Starting phenix.real_space_refine on Thu Mar 5 13:23:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9un2_64337/03_2026/9un2_64337.cif Found real_map, /net/cci-nas-00/data/ceres_data/9un2_64337/03_2026/9un2_64337.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9un2_64337/03_2026/9un2_64337.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9un2_64337/03_2026/9un2_64337.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9un2_64337/03_2026/9un2_64337.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9un2_64337/03_2026/9un2_64337.map" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.009 sd= 0.051 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: 4 Type Number sf(0) Gaussians S 127 5.16 5 C 14046 2.51 5 N 3618 2.21 5 O 4070 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21861 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 5480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 797, 5480 Classifications: {'peptide': 797} Incomplete info: {'truncation_to_alanine': 193} Link IDs: {'PTRANS': 34, 'TRANS': 762} Chain breaks: 2 Unresolved non-hydrogen bonds: 853 Unresolved non-hydrogen angles: 1041 Unresolved non-hydrogen dihedrals: 738 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'ARG:plan': 32, 'GLU:plan': 35, 'GLN:plan1': 7, 'HIS:plan': 10, 'TRP:plan': 3, 'ASN:plan1': 14, 'ASP:plan': 18, 'TYR:plan': 6, 'PHE:plan': 7} Unresolved non-hydrogen planarities: 585 Chain: "B" Number of atoms: 5211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 779, 5211 Classifications: {'peptide': 779} Incomplete info: {'truncation_to_alanine': 240} Link IDs: {'PTRANS': 29, 'TRANS': 749} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 978 Unresolved non-hydrogen angles: 1227 Unresolved non-hydrogen dihedrals: 844 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'ASP:plan': 31, 'GLU:plan': 42, 'HIS:plan': 8, 'PHE:plan': 14, 'ARG:plan': 18, 'GLN:plan1': 10, 'TYR:plan': 14, 'TRP:plan': 4, 'ASN:plan1': 6} Unresolved non-hydrogen planarities: 667 Chain: "C" Number of atoms: 5528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 789, 5528 Classifications: {'peptide': 789} Incomplete info: {'truncation_to_alanine': 164} Link IDs: {'PTRANS': 33, 'TRANS': 755} Chain breaks: 3 Unresolved non-hydrogen bonds: 732 Unresolved non-hydrogen angles: 893 Unresolved non-hydrogen dihedrals: 633 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ARG:plan': 28, 'GLU:plan': 34, 'GLN:plan1': 12, 'TRP:plan': 6, 'ASP:plan': 19, 'ASN:plan1': 9, 'HIS:plan': 3, 'PHE:plan': 4, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 515 Chain: "D" Number of atoms: 5404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 791, 5404 Classifications: {'peptide': 791} Incomplete info: {'truncation_to_alanine': 216} Link IDs: {'PTRANS': 28, 'TRANS': 762} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 873 Unresolved non-hydrogen angles: 1088 Unresolved non-hydrogen dihedrals: 750 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'ASP:plan': 30, 'HIS:plan': 8, 'GLU:plan': 42, 'ARG:plan': 18, 'TRP:plan': 4, 'TYR:plan': 11, 'GLN:plan1': 5, 'PHE:plan': 7, 'ASN:plan1': 9} Unresolved non-hydrogen planarities: 590 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 4.60, per 1000 atoms: 0.21 Number of scatterers: 21861 At special positions: 0 Unit cell: (108.665, 141.37, 181.46, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 127 16.00 O 4070 8.00 N 3618 7.00 C 14046 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 79 " - pdb=" SG CYS A 308 " distance=2.03 Simple disulfide: pdb=" SG CYS A 420 " - pdb=" SG CYS A 454 " distance=2.03 Simple disulfide: pdb=" SG CYS A 436 " - pdb=" SG CYS A 455 " distance=2.03 Simple disulfide: pdb=" SG CYS A 744 " - pdb=" SG CYS A 798 " distance=2.03 Simple disulfide: pdb=" SG CYS B 429 " - pdb=" SG CYS B 456 " distance=2.03 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 457 " distance=2.03 Simple disulfide: pdb=" SG CYS B 746 " - pdb=" SG CYS B 801 " distance=2.03 Simple disulfide: pdb=" SG CYS C 79 " - pdb=" SG CYS C 308 " distance=2.03 Simple disulfide: pdb=" SG CYS C 420 " - pdb=" SG CYS C 454 " distance=2.03 Simple disulfide: pdb=" SG CYS C 436 " - pdb=" SG CYS C 455 " distance=2.03 Simple disulfide: pdb=" SG CYS C 744 " - pdb=" SG CYS C 798 " distance=2.03 Simple disulfide: pdb=" SG CYS D 429 " - pdb=" SG CYS D 456 " distance=2.03 Simple disulfide: pdb=" SG CYS D 436 " - pdb=" SG CYS D 457 " distance=2.03 Simple disulfide: pdb=" SG CYS D 746 " - pdb=" SG CYS D 801 " distance=2.03 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 Links applied NAG-ASN " NAG A 901 " - " ASN A 203 " " NAG A 902 " - " ASN A 239 " " NAG A 903 " - " ASN A 276 " " NAG A 904 " - " ASN A 350 " " NAG A 905 " - " ASN A 471 " " NAG A 906 " - " ASN A 771 " " NAG C 901 " - " ASN C 61 " " NAG C 902 " - " ASN C 203 " " NAG C 903 " - " ASN C 239 " " NAG C 904 " - " ASN C 276 " " NAG C 905 " - " ASN C 350 " " NAG C 906 " - " ASN C 368 " " NAG C 907 " - " ASN C 471 " " NAG C 908 " - " ASN C 771 " " NAG D 901 " - " ASN D 341 " " NAG D 902 " - " ASN D 348 " " NAG D 903 " - " ASN D 688 " Time building additional restraints: 1.61 Conformation dependent library (CDL) restraints added in 952.8 milliseconds 6264 Ramachandran restraints generated. 3132 Oldfield, 0 Emsley, 3132 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5892 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 26 sheets defined 45.9% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 36 through 51 Processing helix chain 'A' and resid 72 through 82 Processing helix chain 'A' and resid 104 through 114 removed outlier: 4.233A pdb=" N TYR A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 145 No H-bonds generated for 'chain 'A' and resid 143 through 145' Processing helix chain 'A' and resid 146 through 158 removed outlier: 4.244A pdb=" N VAL A 150 " --> pdb=" O HIS A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 187 Processing helix chain 'A' and resid 204 through 210 removed outlier: 4.150A pdb=" N GLU A 210 " --> pdb=" O ALA A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 238 Processing helix chain 'A' and resid 255 through 261 Processing helix chain 'A' and resid 276 through 298 removed outlier: 3.846A pdb=" N HIS A 280 " --> pdb=" O ASN A 276 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLU A 297 " --> pdb=" O HIS A 293 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LYS A 298 " --> pdb=" O GLU A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 328 Processing helix chain 'A' and resid 381 through 385 removed outlier: 4.136A pdb=" N GLU A 385 " --> pdb=" O PRO A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 471 Processing helix chain 'A' and resid 499 through 507 Processing helix chain 'A' and resid 520 through 527 removed outlier: 4.087A pdb=" N TYR A 526 " --> pdb=" O GLU A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 583 removed outlier: 4.092A pdb=" N LEU A 564 " --> pdb=" O SER A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 616 Processing helix chain 'A' and resid 626 through 658 Processing helix chain 'A' and resid 669 through 674 Processing helix chain 'A' and resid 687 through 696 Processing helix chain 'A' and resid 699 through 709 removed outlier: 3.775A pdb=" N HIS A 709 " --> pdb=" O HIS A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 723 Processing helix chain 'A' and resid 733 through 743 Processing helix chain 'A' and resid 768 through 782 Processing helix chain 'A' and resid 783 through 792 Processing helix chain 'A' and resid 808 through 826 removed outlier: 3.595A pdb=" N ASN A 812 " --> pdb=" O LEU A 808 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N GLY A 815 " --> pdb=" O GLU A 811 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N VAL A 816 " --> pdb=" O ASN A 812 " (cutoff:3.500A) Processing helix chain 'A' and resid 828 through 844 Processing helix chain 'B' and resid 46 through 58 Processing helix chain 'B' and resid 78 through 92 Processing helix chain 'B' and resid 107 through 120 Processing helix chain 'B' and resid 149 through 164 Processing helix chain 'B' and resid 178 through 192 Processing helix chain 'B' and resid 212 through 223 Processing helix chain 'B' and resid 233 through 248 Processing helix chain 'B' and resid 260 through 264 Processing helix chain 'B' and resid 288 through 311 Processing helix chain 'B' and resid 324 through 330 Processing helix chain 'B' and resid 332 through 340 Processing helix chain 'B' and resid 459 through 472 Processing helix chain 'B' and resid 489 through 493 removed outlier: 3.592A pdb=" N GLY B 492 " --> pdb=" O LYS B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 503 removed outlier: 3.642A pdb=" N MET B 503 " --> pdb=" O GLY B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 523 Processing helix chain 'B' and resid 546 through 552 Processing helix chain 'B' and resid 555 through 565 removed outlier: 3.657A pdb=" N TRP B 559 " --> pdb=" O SER B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 581 Processing helix chain 'B' and resid 601 through 615 Processing helix chain 'B' and resid 625 through 657 Processing helix chain 'B' and resid 668 through 673 Processing helix chain 'B' and resid 674 through 677 removed outlier: 3.802A pdb=" N PHE B 677 " --> pdb=" O PRO B 674 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 674 through 677' Processing helix chain 'B' and resid 689 through 699 Processing helix chain 'B' and resid 699 through 708 removed outlier: 3.797A pdb=" N LYS B 708 " --> pdb=" O ALA B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 724 Processing helix chain 'B' and resid 733 through 743 Processing helix chain 'B' and resid 744 through 747 removed outlier: 4.056A pdb=" N LYS B 747 " --> pdb=" O GLU B 744 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 744 through 747' Processing helix chain 'B' and resid 771 through 787 Processing helix chain 'B' and resid 787 through 796 removed outlier: 4.121A pdb=" N GLU B 791 " --> pdb=" O GLY B 787 " (cutoff:3.500A) Processing helix chain 'B' and resid 818 through 839 Processing helix chain 'C' and resid 35 through 51 Processing helix chain 'C' and resid 70 through 82 Processing helix chain 'C' and resid 103 through 114 removed outlier: 4.021A pdb=" N VAL C 107 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 145 No H-bonds generated for 'chain 'C' and resid 143 through 145' Processing helix chain 'C' and resid 146 through 158 removed outlier: 4.038A pdb=" N VAL C 150 " --> pdb=" O HIS C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 187 Processing helix chain 'C' and resid 204 through 213 Processing helix chain 'C' and resid 224 through 237 removed outlier: 3.796A pdb=" N MET C 237 " --> pdb=" O ARG C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 240 No H-bonds generated for 'chain 'C' and resid 238 through 240' Processing helix chain 'C' and resid 250 through 255 Processing helix chain 'C' and resid 255 through 261 removed outlier: 3.881A pdb=" N ARG C 260 " --> pdb=" O GLY C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 295 Processing helix chain 'C' and resid 316 through 328 removed outlier: 3.744A pdb=" N LEU C 320 " --> pdb=" O LYS C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 385 removed outlier: 3.918A pdb=" N GLU C 385 " --> pdb=" O PRO C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 457 through 471 Processing helix chain 'C' and resid 499 through 507 Processing helix chain 'C' and resid 520 through 526 removed outlier: 3.540A pdb=" N GLN C 525 " --> pdb=" O ASN C 521 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N TYR C 526 " --> pdb=" O GLU C 522 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 584 Processing helix chain 'C' and resid 602 through 616 Processing helix chain 'C' and resid 626 through 657 removed outlier: 3.529A pdb=" N LEU C 657 " --> pdb=" O ALA C 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 669 through 674 Processing helix chain 'C' and resid 687 through 696 Processing helix chain 'C' and resid 699 through 709 Processing helix chain 'C' and resid 713 through 723 Processing helix chain 'C' and resid 733 through 743 Processing helix chain 'C' and resid 768 through 782 Processing helix chain 'C' and resid 783 through 791 Processing helix chain 'C' and resid 814 through 843 Processing helix chain 'D' and resid 48 through 57 Processing helix chain 'D' and resid 78 through 92 removed outlier: 3.587A pdb=" N ILE D 82 " --> pdb=" O PRO D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 120 removed outlier: 3.948A pdb=" N GLN D 110 " --> pdb=" O GLU D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 131 removed outlier: 3.947A pdb=" N SER D 130 " --> pdb=" O HIS D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 164 Processing helix chain 'D' and resid 178 through 193 Processing helix chain 'D' and resid 212 through 223 Processing helix chain 'D' and resid 233 through 248 Processing helix chain 'D' and resid 259 through 264 removed outlier: 4.054A pdb=" N ALA D 263 " --> pdb=" O PRO D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 311 Processing helix chain 'D' and resid 332 through 341 Processing helix chain 'D' and resid 459 through 473 Processing helix chain 'D' and resid 489 through 493 removed outlier: 4.032A pdb=" N GLY D 492 " --> pdb=" O LYS D 489 " (cutoff:3.500A) Processing helix chain 'D' and resid 495 through 503 Processing helix chain 'D' and resid 516 through 523 Processing helix chain 'D' and resid 556 through 563 Processing helix chain 'D' and resid 565 through 581 Processing helix chain 'D' and resid 601 through 615 Processing helix chain 'D' and resid 625 through 656 Processing helix chain 'D' and resid 689 through 699 Processing helix chain 'D' and resid 702 through 709 Processing helix chain 'D' and resid 713 through 724 Processing helix chain 'D' and resid 732 through 743 Processing helix chain 'D' and resid 771 through 787 removed outlier: 4.489A pdb=" N GLN D 775 " --> pdb=" O GLY D 771 " (cutoff:3.500A) Processing helix chain 'D' and resid 787 through 797 removed outlier: 4.137A pdb=" N GLU D 791 " --> pdb=" O GLY D 787 " (cutoff:3.500A) Processing helix chain 'D' and resid 799 through 804 Processing helix chain 'D' and resid 814 through 842 removed outlier: 3.980A pdb=" N MET D 818 " --> pdb=" O ASP D 814 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLY D 820 " --> pdb=" O ASP D 816 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N VAL D 821 " --> pdb=" O ASN D 817 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 119 through 120 Processing sheet with id=AA2, first strand: chain 'A' and resid 193 through 197 removed outlier: 6.251A pdb=" N LEU A 165 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N PHE A 197 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N VAL A 167 " --> pdb=" O PHE A 197 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE A 164 " --> pdb=" O ILE A 220 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N SER A 222 " --> pdb=" O ILE A 164 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N LEU A 166 " --> pdb=" O SER A 222 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ILE A 219 " --> pdb=" O LEU A 248 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 267 through 271 removed outlier: 6.260A pdb=" N TYR A 351 " --> pdb=" O ILE A 366 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ILE A 366 " --> pdb=" O TYR A 351 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ILE A 353 " --> pdb=" O VAL A 364 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 339 through 340 removed outlier: 4.274A pdb=" N GLU A 339 " --> pdb=" O LYS A 347 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 473 through 478 removed outlier: 7.692A pdb=" N ALA A 515 " --> pdb=" O GLY A 761 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N GLY A 761 " --> pdb=" O ALA A 515 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU A 517 " --> pdb=" O GLY A 759 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 410 through 413 removed outlier: 3.720A pdb=" N CYS A 455 " --> pdb=" O VAL A 434 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N VAL A 434 " --> pdb=" O CYS A 455 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 681 through 683 removed outlier: 3.708A pdb=" N TRP A 731 " --> pdb=" O THR A 539 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 124 through 125 Processing sheet with id=AA9, first strand: chain 'B' and resid 202 through 205 removed outlier: 6.572A pdb=" N ILE B 171 " --> pdb=" O LEU B 203 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N LEU B 205 " --> pdb=" O ILE B 171 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N THR B 173 " --> pdb=" O LEU B 205 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR B 174 " --> pdb=" O TYR B 231 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL B 280 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU B 277 " --> pdb=" O LEU B 367 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N LEU B 362 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N LYS B 378 " --> pdb=" O LEU B 362 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ILE B 364 " --> pdb=" O VAL B 376 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 343 through 344 removed outlier: 3.559A pdb=" N PHE B 344 " --> pdb=" O ARG B 347 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 476 through 479 removed outlier: 3.572A pdb=" N ASP B 477 " --> pdb=" O LEU B 406 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N SER B 407 " --> pdb=" O MET B 508 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N VAL B 510 " --> pdb=" O SER B 407 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N VAL B 409 " --> pdb=" O VAL B 510 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 418 through 420 Processing sheet with id=AB4, first strand: chain 'B' and resid 534 through 537 removed outlier: 3.526A pdb=" N SER B 535 " --> pdb=" O TYR B 731 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 30 through 32 removed outlier: 3.584A pdb=" N SER C 93 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N ILE C 90 " --> pdb=" O LEU C 119 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LEU C 121 " --> pdb=" O ILE C 90 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N VAL C 92 " --> pdb=" O LEU C 121 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 194 through 197 removed outlier: 3.651A pdb=" N SER C 168 " --> pdb=" O SER C 222 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N TRP C 247 " --> pdb=" O ILE C 267 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N LEU C 269 " --> pdb=" O TRP C 247 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N VAL C 249 " --> pdb=" O LEU C 269 " (cutoff:3.500A) removed outlier: 9.967A pdb=" N LEU C 271 " --> pdb=" O VAL C 249 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N GLY C 365 " --> pdb=" O ILE C 353 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ASN C 355 " --> pdb=" O GLN C 363 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N GLN C 363 " --> pdb=" O ASN C 355 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N GLN C 357 " --> pdb=" O LEU C 361 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N LEU C 361 " --> pdb=" O GLN C 357 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 473 through 478 removed outlier: 6.515A pdb=" N LEU C 398 " --> pdb=" O GLU C 475 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N HIS C 477 " --> pdb=" O LEU C 398 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ILE C 400 " --> pdb=" O HIS C 477 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N MET C 512 " --> pdb=" O ARG C 397 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N LYS C 399 " --> pdb=" O MET C 512 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N ILE C 760 " --> pdb=" O PRO C 532 " (cutoff:3.500A) removed outlier: 8.689A pdb=" N MET C 762 " --> pdb=" O SER C 530 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N SER C 530 " --> pdb=" O MET C 762 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 434 through 435 removed outlier: 3.607A pdb=" N VAL C 434 " --> pdb=" O CYS C 455 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 487 through 489 removed outlier: 3.703A pdb=" N GLU C 488 " --> pdb=" O GLU C 497 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 710 through 711 removed outlier: 7.580A pdb=" N TYR C 711 " --> pdb=" O TYR C 681 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N THR C 683 " --> pdb=" O TYR C 711 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ALA C 682 " --> pdb=" O ILE C 730 " (cutoff:3.500A) removed outlier: 9.154A pdb=" N ASP C 732 " --> pdb=" O ALA C 682 " (cutoff:3.500A) removed outlier: 10.652A pdb=" N VAL C 684 " --> pdb=" O ASP C 732 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N TRP C 731 " --> pdb=" O THR C 539 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL C 542 " --> pdb=" O VAL C 747 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL C 747 " --> pdb=" O VAL C 542 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 67 through 72 removed outlier: 6.253A pdb=" N GLY D 36 " --> pdb=" O GLY D 96 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N VAL D 98 " --> pdb=" O GLY D 36 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N ALA D 38 " --> pdb=" O VAL D 98 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ALA D 100 " --> pdb=" O ALA D 38 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N ILE D 40 " --> pdb=" O ALA D 100 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 198 through 205 removed outlier: 7.647A pdb=" N PHE D 169 " --> pdb=" O GLU D 200 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N VAL D 202 " --> pdb=" O PHE D 169 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ILE D 171 " --> pdb=" O VAL D 202 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N LEU D 204 " --> pdb=" O ILE D 171 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N THR D 173 " --> pdb=" O LEU D 204 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N ILE D 227 " --> pdb=" O ILE D 168 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N SER D 170 " --> pdb=" O ILE D 227 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ILE D 228 " --> pdb=" O ILE D 257 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N TRP D 256 " --> pdb=" O ILE D 278 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N VAL D 280 " --> pdb=" O TRP D 256 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N VAL D 258 " --> pdb=" O VAL D 280 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N LEU D 277 " --> pdb=" O LEU D 367 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 343 through 344 Processing sheet with id=AC5, first strand: chain 'D' and resid 378 through 379 Processing sheet with id=AC6, first strand: chain 'D' and resid 476 through 477 removed outlier: 6.985A pdb=" N SER D 407 " --> pdb=" O MET D 508 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 418 through 421 removed outlier: 3.865A pdb=" N VAL D 434 " --> pdb=" O CYS D 457 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 728 through 731 removed outlier: 3.832A pdb=" N VAL D 538 " --> pdb=" O VAL D 749 " (cutoff:3.500A) 1110 hydrogen bonds defined for protein. 3255 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.66 Time building geometry restraints manager: 2.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 7100 1.34 - 1.46: 5102 1.46 - 1.58: 9868 1.58 - 1.70: 0 1.70 - 1.82: 215 Bond restraints: 22285 Sorted by residual: bond pdb=" C1 NAG A 904 " pdb=" O5 NAG A 904 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.55e+00 bond pdb=" C1 NAG A 901 " pdb=" O5 NAG A 901 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.32e+00 bond pdb=" C1 NAG C 902 " pdb=" O5 NAG C 902 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.21e+00 bond pdb=" C1 NAG A 903 " pdb=" O5 NAG A 903 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.14e+00 bond pdb=" C1 NAG D 903 " pdb=" O5 NAG D 903 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.04e+00 ... (remaining 22280 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 30226 2.13 - 4.26: 316 4.26 - 6.38: 40 6.38 - 8.51: 8 8.51 - 10.64: 2 Bond angle restraints: 30592 Sorted by residual: angle pdb=" N VAL B 538 " pdb=" CA VAL B 538 " pdb=" C VAL B 538 " ideal model delta sigma weight residual 113.20 108.89 4.31 9.60e-01 1.09e+00 2.01e+01 angle pdb=" CA MET D 818 " pdb=" CB MET D 818 " pdb=" CG MET D 818 " ideal model delta sigma weight residual 114.10 121.81 -7.71 2.00e+00 2.50e-01 1.49e+01 angle pdb=" CB MET D 818 " pdb=" CG MET D 818 " pdb=" SD MET D 818 " ideal model delta sigma weight residual 112.70 123.34 -10.64 3.00e+00 1.11e-01 1.26e+01 angle pdb=" N GLY B 147 " pdb=" CA GLY B 147 " pdb=" C GLY B 147 " ideal model delta sigma weight residual 112.34 119.56 -7.22 2.04e+00 2.40e-01 1.25e+01 angle pdb=" C VAL B 564 " pdb=" N MET B 565 " pdb=" CA MET B 565 " ideal model delta sigma weight residual 122.46 116.86 5.60 1.80e+00 3.09e-01 9.66e+00 ... (remaining 30587 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 12418 17.84 - 35.67: 681 35.67 - 53.51: 119 53.51 - 71.35: 50 71.35 - 89.19: 5 Dihedral angle restraints: 13273 sinusoidal: 4160 harmonic: 9113 Sorted by residual: dihedral pdb=" CB CYS D 429 " pdb=" SG CYS D 429 " pdb=" SG CYS D 456 " pdb=" CB CYS D 456 " ideal model delta sinusoidal sigma weight residual -86.00 -175.19 89.19 1 1.00e+01 1.00e-02 9.46e+01 dihedral pdb=" CB CYS C 436 " pdb=" SG CYS C 436 " pdb=" SG CYS C 455 " pdb=" CB CYS C 455 " ideal model delta sinusoidal sigma weight residual 93.00 174.42 -81.42 1 1.00e+01 1.00e-02 8.17e+01 dihedral pdb=" CB CYS A 744 " pdb=" SG CYS A 744 " pdb=" SG CYS A 798 " pdb=" CB CYS A 798 " ideal model delta sinusoidal sigma weight residual 93.00 156.81 -63.81 1 1.00e+01 1.00e-02 5.36e+01 ... (remaining 13270 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 3462 0.070 - 0.140: 387 0.140 - 0.210: 5 0.210 - 0.280: 1 0.280 - 0.350: 2 Chirality restraints: 3857 Sorted by residual: chirality pdb=" CB ILE D 766 " pdb=" CA ILE D 766 " pdb=" CG1 ILE D 766 " pdb=" CG2 ILE D 766 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.35 2.00e-01 2.50e+01 3.06e+00 chirality pdb=" C1 NAG C 907 " pdb=" ND2 ASN C 471 " pdb=" C2 NAG C 907 " pdb=" O5 NAG C 907 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CB ILE A 90 " pdb=" CA ILE A 90 " pdb=" CG1 ILE A 90 " pdb=" CG2 ILE A 90 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.48e+00 ... (remaining 3854 not shown) Planarity restraints: 3905 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO C 95 " 0.037 5.00e-02 4.00e+02 5.62e-02 5.06e+00 pdb=" N PRO C 96 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO C 96 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 96 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 258 " -0.031 5.00e-02 4.00e+02 4.69e-02 3.51e+00 pdb=" N PRO B 259 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO B 259 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 259 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 832 " -0.012 2.00e-02 2.50e+03 1.40e-02 3.45e+00 pdb=" CG PHE A 832 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 PHE A 832 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE A 832 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE A 832 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 832 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 832 " 0.000 2.00e-02 2.50e+03 ... (remaining 3902 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4069 2.77 - 3.30: 22881 3.30 - 3.84: 37896 3.84 - 4.37: 40670 4.37 - 4.90: 69177 Nonbonded interactions: 174693 Sorted by model distance: nonbonded pdb=" O PHE D 114 " pdb=" NE2 GLN D 118 " model vdw 2.238 3.120 nonbonded pdb=" O ILE C 540 " pdb=" OG1 THR C 748 " model vdw 2.253 3.040 nonbonded pdb=" O PRO D 226 " pdb=" OG1 THR D 255 " model vdw 2.269 3.040 nonbonded pdb=" O ASP A 81 " pdb=" OG SER A 85 " model vdw 2.277 3.040 nonbonded pdb=" O ILE B 340 " pdb=" OG SER B 350 " model vdw 2.280 3.040 ... (remaining 174688 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' and (resid 29 through 159 or (resid 160 and (name N or name CA or nam \ e C or name O or name CB )) or resid 161 through 178 or (resid 179 and (name N o \ r name CA or name C or name O or name CB )) or resid 180 through 195 or (resid 1 \ 96 and (name N or name CA or name C or name O or name CB )) or resid 197 through \ 263 or (resid 264 and (name N or name CA or name C or name O or name CB )) or r \ esid 265 through 310 or (resid 311 and (name N or name CA or name C or name O or \ name CB )) or resid 312 through 314 or (resid 315 through 316 and (name N or na \ me CA or name C or name O or name CB )) or resid 317 through 319 or (resid 320 a \ nd (name N or name CA or name C or name O or name CB )) or resid 321 through 322 \ or (resid 323 and (name N or name CA or name C or name O or name CB )) or resid \ 324 through 369 or (resid 370 through 371 and (name N or name CA or name C or n \ ame O or name CB )) or resid 372 through 387 or (resid 388 and (name N or name C \ A or name C or name O or name CB )) or resid 389 or (resid 390 and (name N or na \ me CA or name C or name O or name CB )) or resid 391 through 396 or (resid 397 a \ nd (name N or name CA or name C or name O or name CB )) or resid 398 through 411 \ or (resid 412 and (name N or name CA or name C or name O or name CB )) or resid \ 413 through 432 or (resid 433 and (name N or name CA or name C or name O or nam \ e CB )) or resid 434 through 452 or (resid 453 and (name N or name CA or name C \ or name O or name CB )) or resid 454 through 480 or (resid 481 and (name N or na \ me CA or name C or name O or name CB )) or (resid 482 through 484 and (name N or \ name CA or name C or name O or name CB )) or resid 485 through 497 or (resid 49 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 499 through \ 503 or (resid 504 and (name N or name CA or name C or name O or name CB )) or re \ sid 505 through 508 or (resid 509 through 510 and (name N or name CA or name C o \ r name O or name CB )) or resid 511 through 525 or (resid 526 and (name N or nam \ e CA or name C or name O or name CB )) or resid 527 through 544 or resid 552 thr \ ough 607 or (resid 608 and (name N or name CA or name C or name O or name CB )) \ or resid 609 through 678 or (resid 679 and (name N or name CA or name C or name \ O or name CB )) or resid 680 through 695 or (resid 696 through 698 and (name N o \ r name CA or name C or name O or name CB )) or resid 699 through 706 or (resid 7 \ 07 through 709 and (name N or name CA or name C or name O or name CB )) or resid \ 710 through 715 or (resid 716 through 717 and (name N or name CA or name C or n \ ame O or name CB )) or resid 718 or (resid 719 through 720 and (name N or name C \ A or name C or name O or name CB )) or resid 721 through 722 or (resid 723 throu \ gh 725 and (name N or name CA or name C or name O or name CB )) or resid 726 thr \ ough 741 or (resid 742 through 743 and (name N or name CA or name C or name O or \ name CB )) or resid 744 through 769 or (resid 770 and (name N or name CA or nam \ e C or name O or name CB )) or resid 771 through 798 or resid 808 through 812 or \ (resid 813 through 814 and (name N or name CA or name C or name O or name CB )) \ or resid 815 through 843 or resid 901 through 906)) selection = (chain 'C' and (resid 29 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 60 or (resid 61 through 62 and (na \ me N or name CA or name C or name O or name CB )) or resid 63 through 69 or (res \ id 70 through 71 and (name N or name CA or name C or name O or name CB )) or res \ id 72 or (resid 73 and (name N or name CA or name C or name O or name CB )) or r \ esid 74 through 87 or (resid 88 through 89 and (name N or name CA or name C or n \ ame O or name CB )) or resid 90 through 93 or (resid 94 and (name N or name CA o \ r name C or name O or name CB )) or resid 95 through 100 or (resid 101 through 1 \ 03 and (name N or name CA or name C or name O or name CB )) or resid 104 through \ 108 or (resid 109 and (name N or name CA or name C or name O or name CB )) or r \ esid 110 through 112 or (resid 113 through 115 and (name N or name CA or name C \ or name O or name CB )) or resid 116 through 123 or (resid 124 and (name N or na \ me CA or name C or name O or name CB )) or resid 125 through 133 or (resid 134 t \ hrough 135 and (name N or name CA or name C or name O or name CB )) or resid 136 \ or (resid 137 and (name N or name CA or name C or name O or name CB )) or resid \ 138 through 173 or (resid 174 through 176 and (name N or name CA or name C or n \ ame O or name CB )) or resid 177 through 216 or (resid 217 and (name N or name C \ A or name C or name O or name CB )) or resid 218 through 236 or (resid 237 and ( \ name N or name CA or name C or name O or name CB )) or resid 238 through 244 or \ (resid 245 and (name N or name CA or name C or name O or name CB )) or resid 246 \ through 256 or (resid 257 through 260 and (name N or name CA or name C or name \ O or name CB )) or resid 261 through 276 or (resid 277 and (name N or name CA or \ name C or name O or name CB )) or resid 278 through 279 or (resid 280 and (name \ N or name CA or name C or name O or name CB )) or resid 281 through 299 or (res \ id 300 through 303 and (name N or name CA or name C or name O or name CB )) or r \ esid 304 through 325 or (resid 326 and (name N or name CA or name C or name O or \ name CB )) or resid 327 through 374 or (resid 375 through 378 and (name N or na \ me CA or name C or name O or name CB )) or resid 379 through 420 or (resid 421 t \ hrough 422 and (name N or name CA or name C or name O or name CB )) or resid 423 \ through 439 or (resid 440 through 441 and (name N or name CA or name C or name \ O or name CB )) or resid 442 through 467 or (resid 468 and (name N or name CA or \ name C or name O or name CB )) or resid 469 through 500 or (resid 501 through 5 \ 02 and (name N or name CA or name C or name O or name CB )) or resid 503 through \ 527 or (resid 528 and (name N or name CA or name C or name O or name CB )) or r \ esid 529 through 530 or (resid 531 and (name N or name CA or name C or name O or \ name CB )) or resid 532 through 557 or (resid 558 and (name N or name CA or nam \ e C or name O or name CB )) or resid 559 through 586 or resid 601 through 602 or \ (resid 603 and (name N or name CA or name C or name O or name CB )) or resid 60 \ 4 through 606 or (resid 607 through 608 and (name N or name CA or name C or name \ O or name CB )) or resid 609 through 610 or (resid 611 and (name N or name CA o \ r name C or name O or name CB )) or resid 612 through 670 or (resid 671 and (nam \ e N or name CA or name C or name O or name CB )) or resid 672 through 685 or (re \ sid 686 and (name N or name CA or name C or name O or name CB )) or resid 687 th \ rough 708 or (resid 709 and (name N or name CA or name C or name O or name CB )) \ or resid 710 through 726 or (resid 727 through 728 and (name N or name CA or na \ me C or name O or name CB )) or resid 729 through 745 or (resid 746 and (name N \ or name CA or name C or name O or name CB )) or resid 747 through 777 or (resid \ 778 and (name N or name CA or name C or name O or name CB )) or resid 779 throug \ h 789 or (resid 790 and (name N or name CA or name C or name O or name CB )) or \ resid 791 through 794 or (resid 795 through 797 and (name N or name CA or name C \ or name O or name CB )) or resid 798 through 817 or (resid 818 and (name N or n \ ame CA or name C or name O or name CB )) or resid 819 through 828 or (resid 829 \ and (name N or name CA or name C or name O or name CB )) or resid 830 through 83 \ 7 or (resid 838 through 839 and (name N or name CA or name C or name O or name C \ B )) or resid 840 through 843 or resid 902 through 907)) } ncs_group { reference = (chain 'B' and (resid 35 through 75 or (resid 76 through 77 and (name N or name \ CA or name C or name O or name CB )) or resid 78 through 115 or (resid 116 throu \ gh 117 and (name N or name CA or name C or name O or name CB )) or resid 118 thr \ ough 165 or (resid 166 through 167 and (name N or name CA or name C or name O or \ name CB )) or resid 168 through 174 or (resid 175 and (name N or name CA or nam \ e C or name O or name CB )) or resid 176 through 196 or (resid 197 through 198 a \ nd (name N or name CA or name C or name O or name CB )) or resid 199 through 213 \ or (resid 214 and (name N or name CA or name C or name O or name CB )) or resid \ 215 through 220 or (resid 221 through 222 and (name N or name CA or name C or n \ ame O or name CB )) or resid 223 or (resid 224 and (name N or name CA or name C \ or name O or name CB )) or resid 225 through 248 or (resid 249 and (name N or na \ me CA or name C or name O or name CB )) or resid 250 through 253 or (resid 254 a \ nd (name N or name CA or name C or name O or name CB )) or resid 255 or (resid 2 \ 56 and (name N or name CA or name C or name O or name CB )) or resid 257 through \ 281 or (resid 282 and (name N or name CA or name C or name O or name CB )) or r \ esid 283 or (resid 284 and (name N or name CA or name C or name O or name CB )) \ or resid 285 through 291 or (resid 292 and (name N or name CA or name C or name \ O or name CB )) or resid 293 through 322 or (resid 323 through 330 and (name N o \ r name CA or name C or name O or name CB )) or resid 331 through 367 or (resid 3 \ 68 through 375 and (name N or name CA or name C or name O or name CB )) or resid \ 376 through 379 or (resid 380 through 382 and (name N or name CA or name C or n \ ame O or name CB )) or resid 383 through 403 or (resid 404 through 405 and (name \ N or name CA or name C or name O or name CB )) or resid 406 through 478 or (res \ id 479 and (name N or name CA or name C or name O or name CB )) or resid 480 thr \ ough 487 or (resid 488 and (name N or name CA or name C or name O or name CB )) \ or resid 489 through 496 or (resid 497 and (name N or name CA or name C or name \ O or name CB )) or resid 498 through 499 or (resid 500 and (name N or name CA or \ name C or name O or name CB )) or resid 501 through 502 or (resid 503 through 5 \ 09 and (name N or name CA or name C or name O or name CB )) or resid 510 through \ 541 or (resid 542 and (name N or name CA or name C or name O or name CB )) or r \ esid 543 through 551 or (resid 552 and (name N or name CA or name C or name O or \ name CB )) or resid 553 through 574 or (resid 575 and (name N or name CA or nam \ e C or name O or name CB )) or resid 576 through 581 or (resid 600 and (name N o \ r name CA or name C or name O or name CB )) or resid 601 through 628 or (resid 6 \ 29 and (name N or name CA or name C or name O or name CB )) or resid 630 through \ 660 or (resid 661 and (name N or name CA or name C or name O or name CB )) or r \ esid 662 through 705 or (resid 706 and (name N or name CA or name C or name O or \ name CB )) or resid 707 through 746 or (resid 747 and (name N or name CA or nam \ e C or name O or name CB )) or resid 748 through 750 or (resid 751 and (name N o \ r name CA or name C or name O or name CB )) or resid 752 through 773 or (resid 7 \ 74 and (name N or name CA or name C or name O or name CB )) or resid 775 through \ 823 or (resid 824 and (name N or name CA or name C or name O or name CB )) or r \ esid 825 through 839)) selection = (chain 'D' and ((resid 35 through 42 and (name N or name CA or name C or name O \ or name CB )) or (resid 43 through 57 and (name N or name CA or name C or name O \ or name CB )) or resid 58 or (resid 59 through 63 and (name N or name CA or nam \ e C or name O or name CB )) or resid 64 through 68 or (resid 69 and (name N or n \ ame CA or name C or name O or name CB )) or resid 70 through 88 or (resid 89 thr \ ough 95 and (name N or name CA or name C or name O or name CB )) or resid 96 thr \ ough 97 or (resid 98 and (name N or name CA or name C or name O or name CB )) or \ resid 99 through 104 or (resid 105 through 107 and (name N or name CA or name C \ or name O or name CB )) or resid 108 through 110 or (resid 111 and (name N or n \ ame CA or name C or name O or name CB )) or resid 112 through 118 or (resid 119 \ and (name N or name CA or name C or name O or name CB )) or resid 120 through 13 \ 3 or (resid 134 through 141 and (name N or name CA or name C or name O or name C \ B )) or resid 142 through 145 or (resid 146 and (name N or name CA or name C or \ name O or name CB )) or resid 147 through 151 or (resid 152 and (name N or name \ CA or name C or name O or name CB )) or resid 153 through 163 or (resid 164 thro \ ugh 167 and (name N or name CA or name C or name O or name CB )) or resid 168 or \ (resid 169 and (name N or name CA or name C or name O or name CB )) or resid 17 \ 0 through 186 or (resid 187 and (name N or name CA or name C or name O or name C \ B )) or resid 188 through 206 or (resid 207 through 211 and (name N or name CA o \ r name C or name O or name CB )) or resid 212 through 230 or (resid 231 and (nam \ e N or name CA or name C or name O or name CB )) or resid 232 through 266 or (re \ sid 267 through 268 and (name N or name CA or name C or name O or name CB )) or \ resid 269 through 272 or (resid 273 and (name N or name CA or name C or name O o \ r name CB )) or resid 274 through 308 or (resid 309 through 313 and (name N or n \ ame CA or name C or name O or name CB )) or resid 314 through 337 or (resid 338 \ and (name N or name CA or name C or name O or name CB )) or resid 339 through 34 \ 3 or (resid 344 through 345 and (name N or name CA or name C or name O or name C \ B )) or resid 346 through 350 or (resid 351 and (name N or name CA or name C or \ name O or name CB )) or resid 352 through 372 or (resid 373 through 375 and (nam \ e N or name CA or name C or name O or name CB )) or resid 376 through 377 or (re \ sid 378 and (name N or name CA or name C or name O or name CB )) or resid 379 th \ rough 384 or (resid 385 through 386 and (name N or name CA or name C or name O o \ r name CB )) or resid 387 or (resid 388 through 394 and (name N or name CA or na \ me C or name O or name CB )) or resid 395 through 412 or (resid 413 through 414 \ and (name N or name CA or name C or name O or name CB )) or resid 415 through 47 \ 3 or (resid 474 through 475 and (name N or name CA or name C or name O or name C \ B )) or resid 476 through 506 or (resid 507 through 509 and (name N or name CA o \ r name C or name O or name CB )) or resid 510 through 530 or (resid 531 and (nam \ e N or name CA or name C or name O or name CB )) or resid 532 through 539 or (re \ sid 540 and (name N or name CA or name C or name O or name CB )) or resid 541 th \ rough 558 or (resid 559 and (name N or name CA or name C or name O or name CB )) \ or resid 560 through 578 or (resid 579 through 580 and (name N or name CA or na \ me C or name O or name CB )) or resid 581 through 620 or (resid 621 and (name N \ or name CA or name C or name O or name CB )) or resid 622 through 666 or (resid \ 667 and (name N or name CA or name C or name O or name CB )) or resid 668 throug \ h 669 or (resid 670 and (name N or name CA or name C or name O or name CB )) or \ resid 671 through 675 or (resid 676 through 678 and (name N or name CA or name C \ or name O or name CB )) or resid 679 through 687 or (resid 688 and (name N or n \ ame CA or name C or name O or name CB )) or resid 689 through 701 or (resid 702 \ through 706 and (name N or name CA or name C or name O or name CB )) or resid 70 \ 7 through 709 or (resid 710 and (name N or name CA or name C or name O or name C \ B )) or resid 711 through 754 or (resid 755 and (name N or name CA or name C or \ name O or name CB )) or resid 756 through 767 or (resid 768 and (name N or name \ CA or name C or name O or name CB )) or resid 769 through 771 or (resid 772 and \ (name N or name CA or name C or name O or name CB )) or resid 773 through 802 or \ (resid 812 and (name N or name CA or name C or name O or name CB )) or resid 81 \ 3 through 835 or (resid 836 through 839 and (name N or name CA or name C or name \ O or name CB )))) } 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: 6.190 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: 0.260 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 19.640 Find NCS groups from input model: 0.650 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 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 : 0.002 0.032 22316 Z= 0.117 Angle : 0.531 10.638 30671 Z= 0.263 Chirality : 0.041 0.350 3857 Planarity : 0.003 0.056 3888 Dihedral : 11.973 76.501 7339 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.16), residues: 3132 helix: 1.87 (0.14), residues: 1350 sheet: -0.45 (0.32), residues: 296 loop : -0.63 (0.17), residues: 1486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 337 TYR 0.006 0.001 TYR C 410 PHE 0.033 0.001 PHE A 832 TRP 0.027 0.001 TRP B 610 HIS 0.002 0.000 HIS B 359 Details of bonding type rmsd covalent geometry : bond 0.00234 (22285) covalent geometry : angle 0.52682 (30592) SS BOND : bond 0.00089 ( 14) SS BOND : angle 0.41204 ( 28) hydrogen bonds : bond 0.15507 ( 1110) hydrogen bonds : angle 6.26620 ( 3255) link_NAG-ASN : bond 0.00408 ( 17) link_NAG-ASN : angle 1.72787 ( 51) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6264 Ramachandran restraints generated. 3132 Oldfield, 0 Emsley, 3132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6264 Ramachandran restraints generated. 3132 Oldfield, 0 Emsley, 3132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 2740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 LYS cc_start: 0.9696 (tmtt) cc_final: 0.9418 (tptp) REVERT: A 354 MET cc_start: 0.6568 (mmp) cc_final: 0.6308 (mmp) REVERT: B 430 MET cc_start: 0.7012 (pmm) cc_final: 0.6592 (pmm) REVERT: C 41 MET cc_start: 0.9073 (mmp) cc_final: 0.8759 (mmp) REVERT: C 408 PHE cc_start: 0.8744 (m-80) cc_final: 0.8493 (m-80) REVERT: C 642 ILE cc_start: 0.8998 (mt) cc_final: 0.8705 (mt) REVERT: D 161 MET cc_start: 0.7773 (ppp) cc_final: 0.7549 (ppp) REVERT: D 307 MET cc_start: 0.8250 (ppp) cc_final: 0.7880 (ppp) REVERT: D 537 MET cc_start: 0.7380 (tpt) cc_final: 0.7028 (tpp) REVERT: D 565 MET cc_start: 0.8092 (ttp) cc_final: 0.7865 (ttt) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.1185 time to fit residues: 35.5201 Evaluate side-chains 157 residues out of total 2740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 197 optimal weight: 30.0000 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.5980 chunk 183 optimal weight: 0.6980 chunk 298 optimal weight: 0.9980 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 363 GLN A 477 HIS A 650 ASN ** B 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 649 ASN ** C 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 616 ASN C 780 HIS D 118 GLN D 159 ASN D 615 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.055008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.044450 restraints weight = 227179.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.045558 restraints weight = 156606.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.046303 restraints weight = 118186.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.046846 restraints weight = 96008.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.047224 restraints weight = 81759.739| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.0657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 22316 Z= 0.098 Angle : 0.492 7.990 30671 Z= 0.253 Chirality : 0.041 0.284 3857 Planarity : 0.003 0.055 3888 Dihedral : 4.764 55.055 3616 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.16), residues: 3132 helix: 1.85 (0.14), residues: 1367 sheet: -0.51 (0.31), residues: 306 loop : -0.60 (0.17), residues: 1459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 337 TYR 0.013 0.001 TYR D 646 PHE 0.020 0.001 PHE A 832 TRP 0.016 0.001 TRP B 610 HIS 0.007 0.001 HIS A 67 Details of bonding type rmsd covalent geometry : bond 0.00199 (22285) covalent geometry : angle 0.48745 (30592) SS BOND : bond 0.00121 ( 14) SS BOND : angle 0.88544 ( 28) hydrogen bonds : bond 0.03535 ( 1110) hydrogen bonds : angle 5.09839 ( 3255) link_NAG-ASN : bond 0.00314 ( 17) link_NAG-ASN : angle 1.67761 ( 51) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6264 Ramachandran restraints generated. 3132 Oldfield, 0 Emsley, 3132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6264 Ramachandran restraints generated. 3132 Oldfield, 0 Emsley, 3132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 LYS cc_start: 0.9709 (tmtt) cc_final: 0.9500 (tptp) REVERT: A 209 MET cc_start: 0.8345 (mmp) cc_final: 0.8061 (mmm) REVERT: B 565 MET cc_start: 0.6093 (ppp) cc_final: 0.5725 (ppp) REVERT: C 41 MET cc_start: 0.9085 (mmp) cc_final: 0.8761 (mmp) REVERT: C 642 ILE cc_start: 0.9132 (mt) cc_final: 0.8857 (mt) REVERT: D 161 MET cc_start: 0.7815 (ppp) cc_final: 0.7596 (ppp) REVERT: D 307 MET cc_start: 0.8339 (ppp) cc_final: 0.7985 (ppp) REVERT: D 386 MET cc_start: 0.8019 (pmm) cc_final: 0.7676 (mmt) REVERT: D 537 MET cc_start: 0.6680 (tpt) cc_final: 0.6281 (tpp) REVERT: D 783 LEU cc_start: 0.9367 (tp) cc_final: 0.9131 (tp) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.1256 time to fit residues: 36.5066 Evaluate side-chains 155 residues out of total 2740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 276 optimal weight: 3.9990 chunk 26 optimal weight: 9.9990 chunk 85 optimal weight: 10.0000 chunk 158 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 303 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 214 optimal weight: 0.9990 chunk 301 optimal weight: 6.9990 chunk 282 optimal weight: 0.6980 chunk 216 optimal weight: 3.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 650 ASN ** B 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 649 ASN B 817 ASN ** C 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 616 ASN D 615 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.053602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.042885 restraints weight = 232112.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.043991 restraints weight = 157769.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.044771 restraints weight = 118317.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.045320 restraints weight = 94916.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.045660 restraints weight = 80641.832| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.1256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 22316 Z= 0.128 Angle : 0.512 8.213 30671 Z= 0.264 Chirality : 0.041 0.274 3857 Planarity : 0.003 0.053 3888 Dihedral : 4.396 51.490 3616 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.16), residues: 3132 helix: 1.85 (0.14), residues: 1364 sheet: -0.57 (0.31), residues: 313 loop : -0.51 (0.17), residues: 1455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 67 TYR 0.017 0.001 TYR D 646 PHE 0.023 0.001 PHE A 832 TRP 0.017 0.001 TRP B 610 HIS 0.005 0.001 HIS C 780 Details of bonding type rmsd covalent geometry : bond 0.00267 (22285) covalent geometry : angle 0.50772 (30592) SS BOND : bond 0.00352 ( 14) SS BOND : angle 1.04423 ( 28) hydrogen bonds : bond 0.03447 ( 1110) hydrogen bonds : angle 4.83439 ( 3255) link_NAG-ASN : bond 0.00292 ( 17) link_NAG-ASN : angle 1.55803 ( 51) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6264 Ramachandran restraints generated. 3132 Oldfield, 0 Emsley, 3132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6264 Ramachandran restraints generated. 3132 Oldfield, 0 Emsley, 3132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 2740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 639 PHE cc_start: 0.7981 (m-80) cc_final: 0.7673 (m-80) REVERT: B 565 MET cc_start: 0.5836 (ppp) cc_final: 0.5526 (ppp) REVERT: B 606 ILE cc_start: 0.8892 (pt) cc_final: 0.8387 (pt) REVERT: B 610 TRP cc_start: 0.7100 (m100) cc_final: 0.6037 (m100) REVERT: C 41 MET cc_start: 0.9087 (mmp) cc_final: 0.8764 (mmp) REVERT: C 642 ILE cc_start: 0.9289 (mt) cc_final: 0.9071 (mt) REVERT: C 790 LYS cc_start: 0.9094 (mppt) cc_final: 0.8850 (mmtt) REVERT: D 134 MET cc_start: 0.7525 (ppp) cc_final: 0.7251 (ppp) REVERT: D 161 MET cc_start: 0.7913 (ppp) cc_final: 0.7707 (ppp) REVERT: D 307 MET cc_start: 0.8363 (ppp) cc_final: 0.8044 (ppp) REVERT: D 386 MET cc_start: 0.8087 (pmm) cc_final: 0.7692 (mmt) REVERT: D 537 MET cc_start: 0.6724 (tpt) cc_final: 0.6414 (tpp) REVERT: D 783 LEU cc_start: 0.9446 (tp) cc_final: 0.9222 (tp) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.1259 time to fit residues: 36.9339 Evaluate side-chains 158 residues out of total 2740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 5 optimal weight: 0.0980 chunk 217 optimal weight: 0.0570 chunk 70 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 chunk 114 optimal weight: 8.9990 chunk 246 optimal weight: 10.0000 chunk 136 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 103 optimal weight: 30.0000 chunk 83 optimal weight: 0.9990 chunk 3 optimal weight: 20.0000 overall best weight: 1.8304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 650 ASN ** B 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 649 ASN ** C 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 616 ASN ** 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 = 0.3568 r_free = 0.3568 target = 0.053074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.042312 restraints weight = 227109.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.043409 restraints weight = 153154.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.044179 restraints weight = 114959.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.044686 restraints weight = 93043.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.045112 restraints weight = 79500.348| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 22316 Z= 0.120 Angle : 0.511 8.253 30671 Z= 0.261 Chirality : 0.041 0.263 3857 Planarity : 0.003 0.053 3888 Dihedral : 4.103 41.289 3616 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.16), residues: 3132 helix: 1.83 (0.14), residues: 1363 sheet: -0.59 (0.30), residues: 331 loop : -0.55 (0.17), residues: 1438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 67 TYR 0.013 0.001 TYR C 692 PHE 0.020 0.001 PHE D 638 TRP 0.010 0.001 TRP B 610 HIS 0.005 0.001 HIS C 780 Details of bonding type rmsd covalent geometry : bond 0.00246 (22285) covalent geometry : angle 0.50598 (30592) SS BOND : bond 0.00434 ( 14) SS BOND : angle 1.28194 ( 28) hydrogen bonds : bond 0.03271 ( 1110) hydrogen bonds : angle 4.67195 ( 3255) link_NAG-ASN : bond 0.00274 ( 17) link_NAG-ASN : angle 1.56579 ( 51) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6264 Ramachandran restraints generated. 3132 Oldfield, 0 Emsley, 3132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6264 Ramachandran restraints generated. 3132 Oldfield, 0 Emsley, 3132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 2740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 LYS cc_start: 0.9415 (mtmm) cc_final: 0.9158 (mttt) REVERT: A 209 MET cc_start: 0.8496 (mmp) cc_final: 0.8234 (mmm) REVERT: A 354 MET cc_start: 0.6926 (mmp) cc_final: 0.6636 (mmm) REVERT: A 639 PHE cc_start: 0.8005 (m-80) cc_final: 0.7726 (m-80) REVERT: C 41 MET cc_start: 0.9132 (mmp) cc_final: 0.8801 (mmp) REVERT: D 134 MET cc_start: 0.7645 (ppp) cc_final: 0.7231 (ppp) REVERT: D 161 MET cc_start: 0.7950 (ppp) cc_final: 0.7517 (ppp) REVERT: D 307 MET cc_start: 0.8451 (ppp) cc_final: 0.8103 (ppp) REVERT: D 386 MET cc_start: 0.8064 (pmm) cc_final: 0.7682 (mmt) REVERT: D 537 MET cc_start: 0.6631 (tpt) cc_final: 0.6342 (tpp) REVERT: D 783 LEU cc_start: 0.9467 (tp) cc_final: 0.9234 (tp) REVERT: D 833 LEU cc_start: 0.9247 (mp) cc_final: 0.9032 (mm) outliers start: 0 outliers final: 0 residues processed: 172 average time/residue: 0.1204 time to fit residues: 34.3263 Evaluate side-chains 155 residues out of total 2740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 292 optimal weight: 0.9990 chunk 109 optimal weight: 0.0670 chunk 288 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 87 optimal weight: 7.9990 chunk 39 optimal weight: 8.9990 chunk 238 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 243 optimal weight: 9.9990 chunk 17 optimal weight: 4.9990 chunk 208 optimal weight: 8.9990 overall best weight: 0.9522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 650 ASN ** B 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 649 ASN ** C 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 159 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.053329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.042593 restraints weight = 224437.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.043722 restraints weight = 152165.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.044497 restraints weight = 114141.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.045053 restraints weight = 91752.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.045429 restraints weight = 77860.788| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 22316 Z= 0.096 Angle : 0.510 10.820 30671 Z= 0.256 Chirality : 0.041 0.239 3857 Planarity : 0.003 0.053 3888 Dihedral : 3.850 32.271 3616 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.16), residues: 3132 helix: 1.87 (0.14), residues: 1365 sheet: -0.49 (0.30), residues: 326 loop : -0.55 (0.17), residues: 1441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 346 TYR 0.010 0.001 TYR C 692 PHE 0.029 0.001 PHE D 784 TRP 0.011 0.001 TRP D 796 HIS 0.004 0.001 HIS C 780 Details of bonding type rmsd covalent geometry : bond 0.00204 (22285) covalent geometry : angle 0.50134 (30592) SS BOND : bond 0.00154 ( 14) SS BOND : angle 0.82273 ( 28) hydrogen bonds : bond 0.03050 ( 1110) hydrogen bonds : angle 4.56292 ( 3255) link_NAG-ASN : bond 0.00380 ( 17) link_NAG-ASN : angle 2.35198 ( 51) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6264 Ramachandran restraints generated. 3132 Oldfield, 0 Emsley, 3132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6264 Ramachandran restraints generated. 3132 Oldfield, 0 Emsley, 3132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 MET cc_start: 0.8461 (mmp) cc_final: 0.8216 (mmm) REVERT: A 639 PHE cc_start: 0.8016 (m-80) cc_final: 0.7792 (m-80) REVERT: C 41 MET cc_start: 0.9151 (mmp) cc_final: 0.8799 (mmp) REVERT: C 74 MET cc_start: 0.8174 (mmm) cc_final: 0.7958 (mmm) REVERT: C 555 MET cc_start: 0.7564 (ttt) cc_final: 0.7325 (ttt) REVERT: C 790 LYS cc_start: 0.9097 (mppt) cc_final: 0.8850 (mmtt) REVERT: D 134 MET cc_start: 0.7774 (ppp) cc_final: 0.7291 (ppp) REVERT: D 161 MET cc_start: 0.7745 (ppp) cc_final: 0.7485 (ppp) REVERT: D 307 MET cc_start: 0.8429 (ppp) cc_final: 0.8088 (ppp) REVERT: D 386 MET cc_start: 0.8125 (pmm) cc_final: 0.7785 (mmt) REVERT: D 537 MET cc_start: 0.6502 (tpt) cc_final: 0.6274 (tpp) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.1218 time to fit residues: 35.5781 Evaluate side-chains 155 residues out of total 2740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 119 optimal weight: 8.9990 chunk 181 optimal weight: 0.9980 chunk 208 optimal weight: 7.9990 chunk 254 optimal weight: 6.9990 chunk 239 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 115 optimal weight: 0.0870 chunk 166 optimal weight: 10.0000 chunk 148 optimal weight: 5.9990 chunk 196 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 overall best weight: 1.3762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 650 ASN ** B 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 649 ASN ** C 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 159 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.052932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.042173 restraints weight = 227215.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.043292 restraints weight = 153217.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.044089 restraints weight = 114617.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.044635 restraints weight = 92082.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.045030 restraints weight = 78289.711| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 22316 Z= 0.107 Angle : 0.517 9.361 30671 Z= 0.260 Chirality : 0.041 0.279 3857 Planarity : 0.003 0.053 3888 Dihedral : 3.768 27.402 3616 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.16), residues: 3132 helix: 1.89 (0.14), residues: 1359 sheet: -0.49 (0.30), residues: 330 loop : -0.51 (0.17), residues: 1443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 346 TYR 0.010 0.001 TYR C 692 PHE 0.025 0.001 PHE C 832 TRP 0.009 0.001 TRP B 610 HIS 0.004 0.001 HIS C 780 Details of bonding type rmsd covalent geometry : bond 0.00226 (22285) covalent geometry : angle 0.51028 (30592) SS BOND : bond 0.00182 ( 14) SS BOND : angle 0.80733 ( 28) hydrogen bonds : bond 0.03035 ( 1110) hydrogen bonds : angle 4.53519 ( 3255) link_NAG-ASN : bond 0.00352 ( 17) link_NAG-ASN : angle 2.07570 ( 51) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6264 Ramachandran restraints generated. 3132 Oldfield, 0 Emsley, 3132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6264 Ramachandran restraints generated. 3132 Oldfield, 0 Emsley, 3132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 2740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 MET cc_start: 0.8484 (mmp) cc_final: 0.8272 (mmm) REVERT: A 354 MET cc_start: 0.6878 (mmp) cc_final: 0.6615 (mmm) REVERT: A 639 PHE cc_start: 0.8050 (m-80) cc_final: 0.7832 (m-80) REVERT: B 565 MET cc_start: 0.6225 (ppp) cc_final: 0.5951 (ppp) REVERT: C 41 MET cc_start: 0.9128 (mmp) cc_final: 0.8783 (mmp) REVERT: C 642 ILE cc_start: 0.9296 (mt) cc_final: 0.9064 (mt) REVERT: C 790 LYS cc_start: 0.9095 (mppt) cc_final: 0.8856 (mmtt) REVERT: D 134 MET cc_start: 0.7766 (ppp) cc_final: 0.7238 (ppp) REVERT: D 142 MET cc_start: 0.7021 (ptt) cc_final: 0.6777 (ptt) REVERT: D 161 MET cc_start: 0.7770 (ppp) cc_final: 0.7531 (ppp) REVERT: D 307 MET cc_start: 0.8490 (ppp) cc_final: 0.8171 (ppp) REVERT: D 386 MET cc_start: 0.8138 (pmm) cc_final: 0.7769 (mmt) REVERT: D 537 MET cc_start: 0.6515 (tpt) cc_final: 0.6219 (tpp) REVERT: D 702 MET cc_start: 0.7932 (pmm) cc_final: 0.7653 (pmm) REVERT: D 783 LEU cc_start: 0.9458 (tp) cc_final: 0.9250 (tp) outliers start: 0 outliers final: 0 residues processed: 172 average time/residue: 0.1240 time to fit residues: 35.4192 Evaluate side-chains 153 residues out of total 2740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 243 optimal weight: 0.4980 chunk 221 optimal weight: 5.9990 chunk 27 optimal weight: 30.0000 chunk 250 optimal weight: 0.1980 chunk 154 optimal weight: 4.9990 chunk 279 optimal weight: 6.9990 chunk 179 optimal weight: 7.9990 chunk 161 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 chunk 232 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 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 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 650 ASN ** B 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 616 ASN B 649 ASN ** C 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 159 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.053107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.042362 restraints weight = 225798.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.043480 restraints weight = 152176.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.044279 restraints weight = 113758.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.044824 restraints weight = 91649.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.045214 restraints weight = 78060.741| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 22316 Z= 0.094 Angle : 0.509 8.905 30671 Z= 0.255 Chirality : 0.041 0.270 3857 Planarity : 0.003 0.054 3888 Dihedral : 3.669 24.463 3616 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.16), residues: 3132 helix: 1.86 (0.14), residues: 1365 sheet: -0.51 (0.30), residues: 331 loop : -0.52 (0.17), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 346 TYR 0.008 0.001 TYR C 692 PHE 0.025 0.001 PHE A 832 TRP 0.010 0.001 TRP B 610 HIS 0.004 0.001 HIS C 134 Details of bonding type rmsd covalent geometry : bond 0.00201 (22285) covalent geometry : angle 0.50275 (30592) SS BOND : bond 0.00107 ( 14) SS BOND : angle 0.67133 ( 28) hydrogen bonds : bond 0.02962 ( 1110) hydrogen bonds : angle 4.45093 ( 3255) link_NAG-ASN : bond 0.00379 ( 17) link_NAG-ASN : angle 1.97331 ( 51) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6264 Ramachandran restraints generated. 3132 Oldfield, 0 Emsley, 3132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6264 Ramachandran restraints generated. 3132 Oldfield, 0 Emsley, 3132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 2740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.635 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 178 LYS cc_start: 0.9450 (mtmm) cc_final: 0.9187 (mttt) REVERT: A 209 MET cc_start: 0.8473 (mmp) cc_final: 0.8256 (mmm) REVERT: A 555 MET cc_start: 0.7538 (tpt) cc_final: 0.7295 (mmm) REVERT: A 639 PHE cc_start: 0.8019 (m-80) cc_final: 0.7812 (m-80) REVERT: B 565 MET cc_start: 0.6291 (ppp) cc_final: 0.5932 (ppp) REVERT: C 41 MET cc_start: 0.9120 (mmp) cc_final: 0.8775 (mmp) REVERT: C 74 MET cc_start: 0.8419 (mmm) cc_final: 0.8017 (mmm) REVERT: C 178 LYS cc_start: 0.9446 (tmtt) cc_final: 0.9238 (tptp) REVERT: C 642 ILE cc_start: 0.9251 (mt) cc_final: 0.9007 (mt) REVERT: D 134 MET cc_start: 0.7763 (ppp) cc_final: 0.7358 (ppp) REVERT: D 142 MET cc_start: 0.6928 (ptt) cc_final: 0.6648 (ptt) REVERT: D 161 MET cc_start: 0.7840 (ppp) cc_final: 0.7639 (ppp) REVERT: D 307 MET cc_start: 0.8494 (ppp) cc_final: 0.8165 (ppp) REVERT: D 386 MET cc_start: 0.8073 (pmm) cc_final: 0.7766 (mmt) REVERT: D 537 MET cc_start: 0.6398 (tpt) cc_final: 0.6146 (tpp) REVERT: D 702 MET cc_start: 0.7958 (pmm) cc_final: 0.7695 (pmm) REVERT: D 783 LEU cc_start: 0.9466 (tp) cc_final: 0.9247 (tp) outliers start: 0 outliers final: 0 residues processed: 172 average time/residue: 0.1255 time to fit residues: 35.9428 Evaluate side-chains 157 residues out of total 2740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 65 optimal weight: 8.9990 chunk 85 optimal weight: 50.0000 chunk 188 optimal weight: 10.0000 chunk 142 optimal weight: 7.9990 chunk 299 optimal weight: 1.9990 chunk 280 optimal weight: 0.0470 chunk 19 optimal weight: 5.9990 chunk 178 optimal weight: 10.0000 chunk 208 optimal weight: 0.9990 chunk 158 optimal weight: 10.0000 chunk 213 optimal weight: 7.9990 overall best weight: 3.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 650 ASN A 742 GLN B 649 ASN ** C 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 477 HIS ** C 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 105 GLN D 159 ASN ** D 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.050790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.040111 restraints weight = 227980.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.041175 restraints weight = 153132.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.041881 restraints weight = 115102.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.042408 restraints weight = 93689.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.042790 restraints weight = 80094.762| |-----------------------------------------------------------------------------| r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 22316 Z= 0.201 Angle : 0.603 10.481 30671 Z= 0.313 Chirality : 0.043 0.301 3857 Planarity : 0.004 0.053 3888 Dihedral : 4.129 25.515 3616 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.16), residues: 3132 helix: 1.64 (0.14), residues: 1370 sheet: -0.67 (0.30), residues: 340 loop : -0.53 (0.17), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 346 TYR 0.014 0.001 TYR C 692 PHE 0.055 0.002 PHE B 577 TRP 0.024 0.002 TRP D 559 HIS 0.006 0.001 HIS A 571 Details of bonding type rmsd covalent geometry : bond 0.00401 (22285) covalent geometry : angle 0.59690 (30592) SS BOND : bond 0.00185 ( 14) SS BOND : angle 0.86321 ( 28) hydrogen bonds : bond 0.03729 ( 1110) hydrogen bonds : angle 4.81515 ( 3255) link_NAG-ASN : bond 0.00380 ( 17) link_NAG-ASN : angle 2.05748 ( 51) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6264 Ramachandran restraints generated. 3132 Oldfield, 0 Emsley, 3132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6264 Ramachandran restraints generated. 3132 Oldfield, 0 Emsley, 3132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 2740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 LYS cc_start: 0.9457 (mtmm) cc_final: 0.9215 (mttt) REVERT: A 209 MET cc_start: 0.8861 (mmp) cc_final: 0.8390 (mmm) REVERT: A 354 MET cc_start: 0.7414 (mmp) cc_final: 0.6967 (mmm) REVERT: A 639 PHE cc_start: 0.8303 (m-80) cc_final: 0.8058 (m-80) REVERT: B 824 MET cc_start: 0.5042 (mmt) cc_final: 0.4803 (mmt) REVERT: C 41 MET cc_start: 0.9264 (mmp) cc_final: 0.8912 (mmp) REVERT: C 209 MET cc_start: 0.9112 (ptp) cc_final: 0.8806 (ptp) REVERT: C 818 MET cc_start: 0.5563 (mpp) cc_final: 0.5203 (mpp) REVERT: D 134 MET cc_start: 0.7846 (ppp) cc_final: 0.7475 (ppp) REVERT: D 142 MET cc_start: 0.7439 (ptt) cc_final: 0.7126 (ptt) REVERT: D 161 MET cc_start: 0.7877 (ppp) cc_final: 0.7638 (ppp) REVERT: D 307 MET cc_start: 0.8593 (ppp) cc_final: 0.8252 (ppp) REVERT: D 537 MET cc_start: 0.6758 (tpt) cc_final: 0.6307 (tpp) REVERT: D 562 MET cc_start: 0.7997 (mpp) cc_final: 0.7685 (mtp) REVERT: D 783 LEU cc_start: 0.9473 (tp) cc_final: 0.9244 (tp) REVERT: D 833 LEU cc_start: 0.9277 (mp) cc_final: 0.9075 (mm) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.1282 time to fit residues: 35.2087 Evaluate side-chains 151 residues out of total 2740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 201 optimal weight: 0.5980 chunk 242 optimal weight: 3.9990 chunk 155 optimal weight: 0.3980 chunk 299 optimal weight: 0.0050 chunk 126 optimal weight: 8.9990 chunk 12 optimal weight: 0.9990 chunk 142 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 chunk 258 optimal weight: 6.9990 chunk 100 optimal weight: 10.0000 chunk 163 optimal weight: 0.6980 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN A 357 GLN ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 650 ASN ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 649 ASN ** C 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 159 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.052149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.041448 restraints weight = 225556.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.042569 restraints weight = 150833.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.043327 restraints weight = 112242.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.043850 restraints weight = 90643.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.044248 restraints weight = 77327.265| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 22316 Z= 0.100 Angle : 0.540 9.584 30671 Z= 0.270 Chirality : 0.042 0.277 3857 Planarity : 0.003 0.054 3888 Dihedral : 3.857 25.001 3616 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.16), residues: 3132 helix: 1.74 (0.14), residues: 1374 sheet: -0.52 (0.30), residues: 341 loop : -0.53 (0.17), residues: 1417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 346 TYR 0.012 0.001 TYR B 731 PHE 0.038 0.001 PHE B 577 TRP 0.015 0.001 TRP B 635 HIS 0.003 0.001 HIS C 780 Details of bonding type rmsd covalent geometry : bond 0.00212 (22285) covalent geometry : angle 0.53533 (30592) SS BOND : bond 0.00104 ( 14) SS BOND : angle 0.61834 ( 28) hydrogen bonds : bond 0.03105 ( 1110) hydrogen bonds : angle 4.52336 ( 3255) link_NAG-ASN : bond 0.00379 ( 17) link_NAG-ASN : angle 1.88685 ( 51) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6264 Ramachandran restraints generated. 3132 Oldfield, 0 Emsley, 3132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6264 Ramachandran restraints generated. 3132 Oldfield, 0 Emsley, 3132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 2740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 LYS cc_start: 0.9444 (mtmm) cc_final: 0.9170 (mttt) REVERT: A 209 MET cc_start: 0.8623 (mmp) cc_final: 0.8225 (mmm) REVERT: A 354 MET cc_start: 0.7137 (mmp) cc_final: 0.6785 (mmm) REVERT: A 463 LEU cc_start: 0.9517 (tp) cc_final: 0.9303 (tp) REVERT: B 565 MET cc_start: 0.6421 (ppp) cc_final: 0.6043 (ppp) REVERT: C 41 MET cc_start: 0.9179 (mmp) cc_final: 0.8835 (mmp) REVERT: C 74 MET cc_start: 0.8415 (mmm) cc_final: 0.8143 (mmm) REVERT: C 790 LYS cc_start: 0.9076 (mppt) cc_final: 0.8824 (mmtt) REVERT: D 134 MET cc_start: 0.7923 (ppp) cc_final: 0.7446 (ppp) REVERT: D 142 MET cc_start: 0.7025 (ptt) cc_final: 0.6739 (ptt) REVERT: D 161 MET cc_start: 0.7859 (ppp) cc_final: 0.7636 (ppp) REVERT: D 307 MET cc_start: 0.8482 (ppp) cc_final: 0.8146 (ppp) REVERT: D 537 MET cc_start: 0.6415 (tpt) cc_final: 0.6104 (tpp) outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.1321 time to fit residues: 36.1167 Evaluate side-chains 153 residues out of total 2740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 212 optimal weight: 0.7980 chunk 241 optimal weight: 0.2980 chunk 216 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 279 optimal weight: 5.9990 chunk 215 optimal weight: 0.7980 chunk 303 optimal weight: 0.5980 chunk 70 optimal weight: 9.9990 chunk 101 optimal weight: 6.9990 chunk 140 optimal weight: 7.9990 chunk 39 optimal weight: 20.0000 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 650 ASN ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 649 ASN C 101 HIS D 159 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.051989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.041319 restraints weight = 224907.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.042459 restraints weight = 150440.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.043155 restraints weight = 111795.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.043726 restraints weight = 90694.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.044120 restraints weight = 77154.541| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 22316 Z= 0.099 Angle : 0.529 8.706 30671 Z= 0.266 Chirality : 0.042 0.281 3857 Planarity : 0.003 0.054 3888 Dihedral : 3.733 24.455 3616 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.16), residues: 3132 helix: 1.75 (0.14), residues: 1375 sheet: -0.46 (0.30), residues: 332 loop : -0.54 (0.17), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 346 TYR 0.008 0.001 TYR C 410 PHE 0.038 0.001 PHE B 577 TRP 0.016 0.001 TRP B 610 HIS 0.004 0.001 HIS C 780 Details of bonding type rmsd covalent geometry : bond 0.00213 (22285) covalent geometry : angle 0.52400 (30592) SS BOND : bond 0.00084 ( 14) SS BOND : angle 0.60471 ( 28) hydrogen bonds : bond 0.03087 ( 1110) hydrogen bonds : angle 4.49011 ( 3255) link_NAG-ASN : bond 0.00350 ( 17) link_NAG-ASN : angle 1.85989 ( 51) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6264 Ramachandran restraints generated. 3132 Oldfield, 0 Emsley, 3132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6264 Ramachandran restraints generated. 3132 Oldfield, 0 Emsley, 3132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 2740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 LYS cc_start: 0.9451 (mtmm) cc_final: 0.9175 (mttt) REVERT: A 209 MET cc_start: 0.8616 (mmp) cc_final: 0.8222 (mmm) REVERT: A 354 MET cc_start: 0.7220 (mmp) cc_final: 0.6780 (mmm) REVERT: A 463 LEU cc_start: 0.9534 (tp) cc_final: 0.9309 (tp) REVERT: B 142 MET cc_start: 0.4158 (ptt) cc_final: 0.3710 (ppp) REVERT: C 41 MET cc_start: 0.9187 (mmp) cc_final: 0.8845 (mmp) REVERT: C 74 MET cc_start: 0.8367 (mmm) cc_final: 0.8067 (mmm) REVERT: C 642 ILE cc_start: 0.9275 (mt) cc_final: 0.9018 (mt) REVERT: C 647 TYR cc_start: 0.8785 (t80) cc_final: 0.8584 (t80) REVERT: C 651 LEU cc_start: 0.9268 (mt) cc_final: 0.9045 (mt) REVERT: C 790 LYS cc_start: 0.9079 (mppt) cc_final: 0.8835 (mmtt) REVERT: C 818 MET cc_start: 0.5701 (mpp) cc_final: 0.5461 (mpp) REVERT: D 134 MET cc_start: 0.7853 (ppp) cc_final: 0.7390 (ppp) REVERT: D 142 MET cc_start: 0.7143 (ptt) cc_final: 0.6825 (ptt) REVERT: D 161 MET cc_start: 0.7840 (ppp) cc_final: 0.7615 (ppp) REVERT: D 307 MET cc_start: 0.8474 (ppp) cc_final: 0.8134 (ppp) REVERT: D 537 MET cc_start: 0.6279 (tpt) cc_final: 0.5997 (tpp) REVERT: D 565 MET cc_start: 0.7665 (ttp) cc_final: 0.7431 (ppp) REVERT: D 702 MET cc_start: 0.7904 (pmm) cc_final: 0.7667 (pmm) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.1228 time to fit residues: 34.2391 Evaluate side-chains 153 residues out of total 2740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 72 optimal weight: 4.9990 chunk 78 optimal weight: 0.0370 chunk 300 optimal weight: 2.9990 chunk 257 optimal weight: 8.9990 chunk 11 optimal weight: 0.9980 chunk 245 optimal weight: 10.0000 chunk 197 optimal weight: 0.1980 chunk 230 optimal weight: 3.9990 chunk 175 optimal weight: 4.9990 chunk 190 optimal weight: 7.9990 chunk 178 optimal weight: 0.9980 overall best weight: 1.0460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 650 ASN ** B 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 649 ASN D 159 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.051926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.041243 restraints weight = 224769.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.042388 restraints weight = 151496.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.043131 restraints weight = 112653.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.043637 restraints weight = 90909.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.044040 restraints weight = 77786.582| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 22316 Z= 0.100 Angle : 0.527 9.615 30671 Z= 0.264 Chirality : 0.041 0.282 3857 Planarity : 0.003 0.054 3888 Dihedral : 3.656 24.189 3616 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.16), residues: 3132 helix: 1.76 (0.14), residues: 1376 sheet: -0.48 (0.30), residues: 324 loop : -0.55 (0.17), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 346 TYR 0.011 0.001 TYR D 646 PHE 0.036 0.001 PHE B 577 TRP 0.017 0.001 TRP B 610 HIS 0.004 0.001 HIS C 780 Details of bonding type rmsd covalent geometry : bond 0.00213 (22285) covalent geometry : angle 0.52184 (30592) SS BOND : bond 0.00080 ( 14) SS BOND : angle 0.63098 ( 28) hydrogen bonds : bond 0.03005 ( 1110) hydrogen bonds : angle 4.42255 ( 3255) link_NAG-ASN : bond 0.00353 ( 17) link_NAG-ASN : angle 1.81229 ( 51) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3377.73 seconds wall clock time: 59 minutes 3.39 seconds (3543.39 seconds total)