Starting phenix.real_space_refine on Fri Mar 6 07:55:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rz4_24750/03_2026/7rz4_24750.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rz4_24750/03_2026/7rz4_24750.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7rz4_24750/03_2026/7rz4_24750.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rz4_24750/03_2026/7rz4_24750.map" model { file = "/net/cci-nas-00/data/ceres_data/7rz4_24750/03_2026/7rz4_24750.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rz4_24750/03_2026/7rz4_24750.cif" } resolution = 3.6 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= 0.003 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: 6 Type Number sf(0) Gaussians P 16 5.49 5 S 142 5.16 5 C 18762 2.51 5 N 4678 2.21 5 O 5388 1.98 5 F 12 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28998 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 993, 7823 Classifications: {'peptide': 993} Link IDs: {'PCIS': 4, 'PTRANS': 23, 'TRANS': 965} Chain breaks: 3 Chain: "B" Number of atoms: 6254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 794, 6254 Classifications: {'peptide': 794} Link IDs: {'PCIS': 4, 'PTRANS': 19, 'TRANS': 770} Chain breaks: 1 Chain: "C" Number of atoms: 7823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 993, 7823 Classifications: {'peptide': 993} Link IDs: {'PCIS': 4, 'PTRANS': 23, 'TRANS': 965} Chain breaks: 3 Chain: "D" Number of atoms: 6254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 794, 6254 Classifications: {'peptide': 794} Link IDs: {'PCIS': 4, 'PTRANS': 19, 'TRANS': 770} Chain breaks: 1 Chain: "A" Number of atoms: 211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 211 Unusual residues: {'NAG': 1, 'PCW': 6, 'ZK1': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 155 Unresolved non-hydrogen angles: 183 Unresolved non-hydrogen dihedrals: 145 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PCW:plan-2': 2, 'PCW:plan-1': 3, 'PCW:plan-3': 3, 'PCW:plan-4': 3} Unresolved non-hydrogen planarities: 38 Chain: "B" Number of atoms: 211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 211 Unusual residues: {'NAG': 1, 'PCW': 6, 'ZK1': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 155 Unresolved non-hydrogen angles: 183 Unresolved non-hydrogen dihedrals: 145 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PCW:plan-2': 2, 'PCW:plan-1': 3, 'PCW:plan-3': 3, 'PCW:plan-4': 3} Unresolved non-hydrogen planarities: 38 Chain: "C" Number of atoms: 211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 211 Unusual residues: {'NAG': 1, 'PCW': 6, 'ZK1': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 155 Unresolved non-hydrogen angles: 183 Unresolved non-hydrogen dihedrals: 145 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PCW:plan-2': 2, 'PCW:plan-1': 3, 'PCW:plan-3': 3, 'PCW:plan-4': 3} Unresolved non-hydrogen planarities: 38 Chain: "D" Number of atoms: 211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 211 Unusual residues: {'NAG': 1, 'PCW': 6, 'ZK1': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 155 Unresolved non-hydrogen angles: 183 Unresolved non-hydrogen dihedrals: 145 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PCW:plan-1': 3, 'PCW:plan-3': 3, 'PCW:plan-4': 3, 'PCW:plan-2': 2} Unresolved non-hydrogen planarities: 38 Time building chain proxies: 6.48, per 1000 atoms: 0.22 Number of scatterers: 28998 At special positions: 0 Unit cell: (124.3, 168.3, 199.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 142 16.00 P 16 15.00 F 12 9.00 O 5388 8.00 N 4678 7.00 C 18762 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 315 " distance=2.03 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.03 Simple disulfide: pdb=" SG CYS A 890 " - pdb=" SG CYS A 900 " distance=2.03 Simple disulfide: pdb=" SG CYS B 63 " - pdb=" SG CYS B 315 " distance=2.04 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.03 Simple disulfide: pdb=" SG CYS C 63 " - pdb=" SG CYS C 315 " distance=2.03 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.03 Simple disulfide: pdb=" SG CYS C 890 " - pdb=" SG CYS C 900 " distance=2.03 Simple disulfide: pdb=" SG CYS D 63 " - pdb=" SG CYS D 315 " distance=2.04 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " 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 A1102 " - " ASN A 355 " " NAG B1102 " - " ASN B 355 " " NAG C1102 " - " ASN C 355 " " NAG D1103 " - " ASN D 355 " Time building additional restraints: 1.72 Conformation dependent library (CDL) restraints added in 1.3 seconds 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6568 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 40 sheets defined 50.4% alpha, 12.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 22 through 36 Processing helix chain 'A' and resid 54 through 69 Processing helix chain 'A' and resid 81 through 93 Processing helix chain 'A' and resid 117 through 129 Processing helix chain 'A' and resid 139 through 142 Processing helix chain 'A' and resid 143 through 157 removed outlier: 3.555A pdb=" N ALA A 153 " --> pdb=" O VAL A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 187 removed outlier: 3.601A pdb=" N PHE A 181 " --> pdb=" O TYR A 177 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS A 187 " --> pdb=" O ASP A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 211 removed outlier: 3.549A pdb=" N ASP A 206 " --> pdb=" O ASN A 202 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE A 211 " --> pdb=" O GLN A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 237 removed outlier: 4.207A pdb=" N PHE A 237 " --> pdb=" O LEU A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 264 removed outlier: 3.552A pdb=" N PHE A 258 " --> pdb=" O LEU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 302 removed outlier: 3.726A pdb=" N GLN A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 335 removed outlier: 3.620A pdb=" N GLN A 335 " --> pdb=" O ARG A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 419 removed outlier: 4.329A pdb=" N GLU A 419 " --> pdb=" O GLU A 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 416 through 419' Processing helix chain 'A' and resid 423 through 437 Processing helix chain 'A' and resid 461 through 469 Processing helix chain 'A' and resid 482 through 487 removed outlier: 3.556A pdb=" N GLU A 487 " --> pdb=" O LEU A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 519 Processing helix chain 'A' and resid 522 through 545 removed outlier: 3.716A pdb=" N VAL A 530 " --> pdb=" O TRP A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 585 Processing helix chain 'A' and resid 595 through 630 removed outlier: 3.735A pdb=" N TRP A 605 " --> pdb=" O VAL A 601 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE A 611 " --> pdb=" O PHE A 607 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE A 613 " --> pdb=" O THR A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 641 removed outlier: 3.554A pdb=" N LEU A 639 " --> pdb=" O SER A 635 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS A 641 " --> pdb=" O GLU A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 661 removed outlier: 3.750A pdb=" N PHE A 659 " --> pdb=" O THR A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 676 Processing helix chain 'A' and resid 685 through 696 removed outlier: 3.530A pdb=" N LYS A 695 " --> pdb=" O ALA A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 714 removed outlier: 3.580A pdb=" N GLN A 714 " --> pdb=" O GLU A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 756 removed outlier: 3.503A pdb=" N VAL A 746 " --> pdb=" O LEU A 742 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 768 Processing helix chain 'A' and resid 775 through 779 Processing helix chain 'A' and resid 792 through 822 removed outlier: 3.987A pdb=" N PHE A 796 " --> pdb=" O VAL A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 858 removed outlier: 3.721A pdb=" N LEU A 852 " --> pdb=" O GLY A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 897 Processing helix chain 'A' and resid 917 through 928 removed outlier: 3.505A pdb=" N MET A 924 " --> pdb=" O ASN A 920 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 952 removed outlier: 4.136A pdb=" N LEU A 933 " --> pdb=" O THR A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 956 through 990 removed outlier: 4.482A pdb=" N PHE A 960 " --> pdb=" O THR A 956 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLU A 987 " --> pdb=" O SER A 983 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N MET A 988 " --> pdb=" O ILE A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1035 removed outlier: 3.558A pdb=" N LEU A1015 " --> pdb=" O ALA A1011 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL A1025 " --> pdb=" O GLY A1021 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR A1026 " --> pdb=" O VAL A1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 36 Processing helix chain 'B' and resid 54 through 69 Processing helix chain 'B' and resid 78 through 80 No H-bonds generated for 'chain 'B' and resid 78 through 80' Processing helix chain 'B' and resid 81 through 93 removed outlier: 3.501A pdb=" N ILE B 85 " --> pdb=" O SER B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 129 removed outlier: 3.630A pdb=" N ILE B 125 " --> pdb=" O LEU B 121 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU B 126 " --> pdb=" O LEU B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 156 removed outlier: 3.803A pdb=" N ALA B 154 " --> pdb=" O LEU B 150 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLU B 155 " --> pdb=" O ASP B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 187 removed outlier: 3.591A pdb=" N THR B 176 " --> pdb=" O LYS B 172 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS B 187 " --> pdb=" O ASP B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 211 removed outlier: 3.671A pdb=" N ILE B 211 " --> pdb=" O GLN B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 264 removed outlier: 3.710A pdb=" N THR B 264 " --> pdb=" O GLU B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 302 removed outlier: 3.584A pdb=" N VAL B 289 " --> pdb=" O THR B 285 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLN B 290 " --> pdb=" O TYR B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 335 removed outlier: 3.862A pdb=" N GLU B 328 " --> pdb=" O GLY B 324 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG B 331 " --> pdb=" O VAL B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 419 removed outlier: 3.719A pdb=" N GLU B 419 " --> pdb=" O GLU B 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 416 through 419' Processing helix chain 'B' and resid 423 through 437 Processing helix chain 'B' and resid 463 through 469 Processing helix chain 'B' and resid 482 through 489 removed outlier: 3.645A pdb=" N GLU B 487 " --> pdb=" O LEU B 483 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N VAL B 488 " --> pdb=" O VAL B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 519 removed outlier: 3.780A pdb=" N LEU B 518 " --> pdb=" O PHE B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 547 Processing helix chain 'B' and resid 572 through 585 removed outlier: 3.611A pdb=" N LEU B 577 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N TRP B 578 " --> pdb=" O PHE B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 626 removed outlier: 3.603A pdb=" N VAL B 601 " --> pdb=" O SER B 597 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE B 611 " --> pdb=" O PHE B 607 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER B 614 " --> pdb=" O LEU B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 641 removed outlier: 3.709A pdb=" N LEU B 639 " --> pdb=" O SER B 635 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS B 641 " --> pdb=" O GLU B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 661 removed outlier: 3.613A pdb=" N PHE B 659 " --> pdb=" O THR B 655 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG B 661 " --> pdb=" O GLU B 657 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 676 removed outlier: 3.511A pdb=" N SER B 676 " --> pdb=" O THR B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 696 Processing helix chain 'B' and resid 706 through 714 removed outlier: 3.503A pdb=" N GLU B 713 " --> pdb=" O ASN B 709 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN B 714 " --> pdb=" O GLU B 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 756 removed outlier: 3.599A pdb=" N LEU B 751 " --> pdb=" O ASN B 747 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 768 removed outlier: 3.523A pdb=" N TYR B 768 " --> pdb=" O ASN B 764 " (cutoff:3.500A) Processing helix chain 'B' and resid 774 through 781 removed outlier: 3.650A pdb=" N SER B 778 " --> pdb=" O GLY B 774 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS B 781 " --> pdb=" O ASP B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 792 through 820 removed outlier: 3.995A pdb=" N PHE B 796 " --> pdb=" O VAL B 792 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA B 806 " --> pdb=" O GLY B 802 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 36 Processing helix chain 'C' and resid 54 through 69 Processing helix chain 'C' and resid 81 through 93 Processing helix chain 'C' and resid 117 through 129 Processing helix chain 'C' and resid 139 through 142 Processing helix chain 'C' and resid 143 through 157 removed outlier: 3.556A pdb=" N ALA C 153 " --> pdb=" O VAL C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 187 removed outlier: 3.601A pdb=" N PHE C 181 " --> pdb=" O TYR C 177 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS C 187 " --> pdb=" O ASP C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 211 removed outlier: 3.549A pdb=" N ASP C 206 " --> pdb=" O ASN C 202 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE C 211 " --> pdb=" O GLN C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 237 removed outlier: 4.208A pdb=" N PHE C 237 " --> pdb=" O LEU C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 264 removed outlier: 3.551A pdb=" N PHE C 258 " --> pdb=" O LEU C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 302 removed outlier: 3.726A pdb=" N GLN C 290 " --> pdb=" O TYR C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 335 removed outlier: 3.621A pdb=" N GLN C 335 " --> pdb=" O ARG C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 419 removed outlier: 4.329A pdb=" N GLU C 419 " --> pdb=" O GLU C 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 416 through 419' Processing helix chain 'C' and resid 423 through 437 Processing helix chain 'C' and resid 461 through 469 Processing helix chain 'C' and resid 482 through 487 removed outlier: 3.556A pdb=" N GLU C 487 " --> pdb=" O LEU C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 515 through 519 Processing helix chain 'C' and resid 522 through 545 removed outlier: 3.716A pdb=" N VAL C 530 " --> pdb=" O TRP C 526 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 585 Processing helix chain 'C' and resid 595 through 630 removed outlier: 3.735A pdb=" N TRP C 605 " --> pdb=" O VAL C 601 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE C 611 " --> pdb=" O PHE C 607 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE C 613 " --> pdb=" O THR C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 635 through 641 removed outlier: 3.553A pdb=" N LEU C 639 " --> pdb=" O SER C 635 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS C 641 " --> pdb=" O GLU C 637 " (cutoff:3.500A) Processing helix chain 'C' and resid 653 through 661 removed outlier: 3.749A pdb=" N PHE C 659 " --> pdb=" O THR C 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 676 Processing helix chain 'C' and resid 685 through 696 removed outlier: 3.531A pdb=" N LYS C 695 " --> pdb=" O ALA C 691 " (cutoff:3.500A) Processing helix chain 'C' and resid 706 through 714 removed outlier: 3.580A pdb=" N GLN C 714 " --> pdb=" O GLU C 710 " (cutoff:3.500A) Processing helix chain 'C' and resid 742 through 756 removed outlier: 3.503A pdb=" N VAL C 746 " --> pdb=" O LEU C 742 " (cutoff:3.500A) Processing helix chain 'C' and resid 757 through 768 Processing helix chain 'C' and resid 775 through 779 Processing helix chain 'C' and resid 792 through 822 removed outlier: 3.987A pdb=" N PHE C 796 " --> pdb=" O VAL C 792 " (cutoff:3.500A) Processing helix chain 'C' and resid 832 through 858 removed outlier: 3.722A pdb=" N LEU C 852 " --> pdb=" O GLY C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 893 through 897 Processing helix chain 'C' and resid 917 through 928 removed outlier: 3.505A pdb=" N MET C 924 " --> pdb=" O ASN C 920 " (cutoff:3.500A) Processing helix chain 'C' and resid 929 through 952 removed outlier: 4.137A pdb=" N LEU C 933 " --> pdb=" O THR C 929 " (cutoff:3.500A) Processing helix chain 'C' and resid 956 through 990 removed outlier: 4.481A pdb=" N PHE C 960 " --> pdb=" O THR C 956 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLU C 987 " --> pdb=" O SER C 983 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N MET C 988 " --> pdb=" O ILE C 984 " (cutoff:3.500A) Processing helix chain 'C' and resid 1004 through 1035 removed outlier: 3.559A pdb=" N LEU C1015 " --> pdb=" O ALA C1011 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL C1025 " --> pdb=" O GLY C1021 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR C1026 " --> pdb=" O VAL C1022 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 36 Processing helix chain 'D' and resid 54 through 69 Processing helix chain 'D' and resid 78 through 80 No H-bonds generated for 'chain 'D' and resid 78 through 80' Processing helix chain 'D' and resid 81 through 93 removed outlier: 3.502A pdb=" N ILE D 85 " --> pdb=" O SER D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 129 removed outlier: 3.630A pdb=" N ILE D 125 " --> pdb=" O LEU D 121 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU D 126 " --> pdb=" O LEU D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 156 removed outlier: 3.803A pdb=" N ALA D 154 " --> pdb=" O LEU D 150 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLU D 155 " --> pdb=" O ASP D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 187 removed outlier: 3.590A pdb=" N THR D 176 " --> pdb=" O LYS D 172 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS D 187 " --> pdb=" O ASP D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 211 removed outlier: 3.671A pdb=" N ILE D 211 " --> pdb=" O GLN D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 264 removed outlier: 3.710A pdb=" N THR D 264 " --> pdb=" O GLU D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 302 removed outlier: 3.585A pdb=" N VAL D 289 " --> pdb=" O THR D 285 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLN D 290 " --> pdb=" O TYR D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 335 removed outlier: 3.863A pdb=" N GLU D 328 " --> pdb=" O GLY D 324 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG D 331 " --> pdb=" O VAL D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 419 removed outlier: 3.720A pdb=" N GLU D 419 " --> pdb=" O GLU D 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 416 through 419' Processing helix chain 'D' and resid 423 through 437 Processing helix chain 'D' and resid 463 through 469 Processing helix chain 'D' and resid 482 through 489 removed outlier: 3.645A pdb=" N GLU D 487 " --> pdb=" O LEU D 483 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N VAL D 488 " --> pdb=" O VAL D 484 " (cutoff:3.500A) Processing helix chain 'D' and resid 515 through 519 removed outlier: 3.779A pdb=" N LEU D 518 " --> pdb=" O PHE D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 547 Processing helix chain 'D' and resid 572 through 585 removed outlier: 3.611A pdb=" N LEU D 577 " --> pdb=" O ILE D 573 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N TRP D 578 " --> pdb=" O PHE D 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 595 through 626 removed outlier: 3.603A pdb=" N VAL D 601 " --> pdb=" O SER D 597 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE D 611 " --> pdb=" O PHE D 607 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER D 614 " --> pdb=" O LEU D 610 " (cutoff:3.500A) Processing helix chain 'D' and resid 635 through 641 removed outlier: 3.709A pdb=" N LEU D 639 " --> pdb=" O SER D 635 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS D 641 " --> pdb=" O GLU D 637 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 661 removed outlier: 3.614A pdb=" N PHE D 659 " --> pdb=" O THR D 655 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG D 661 " --> pdb=" O GLU D 657 " (cutoff:3.500A) Processing helix chain 'D' and resid 664 through 676 removed outlier: 3.511A pdb=" N SER D 676 " --> pdb=" O THR D 672 " (cutoff:3.500A) Processing helix chain 'D' and resid 685 through 696 Processing helix chain 'D' and resid 706 through 714 removed outlier: 3.503A pdb=" N GLU D 713 " --> pdb=" O ASN D 709 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLN D 714 " --> pdb=" O GLU D 710 " (cutoff:3.500A) Processing helix chain 'D' and resid 742 through 756 removed outlier: 3.599A pdb=" N LEU D 751 " --> pdb=" O ASN D 747 " (cutoff:3.500A) Processing helix chain 'D' and resid 757 through 768 removed outlier: 3.522A pdb=" N TYR D 768 " --> pdb=" O ASN D 764 " (cutoff:3.500A) Processing helix chain 'D' and resid 774 through 781 removed outlier: 3.651A pdb=" N SER D 778 " --> pdb=" O GLY D 774 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS D 781 " --> pdb=" O ASP D 777 " (cutoff:3.500A) Processing helix chain 'D' and resid 792 through 820 removed outlier: 3.995A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA D 806 " --> pdb=" O GLY D 802 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 50 removed outlier: 4.409A pdb=" N ALA A 72 " --> pdb=" O GLN A 13 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ILE A 73 " --> pdb=" O ILE A 97 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N PHE A 96 " --> pdb=" O ILE A 111 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 159 through 164 removed outlier: 3.554A pdb=" N TYR A 137 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N ARG A 191 " --> pdb=" O LYS A 132 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N PHE A 245 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N VAL A 242 " --> pdb=" O LEU A 363 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 338 through 339 removed outlier: 3.836A pdb=" N VAL A 338 " --> pdb=" O ILE A 345 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS A 346 " --> pdb=" O ILE A 354 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 372 through 374 removed outlier: 3.532A pdb=" N VAL A 381 " --> pdb=" O TYR A 373 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 440 through 444 Processing sheet with id=AA6, first strand: chain 'A' and resid 407 through 408 Processing sheet with id=AA7, first strand: chain 'A' and resid 489 through 491 Processing sheet with id=AA8, first strand: chain 'A' and resid 496 through 498 removed outlier: 4.080A pdb=" N MET A 496 " --> pdb=" O TYR A 732 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU A 498 " --> pdb=" O LYS A 730 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 646 through 648 removed outlier: 6.673A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 9.506A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 8.678A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 900 through 902 removed outlier: 4.013A pdb=" N SER A 875 " --> pdb=" O LEU A 870 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N GLU A 866 " --> pdb=" O LYS A 879 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N SER A 881 " --> pdb=" O LEU A 864 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N LEU A 864 " --> pdb=" O SER A 881 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N HIS A 883 " --> pdb=" O LEU A 862 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU A 862 " --> pdb=" O HIS A 883 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 11 through 13 Processing sheet with id=AB3, first strand: chain 'B' and resid 47 through 50 removed outlier: 6.568A pdb=" N ILE B 73 " --> pdb=" O ILE B 97 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N PHE B 96 " --> pdb=" O ILE B 111 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 159 through 164 removed outlier: 5.398A pdb=" N ARG B 191 " --> pdb=" O LYS B 132 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N TYR B 220 " --> pdb=" O SER B 243 " (cutoff:3.500A) removed outlier: 8.798A pdb=" N PHE B 245 " --> pdb=" O TYR B 220 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N ILE B 222 " --> pdb=" O PHE B 245 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N VAL B 242 " --> pdb=" O LEU B 363 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ILE B 358 " --> pdb=" O TYR B 373 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N TYR B 373 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ILE B 360 " --> pdb=" O ILE B 371 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU B 362 " --> pdb=" O ARG B 369 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 338 through 339 removed outlier: 3.786A pdb=" N VAL B 338 " --> pdb=" O ILE B 345 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LYS B 346 " --> pdb=" O ILE B 354 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 439 through 444 removed outlier: 6.573A pdb=" N VAL B 395 " --> pdb=" O LYS B 441 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N THR B 443 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N VAL B 397 " --> pdb=" O THR B 443 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AB8, first strand: chain 'B' and resid 451 through 453 removed outlier: 3.711A pdb=" N ALA B 452 " --> pdb=" O ASN B 461 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 490 through 491 Processing sheet with id=AC1, first strand: chain 'B' and resid 496 through 498 removed outlier: 4.119A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 646 through 648 removed outlier: 6.878A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 9.559A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 42 through 50 removed outlier: 4.409A pdb=" N ALA C 72 " --> pdb=" O GLN C 13 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ILE C 73 " --> pdb=" O ILE C 97 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N PHE C 96 " --> pdb=" O ILE C 111 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 159 through 164 removed outlier: 3.554A pdb=" N TYR C 137 " --> pdb=" O ILE C 163 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N ARG C 191 " --> pdb=" O LYS C 132 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N PHE C 245 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N VAL C 242 " --> pdb=" O LEU C 363 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 338 through 339 removed outlier: 3.836A pdb=" N VAL C 338 " --> pdb=" O ILE C 345 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS C 346 " --> pdb=" O ILE C 354 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 372 through 374 removed outlier: 3.533A pdb=" N VAL C 381 " --> pdb=" O TYR C 373 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 440 through 444 Processing sheet with id=AC8, first strand: chain 'C' and resid 407 through 408 Processing sheet with id=AC9, first strand: chain 'C' and resid 489 through 491 Processing sheet with id=AD1, first strand: chain 'C' and resid 496 through 498 removed outlier: 4.080A pdb=" N MET C 496 " --> pdb=" O TYR C 732 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU C 498 " --> pdb=" O LYS C 730 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 646 through 648 removed outlier: 6.672A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 9.507A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) removed outlier: 8.678A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 900 through 902 removed outlier: 4.012A pdb=" N SER C 875 " --> pdb=" O LEU C 870 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N GLU C 866 " --> pdb=" O LYS C 879 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N SER C 881 " --> pdb=" O LEU C 864 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N LEU C 864 " --> pdb=" O SER C 881 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N HIS C 883 " --> pdb=" O LEU C 862 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU C 862 " --> pdb=" O HIS C 883 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 11 through 13 Processing sheet with id=AD5, first strand: chain 'D' and resid 47 through 50 removed outlier: 6.568A pdb=" N ILE D 73 " --> pdb=" O ILE D 97 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N PHE D 96 " --> pdb=" O ILE D 111 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 159 through 164 removed outlier: 5.399A pdb=" N ARG D 191 " --> pdb=" O LYS D 132 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N TYR D 220 " --> pdb=" O SER D 243 " (cutoff:3.500A) removed outlier: 8.797A pdb=" N PHE D 245 " --> pdb=" O TYR D 220 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N ILE D 222 " --> pdb=" O PHE D 245 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N VAL D 242 " --> pdb=" O LEU D 363 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ILE D 358 " --> pdb=" O TYR D 373 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N TYR D 373 " --> pdb=" O ILE D 358 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ILE D 360 " --> pdb=" O ILE D 371 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU D 362 " --> pdb=" O ARG D 369 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 338 through 339 removed outlier: 3.786A pdb=" N VAL D 338 " --> pdb=" O ILE D 345 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LYS D 346 " --> pdb=" O ILE D 354 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 439 through 444 removed outlier: 6.573A pdb=" N VAL D 395 " --> pdb=" O LYS D 441 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N THR D 443 " --> pdb=" O VAL D 395 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N VAL D 397 " --> pdb=" O THR D 443 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AE1, first strand: chain 'D' and resid 451 through 453 removed outlier: 3.712A pdb=" N ALA D 452 " --> pdb=" O ASN D 461 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 490 through 491 Processing sheet with id=AE3, first strand: chain 'D' and resid 496 through 498 removed outlier: 4.119A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 646 through 648 removed outlier: 6.878A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 9.559A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) 1414 hydrogen bonds defined for protein. 4140 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: 5.62 Time building geometry restraints manager: 2.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4646 1.32 - 1.46: 8707 1.46 - 1.59: 15969 1.59 - 1.73: 24 1.73 - 1.86: 236 Bond restraints: 29582 Sorted by residual: bond pdb=" CAT ZK1 B1101 " pdb=" OAA ZK1 B1101 " ideal model delta sigma weight residual 1.214 1.401 -0.187 2.00e-02 2.50e+03 8.70e+01 bond pdb=" CAT ZK1 D1102 " pdb=" OAA ZK1 D1102 " ideal model delta sigma weight residual 1.214 1.399 -0.185 2.00e-02 2.50e+03 8.59e+01 bond pdb=" CAT ZK1 C1101 " pdb=" OAA ZK1 C1101 " ideal model delta sigma weight residual 1.214 1.399 -0.185 2.00e-02 2.50e+03 8.56e+01 bond pdb=" CAT ZK1 A1101 " pdb=" OAA ZK1 A1101 " ideal model delta sigma weight residual 1.214 1.398 -0.184 2.00e-02 2.50e+03 8.50e+01 bond pdb=" CAU ZK1 B1101 " pdb=" OAB ZK1 B1101 " ideal model delta sigma weight residual 1.215 1.398 -0.183 2.00e-02 2.50e+03 8.39e+01 ... (remaining 29577 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.82: 39104 2.82 - 5.63: 547 5.63 - 8.45: 129 8.45 - 11.27: 46 11.27 - 14.09: 20 Bond angle restraints: 39846 Sorted by residual: angle pdb=" C ASP D 378 " pdb=" N LYS D 379 " pdb=" CA LYS D 379 " ideal model delta sigma weight residual 121.19 128.95 -7.76 1.59e+00 3.96e-01 2.38e+01 angle pdb=" C ASP B 378 " pdb=" N LYS B 379 " pdb=" CA LYS B 379 " ideal model delta sigma weight residual 121.19 128.89 -7.70 1.59e+00 3.96e-01 2.35e+01 angle pdb=" C ALA C 928 " pdb=" N THR C 929 " pdb=" CA THR C 929 " ideal model delta sigma weight residual 120.26 126.34 -6.08 1.34e+00 5.57e-01 2.06e+01 angle pdb=" C ALA A 928 " pdb=" N THR A 929 " pdb=" CA THR A 929 " ideal model delta sigma weight residual 120.26 126.30 -6.04 1.34e+00 5.57e-01 2.03e+01 angle pdb=" N ASP C 519 " pdb=" CA ASP C 519 " pdb=" C ASP C 519 " ideal model delta sigma weight residual 109.81 119.47 -9.66 2.21e+00 2.05e-01 1.91e+01 ... (remaining 39841 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 17380 35.95 - 71.90: 336 71.90 - 107.86: 36 107.86 - 143.81: 3 143.81 - 179.76: 9 Dihedral angle restraints: 17764 sinusoidal: 7476 harmonic: 10288 Sorted by residual: dihedral pdb=" CA ASP C 378 " pdb=" C ASP C 378 " pdb=" N LYS C 379 " pdb=" CA LYS C 379 " ideal model delta harmonic sigma weight residual -180.00 -140.62 -39.38 0 5.00e+00 4.00e-02 6.20e+01 dihedral pdb=" CA ASP A 378 " pdb=" C ASP A 378 " pdb=" N LYS A 379 " pdb=" CA LYS A 379 " ideal model delta harmonic sigma weight residual -180.00 -140.67 -39.33 0 5.00e+00 4.00e-02 6.19e+01 dihedral pdb=" CA ASP B 378 " pdb=" C ASP B 378 " pdb=" N LYS B 379 " pdb=" CA LYS B 379 " ideal model delta harmonic sigma weight residual -180.00 -142.16 -37.84 0 5.00e+00 4.00e-02 5.73e+01 ... (remaining 17761 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.133: 4278 0.133 - 0.265: 74 0.265 - 0.398: 0 0.398 - 0.530: 0 0.530 - 0.663: 2 Chirality restraints: 4354 Sorted by residual: chirality pdb=" C1 NAG B1102 " pdb=" ND2 ASN B 355 " pdb=" C2 NAG B1102 " pdb=" O5 NAG B1102 " both_signs ideal model delta sigma weight residual False -2.40 -1.74 -0.66 2.00e-01 2.50e+01 1.10e+01 chirality pdb=" C1 NAG D1103 " pdb=" ND2 ASN D 355 " pdb=" C2 NAG D1103 " pdb=" O5 NAG D1103 " both_signs ideal model delta sigma weight residual False -2.40 -1.82 -0.58 2.00e-01 2.50e+01 8.37e+00 chirality pdb=" CG LEU C 989 " pdb=" CB LEU C 989 " pdb=" CD1 LEU C 989 " pdb=" CD2 LEU C 989 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.41e+00 ... (remaining 4351 not shown) Planarity restraints: 4964 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 98 " -0.057 5.00e-02 4.00e+02 8.62e-02 1.19e+01 pdb=" N PRO D 99 " 0.149 5.00e-02 4.00e+02 pdb=" CA PRO D 99 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO D 99 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 98 " 0.056 5.00e-02 4.00e+02 8.59e-02 1.18e+01 pdb=" N PRO B 99 " -0.149 5.00e-02 4.00e+02 pdb=" CA PRO B 99 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO B 99 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 98 " -0.056 5.00e-02 4.00e+02 8.55e-02 1.17e+01 pdb=" N PRO A 99 " 0.148 5.00e-02 4.00e+02 pdb=" CA PRO A 99 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO A 99 " -0.046 5.00e-02 4.00e+02 ... (remaining 4961 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 9052 2.84 - 3.35: 24474 3.35 - 3.87: 43601 3.87 - 4.38: 49459 4.38 - 4.90: 88939 Nonbonded interactions: 215525 Sorted by model distance: nonbonded pdb=" O MET C 33 " pdb=" OG SER C 37 " model vdw 2.325 3.040 nonbonded pdb=" O MET A 33 " pdb=" OG SER A 37 " model vdw 2.325 3.040 nonbonded pdb=" OH TYR D 77 " pdb=" O PHE D 101 " model vdw 2.346 3.040 nonbonded pdb=" OH TYR B 77 " pdb=" O PHE B 101 " model vdw 2.346 3.040 nonbonded pdb=" OG SER C 544 " pdb=" ND2 ASN C 569 " model vdw 2.357 3.120 ... (remaining 215520 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = (chain 'B' and (resid 10 through 820 or resid 1104 through 1105 or (resid 1106 a \ nd (name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name \ C19)) or (resid 1107 through 1108 and (name C13 or name C14 or name C15 or name \ C16 or name C17 or name C18 or name C19 or name C20 or name C21 or name C22 or \ name C23)))) selection = (chain 'D' and (resid 10 through 820 or (resid 1104 and (name N or name C1 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 o \ r name C18 or name C19 or name C2 or name C20 or name C3 or name C31 or name C32 \ or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name \ C39 or name C4 or name C40 or name C41 or name C42 or name C43 or name C44 or n \ ame C45 or name C5 or name C6 or name C7 or name C8 or name O11 or name O1P or n \ ame O2 or name O2P or name O3 or name O31 or name O3P or name O4P or name P )) o \ r (resid 1105 and (name N or name C1 or name C11 or name C12 or name C13 or name \ C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C2 or n \ ame C3 or name C31 or name C32 or name C33 or name C34 or name C35 or name C36 o \ r name C37 or name C38 or name C39 or name C4 or name C40 or name C41 or name C4 \ 2 or name C43 or name C44 or name C5 or name C6 or name C7 or name C8 or name O1 \ 1 or name O1P or name O2 or name O2P or name O3 or name O31 or name O3P or name \ O4P or name P )) or (resid 1106 and (name C13 or name C14 or name C15 or name C1 \ 6 or name C17 or name C18 or name C19)) or (resid 1107 through 1108 and (name C1 \ 3 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or nam \ e C20 or name C21 or name C22 or name C23)))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.430 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 25.170 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 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 : 0.007 0.187 29596 Z= 0.370 Angle : 0.983 15.266 39878 Z= 0.472 Chirality : 0.050 0.663 4354 Planarity : 0.006 0.086 4960 Dihedral : 14.069 179.761 11166 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.26 % Allowed : 4.33 % Favored : 95.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -3.94 (0.10), residues: 3550 helix: -3.58 (0.06), residues: 1700 sheet: 0.10 (0.24), residues: 456 loop : -2.01 (0.12), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 485 TYR 0.024 0.002 TYR B 177 PHE 0.021 0.002 PHE A 245 TRP 0.027 0.003 TRP D 323 HIS 0.011 0.002 HIS D 93 Details of bonding type rmsd covalent geometry : bond 0.00735 (29582) covalent geometry : angle 0.97361 (39846) SS BOND : bond 0.00286 ( 10) SS BOND : angle 0.52711 ( 20) hydrogen bonds : bond 0.32613 ( 1414) hydrogen bonds : angle 8.52550 ( 4140) link_NAG-ASN : bond 0.01816 ( 4) link_NAG-ASN : angle 7.78925 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 717 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 709 time to evaluate : 1.187 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 SER cc_start: 0.8758 (m) cc_final: 0.8405 (p) REVERT: A 591 ILE cc_start: 0.5789 (OUTLIER) cc_final: 0.5539 (pp) REVERT: A 638 ASP cc_start: 0.8505 (m-30) cc_final: 0.8089 (m-30) REVERT: A 663 LYS cc_start: 0.8311 (mtmt) cc_final: 0.8039 (mptt) REVERT: A 705 GLU cc_start: 0.7190 (mm-30) cc_final: 0.6908 (mm-30) REVERT: A 989 LEU cc_start: 0.8017 (tm) cc_final: 0.7734 (tp) REVERT: B 26 TYR cc_start: 0.8172 (t80) cc_final: 0.7806 (t80) REVERT: B 41 PHE cc_start: 0.5709 (p90) cc_final: 0.5413 (p90) REVERT: B 42 ARG cc_start: 0.6417 (mtp-110) cc_final: 0.5800 (mpt180) REVERT: B 293 THR cc_start: 0.7349 (m) cc_final: 0.7148 (p) REVERT: B 629 MET cc_start: 0.6394 (mtm) cc_final: 0.5982 (mmt) REVERT: B 712 ILE cc_start: 0.8716 (mm) cc_final: 0.8469 (mt) REVERT: C 297 ARG cc_start: 0.6322 (ttm170) cc_final: 0.6109 (ttm170) REVERT: C 373 TYR cc_start: 0.7949 (p90) cc_final: 0.7603 (p90) REVERT: C 511 LYS cc_start: 0.8277 (tttm) cc_final: 0.8022 (ttpt) REVERT: C 597 SER cc_start: 0.8472 (p) cc_final: 0.8100 (t) REVERT: C 642 GLN cc_start: 0.8075 (tm-30) cc_final: 0.7745 (tm-30) REVERT: C 663 LYS cc_start: 0.8631 (mtmt) cc_final: 0.8262 (mptt) REVERT: C 859 ASP cc_start: 0.6787 (p0) cc_final: 0.6252 (m-30) REVERT: C 866 GLU cc_start: 0.6576 (tt0) cc_final: 0.6273 (pt0) REVERT: C 924 MET cc_start: 0.7243 (mmt) cc_final: 0.6656 (mmt) REVERT: C 983 SER cc_start: 0.8032 (m) cc_final: 0.7248 (p) REVERT: C 1023 MET cc_start: 0.6490 (mtt) cc_final: 0.6261 (mtp) REVERT: D 34 VAL cc_start: 0.7926 (t) cc_final: 0.7702 (m) REVERT: D 172 LYS cc_start: 0.7960 (mtmm) cc_final: 0.7744 (mtpp) REVERT: D 266 GLU cc_start: 0.7096 (mp0) cc_final: 0.6344 (mm-30) REVERT: D 438 PHE cc_start: 0.6871 (p90) cc_final: 0.6618 (p90) REVERT: D 515 PHE cc_start: 0.8569 (m-10) cc_final: 0.8274 (m-80) outliers start: 8 outliers final: 1 residues processed: 715 average time/residue: 0.2215 time to fit residues: 237.1513 Evaluate side-chains 351 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 349 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 882 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.1980 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 ASN A 311 ASN A 642 GLN A 873 ASN A 874 GLN ** A 883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 920 ASN A 947 ASN ** B 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 GLN B 60 ASN B 318 ASN B 344 ASN B 587 GLN B 764 ASN C 10 ASN C 46 HIS C 170 ASN C 311 ASN C 873 ASN C 874 GLN C 920 ASN C 947 ASN D 318 ASN D 344 ASN D 508 GLN D 586 GLN D 587 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.150035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.115005 restraints weight = 41779.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.112720 restraints weight = 42379.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.114670 restraints weight = 42578.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.115193 restraints weight = 27213.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.117004 restraints weight = 24536.299| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 29596 Z= 0.142 Angle : 0.565 13.290 39878 Z= 0.300 Chirality : 0.042 0.311 4354 Planarity : 0.005 0.077 4960 Dihedral : 13.955 179.859 4582 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.77 % Allowed : 8.73 % Favored : 89.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % 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: -0.75 (0.13), residues: 3550 helix: 0.04 (0.11), residues: 1734 sheet: 0.47 (0.24), residues: 496 loop : -1.52 (0.14), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 178 TYR 0.022 0.002 TYR C 523 PHE 0.030 0.002 PHE D 546 TRP 0.018 0.002 TRP A 262 HIS 0.006 0.001 HIS C 46 Details of bonding type rmsd covalent geometry : bond 0.00304 (29582) covalent geometry : angle 0.55138 (39846) SS BOND : bond 0.00230 ( 10) SS BOND : angle 0.89017 ( 20) hydrogen bonds : bond 0.06192 ( 1414) hydrogen bonds : angle 4.19499 ( 4140) link_NAG-ASN : bond 0.01471 ( 4) link_NAG-ASN : angle 7.07789 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 377 time to evaluate : 1.000 Fit side-chains revert: symmetry clash REVERT: A 44 THR cc_start: 0.8234 (p) cc_final: 0.7961 (m) REVERT: A 297 ARG cc_start: 0.6221 (ttm170) cc_final: 0.5361 (ttp80) REVERT: A 591 ILE cc_start: 0.6140 (OUTLIER) cc_final: 0.5814 (pp) REVERT: A 642 GLN cc_start: 0.7845 (OUTLIER) cc_final: 0.7589 (pp30) REVERT: A 716 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.8085 (mtmt) REVERT: A 719 ASP cc_start: 0.8176 (p0) cc_final: 0.7200 (p0) REVERT: A 984 ILE cc_start: 0.7683 (mt) cc_final: 0.7432 (mt) REVERT: B 26 TYR cc_start: 0.7984 (t80) cc_final: 0.7469 (t80) REVERT: B 42 ARG cc_start: 0.6193 (mtp-110) cc_final: 0.5800 (mpt180) REVERT: B 195 ASP cc_start: 0.7551 (t0) cc_final: 0.7132 (t70) REVERT: B 414 MET cc_start: 0.5472 (mmt) cc_final: 0.5270 (mmt) REVERT: B 473 ASP cc_start: 0.6321 (t0) cc_final: 0.6081 (t0) REVERT: B 649 THR cc_start: 0.9167 (p) cc_final: 0.8948 (p) REVERT: C 323 TRP cc_start: 0.7578 (p-90) cc_final: 0.6863 (p-90) REVERT: C 373 TYR cc_start: 0.7987 (p90) cc_final: 0.7675 (p90) REVERT: C 490 ASP cc_start: 0.7814 (OUTLIER) cc_final: 0.7607 (m-30) REVERT: C 511 LYS cc_start: 0.8258 (tttm) cc_final: 0.8049 (ttpt) REVERT: C 642 GLN cc_start: 0.7817 (tm-30) cc_final: 0.7605 (tm-30) REVERT: C 663 LYS cc_start: 0.8567 (mtmt) cc_final: 0.8278 (mptt) REVERT: C 866 GLU cc_start: 0.6635 (tt0) cc_final: 0.5831 (mp0) REVERT: C 888 ARG cc_start: 0.6102 (mpt180) cc_final: 0.5840 (mpt180) REVERT: C 924 MET cc_start: 0.6887 (mmt) cc_final: 0.6459 (mmt) REVERT: C 983 SER cc_start: 0.8196 (m) cc_final: 0.7556 (p) REVERT: C 1029 MET cc_start: 0.5631 (mtp) cc_final: 0.5309 (mtm) outliers start: 54 outliers final: 25 residues processed: 415 average time/residue: 0.2022 time to fit residues: 131.7807 Evaluate side-chains 323 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 294 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 642 GLN Chi-restraints excluded: chain A residue 644 GLU Chi-restraints excluded: chain A residue 716 LYS Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain A residue 907 MET Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 525 ILE Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 170 ASN Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 490 ASP Chi-restraints excluded: chain C residue 748 LEU Chi-restraints excluded: chain C residue 773 CYS Chi-restraints excluded: chain C residue 789 LEU Chi-restraints excluded: chain C residue 790 SER Chi-restraints excluded: chain C residue 907 MET Chi-restraints excluded: chain C residue 1022 VAL Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 199 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 223 optimal weight: 0.8980 chunk 181 optimal weight: 5.9990 chunk 31 optimal weight: 0.0980 chunk 146 optimal weight: 1.9990 chunk 176 optimal weight: 0.6980 chunk 254 optimal weight: 0.8980 chunk 147 optimal weight: 0.9990 chunk 267 optimal weight: 3.9990 chunk 56 optimal weight: 0.5980 chunk 76 optimal weight: 3.9990 chunk 244 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 ASN A 642 GLN ** A 883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 46 HIS ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 10 ASN D 60 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.148961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.114070 restraints weight = 41584.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.113604 restraints weight = 41558.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.114043 restraints weight = 43274.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.114924 restraints weight = 25613.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.116143 restraints weight = 22250.515| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.3727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 29596 Z= 0.119 Angle : 0.500 13.070 39878 Z= 0.262 Chirality : 0.040 0.296 4354 Planarity : 0.004 0.069 4960 Dihedral : 12.720 178.213 4582 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.07 % Allowed : 10.30 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % 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: 0.63 (0.14), residues: 3550 helix: 1.63 (0.12), residues: 1728 sheet: 0.54 (0.24), residues: 492 loop : -1.28 (0.15), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 660 TYR 0.021 0.001 TYR A 980 PHE 0.020 0.001 PHE A 999 TRP 0.015 0.001 TRP A 262 HIS 0.004 0.001 HIS D 219 Details of bonding type rmsd covalent geometry : bond 0.00257 (29582) covalent geometry : angle 0.48572 (39846) SS BOND : bond 0.00342 ( 10) SS BOND : angle 0.78414 ( 20) hydrogen bonds : bond 0.05002 ( 1414) hydrogen bonds : angle 3.76500 ( 4140) link_NAG-ASN : bond 0.01693 ( 4) link_NAG-ASN : angle 6.92514 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 314 time to evaluate : 1.090 Fit side-chains revert: symmetry clash REVERT: A 591 ILE cc_start: 0.6312 (OUTLIER) cc_final: 0.5879 (pp) REVERT: A 642 GLN cc_start: 0.7423 (OUTLIER) cc_final: 0.7202 (pp30) REVERT: A 984 ILE cc_start: 0.7648 (mt) cc_final: 0.7408 (mt) REVERT: A 1005 TRP cc_start: 0.6528 (m-90) cc_final: 0.5894 (m100) REVERT: B 42 ARG cc_start: 0.6218 (mtp-110) cc_final: 0.5846 (mpt180) REVERT: B 344 ASN cc_start: 0.6425 (t0) cc_final: 0.6191 (t0) REVERT: B 378 ASP cc_start: 0.6920 (p0) cc_final: 0.6379 (p0) REVERT: B 473 ASP cc_start: 0.6019 (t0) cc_final: 0.5781 (t0) REVERT: B 649 THR cc_start: 0.9262 (p) cc_final: 0.8974 (p) REVERT: C 268 LYS cc_start: 0.7875 (mppt) cc_final: 0.7612 (mmmt) REVERT: C 323 TRP cc_start: 0.7682 (p-90) cc_final: 0.7066 (p-90) REVERT: C 373 TYR cc_start: 0.8010 (p90) cc_final: 0.7664 (p90) REVERT: C 511 LYS cc_start: 0.8250 (tttm) cc_final: 0.8040 (ttpt) REVERT: C 663 LYS cc_start: 0.8472 (mtmt) cc_final: 0.8212 (mptt) REVERT: C 866 GLU cc_start: 0.6499 (tt0) cc_final: 0.5801 (mp0) REVERT: C 888 ARG cc_start: 0.5923 (mpt180) cc_final: 0.5638 (mpt180) REVERT: C 983 SER cc_start: 0.8330 (m) cc_final: 0.7777 (p) REVERT: C 991 ARG cc_start: 0.6424 (ptm-80) cc_final: 0.5957 (ttt-90) REVERT: D 71 TYR cc_start: 0.8241 (m-80) cc_final: 0.7998 (m-80) REVERT: D 438 PHE cc_start: 0.7912 (p90) cc_final: 0.7590 (p90) outliers start: 63 outliers final: 38 residues processed: 358 average time/residue: 0.2023 time to fit residues: 114.3955 Evaluate side-chains 325 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 285 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 642 GLN Chi-restraints excluded: chain A residue 644 GLU Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain A residue 883 HIS Chi-restraints excluded: chain A residue 907 MET Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 544 SER Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain C residue 315 CYS Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 644 GLU Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 708 MET Chi-restraints excluded: chain C residue 748 LEU Chi-restraints excluded: chain C residue 773 CYS Chi-restraints excluded: chain C residue 790 SER Chi-restraints excluded: chain C residue 907 MET Chi-restraints excluded: chain C residue 1022 VAL Chi-restraints excluded: chain D residue 10 ASN Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 199 ASP Chi-restraints excluded: chain D residue 443 THR Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 545 ARG Chi-restraints excluded: chain D residue 788 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 46 optimal weight: 0.8980 chunk 347 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 161 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 45 optimal weight: 0.4980 chunk 272 optimal weight: 0.8980 chunk 230 optimal weight: 2.9990 chunk 337 optimal weight: 4.9990 chunk 168 optimal weight: 0.9980 chunk 299 optimal weight: 0.0000 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 642 GLN A 883 HIS B 10 ASN C 46 HIS ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.147794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.112704 restraints weight = 41368.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.111403 restraints weight = 41257.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.112492 restraints weight = 44095.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.113545 restraints weight = 26922.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.115245 restraints weight = 23436.272| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.4074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 29596 Z= 0.111 Angle : 0.486 13.031 39878 Z= 0.251 Chirality : 0.041 0.300 4354 Planarity : 0.004 0.065 4960 Dihedral : 12.263 177.341 4582 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.33 % Allowed : 11.02 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % 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: 1.05 (0.14), residues: 3550 helix: 2.15 (0.13), residues: 1732 sheet: 0.37 (0.24), residues: 474 loop : -1.18 (0.15), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 660 TYR 0.018 0.001 TYR C 998 PHE 0.016 0.001 PHE A 999 TRP 0.014 0.001 TRP B 323 HIS 0.004 0.001 HIS D 219 Details of bonding type rmsd covalent geometry : bond 0.00245 (29582) covalent geometry : angle 0.46824 (39846) SS BOND : bond 0.00160 ( 10) SS BOND : angle 0.68008 ( 20) hydrogen bonds : bond 0.04454 ( 1414) hydrogen bonds : angle 3.62713 ( 4140) link_NAG-ASN : bond 0.01566 ( 4) link_NAG-ASN : angle 7.44291 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 297 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 323 TRP cc_start: 0.7719 (p-90) cc_final: 0.7486 (p-90) REVERT: A 591 ILE cc_start: 0.6332 (OUTLIER) cc_final: 0.5874 (pp) REVERT: A 866 GLU cc_start: 0.6132 (tt0) cc_final: 0.5353 (mp0) REVERT: A 939 MET cc_start: 0.5594 (OUTLIER) cc_final: 0.5195 (mtm) REVERT: A 984 ILE cc_start: 0.7325 (mt) cc_final: 0.6954 (mt) REVERT: A 989 LEU cc_start: 0.7645 (OUTLIER) cc_final: 0.7284 (tp) REVERT: A 1005 TRP cc_start: 0.6545 (m-90) cc_final: 0.5920 (m100) REVERT: A 1029 MET cc_start: 0.6259 (tmm) cc_final: 0.5615 (ttm) REVERT: B 10 ASN cc_start: 0.3611 (OUTLIER) cc_final: 0.3160 (t160) REVERT: B 42 ARG cc_start: 0.6216 (mtp-110) cc_final: 0.5828 (mpt180) REVERT: B 344 ASN cc_start: 0.6496 (t0) cc_final: 0.6268 (t0) REVERT: B 378 ASP cc_start: 0.6916 (p0) cc_final: 0.6415 (p0) REVERT: B 649 THR cc_start: 0.9236 (p) cc_final: 0.8997 (p) REVERT: B 719 ASP cc_start: 0.7687 (t70) cc_final: 0.7264 (t0) REVERT: C 268 LYS cc_start: 0.7855 (mppt) cc_final: 0.7626 (mmmt) REVERT: C 323 TRP cc_start: 0.7650 (p-90) cc_final: 0.7080 (p-90) REVERT: C 373 TYR cc_start: 0.7926 (p90) cc_final: 0.7622 (p90) REVERT: C 511 LYS cc_start: 0.8285 (tttm) cc_final: 0.8008 (ttpt) REVERT: C 663 LYS cc_start: 0.8535 (mtmt) cc_final: 0.8321 (mptt) REVERT: C 866 GLU cc_start: 0.6304 (tt0) cc_final: 0.5762 (mp0) REVERT: C 888 ARG cc_start: 0.5945 (mpt180) cc_final: 0.5664 (mpt180) REVERT: C 983 SER cc_start: 0.8374 (m) cc_final: 0.7831 (p) REVERT: C 991 ARG cc_start: 0.6181 (ptm-80) cc_final: 0.5793 (ttt-90) REVERT: D 71 TYR cc_start: 0.8189 (m-80) cc_final: 0.7922 (m-80) outliers start: 71 outliers final: 50 residues processed: 344 average time/residue: 0.2050 time to fit residues: 110.9105 Evaluate side-chains 335 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 281 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 644 GLU Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain A residue 883 HIS Chi-restraints excluded: chain A residue 907 MET Chi-restraints excluded: chain A residue 939 MET Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain B residue 10 ASN Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 544 SER Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain B residue 708 MET Chi-restraints excluded: chain C residue 116 ASP Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain C residue 315 CYS Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 408 MET Chi-restraints excluded: chain C residue 410 LYS Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 637 GLU Chi-restraints excluded: chain C residue 644 GLU Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 708 MET Chi-restraints excluded: chain C residue 748 LEU Chi-restraints excluded: chain C residue 773 CYS Chi-restraints excluded: chain C residue 787 LEU Chi-restraints excluded: chain C residue 790 SER Chi-restraints excluded: chain C residue 907 MET Chi-restraints excluded: chain C residue 1022 VAL Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 199 ASP Chi-restraints excluded: chain D residue 443 THR Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 545 ARG Chi-restraints excluded: chain D residue 708 MET Chi-restraints excluded: chain D residue 788 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 327 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 86 optimal weight: 7.9990 chunk 173 optimal weight: 3.9990 chunk 128 optimal weight: 0.0970 chunk 299 optimal weight: 0.1980 chunk 348 optimal weight: 0.7980 chunk 350 optimal weight: 0.7980 chunk 135 optimal weight: 1.9990 chunk 276 optimal weight: 0.8980 chunk 151 optimal weight: 0.9980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 GLN ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.148029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.113398 restraints weight = 41678.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.112131 restraints weight = 42193.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.113451 restraints weight = 44200.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.113958 restraints weight = 26407.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.115181 restraints weight = 23545.134| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.4309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 29596 Z= 0.102 Angle : 0.470 12.998 39878 Z= 0.242 Chirality : 0.040 0.290 4354 Planarity : 0.003 0.061 4960 Dihedral : 11.832 176.362 4582 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.20 % Allowed : 11.84 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % 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: 1.31 (0.14), residues: 3550 helix: 2.48 (0.13), residues: 1718 sheet: 0.31 (0.24), residues: 474 loop : -1.09 (0.15), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 303 TYR 0.014 0.001 TYR C 998 PHE 0.019 0.001 PHE A 999 TRP 0.012 0.001 TRP A 262 HIS 0.010 0.001 HIS A 883 Details of bonding type rmsd covalent geometry : bond 0.00220 (29582) covalent geometry : angle 0.45309 (39846) SS BOND : bond 0.00135 ( 10) SS BOND : angle 0.57467 ( 20) hydrogen bonds : bond 0.04125 ( 1414) hydrogen bonds : angle 3.52704 ( 4140) link_NAG-ASN : bond 0.01572 ( 4) link_NAG-ASN : angle 7.19553 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 299 time to evaluate : 1.147 Fit side-chains revert: symmetry clash REVERT: A 323 TRP cc_start: 0.7815 (p-90) cc_final: 0.7589 (p-90) REVERT: A 523 TYR cc_start: 0.7599 (p90) cc_final: 0.7336 (p90) REVERT: A 591 ILE cc_start: 0.6405 (OUTLIER) cc_final: 0.5938 (pp) REVERT: A 866 GLU cc_start: 0.6074 (tt0) cc_final: 0.5582 (mp0) REVERT: A 892 LEU cc_start: 0.6588 (tt) cc_final: 0.6382 (mm) REVERT: A 939 MET cc_start: 0.5797 (OUTLIER) cc_final: 0.5402 (mtm) REVERT: A 984 ILE cc_start: 0.7342 (mt) cc_final: 0.7133 (mt) REVERT: A 1005 TRP cc_start: 0.6604 (m-90) cc_final: 0.5966 (m100) REVERT: A 1029 MET cc_start: 0.6255 (tmm) cc_final: 0.5469 (ttm) REVERT: B 42 ARG cc_start: 0.6266 (mtp-110) cc_final: 0.5886 (mpt180) REVERT: B 344 ASN cc_start: 0.6482 (t0) cc_final: 0.6275 (t0) REVERT: B 378 ASP cc_start: 0.7060 (p0) cc_final: 0.6528 (p0) REVERT: B 473 ASP cc_start: 0.6055 (t0) cc_final: 0.5832 (t0) REVERT: B 649 THR cc_start: 0.9215 (p) cc_final: 0.8993 (p) REVERT: B 719 ASP cc_start: 0.7702 (t70) cc_final: 0.7315 (t0) REVERT: C 268 LYS cc_start: 0.7862 (mppt) cc_final: 0.7622 (mmmt) REVERT: C 323 TRP cc_start: 0.7579 (p-90) cc_final: 0.7076 (p-90) REVERT: C 373 TYR cc_start: 0.7858 (p90) cc_final: 0.7624 (p90) REVERT: C 511 LYS cc_start: 0.8335 (tttm) cc_final: 0.8012 (ttpt) REVERT: C 663 LYS cc_start: 0.8450 (mtmt) cc_final: 0.8134 (tppt) REVERT: C 866 GLU cc_start: 0.6209 (tt0) cc_final: 0.5707 (mp0) REVERT: C 880 MET cc_start: 0.6448 (tmm) cc_final: 0.6151 (tmm) REVERT: C 983 SER cc_start: 0.8461 (m) cc_final: 0.7930 (p) REVERT: C 991 ARG cc_start: 0.6161 (ptm-80) cc_final: 0.5848 (ttt-90) REVERT: D 71 TYR cc_start: 0.8043 (m-80) cc_final: 0.7762 (m-80) REVERT: D 543 VAL cc_start: 0.8100 (t) cc_final: 0.7889 (t) REVERT: D 705 GLU cc_start: 0.6522 (mt-10) cc_final: 0.6133 (mt-10) REVERT: D 719 ASP cc_start: 0.7718 (t70) cc_final: 0.7381 (t0) REVERT: D 788 SER cc_start: 0.8844 (OUTLIER) cc_final: 0.8394 (m) outliers start: 67 outliers final: 46 residues processed: 341 average time/residue: 0.2058 time to fit residues: 110.4280 Evaluate side-chains 333 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 284 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 644 GLU Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain A residue 883 HIS Chi-restraints excluded: chain A residue 907 MET Chi-restraints excluded: chain A residue 939 MET Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 33 MET Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 708 MET Chi-restraints excluded: chain C residue 116 ASP Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain C residue 306 ILE Chi-restraints excluded: chain C residue 315 CYS Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 644 GLU Chi-restraints excluded: chain C residue 708 MET Chi-restraints excluded: chain C residue 748 LEU Chi-restraints excluded: chain C residue 773 CYS Chi-restraints excluded: chain C residue 787 LEU Chi-restraints excluded: chain C residue 790 SER Chi-restraints excluded: chain C residue 907 MET Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 1022 VAL Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 545 ARG Chi-restraints excluded: chain D residue 788 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 178 optimal weight: 4.9990 chunk 293 optimal weight: 0.3980 chunk 346 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 306 optimal weight: 8.9990 chunk 164 optimal weight: 5.9990 chunk 331 optimal weight: 6.9990 chunk 292 optimal weight: 0.9990 chunk 215 optimal weight: 0.0980 chunk 61 optimal weight: 3.9990 chunk 110 optimal weight: 0.8980 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 883 HIS ** B 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.146849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.112152 restraints weight = 41623.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.111022 restraints weight = 41908.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.112102 restraints weight = 44057.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.112808 restraints weight = 26046.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.114064 restraints weight = 23112.812| |-----------------------------------------------------------------------------| r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.4573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 29596 Z= 0.109 Angle : 0.473 12.955 39878 Z= 0.244 Chirality : 0.040 0.300 4354 Planarity : 0.003 0.060 4960 Dihedral : 11.553 175.981 4582 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.43 % Allowed : 11.94 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % 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: 1.39 (0.14), residues: 3550 helix: 2.57 (0.13), residues: 1726 sheet: 0.29 (0.24), residues: 470 loop : -1.10 (0.15), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 303 TYR 0.012 0.001 TYR A 980 PHE 0.017 0.001 PHE A 999 TRP 0.017 0.001 TRP C 262 HIS 0.004 0.001 HIS D 219 Details of bonding type rmsd covalent geometry : bond 0.00245 (29582) covalent geometry : angle 0.45694 (39846) SS BOND : bond 0.00163 ( 10) SS BOND : angle 0.60171 ( 20) hydrogen bonds : bond 0.04200 ( 1414) hydrogen bonds : angle 3.51188 ( 4140) link_NAG-ASN : bond 0.01678 ( 4) link_NAG-ASN : angle 7.11787 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 293 time to evaluate : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 262 TRP cc_start: 0.8384 (t-100) cc_final: 0.8010 (t-100) REVERT: A 399 THR cc_start: 0.8897 (m) cc_final: 0.8599 (p) REVERT: A 591 ILE cc_start: 0.6551 (OUTLIER) cc_final: 0.6116 (pp) REVERT: A 866 GLU cc_start: 0.6052 (tt0) cc_final: 0.5529 (mp0) REVERT: A 892 LEU cc_start: 0.6643 (tt) cc_final: 0.6244 (pp) REVERT: A 984 ILE cc_start: 0.7244 (mt) cc_final: 0.7041 (mt) REVERT: A 1005 TRP cc_start: 0.6741 (m-90) cc_final: 0.5938 (m100) REVERT: A 1029 MET cc_start: 0.6273 (tmm) cc_final: 0.5515 (ttm) REVERT: B 42 ARG cc_start: 0.6293 (mtp-110) cc_final: 0.5914 (mpt180) REVERT: B 378 ASP cc_start: 0.7057 (p0) cc_final: 0.6527 (p0) REVERT: B 531 PHE cc_start: 0.8276 (m-10) cc_final: 0.7980 (m-80) REVERT: B 719 ASP cc_start: 0.7687 (t70) cc_final: 0.7371 (t0) REVERT: C 373 TYR cc_start: 0.7859 (p90) cc_final: 0.7645 (p90) REVERT: C 511 LYS cc_start: 0.8360 (tttm) cc_final: 0.8042 (ttpt) REVERT: C 591 ILE cc_start: 0.6485 (OUTLIER) cc_final: 0.6231 (pp) REVERT: C 663 LYS cc_start: 0.8473 (mtmt) cc_final: 0.8132 (tppt) REVERT: C 805 LEU cc_start: 0.8090 (tp) cc_final: 0.7670 (tt) REVERT: C 849 LEU cc_start: 0.6854 (OUTLIER) cc_final: 0.6296 (mt) REVERT: C 866 GLU cc_start: 0.5872 (tt0) cc_final: 0.5333 (mp0) REVERT: C 880 MET cc_start: 0.6511 (tmm) cc_final: 0.6243 (tmm) REVERT: C 983 SER cc_start: 0.8363 (m) cc_final: 0.7916 (p) REVERT: C 991 ARG cc_start: 0.6318 (ptm-80) cc_final: 0.5966 (ttt-90) REVERT: D 542 LEU cc_start: 0.7896 (mm) cc_final: 0.7487 (tt) REVERT: D 705 GLU cc_start: 0.6600 (mt-10) cc_final: 0.6223 (mt-10) REVERT: D 719 ASP cc_start: 0.7741 (t70) cc_final: 0.7404 (t0) REVERT: D 788 SER cc_start: 0.8786 (OUTLIER) cc_final: 0.8336 (m) outliers start: 74 outliers final: 52 residues processed: 347 average time/residue: 0.2063 time to fit residues: 112.9827 Evaluate side-chains 331 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 275 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 644 GLU Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain A residue 883 HIS Chi-restraints excluded: chain A residue 907 MET Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 544 SER Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 708 MET Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain C residue 306 ILE Chi-restraints excluded: chain C residue 315 CYS Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 410 LYS Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 644 GLU Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain C residue 708 MET Chi-restraints excluded: chain C residue 748 LEU Chi-restraints excluded: chain C residue 773 CYS Chi-restraints excluded: chain C residue 787 LEU Chi-restraints excluded: chain C residue 790 SER Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 907 MET Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 1022 VAL Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 443 THR Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 545 ARG Chi-restraints excluded: chain D residue 788 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 255 optimal weight: 3.9990 chunk 219 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 126 optimal weight: 0.9990 chunk 301 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 chunk 347 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 chunk 266 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 216 optimal weight: 0.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 HIS A 412 HIS A 883 HIS C 412 HIS ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.142178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.104911 restraints weight = 41715.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.105691 restraints weight = 50630.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.106926 restraints weight = 45247.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.107401 restraints weight = 29191.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.109100 restraints weight = 26286.612| |-----------------------------------------------------------------------------| r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.4819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 29596 Z= 0.203 Angle : 0.583 13.470 39878 Z= 0.303 Chirality : 0.044 0.391 4354 Planarity : 0.004 0.067 4960 Dihedral : 12.006 178.915 4582 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.49 % Allowed : 12.24 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.87 (0.14), residues: 3550 helix: 2.11 (0.13), residues: 1728 sheet: 0.07 (0.25), residues: 448 loop : -1.31 (0.15), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 897 TYR 0.018 0.002 TYR A 77 PHE 0.024 0.002 PHE A 891 TRP 0.021 0.002 TRP D 323 HIS 0.010 0.001 HIS D 219 Details of bonding type rmsd covalent geometry : bond 0.00495 (29582) covalent geometry : angle 0.56754 (39846) SS BOND : bond 0.00422 ( 10) SS BOND : angle 1.12848 ( 20) hydrogen bonds : bond 0.05949 ( 1414) hydrogen bonds : angle 3.89071 ( 4140) link_NAG-ASN : bond 0.01572 ( 4) link_NAG-ASN : angle 7.61469 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 289 time to evaluate : 1.083 Fit side-chains revert: symmetry clash REVERT: A 262 TRP cc_start: 0.8423 (t-100) cc_final: 0.8147 (t-100) REVERT: A 330 GLU cc_start: 0.8123 (pt0) cc_final: 0.7754 (pt0) REVERT: A 399 THR cc_start: 0.8953 (m) cc_final: 0.8653 (p) REVERT: A 591 ILE cc_start: 0.6548 (OUTLIER) cc_final: 0.6126 (pp) REVERT: A 630 VAL cc_start: 0.8660 (OUTLIER) cc_final: 0.8427 (t) REVERT: A 866 GLU cc_start: 0.6190 (tt0) cc_final: 0.5709 (mp0) REVERT: A 892 LEU cc_start: 0.6530 (tt) cc_final: 0.6183 (pp) REVERT: A 1005 TRP cc_start: 0.6689 (m-90) cc_final: 0.5958 (m100) REVERT: B 42 ARG cc_start: 0.6252 (mtp-110) cc_final: 0.5898 (mpt180) REVERT: B 378 ASP cc_start: 0.7204 (p0) cc_final: 0.6634 (p0) REVERT: B 531 PHE cc_start: 0.8304 (m-10) cc_final: 0.8044 (m-80) REVERT: B 719 ASP cc_start: 0.7794 (t70) cc_final: 0.7473 (t0) REVERT: C 323 TRP cc_start: 0.7185 (p-90) cc_final: 0.6888 (p-90) REVERT: C 591 ILE cc_start: 0.6551 (OUTLIER) cc_final: 0.6271 (pp) REVERT: C 663 LYS cc_start: 0.8618 (mtmt) cc_final: 0.8365 (mptt) REVERT: C 805 LEU cc_start: 0.8154 (tp) cc_final: 0.7782 (tt) REVERT: C 849 LEU cc_start: 0.6874 (OUTLIER) cc_final: 0.6352 (mt) REVERT: C 866 GLU cc_start: 0.6073 (tt0) cc_final: 0.5799 (mp0) REVERT: C 983 SER cc_start: 0.8517 (m) cc_final: 0.8000 (p) REVERT: C 991 ARG cc_start: 0.6338 (ptm-80) cc_final: 0.5828 (ttt-90) REVERT: D 542 LEU cc_start: 0.7870 (mm) cc_final: 0.7476 (tt) REVERT: D 705 GLU cc_start: 0.6705 (mt-10) cc_final: 0.6352 (mt-10) outliers start: 76 outliers final: 55 residues processed: 342 average time/residue: 0.2043 time to fit residues: 109.8563 Evaluate side-chains 330 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 271 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 410 LYS Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 644 GLU Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain A residue 907 MET Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 544 SER Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 708 MET Chi-restraints excluded: chain B residue 760 ASP Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain C residue 306 ILE Chi-restraints excluded: chain C residue 315 CYS Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 644 GLU Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain C residue 708 MET Chi-restraints excluded: chain C residue 748 LEU Chi-restraints excluded: chain C residue 773 CYS Chi-restraints excluded: chain C residue 787 LEU Chi-restraints excluded: chain C residue 789 LEU Chi-restraints excluded: chain C residue 790 SER Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 907 MET Chi-restraints excluded: chain C residue 939 MET Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 1022 VAL Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 443 THR Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 529 ILE Chi-restraints excluded: chain D residue 708 MET Chi-restraints excluded: chain D residue 760 ASP Chi-restraints excluded: chain D residue 788 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 73 optimal weight: 2.9990 chunk 355 optimal weight: 4.9990 chunk 235 optimal weight: 0.9980 chunk 229 optimal weight: 2.9990 chunk 310 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 83 optimal weight: 10.0000 chunk 276 optimal weight: 2.9990 chunk 330 optimal weight: 7.9990 chunk 208 optimal weight: 10.0000 chunk 7 optimal weight: 3.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 10 ASN B 587 GLN ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 587 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.140752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.106722 restraints weight = 41771.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.104829 restraints weight = 43899.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.105986 restraints weight = 46404.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.106544 restraints weight = 27611.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.107964 restraints weight = 24241.593| |-----------------------------------------------------------------------------| r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.5077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 29596 Z= 0.238 Angle : 0.622 13.526 39878 Z= 0.322 Chirality : 0.046 0.435 4354 Planarity : 0.004 0.065 4960 Dihedral : 12.316 178.393 4582 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.76 % Allowed : 12.73 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % 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: 0.53 (0.14), residues: 3550 helix: 1.81 (0.12), residues: 1718 sheet: 0.03 (0.26), residues: 434 loop : -1.46 (0.14), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 897 TYR 0.022 0.002 TYR C 980 PHE 0.018 0.002 PHE A 999 TRP 0.028 0.002 TRP D 323 HIS 0.012 0.002 HIS D 219 Details of bonding type rmsd covalent geometry : bond 0.00585 (29582) covalent geometry : angle 0.60673 (39846) SS BOND : bond 0.00341 ( 10) SS BOND : angle 1.04221 ( 20) hydrogen bonds : bond 0.06250 ( 1414) hydrogen bonds : angle 4.02286 ( 4140) link_NAG-ASN : bond 0.01562 ( 4) link_NAG-ASN : angle 7.76387 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 280 time to evaluate : 1.207 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 399 THR cc_start: 0.8987 (m) cc_final: 0.8677 (p) REVERT: A 591 ILE cc_start: 0.6535 (OUTLIER) cc_final: 0.6147 (pp) REVERT: A 630 VAL cc_start: 0.8720 (OUTLIER) cc_final: 0.8468 (t) REVERT: A 866 GLU cc_start: 0.6095 (tt0) cc_final: 0.5808 (mp0) REVERT: A 1005 TRP cc_start: 0.6783 (m-90) cc_final: 0.6014 (m100) REVERT: A 1029 MET cc_start: 0.5742 (tmm) cc_final: 0.4943 (ttm) REVERT: B 26 TYR cc_start: 0.8471 (t80) cc_final: 0.8250 (t80) REVERT: B 42 ARG cc_start: 0.6344 (mtp-110) cc_final: 0.5996 (mpt180) REVERT: B 378 ASP cc_start: 0.7251 (p0) cc_final: 0.6669 (p0) REVERT: B 414 MET cc_start: 0.5914 (mmt) cc_final: 0.5453 (mtp) REVERT: B 523 TYR cc_start: 0.7530 (m-80) cc_final: 0.7170 (m-80) REVERT: B 531 PHE cc_start: 0.8307 (m-10) cc_final: 0.8016 (m-80) REVERT: C 268 LYS cc_start: 0.7841 (mppt) cc_final: 0.7636 (mmmt) REVERT: C 323 TRP cc_start: 0.7450 (p-90) cc_final: 0.7005 (p-90) REVERT: C 591 ILE cc_start: 0.6602 (OUTLIER) cc_final: 0.6221 (pp) REVERT: C 663 LYS cc_start: 0.8666 (mtmt) cc_final: 0.8410 (mptt) REVERT: C 805 LEU cc_start: 0.8066 (tp) cc_final: 0.7741 (tt) REVERT: C 849 LEU cc_start: 0.6866 (OUTLIER) cc_final: 0.6450 (mt) REVERT: C 983 SER cc_start: 0.8376 (m) cc_final: 0.7860 (p) REVERT: C 991 ARG cc_start: 0.6274 (ptm-80) cc_final: 0.6050 (ttp80) REVERT: D 542 LEU cc_start: 0.7874 (mm) cc_final: 0.7452 (tt) REVERT: D 705 GLU cc_start: 0.6815 (mt-10) cc_final: 0.6443 (mt-10) outliers start: 84 outliers final: 65 residues processed: 339 average time/residue: 0.1983 time to fit residues: 107.1834 Evaluate side-chains 337 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 268 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 410 LYS Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 644 GLU Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain A residue 907 MET Chi-restraints excluded: chain B residue 10 ASN Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 544 SER Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 708 MET Chi-restraints excluded: chain B residue 760 ASP Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain C residue 306 ILE Chi-restraints excluded: chain C residue 315 CYS Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 408 MET Chi-restraints excluded: chain C residue 410 LYS Chi-restraints excluded: chain C residue 496 MET Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 644 GLU Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain C residue 708 MET Chi-restraints excluded: chain C residue 748 LEU Chi-restraints excluded: chain C residue 773 CYS Chi-restraints excluded: chain C residue 787 LEU Chi-restraints excluded: chain C residue 789 LEU Chi-restraints excluded: chain C residue 790 SER Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 907 MET Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 1022 VAL Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 443 THR Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 529 ILE Chi-restraints excluded: chain D residue 708 MET Chi-restraints excluded: chain D residue 760 ASP Chi-restraints excluded: chain D residue 788 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 42 optimal weight: 0.9980 chunk 262 optimal weight: 10.0000 chunk 164 optimal weight: 0.0980 chunk 73 optimal weight: 1.9990 chunk 254 optimal weight: 0.9980 chunk 59 optimal weight: 0.5980 chunk 58 optimal weight: 0.6980 chunk 165 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 156 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.144723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.109733 restraints weight = 41598.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.107473 restraints weight = 40933.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.108791 restraints weight = 45833.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.109427 restraints weight = 28467.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.110860 restraints weight = 25070.389| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.5188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 29596 Z= 0.112 Angle : 0.491 13.124 39878 Z= 0.254 Chirality : 0.041 0.338 4354 Planarity : 0.003 0.060 4960 Dihedral : 11.683 179.928 4582 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.97 % Allowed : 13.52 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % 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: 1.05 (0.14), residues: 3550 helix: 2.37 (0.13), residues: 1712 sheet: 0.02 (0.25), residues: 454 loop : -1.30 (0.15), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 715 TYR 0.018 0.001 TYR C 980 PHE 0.019 0.001 PHE A 999 TRP 0.020 0.001 TRP C 262 HIS 0.004 0.001 HIS B 93 Details of bonding type rmsd covalent geometry : bond 0.00251 (29582) covalent geometry : angle 0.47468 (39846) SS BOND : bond 0.00125 ( 10) SS BOND : angle 0.61210 ( 20) hydrogen bonds : bond 0.04421 ( 1414) hydrogen bonds : angle 3.61042 ( 4140) link_NAG-ASN : bond 0.01567 ( 4) link_NAG-ASN : angle 7.33816 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 280 time to evaluate : 1.026 Fit side-chains revert: symmetry clash REVERT: A 399 THR cc_start: 0.8900 (m) cc_final: 0.8645 (p) REVERT: A 591 ILE cc_start: 0.6584 (OUTLIER) cc_final: 0.6278 (pp) REVERT: A 866 GLU cc_start: 0.5907 (tt0) cc_final: 0.5519 (mp0) REVERT: A 1005 TRP cc_start: 0.6665 (m-90) cc_final: 0.5769 (m100) REVERT: A 1029 MET cc_start: 0.5665 (tmm) cc_final: 0.5065 (ttm) REVERT: B 26 TYR cc_start: 0.8341 (t80) cc_final: 0.8114 (t80) REVERT: B 42 ARG cc_start: 0.6255 (mtp-110) cc_final: 0.5814 (mpt180) REVERT: B 378 ASP cc_start: 0.7221 (p0) cc_final: 0.6650 (p0) REVERT: B 523 TYR cc_start: 0.7365 (m-80) cc_final: 0.6979 (m-80) REVERT: C 268 LYS cc_start: 0.7926 (mppt) cc_final: 0.7722 (mmmt) REVERT: C 323 TRP cc_start: 0.7410 (p-90) cc_final: 0.7034 (p-90) REVERT: C 591 ILE cc_start: 0.6427 (OUTLIER) cc_final: 0.6120 (pp) REVERT: C 663 LYS cc_start: 0.8547 (mtmt) cc_final: 0.8257 (mptt) REVERT: C 805 LEU cc_start: 0.8029 (tp) cc_final: 0.7684 (tt) REVERT: C 849 LEU cc_start: 0.6881 (OUTLIER) cc_final: 0.6374 (mt) REVERT: C 866 GLU cc_start: 0.5982 (tt0) cc_final: 0.5583 (mp0) REVERT: C 983 SER cc_start: 0.8411 (m) cc_final: 0.7867 (p) REVERT: C 991 ARG cc_start: 0.6518 (ptm-80) cc_final: 0.5919 (ttt-90) REVERT: D 542 LEU cc_start: 0.7739 (mm) cc_final: 0.7379 (tt) REVERT: D 705 GLU cc_start: 0.6714 (mt-10) cc_final: 0.6439 (mt-10) outliers start: 60 outliers final: 46 residues processed: 321 average time/residue: 0.1908 time to fit residues: 97.1208 Evaluate side-chains 319 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 270 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 644 GLU Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain A residue 907 MET Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 544 SER Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 708 MET Chi-restraints excluded: chain C residue 116 ASP Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain C residue 306 ILE Chi-restraints excluded: chain C residue 315 CYS Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 496 MET Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 644 GLU Chi-restraints excluded: chain C residue 708 MET Chi-restraints excluded: chain C residue 748 LEU Chi-restraints excluded: chain C residue 773 CYS Chi-restraints excluded: chain C residue 789 LEU Chi-restraints excluded: chain C residue 790 SER Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 907 MET Chi-restraints excluded: chain C residue 1022 VAL Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 443 THR Chi-restraints excluded: chain D residue 629 MET Chi-restraints excluded: chain D residue 788 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 134 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 153 optimal weight: 3.9990 chunk 270 optimal weight: 0.8980 chunk 25 optimal weight: 0.0870 chunk 171 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 207 optimal weight: 0.0030 chunk 244 optimal weight: 0.8980 chunk 230 optimal weight: 0.7980 chunk 161 optimal weight: 3.9990 overall best weight: 0.5368 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 337 GLN ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 10 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 = 0.3661 r_free = 0.3661 target = 0.145506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.110519 restraints weight = 41503.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.108173 restraints weight = 40862.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.109610 restraints weight = 45404.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.110143 restraints weight = 28342.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.111499 restraints weight = 25037.289| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.5268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 29596 Z= 0.101 Angle : 0.479 13.017 39878 Z= 0.246 Chirality : 0.040 0.319 4354 Planarity : 0.003 0.059 4960 Dihedral : 11.263 177.866 4582 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.61 % Allowed : 13.91 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % 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: 1.26 (0.14), residues: 3550 helix: 2.59 (0.13), residues: 1714 sheet: 0.10 (0.25), residues: 444 loop : -1.24 (0.15), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 715 TYR 0.018 0.001 TYR C 980 PHE 0.019 0.001 PHE A 999 TRP 0.021 0.001 TRP B 323 HIS 0.004 0.001 HIS B 93 Details of bonding type rmsd covalent geometry : bond 0.00223 (29582) covalent geometry : angle 0.46225 (39846) SS BOND : bond 0.00141 ( 10) SS BOND : angle 0.57265 ( 20) hydrogen bonds : bond 0.04041 ( 1414) hydrogen bonds : angle 3.51270 ( 4140) link_NAG-ASN : bond 0.01429 ( 4) link_NAG-ASN : angle 7.17019 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 285 time to evaluate : 1.188 Fit side-chains revert: symmetry clash REVERT: A 399 THR cc_start: 0.8876 (m) cc_final: 0.8624 (p) REVERT: A 591 ILE cc_start: 0.6561 (OUTLIER) cc_final: 0.6279 (pp) REVERT: A 866 GLU cc_start: 0.5584 (tt0) cc_final: 0.5338 (mp0) REVERT: A 1005 TRP cc_start: 0.6498 (m-90) cc_final: 0.5772 (m100) REVERT: A 1029 MET cc_start: 0.5729 (tmm) cc_final: 0.5138 (ttm) REVERT: B 42 ARG cc_start: 0.6221 (mtp-110) cc_final: 0.5776 (mpt180) REVERT: B 268 LYS cc_start: 0.8626 (mttm) cc_final: 0.8316 (mmmm) REVERT: B 378 ASP cc_start: 0.7170 (p0) cc_final: 0.6592 (p0) REVERT: B 414 MET cc_start: 0.5805 (mmt) cc_final: 0.5347 (mtp) REVERT: B 523 TYR cc_start: 0.7233 (m-80) cc_final: 0.6833 (m-80) REVERT: C 262 TRP cc_start: 0.8748 (t-100) cc_final: 0.8435 (t-100) REVERT: C 268 LYS cc_start: 0.7955 (mppt) cc_final: 0.7716 (mmmt) REVERT: C 323 TRP cc_start: 0.7353 (p-90) cc_final: 0.7085 (p-90) REVERT: C 399 THR cc_start: 0.8883 (m) cc_final: 0.8598 (p) REVERT: C 591 ILE cc_start: 0.6469 (OUTLIER) cc_final: 0.6139 (pp) REVERT: C 663 LYS cc_start: 0.8460 (mtmt) cc_final: 0.8148 (mptt) REVERT: C 805 LEU cc_start: 0.8047 (tp) cc_final: 0.7720 (tt) REVERT: C 866 GLU cc_start: 0.5973 (tt0) cc_final: 0.5615 (mp0) REVERT: C 983 SER cc_start: 0.8447 (m) cc_final: 0.7866 (p) REVERT: C 991 ARG cc_start: 0.6467 (ptm-80) cc_final: 0.5952 (ttt-90) REVERT: D 71 TYR cc_start: 0.7757 (m-80) cc_final: 0.7438 (m-80) REVERT: D 542 LEU cc_start: 0.7772 (mm) cc_final: 0.7398 (tt) REVERT: D 705 GLU cc_start: 0.6636 (mt-10) cc_final: 0.6263 (mt-10) REVERT: D 800 VAL cc_start: 0.7742 (t) cc_final: 0.7539 (p) outliers start: 49 outliers final: 37 residues processed: 315 average time/residue: 0.2000 time to fit residues: 99.9620 Evaluate side-chains 319 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 280 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain A residue 907 MET Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 33 MET Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 708 MET Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain C residue 306 ILE Chi-restraints excluded: chain C residue 315 CYS Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 496 MET Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 644 GLU Chi-restraints excluded: chain C residue 708 MET Chi-restraints excluded: chain C residue 748 LEU Chi-restraints excluded: chain C residue 773 CYS Chi-restraints excluded: chain C residue 790 SER Chi-restraints excluded: chain C residue 1022 VAL Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 443 THR Chi-restraints excluded: chain D residue 788 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 23 optimal weight: 3.9990 chunk 293 optimal weight: 0.7980 chunk 54 optimal weight: 3.9990 chunk 149 optimal weight: 0.9980 chunk 181 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 233 optimal weight: 1.9990 chunk 25 optimal weight: 0.4980 chunk 160 optimal weight: 0.6980 chunk 146 optimal weight: 2.9990 chunk 336 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 337 GLN ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 10 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 = 0.3654 r_free = 0.3654 target = 0.144937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.109616 restraints weight = 41568.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.108122 restraints weight = 42441.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.109341 restraints weight = 45126.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.110153 restraints weight = 28377.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.111639 restraints weight = 24975.104| |-----------------------------------------------------------------------------| r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.5297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 29596 Z= 0.114 Angle : 0.489 13.035 39878 Z= 0.251 Chirality : 0.041 0.326 4354 Planarity : 0.003 0.061 4960 Dihedral : 11.029 178.060 4582 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.61 % Allowed : 13.98 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % 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: 1.27 (0.14), residues: 3550 helix: 2.56 (0.13), residues: 1722 sheet: 0.16 (0.25), residues: 444 loop : -1.23 (0.15), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 991 TYR 0.018 0.001 TYR C 980 PHE 0.018 0.001 PHE A 999 TRP 0.021 0.001 TRP B 323 HIS 0.005 0.001 HIS D 219 Details of bonding type rmsd covalent geometry : bond 0.00261 (29582) covalent geometry : angle 0.47320 (39846) SS BOND : bond 0.00159 ( 10) SS BOND : angle 0.59949 ( 20) hydrogen bonds : bond 0.04296 ( 1414) hydrogen bonds : angle 3.53756 ( 4140) link_NAG-ASN : bond 0.01386 ( 4) link_NAG-ASN : angle 7.16240 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4599.56 seconds wall clock time: 80 minutes 22.73 seconds (4822.73 seconds total)