Starting phenix.real_space_refine on Sat Jul 4 05:12:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7eu8_31309/07_2026/7eu8_31309_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7eu8_31309/07_2026/7eu8_31309.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7eu8_31309/07_2026/7eu8_31309.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7eu8_31309/07_2026/7eu8_31309.map" model { file = "/net/cci-nas-00/data/ceres_data/7eu8_31309/07_2026/7eu8_31309_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7eu8_31309/07_2026/7eu8_31309_neut.cif" } resolution = 4.07 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= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 55 5.16 5 Cl 1 4.86 5 C 11880 2.51 5 N 3207 2.21 5 O 3527 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18670 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 761, 4607 Classifications: {'peptide': 761} Incomplete info: {'truncation_to_alanine': 409} Link IDs: {'PTRANS': 31, 'TRANS': 729} Chain breaks: 7 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 1452 Unresolved non-hydrogen angles: 1816 Unresolved non-hydrogen dihedrals: 1171 Unresolved non-hydrogen chiralities: 124 Planarities with less than four sites: {'ASN:plan1': 28, 'ARG:plan': 35, 'HIS:plan': 10, 'GLU:plan': 43, 'GLN:plan1': 23, 'PHE:plan': 11, 'ASP:plan': 32, 'TYR:plan': 7, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 802 Chain: "B" Number of atoms: 4546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 743, 4546 Classifications: {'peptide': 743} Incomplete info: {'truncation_to_alanine': 355} Link IDs: {'PTRANS': 26, 'TRANS': 716} Chain breaks: 7 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1353 Unresolved non-hydrogen angles: 1690 Unresolved non-hydrogen dihedrals: 1135 Unresolved non-hydrogen chiralities: 91 Planarities with less than four sites: {'ASP:plan': 32, 'GLU:plan': 38, 'HIS:plan': 7, 'PHE:plan': 22, 'ARG:plan': 21, 'GLN:plan1': 22, 'ASN:plan1': 19, 'TYR:plan': 15, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 788 Chain: "C" Number of atoms: 4844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 772, 4844 Classifications: {'peptide': 772} Incomplete info: {'truncation_to_alanine': 323} Link IDs: {'PTRANS': 32, 'TRANS': 739} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1294 Unresolved non-hydrogen angles: 1603 Unresolved non-hydrogen dihedrals: 1075 Unresolved non-hydrogen chiralities: 63 Planarities with less than four sites: {'ASN:plan1': 24, 'ARG:plan': 35, 'HIS:plan': 12, 'GLU:plan': 47, 'GLN:plan1': 25, 'PHE:plan': 10, 'TYR:plan': 8, 'ASP:plan': 31, 'TRP:plan': 3} Unresolved non-hydrogen planarities: 831 Chain: "D" Number of atoms: 4559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 734, 4559 Classifications: {'peptide': 734} Incomplete info: {'truncation_to_alanine': 322} Link IDs: {'PTRANS': 26, 'TRANS': 707} Chain breaks: 7 Unresolved non-hydrogen bonds: 1274 Unresolved non-hydrogen angles: 1581 Unresolved non-hydrogen dihedrals: 1081 Unresolved non-hydrogen chiralities: 76 Planarities with less than four sites: {'GLU:plan': 36, 'ASP:plan': 29, 'PHE:plan': 21, 'HIS:plan': 8, 'ARG:plan': 22, 'GLN:plan1': 20, 'ASN:plan1': 14, 'TYR:plan': 14, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 745 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 44 Unusual residues: {'JC9': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 4.76, per 1000 atoms: 0.25 Number of scatterers: 18670 At special positions: 0 Unit cell: (129.256, 146.376, 181.472, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 55 16.00 O 3527 8.00 N 3207 7.00 C 11880 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 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 436 " - pdb=" SG CYS B 457 " distance=2.03 Simple disulfide: pdb=" SG CYS C 744 " - pdb=" SG CYS C 798 " distance=2.03 Simple disulfide: pdb=" SG CYS D 429 " - pdb=" SG CYS D 456 " distance=2.03 Simple disulfide: pdb=" SG CYS D 436 " - pdb=" SG CYS D 457 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 901 " - " ASN A 203 " " NAG B 901 " - " ASN B 688 " " NAG B 902 " - " ASN B 341 " " NAG C 901 " - " ASN C 203 " " NAG D 901 " - " ASN D 542 " " NAG D 902 " - " ASN D 688 " " NAG D 903 " - " ASN D 348 " Time building additional restraints: 1.49 Conformation dependent library (CDL) restraints added in 973.9 milliseconds 5896 Ramachandran restraints generated. 2948 Oldfield, 0 Emsley, 2948 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5618 Finding SS restraints... Secondary structure from input PDB file: 109 helices and 29 sheets defined 45.1% alpha, 7.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 35 through 52 Processing helix chain 'A' and resid 70 through 86 removed outlier: 3.838A pdb=" N LEU A 76 " --> pdb=" O ILE A 72 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N CYS A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 114 removed outlier: 4.191A pdb=" N TYR A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 132 removed outlier: 3.946A pdb=" N LYS A 131 " --> pdb=" O ILE A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 159 Processing helix chain 'A' and resid 170 through 184 Processing helix chain 'A' and resid 205 through 215 Processing helix chain 'A' and resid 224 through 238 Processing helix chain 'A' and resid 255 through 262 removed outlier: 3.872A pdb=" N TYR A 261 " --> pdb=" O ASN A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 297 removed outlier: 3.761A pdb=" N ASP A 283 " --> pdb=" O ALA A 279 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLU A 297 " --> pdb=" O HIS A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 328 Processing helix chain 'A' and resid 458 through 471 Processing helix chain 'A' and resid 503 through 508 removed outlier: 4.206A pdb=" N GLY A 508 " --> pdb=" O GLU A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 582 removed outlier: 4.208A pdb=" N VAL A 570 " --> pdb=" O VAL A 566 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N HIS A 571 " --> pdb=" O GLY A 567 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N VAL A 572 " --> pdb=" O LEU A 568 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N VAL A 573 " --> pdb=" O SER A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 615 removed outlier: 3.964A pdb=" N LEU A 614 " --> pdb=" O SER A 610 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU A 615 " --> pdb=" O TRP A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 656 removed outlier: 4.154A pdb=" N VAL A 635 " --> pdb=" O ILE A 631 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY A 638 " --> pdb=" O MET A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 668 removed outlier: 3.941A pdb=" N ASN A 668 " --> pdb=" O THR A 665 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 665 through 668' Processing helix chain 'A' and resid 669 through 674 Processing helix chain 'A' and resid 687 through 696 removed outlier: 3.931A pdb=" N ILE A 691 " --> pdb=" O SER A 687 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLN A 696 " --> pdb=" O TYR A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 700 Processing helix chain 'A' and resid 713 through 723 removed outlier: 3.536A pdb=" N ASP A 723 " --> pdb=" O GLN A 719 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 743 removed outlier: 4.509A pdb=" N PHE A 738 " --> pdb=" O ALA A 734 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N SER A 741 " --> pdb=" O GLU A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 782 Processing helix chain 'A' and resid 783 through 793 Processing helix chain 'A' and resid 813 through 841 removed outlier: 3.815A pdb=" N PHE A 817 " --> pdb=" O MET A 813 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N VAL A 825 " --> pdb=" O ALA A 821 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA A 826 " --> pdb=" O GLY A 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 57 removed outlier: 4.149A pdb=" N ASP B 52 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 92 Processing helix chain 'B' and resid 106 through 120 removed outlier: 3.735A pdb=" N GLN B 110 " --> pdb=" O GLU B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 165 Processing helix chain 'B' and resid 179 through 193 Processing helix chain 'B' and resid 214 through 223 Processing helix chain 'B' and resid 233 through 248 removed outlier: 3.943A pdb=" N TYR B 239 " --> pdb=" O GLU B 235 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU B 242 " --> pdb=" O THR B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 312 Processing helix chain 'B' and resid 332 through 340 removed outlier: 3.610A pdb=" N ASN B 336 " --> pdb=" O SER B 332 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N TYR B 338 " --> pdb=" O MET B 334 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE B 340 " --> pdb=" O ASN B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 383 removed outlier: 3.532A pdb=" N LYS B 382 " --> pdb=" O TRP B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 417 removed outlier: 3.761A pdb=" N PHE B 416 " --> pdb=" O GLU B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 472 Processing helix chain 'B' and resid 495 through 503 removed outlier: 3.842A pdb=" N MET B 503 " --> pdb=" O GLY B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 523 removed outlier: 3.757A pdb=" N VAL B 522 " --> pdb=" O GLU B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 566 removed outlier: 3.578A pdb=" N VAL B 564 " --> pdb=" O VAL B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 576 removed outlier: 3.727A pdb=" N ALA B 571 " --> pdb=" O LEU B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 614 removed outlier: 4.185A pdb=" N ILE B 606 " --> pdb=" O ILE B 602 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N TRP B 607 " --> pdb=" O GLY B 603 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU B 612 " --> pdb=" O LEU B 608 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL B 613 " --> pdb=" O LEU B 609 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE B 614 " --> pdb=" O TRP B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 655 removed outlier: 4.115A pdb=" N VAL B 632 " --> pdb=" O SER B 628 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE B 655 " --> pdb=" O ALA B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 673 removed outlier: 3.516A pdb=" N GLN B 672 " --> pdb=" O ASP B 668 " (cutoff:3.500A) Processing helix chain 'B' and resid 673 through 678 Processing helix chain 'B' and resid 689 through 699 removed outlier: 3.837A pdb=" N ARG B 693 " --> pdb=" O GLY B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 700 through 709 removed outlier: 3.513A pdb=" N LYS B 708 " --> pdb=" O ALA B 704 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE B 709 " --> pdb=" O TYR B 705 " (cutoff:3.500A) Processing helix chain 'B' and resid 714 through 724 Processing helix chain 'B' and resid 733 through 741 Processing helix chain 'B' and resid 772 through 785 removed outlier: 3.836A pdb=" N LEU B 778 " --> pdb=" O ARG B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 797 removed outlier: 3.788A pdb=" N TRP B 796 " --> pdb=" O LEU B 792 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU B 797 " --> pdb=" O GLU B 793 " (cutoff:3.500A) Processing helix chain 'B' and resid 821 through 831 removed outlier: 3.872A pdb=" N ALA B 828 " --> pdb=" O MET B 824 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N MET B 829 " --> pdb=" O LEU B 825 " (cutoff:3.500A) Processing helix chain 'B' and resid 831 through 836 removed outlier: 3.798A pdb=" N THR B 835 " --> pdb=" O LEU B 831 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 51 Processing helix chain 'C' and resid 70 through 86 Processing helix chain 'C' and resid 104 through 114 removed outlier: 4.185A pdb=" N TYR C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 131 removed outlier: 3.899A pdb=" N LYS C 131 " --> pdb=" O ILE C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 159 removed outlier: 3.652A pdb=" N TRP C 151 " --> pdb=" O GLN C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 185 Processing helix chain 'C' and resid 204 through 213 removed outlier: 3.757A pdb=" N LEU C 208 " --> pdb=" O VAL C 204 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU C 213 " --> pdb=" O MET C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 239 Processing helix chain 'C' and resid 257 through 262 removed outlier: 3.912A pdb=" N TYR C 261 " --> pdb=" O ASN C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 298 removed outlier: 4.114A pdb=" N ASP C 283 " --> pdb=" O ALA C 279 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLU C 297 " --> pdb=" O HIS C 293 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N LYS C 298 " --> pdb=" O GLU C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 328 Processing helix chain 'C' and resid 458 through 471 removed outlier: 4.231A pdb=" N LEU C 462 " --> pdb=" O PHE C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 500 through 507 Processing helix chain 'C' and resid 520 through 527 Processing helix chain 'C' and resid 559 through 582 removed outlier: 3.648A pdb=" N TYR C 578 " --> pdb=" O ALA C 574 " (cutoff:3.500A) Processing helix chain 'C' and resid 604 through 615 removed outlier: 3.762A pdb=" N TRP C 608 " --> pdb=" O SER C 604 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N LEU C 615 " --> pdb=" O TRP C 611 " (cutoff:3.500A) Processing helix chain 'C' and resid 628 through 636 Processing helix chain 'C' and resid 638 through 656 Processing helix chain 'C' and resid 665 through 668 Processing helix chain 'C' and resid 669 through 674 Processing helix chain 'C' and resid 687 through 696 removed outlier: 4.090A pdb=" N ILE C 691 " --> pdb=" O SER C 687 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLN C 696 " --> pdb=" O TYR C 692 " (cutoff:3.500A) Processing helix chain 'C' and resid 699 through 705 removed outlier: 3.656A pdb=" N HIS C 705 " --> pdb=" O THR C 701 " (cutoff:3.500A) Processing helix chain 'C' and resid 713 through 723 removed outlier: 3.573A pdb=" N ALA C 717 " --> pdb=" O SER C 713 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP C 723 " --> pdb=" O GLN C 719 " (cutoff:3.500A) Processing helix chain 'C' and resid 732 through 744 removed outlier: 4.525A pdb=" N PHE C 738 " --> pdb=" O ALA C 734 " (cutoff:3.500A) Processing helix chain 'C' and resid 768 through 782 Processing helix chain 'C' and resid 783 through 793 Processing helix chain 'C' and resid 810 through 841 removed outlier: 4.457A pdb=" N GLY C 815 " --> pdb=" O GLU C 811 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N VAL C 816 " --> pdb=" O ASN C 812 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 52 removed outlier: 3.684A pdb=" N LYS D 51 " --> pdb=" O GLU D 47 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASP D 52 " --> pdb=" O VAL D 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 47 through 52' Processing helix chain 'D' and resid 77 through 91 removed outlier: 3.627A pdb=" N ILE D 81 " --> pdb=" O ASP D 77 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N MET D 89 " --> pdb=" O ILE D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 120 removed outlier: 4.049A pdb=" N GLN D 110 " --> pdb=" O GLU D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 165 Processing helix chain 'D' and resid 176 through 178 No H-bonds generated for 'chain 'D' and resid 176 through 178' Processing helix chain 'D' and resid 179 through 193 removed outlier: 3.647A pdb=" N VAL D 183 " --> pdb=" O TYR D 179 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ASN D 184 " --> pdb=" O GLN D 180 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER D 193 " --> pdb=" O THR D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 223 Processing helix chain 'D' and resid 233 through 248 removed outlier: 4.079A pdb=" N TYR D 239 " --> pdb=" O GLU D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 312 Processing helix chain 'D' and resid 320 through 325 removed outlier: 4.182A pdb=" N THR D 324 " --> pdb=" O CYS D 321 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N HIS D 325 " --> pdb=" O TYR D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 341 Processing helix chain 'D' and resid 413 through 417 removed outlier: 3.761A pdb=" N PHE D 416 " --> pdb=" O GLU D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 472 Processing helix chain 'D' and resid 495 through 503 Processing helix chain 'D' and resid 516 through 523 removed outlier: 3.668A pdb=" N VAL D 522 " --> pdb=" O GLU D 518 " (cutoff:3.500A) Processing helix chain 'D' and resid 555 through 579 removed outlier: 3.850A pdb=" N TRP D 559 " --> pdb=" O SER D 555 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N VAL D 560 " --> pdb=" O ALA D 556 " (cutoff:3.500A) Processing helix chain 'D' and resid 601 through 615 Processing helix chain 'D' and resid 628 through 655 removed outlier: 3.728A pdb=" N VAL D 632 " --> pdb=" O SER D 628 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE D 655 " --> pdb=" O ALA D 651 " (cutoff:3.500A) Processing helix chain 'D' and resid 668 through 673 Processing helix chain 'D' and resid 673 through 678 Processing helix chain 'D' and resid 689 through 699 Processing helix chain 'D' and resid 699 through 707 Processing helix chain 'D' and resid 708 through 710 No H-bonds generated for 'chain 'D' and resid 708 through 710' Processing helix chain 'D' and resid 714 through 723 Processing helix chain 'D' and resid 732 through 741 Processing helix chain 'D' and resid 742 through 746 removed outlier: 4.097A pdb=" N CYS D 746 " --> pdb=" O ASP D 743 " (cutoff:3.500A) Processing helix chain 'D' and resid 772 through 786 Processing helix chain 'D' and resid 787 through 797 Processing helix chain 'D' and resid 814 through 837 removed outlier: 3.609A pdb=" N MET D 818 " --> pdb=" O ASP D 814 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N GLY D 820 " --> pdb=" O ASP D 816 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N VAL D 821 " --> pdb=" O ASN D 817 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N PHE D 822 " --> pdb=" O MET D 818 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 118 through 120 removed outlier: 3.637A pdb=" N LEU A 138 " --> pdb=" O VAL A 118 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 164 through 167 removed outlier: 3.505A pdb=" N SER A 222 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N ILE A 219 " --> pdb=" O LEU A 248 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 267 through 271 removed outlier: 6.385A pdb=" N TYR A 351 " --> pdb=" O ILE A 366 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N ILE A 366 " --> pdb=" O TYR A 351 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N ILE A 353 " --> pdb=" O VAL A 364 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 397 through 401 removed outlier: 7.200A pdb=" N LEU A 398 " --> pdb=" O GLU A 475 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N HIS A 477 " --> pdb=" O LEU A 398 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N ILE A 400 " --> pdb=" O HIS A 477 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 409 through 413 removed outlier: 3.862A pdb=" N TYR A 456 " --> pdb=" O TYR A 410 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYS A 412 " --> pdb=" O CYS A 454 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 486 through 488 removed outlier: 3.737A pdb=" N GLU A 488 " --> pdb=" O GLU A 497 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLU A 497 " --> pdb=" O GLU A 488 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 534 through 537 removed outlier: 3.859A pdb=" N LYS A 534 " --> pdb=" O PHE A 758 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 728 through 729 removed outlier: 3.650A pdb=" N ILE A 540 " --> pdb=" O THR A 749 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 39 through 40 removed outlier: 3.739A pdb=" N ILE B 40 " --> pdb=" O VAL B 98 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 227 through 229 Processing sheet with id=AB2, first strand: chain 'B' and resid 278 through 282 removed outlier: 3.787A pdb=" N LEU B 366 " --> pdb=" O GLU B 374 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 343 through 344 Processing sheet with id=AB4, first strand: chain 'B' and resid 475 through 480 removed outlier: 8.298A pdb=" N MET B 508 " --> pdb=" O HIS B 405 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N SER B 407 " --> pdb=" O MET B 508 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 434 through 437 Processing sheet with id=AB6, first strand: chain 'B' and resid 729 through 732 removed outlier: 4.227A pdb=" N PHE B 729 " --> pdb=" O MET B 537 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N MET B 537 " --> pdb=" O PHE B 729 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N TYR B 731 " --> pdb=" O SER B 535 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N SER B 535 " --> pdb=" O TYR B 731 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ILE B 530 " --> pdb=" O TYR B 762 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR B 762 " --> pdb=" O ILE B 530 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N ILE B 534 " --> pdb=" O ALA B 758 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ALA B 758 " --> pdb=" O ILE B 534 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 91 through 93 removed outlier: 6.013A pdb=" N VAL C 92 " --> pdb=" O LEU C 121 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU C 138 " --> pdb=" O VAL C 118 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 163 through 167 removed outlier: 6.369A pdb=" N ILE C 219 " --> pdb=" O LEU C 248 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU C 267 " --> pdb=" O TRP C 247 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU C 269 " --> pdb=" O VAL C 249 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ILE C 266 " --> pdb=" O LEU C 356 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N TYR C 351 " --> pdb=" O ILE C 366 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N ILE C 366 " --> pdb=" O TYR C 351 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N ILE C 353 " --> pdb=" O VAL C 364 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 397 through 401 removed outlier: 3.900A pdb=" N LEU C 398 " --> pdb=" O THR C 473 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLU C 475 " --> pdb=" O LEU C 398 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 412 through 413 Processing sheet with id=AC2, first strand: chain 'C' and resid 512 through 513 Processing sheet with id=AC3, first strand: chain 'C' and resid 534 through 537 removed outlier: 3.959A pdb=" N LYS C 534 " --> pdb=" O PHE C 758 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N SER C 756 " --> pdb=" O GLN C 536 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 681 through 682 removed outlier: 4.147A pdb=" N ALA C 682 " --> pdb=" O ALA C 728 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 67 through 72 removed outlier: 3.868A pdb=" N VAL D 39 " --> pdb=" O GLU D 69 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N LEU D 41 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N VAL D 98 " --> pdb=" O GLY D 36 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ALA D 38 " --> pdb=" O VAL D 98 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N ALA D 100 " --> pdb=" O ALA D 38 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ILE D 40 " --> pdb=" O ALA D 100 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 227 through 228 removed outlier: 3.771A pdb=" N ILE D 228 " --> pdb=" O THR D 255 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'D' and resid 278 through 282 Processing sheet with id=AC8, first strand: chain 'D' and resid 343 through 344 Processing sheet with id=AC9, first strand: chain 'D' and resid 478 through 480 removed outlier: 5.910A pdb=" N ILE D 408 " --> pdb=" O TYR D 479 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N VAL D 409 " --> pdb=" O VAL D 510 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 434 through 435 Processing sheet with id=AD2, first strand: chain 'D' and resid 531 through 534 removed outlier: 4.437A pdb=" N ILE D 534 " --> pdb=" O ALA D 758 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N ALA D 758 " --> pdb=" O ILE D 534 " (cutoff:3.500A) 938 hydrogen bonds defined for protein. 2751 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.72 Time building geometry restraints manager: 2.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6288 1.34 - 1.46: 4439 1.46 - 1.58: 8207 1.58 - 1.70: 0 1.70 - 1.81: 77 Bond restraints: 19011 Sorted by residual: bond pdb=" C1 NAG A 901 " pdb=" O5 NAG A 901 " ideal model delta sigma weight residual 1.406 1.495 -0.089 2.00e-02 2.50e+03 1.96e+01 bond pdb=" C GLN C 556 " pdb=" N PRO C 557 " ideal model delta sigma weight residual 1.335 1.385 -0.050 1.28e-02 6.10e+03 1.55e+01 bond pdb=" C ALA D 414 " pdb=" N PRO D 415 " ideal model delta sigma weight residual 1.336 1.382 -0.046 1.25e-02 6.40e+03 1.38e+01 bond pdb=" C ALA B 414 " pdb=" N PRO B 415 " ideal model delta sigma weight residual 1.336 1.382 -0.046 1.25e-02 6.40e+03 1.35e+01 bond pdb=" C10 JC9 B 903 " pdb=" N1 JC9 B 903 " ideal model delta sigma weight residual 1.493 1.454 0.039 2.00e-02 2.50e+03 3.80e+00 ... (remaining 19006 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 26104 2.05 - 4.10: 168 4.10 - 6.15: 31 6.15 - 8.21: 1 8.21 - 10.26: 1 Bond angle restraints: 26305 Sorted by residual: angle pdb=" C HIS D 325 " pdb=" CA HIS D 325 " pdb=" CB HIS D 325 " ideal model delta sigma weight residual 116.34 110.42 5.92 1.40e+00 5.10e-01 1.79e+01 angle pdb=" CA LEU C 541 " pdb=" CB LEU C 541 " pdb=" CG LEU C 541 " ideal model delta sigma weight residual 116.30 126.56 -10.26 3.50e+00 8.16e-02 8.59e+00 angle pdb=" CA GLN C 556 " pdb=" C GLN C 556 " pdb=" N PRO C 557 " ideal model delta sigma weight residual 118.44 122.83 -4.39 1.59e+00 3.96e-01 7.61e+00 angle pdb=" CA GLN A 556 " pdb=" C GLN A 556 " pdb=" N PRO A 557 " ideal model delta sigma weight residual 118.44 122.72 -4.28 1.59e+00 3.96e-01 7.23e+00 angle pdb=" CA ALA D 414 " pdb=" C ALA D 414 " pdb=" N PRO D 415 " ideal model delta sigma weight residual 118.44 122.67 -4.23 1.59e+00 3.96e-01 7.08e+00 ... (remaining 26300 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.48: 10799 23.48 - 46.95: 151 46.95 - 70.43: 14 70.43 - 93.91: 0 93.91 - 117.39: 3 Dihedral angle restraints: 10967 sinusoidal: 2306 harmonic: 8661 Sorted by residual: dihedral pdb=" CA ALA B 414 " pdb=" C ALA B 414 " pdb=" N PRO B 415 " pdb=" CA PRO B 415 " ideal model delta harmonic sigma weight residual 180.00 -157.69 -22.31 0 5.00e+00 4.00e-02 1.99e+01 dihedral pdb=" CA ALA D 414 " pdb=" C ALA D 414 " pdb=" N PRO D 415 " pdb=" CA PRO D 415 " ideal model delta harmonic sigma weight residual -180.00 -158.68 -21.32 0 5.00e+00 4.00e-02 1.82e+01 dihedral pdb=" C2 NAG A 901 " pdb=" C1 NAG A 901 " pdb=" O5 NAG A 901 " pdb=" C5 NAG A 901 " ideal model delta sinusoidal sigma weight residual -62.96 54.43 -117.39 1 3.00e+01 1.11e-03 1.56e+01 ... (remaining 10964 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 3054 0.072 - 0.144: 315 0.144 - 0.216: 1 0.216 - 0.287: 1 0.287 - 0.359: 1 Chirality restraints: 3372 Sorted by residual: chirality pdb=" C1 NAG A 901 " pdb=" ND2 ASN A 203 " pdb=" C2 NAG A 901 " pdb=" O5 NAG A 901 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.23e+00 chirality pdb=" C1 NAG D 903 " pdb=" ND2 ASN D 348 " pdb=" C2 NAG D 903 " pdb=" O5 NAG D 903 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" C1 JC9 B 903 " pdb=" C2 JC9 B 903 " pdb=" C5 JC9 B 903 " pdb=" C7 JC9 B 903 " both_signs ideal model delta sigma weight residual False -2.77 -2.61 -0.16 2.00e-01 2.50e+01 6.17e-01 ... (remaining 3369 not shown) Planarity restraints: 3438 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 556 " -0.048 5.00e-02 4.00e+02 7.11e-02 8.10e+00 pdb=" N PRO A 557 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO A 557 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 557 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 414 " 0.044 5.00e-02 4.00e+02 6.64e-02 7.06e+00 pdb=" N PRO B 415 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO B 415 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 415 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 414 " 0.042 5.00e-02 4.00e+02 6.38e-02 6.51e+00 pdb=" N PRO D 415 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO D 415 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 415 " 0.037 5.00e-02 4.00e+02 ... (remaining 3435 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 1722 2.74 - 3.28: 18465 3.28 - 3.82: 30829 3.82 - 4.36: 28607 4.36 - 4.90: 53030 Nonbonded interactions: 132653 Sorted by model distance: nonbonded pdb=" O ALA D 794 " pdb=" OG1 THR D 798 " model vdw 2.206 3.040 nonbonded pdb=" O LEU A 672 " pdb=" OH TYR A 681 " model vdw 2.232 3.040 nonbonded pdb=" O ARG C 671 " pdb=" OH TYR C 681 " model vdw 2.262 3.040 nonbonded pdb=" N GLY A 250 " pdb=" OE2 GLU A 253 " model vdw 2.266 3.120 nonbonded pdb=" OG SER C 126 " pdb=" OG SER C 129 " model vdw 2.293 3.040 ... (remaining 132648 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 28 through 81 or (resid 82 through 92 and (name N or name \ CA or name C or name O or name CB )) or resid 93 through 108 or (resid 109 throu \ gh 111 and (name N or name CA or name C or name O or name CB )) or resid 112 thr \ ough 186 or (resid 189 through 198 and (name N or name CA or name C or name O or \ name CB )) or resid 199 through 244 or (resid 245 through 246 and (name N or na \ me CA or name C or name O or name CB )) or resid 247 through 252 or (resid 253 t \ hrough 255 and (name N or name CA or name C or name O or name CB )) or resid 256 \ through 269 or (resid 270 through 273 and (name N or name CA or name C or name \ O or name CB )) or resid 274 through 370 or (resid 371 through 381 and (name N o \ r name CA or name C or name O or name CB )) or resid 382 through 433 or (resid 4 \ 34 through 435 and (name N or name CA or name C or name O or name CB )) or resid \ 436 through 449 or (resid 450 and (name N or name CA or name C or name O or nam \ e CB )) or resid 451 through 486 or (resid 487 through 497 and (name N or name C \ A or name C or name O or name CB )) or resid 498 through 503 or (resid 504 throu \ gh 507 and (name N or name CA or name C or name O or name CB )) or resid 508 thr \ ough 511 or (resid 512 and (name N or name CA or name C or name O or name CB )) \ or resid 513 through 518 or (resid 519 and (name N or name CA or name C or name \ O or name CB )) or resid 520 through 562 or (resid 563 through 564 and (name N o \ r name CA or name C or name O or name CB )) or resid 565 through 570 or (resid 5 \ 71 through 572 and (name N or name CA or name C or name O or name CB )) or resid \ 573 through 618 or (resid 626 through 627 and (name N or name CA or name C or n \ ame O or name CB )) or resid 628 through 630 or (resid 631 through 632 and (name \ N or name CA or name C or name O or name CB )) or resid 633 or (resid 634 and ( \ name N or name CA or name C or name O or name CB )) or resid 635 through 663 or \ (resid 664 and (name N or name CA or name C or name O or name CB )) or resid 665 \ through 666 or (resid 667 through 668 and (name N or name CA or name C or name \ O or name CB )) or resid 669 through 671 or (resid 672 through 674 and (name N o \ r name CA or name C or name O or name CB )) or resid 675 through 695 or (resid 6 \ 96 and (name N or name CA or name C or name O or name CB )) or resid 697 through \ 706 or (resid 707 through 708 and (name N or name CA or name C or name O or nam \ e CB )) or resid 709 through 737 or (resid 738 through 740 and (name N or name C \ A or name C or name O or name CB )) or resid 741 through 762 or (resid 763 throu \ gh 766 and (name N or name CA or name C or name O or name CB )) or resid 767 thr \ ough 790 or (resid 791 and (name N or name CA or name C or name O or name CB )) \ or resid 792 through 809 or (resid 810 through 814 and (name N or name CA or nam \ e C or name O or name CB )) or resid 815 through 818 or (resid 819 and (name N o \ r name CA or name C or name O or name CB )) or resid 820 through 901)) selection = (chain 'C' and (resid 28 through 32 or (resid 33 through 60 and (name N or name \ CA or name C or name O or name CB )) or resid 61 through 63 or (resid 64 through \ 66 and (name N or name CA or name C or name O or name CB )) or resid 67 through \ 68 or (resid 69 through 77 and (name N or name CA or name C or name O or name C \ B )) or resid 78 or (resid 79 through 92 and (name N or name CA or name C or nam \ e O or name CB )) or resid 93 through 97 or (resid 98 through 103 and (name N or \ name CA or name C or name O or name CB )) or resid 104 through 106 or (resid 10 \ 7 and (name N or name CA or name C or name O or name CB )) or resid 108 through \ 109 or (resid 110 through 111 and (name N or name CA or name C or name O or name \ CB )) or resid 112 through 118 or (resid 119 and (name N or name CA or name C o \ r name O or name CB )) or resid 120 or (resid 121 through 122 and (name N or nam \ e CA or name C or name O or name CB )) or resid 123 through 124 or (resid 125 th \ rough 127 and (name N or name CA or name C or name O or name CB )) or resid 128 \ or (resid 129 through 131 and (name N or name CA or name C or name O or name CB \ )) or resid 132 or (resid 133 and (name N or name CA or name C or name O or name \ CB )) or resid 134 or (resid 135 through 137 and (name N or name CA or name C o \ r name O or name CB )) or resid 138 through 139 or (resid 140 and (name N or nam \ e CA or name C or name O or name CB )) or resid 141 through 146 or (resid 147 an \ d (name N or name CA or name C or name O or name CB )) or resid 148 or (resid 14 \ 9 through 150 and (name N or name CA or name C or name O or name CB )) or resid \ 151 or (resid 152 through 157 and (name N or name CA or name C or name O or name \ CB )) or resid 158 or (resid 159 and (name N or name CA or name C or name O or \ name CB )) or resid 160 through 162 or (resid 163 and (name N or name CA or name \ C or name O or name CB )) or resid 164 or (resid 165 through 172 and (name N or \ name CA or name C or name O or name CB )) or resid 173 through 181 or (resid 18 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 183 or (resi \ d 184 through 198 and (name N or name CA or name C or name O or name CB )) or re \ sid 199 through 203 or (resid 204 and (name N or name CA or name C or name O or \ name CB )) or resid 205 through 220 or (resid 221 through 229 and (name N or nam \ e CA or name C or name O or name CB )) or resid 230 through 237 or (resid 238 th \ rough 241 and (name N or name CA or name C or name O or name CB )) or resid 242 \ or (resid 243 and (name N or name CA or name C or name O or name CB )) or (resid \ 244 through 246 and (name N or name CA or name C or name O or name CB )) or res \ id 247 or (resid 248 through 249 and (name N or name CA or name C or name O or n \ ame CB )) or (resid 250 through 255 and (name N or name CA or name C or name O o \ r name CB )) or (resid 256 through 260 and (name N or name CA or name C or name \ O or name CB )) or resid 261 through 266 or (resid 267 and (name N or name CA or \ name C or name O or name CB )) or resid 268 through 271 or (resid 272 through 2 \ 73 and (name N or name CA or name C or name O or name CB )) or (resid 274 throug \ h 279 and (name N or name CA or name C or name O or name CB )) or resid 280 thro \ ugh 281 or (resid 282 through 285 and (name N or name CA or name C or name O or \ name CB )) or (resid 286 through 303 and (name N or name CA or name C or name O \ or name CB )) or resid 304 through 311 or (resid 312 through 314 and (name N or \ name CA or name C or name O or name CB )) or resid 315 through 318 or (resid 319 \ through 320 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 21 through 324 or (resid 325 through 326 and (name N or name CA or name C or nam \ e O or name CB )) or resid 327 or (resid 328 through 332 and (name N or name CA \ or name C or name O or name CB )) or resid 333 or (resid 334 through 335 and (na \ me N or name CA or name C or name O or name CB )) or resid 336 through 339 or (r \ esid 340 through 343 and (name N or name CA or name C or name O or name CB )) or \ (resid 344 through 351 and (name N or name CA or name C or name O or name CB )) \ or resid 352 or (resid 353 through 364 and (name N or name CA or name C or name \ O or name CB )) or resid 365 through 372 or (resid 373 through 381 and (name N \ or name CA or name C or name O or name CB )) or resid 382 through 396 or (resid \ 397 and (name N or name CA or name C or name O or name CB )) or resid 398 throug \ h 410 or (resid 411 through 412 and (name N or name CA or name C or name O or na \ me CB )) or resid 413 or (resid 414 through 417 and (name N or name CA or name C \ or name O or name CB )) or resid 418 through 424 or (resid 425 through 427 and \ (name N or name CA or name C or name O or name CB )) or resid 428 through 430 or \ (resid 431 through 435 and (name N or name CA or name C or name O or name CB )) \ or resid 436 through 442 or (resid 443 through 444 and (name N or name CA or na \ me C or name O or name CB )) or resid 445 or (resid 446 through 450 and (name N \ or name CA or name C or name O or name CB )) or resid 451 through 458 or (resid \ 459 through 471 and (name N or name CA or name C or name O or name CB )) or resi \ d 472 or (resid 473 and (name N or name CA or name C or name O or name CB )) or \ resid 474 through 475 or (resid 476 and (name N or name CA or name C or name O o \ r name CB )) or resid 477 or (resid 478 through 481 and (name N or name CA or na \ me C or name O or name CB )) or resid 482 through 485 or (resid 486 through 497 \ and (name N or name CA or name C or name O or name CB )) or resid 498 or (resid \ 499 and (name N or name CA or name C or name O or name CB )) or resid 500 throug \ h 501 or (resid 502 and (name N or name CA or name C or name O or name CB )) or \ (resid 503 through 507 and (name N or name CA or name C or name O or name CB )) \ or resid 508 through 517 or (resid 518 through 519 and (name N or name CA or nam \ e C or name O or name CB )) or resid 520 or (resid 521 through 522 and (name N o \ r name CA or name C or name O or name CB )) or resid 523 through 538 or (resid 5 \ 39 through 545 and (name N or name CA or name C or name O or name CB )) or (resi \ d 552 through 556 and (name N or name CA or name C or name O or name CB )) or re \ sid 557 through 559 or (resid 560 and (name N or name CA or name C or name O or \ name CB )) or resid 561 through 563 or (resid 564 and (name N or name CA or name \ C or name O or name CB )) or resid 565 through 577 or (resid 578 through 603 an \ d (name N or name CA or name C or name O or name CB )) or resid 604 through 609 \ or (resid 610 and (name N or name CA or name C or name O or name CB )) or resid \ 611 through 618 or resid 626 through 670 or (resid 671 through 674 and (name N o \ r name CA or name C or name O or name CB )) or resid 675 through 729 or (resid 7 \ 30 through 732 and (name N or name CA or name C or name O or name CB )) or resid \ 733 through 770 or (resid 771 and (name N or name CA or name C or name O or nam \ e CB )) or resid 772 through 784 or (resid 785 through 787 and (name N or name C \ A or name C or name O or name CB )) or resid 788 through 807 or (resid 808 and ( \ name N or name CA or name C or name O or name CB )) or resid 809 through 901)) } ncs_group { reference = (chain 'B' and ((resid 34 and (name N or name CA or name C or name O or name CB \ )) or resid 35 through 57 or (resid 58 through 65 and (name N or name CA or name \ C or name O or name CB )) or resid 66 through 69 or (resid 70 and (name N or na \ me CA or name C or name O or name CB )) or resid 71 through 84 or (resid 85 thro \ ugh 89 and (name N or name CA or name C or name O or name CB )) or resid 90 thro \ ugh 107 or (resid 108 through 110 and (name N or name CA or name C or name O or \ name CB )) or resid 111 through 123 or (resid 124 and (name N or name CA or name \ C or name O or name CB )) or (resid 125 through 127 and (name N or name CA or n \ ame C or name O or name CB )) or resid 128 through 145 or (resid 146 and (name N \ or name CA or name C or name O or name CB )) or resid 147 through 148 or (resid \ 149 through 155 and (name N or name CA or name C or name O or name CB )) or res \ id 156 through 159 or (resid 160 and (name N or name CA or name C or name O or n \ ame CB )) or resid 161 through 165 or (resid 166 and (name N or name CA or name \ C or name O or name CB )) or resid 167 through 173 or (resid 174 through 176 and \ (name N or name CA or name C or name O or name CB )) or resid 177 through 200 o \ r resid 215 through 237 or (resid 238 through 239 and (name N or name CA or name \ C or name O or name CB )) or resid 240 or (resid 241 through 242 and (name N or \ name CA or name C or name O or name CB )) or resid 243 through 244 or (resid 24 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 246 through \ 248 or resid 253 through 261 or (resid 262 through 263 and (name N or name CA or \ name C or name O or name CB )) or (resid 264 through 269 and (name N or name CA \ or name C or name O or name CB )) or resid 270 through 277 or (resid 278 and (n \ ame N or name CA or name C or name O or name CB )) or resid 279 through 296 or ( \ resid 297 through 300 and (name N or name CA or name C or name O or name CB )) o \ r resid 301 through 305 or (resid 306 through 308 and (name N or name CA or name \ C or name O or name CB )) or resid 309 through 310 or (resid 311 through 314 an \ d (name N or name CA or name C or name O or name CB )) or resid 315 through 349 \ or (resid 350 and (name N or name CA or name C or name O or name CB )) or resid \ 351 through 358 or (resid 359 and (name N or name CA or name C or name O or name \ CB )) or resid 360 through 362 or (resid 363 through 366 and (name N or name CA \ or name C or name O or name CB )) or resid 367 through 392 or (resid 406 and (n \ ame N or name CA or name C or name O or name CB )) or resid 407 through 422 or ( \ resid 423 and (name N or name CA or name C or name O or name CB )) or resid 424 \ through 431 or (resid 432 through 433 and (name N or name CA or name C or name O \ or name CB )) or resid 434 through 438 or resid 451 or (resid 452 through 455 a \ nd (name N or name CA or name C or name O or name CB )) or resid 456 through 474 \ or (resid 475 and (name N or name CA or name C or name O or name CB )) or resid \ 476 through 479 or (resid 480 and (name N or name CA or name C or name O or nam \ e CB )) or resid 481 through 499 or (resid 500 and (name N or name CA or name C \ or name O or name CB )) or resid 501 through 507 or (resid 508 through 509 and ( \ name N or name CA or name C or name O or name CB )) or resid 510 through 518 or \ (resid 519 and (name N or name CA or name C or name O or name CB )) or resid 520 \ through 524 or (resid 525 and (name N or name CA or name C or name O or name CB \ )) or resid 526 through 544 or (resid 545 and (name N or name CA or name C or n \ ame O or name CB )) or resid 546 through 554 or (resid 555 through 556 and (name \ N or name CA or name C or name O or name CB )) or resid 557 through 566 or (res \ id 567 through 568 and (name N or name CA or name C or name O or name CB )) or r \ esid 569 or (resid 570 through 571 and (name N or name CA or name C or name O or \ name CB )) or resid 572 through 573 or (resid 574 through 575 and (name N or na \ me CA or name C or name O or name CB )) or resid 576 through 601 or (resid 602 a \ nd (name N or name CA or name C or name O or name CB )) or resid 603 through 613 \ or (resid 614 through 615 and (name N or name CA or name C or name O or name CB \ )) or resid 616 or (resid 617 through 618 and (name N or name CA or name C or n \ ame O or name CB )) or resid 619 through 629 or (resid 630 through 631 and (name \ N or name CA or name C or name O or name CB )) or resid 632 through 637 or (res \ id 638 through 639 and (name N or name CA or name C or name O or name CB )) or r \ esid 640 through 642 or (resid 643 through 644 and (name N or name CA or name C \ or name O or name CB )) or resid 645 through 696 or (resid 697 through 698 and ( \ name N or name CA or name C or name O or name CB )) or resid 699 through 704 or \ (resid 705 through 706 and (name N or name CA or name C or name O or name CB )) \ or resid 707 through 768 or (resid 769 and (name N or name CA or name C or name \ O or name CB )) or resid 770 through 772 or (resid 773 through 775 and (name N o \ r name CA or name C or name O or name CB )) or resid 776 through 788 or (resid 7 \ 89 through 791 and (name N or name CA or name C or name O or name CB )) or resid \ 792 through 815 or (resid 816 through 819 and (name N or name CA or name C or n \ ame O or name CB )) or resid 820 through 830 or (resid 831 and (name N or name C \ A or name C or name O or name CB )) or resid 832 through 837 or resid 901 throug \ h 902)) selection = (chain 'D' and (resid 34 through 36 or (resid 37 through 38 and (name N or name \ CA or name C or name O or name CB )) or resid 39 through 40 or (resid 41 and (na \ me N or name CA or name C or name O or name CB )) or resid 42 through 45 or (res \ id 46 through 51 and (name N or name CA or name C or name O or name CB )) or res \ id 52 through 53 or (resid 54 through 65 and (name N or name CA or name C or nam \ e O or name CB )) or resid 66 through 75 or (resid 76 through 77 and (name N or \ name CA or name C or name O or name CB )) or resid 78 through 79 or (resid 80 an \ d (name N or name CA or name C or name O or name CB )) or resid 81 or (resid 82 \ through 89 and (name N or name CA or name C or name O or name CB )) or resid 90 \ or (resid 91 through 95 and (name N or name CA or name C or name O or name CB )) \ or resid 96 through 102 or (resid 103 through 110 and (name N or name CA or nam \ e C or name O or name CB )) or resid 111 through 113 or (resid 114 and (name N o \ r name CA or name C or name O or name CB )) or resid 115 through 117 or (resid 1 \ 18 through 120 and (name N or name CA or name C or name O or name CB )) or resid \ 121 through 125 or (resid 126 through 127 and (name N or name CA or name C or n \ ame O or name CB )) or resid 128 through 130 or (resid 131 through 142 and (name \ N or name CA or name C or name O or name CB )) or resid 143 through 149 or (res \ id 150 through 155 and (name N or name CA or name C or name O or name CB )) or r \ esid 156 through 174 or (resid 175 through 176 and (name N or name CA or name C \ or name O or name CB )) or resid 177 through 180 or (resid 181 through 182 and ( \ name N or name CA or name C or name O or name CB )) or resid 183 through 185 or \ (resid 186 through 187 and (name N or name CA or name C or name O or name CB )) \ or resid 188 through 190 or (resid 191 through 192 and (name N or name CA or nam \ e C or name O or name CB )) or resid 193 through 198 or (resid 199 through 215 a \ nd (name N or name CA or name C or name O or name CB )) or resid 216 through 217 \ or (resid 218 through 224 and (name N or name CA or name C or name O or name CB \ )) or resid 225 through 227 or (resid 228 and (name N or name CA or name C or n \ ame O or name CB )) or resid 229 or (resid 230 and (name N or name CA or name C \ or name O or name CB )) or resid 231 or (resid 232 through 239 and (name N or na \ me CA or name C or name O or name CB )) or resid 240 through 255 or (resid 256 a \ nd (name N or name CA or name C or name O or name CB )) or resid 257 through 259 \ or (resid 260 through 263 and (name N or name CA or name C or name O or name CB \ )) or (resid 264 through 269 and (name N or name CA or name C or name O or name \ CB )) or resid 270 through 274 or (resid 275 and (name N or name CA or name C o \ r name O or name CB )) or resid 276 through 279 or (resid 280 through 287 and (n \ ame N or name CA or name C or name O or name CB )) or resid 288 through 292 or ( \ resid 293 through 295 and (name N or name CA or name C or name O or name CB )) o \ r (resid 296 through 300 and (name N or name CA or name C or name O or name CB ) \ ) or resid 301 through 311 or (resid 312 through 314 and (name N or name CA or n \ ame C or name O or name CB )) or resid 315 through 320 or (resid 321 through 327 \ and (name N or name CA or name C or name O or name CB )) or (resid 331 through \ 334 and (name N or name CA or name C or name O or name CB )) or resid 335 throug \ h 338 or (resid 339 and (name N or name CA or name C or name O or name CB )) or \ (resid 340 and (name N or name CA or name C or name O or name CB or name CG1 or \ name CG2)) or resid 341 through 347 or (resid 348 through 350 and (name N or nam \ e CA or name C or name O or name CB )) or resid 351 through 353 or (resid 354 an \ d (name N or name CA or name C or name O or name CB )) or resid 355 or (resid 35 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 357 through \ 361 or (resid 362 through 366 and (name N or name CA or name C or name O or name \ CB )) or (resid 367 and (name N or name CA or name C or name O or name CB or na \ me CG or name CD2)) or (resid 368 through 372 and (name N or name CA or name C o \ r name O or name CB )) or resid 373 through 385 or (resid 386 through 387 and (n \ ame N or name CA or name C or name O or name CB )) or resid 388 through 389 or ( \ resid 390 and (name N or name CA or name C or name O or name CB )) or resid 391 \ or (resid 392 through 406 and (name N or name CA or name C or name O or name CB \ )) or resid 407 through 420 or (resid 421 and (name N or name CA or name C or na \ me O or name CB )) or resid 422 through 462 or (resid 463 and (name N or name CA \ or name C or name O or name CB )) or resid 464 through 478 or (resid 479 throug \ h 480 and (name N or name CA or name C or name O or name CB )) or resid 481 thro \ ugh 492 or (resid 493 and (name N or name CA or name C or name O or name CB )) o \ r resid 494 or (resid 495 and (name N or name CA or name C or name O or name CB \ )) or (resid 496 through 498 and (name N or name CA or name C or name O or name \ CB )) or resid 499 through 501 or (resid 502 through 506 and (name N or name CA \ or name C or name O or name CB )) or resid 507 through 511 or (resid 512 and (na \ me N or name CA or name C or name O or name CB )) or resid 513 or (resid 514 and \ (name N or name CA or name C or name O or name CB )) or resid 515 or (resid 516 \ through 519 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 20 through 521 or (resid 522 and (name N or name CA or name C or name O or name \ CB )) or resid 523 through 529 or (resid 530 through 531 and (name N or name CA \ or name C or name O or name CB )) or (resid 532 and (name N or name CA or name C \ or name O or name CB or name OG1)) or resid 533 through 537 or (resid 538 throu \ gh 540 and (name N or name CA or name C or name O or name CB )) or resid 541 thr \ ough 547 or (resid 548 through 549 and (name N or name CA or name C or name O or \ name CB )) or resid 550 through 600 or (resid 601 through 602 and (name N or na \ me CA or name C or name O or name CB )) or resid 603 through 607 or (resid 608 t \ hrough 609 and (name N or name CA or name C or name O or name CB )) or resid 610 \ through 614 or (resid 615 and (name N or name CA or name C or name O or name CB \ )) or resid 616 through 652 or (resid 653 through 654 and (name N or name CA or \ name C or name O or name CB )) or resid 655 through 662 or (resid 663 through 6 \ 64 and (name N or name CA or name C or name O or name CB )) or resid 665 through \ 670 or (resid 671 through 673 and (name N or name CA or name C or name O or nam \ e CB )) or resid 674 through 708 or (resid 709 through 712 and (name N or name C \ A or name C or name O or name CB )) or resid 713 through 725 or (resid 726 throu \ gh 728 and (name N or name CA or name C or name O or name CB )) or resid 729 thr \ ough 756 or (resid 757 through 758 and (name N or name CA or name C or name O or \ name CB )) or resid 759 through 781 or (resid 782 and (name N or name CA or nam \ e C or name O or name CB )) or resid 783 through 790 or (resid 791 and (name N o \ r name CA or name C or name O or name CB )) or resid 792 or (resid 793 through 7 \ 94 and (name N or name CA or name C or name O or name CB )) or resid 795 through \ 803 or (resid 810 through 819 and (name N or name CA or name C or name O or nam \ e CB )) or resid 820 through 902)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.250 Find NCS groups from input model: 0.600 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: 0.010 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6092 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.089 19024 Z= 0.109 Angle : 0.425 10.258 26338 Z= 0.214 Chirality : 0.041 0.359 3372 Planarity : 0.003 0.071 3431 Dihedral : 8.163 117.386 5331 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.00 % Favored : 97.86 % Rotamer: Outliers : 3.51 % Allowed : 8.87 % Favored : 87.62 % 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: 1.10 (0.16), residues: 2948 helix: 2.76 (0.15), residues: 1209 sheet: -0.18 (0.35), residues: 239 loop : -0.88 (0.16), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 523 TYR 0.009 0.000 TYR C 578 PHE 0.005 0.001 PHE B 550 TRP 0.007 0.000 TRP D 635 HIS 0.002 0.000 HIS D 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00195 / 0.11 (19011) covalent geometry : angle 0.41647 / 0.21 (26305) SS BOND : bond 0.00083 / 0.04 ( 6) SS BOND : angle 0.55467 / 0.43 ( 12) hydrogen bonds : bond 0.12102 / 8.66 ( 938) hydrogen bonds : angle 4.93226 / 3.80 ( 2751) link_NAG-ASN : bond 0.00874 / 0.55 ( 7) link_NAG-ASN : angle 2.93353 / 2.57 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5896 Ramachandran restraints generated. 2948 Oldfield, 0 Emsley, 2948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5896 Ramachandran restraints generated. 2948 Oldfield, 0 Emsley, 2948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 289 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 650 ASN cc_start: 0.8141 (t0) cc_final: 0.7914 (t0) REVERT: A 738 PHE cc_start: 0.5625 (OUTLIER) cc_final: 0.4773 (t80) REVERT: B 358 MET cc_start: 0.6008 (ttt) cc_final: 0.5637 (ttm) REVERT: C 636 TRP cc_start: 0.6439 (OUTLIER) cc_final: 0.6227 (t60) REVERT: D 181 ASP cc_start: 0.7460 (p0) cc_final: 0.6898 (p0) outliers start: 42 outliers final: 21 residues processed: 327 average time/residue: 0.1017 time to fit residues: 57.9307 Evaluate side-chains 213 residues out of total 2606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 190 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 7.9990 chunk 298 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 94 HIS C 780 HIS ** D 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.088778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.079669 restraints weight = 104865.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.079401 restraints weight = 150405.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.079869 restraints weight = 141154.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.080047 restraints weight = 95054.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.080348 restraints weight = 85263.687| |-----------------------------------------------------------------------------| r_work (final): 0.3803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6622 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 19024 Z= 0.208 Angle : 0.633 14.375 26338 Z= 0.333 Chirality : 0.047 0.426 3372 Planarity : 0.004 0.064 3431 Dihedral : 5.070 82.687 3223 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.61 % Favored : 95.18 % Rotamer: Outliers : 0.42 % Allowed : 5.69 % Favored : 93.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.34 (0.16), residues: 2948 helix: 1.87 (0.15), residues: 1238 sheet: -0.84 (0.31), residues: 273 loop : -1.06 (0.17), residues: 1437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 671 TYR 0.045 0.003 TYR D 731 PHE 0.027 0.003 PHE A 738 TRP 0.024 0.003 TRP A 247 HIS 0.013 0.002 HIS A 780 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.21 (19011) covalent geometry : angle 0.62665 / 0.33 (26305) SS BOND : bond 0.00218 / 0.14 ( 6) SS BOND : angle 1.11327 / 0.83 ( 12) hydrogen bonds : bond 0.03115 / 2.29 ( 938) hydrogen bonds : angle 4.41479 / 3.42 ( 2751) link_NAG-ASN : bond 0.01030 / 0.68 ( 7) link_NAG-ASN : angle 3.09862 / 2.62 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5896 Ramachandran restraints generated. 2948 Oldfield, 0 Emsley, 2948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5896 Ramachandran restraints generated. 2948 Oldfield, 0 Emsley, 2948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 218 time to evaluate : 0.657 Fit side-chains REVERT: A 403 ILE cc_start: 0.8872 (mm) cc_final: 0.8633 (mm) REVERT: D 777 ASP cc_start: 0.7266 (m-30) cc_final: 0.7010 (m-30) outliers start: 5 outliers final: 2 residues processed: 222 average time/residue: 0.0936 time to fit residues: 37.2768 Evaluate side-chains 181 residues out of total 2606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 179 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 40 optimal weight: 8.9990 chunk 160 optimal weight: 3.9990 chunk 52 optimal weight: 0.4980 chunk 158 optimal weight: 0.8980 chunk 20 optimal weight: 20.0000 chunk 44 optimal weight: 1.9990 chunk 268 optimal weight: 8.9990 chunk 249 optimal weight: 0.1980 chunk 15 optimal weight: 5.9990 chunk 184 optimal weight: 6.9990 chunk 289 optimal weight: 9.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 650 ASN B 357 GLN C 650 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.089527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.080225 restraints weight = 104854.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.080303 restraints weight = 119233.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.080581 restraints weight = 114897.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.080663 restraints weight = 77035.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.080839 restraints weight = 71492.884| |-----------------------------------------------------------------------------| r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6577 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 19024 Z= 0.108 Angle : 0.498 10.504 26338 Z= 0.255 Chirality : 0.043 0.376 3372 Planarity : 0.004 0.065 3431 Dihedral : 4.066 49.517 3223 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.02 % Favored : 96.85 % Rotamer: Outliers : 0.17 % Allowed : 3.85 % Favored : 95.98 % 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: 0.60 (0.16), residues: 2948 helix: 2.20 (0.15), residues: 1234 sheet: -0.88 (0.30), residues: 276 loop : -0.99 (0.17), residues: 1438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 722 TYR 0.018 0.001 TYR D 731 PHE 0.017 0.001 PHE D 529 TRP 0.013 0.001 TRP D 373 HIS 0.004 0.001 HIS C 780 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (19011) covalent geometry : angle 0.48789 / 0.25 (26305) SS BOND : bond 0.00211 / 0.11 ( 6) SS BOND : angle 1.51057 / 1.32 ( 12) hydrogen bonds : bond 0.02322 / 1.69 ( 938) hydrogen bonds : angle 3.92215 / 3.04 ( 2751) link_NAG-ASN : bond 0.00791 / 0.56 ( 7) link_NAG-ASN : angle 3.48434 / 2.92 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5896 Ramachandran restraints generated. 2948 Oldfield, 0 Emsley, 2948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5896 Ramachandran restraints generated. 2948 Oldfield, 0 Emsley, 2948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 220 time to evaluate : 0.687 Fit side-chains REVERT: A 701 THR cc_start: 0.8130 (t) cc_final: 0.7904 (m) REVERT: B 358 MET cc_start: 0.4297 (ttt) cc_final: 0.3591 (ttm) REVERT: D 126 ILE cc_start: 0.6605 (mp) cc_final: 0.6115 (mm) REVERT: D 777 ASP cc_start: 0.7126 (m-30) cc_final: 0.6925 (m-30) outliers start: 2 outliers final: 0 residues processed: 221 average time/residue: 0.0895 time to fit residues: 35.0223 Evaluate side-chains 167 residues out of total 2606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 41 optimal weight: 8.9990 chunk 71 optimal weight: 8.9990 chunk 26 optimal weight: 50.0000 chunk 21 optimal weight: 30.0000 chunk 66 optimal weight: 5.9990 chunk 30 optimal weight: 0.0170 chunk 48 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 150 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 98 optimal weight: 8.9990 overall best weight: 3.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 487 GLN A 709 HIS B 359 HIS ** C 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 650 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.085485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.075201 restraints weight = 104502.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.074401 restraints weight = 146096.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.074933 restraints weight = 137397.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.075608 restraints weight = 90577.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.075694 restraints weight = 80765.325| |-----------------------------------------------------------------------------| r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6928 moved from start: 0.3738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 19024 Z= 0.197 Angle : 0.630 13.695 26338 Z= 0.328 Chirality : 0.046 0.388 3372 Planarity : 0.004 0.064 3431 Dihedral : 4.486 31.181 3223 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.50 % Favored : 94.30 % Rotamer: Outliers : 0.25 % Allowed : 6.28 % Favored : 93.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.03 (0.16), residues: 2948 helix: 1.76 (0.15), residues: 1232 sheet: -1.53 (0.29), residues: 275 loop : -1.25 (0.16), residues: 1441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 671 TYR 0.038 0.003 TYR D 731 PHE 0.029 0.002 PHE D 529 TRP 0.027 0.002 TRP A 247 HIS 0.015 0.002 HIS C 780 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.20 (19011) covalent geometry : angle 0.62032 / 0.33 (26305) SS BOND : bond 0.01431 / 0.73 ( 6) SS BOND : angle 1.51276 / 1.19 ( 12) hydrogen bonds : bond 0.03034 / 2.23 ( 938) hydrogen bonds : angle 4.33101 / 3.33 ( 2751) link_NAG-ASN : bond 0.00722 / 0.46 ( 7) link_NAG-ASN : angle 3.78352 / 3.51 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5896 Ramachandran restraints generated. 2948 Oldfield, 0 Emsley, 2948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5896 Ramachandran restraints generated. 2948 Oldfield, 0 Emsley, 2948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 194 time to evaluate : 0.748 Fit side-chains revert: symmetry clash REVERT: D 126 ILE cc_start: 0.6924 (mp) cc_final: 0.6474 (mm) REVERT: D 462 ILE cc_start: 0.8739 (mm) cc_final: 0.8425 (mm) outliers start: 3 outliers final: 1 residues processed: 196 average time/residue: 0.0924 time to fit residues: 32.6960 Evaluate side-chains 157 residues out of total 2606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 156 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 207 optimal weight: 5.9990 chunk 184 optimal weight: 20.0000 chunk 213 optimal weight: 7.9990 chunk 99 optimal weight: 8.9990 chunk 294 optimal weight: 10.0000 chunk 120 optimal weight: 0.6980 chunk 2 optimal weight: 40.0000 chunk 153 optimal weight: 50.0000 chunk 214 optimal weight: 0.9990 chunk 200 optimal weight: 10.0000 chunk 174 optimal weight: 30.0000 overall best weight: 4.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 650 ASN C 650 ASN ** D 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 649 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.083400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.073215 restraints weight = 100314.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.073108 restraints weight = 138047.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.073528 restraints weight = 131660.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.073749 restraints weight = 87641.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.073895 restraints weight = 83449.133| |-----------------------------------------------------------------------------| r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7010 moved from start: 0.4741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 19024 Z= 0.226 Angle : 0.645 10.600 26338 Z= 0.344 Chirality : 0.047 0.382 3372 Planarity : 0.005 0.066 3431 Dihedral : 4.993 34.701 3223 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.65 % Favored : 95.18 % Rotamer: Outliers : 0.08 % Allowed : 4.35 % Favored : 95.56 % 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: -0.49 (0.16), residues: 2948 helix: 1.38 (0.15), residues: 1231 sheet: -2.06 (0.28), residues: 261 loop : -1.54 (0.16), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 671 TYR 0.051 0.003 TYR D 388 PHE 0.033 0.003 PHE D 784 TRP 0.037 0.003 TRP D 391 HIS 0.015 0.002 HIS B 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00501 / 0.23 (19011) covalent geometry : angle 0.63554 / 0.34 (26305) SS BOND : bond 0.00885 / 0.58 ( 6) SS BOND : angle 2.03394 / 1.63 ( 12) hydrogen bonds : bond 0.03241 / 2.37 ( 938) hydrogen bonds : angle 4.65500 / 3.59 ( 2751) link_NAG-ASN : bond 0.00938 / 0.67 ( 7) link_NAG-ASN : angle 3.66789 / 3.26 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5896 Ramachandran restraints generated. 2948 Oldfield, 0 Emsley, 2948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5896 Ramachandran restraints generated. 2948 Oldfield, 0 Emsley, 2948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 2606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 187 time to evaluate : 0.555 Fit side-chains REVERT: C 690 ASP cc_start: 0.8059 (m-30) cc_final: 0.7833 (m-30) REVERT: D 126 ILE cc_start: 0.7014 (mp) cc_final: 0.6655 (mm) outliers start: 1 outliers final: 0 residues processed: 188 average time/residue: 0.0873 time to fit residues: 29.5556 Evaluate side-chains 154 residues out of total 2606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 204 optimal weight: 10.0000 chunk 67 optimal weight: 0.2980 chunk 222 optimal weight: 6.9990 chunk 252 optimal weight: 40.0000 chunk 229 optimal weight: 9.9990 chunk 102 optimal weight: 0.3980 chunk 26 optimal weight: 50.0000 chunk 41 optimal weight: 0.2980 chunk 244 optimal weight: 0.0670 chunk 273 optimal weight: 0.9990 chunk 92 optimal weight: 0.9980 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 650 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.085969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.076362 restraints weight = 101922.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.076299 restraints weight = 110015.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.076587 restraints weight = 111011.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.076756 restraints weight = 78765.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.076862 restraints weight = 74010.339| |-----------------------------------------------------------------------------| r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6868 moved from start: 0.4509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 19024 Z= 0.102 Angle : 0.518 9.426 26338 Z= 0.267 Chirality : 0.044 0.338 3372 Planarity : 0.004 0.069 3431 Dihedral : 4.196 29.038 3223 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.87 % Favored : 95.96 % Rotamer: Outliers : 0.08 % Allowed : 3.01 % Favored : 96.90 % 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: -0.01 (0.16), residues: 2948 helix: 1.87 (0.15), residues: 1224 sheet: -1.68 (0.29), residues: 271 loop : -1.37 (0.16), residues: 1453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 763 TYR 0.016 0.001 TYR C 456 PHE 0.014 0.001 PHE D 529 TRP 0.039 0.001 TRP A 247 HIS 0.005 0.001 HIS C 780 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 (19011) covalent geometry : angle 0.50702 / 0.26 (26305) SS BOND : bond 0.00527 / 0.35 ( 6) SS BOND : angle 1.84126 / 1.52 ( 12) hydrogen bonds : bond 0.02318 / 1.68 ( 938) hydrogen bonds : angle 4.05179 / 3.11 ( 2751) link_NAG-ASN : bond 0.00744 / 0.53 ( 7) link_NAG-ASN : angle 3.60971 / 2.79 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5896 Ramachandran restraints generated. 2948 Oldfield, 0 Emsley, 2948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5896 Ramachandran restraints generated. 2948 Oldfield, 0 Emsley, 2948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 194 time to evaluate : 0.766 Fit side-chains revert: symmetry clash REVERT: A 501 MET cc_start: 0.7930 (ttm) cc_final: 0.7675 (ttm) REVERT: B 358 MET cc_start: 0.4060 (ttt) cc_final: 0.3202 (ttm) REVERT: C 520 ASN cc_start: 0.7298 (p0) cc_final: 0.6394 (m110) REVERT: D 126 ILE cc_start: 0.6853 (mp) cc_final: 0.6555 (mm) outliers start: 1 outliers final: 0 residues processed: 195 average time/residue: 0.0947 time to fit residues: 33.2355 Evaluate side-chains 155 residues out of total 2606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 30 optimal weight: 30.0000 chunk 143 optimal weight: 4.9990 chunk 1 optimal weight: 20.0000 chunk 159 optimal weight: 9.9990 chunk 133 optimal weight: 20.0000 chunk 197 optimal weight: 5.9990 chunk 184 optimal weight: 6.9990 chunk 26 optimal weight: 50.0000 chunk 207 optimal weight: 5.9990 chunk 234 optimal weight: 10.0000 chunk 163 optimal weight: 8.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 650 ASN C 477 HIS C 650 ASN C 709 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.081386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.071153 restraints weight = 100943.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.071072 restraints weight = 155910.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.071465 restraints weight = 144084.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.071781 restraints weight = 94577.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.071921 restraints weight = 91206.476| |-----------------------------------------------------------------------------| r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.5565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.092 19024 Z= 0.305 Angle : 0.734 9.495 26338 Z= 0.398 Chirality : 0.049 0.377 3372 Planarity : 0.005 0.063 3431 Dihedral : 5.417 36.099 3223 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.39 % Favored : 92.40 % Rotamer: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.89 (0.15), residues: 2948 helix: 1.11 (0.15), residues: 1225 sheet: -2.20 (0.27), residues: 274 loop : -1.82 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 671 TYR 0.047 0.003 TYR D 731 PHE 0.043 0.004 PHE D 729 TRP 0.062 0.003 TRP A 247 HIS 0.012 0.002 HIS C 780 Details of bonding type rmsd/Z covalent geometry : bond 0.00681 / 0.31 (19011) covalent geometry : angle 0.72624 / 0.40 (26305) SS BOND : bond 0.00590 / 0.37 ( 6) SS BOND : angle 2.52991 / 2.04 ( 12) hydrogen bonds : bond 0.03910 / 2.88 ( 938) hydrogen bonds : angle 5.06912 / 3.87 ( 2751) link_NAG-ASN : bond 0.00847 / 0.60 ( 7) link_NAG-ASN : angle 3.50353 / 2.94 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5896 Ramachandran restraints generated. 2948 Oldfield, 0 Emsley, 2948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5896 Ramachandran restraints generated. 2948 Oldfield, 0 Emsley, 2948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 2606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 0.750 Fit side-chains REVERT: B 35 ILE cc_start: 0.7778 (mm) cc_final: 0.7271 (pt) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.0955 time to fit residues: 30.6323 Evaluate side-chains 147 residues out of total 2606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 110 optimal weight: 0.4980 chunk 103 optimal weight: 30.0000 chunk 78 optimal weight: 0.0000 chunk 47 optimal weight: 0.8980 chunk 199 optimal weight: 4.9990 chunk 145 optimal weight: 0.9980 chunk 232 optimal weight: 7.9990 chunk 228 optimal weight: 40.0000 chunk 106 optimal weight: 8.9990 chunk 118 optimal weight: 5.9990 chunk 196 optimal weight: 6.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 650 ASN C 650 ASN 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 = 0.083801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.073637 restraints weight = 100955.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.073296 restraints weight = 124847.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.073663 restraints weight = 124712.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.073811 restraints weight = 83321.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.073935 restraints weight = 74654.940| |-----------------------------------------------------------------------------| r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 moved from start: 0.5351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19024 Z= 0.117 Angle : 0.538 9.395 26338 Z= 0.281 Chirality : 0.044 0.340 3372 Planarity : 0.004 0.069 3431 Dihedral : 4.536 29.603 3223 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.17 % Favored : 95.66 % Rotamer: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % 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 (0.16), residues: 2948 helix: 1.66 (0.15), residues: 1227 sheet: -2.08 (0.28), residues: 252 loop : -1.65 (0.16), residues: 1469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 523 TYR 0.017 0.001 TYR A 703 PHE 0.019 0.001 PHE D 729 TRP 0.035 0.002 TRP B 772 HIS 0.003 0.001 HIS A 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (19011) covalent geometry : angle 0.53084 / 0.28 (26305) SS BOND : bond 0.00284 / 0.18 ( 6) SS BOND : angle 1.84065 / 1.63 ( 12) hydrogen bonds : bond 0.02593 / 1.89 ( 938) hydrogen bonds : angle 4.33002 / 3.32 ( 2751) link_NAG-ASN : bond 0.00740 / 0.53 ( 7) link_NAG-ASN : angle 2.81848 / 2.62 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5896 Ramachandran restraints generated. 2948 Oldfield, 0 Emsley, 2948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5896 Ramachandran restraints generated. 2948 Oldfield, 0 Emsley, 2948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 2606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 0.702 Fit side-chains REVERT: B 358 MET cc_start: 0.4095 (ttt) cc_final: 0.3738 (ttt) REVERT: C 520 ASN cc_start: 0.7261 (p0) cc_final: 0.6194 (m110) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.0919 time to fit residues: 29.5639 Evaluate side-chains 148 residues out of total 2606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 3 optimal weight: 30.0000 chunk 16 optimal weight: 7.9990 chunk 43 optimal weight: 20.0000 chunk 242 optimal weight: 0.0670 chunk 49 optimal weight: 0.8980 chunk 272 optimal weight: 0.9990 chunk 291 optimal weight: 1.9990 chunk 276 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 chunk 93 optimal weight: 0.3980 chunk 201 optimal weight: 0.9980 overall best weight: 0.6720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 650 ASN ** C 650 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 = 0.3910 r_free = 0.3910 target = 0.084828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.074590 restraints weight = 102479.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.074083 restraints weight = 123862.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.074480 restraints weight = 120503.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.074815 restraints weight = 82610.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.074922 restraints weight = 77454.467| |-----------------------------------------------------------------------------| r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6968 moved from start: 0.5233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 19024 Z= 0.099 Angle : 0.512 9.148 26338 Z= 0.264 Chirality : 0.043 0.329 3372 Planarity : 0.004 0.070 3431 Dihedral : 4.081 28.323 3223 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.61 % Favored : 95.22 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.16), residues: 2948 helix: 1.88 (0.15), residues: 1227 sheet: -1.84 (0.29), residues: 262 loop : -1.54 (0.16), residues: 1459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 397 TYR 0.016 0.001 TYR A 703 PHE 0.016 0.001 PHE C 554 TRP 0.021 0.001 TRP A 247 HIS 0.003 0.001 HIS A 780 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.10 (19011) covalent geometry : angle 0.50544 / 0.26 (26305) SS BOND : bond 0.00901 / 0.48 ( 6) SS BOND : angle 1.69231 / 1.54 ( 12) hydrogen bonds : bond 0.02333 / 1.70 ( 938) hydrogen bonds : angle 4.06563 / 3.11 ( 2751) link_NAG-ASN : bond 0.00675 / 0.48 ( 7) link_NAG-ASN : angle 2.62431 / 2.51 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5896 Ramachandran restraints generated. 2948 Oldfield, 0 Emsley, 2948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5896 Ramachandran restraints generated. 2948 Oldfield, 0 Emsley, 2948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.761 Fit side-chains REVERT: B 161 MET cc_start: 0.6229 (ttp) cc_final: 0.5899 (ttp) REVERT: B 358 MET cc_start: 0.4386 (ttt) cc_final: 0.4034 (ttt) REVERT: C 520 ASN cc_start: 0.7367 (p0) cc_final: 0.6462 (m110) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.0939 time to fit residues: 31.2349 Evaluate side-chains 153 residues out of total 2606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 42 optimal weight: 0.9990 chunk 152 optimal weight: 40.0000 chunk 99 optimal weight: 10.0000 chunk 163 optimal weight: 9.9990 chunk 210 optimal weight: 5.9990 chunk 1 optimal weight: 20.0000 chunk 230 optimal weight: 6.9990 chunk 57 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 108 optimal weight: 20.0000 chunk 120 optimal weight: 6.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 650 ASN C 650 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.082423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.072167 restraints weight = 102315.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.071534 restraints weight = 135687.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.072007 restraints weight = 127208.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.072405 restraints weight = 84735.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.072519 restraints weight = 80529.095| |-----------------------------------------------------------------------------| r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7097 moved from start: 0.5665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 19024 Z= 0.184 Angle : 0.587 9.175 26338 Z= 0.309 Chirality : 0.045 0.343 3372 Planarity : 0.004 0.066 3431 Dihedral : 4.544 31.496 3223 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.38 % Favored : 93.42 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % 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: -0.36 (0.16), residues: 2948 helix: 1.70 (0.15), residues: 1236 sheet: -2.13 (0.28), residues: 262 loop : -1.67 (0.16), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 671 TYR 0.032 0.002 TYR B 731 PHE 0.023 0.002 PHE A 533 TRP 0.044 0.002 TRP A 247 HIS 0.004 0.001 HIS A 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.18 (19011) covalent geometry : angle 0.58009 / 0.31 (26305) SS BOND : bond 0.00359 / 0.22 ( 6) SS BOND : angle 1.84733 / 1.62 ( 12) hydrogen bonds : bond 0.02908 / 2.14 ( 938) hydrogen bonds : angle 4.37102 / 3.33 ( 2751) link_NAG-ASN : bond 0.00743 / 0.53 ( 7) link_NAG-ASN : angle 2.86752 / 2.62 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5896 Ramachandran restraints generated. 2948 Oldfield, 0 Emsley, 2948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5896 Ramachandran restraints generated. 2948 Oldfield, 0 Emsley, 2948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 0.738 Fit side-chains REVERT: B 35 ILE cc_start: 0.7735 (mm) cc_final: 0.7242 (pt) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.0913 time to fit residues: 28.9919 Evaluate side-chains 145 residues out of total 2606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 278 optimal weight: 8.9990 chunk 132 optimal weight: 8.9990 chunk 91 optimal weight: 9.9990 chunk 65 optimal weight: 6.9990 chunk 266 optimal weight: 3.9990 chunk 279 optimal weight: 0.8980 chunk 205 optimal weight: 6.9990 chunk 127 optimal weight: 4.9990 chunk 137 optimal weight: 3.9990 chunk 249 optimal weight: 0.2980 chunk 169 optimal weight: 20.0000 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 650 ASN C 650 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.082839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.072339 restraints weight = 102685.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.072032 restraints weight = 119036.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.072455 restraints weight = 110587.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.072678 restraints weight = 75528.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.072827 restraints weight = 71500.276| |-----------------------------------------------------------------------------| r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7087 moved from start: 0.5779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19024 Z= 0.144 Angle : 0.545 9.237 26338 Z= 0.285 Chirality : 0.045 0.343 3372 Planarity : 0.004 0.069 3431 Dihedral : 4.404 30.241 3223 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.73 % Favored : 94.06 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % 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: -0.32 (0.16), residues: 2948 helix: 1.77 (0.15), residues: 1231 sheet: -2.10 (0.29), residues: 265 loop : -1.67 (0.16), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 671 TYR 0.023 0.002 TYR B 731 PHE 0.017 0.002 PHE C 753 TRP 0.031 0.002 TRP A 247 HIS 0.004 0.001 HIS A 780 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (19011) covalent geometry : angle 0.53816 / 0.28 (26305) SS BOND : bond 0.00290 / 0.19 ( 6) SS BOND : angle 1.66911 / 1.49 ( 12) hydrogen bonds : bond 0.02626 / 1.93 ( 938) hydrogen bonds : angle 4.28884 / 3.28 ( 2751) link_NAG-ASN : bond 0.00705 / 0.50 ( 7) link_NAG-ASN : angle 2.81050 / 2.61 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2587.16 seconds wall clock time: 45 minutes 26.64 seconds (2726.64 seconds total)