Starting phenix.real_space_refine on Sun Aug 4 22:36:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9asj_43816/08_2024/9asj_43816.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9asj_43816/08_2024/9asj_43816.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9asj_43816/08_2024/9asj_43816.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9asj_43816/08_2024/9asj_43816.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9asj_43816/08_2024/9asj_43816.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9asj_43816/08_2024/9asj_43816.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= 0.000 sd= 0.013 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 6 5.49 5 S 74 5.16 5 C 7434 2.51 5 N 1990 2.21 5 O 2122 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 126": "OE1" <-> "OE2" Residue "A GLU 163": "OE1" <-> "OE2" Residue "A GLU 500": "OE1" <-> "OE2" Residue "A GLU 593": "OE1" <-> "OE2" Residue "A GLU 685": "OE1" <-> "OE2" Residue "A GLU 792": "OE1" <-> "OE2" Residue "B GLU 126": "OE1" <-> "OE2" Residue "B GLU 163": "OE1" <-> "OE2" Residue "B GLU 500": "OE1" <-> "OE2" Residue "B GLU 593": "OE1" <-> "OE2" Residue "B GLU 685": "OE1" <-> "OE2" Residue "B GLU 792": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 11626 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 5782 Classifications: {'peptide': 741} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 21, 'TRANS': 719} Chain breaks: 8 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 56 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 5782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 5782 Classifications: {'peptide': 741} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 21, 'TRANS': 719} Chain breaks: 8 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 56 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 23 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.35, per 1000 atoms: 0.63 Number of scatterers: 11626 At special positions: 0 Unit cell: (96.6, 155.48, 83.72, 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 74 16.00 P 6 15.00 O 2122 8.00 N 1990 7.00 C 7434 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.61 Conformation dependent library (CDL) restraints added in 2.1 seconds 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2784 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 10 sheets defined 57.4% alpha, 8.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.37 Creating SS restraints... Processing helix chain 'A' and resid 70 through 74 Processing helix chain 'A' and resid 77 through 87 Processing helix chain 'A' and resid 93 through 101 Processing helix chain 'A' and resid 120 through 136 removed outlier: 4.218A pdb=" N VAL A 124 " --> pdb=" O GLY A 120 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ALA A 125 " --> pdb=" O LYS A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 162 Processing helix chain 'A' and resid 191 through 204 removed outlier: 3.897A pdb=" N GLY A 196 " --> pdb=" O GLU A 192 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU A 204 " --> pdb=" O ARG A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 222 removed outlier: 3.558A pdb=" N GLY A 222 " --> pdb=" O HIS A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 245 removed outlier: 3.532A pdb=" N ALA A 245 " --> pdb=" O THR A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 278 Processing helix chain 'A' and resid 325 through 336 removed outlier: 3.894A pdb=" N LEU A 329 " --> pdb=" O HIS A 325 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N CYS A 330 " --> pdb=" O VAL A 326 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR A 333 " --> pdb=" O LEU A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 367 removed outlier: 3.656A pdb=" N TYR A 362 " --> pdb=" O ALA A 358 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ASN A 363 " --> pdb=" O ARG A 359 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N HIS A 365 " --> pdb=" O PHE A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 396 removed outlier: 3.837A pdb=" N ARG A 396 " --> pdb=" O ASP A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 407 removed outlier: 3.876A pdb=" N LYS A 407 " --> pdb=" O SER A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 411 Processing helix chain 'A' and resid 421 through 434 Processing helix chain 'A' and resid 444 through 449 removed outlier: 3.584A pdb=" N SER A 448 " --> pdb=" O THR A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 479 Processing helix chain 'A' and resid 497 through 499 No H-bonds generated for 'chain 'A' and resid 497 through 499' Processing helix chain 'A' and resid 500 through 510 Processing helix chain 'A' and resid 528 through 540 removed outlier: 3.892A pdb=" N ILE A 538 " --> pdb=" O ALA A 534 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL A 540 " --> pdb=" O LEU A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 556 Processing helix chain 'A' and resid 557 through 563 removed outlier: 3.924A pdb=" N MET A 563 " --> pdb=" O LEU A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 592 removed outlier: 3.710A pdb=" N VAL A 586 " --> pdb=" O ILE A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 622 removed outlier: 3.596A pdb=" N SER A 620 " --> pdb=" O SER A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 637 removed outlier: 3.524A pdb=" N LEU A 629 " --> pdb=" O PRO A 625 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ASP A 630 " --> pdb=" O ALA A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 653 Processing helix chain 'A' and resid 665 through 676 Processing helix chain 'A' and resid 679 through 687 removed outlier: 3.506A pdb=" N ALA A 684 " --> pdb=" O MET A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 730 removed outlier: 3.709A pdb=" N ILE A 715 " --> pdb=" O ARG A 711 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ARG A 718 " --> pdb=" O ALA A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 742 Processing helix chain 'A' and resid 744 through 769 removed outlier: 3.909A pdb=" N LEU A 751 " --> pdb=" O GLN A 747 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N SER A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N VAL A 757 " --> pdb=" O GLN A 753 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR A 758 " --> pdb=" O SER A 754 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N VAL A 764 " --> pdb=" O GLY A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 779 removed outlier: 3.504A pdb=" N GLU A 775 " --> pdb=" O TRP A 771 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU A 776 " --> pdb=" O HIS A 772 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU A 777 " --> pdb=" O ASN A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 780 through 787 removed outlier: 3.627A pdb=" N PHE A 787 " --> pdb=" O LYS A 783 " (cutoff:3.500A) Processing helix chain 'A' and resid 795 through 799 removed outlier: 3.525A pdb=" N ARG A 798 " --> pdb=" O ASP A 795 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL A 799 " --> pdb=" O LEU A 796 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 795 through 799' Processing helix chain 'A' and resid 807 through 812 Processing helix chain 'A' and resid 817 through 823 removed outlier: 3.545A pdb=" N ARG A 823 " --> pdb=" O ALA A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 835 removed outlier: 3.904A pdb=" N VAL A 831 " --> pdb=" O VAL A 827 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE A 832 " --> pdb=" O GLU A 828 " (cutoff:3.500A) Processing helix chain 'A' and resid 871 through 890 removed outlier: 3.706A pdb=" N VAL A 880 " --> pdb=" O ALA A 876 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 74 Processing helix chain 'B' and resid 77 through 87 Processing helix chain 'B' and resid 93 through 101 Processing helix chain 'B' and resid 120 through 136 removed outlier: 4.218A pdb=" N VAL B 124 " --> pdb=" O GLY B 120 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA B 125 " --> pdb=" O LYS B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 162 Processing helix chain 'B' and resid 191 through 204 removed outlier: 3.897A pdb=" N GLY B 196 " --> pdb=" O GLU B 192 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU B 204 " --> pdb=" O ARG B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 222 removed outlier: 3.558A pdb=" N GLY B 222 " --> pdb=" O HIS B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 245 removed outlier: 3.532A pdb=" N ALA B 245 " --> pdb=" O THR B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 278 Processing helix chain 'B' and resid 325 through 336 removed outlier: 3.894A pdb=" N LEU B 329 " --> pdb=" O HIS B 325 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N CYS B 330 " --> pdb=" O VAL B 326 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR B 333 " --> pdb=" O LEU B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 367 removed outlier: 3.655A pdb=" N TYR B 362 " --> pdb=" O ALA B 358 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASN B 363 " --> pdb=" O ARG B 359 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N HIS B 365 " --> pdb=" O PHE B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 396 removed outlier: 3.836A pdb=" N ARG B 396 " --> pdb=" O ASP B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 407 removed outlier: 3.877A pdb=" N LYS B 407 " --> pdb=" O SER B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 411 Processing helix chain 'B' and resid 421 through 434 Processing helix chain 'B' and resid 444 through 449 removed outlier: 3.584A pdb=" N SER B 448 " --> pdb=" O THR B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 479 Processing helix chain 'B' and resid 497 through 499 No H-bonds generated for 'chain 'B' and resid 497 through 499' Processing helix chain 'B' and resid 500 through 510 Processing helix chain 'B' and resid 528 through 540 removed outlier: 3.893A pdb=" N ILE B 538 " --> pdb=" O ALA B 534 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL B 540 " --> pdb=" O LEU B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 556 Processing helix chain 'B' and resid 557 through 563 removed outlier: 3.924A pdb=" N MET B 563 " --> pdb=" O LEU B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 592 removed outlier: 3.710A pdb=" N VAL B 586 " --> pdb=" O ILE B 582 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 622 removed outlier: 3.596A pdb=" N SER B 620 " --> pdb=" O SER B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 637 removed outlier: 3.524A pdb=" N LEU B 629 " --> pdb=" O PRO B 625 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ASP B 630 " --> pdb=" O ALA B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 647 through 653 Processing helix chain 'B' and resid 665 through 676 Processing helix chain 'B' and resid 679 through 687 removed outlier: 3.507A pdb=" N ALA B 684 " --> pdb=" O MET B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 710 through 730 removed outlier: 3.710A pdb=" N ILE B 715 " --> pdb=" O ARG B 711 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ARG B 718 " --> pdb=" O ALA B 714 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 742 Processing helix chain 'B' and resid 744 through 769 removed outlier: 3.909A pdb=" N LEU B 751 " --> pdb=" O GLN B 747 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N SER B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N VAL B 757 " --> pdb=" O GLN B 753 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR B 758 " --> pdb=" O SER B 754 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N VAL B 764 " --> pdb=" O GLY B 760 " (cutoff:3.500A) Processing helix chain 'B' and resid 771 through 779 removed outlier: 3.504A pdb=" N GLU B 775 " --> pdb=" O TRP B 771 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU B 776 " --> pdb=" O HIS B 772 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU B 777 " --> pdb=" O ASN B 773 " (cutoff:3.500A) Processing helix chain 'B' and resid 780 through 787 removed outlier: 3.628A pdb=" N PHE B 787 " --> pdb=" O LYS B 783 " (cutoff:3.500A) Processing helix chain 'B' and resid 795 through 799 removed outlier: 3.525A pdb=" N ARG B 798 " --> pdb=" O ASP B 795 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL B 799 " --> pdb=" O LEU B 796 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 795 through 799' Processing helix chain 'B' and resid 807 through 812 Processing helix chain 'B' and resid 817 through 823 removed outlier: 3.545A pdb=" N ARG B 823 " --> pdb=" O ALA B 819 " (cutoff:3.500A) Processing helix chain 'B' and resid 827 through 835 removed outlier: 3.903A pdb=" N VAL B 831 " --> pdb=" O VAL B 827 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE B 832 " --> pdb=" O GLU B 828 " (cutoff:3.500A) Processing helix chain 'B' and resid 871 through 890 removed outlier: 3.707A pdb=" N VAL B 880 " --> pdb=" O ALA B 876 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 168 through 169 removed outlier: 7.070A pdb=" N ALA A 140 " --> pdb=" O ALA A 187 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N CYS A 189 " --> pdb=" O ALA A 140 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N PHE A 142 " --> pdb=" O CYS A 189 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N LYS A 139 " --> pdb=" O LEU A 210 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N MET A 212 " --> pdb=" O LYS A 139 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL A 214 " --> pdb=" O LEU A 141 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 309 through 311 removed outlier: 7.536A pdb=" N ILE A 302 " --> pdb=" O VAL A 310 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER A 492 " --> pdb=" O LEU A 293 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS A 297 " --> pdb=" O LEU A 494 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL A 457 " --> pdb=" O ILE A 493 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N LEU A 341 " --> pdb=" O ILE A 458 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 463 through 464 Processing sheet with id=AA4, first strand: chain 'A' and resid 595 through 598 Processing sheet with id=AA5, first strand: chain 'A' and resid 862 through 863 Processing sheet with id=AA6, first strand: chain 'B' and resid 168 through 169 removed outlier: 7.069A pdb=" N ALA B 140 " --> pdb=" O ALA B 187 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N CYS B 189 " --> pdb=" O ALA B 140 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N PHE B 142 " --> pdb=" O CYS B 189 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N LYS B 139 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N MET B 212 " --> pdb=" O LYS B 139 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL B 214 " --> pdb=" O LEU B 141 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 309 through 311 removed outlier: 7.536A pdb=" N ILE B 302 " --> pdb=" O VAL B 310 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER B 492 " --> pdb=" O LEU B 293 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS B 297 " --> pdb=" O LEU B 494 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL B 457 " --> pdb=" O ILE B 493 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N LEU B 341 " --> pdb=" O ILE B 458 " (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 Processing sheet with id=AB1, first strand: chain 'B' and resid 862 through 863 556 hydrogen bonds defined for protein. 1596 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.83 Time building geometry restraints manager: 5.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3768 1.34 - 1.46: 2622 1.46 - 1.58: 5310 1.58 - 1.70: 8 1.70 - 1.82: 122 Bond restraints: 11830 Sorted by residual: bond pdb=" C2' ANP A 901 " pdb=" C3' ANP A 901 " ideal model delta sigma weight residual 1.520 1.292 0.228 2.00e-02 2.50e+03 1.30e+02 bond pdb=" C2' ANP B 901 " pdb=" C3' ANP B 901 " ideal model delta sigma weight residual 1.520 1.292 0.228 2.00e-02 2.50e+03 1.30e+02 bond pdb=" C6 ANP A 901 " pdb=" N6 ANP A 901 " ideal model delta sigma weight residual 1.340 1.491 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" C6 ANP B 901 " pdb=" N6 ANP B 901 " ideal model delta sigma weight residual 1.340 1.491 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" C1' ANP B 901 " pdb=" O4' ANP B 901 " ideal model delta sigma weight residual 1.394 1.514 -0.120 2.00e-02 2.50e+03 3.62e+01 ... (remaining 11825 not shown) Histogram of bond angle deviations from ideal: 98.06 - 105.26: 152 105.26 - 112.46: 6295 112.46 - 119.66: 3939 119.66 - 126.86: 5488 126.86 - 134.06: 142 Bond angle restraints: 16016 Sorted by residual: angle pdb=" O3A ANP A 901 " pdb=" PA ANP A 901 " pdb=" O5' ANP A 901 " ideal model delta sigma weight residual 98.09 109.28 -11.19 3.00e+00 1.11e-01 1.39e+01 angle pdb=" O3A ANP B 901 " pdb=" PA ANP B 901 " pdb=" O5' ANP B 901 " ideal model delta sigma weight residual 98.09 109.25 -11.16 3.00e+00 1.11e-01 1.38e+01 angle pdb=" CB MET B 885 " pdb=" CG MET B 885 " pdb=" SD MET B 885 " ideal model delta sigma weight residual 112.70 123.81 -11.11 3.00e+00 1.11e-01 1.37e+01 angle pdb=" CB MET A 885 " pdb=" CG MET A 885 " pdb=" SD MET A 885 " ideal model delta sigma weight residual 112.70 123.78 -11.08 3.00e+00 1.11e-01 1.36e+01 angle pdb=" O1B ANP B 901 " pdb=" PB ANP B 901 " pdb=" O2B ANP B 901 " ideal model delta sigma weight residual 120.08 109.67 10.41 3.00e+00 1.11e-01 1.20e+01 ... (remaining 16011 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.09: 5879 17.09 - 34.18: 879 34.18 - 51.27: 296 51.27 - 68.36: 58 68.36 - 85.45: 28 Dihedral angle restraints: 7140 sinusoidal: 2854 harmonic: 4286 Sorted by residual: dihedral pdb=" CG ARG A 637 " pdb=" CD ARG A 637 " pdb=" NE ARG A 637 " pdb=" CZ ARG A 637 " ideal model delta sinusoidal sigma weight residual -180.00 -136.23 -43.77 2 1.50e+01 4.44e-03 1.02e+01 dihedral pdb=" CG ARG B 637 " pdb=" CD ARG B 637 " pdb=" NE ARG B 637 " pdb=" CZ ARG B 637 " ideal model delta sinusoidal sigma weight residual -180.00 -136.29 -43.71 2 1.50e+01 4.44e-03 1.02e+01 dihedral pdb=" CA ASP A 630 " pdb=" CB ASP A 630 " pdb=" CG ASP A 630 " pdb=" OD1 ASP A 630 " ideal model delta sinusoidal sigma weight residual -30.00 -84.55 54.55 1 2.00e+01 2.50e-03 1.01e+01 ... (remaining 7137 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1729 0.069 - 0.138: 147 0.138 - 0.207: 6 0.207 - 0.276: 0 0.276 - 0.345: 2 Chirality restraints: 1884 Sorted by residual: chirality pdb=" C2' ANP B 901 " pdb=" C1' ANP B 901 " pdb=" C3' ANP B 901 " pdb=" O2' ANP B 901 " both_signs ideal model delta sigma weight residual False -2.72 -2.38 -0.35 2.00e-01 2.50e+01 2.98e+00 chirality pdb=" C2' ANP A 901 " pdb=" C1' ANP A 901 " pdb=" C3' ANP A 901 " pdb=" O2' ANP A 901 " both_signs ideal model delta sigma weight residual False -2.72 -2.38 -0.34 2.00e-01 2.50e+01 2.94e+00 chirality pdb=" C4' ANP A 901 " pdb=" C3' ANP A 901 " pdb=" C5' ANP A 901 " pdb=" O4' ANP A 901 " both_signs ideal model delta sigma weight residual False -2.45 -2.62 0.16 2.00e-01 2.50e+01 6.77e-01 ... (remaining 1881 not shown) Planarity restraints: 1992 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 290 " -0.042 5.00e-02 4.00e+02 6.44e-02 6.63e+00 pdb=" N PRO B 291 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO B 291 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 291 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 290 " 0.042 5.00e-02 4.00e+02 6.40e-02 6.54e+00 pdb=" N PRO A 291 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 291 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 291 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 397 " -0.027 5.00e-02 4.00e+02 4.06e-02 2.64e+00 pdb=" N PRO A 398 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 398 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 398 " -0.023 5.00e-02 4.00e+02 ... (remaining 1989 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 513 2.73 - 3.27: 11971 3.27 - 3.81: 19118 3.81 - 4.36: 22808 4.36 - 4.90: 38879 Nonbonded interactions: 93289 Sorted by model distance: nonbonded pdb=" OE1 GLU A 98 " pdb=" OH TYR A 283 " model vdw 2.184 3.040 nonbonded pdb=" OE1 GLU B 98 " pdb=" OH TYR B 283 " model vdw 2.184 3.040 nonbonded pdb=" NZ LYS B 109 " pdb=" OD1 ASN B 279 " model vdw 2.236 3.120 nonbonded pdb=" NZ LYS A 109 " pdb=" OD1 ASN A 279 " model vdw 2.236 3.120 nonbonded pdb=" O ALA A 617 " pdb=" OG SER A 621 " model vdw 2.240 3.040 ... (remaining 93284 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: 3.750 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: 0.450 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 34.580 Find NCS groups from input model: 0.340 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: 0.010 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 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 : 0.005 0.228 11830 Z= 0.368 Angle : 0.706 11.192 16016 Z= 0.315 Chirality : 0.041 0.345 1884 Planarity : 0.004 0.064 1992 Dihedral : 18.824 85.447 4356 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 0.24 % Allowed : 34.42 % Favored : 65.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.22), residues: 1446 helix: -0.41 (0.19), residues: 758 sheet: 0.33 (0.46), residues: 126 loop : -1.10 (0.26), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 411 HIS 0.004 0.001 HIS A 610 PHE 0.012 0.001 PHE A 313 TYR 0.012 0.001 TYR A 239 ARG 0.006 0.000 ARG B 798 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 201 time to evaluate : 1.215 Fit side-chains REVERT: A 639 MET cc_start: 0.4324 (mmp) cc_final: 0.4011 (mmp) REVERT: B 639 MET cc_start: 0.4339 (mmp) cc_final: 0.4026 (mmp) outliers start: 3 outliers final: 0 residues processed: 204 average time/residue: 0.2412 time to fit residues: 70.2207 Evaluate side-chains 158 residues out of total 1282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 0.6980 chunk 112 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 75 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 116 optimal weight: 0.0050 chunk 44 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 134 optimal weight: 0.0980 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 300 ASN A 498 ASN A 551 HIS A 610 HIS A 753 GLN B 300 ASN B 451 ASN B 498 ASN B 551 HIS B 610 HIS B 753 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7000 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11830 Z= 0.191 Angle : 0.631 10.007 16016 Z= 0.310 Chirality : 0.041 0.155 1884 Planarity : 0.004 0.051 1992 Dihedral : 8.136 75.602 1644 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 4.63 % Allowed : 30.67 % Favored : 64.70 % 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: -0.61 (0.22), residues: 1446 helix: 0.13 (0.18), residues: 794 sheet: 0.47 (0.45), residues: 130 loop : -1.36 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 411 HIS 0.003 0.001 HIS A 417 PHE 0.013 0.001 PHE B 670 TYR 0.011 0.002 TYR B 113 ARG 0.006 0.000 ARG A 226 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 185 time to evaluate : 1.413 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 91 LYS cc_start: 0.7097 (tptt) cc_final: 0.6686 (pttt) REVERT: A 639 MET cc_start: 0.4703 (mmp) cc_final: 0.4378 (mmp) REVERT: A 680 MET cc_start: 0.7837 (OUTLIER) cc_final: 0.7041 (mpp) REVERT: A 741 TYR cc_start: 0.7112 (m-80) cc_final: 0.6864 (m-80) REVERT: B 639 MET cc_start: 0.4645 (mmp) cc_final: 0.4304 (mmp) REVERT: B 680 MET cc_start: 0.7835 (OUTLIER) cc_final: 0.7028 (mpp) REVERT: B 741 TYR cc_start: 0.7261 (m-80) cc_final: 0.6949 (m-80) outliers start: 58 outliers final: 33 residues processed: 223 average time/residue: 0.2058 time to fit residues: 68.8650 Evaluate side-chains 192 residues out of total 1282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 157 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 667 TYR Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 722 SER Chi-restraints excluded: chain A residue 763 THR Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain B residue 360 GLU Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 662 THR Chi-restraints excluded: chain B residue 667 TYR Chi-restraints excluded: chain B residue 680 MET Chi-restraints excluded: chain B residue 715 ILE Chi-restraints excluded: chain B residue 722 SER Chi-restraints excluded: chain B residue 763 THR Chi-restraints excluded: chain B residue 793 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 74 optimal weight: 10.0000 chunk 41 optimal weight: 0.8980 chunk 111 optimal weight: 0.6980 chunk 91 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 134 optimal weight: 0.9990 chunk 145 optimal weight: 4.9990 chunk 119 optimal weight: 3.9990 chunk 133 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 551 HIS A 649 HIS ** A 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 551 HIS B 649 HIS ** B 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 11830 Z= 0.244 Angle : 0.621 9.504 16016 Z= 0.307 Chirality : 0.042 0.163 1884 Planarity : 0.004 0.052 1992 Dihedral : 7.978 72.577 1644 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 4.87 % Allowed : 30.67 % Favored : 64.46 % 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: -0.63 (0.22), residues: 1446 helix: 0.13 (0.18), residues: 806 sheet: 0.29 (0.43), residues: 130 loop : -1.38 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 411 HIS 0.005 0.001 HIS A 417 PHE 0.012 0.001 PHE A 432 TYR 0.013 0.002 TYR A 171 ARG 0.005 0.000 ARG A 873 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 167 time to evaluate : 1.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7510 (tp30) REVERT: A 300 ASN cc_start: 0.8169 (OUTLIER) cc_final: 0.7621 (t0) REVERT: A 639 MET cc_start: 0.4984 (mmp) cc_final: 0.4473 (mmp) REVERT: A 680 MET cc_start: 0.7956 (OUTLIER) cc_final: 0.7432 (mpp) REVERT: A 775 GLU cc_start: 0.7259 (tm-30) cc_final: 0.6988 (tt0) REVERT: B 152 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7515 (tp30) REVERT: B 300 ASN cc_start: 0.8164 (OUTLIER) cc_final: 0.7596 (t0) REVERT: B 639 MET cc_start: 0.4984 (mmp) cc_final: 0.4472 (mmp) REVERT: B 680 MET cc_start: 0.7947 (OUTLIER) cc_final: 0.7429 (mpp) REVERT: B 775 GLU cc_start: 0.7323 (tm-30) cc_final: 0.7069 (tt0) outliers start: 61 outliers final: 38 residues processed: 213 average time/residue: 0.1950 time to fit residues: 64.1491 Evaluate side-chains 194 residues out of total 1282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 150 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 667 TYR Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 722 SER Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 300 ASN Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 360 GLU Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 667 TYR Chi-restraints excluded: chain B residue 680 MET Chi-restraints excluded: chain B residue 722 SER Chi-restraints excluded: chain B residue 752 GLN Chi-restraints excluded: chain B residue 793 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 133 optimal weight: 0.2980 chunk 101 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 64 optimal weight: 0.5980 chunk 90 optimal weight: 2.9990 chunk 135 optimal weight: 0.6980 chunk 143 optimal weight: 10.0000 chunk 70 optimal weight: 0.0570 chunk 128 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7030 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 11830 Z= 0.176 Angle : 0.574 9.572 16016 Z= 0.283 Chirality : 0.041 0.153 1884 Planarity : 0.004 0.052 1992 Dihedral : 7.779 72.466 1644 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 5.03 % Allowed : 30.75 % Favored : 64.22 % 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 (0.22), residues: 1446 helix: 0.27 (0.18), residues: 804 sheet: 0.31 (0.44), residues: 130 loop : -1.47 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 411 HIS 0.004 0.001 HIS A 417 PHE 0.010 0.001 PHE A 432 TYR 0.015 0.001 TYR B 113 ARG 0.005 0.000 ARG A 873 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 183 time to evaluate : 1.365 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 152 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.7464 (tp30) REVERT: A 300 ASN cc_start: 0.8154 (OUTLIER) cc_final: 0.7730 (t0) REVERT: A 361 PHE cc_start: 0.5792 (OUTLIER) cc_final: 0.4497 (t80) REVERT: A 550 MET cc_start: 0.6668 (tmm) cc_final: 0.6163 (tmm) REVERT: A 741 TYR cc_start: 0.7412 (m-80) cc_final: 0.6965 (m-80) REVERT: A 775 GLU cc_start: 0.7127 (tm-30) cc_final: 0.6627 (tt0) REVERT: B 152 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7485 (tp30) REVERT: B 300 ASN cc_start: 0.8148 (OUTLIER) cc_final: 0.7621 (t0) REVERT: B 361 PHE cc_start: 0.5750 (OUTLIER) cc_final: 0.4433 (t80) REVERT: B 741 TYR cc_start: 0.7444 (m-80) cc_final: 0.6975 (m-80) REVERT: B 775 GLU cc_start: 0.7135 (tm-30) cc_final: 0.6634 (tt0) outliers start: 63 outliers final: 41 residues processed: 226 average time/residue: 0.2119 time to fit residues: 71.9414 Evaluate side-chains 202 residues out of total 1282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 155 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain A residue 361 PHE Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 551 HIS Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 667 TYR Chi-restraints excluded: chain A residue 722 SER Chi-restraints excluded: chain A residue 752 GLN Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 300 ASN Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain B residue 360 GLU Chi-restraints excluded: chain B residue 361 PHE Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 551 HIS Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 662 THR Chi-restraints excluded: chain B residue 667 TYR Chi-restraints excluded: chain B residue 722 SER Chi-restraints excluded: chain B residue 793 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 119 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 2 optimal weight: 0.4980 chunk 106 optimal weight: 0.6980 chunk 59 optimal weight: 0.6980 chunk 122 optimal weight: 0.0870 chunk 98 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 chunk 128 optimal weight: 0.6980 chunk 36 optimal weight: 0.0670 overall best weight: 0.4096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 753 GLN B 753 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11830 Z= 0.173 Angle : 0.599 9.835 16016 Z= 0.292 Chirality : 0.040 0.150 1884 Planarity : 0.004 0.053 1992 Dihedral : 7.624 71.913 1644 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.33 % Favored : 94.54 % Rotamer: Outliers : 4.87 % Allowed : 30.99 % Favored : 64.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.22), residues: 1446 helix: 0.40 (0.18), residues: 800 sheet: 0.36 (0.44), residues: 130 loop : -1.40 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 411 HIS 0.004 0.001 HIS A 416 PHE 0.010 0.001 PHE A 670 TYR 0.012 0.001 TYR A 171 ARG 0.004 0.000 ARG A 873 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 174 time to evaluate : 1.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7397 (tp30) REVERT: A 300 ASN cc_start: 0.8144 (OUTLIER) cc_final: 0.7581 (t0) REVERT: A 361 PHE cc_start: 0.5857 (OUTLIER) cc_final: 0.4630 (t80) REVERT: A 550 MET cc_start: 0.6657 (tmm) cc_final: 0.6170 (tmm) REVERT: A 680 MET cc_start: 0.7894 (OUTLIER) cc_final: 0.7266 (mpp) REVERT: A 729 ILE cc_start: 0.6870 (pt) cc_final: 0.6482 (mm) REVERT: A 775 GLU cc_start: 0.7055 (tm-30) cc_final: 0.6643 (tt0) REVERT: B 152 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7456 (tp30) REVERT: B 300 ASN cc_start: 0.8168 (OUTLIER) cc_final: 0.7597 (t0) REVERT: B 361 PHE cc_start: 0.5720 (OUTLIER) cc_final: 0.4472 (t80) REVERT: B 680 MET cc_start: 0.7883 (OUTLIER) cc_final: 0.7237 (mpp) REVERT: B 729 ILE cc_start: 0.6847 (pt) cc_final: 0.6453 (mm) outliers start: 61 outliers final: 38 residues processed: 219 average time/residue: 0.2055 time to fit residues: 68.1088 Evaluate side-chains 205 residues out of total 1282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 159 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain A residue 361 PHE Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 551 HIS Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 667 TYR Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 722 SER Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 300 ASN Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 360 GLU Chi-restraints excluded: chain B residue 361 PHE Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 551 HIS Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 667 TYR Chi-restraints excluded: chain B residue 680 MET Chi-restraints excluded: chain B residue 722 SER Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 792 GLU Chi-restraints excluded: chain B residue 793 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 48 optimal weight: 0.5980 chunk 128 optimal weight: 0.9990 chunk 28 optimal weight: 0.0370 chunk 83 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 143 optimal weight: 6.9990 chunk 118 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 47 optimal weight: 0.5980 chunk 75 optimal weight: 0.6980 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 888 GLN B 888 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7037 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11830 Z= 0.180 Angle : 0.592 9.696 16016 Z= 0.288 Chirality : 0.040 0.168 1884 Planarity : 0.004 0.053 1992 Dihedral : 7.489 71.058 1644 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.67 % Favored : 94.19 % Rotamer: Outliers : 4.23 % Allowed : 31.23 % Favored : 64.54 % 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: -0.32 (0.22), residues: 1446 helix: 0.50 (0.18), residues: 798 sheet: 0.29 (0.44), residues: 130 loop : -1.39 (0.28), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 411 HIS 0.003 0.001 HIS A 417 PHE 0.015 0.001 PHE B 815 TYR 0.010 0.001 TYR A 283 ARG 0.005 0.000 ARG A 873 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 177 time to evaluate : 1.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.7383 (tp30) REVERT: A 550 MET cc_start: 0.6704 (tmm) cc_final: 0.6227 (tmm) REVERT: A 680 MET cc_start: 0.7919 (OUTLIER) cc_final: 0.7299 (mpp) REVERT: A 729 ILE cc_start: 0.6796 (pt) cc_final: 0.6437 (mm) REVERT: A 741 TYR cc_start: 0.7232 (m-80) cc_final: 0.6878 (m-80) REVERT: A 775 GLU cc_start: 0.7107 (tm-30) cc_final: 0.6665 (tt0) REVERT: B 130 LEU cc_start: 0.8620 (mt) cc_final: 0.8381 (mt) REVERT: B 300 ASN cc_start: 0.8171 (OUTLIER) cc_final: 0.7561 (t0) REVERT: B 680 MET cc_start: 0.7914 (OUTLIER) cc_final: 0.7291 (mpp) REVERT: B 729 ILE cc_start: 0.6705 (pt) cc_final: 0.6349 (mm) REVERT: B 741 TYR cc_start: 0.7201 (m-80) cc_final: 0.6819 (m-80) REVERT: B 775 GLU cc_start: 0.7093 (tm-30) cc_final: 0.6687 (tt0) outliers start: 53 outliers final: 44 residues processed: 213 average time/residue: 0.2001 time to fit residues: 65.2576 Evaluate side-chains 212 residues out of total 1282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 164 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 551 HIS Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 639 MET Chi-restraints excluded: chain A residue 667 TYR Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 722 SER Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 300 ASN Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 360 GLU Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 551 HIS Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 631 ILE Chi-restraints excluded: chain B residue 639 MET Chi-restraints excluded: chain B residue 667 TYR Chi-restraints excluded: chain B residue 680 MET Chi-restraints excluded: chain B residue 722 SER Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 793 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 138 optimal weight: 0.0970 chunk 16 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 chunk 120 optimal weight: 0.1980 chunk 79 optimal weight: 1.9990 chunk 142 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 86 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 888 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7037 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11830 Z= 0.180 Angle : 0.590 10.185 16016 Z= 0.287 Chirality : 0.041 0.189 1884 Planarity : 0.004 0.055 1992 Dihedral : 7.406 70.191 1644 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.60 % Favored : 94.26 % Rotamer: Outliers : 4.71 % Allowed : 31.15 % Favored : 64.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.22), residues: 1446 helix: 0.52 (0.18), residues: 798 sheet: 0.29 (0.44), residues: 130 loop : -1.39 (0.28), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 277 HIS 0.003 0.001 HIS A 416 PHE 0.020 0.001 PHE B 87 TYR 0.011 0.001 TYR A 113 ARG 0.004 0.000 ARG B 456 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 173 time to evaluate : 1.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 LEU cc_start: 0.8659 (mt) cc_final: 0.8398 (mt) REVERT: A 300 ASN cc_start: 0.8207 (OUTLIER) cc_final: 0.7640 (t0) REVERT: A 396 ARG cc_start: 0.6127 (ptt90) cc_final: 0.5580 (mmt180) REVERT: A 550 MET cc_start: 0.6723 (tmm) cc_final: 0.6251 (tmm) REVERT: A 680 MET cc_start: 0.7931 (OUTLIER) cc_final: 0.7308 (mpp) REVERT: A 729 ILE cc_start: 0.6688 (pt) cc_final: 0.6387 (mm) REVERT: A 741 TYR cc_start: 0.7112 (m-80) cc_final: 0.6781 (m-80) REVERT: A 775 GLU cc_start: 0.7102 (tm-30) cc_final: 0.6580 (tm-30) REVERT: B 130 LEU cc_start: 0.8624 (mt) cc_final: 0.8370 (mt) REVERT: B 300 ASN cc_start: 0.8205 (OUTLIER) cc_final: 0.7614 (t0) REVERT: B 361 PHE cc_start: 0.5720 (OUTLIER) cc_final: 0.4630 (t80) REVERT: B 680 MET cc_start: 0.7908 (OUTLIER) cc_final: 0.7267 (mpp) REVERT: B 729 ILE cc_start: 0.6705 (pt) cc_final: 0.6405 (mm) REVERT: B 741 TYR cc_start: 0.7113 (m-80) cc_final: 0.6781 (m-80) REVERT: B 775 GLU cc_start: 0.7081 (tm-30) cc_final: 0.6692 (tt0) outliers start: 59 outliers final: 42 residues processed: 217 average time/residue: 0.1973 time to fit residues: 65.6881 Evaluate side-chains 210 residues out of total 1282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 163 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 551 HIS Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 667 TYR Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 722 SER Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 792 GLU Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain B residue 300 ASN Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 360 GLU Chi-restraints excluded: chain B residue 361 PHE Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 551 HIS Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 631 ILE Chi-restraints excluded: chain B residue 639 MET Chi-restraints excluded: chain B residue 667 TYR Chi-restraints excluded: chain B residue 680 MET Chi-restraints excluded: chain B residue 722 SER Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 792 GLU Chi-restraints excluded: chain B residue 793 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 56 optimal weight: 1.9990 chunk 85 optimal weight: 0.5980 chunk 42 optimal weight: 0.0020 chunk 28 optimal weight: 0.0980 chunk 27 optimal weight: 0.5980 chunk 90 optimal weight: 0.8980 chunk 97 optimal weight: 0.0020 chunk 70 optimal weight: 0.7980 chunk 13 optimal weight: 0.0570 chunk 112 optimal weight: 2.9990 chunk 129 optimal weight: 0.9990 overall best weight: 0.1514 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6972 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 11830 Z= 0.148 Angle : 0.601 12.009 16016 Z= 0.288 Chirality : 0.040 0.157 1884 Planarity : 0.004 0.054 1992 Dihedral : 7.251 68.836 1644 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.46 % Favored : 94.40 % Rotamer: Outliers : 2.88 % Allowed : 32.99 % Favored : 64.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.22), residues: 1446 helix: 0.60 (0.18), residues: 798 sheet: 0.48 (0.45), residues: 130 loop : -1.48 (0.27), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 411 HIS 0.003 0.001 HIS A 416 PHE 0.015 0.001 PHE A 815 TYR 0.010 0.001 TYR A 113 ARG 0.007 0.000 ARG B 396 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 161 time to evaluate : 1.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 LYS cc_start: 0.8039 (OUTLIER) cc_final: 0.7811 (tptt) REVERT: A 300 ASN cc_start: 0.8114 (OUTLIER) cc_final: 0.7613 (t0) REVERT: A 440 LEU cc_start: 0.7732 (OUTLIER) cc_final: 0.7197 (tp) REVERT: A 550 MET cc_start: 0.6668 (tmm) cc_final: 0.6263 (tmm) REVERT: A 680 MET cc_start: 0.7786 (OUTLIER) cc_final: 0.6918 (mpp) REVERT: A 729 ILE cc_start: 0.6639 (pt) cc_final: 0.6385 (mm) REVERT: A 741 TYR cc_start: 0.6966 (m-80) cc_final: 0.6680 (m-80) REVERT: A 775 GLU cc_start: 0.6986 (tm-30) cc_final: 0.6491 (tm-30) REVERT: B 130 LEU cc_start: 0.8624 (mt) cc_final: 0.8377 (mt) REVERT: B 300 ASN cc_start: 0.8109 (OUTLIER) cc_final: 0.7604 (t0) REVERT: B 680 MET cc_start: 0.7769 (OUTLIER) cc_final: 0.6989 (mpp) REVERT: B 729 ILE cc_start: 0.6613 (pt) cc_final: 0.6372 (mm) REVERT: B 741 TYR cc_start: 0.6848 (m-80) cc_final: 0.6470 (m-80) REVERT: B 775 GLU cc_start: 0.6930 (tm-30) cc_final: 0.6590 (tt0) outliers start: 36 outliers final: 27 residues processed: 182 average time/residue: 0.2012 time to fit residues: 56.6469 Evaluate side-chains 185 residues out of total 1282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 152 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 LYS Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 551 HIS Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 639 MET Chi-restraints excluded: chain A residue 667 TYR Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain B residue 300 ASN Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 360 GLU Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain B residue 551 HIS Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 639 MET Chi-restraints excluded: chain B residue 667 TYR Chi-restraints excluded: chain B residue 680 MET Chi-restraints excluded: chain B residue 793 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 136 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 132 optimal weight: 0.6980 chunk 80 optimal weight: 0.5980 chunk 57 optimal weight: 0.0770 chunk 104 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 120 optimal weight: 4.9990 chunk 125 optimal weight: 0.7980 chunk 87 optimal weight: 0.9980 chunk 140 optimal weight: 0.7980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11830 Z= 0.201 Angle : 0.631 12.335 16016 Z= 0.303 Chirality : 0.041 0.152 1884 Planarity : 0.004 0.051 1992 Dihedral : 7.187 67.115 1644 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.81 % Favored : 94.05 % Rotamer: Outliers : 2.96 % Allowed : 32.91 % Favored : 64.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.22), residues: 1446 helix: 0.53 (0.18), residues: 800 sheet: 0.39 (0.44), residues: 130 loop : -1.36 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 411 HIS 0.004 0.001 HIS A 417 PHE 0.027 0.001 PHE B 87 TYR 0.013 0.001 TYR A 171 ARG 0.004 0.000 ARG A 226 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 152 time to evaluate : 1.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 LEU cc_start: 0.8658 (mt) cc_final: 0.8368 (mt) REVERT: A 153 LYS cc_start: 0.7975 (OUTLIER) cc_final: 0.7754 (tptt) REVERT: A 300 ASN cc_start: 0.8176 (OUTLIER) cc_final: 0.7599 (t0) REVERT: A 550 MET cc_start: 0.6572 (tmm) cc_final: 0.6174 (tmm) REVERT: A 680 MET cc_start: 0.7935 (OUTLIER) cc_final: 0.7261 (mpp) REVERT: A 729 ILE cc_start: 0.6655 (pt) cc_final: 0.6390 (mm) REVERT: A 741 TYR cc_start: 0.7116 (m-80) cc_final: 0.6848 (m-80) REVERT: A 775 GLU cc_start: 0.7098 (tm-30) cc_final: 0.6630 (tm-30) REVERT: B 130 LEU cc_start: 0.8649 (mt) cc_final: 0.8374 (mt) REVERT: B 595 ILE cc_start: 0.6652 (mm) cc_final: 0.6327 (mt) REVERT: B 680 MET cc_start: 0.7966 (OUTLIER) cc_final: 0.7360 (mpp) REVERT: B 729 ILE cc_start: 0.6673 (pt) cc_final: 0.6404 (mm) REVERT: B 741 TYR cc_start: 0.6988 (m-80) cc_final: 0.6616 (m-80) outliers start: 37 outliers final: 32 residues processed: 175 average time/residue: 0.1936 time to fit residues: 52.7759 Evaluate side-chains 185 residues out of total 1282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 149 time to evaluate : 1.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 LYS Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 551 HIS Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 639 MET Chi-restraints excluded: chain A residue 667 TYR Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 360 GLU Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain B residue 551 HIS Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 639 MET Chi-restraints excluded: chain B residue 667 TYR Chi-restraints excluded: chain B residue 680 MET Chi-restraints excluded: chain B residue 774 MET Chi-restraints excluded: chain B residue 792 GLU Chi-restraints excluded: chain B residue 793 LEU Chi-restraints excluded: chain B residue 862 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 85 optimal weight: 0.4980 chunk 66 optimal weight: 1.9990 chunk 97 optimal weight: 0.0570 chunk 147 optimal weight: 0.0570 chunk 135 optimal weight: 0.9990 chunk 117 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 90 optimal weight: 0.5980 chunk 71 optimal weight: 5.9990 chunk 93 optimal weight: 0.6980 chunk 125 optimal weight: 0.7980 overall best weight: 0.3816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7009 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11830 Z= 0.171 Angle : 0.623 12.249 16016 Z= 0.298 Chirality : 0.040 0.148 1884 Planarity : 0.004 0.051 1992 Dihedral : 7.081 65.559 1644 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.33 % Favored : 94.54 % Rotamer: Outliers : 2.96 % Allowed : 32.99 % Favored : 64.06 % 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: -0.23 (0.22), residues: 1446 helix: 0.57 (0.18), residues: 800 sheet: 0.33 (0.45), residues: 132 loop : -1.35 (0.28), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 411 HIS 0.004 0.001 HIS B 417 PHE 0.014 0.001 PHE A 815 TYR 0.012 0.001 TYR A 171 ARG 0.004 0.000 ARG A 226 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 155 time to evaluate : 1.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 LEU cc_start: 0.8671 (mt) cc_final: 0.8370 (mt) REVERT: A 153 LYS cc_start: 0.7923 (OUTLIER) cc_final: 0.7711 (tptt) REVERT: A 300 ASN cc_start: 0.8161 (OUTLIER) cc_final: 0.7634 (t0) REVERT: A 440 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7297 (tp) REVERT: A 550 MET cc_start: 0.6689 (tmm) cc_final: 0.6293 (tmm) REVERT: A 680 MET cc_start: 0.7846 (OUTLIER) cc_final: 0.7075 (mpp) REVERT: A 729 ILE cc_start: 0.6617 (pt) cc_final: 0.6388 (mm) REVERT: A 741 TYR cc_start: 0.6966 (m-80) cc_final: 0.6656 (m-80) REVERT: A 775 GLU cc_start: 0.7052 (tm-30) cc_final: 0.6575 (tm-30) REVERT: B 130 LEU cc_start: 0.8633 (mt) cc_final: 0.8336 (mt) REVERT: B 440 LEU cc_start: 0.7590 (mp) cc_final: 0.7237 (tt) REVERT: B 595 ILE cc_start: 0.6676 (mm) cc_final: 0.6314 (mt) REVERT: B 680 MET cc_start: 0.7859 (OUTLIER) cc_final: 0.7171 (mpp) REVERT: B 729 ILE cc_start: 0.6726 (pt) cc_final: 0.6422 (mm) REVERT: B 741 TYR cc_start: 0.6881 (m-80) cc_final: 0.6527 (m-80) REVERT: B 775 GLU cc_start: 0.7008 (tm-30) cc_final: 0.6647 (tt0) outliers start: 37 outliers final: 31 residues processed: 177 average time/residue: 0.1950 time to fit residues: 54.1435 Evaluate side-chains 188 residues out of total 1282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 152 time to evaluate : 1.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 LYS Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain A residue 363 ASN Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 551 HIS Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 639 MET Chi-restraints excluded: chain A residue 667 TYR Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 360 GLU Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 551 HIS Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 639 MET Chi-restraints excluded: chain B residue 667 TYR Chi-restraints excluded: chain B residue 680 MET Chi-restraints excluded: chain B residue 774 MET Chi-restraints excluded: chain B residue 793 LEU Chi-restraints excluded: chain B residue 862 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 35 optimal weight: 0.5980 chunk 108 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 117 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 120 optimal weight: 0.7980 chunk 14 optimal weight: 0.3980 chunk 21 optimal weight: 0.0980 chunk 103 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.188991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.158245 restraints weight = 17560.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.163011 restraints weight = 9893.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.166235 restraints weight = 6808.229| |-----------------------------------------------------------------------------| r_work (final): 0.4215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7056 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11830 Z= 0.189 Angle : 0.627 11.990 16016 Z= 0.299 Chirality : 0.040 0.148 1884 Planarity : 0.004 0.051 1992 Dihedral : 6.903 62.196 1644 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.53 % Favored : 94.33 % Rotamer: Outliers : 3.35 % Allowed : 32.99 % Favored : 63.66 % 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: -0.19 (0.22), residues: 1446 helix: 0.59 (0.18), residues: 800 sheet: 0.31 (0.45), residues: 130 loop : -1.30 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 411 HIS 0.004 0.001 HIS B 417 PHE 0.014 0.001 PHE A 815 TYR 0.011 0.001 TYR A 171 ARG 0.005 0.000 ARG A 226 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2413.12 seconds wall clock time: 45 minutes 2.34 seconds (2702.34 seconds total)