B 436 LEU cc_start: 0.7753 (OUTLIER) cc_final: 0.7547 (mp) outliers start: 23 outliers final: 13 residues processed: 183 average time/residue: 0.2858 time to fit residues: 73.7499 Evaluate side-chains 176 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 160 time to evaluate : 1.436 ------------------------------------------------------------------------------- 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 290 VAL Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 655 THR 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 436 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 776 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 81 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 131 optimal weight: 0.8980 chunk 111 optimal weight: 4.9990 chunk 153 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 148 optimal weight: 5.9990 chunk 150 optimal weight: 9.9990 chunk 74 optimal weight: 7.9990 chunk 15 optimal weight: 0.5980 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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 85 HIS ** B 96 GLN ** 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 = 0.4100 r_free = 0.4100 target = 0.178112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.132634 restraints weight = 16385.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.131512 restraints weight = 20294.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.132664 restraints weight = 20180.724| |-----------------------------------------------------------------------------| r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.4154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13445 Z= 0.287 Angle : 0.615 10.324 18297 Z= 0.315 Chirality : 0.042 0.247 2152 Planarity : 0.004 0.062 2165 Dihedral : 14.582 163.978 2178 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.06 % Allowed : 13.94 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.21), residues: 1550 helix: 0.54 (0.18), residues: 850 sheet: 0.63 (0.42), residues: 146 loop : 0.28 (0.28), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP A 95 HIS 0.005 0.001 HIS A 417 PHE 0.021 0.002 PHE A 765 TYR 0.013 0.002 TYR B 113 ARG 0.010 0.001 ARG B 808 *********************** 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 to be fit. rotamer outliers: 28 poor density : 170 time to evaluate : 1.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8152 (tt) REVERT: A 293 LEU cc_start: 0.8232 (mp) cc_final: 0.7800 (tt) REVERT: A 803 ASN cc_start: 0.7636 (m110) cc_final: 0.6933 (p0) REVERT: B 73 ASN cc_start: 0.8352 (t0) cc_final: 0.8103 (t0) REVERT: B 392 ASP cc_start: 0.6523 (t70) cc_final: 0.6125 (t0) REVERT: B 396 ARG cc_start: 0.7505 (ptt-90) cc_final: 0.7168 (ptt90) REVERT: B 672 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.8003 (tp) REVERT: B 784 ARG cc_start: 0.8490 (ttm110) cc_final: 0.8012 (ttm-80) outliers start: 28 outliers final: 17 residues processed: 187 average time/residue: 0.2745 time to fit residues: 74.5224 Evaluate side-chains 178 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 159 time to evaluate : 1.388 ------------------------------------------------------------------------------- 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 164 VAL Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 356 ILE 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 655 THR Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 385 LYS 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 672 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 99 optimal weight: 4.9990 chunk 87 optimal weight: 0.2980 chunk 14 optimal weight: 0.0050 chunk 133 optimal weight: 0.5980 chunk 124 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 126 optimal weight: 0.9980 chunk 24 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 overall best weight: 0.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 739 GLN B 85 HIS ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.183945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.141620 restraints weight = 16701.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.140566 restraints weight = 21463.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.141644 restraints weight = 20103.439| |-----------------------------------------------------------------------------| r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.4345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13445 Z= 0.194 Angle : 0.580 9.643 18297 Z= 0.297 Chirality : 0.040 0.207 2152 Planarity : 0.004 0.053 2165 Dihedral : 14.495 164.197 2178 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.92 % Allowed : 15.19 % Favored : 82.89 % 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: 0.66 (0.22), residues: 1550 helix: 0.72 (0.18), residues: 852 sheet: 0.61 (0.43), residues: 150 loop : 0.18 (0.28), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP A 95 HIS 0.004 0.001 HIS A 417 PHE 0.011 0.001 PHE A 765 TYR 0.010 0.001 TYR A 171 ARG 0.006 0.000 ARG B 705 *********************** 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 197 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 171 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: 0.8599 (OUTLIER) cc_final: 0.8149 (tt) REVERT: A 293 LEU cc_start: 0.8042 (mp) cc_final: 0.7802 (tt) REVERT: A 640 LYS cc_start: 0.6719 (OUTLIER) cc_final: 0.6382 (pttt) REVERT: A 655 THR cc_start: 0.8731 (OUTLIER) cc_final: 0.8464 (m) REVERT: A 803 ASN cc_start: 0.7529 (m110) cc_final: 0.7000 (p0) REVERT: B 73 ASN cc_start: 0.8236 (t0) cc_final: 0.7903 (t0) REVERT: B 392 ASP cc_start: 0.6165 (t70) cc_final: 0.5769 (t0) REVERT: B 396 ARG cc_start: 0.7295 (ptt-90) cc_final: 0.7056 (ptt90) REVERT: B 784 ARG cc_start: 0.8443 (ttm110) cc_final: 0.7972 (ttm-80) outliers start: 26 outliers final: 17 residues processed: 185 average time/residue: 0.2779 time to fit residues: 73.2751 Evaluate side-chains 187 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 167 time to evaluate : 1.468 ------------------------------------------------------------------------------- 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 164 VAL Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 180 HIS 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 640 LYS Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 815 PHE Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 307 MET 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 79 optimal weight: 6.9990 chunk 84 optimal weight: 2.9990 chunk 143 optimal weight: 0.6980 chunk 117 optimal weight: 4.9990 chunk 148 optimal weight: 1.9990 chunk 133 optimal weight: 0.5980 chunk 21 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 51 optimal weight: 0.0980 chunk 14 optimal weight: 0.9990 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 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 HIS ** 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 = 0.4175 r_free = 0.4175 target = 0.184679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.144093 restraints weight = 16603.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.143008 restraints weight = 26897.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.144324 restraints weight = 24781.405| |-----------------------------------------------------------------------------| r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.4462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13445 Z= 0.204 Angle : 0.578 10.320 18297 Z= 0.299 Chirality : 0.040 0.200 2152 Planarity : 0.004 0.073 2165 Dihedral : 14.465 164.683 2178 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.70 % Allowed : 15.34 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.22), residues: 1550 helix: 0.73 (0.18), residues: 852 sheet: 0.60 (0.43), residues: 150 loop : 0.17 (0.28), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP A 95 HIS 0.004 0.001 HIS A 417 PHE 0.013 0.001 PHE A 765 TYR 0.010 0.001 TYR A 331 ARG 0.006 0.000 ARG B 395 *********************** 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 189 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 166 time to evaluate : 1.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8282 (tt) REVERT: A 640 LYS cc_start: 0.6580 (OUTLIER) cc_final: 0.6168 (pttt) REVERT: A 655 THR cc_start: 0.8817 (OUTLIER) cc_final: 0.8545 (m) REVERT: A 803 ASN cc_start: 0.7454 (m110) cc_final: 0.6968 (p0) REVERT: B 73 ASN cc_start: 0.8088 (t0) cc_final: 0.7766 (t0) REVERT: B 307 MET cc_start: 0.7087 (OUTLIER) cc_final: 0.6790 (tpt) REVERT: B 396 ARG cc_start: 0.7260 (ptt-90) cc_final: 0.6971 (ptt90) REVERT: B 784 ARG cc_start: 0.8465 (ttm110) cc_final: 0.7992 (ttm-80) outliers start: 23 outliers final: 15 residues processed: 180 average time/residue: 0.2913 time to fit residues: 73.6977 Evaluate side-chains 179 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 160 time to evaluate : 1.349 ------------------------------------------------------------------------------- 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 290 VAL 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 640 LYS Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 815 PHE Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 307 MET 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 528 THR Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 793 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 29 optimal weight: 7.9990 chunk 19 optimal weight: 0.7980 chunk 128 optimal weight: 0.9980 chunk 153 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 chunk 132 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 39 optimal weight: 0.1980 chunk 151 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 HIS ** 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 = 0.4185 r_free = 0.4185 target = 0.185690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.145610 restraints weight = 16483.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.144259 restraints weight = 26787.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.145343 restraints weight = 24239.923| |-----------------------------------------------------------------------------| r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.4608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13445 Z= 0.182 Angle : 0.587 10.103 18297 Z= 0.300 Chirality : 0.040 0.184 2152 Planarity : 0.004 0.096 2165 Dihedral : 14.428 164.823 2178 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.62 % Allowed : 15.34 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.22), residues: 1550 helix: 0.84 (0.18), residues: 854 sheet: 0.60 (0.43), residues: 150 loop : 0.12 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP A 95 HIS 0.004 0.001 HIS A 417 PHE 0.013 0.001 PHE A 343 TYR 0.010 0.001 TYR A 171 ARG 0.006 0.000 ARG A 884 ********************** 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 189 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 167 time to evaluate : 1.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8307 (tt) REVERT: A 640 LYS cc_start: 0.6492 (OUTLIER) cc_final: 0.6164 (pttt) REVERT: A 655 THR cc_start: 0.8778 (OUTLIER) cc_final: 0.8514 (m) REVERT: A 803 ASN cc_start: 0.7476 (m110) cc_final: 0.6978 (p0) REVERT: B 73 ASN cc_start: 0.8117 (t0) cc_final: 0.7773 (t0) REVERT: B 101 LEU cc_start: 0.7921 (OUTLIER) cc_final: 0.7591 (mt) REVERT: B 784 ARG cc_start: 0.8451 (ttm110) cc_final: 0.7987 (ttm-80) outliers start: 22 outliers final: 16 residues processed: 182 average time/residue: 0.2958 time to fit residues: 75.8212 Evaluate side-chains 179 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 159 time to evaluate : 1.350 ------------------------------------------------------------------------------- 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 164 VAL Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 290 VAL 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 640 LYS Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 815 PHE Chi-restraints excluded: chain B residue 101 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 527 VAL Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 793 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 42 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 151 optimal weight: 0.6980 chunk 45 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 chunk 148 optimal weight: 8.9990 chunk 39 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 HIS ** 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 = 0.4177 r_free = 0.4177 target = 0.184840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.144544 restraints weight = 16662.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.143355 restraints weight = 28955.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.144578 restraints weight = 25221.643| |-----------------------------------------------------------------------------| r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.4653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13445 Z= 0.208 Angle : 0.594 10.052 18297 Z= 0.305 Chirality : 0.040 0.188 2152 Planarity : 0.004 0.084 2165 Dihedral : 14.443 164.983 2178 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.55 % Allowed : 15.78 % Favored : 82.67 % 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: 0.73 (0.22), residues: 1550 helix: 0.82 (0.18), residues: 850 sheet: 0.61 (0.43), residues: 150 loop : 0.12 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP A 95 HIS 0.022 0.001 HIS A 85 PHE 0.022 0.002 PHE B 287 TYR 0.022 0.001 TYR A 811 ARG 0.009 0.001 ARG B 705 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3574.16 seconds wall clock time: 65 minutes 28.12 seconds (3928.12 seconds total)