Starting phenix.real_space_refine on Thu Mar 5 16:12:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uno_64358/03_2026/9uno_64358.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uno_64358/03_2026/9uno_64358.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9uno_64358/03_2026/9uno_64358.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uno_64358/03_2026/9uno_64358.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9uno_64358/03_2026/9uno_64358.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uno_64358/03_2026/9uno_64358.map" } resolution = 3.55 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= 0.012 sd= 0.065 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 124 5.16 5 C 14761 2.51 5 N 3833 2.21 5 O 4223 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.03s 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: 22941 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 786, 5722 Classifications: {'peptide': 786} Incomplete info: {'truncation_to_alanine': 116} Link IDs: {'PTRANS': 33, 'TRANS': 752} Chain breaks: 3 Unresolved non-hydrogen bonds: 489 Unresolved non-hydrogen angles: 586 Unresolved non-hydrogen dihedrals: 418 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 16, 'GLU:plan': 29, 'TRP:plan': 1, 'ASN:plan1': 6, 'GLN:plan1': 6, 'ASP:plan': 11, 'HIS:plan': 3, 'PHE:plan': 5, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 332 Chain: "B" Number of atoms: 5586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 789, 5586 Classifications: {'peptide': 789} Incomplete info: {'truncation_to_alanine': 164} Link IDs: {'PTRANS': 29, 'TRANS': 759} Chain breaks: 1 Unresolved non-hydrogen bonds: 684 Unresolved non-hydrogen angles: 845 Unresolved non-hydrogen dihedrals: 587 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLU:plan': 35, 'ARG:plan': 16, 'TRP:plan': 3, 'GLN:plan1': 9, 'ASP:plan': 16, 'PHE:plan': 12, 'TYR:plan': 5, 'HIS:plan': 2, 'ASN:plan1': 12} Unresolved non-hydrogen planarities: 484 Chain: "C" Number of atoms: 5658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 786, 5658 Classifications: {'peptide': 786} Incomplete info: {'truncation_to_alanine': 135} Link IDs: {'PTRANS': 34, 'TRANS': 751} Chain breaks: 3 Unresolved non-hydrogen bonds: 551 Unresolved non-hydrogen angles: 663 Unresolved non-hydrogen dihedrals: 469 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'ARG:plan': 13, 'GLU:plan': 35, 'TRP:plan': 1, 'ASN:plan1': 8, 'GLN:plan1': 6, 'ASP:plan': 11, 'HIS:plan': 4, 'PHE:plan': 3, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 354 Chain: "D" Number of atoms: 5627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 779, 5627 Classifications: {'peptide': 779} Incomplete info: {'truncation_to_alanine': 143} Link IDs: {'PTRANS': 27, 'TRANS': 751} Chain breaks: 2 Unresolved non-hydrogen bonds: 555 Unresolved non-hydrogen angles: 681 Unresolved non-hydrogen dihedrals: 468 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLU:plan': 36, 'ARG:plan': 11, 'TRP:plan': 1, 'ASP:plan': 15, 'PHE:plan': 7, 'ASN:plan1': 6, 'HIS:plan': 3, 'TYR:plan': 4, 'GLN:plan1': 6} Unresolved non-hydrogen planarities: 380 Chain: "A" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 116 Unusual residues: {'NAG': 8} Classifications: {'peptide': 1, 'undetermined': 8} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 51 Unusual residues: {'NAG': 3} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 116 Unusual residues: {'NAG': 8} Classifications: {'peptide': 1, 'undetermined': 8} Link IDs: {None: 8} 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: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 65 Unusual residues: {'NAG': 4} Classifications: {'peptide': 1, 'undetermined': 4} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 5.17, per 1000 atoms: 0.23 Number of scatterers: 22941 At special positions: 0 Unit cell: (107.61, 142.425, 177.24, 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 124 16.00 O 4223 8.00 N 3833 7.00 C 14761 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, 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 87 " - pdb=" SG CYS B 320 " distance=2.03 Simple disulfide: pdb=" SG CYS B 429 " - pdb=" SG CYS B 455 " distance=2.03 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 456 " distance=2.03 Simple disulfide: pdb=" SG CYS B 745 " - pdb=" SG CYS B 800 " 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 D 87 " - pdb=" SG CYS D 320 " distance=2.03 Simple disulfide: pdb=" SG CYS D 429 " - pdb=" SG CYS D 455 " distance=2.03 Simple disulfide: pdb=" SG CYS D 436 " - pdb=" SG CYS D 456 " distance=2.03 Simple disulfide: pdb=" SG CYS D 745 " - pdb=" SG CYS D 800 " 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 61 " " NAG A 902 " - " ASN A 276 " " NAG A 903 " - " ASN A 350 " " NAG A 904 " - " ASN A 471 " " NAG A 905 " - " ASN A 771 " " NAG A 906 " - " ASN A 203 " " NAG A 907 " - " ASN A 239 " " NAG A 908 " - " ASN A 368 " " NAG B 901 " - " ASN B 340 " " NAG B 902 " - " ASN B 687 " " NAG B 903 " - " ASN B 75 " " NAG C 901 " - " ASN C 61 " " NAG C 902 " - " ASN C 203 " " NAG C 903 " - " ASN C 368 " " NAG C 904 " - " ASN C 771 " " NAG C 905 " - " ASN C 471 " " NAG C 906 " - " ASN C 239 " " NAG C 907 " - " ASN C 276 " " NAG C 908 " - " ASN C 350 " " NAG D 901 " - " ASN D 340 " " NAG D 902 " - " ASN D 380 " " NAG D 903 " - " ASN D 75 " " NAG D 904 " - " ASN D 687 " Time building additional restraints: 1.96 Conformation dependent library (CDL) restraints added in 1.1 seconds 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5872 Finding SS restraints... Secondary structure from input PDB file: 115 helices and 30 sheets defined 45.0% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 35 through 54 Processing helix chain 'A' and resid 70 through 81 Processing helix chain 'A' and resid 82 through 85 Processing helix chain 'A' and resid 103 through 114 removed outlier: 4.380A pdb=" N VAL A 107 " --> pdb=" O THR A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 129 removed outlier: 3.641A pdb=" N TYR A 128 " --> pdb=" O MET A 125 " (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: 4.164A pdb=" N VAL A 150 " --> pdb=" O HIS A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 185 Processing helix chain 'A' and resid 204 through 214 Processing helix chain 'A' and resid 224 through 238 Processing helix chain 'A' and resid 251 through 255 removed outlier: 3.566A pdb=" N ILE A 254 " --> pdb=" O GLU A 251 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N SER A 255 " --> pdb=" O ARG A 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 251 through 255' Processing helix chain 'A' and resid 256 through 261 Processing helix chain 'A' and resid 276 through 298 removed outlier: 3.589A pdb=" N HIS A 280 " --> pdb=" O ASN A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 328 Processing helix chain 'A' and resid 381 through 385 removed outlier: 4.192A pdb=" N GLU A 385 " --> pdb=" O PRO A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 470 Processing helix chain 'A' and resid 500 through 508 removed outlier: 3.841A pdb=" N GLY A 508 " --> pdb=" O GLU A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 525 removed outlier: 3.590A pdb=" N GLN A 525 " --> pdb=" O ASN A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 583 removed outlier: 3.586A pdb=" N LEU A 564 " --> pdb=" O SER A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 615 Processing helix chain 'A' and resid 626 through 657 Processing helix chain 'A' and resid 669 through 674 Processing helix chain 'A' and resid 687 through 696 removed outlier: 3.581A pdb=" N ILE A 691 " --> pdb=" O SER A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 709 removed outlier: 3.942A 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 793 Processing helix chain 'A' and resid 809 through 811 No H-bonds generated for 'chain 'A' and resid 809 through 811' Processing helix chain 'A' and resid 812 through 836 removed outlier: 3.681A pdb=" N GLY A 823 " --> pdb=" O LEU A 819 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ILE A 824 " --> pdb=" O VAL A 820 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE A 829 " --> pdb=" O VAL A 825 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 55 Processing helix chain 'B' and resid 78 through 92 removed outlier: 3.628A pdb=" N GLY B 92 " --> pdb=" O ASP B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 121 Processing helix chain 'B' and resid 150 through 165 Processing helix chain 'B' and resid 179 through 193 Processing helix chain 'B' and resid 211 through 220 Processing helix chain 'B' and resid 232 through 247 Processing helix chain 'B' and resid 258 through 263 Processing helix chain 'B' and resid 287 through 310 Processing helix chain 'B' and resid 334 through 340 Processing helix chain 'B' and resid 367 through 371 removed outlier: 4.185A pdb=" N ARG B 370 " --> pdb=" O ASN B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 472 Processing helix chain 'B' and resid 495 through 502 Processing helix chain 'B' and resid 515 through 522 Processing helix chain 'B' and resid 556 through 579 Processing helix chain 'B' and resid 600 through 613 Processing helix chain 'B' and resid 624 through 655 removed outlier: 3.928A pdb=" N PHE B 637 " --> pdb=" O VAL B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 672 Processing helix chain 'B' and resid 688 through 698 Processing helix chain 'B' and resid 698 through 706 Processing helix chain 'B' and resid 707 through 709 No H-bonds generated for 'chain 'B' and resid 707 through 709' Processing helix chain 'B' and resid 712 through 722 Processing helix chain 'B' and resid 732 through 742 Processing helix chain 'B' and resid 771 through 785 Processing helix chain 'B' and resid 786 through 796 Processing helix chain 'B' and resid 798 through 803 Processing helix chain 'B' and resid 817 through 838 Processing helix chain 'C' and resid 35 through 54 Processing helix chain 'C' and resid 70 through 82 Processing helix chain 'C' and resid 103 through 114 removed outlier: 3.876A pdb=" N VAL C 107 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 129 removed outlier: 3.635A pdb=" N TYR C 128 " --> pdb=" O MET C 125 " (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 159 removed outlier: 4.171A pdb=" N VAL C 150 " --> pdb=" O HIS C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 185 Processing helix chain 'C' and resid 204 through 214 Processing helix chain 'C' and resid 224 through 239 Processing helix chain 'C' and resid 256 through 261 Processing helix chain 'C' and resid 278 through 298 Processing helix chain 'C' and resid 317 through 328 Processing helix chain 'C' and resid 381 through 385 removed outlier: 4.187A pdb=" N GLU C 385 " --> pdb=" O PRO C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 419 Processing helix chain 'C' and resid 458 through 470 Processing helix chain 'C' and resid 500 through 507 Processing helix chain 'C' and resid 520 through 525 removed outlier: 3.895A pdb=" N GLN C 525 " --> pdb=" O ASN C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 583 removed outlier: 3.605A pdb=" N LEU C 564 " --> pdb=" O SER C 560 " (cutoff:3.500A) Processing helix chain 'C' and resid 602 through 615 Processing helix chain 'C' and resid 626 through 656 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 710 Processing helix chain 'C' and resid 713 through 723 Processing helix chain 'C' and resid 733 through 743 Processing helix chain 'C' and resid 769 through 782 Processing helix chain 'C' and resid 783 through 792 Processing helix chain 'C' and resid 813 through 837 removed outlier: 4.554A pdb=" N ILE C 824 " --> pdb=" O VAL C 820 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N VAL C 825 " --> pdb=" O ALA C 821 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 55 Processing helix chain 'D' and resid 56 through 60 Processing helix chain 'D' and resid 78 through 91 Processing helix chain 'D' and resid 107 through 121 removed outlier: 4.078A pdb=" N GLN D 111 " --> pdb=" O GLU D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 165 Processing helix chain 'D' and resid 179 through 193 Processing helix chain 'D' and resid 212 through 221 Processing helix chain 'D' and resid 232 through 247 Processing helix chain 'D' and resid 258 through 263 removed outlier: 4.163A pdb=" N SER D 262 " --> pdb=" O PRO D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 310 Processing helix chain 'D' and resid 329 through 332 Processing helix chain 'D' and resid 333 through 340 removed outlier: 3.787A pdb=" N PHE D 337 " --> pdb=" O THR D 333 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASN D 340 " --> pdb=" O GLN D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 346 removed outlier: 3.531A pdb=" N GLY D 345 " --> pdb=" O THR D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 458 through 471 Processing helix chain 'D' and resid 494 through 502 Processing helix chain 'D' and resid 515 through 520 Processing helix chain 'D' and resid 555 through 579 removed outlier: 3.830A pdb=" N VAL D 559 " --> pdb=" O ALA D 555 " (cutoff:3.500A) Processing helix chain 'D' and resid 603 through 613 Processing helix chain 'D' and resid 624 through 655 removed outlier: 3.673A pdb=" N ILE D 654 " --> pdb=" O ALA D 650 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLN D 655 " --> pdb=" O ALA D 651 " (cutoff:3.500A) Processing helix chain 'D' and resid 667 through 672 Processing helix chain 'D' and resid 687 through 698 removed outlier: 3.798A pdb=" N GLU D 691 " --> pdb=" O ASN D 687 " (cutoff:3.500A) Processing helix chain 'D' and resid 698 through 706 Processing helix chain 'D' and resid 707 through 709 No H-bonds generated for 'chain 'D' and resid 707 through 709' Processing helix chain 'D' and resid 712 through 723 Processing helix chain 'D' and resid 732 through 741 Processing helix chain 'D' and resid 742 through 745 removed outlier: 3.666A pdb=" N CYS D 745 " --> pdb=" O ASP D 742 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 742 through 745' Processing helix chain 'D' and resid 770 through 785 removed outlier: 4.614A pdb=" N GLN D 774 " --> pdb=" O PRO D 770 " (cutoff:3.500A) Processing helix chain 'D' and resid 786 through 796 Processing helix chain 'D' and resid 816 through 818 No H-bonds generated for 'chain 'D' and resid 816 through 818' Processing helix chain 'D' and resid 819 through 841 Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 65 removed outlier: 8.293A pdb=" N ASN A 28 " --> pdb=" O TYR A 88 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N ILE A 90 " --> pdb=" O ASN A 28 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N GLY A 30 " --> pdb=" O ILE A 90 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N VAL A 92 " --> pdb=" O GLY A 30 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL A 32 " --> pdb=" O VAL A 92 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N VAL A 118 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 194 through 197 removed outlier: 8.306A pdb=" N LEU A 195 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LEU A 165 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N PHE A 197 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N VAL A 167 " --> pdb=" O PHE A 197 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER A 222 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER A 168 " --> pdb=" O SER A 222 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU A 269 " --> pdb=" O VAL A 249 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY A 365 " --> pdb=" O ILE A 353 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ASN A 355 " --> pdb=" O GLN A 363 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N GLN A 363 " --> pdb=" O ASN A 355 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 474 through 478 removed outlier: 6.296A pdb=" N LEU A 398 " --> pdb=" O GLU A 475 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N HIS A 477 " --> pdb=" O LEU A 398 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N ILE A 400 " --> pdb=" O HIS A 477 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 410 through 413 Processing sheet with id=AA5, first strand: chain 'A' and resid 486 through 489 Processing sheet with id=AA6, first strand: chain 'A' and resid 681 through 682 removed outlier: 3.665A pdb=" N ALA A 682 " --> pdb=" O ALA A 728 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ILE A 730 " --> pdb=" O ALA A 682 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TRP A 731 " --> pdb=" O THR A 539 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N LEU A 538 " --> pdb=" O GLU A 751 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N GLU A 751 " --> pdb=" O LEU A 538 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 68 through 69 removed outlier: 3.631A pdb=" N ILE B 36 " --> pdb=" O ASN B 68 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 68 through 69 removed outlier: 3.631A pdb=" N ILE B 36 " --> pdb=" O ASN B 68 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N LEU B 98 " --> pdb=" O LEU B 125 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ILE B 124 " --> pdb=" O PHE B 145 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 199 through 204 removed outlier: 7.472A pdb=" N PHE B 170 " --> pdb=" O ASN B 202 " (cutoff:3.500A) removed outlier: 8.977A pdb=" N ILE B 204 " --> pdb=" O PHE B 170 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LEU B 172 " --> pdb=" O ILE B 204 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N VAL B 169 " --> pdb=" O VAL B 226 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N LEU B 228 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N SER B 171 " --> pdb=" O LEU B 228 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ILE B 227 " --> pdb=" O ILE B 256 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL B 279 " --> pdb=" O VAL B 257 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 342 through 343 Processing sheet with id=AB2, first strand: chain 'B' and resid 475 through 479 removed outlier: 6.710A pdb=" N LEU B 406 " --> pdb=" O ASP B 476 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N TYR B 478 " --> pdb=" O LEU B 406 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N ILE B 408 " --> pdb=" O TYR B 478 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N SER B 407 " --> pdb=" O MET B 507 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 418 through 419 Processing sheet with id=AB4, first strand: chain 'B' and resid 437 through 441 Processing sheet with id=AB5, first strand: chain 'B' and resid 488 through 489 Processing sheet with id=AB6, first strand: chain 'B' and resid 523 through 524 Processing sheet with id=AB7, first strand: chain 'B' and resid 682 through 683 removed outlier: 6.591A pdb=" N GLY B 683 " --> pdb=" O ILE B 729 " (cutoff:3.500A) removed outlier: 8.981A pdb=" N ASP B 731 " --> pdb=" O GLY B 683 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL B 748 " --> pdb=" O VAL B 537 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 60 through 66 Processing sheet with id=AB9, first strand: chain 'C' and resid 194 through 197 removed outlier: 6.454A pdb=" N ILE C 164 " --> pdb=" O ILE C 220 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N SER C 222 " --> pdb=" O ILE C 164 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N LEU C 166 " --> pdb=" O SER C 222 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N ILE C 219 " --> pdb=" O LEU C 248 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 267 through 268 removed outlier: 4.011A pdb=" N GLY C 365 " --> pdb=" O ILE C 353 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ASN C 355 " --> pdb=" O GLN C 363 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N GLN C 363 " --> pdb=" O ASN C 355 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 474 through 478 removed outlier: 6.490A pdb=" N LEU C 398 " --> pdb=" O GLU C 475 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N HIS C 477 " --> pdb=" O LEU C 398 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N ILE C 400 " --> pdb=" O HIS C 477 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N LYS C 399 " --> pdb=" O MET C 512 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 409 through 413 Processing sheet with id=AC4, first strand: chain 'C' and resid 486 through 489 Processing sheet with id=AC5, first strand: chain 'C' and resid 681 through 683 removed outlier: 6.382A pdb=" N LEU C 538 " --> pdb=" O GLU C 751 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N GLU C 751 " --> pdb=" O LEU C 538 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE C 540 " --> pdb=" O THR C 749 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 67 through 71 removed outlier: 6.756A pdb=" N ASN D 35 " --> pdb=" O GLY D 97 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N VAL D 99 " --> pdb=" O ASN D 35 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ALA D 37 " --> pdb=" O VAL D 99 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N ILE D 124 " --> pdb=" O PHE D 145 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 199 through 205 removed outlier: 8.227A pdb=" N PHE D 170 " --> pdb=" O ASN D 202 " (cutoff:3.500A) removed outlier: 9.007A pdb=" N ILE D 204 " --> pdb=" O PHE D 170 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LEU D 172 " --> pdb=" O ILE D 204 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N VAL D 169 " --> pdb=" O VAL D 226 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N LEU D 228 " --> pdb=" O VAL D 169 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N SER D 171 " --> pdb=" O LEU D 228 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N TYR D 230 " --> pdb=" O SER D 171 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N VAL D 173 " --> pdb=" O TYR D 230 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU D 229 " --> pdb=" O ILE D 256 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL D 279 " --> pdb=" O VAL D 257 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N VAL D 363 " --> pdb=" O VAL D 375 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 405 through 406 Processing sheet with id=AC9, first strand: chain 'D' and resid 409 through 410 Processing sheet with id=AD1, first strand: chain 'D' and resid 418 through 420 removed outlier: 3.696A pdb=" N VAL D 434 " --> pdb=" O CYS D 456 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 533 through 534 Processing sheet with id=AD3, first strand: chain 'D' and resid 536 through 538 1094 hydrogen bonds defined for protein. 3177 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: 4.36 Time building geometry restraints manager: 2.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7351 1.34 - 1.46: 5184 1.46 - 1.58: 10698 1.58 - 1.70: 0 1.70 - 1.82: 211 Bond restraints: 23444 Sorted by residual: bond pdb=" N LEU C 33 " pdb=" CA LEU C 33 " ideal model delta sigma weight residual 1.452 1.489 -0.036 1.22e-02 6.72e+03 8.75e+00 bond pdb=" N GLY C 30 " pdb=" CA GLY C 30 " ideal model delta sigma weight residual 1.444 1.475 -0.031 1.06e-02 8.90e+03 8.54e+00 bond pdb=" N ILE C 642 " pdb=" CA ILE C 642 " ideal model delta sigma weight residual 1.461 1.494 -0.032 1.17e-02 7.31e+03 7.68e+00 bond pdb=" N ILE C 631 " pdb=" CA ILE C 631 " ideal model delta sigma weight residual 1.461 1.494 -0.032 1.17e-02 7.31e+03 7.63e+00 bond pdb=" N VAL C 644 " pdb=" CA VAL C 644 " ideal model delta sigma weight residual 1.461 1.493 -0.033 1.19e-02 7.06e+03 7.55e+00 ... (remaining 23439 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 31487 1.76 - 3.52: 536 3.52 - 5.29: 68 5.29 - 7.05: 14 7.05 - 8.81: 4 Bond angle restraints: 32109 Sorted by residual: angle pdb=" C VAL D 257 " pdb=" CA VAL D 257 " pdb=" CB VAL D 257 " ideal model delta sigma weight residual 109.33 112.70 -3.37 9.80e-01 1.04e+00 1.19e+01 angle pdb=" CA SER C 34 " pdb=" C SER C 34 " pdb=" O SER C 34 " ideal model delta sigma weight residual 120.70 117.46 3.24 1.03e+00 9.43e-01 9.89e+00 angle pdb=" CA MET B 564 " pdb=" CB MET B 564 " pdb=" CG MET B 564 " ideal model delta sigma weight residual 114.10 120.31 -6.21 2.00e+00 2.50e-01 9.63e+00 angle pdb=" CA GLU D 379 " pdb=" CB GLU D 379 " pdb=" CG GLU D 379 " ideal model delta sigma weight residual 114.10 120.31 -6.21 2.00e+00 2.50e-01 9.63e+00 angle pdb=" CA THR C 35 " pdb=" CB THR C 35 " pdb=" OG1 THR C 35 " ideal model delta sigma weight residual 109.60 104.99 4.61 1.50e+00 4.44e-01 9.43e+00 ... (remaining 32104 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.22: 12897 17.22 - 34.44: 847 34.44 - 51.66: 157 51.66 - 68.88: 52 68.88 - 86.10: 12 Dihedral angle restraints: 13965 sinusoidal: 4880 harmonic: 9085 Sorted by residual: 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 -86.00 -147.58 61.58 1 1.00e+01 1.00e-02 5.03e+01 dihedral pdb=" CB CYS C 420 " pdb=" SG CYS C 420 " pdb=" SG CYS C 454 " pdb=" CB CYS C 454 " ideal model delta sinusoidal sigma weight residual 93.00 43.57 49.43 1 1.00e+01 1.00e-02 3.36e+01 dihedral pdb=" CB CYS D 87 " pdb=" SG CYS D 87 " pdb=" SG CYS D 320 " pdb=" CB CYS D 320 " ideal model delta sinusoidal sigma weight residual 93.00 141.69 -48.69 1 1.00e+01 1.00e-02 3.26e+01 ... (remaining 13962 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 3465 0.067 - 0.135: 453 0.135 - 0.202: 23 0.202 - 0.269: 6 0.269 - 0.337: 2 Chirality restraints: 3949 Sorted by residual: chirality pdb=" C1 NAG A 905 " pdb=" ND2 ASN A 771 " pdb=" C2 NAG A 905 " pdb=" O5 NAG A 905 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.83e+00 chirality pdb=" C1 NAG C 906 " pdb=" ND2 ASN C 239 " pdb=" C2 NAG C 906 " pdb=" O5 NAG C 906 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CB VAL C 32 " pdb=" CA VAL C 32 " pdb=" CG1 VAL C 32 " pdb=" CG2 VAL C 32 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 3946 not shown) Planarity restraints: 4061 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 630 " -0.202 9.50e-02 1.11e+02 9.04e-02 5.04e+00 pdb=" NE ARG C 630 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG C 630 " -0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG C 630 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG C 630 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL D 257 " -0.027 5.00e-02 4.00e+02 4.11e-02 2.70e+00 pdb=" N PRO D 258 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO D 258 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO D 258 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 160 " 0.013 2.00e-02 2.50e+03 1.03e-02 2.63e+00 pdb=" CG TRP C 160 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 TRP C 160 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP C 160 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 160 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP C 160 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 160 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 160 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 160 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP C 160 " 0.003 2.00e-02 2.50e+03 ... (remaining 4058 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 2177 2.74 - 3.28: 24273 3.28 - 3.82: 39450 3.82 - 4.36: 43117 4.36 - 4.90: 75699 Nonbonded interactions: 184716 Sorted by model distance: nonbonded pdb=" O PRO C 104 " pdb=" OG SER C 108 " model vdw 2.206 3.040 nonbonded pdb=" O PRO A 104 " pdb=" OG SER A 108 " model vdw 2.235 3.040 nonbonded pdb=" O VAL B 339 " pdb=" OG SER B 349 " model vdw 2.238 3.040 nonbonded pdb=" O THR B 793 " pdb=" OG1 THR B 797 " model vdw 2.254 3.040 nonbonded pdb=" O THR D 793 " pdb=" OG1 THR D 797 " model vdw 2.264 3.040 ... (remaining 184711 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 25 through 50 or (resid 51 and (name N or name CA or name \ C or name O or name CB )) or resid 52 through 67 or (resid 68 and (name N or nam \ e CA or name C or name O or name CB )) or resid 69 through 72 or (resid 73 and ( \ name N or name CA or name C or name O or name CB )) or resid 74 through 100 or ( \ resid 101 and (name N or name CA or name C or name O or name CB )) or resid 102 \ through 168 or (resid 169 and (name N or name CA or name C or name O or name CB \ )) or resid 170 through 191 or (resid 192 through 193 and (name N or name CA or \ name C or name O or name CB )) or resid 194 through 225 or (resid 226 and (name \ N or name CA or name C or name O or name CB )) or resid 227 through 236 or (resi \ d 237 and (name N or name CA or name C or name O or name CB )) or resid 238 thro \ ugh 293 or (resid 294 and (name N or name CA or name C or name O or name CB )) o \ r resid 295 or (resid 296 through 299 and (name N or name CA or name C or name O \ or name CB )) or resid 300 through 321 or (resid 322 and (name N or name CA or \ name C or name O or name CB )) or resid 323 through 338 or (resid 339 through 34 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 343 through \ 346 or (resid 347 and (name N or name CA or name C or name O or name CB )) or re \ sid 348 through 387 or (resid 388 and (name N or name CA or name C or name O or \ name CB )) or resid 389 through 393 or (resid 394 and (name N or name CA or name \ C or name O or name CB )) or resid 395 through 405 or (resid 406 and (name N or \ name CA or name C or name O or name CB )) or resid 407 through 421 or (resid 42 \ 2 through 423 and (name N or name CA or name C or name O or name CB )) or resid \ 424 through 489 or (resid 490 through 492 and (name N or name CA or name C or na \ me O or name CB )) or resid 493 or (resid 494 through 497 and (name N or name CA \ or name C or name O or name CB )) or resid 498 through 501 or (resid 502 and (n \ ame N or name CA or name C or name O or name CB )) or resid 503 through 510 or ( \ resid 511 and (name N or name CA or name C or name O or name CB )) or resid 512 \ through 527 or (resid 528 and (name N or name CA or name C or name O or name CB \ )) or resid 529 through 542 or (resid 543 through 545 and (name N or name CA or \ name C or name O or name CB )) or resid 546 through 555 or (resid 556 and (name \ N or name CA or name C or name O or name CB )) or resid 557 through 576 or (resi \ d 577 through 578 and (name N or name CA or name C or name O or name CB )) or re \ sid 579 through 583 or (resid 601 through 602 and (name N or name CA or name C o \ r name O or name CB )) or resid 603 through 634 or (resid 635 and (name N or nam \ e CA or name C or name O or name CB )) or resid 636 through 656 or resid 664 thr \ ough 671 or (resid 672 and (name N or name CA or name C or name O or name CB )) \ or resid 673 through 678 or (resid 679 and (name N or name CA or name C or name \ O or name CB )) or resid 680 through 684 or (resid 685 and (name N or name CA or \ name C or name O or name CB )) or resid 686 through 696 or (resid 697 through 6 \ 99 and (name N or name CA or name C or name O or name CB )) or resid 700 through \ 702 or (resid 703 through 704 and (name N or name CA or name C or name O or nam \ e CB )) or resid 705 through 793 or (resid 794 through 804 and (name N or name C \ A or name C or name O or name CB )) or resid 805 through 810 or (resid 811 throu \ gh 814 and (name N or name CA or name C or name O or name CB )) or resid 815 thr \ ough 817 or (resid 818 through 819 and (name N or name CA or name C or name O or \ name CB )) or resid 820 through 909)) selection = (chain 'C' and (resid 25 through 182 or (resid 183 and (name N or name CA or nam \ e C or name O or name CB )) or resid 184 through 274 or (resid 275 and (name N o \ r name CA or name C or name O or name CB )) or resid 276 through 305 or (resid 3 \ 06 and (name N or name CA or name C or name O or name CB )) or resid 307 through \ 339 or (resid 340 through 342 and (name N or name CA or name C or name O or nam \ e CB )) or resid 343 through 357 or (resid 358 and (name N or name CA or name C \ or name O or name CB )) or resid 359 through 422 or (resid 423 and (name N or na \ me CA or name C or name O or name CB )) or resid 424 through 480 or (resid 481 a \ nd (name N or name CA or name C or name O or name CB )) or resid 482 or (resid 4 \ 83 and (name N or name CA or name C or name O or name CB )) or resid 484 through \ 535 or (resid 536 and (name N or name CA or name C or name O or name CB )) or r \ esid 537 through 550 or (resid 551 through 552 and (name N or name CA or name C \ or name O or name CB )) or resid 553 through 567 or (resid 568 and (name N or na \ me CA or name C or name O or name CB )) or resid 569 through 575 or (resid 576 t \ hrough 578 and (name N or name CA or name C or name O or name CB )) or resid 579 \ through 581 or (resid 582 through 583 and (name N or name CA or name C or name \ O or name CB )) or resid 601 through 629 or (resid 630 and (name N or name CA or \ name C or name O or name CB )) or resid 631 through 676 or (resid 677 through 6 \ 79 and (name N or name CA or name C or name O or name CB )) or resid 680 through \ 701 or (resid 702 through 704 and (name N or name CA or name C or name O or nam \ e CB )) or resid 705 through 741 or (resid 742 through 743 and (name N or name C \ A or name C or name O or name CB )) or resid 744 through 755 or (resid 756 and ( \ name N or name CA or name C or name O or name CB )) or resid 757 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 816 or (resid 817 through 819 and (name N or name CA or nam \ e C or name O or name CB )) or resid 820 through 828 or (resid 829 and (name N o \ r name CA or name C or name O or name CB )) or resid 830 through 836 or resid 90 \ 1 through 909)) } ncs_group { reference = (chain 'B' and (resid 34 through 42 or (resid 43 and (name N or name CA or name \ C or name O or name CB )) or resid 44 through 64 or (resid 65 through 66 and (na \ me N or name CA or name C or name O or name CB )) or resid 67 through 90 or (res \ id 91 and (name N or name CA or name C or name O or name CB )) or resid 92 throu \ gh 106 or (resid 107 through 108 and (name N or name CA or name C or name O or n \ ame CB )) or resid 109 through 180 or (resid 181 and (name N or name CA or name \ C or name O or name CB )) or resid 182 through 201 or (resid 202 and (name N or \ name CA or name C or name O or name CB )) or resid 203 through 219 or (resid 220 \ through 221 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 22 or (resid 223 and (name N or name CA or name C or name O or name CB )) or res \ id 224 through 231 or (resid 232 and (name N or name CA or name C or name O or n \ ame CB )) or resid 233 through 234 or (resid 235 through 236 and (name N or name \ CA or name C or name O or name CB )) or resid 237 through 241 or (resid 242 thr \ ough 243 and (name N or name CA or name C or name O or name CB )) or resid 244 o \ r (resid 245 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 46 through 282 or (resid 283 through 285 and (name N or name CA or name C or nam \ e O or name CB )) or resid 286 through 288 or (resid 289 through 290 and (name N \ or name CA or name C or name O or name CB )) or resid 291 through 305 or (resid \ 306 and (name N or name CA or name C or name O or name CB )) or resid 307 throu \ gh 314 or (resid 315 through 319 and (name N or name CA or name C or name O or n \ ame CB )) or resid 320 through 330 or (resid 331 through 333 and (name N or name \ CA or name C or name O or name CB )) or resid 334 through 381 or (resid 382 and \ (name N or name CA or name C or name O or name CB )) or resid 383 or (resid 384 \ and (name N or name CA or name C or name O or name CB )) or resid 385 through 3 \ 94 or (resid 395 through 398 and (name N or name CA or name C or name O or name \ CB )) or resid 399 through 402 or (resid 403 through 404 and (name N or name CA \ or name C or name O or name CB )) or resid 405 through 425 or (resid 426 through \ 428 and (name N or name CA or name C or name O or name CB )) or resid 429 throu \ gh 517 or (resid 518 and (name N or name CA or name C or name O or name CB )) or \ resid 519 through 543 or resid 553 through 575 or (resid 576 and (name N or nam \ e CA or name C or name O or name CB )) or resid 577 through 579 or resid 601 thr \ ough 625 or (resid 626 and (name N or name CA or name C or name O or name CB )) \ or resid 627 through 652 or (resid 653 and (name N or name CA or name C or name \ O or name CB )) or resid 654 through 659 or (resid 660 and (name N or name CA or \ name C or name O or name CB )) or resid 661 through 690 or (resid 691 and (name \ N or name CA or name C or name O or name CB )) or resid 692 through 699 or (res \ id 700 and (name N or name CA or name C or name O or name CB )) or resid 701 thr \ ough 725 or (resid 726 through 727 and (name N or name CA or name C or name O or \ name CB )) or resid 728 through 741 or (resid 742 through 743 and (name N or na \ me CA or name C or name O or name CB )) or resid 744 through 751 or (resid 752 a \ nd (name N or name CA or name C or name O or name CB )) or resid 753 or (resid 7 \ 54 and (name N or name CA or name C or name O or name CB )) or resid 755 through \ 765 or (resid 766 and (name N or name CA or name C or name O or name CB )) or r \ esid 767 through 773 or (resid 774 and (name N or name CA or name C or name O or \ name CB )) or resid 775 through 816 or (resid 817 through 818 and (name N or na \ me CA or name C or name O or name CB )) or resid 819 through 904)) selection = (chain 'D' and ((resid 34 and (name N or name CA or name C or name O or name CB \ )) or resid 35 through 51 or (resid 52 and (name N or name CA or name C or name \ O or name CB )) or resid 53 through 58 or (resid 59 through 60 and (name N or na \ me CA or name C or name O or name CB )) or resid 61 through 75 or (resid 76 and \ (name N or name CA or name C or name O or name CB )) or resid 77 through 105 or \ (resid 106 through 108 and (name N or name CA or name C or name O or name CB )) \ or resid 109 through 137 or (resid 138 and (name N or name CA or name C or name \ O or name CB )) or resid 139 through 155 or (resid 156 and (name N or name CA or \ name C or name O or name CB )) or resid 157 through 159 or (resid 160 and (name \ N or name CA or name C or name O or name CB )) or resid 161 through 162 or (res \ id 163 and (name N or name CA or name C or name O or name CB )) or resid 164 thr \ ough 165 or (resid 166 and (name N or name CA or name C or name O or name CB )) \ or resid 167 through 215 or (resid 216 and (name N or name CA or name C or name \ O or name CB )) or resid 217 through 233 or (resid 234 through 236 and (name N o \ r name CA or name C or name O or name CB )) or resid 237 through 250 or (resid 2 \ 51 through 252 and (name N or name CA or name C or name O or name CB )) or resid \ 253 through 266 or (resid 267 and (name N or name CA or name C or name O or nam \ e CB )) or resid 268 through 271 or (resid 272 and (name N or name CA or name C \ or name O or name CB )) or resid 273 through 283 or (resid 284 through 285 and ( \ name N or name CA or name C or name O or name CB )) or resid 286 or (resid 287 a \ nd (name N or name CA or name C or name O or name CB )) or resid 288 through 292 \ or (resid 293 and (name N or name CA or name C or name O or name CB )) or resid \ 294 through 359 or (resid 360 and (name N or name CA or name C or name O or nam \ e CB )) or resid 361 through 369 or (resid 370 through 371 and (name N or name C \ A or name C or name O or name CB )) or resid 372 through 373 or (resid 374 and ( \ name N or name CA or name C or name O or name CB )) or resid 375 through 377 or \ (resid 378 and (name N or name CA or name C or name O or name CB )) or resid 379 \ or (resid 380 and (name N or name CA or name C or name O or name CB )) or resid \ 381 through 391 or (resid 392 through 398 and (name N or name CA or name C or n \ ame O or name CB )) or resid 399 through 403 or (resid 404 and (name N or name C \ A or name C or name O or name CB )) or resid 405 through 420 or (resid 421 and ( \ name N or name CA or name C or name O or name CB )) or resid 422 through 449 or \ (resid 450 and (name N or name CA or name C or name O or name CB )) or resid 451 \ through 475 or (resid 476 and (name N or name CA or name C or name O or name CB \ )) or resid 477 through 481 or (resid 482 and (name N or name CA or name C or n \ ame O or name CB )) or resid 483 through 515 or (resid 516 through 518 and (name \ N or name CA or name C or name O or name CB )) or resid 519 through 540 or (res \ id 541 and (name N or name CA or name C or name O or name CB )) or resid 542 thr \ ough 573 or (resid 574 and (name N or name CA or name C or name O or name CB )) \ or resid 575 through 577 or (resid 578 through 579 and (name N or name CA or nam \ e C or name O or name CB )) or resid 601 through 606 or (resid 607 and (name N o \ r name CA or name C or name O or name CB )) or resid 608 through 620 or (resid 6 \ 21 and (name N or name CA or name C or name O or name CB )) or resid 622 through \ 668 or (resid 669 and (name N or name CA or name C or name O or name CB )) or r \ esid 670 through 676 or (resid 677 and (name N or name CA or name C or name O or \ name CB )) or resid 678 through 694 or (resid 695 and (name N or name CA or nam \ e C or name O or name CB )) or resid 696 through 702 or (resid 703 and (name N o \ r name CA or name C or name O or name CB )) or resid 704 through 714 or (resid 7 \ 15 through 716 and (name N or name CA or name C or name O or name CB )) or resid \ 717 through 720 or (resid 721 and (name N or name CA or name C or name O or nam \ e CB )) or resid 722 through 768 or (resid 769 and (name N or name CA or name C \ or name O or name CB )) or resid 770 through 771 or (resid 772 through 774 and ( \ name N or name CA or name C or name O or name CB )) or resid 775 through 786 or \ (resid 787 and (name N or name CA or name C or name O or name CB )) or resid 788 \ through 801 or (resid 802 through 806 and (name N or name CA or name C or name \ O or name CB )) or resid 807 through 837 or (resid 838 and (name N or name CA or \ name C or name O or name CB )) or resid 839 or (resid 840 through 841 and (name \ N or name CA or name C or name O or name CB )) or resid 901 through 903 or resi \ d 905)) } 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: 5.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.280 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 21.370 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.040 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23482 Z= 0.169 Angle : 0.561 12.556 32208 Z= 0.296 Chirality : 0.044 0.337 3949 Planarity : 0.003 0.090 4038 Dihedral : 12.476 86.100 8048 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.14 % Allowed : 0.41 % Favored : 99.45 % 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: 0.30 (0.15), residues: 3114 helix: 1.92 (0.14), residues: 1282 sheet: -0.97 (0.29), residues: 371 loop : -1.07 (0.16), residues: 1461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 437 TYR 0.012 0.001 TYR A 392 PHE 0.022 0.001 PHE B 682 TRP 0.027 0.001 TRP C 160 HIS 0.006 0.001 HIS A 780 Details of bonding type rmsd covalent geometry : bond 0.00313 (23444) covalent geometry : angle 0.54653 (32109) SS BOND : bond 0.00212 ( 15) SS BOND : angle 0.88021 ( 30) hydrogen bonds : bond 0.14673 ( 1094) hydrogen bonds : angle 5.98464 ( 3177) link_NAG-ASN : bond 0.00579 ( 23) link_NAG-ASN : angle 2.72657 ( 69) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 192 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 MET cc_start: 0.8226 (mmp) cc_final: 0.7878 (mmt) REVERT: B 788 MET cc_start: 0.7772 (mpp) cc_final: 0.7498 (mtm) outliers start: 3 outliers final: 0 residues processed: 195 average time/residue: 0.1304 time to fit residues: 43.0059 Evaluate side-chains 172 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 0.5980 chunk 183 optimal weight: 0.0970 chunk 298 optimal weight: 0.0020 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN A 355 ASN A 363 GLN ** B 816 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 HIS D 44 HIS D 615 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.098252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.083060 restraints weight = 90719.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.084910 restraints weight = 56206.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.085071 restraints weight = 39235.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.085486 restraints weight = 35792.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.085526 restraints weight = 33313.593| |-----------------------------------------------------------------------------| r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.0775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 23482 Z= 0.122 Angle : 0.534 13.397 32208 Z= 0.270 Chirality : 0.042 0.305 3949 Planarity : 0.003 0.043 4038 Dihedral : 4.918 57.967 3771 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.55 % Allowed : 6.86 % Favored : 92.59 % 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: 0.38 (0.15), residues: 3114 helix: 1.98 (0.14), residues: 1306 sheet: -1.05 (0.29), residues: 379 loop : -1.03 (0.16), residues: 1429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 692 TYR 0.014 0.001 TYR D 698 PHE 0.020 0.001 PHE C 340 TRP 0.028 0.001 TRP C 498 HIS 0.006 0.001 HIS A 101 Details of bonding type rmsd covalent geometry : bond 0.00268 (23444) covalent geometry : angle 0.52057 (32109) SS BOND : bond 0.00254 ( 15) SS BOND : angle 0.93851 ( 30) hydrogen bonds : bond 0.04088 ( 1094) hydrogen bonds : angle 4.75477 ( 3177) link_NAG-ASN : bond 0.00560 ( 23) link_NAG-ASN : angle 2.54594 ( 69) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 178 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 MET cc_start: 0.8217 (mmp) cc_final: 0.7733 (mmt) REVERT: A 563 TRP cc_start: 0.8178 (m100) cc_final: 0.7760 (m100) REVERT: B 90 MET cc_start: 0.8220 (ptm) cc_final: 0.7794 (ttp) REVERT: C 702 MET cc_start: 0.8722 (mmt) cc_final: 0.8383 (mmp) REVERT: D 251 TYR cc_start: 0.6801 (OUTLIER) cc_final: 0.6131 (m-80) REVERT: D 496 MET cc_start: 0.7785 (mtp) cc_final: 0.7549 (mtp) REVERT: D 560 MET cc_start: 0.8408 (mmp) cc_final: 0.7772 (ptt) outliers start: 12 outliers final: 8 residues processed: 184 average time/residue: 0.1345 time to fit residues: 41.7030 Evaluate side-chains 181 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 172 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 237 MET Chi-restraints excluded: chain A residue 607 MET Chi-restraints excluded: chain B residue 799 ILE Chi-restraints excluded: chain C residue 498 TRP Chi-restraints excluded: chain D residue 251 TYR Chi-restraints excluded: chain D residue 680 PHE Chi-restraints excluded: chain D residue 781 GLN Chi-restraints excluded: chain D residue 799 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 309 optimal weight: 0.0980 chunk 305 optimal weight: 0.6980 chunk 211 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 2 optimal weight: 10.0000 chunk 94 optimal weight: 6.9990 chunk 82 optimal weight: 0.8980 chunk 273 optimal weight: 6.9990 chunk 200 optimal weight: 0.9980 chunk 111 optimal weight: 3.9990 chunk 264 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 381 GLN ** B 816 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 358 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.097639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.082512 restraints weight = 89609.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.084486 restraints weight = 56120.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.084918 restraints weight = 38663.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.085058 restraints weight = 34606.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.085197 restraints weight = 32650.171| |-----------------------------------------------------------------------------| r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.1082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23482 Z= 0.129 Angle : 0.510 11.390 32208 Z= 0.259 Chirality : 0.042 0.313 3949 Planarity : 0.003 0.039 4038 Dihedral : 4.491 55.727 3771 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.06 % Allowed : 9.53 % Favored : 89.41 % 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: 0.38 (0.15), residues: 3114 helix: 1.98 (0.14), residues: 1314 sheet: -1.10 (0.28), residues: 377 loop : -1.02 (0.16), residues: 1423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 673 TYR 0.014 0.001 TYR D 478 PHE 0.021 0.001 PHE A 627 TRP 0.023 0.001 TRP C 498 HIS 0.006 0.001 HIS C 780 Details of bonding type rmsd covalent geometry : bond 0.00292 (23444) covalent geometry : angle 0.49828 (32109) SS BOND : bond 0.00280 ( 15) SS BOND : angle 0.85657 ( 30) hydrogen bonds : bond 0.03587 ( 1094) hydrogen bonds : angle 4.40526 ( 3177) link_NAG-ASN : bond 0.00475 ( 23) link_NAG-ASN : angle 2.38365 ( 69) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 186 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.8661 (ttm) cc_final: 0.8345 (ttt) REVERT: A 240 MET cc_start: 0.8154 (mmp) cc_final: 0.7896 (mmt) REVERT: C 74 MET cc_start: 0.8346 (tpp) cc_final: 0.8011 (tpp) REVERT: C 702 MET cc_start: 0.8761 (mmt) cc_final: 0.8501 (mmp) REVERT: D 251 TYR cc_start: 0.6803 (OUTLIER) cc_final: 0.5976 (m-80) REVERT: D 560 MET cc_start: 0.8464 (mmp) cc_final: 0.7793 (ptt) outliers start: 23 outliers final: 13 residues processed: 201 average time/residue: 0.1399 time to fit residues: 46.3471 Evaluate side-chains 184 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 170 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 237 MET Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain A residue 607 MET Chi-restraints excluded: chain B residue 701 MET Chi-restraints excluded: chain B residue 820 VAL Chi-restraints excluded: chain C residue 576 MET Chi-restraints excluded: chain C residue 607 MET Chi-restraints excluded: chain C residue 619 ILE Chi-restraints excluded: chain C residue 627 PHE Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 251 TYR Chi-restraints excluded: chain D residue 680 PHE Chi-restraints excluded: chain D residue 799 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 82 optimal weight: 0.0050 chunk 158 optimal weight: 6.9990 chunk 105 optimal weight: 9.9990 chunk 129 optimal weight: 9.9990 chunk 284 optimal weight: 2.9990 chunk 100 optimal weight: 0.6980 chunk 294 optimal weight: 0.0870 chunk 262 optimal weight: 20.0000 chunk 178 optimal weight: 0.9980 chunk 224 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 overall best weight: 0.5572 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 816 ASN C 273 ASN C 520 ASN D 693 ASN D 697 ASN D 816 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.098038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.083071 restraints weight = 89524.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.085056 restraints weight = 54911.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.085452 restraints weight = 39974.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.085643 restraints weight = 33441.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.085791 restraints weight = 32211.955| |-----------------------------------------------------------------------------| r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.1274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 23482 Z= 0.106 Angle : 0.508 11.038 32208 Z= 0.256 Chirality : 0.042 0.298 3949 Planarity : 0.003 0.040 4038 Dihedral : 4.253 48.808 3771 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.29 % Allowed : 12.25 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.41 (0.15), residues: 3114 helix: 2.01 (0.14), residues: 1314 sheet: -1.22 (0.28), residues: 362 loop : -0.98 (0.16), residues: 1438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 181 TYR 0.013 0.001 TYR D 478 PHE 0.036 0.001 PHE C 639 TRP 0.016 0.001 TRP D 609 HIS 0.004 0.001 HIS A 101 Details of bonding type rmsd covalent geometry : bond 0.00235 (23444) covalent geometry : angle 0.49724 (32109) SS BOND : bond 0.00218 ( 15) SS BOND : angle 0.77444 ( 30) hydrogen bonds : bond 0.03319 ( 1094) hydrogen bonds : angle 4.28920 ( 3177) link_NAG-ASN : bond 0.00454 ( 23) link_NAG-ASN : angle 2.24688 ( 69) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 177 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 MET cc_start: 0.8140 (mmp) cc_final: 0.7799 (mmt) REVERT: A 401 VAL cc_start: 0.9181 (OUTLIER) cc_final: 0.8843 (m) REVERT: C 74 MET cc_start: 0.8242 (tpp) cc_final: 0.7973 (tpp) REVERT: C 181 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.7978 (mp0) REVERT: C 702 MET cc_start: 0.8751 (mmt) cc_final: 0.8426 (mmp) REVERT: D 251 TYR cc_start: 0.6832 (OUTLIER) cc_final: 0.5976 (m-80) REVERT: D 560 MET cc_start: 0.8312 (mmp) cc_final: 0.7699 (ptt) outliers start: 28 outliers final: 15 residues processed: 196 average time/residue: 0.1329 time to fit residues: 43.6137 Evaluate side-chains 189 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 171 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 607 MET Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 223 HIS Chi-restraints excluded: chain B residue 701 MET Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 607 MET Chi-restraints excluded: chain C residue 619 ILE Chi-restraints excluded: chain C residue 627 PHE Chi-restraints excluded: chain C residue 654 PHE Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 251 TYR Chi-restraints excluded: chain D residue 680 PHE Chi-restraints excluded: chain D residue 799 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 118 optimal weight: 6.9990 chunk 98 optimal weight: 0.9990 chunk 88 optimal weight: 9.9990 chunk 138 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 86 optimal weight: 0.4980 chunk 148 optimal weight: 4.9990 chunk 254 optimal weight: 0.8980 chunk 90 optimal weight: 0.6980 chunk 123 optimal weight: 9.9990 chunk 296 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 134 HIS ** A 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 HIS B 693 ASN ** D 697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.097406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.082303 restraints weight = 88949.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.084317 restraints weight = 56298.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.084766 restraints weight = 38000.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.084895 restraints weight = 34411.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.085042 restraints weight = 32259.270| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23482 Z= 0.133 Angle : 0.519 10.495 32208 Z= 0.261 Chirality : 0.042 0.289 3949 Planarity : 0.003 0.041 4038 Dihedral : 4.052 35.561 3771 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.57 % Allowed : 13.77 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.39 (0.15), residues: 3114 helix: 2.01 (0.14), residues: 1314 sheet: -1.23 (0.27), residues: 390 loop : -1.00 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 181 TYR 0.014 0.001 TYR D 478 PHE 0.040 0.001 PHE C 639 TRP 0.016 0.001 TRP D 609 HIS 0.007 0.001 HIS A 780 Details of bonding type rmsd covalent geometry : bond 0.00306 (23444) covalent geometry : angle 0.50994 (32109) SS BOND : bond 0.00295 ( 15) SS BOND : angle 0.76492 ( 30) hydrogen bonds : bond 0.03338 ( 1094) hydrogen bonds : angle 4.22074 ( 3177) link_NAG-ASN : bond 0.00385 ( 23) link_NAG-ASN : angle 2.13394 ( 69) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 178 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 MET cc_start: 0.8162 (mmp) cc_final: 0.7778 (mmt) REVERT: A 373 ILE cc_start: 0.8923 (OUTLIER) cc_final: 0.8710 (pt) REVERT: B 630 MET cc_start: 0.7097 (tmm) cc_final: 0.6851 (tmm) REVERT: C 74 MET cc_start: 0.8204 (tpp) cc_final: 0.7959 (tpp) REVERT: C 181 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.7942 (mp0) REVERT: C 702 MET cc_start: 0.8757 (mmt) cc_final: 0.8490 (mmp) REVERT: D 74 MET cc_start: 0.8073 (ptm) cc_final: 0.7762 (ptm) REVERT: D 251 TYR cc_start: 0.7006 (OUTLIER) cc_final: 0.6061 (m-80) outliers start: 34 outliers final: 22 residues processed: 201 average time/residue: 0.1345 time to fit residues: 45.2315 Evaluate side-chains 196 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 171 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 237 MET Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 701 MET Chi-restraints excluded: chain B residue 816 ASN Chi-restraints excluded: chain B residue 820 VAL Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 576 MET Chi-restraints excluded: chain C residue 607 MET Chi-restraints excluded: chain C residue 619 ILE Chi-restraints excluded: chain C residue 627 PHE Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 251 TYR Chi-restraints excluded: chain D residue 496 MET Chi-restraints excluded: chain D residue 612 VAL Chi-restraints excluded: chain D residue 680 PHE Chi-restraints excluded: chain D residue 759 THR Chi-restraints excluded: chain D residue 799 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 133 optimal weight: 0.6980 chunk 100 optimal weight: 2.9990 chunk 241 optimal weight: 7.9990 chunk 307 optimal weight: 3.9990 chunk 203 optimal weight: 0.8980 chunk 156 optimal weight: 7.9990 chunk 282 optimal weight: 1.9990 chunk 309 optimal weight: 0.9990 chunk 143 optimal weight: 0.9990 chunk 132 optimal weight: 0.9980 chunk 118 optimal weight: 7.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 GLN C 355 ASN ** D 697 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 = 0.3879 r_free = 0.3879 target = 0.097445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.082269 restraints weight = 89558.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.084517 restraints weight = 56152.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.084827 restraints weight = 38821.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.084981 restraints weight = 33267.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.085133 restraints weight = 32301.038| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23482 Z= 0.124 Angle : 0.519 11.809 32208 Z= 0.258 Chirality : 0.042 0.279 3949 Planarity : 0.003 0.041 4038 Dihedral : 3.907 33.209 3771 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.84 % Allowed : 14.32 % Favored : 83.84 % 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: 0.43 (0.15), residues: 3114 helix: 2.05 (0.14), residues: 1313 sheet: -1.25 (0.26), residues: 404 loop : -0.97 (0.17), residues: 1397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 181 TYR 0.019 0.001 TYR B 754 PHE 0.037 0.001 PHE C 639 TRP 0.017 0.001 TRP D 609 HIS 0.006 0.001 HIS A 780 Details of bonding type rmsd covalent geometry : bond 0.00286 (23444) covalent geometry : angle 0.51026 (32109) SS BOND : bond 0.00273 ( 15) SS BOND : angle 0.73646 ( 30) hydrogen bonds : bond 0.03242 ( 1094) hydrogen bonds : angle 4.16154 ( 3177) link_NAG-ASN : bond 0.00366 ( 23) link_NAG-ASN : angle 2.04322 ( 69) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 179 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 MET cc_start: 0.8141 (mmp) cc_final: 0.7873 (mmt) REVERT: A 373 ILE cc_start: 0.8914 (OUTLIER) cc_final: 0.8696 (pt) REVERT: A 575 VAL cc_start: 0.9245 (OUTLIER) cc_final: 0.8975 (p) REVERT: B 630 MET cc_start: 0.7062 (tmm) cc_final: 0.6810 (tmm) REVERT: B 781 GLN cc_start: 0.7628 (tp40) cc_final: 0.7230 (tp-100) REVERT: C 74 MET cc_start: 0.8145 (tpp) cc_final: 0.7895 (tpp) REVERT: C 181 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7938 (mp0) REVERT: C 580 LEU cc_start: 0.7223 (OUTLIER) cc_final: 0.7000 (tt) REVERT: C 702 MET cc_start: 0.8765 (mmt) cc_final: 0.8482 (mmp) REVERT: D 74 MET cc_start: 0.8114 (ptm) cc_final: 0.7800 (ptm) REVERT: D 251 TYR cc_start: 0.7074 (OUTLIER) cc_final: 0.6122 (m-80) REVERT: D 560 MET cc_start: 0.8341 (mmp) cc_final: 0.7817 (ptt) outliers start: 40 outliers final: 29 residues processed: 204 average time/residue: 0.1322 time to fit residues: 45.5679 Evaluate side-chains 208 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 174 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 237 MET Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 223 HIS Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 701 MET Chi-restraints excluded: chain B residue 820 VAL Chi-restraints excluded: chain B residue 828 MET Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 498 TRP Chi-restraints excluded: chain C residue 576 MET Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain C residue 607 MET Chi-restraints excluded: chain C residue 619 ILE Chi-restraints excluded: chain C residue 627 PHE Chi-restraints excluded: chain C residue 654 PHE Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 251 TYR Chi-restraints excluded: chain D residue 496 MET Chi-restraints excluded: chain D residue 612 VAL Chi-restraints excluded: chain D residue 680 PHE Chi-restraints excluded: chain D residue 747 LEU Chi-restraints excluded: chain D residue 759 THR Chi-restraints excluded: chain D residue 799 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 263 optimal weight: 0.3980 chunk 247 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 chunk 120 optimal weight: 0.7980 chunk 296 optimal weight: 0.9990 chunk 208 optimal weight: 0.6980 chunk 285 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 221 optimal weight: 7.9990 chunk 104 optimal weight: 7.9990 chunk 175 optimal weight: 4.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 693 ASN D 697 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.097646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.082533 restraints weight = 89420.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.084752 restraints weight = 55928.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.085106 restraints weight = 38392.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.085225 restraints weight = 33383.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.085432 restraints weight = 31848.013| |-----------------------------------------------------------------------------| r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23482 Z= 0.113 Angle : 0.516 9.824 32208 Z= 0.257 Chirality : 0.042 0.269 3949 Planarity : 0.003 0.044 4038 Dihedral : 3.820 32.705 3771 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.66 % Allowed : 14.83 % Favored : 83.52 % 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: 0.45 (0.15), residues: 3114 helix: 2.07 (0.14), residues: 1312 sheet: -1.22 (0.27), residues: 399 loop : -0.97 (0.17), residues: 1403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 181 TYR 0.015 0.001 TYR B 754 PHE 0.036 0.001 PHE C 639 TRP 0.017 0.001 TRP D 609 HIS 0.005 0.001 HIS A 780 Details of bonding type rmsd covalent geometry : bond 0.00258 (23444) covalent geometry : angle 0.50825 (32109) SS BOND : bond 0.00250 ( 15) SS BOND : angle 0.71850 ( 30) hydrogen bonds : bond 0.03189 ( 1094) hydrogen bonds : angle 4.13517 ( 3177) link_NAG-ASN : bond 0.00366 ( 23) link_NAG-ASN : angle 1.96952 ( 69) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 179 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 MET cc_start: 0.8113 (mmp) cc_final: 0.7866 (mmt) REVERT: A 373 ILE cc_start: 0.8931 (OUTLIER) cc_final: 0.8725 (pt) REVERT: A 575 VAL cc_start: 0.9242 (m) cc_final: 0.9004 (p) REVERT: B 630 MET cc_start: 0.7047 (tmm) cc_final: 0.6804 (tmm) REVERT: B 781 GLN cc_start: 0.7526 (tp40) cc_final: 0.7119 (tp-100) REVERT: C 74 MET cc_start: 0.8120 (tpp) cc_final: 0.7872 (tpp) REVERT: C 181 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7911 (mp0) REVERT: C 580 LEU cc_start: 0.7267 (OUTLIER) cc_final: 0.7057 (tt) REVERT: C 702 MET cc_start: 0.8761 (mmt) cc_final: 0.8508 (mmp) REVERT: D 74 MET cc_start: 0.8139 (ptm) cc_final: 0.7842 (ptm) REVERT: D 251 TYR cc_start: 0.7079 (OUTLIER) cc_final: 0.6199 (m-80) REVERT: D 560 MET cc_start: 0.8245 (mmp) cc_final: 0.7868 (ptt) outliers start: 36 outliers final: 27 residues processed: 202 average time/residue: 0.1343 time to fit residues: 45.5221 Evaluate side-chains 204 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 173 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 237 MET Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 223 HIS Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 701 MET Chi-restraints excluded: chain B residue 820 VAL Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 498 TRP Chi-restraints excluded: chain C residue 576 MET Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain C residue 607 MET Chi-restraints excluded: chain C residue 619 ILE Chi-restraints excluded: chain C residue 627 PHE Chi-restraints excluded: chain C residue 654 PHE Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 251 TYR Chi-restraints excluded: chain D residue 496 MET Chi-restraints excluded: chain D residue 612 VAL Chi-restraints excluded: chain D residue 680 PHE Chi-restraints excluded: chain D residue 747 LEU Chi-restraints excluded: chain D residue 799 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 174 optimal weight: 3.9990 chunk 137 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 118 optimal weight: 6.9990 chunk 242 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 182 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 269 optimal weight: 7.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.096651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.081477 restraints weight = 88720.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.083471 restraints weight = 56115.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.083925 restraints weight = 39228.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.084013 restraints weight = 34140.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.084192 restraints weight = 32855.325| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 23482 Z= 0.164 Angle : 0.554 11.431 32208 Z= 0.277 Chirality : 0.043 0.274 3949 Planarity : 0.003 0.043 4038 Dihedral : 3.923 30.853 3771 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 1.98 % Allowed : 14.87 % Favored : 83.15 % 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: 0.36 (0.15), residues: 3114 helix: 2.00 (0.14), residues: 1307 sheet: -1.29 (0.27), residues: 399 loop : -1.00 (0.17), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 181 TYR 0.016 0.001 TYR A 392 PHE 0.037 0.002 PHE C 639 TRP 0.019 0.001 TRP D 609 HIS 0.009 0.001 HIS A 780 Details of bonding type rmsd covalent geometry : bond 0.00384 (23444) covalent geometry : angle 0.54717 (32109) SS BOND : bond 0.00369 ( 15) SS BOND : angle 0.77035 ( 30) hydrogen bonds : bond 0.03418 ( 1094) hydrogen bonds : angle 4.22891 ( 3177) link_NAG-ASN : bond 0.00335 ( 23) link_NAG-ASN : angle 1.97560 ( 69) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 178 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 MET cc_start: 0.8148 (mmp) cc_final: 0.7891 (mmt) REVERT: A 373 ILE cc_start: 0.8919 (OUTLIER) cc_final: 0.8696 (pt) REVERT: A 575 VAL cc_start: 0.9252 (m) cc_final: 0.9006 (p) REVERT: B 112 MET cc_start: 0.8446 (mmm) cc_final: 0.8044 (mmm) REVERT: B 781 GLN cc_start: 0.7529 (tp40) cc_final: 0.7046 (tp-100) REVERT: C 74 MET cc_start: 0.8041 (tpp) cc_final: 0.7807 (tpp) REVERT: C 181 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.7932 (mp0) REVERT: C 245 TYR cc_start: 0.6088 (OUTLIER) cc_final: 0.5773 (t80) REVERT: D 74 MET cc_start: 0.8046 (ptm) cc_final: 0.7788 (ptm) REVERT: D 251 TYR cc_start: 0.7199 (OUTLIER) cc_final: 0.6237 (m-80) outliers start: 43 outliers final: 29 residues processed: 209 average time/residue: 0.1313 time to fit residues: 46.4496 Evaluate side-chains 207 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 174 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 237 MET Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 223 HIS Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 701 MET Chi-restraints excluded: chain B residue 820 VAL Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 245 TYR Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 498 TRP Chi-restraints excluded: chain C residue 576 MET Chi-restraints excluded: chain C residue 607 MET Chi-restraints excluded: chain C residue 619 ILE Chi-restraints excluded: chain C residue 627 PHE Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 251 TYR Chi-restraints excluded: chain D residue 496 MET Chi-restraints excluded: chain D residue 612 VAL Chi-restraints excluded: chain D residue 680 PHE Chi-restraints excluded: chain D residue 747 LEU Chi-restraints excluded: chain D residue 759 THR Chi-restraints excluded: chain D residue 799 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 274 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 121 optimal weight: 0.9990 chunk 244 optimal weight: 0.9980 chunk 231 optimal weight: 0.8980 chunk 161 optimal weight: 5.9990 chunk 303 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 124 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 252 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 67 HIS ** A 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.096932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.081799 restraints weight = 89367.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.083810 restraints weight = 56169.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.084284 restraints weight = 38776.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.084386 restraints weight = 34025.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.084523 restraints weight = 32654.654| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 23482 Z= 0.127 Angle : 0.540 11.705 32208 Z= 0.267 Chirality : 0.042 0.268 3949 Planarity : 0.003 0.044 4038 Dihedral : 3.855 30.412 3771 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.80 % Allowed : 15.15 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.39 (0.16), residues: 3114 helix: 2.02 (0.14), residues: 1307 sheet: -1.28 (0.26), residues: 408 loop : -0.97 (0.17), residues: 1399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 181 TYR 0.015 0.001 TYR D 478 PHE 0.025 0.001 PHE B 680 TRP 0.025 0.001 TRP D 609 HIS 0.006 0.001 HIS A 780 Details of bonding type rmsd covalent geometry : bond 0.00295 (23444) covalent geometry : angle 0.53305 (32109) SS BOND : bond 0.00286 ( 15) SS BOND : angle 0.74529 ( 30) hydrogen bonds : bond 0.03270 ( 1094) hydrogen bonds : angle 4.18067 ( 3177) link_NAG-ASN : bond 0.00337 ( 23) link_NAG-ASN : angle 1.88149 ( 69) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 176 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 MET cc_start: 0.8086 (mmp) cc_final: 0.7801 (mmt) REVERT: A 373 ILE cc_start: 0.8919 (OUTLIER) cc_final: 0.8690 (pt) REVERT: A 575 VAL cc_start: 0.9243 (m) cc_final: 0.9005 (p) REVERT: B 630 MET cc_start: 0.7021 (tmm) cc_final: 0.6736 (tmm) REVERT: C 74 MET cc_start: 0.8007 (tpp) cc_final: 0.7760 (tpp) REVERT: C 181 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7909 (mp0) REVERT: C 245 TYR cc_start: 0.5945 (OUTLIER) cc_final: 0.5646 (t80) REVERT: D 74 MET cc_start: 0.8046 (ptm) cc_final: 0.7815 (ptm) REVERT: D 251 TYR cc_start: 0.7118 (OUTLIER) cc_final: 0.6244 (m-80) REVERT: D 282 ASP cc_start: 0.8241 (OUTLIER) cc_final: 0.8031 (t0) REVERT: D 560 MET cc_start: 0.8301 (mmp) cc_final: 0.7880 (ptt) outliers start: 39 outliers final: 29 residues processed: 203 average time/residue: 0.1268 time to fit residues: 43.9405 Evaluate side-chains 204 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 170 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 237 MET Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 223 HIS Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 701 MET Chi-restraints excluded: chain B residue 820 VAL Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 245 TYR Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 498 TRP Chi-restraints excluded: chain C residue 576 MET Chi-restraints excluded: chain C residue 607 MET Chi-restraints excluded: chain C residue 619 ILE Chi-restraints excluded: chain C residue 654 PHE Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 251 TYR Chi-restraints excluded: chain D residue 282 ASP Chi-restraints excluded: chain D residue 496 MET Chi-restraints excluded: chain D residue 612 VAL Chi-restraints excluded: chain D residue 680 PHE Chi-restraints excluded: chain D residue 747 LEU Chi-restraints excluded: chain D residue 759 THR Chi-restraints excluded: chain D residue 799 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 253 optimal weight: 4.9990 chunk 159 optimal weight: 0.0570 chunk 232 optimal weight: 4.9990 chunk 129 optimal weight: 0.5980 chunk 211 optimal weight: 7.9990 chunk 122 optimal weight: 4.9990 chunk 274 optimal weight: 0.9990 chunk 282 optimal weight: 0.9980 chunk 161 optimal weight: 1.9990 chunk 236 optimal weight: 8.9990 chunk 80 optimal weight: 0.5980 overall best weight: 0.6500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.096983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.081934 restraints weight = 89469.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.084403 restraints weight = 55556.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.084588 restraints weight = 38165.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.084684 restraints weight = 32644.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.084818 restraints weight = 31872.007| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23482 Z= 0.111 Angle : 0.537 13.611 32208 Z= 0.264 Chirality : 0.042 0.260 3949 Planarity : 0.003 0.045 4038 Dihedral : 3.765 29.347 3771 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.66 % Allowed : 15.47 % Favored : 82.87 % 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: 0.43 (0.16), residues: 3114 helix: 2.05 (0.14), residues: 1306 sheet: -1.23 (0.27), residues: 400 loop : -0.96 (0.17), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 181 TYR 0.014 0.001 TYR D 478 PHE 0.055 0.001 PHE C 639 TRP 0.024 0.001 TRP D 609 HIS 0.005 0.001 HIS A 780 Details of bonding type rmsd covalent geometry : bond 0.00254 (23444) covalent geometry : angle 0.53075 (32109) SS BOND : bond 0.00242 ( 15) SS BOND : angle 0.72903 ( 30) hydrogen bonds : bond 0.03146 ( 1094) hydrogen bonds : angle 4.13874 ( 3177) link_NAG-ASN : bond 0.00344 ( 23) link_NAG-ASN : angle 1.80885 ( 69) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 173 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 MET cc_start: 0.8026 (mmp) cc_final: 0.7731 (mmt) REVERT: A 373 ILE cc_start: 0.8932 (OUTLIER) cc_final: 0.8698 (pt) REVERT: A 575 VAL cc_start: 0.9234 (m) cc_final: 0.9011 (p) REVERT: C 74 MET cc_start: 0.7992 (tpp) cc_final: 0.7753 (tpp) REVERT: C 181 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7891 (mp0) REVERT: C 245 TYR cc_start: 0.5918 (OUTLIER) cc_final: 0.5642 (t80) REVERT: D 74 MET cc_start: 0.8062 (ptm) cc_final: 0.7834 (ptm) REVERT: D 251 TYR cc_start: 0.7166 (OUTLIER) cc_final: 0.6250 (m-80) REVERT: D 560 MET cc_start: 0.8281 (mmp) cc_final: 0.7871 (ptt) REVERT: D 788 MET cc_start: 0.8922 (mmm) cc_final: 0.8689 (mmm) outliers start: 36 outliers final: 28 residues processed: 199 average time/residue: 0.1357 time to fit residues: 45.7943 Evaluate side-chains 203 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 171 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 237 MET Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 223 HIS Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 701 MET Chi-restraints excluded: chain B residue 820 VAL Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 245 TYR Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 498 TRP Chi-restraints excluded: chain C residue 576 MET Chi-restraints excluded: chain C residue 619 ILE Chi-restraints excluded: chain C residue 627 PHE Chi-restraints excluded: chain C residue 654 PHE Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 251 TYR Chi-restraints excluded: chain D residue 496 MET Chi-restraints excluded: chain D residue 612 VAL Chi-restraints excluded: chain D residue 680 PHE Chi-restraints excluded: chain D residue 747 LEU Chi-restraints excluded: chain D residue 759 THR Chi-restraints excluded: chain D residue 799 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 35 optimal weight: 0.9990 chunk 298 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 235 optimal weight: 8.9990 chunk 202 optimal weight: 0.8980 chunk 281 optimal weight: 4.9990 chunk 302 optimal weight: 1.9990 chunk 217 optimal weight: 0.9990 chunk 125 optimal weight: 2.9990 chunk 140 optimal weight: 0.0570 chunk 211 optimal weight: 7.9990 overall best weight: 0.7502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.097129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.082042 restraints weight = 89237.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.084485 restraints weight = 55333.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.084748 restraints weight = 39033.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.084644 restraints weight = 33789.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.084870 restraints weight = 32588.683| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23482 Z= 0.115 Angle : 0.536 10.837 32208 Z= 0.264 Chirality : 0.042 0.259 3949 Planarity : 0.003 0.044 4038 Dihedral : 3.726 28.250 3771 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.57 % Allowed : 15.52 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.43 (0.16), residues: 3114 helix: 2.04 (0.14), residues: 1307 sheet: -1.23 (0.26), residues: 414 loop : -0.95 (0.17), residues: 1393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 181 TYR 0.014 0.001 TYR D 478 PHE 0.024 0.001 PHE B 680 TRP 0.023 0.001 TRP D 609 HIS 0.005 0.001 HIS A 780 Details of bonding type rmsd covalent geometry : bond 0.00266 (23444) covalent geometry : angle 0.53040 (32109) SS BOND : bond 0.00250 ( 15) SS BOND : angle 0.72339 ( 30) hydrogen bonds : bond 0.03160 ( 1094) hydrogen bonds : angle 4.11709 ( 3177) link_NAG-ASN : bond 0.00328 ( 23) link_NAG-ASN : angle 1.76696 ( 69) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3012.04 seconds wall clock time: 53 minutes 4.74 seconds (3184.74 seconds total)