Starting phenix.real_space_refine on Sun Jul 5 14:15:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dkl_46961/07_2026/9dkl_46961.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dkl_46961/07_2026/9dkl_46961.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dkl_46961/07_2026/9dkl_46961.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dkl_46961/07_2026/9dkl_46961.map" model { file = "/net/cci-nas-00/data/ceres_data/9dkl_46961/07_2026/9dkl_46961.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dkl_46961/07_2026/9dkl_46961.cif" } resolution = 3.4 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= 0.001 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 Ca 8 9.91 5 K 2 8.98 5 S 172 5.16 5 C 18416 2.51 5 N 4664 2.21 5 O 5156 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 165 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 28418 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 899, 7102 Classifications: {'peptide': 899} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 35, 'TRANS': 863} Chain breaks: 5 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 48 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 3, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "B" Number of atoms: 7102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 899, 7102 Classifications: {'peptide': 899} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 35, 'TRANS': 863} Chain breaks: 5 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 48 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 3, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "C" Number of atoms: 7102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 899, 7102 Classifications: {'peptide': 899} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 35, 'TRANS': 863} Chain breaks: 5 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 48 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 3, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "D" Number of atoms: 7102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 899, 7102 Classifications: {'peptide': 899} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 35, 'TRANS': 863} Chain breaks: 5 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 48 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 3, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 0 Ad-hoc single atom residues: {' K': 2, ' CA': 2} Chain breaks: 4 Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 Time building chain proxies: 5.79, per 1000 atoms: 0.20 Number of scatterers: 28418 At special positions: 0 Unit cell: (145.631, 145.631, 123.308, 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) Ca 8 19.99 K 2 19.00 S 172 16.00 O 5156 8.00 N 4664 7.00 C 18416 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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 Time building additional restraints: 2.34 Conformation dependent library (CDL) restraints added in 1.2 seconds 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6784 Finding SS restraints... Secondary structure from input PDB file: 200 helices and 20 sheets defined 57.4% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.19 Creating SS restraints... Processing helix chain 'A' and resid 16 through 44 removed outlier: 3.826A pdb=" N LEU A 20 " --> pdb=" O TRP A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 92 removed outlier: 3.894A pdb=" N LYS A 85 " --> pdb=" O MET A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 123 Processing helix chain 'A' and resid 136 through 160 removed outlier: 3.670A pdb=" N PHE A 148 " --> pdb=" O ALA A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 168 Processing helix chain 'A' and resid 169 through 188 removed outlier: 3.542A pdb=" N PHE A 173 " --> pdb=" O GLU A 169 " (cutoff:3.500A) Proline residue: A 180 - end of helix removed outlier: 3.547A pdb=" N ILE A 186 " --> pdb=" O SER A 182 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TYR A 187 " --> pdb=" O PHE A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 198 through 203 removed outlier: 4.186A pdb=" N ARG A 202 " --> pdb=" O LEU A 198 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU A 203 " --> pdb=" O ARG A 199 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 198 through 203' Processing helix chain 'A' and resid 205 through 213 Processing helix chain 'A' and resid 218 through 249 removed outlier: 4.752A pdb=" N LEU A 234 " --> pdb=" O SER A 230 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N THR A 237 " --> pdb=" O SER A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 254 Processing helix chain 'A' and resid 262 through 275 Processing helix chain 'A' and resid 286 through 303 removed outlier: 3.572A pdb=" N GLY A 302 " --> pdb=" O MET A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 317 Processing helix chain 'A' and resid 341 through 353 removed outlier: 3.682A pdb=" N ASP A 351 " --> pdb=" O ASN A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 383 Processing helix chain 'A' and resid 396 through 403 Processing helix chain 'A' and resid 421 through 440 Processing helix chain 'A' and resid 451 through 453 No H-bonds generated for 'chain 'A' and resid 451 through 453' Processing helix chain 'A' and resid 454 through 461 removed outlier: 3.917A pdb=" N LEU A 458 " --> pdb=" O ASN A 454 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN A 460 " --> pdb=" O ALA A 456 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE A 461 " --> pdb=" O TYR A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 489 removed outlier: 3.524A pdb=" N LEU A 488 " --> pdb=" O ALA A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 500 removed outlier: 3.753A pdb=" N ASN A 498 " --> pdb=" O THR A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 524 removed outlier: 3.817A pdb=" N MET A 524 " --> pdb=" O ARG A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 536 Processing helix chain 'A' and resid 539 through 550 Processing helix chain 'A' and resid 592 through 597 Processing helix chain 'A' and resid 597 through 602 Processing helix chain 'A' and resid 603 through 607 Processing helix chain 'A' and resid 612 through 616 Processing helix chain 'A' and resid 721 through 725 Processing helix chain 'A' and resid 728 through 735 Processing helix chain 'A' and resid 756 through 761 Processing helix chain 'A' and resid 762 through 765 removed outlier: 3.712A pdb=" N ALA A 765 " --> pdb=" O PRO A 762 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 762 through 765' Processing helix chain 'A' and resid 769 through 773 Processing helix chain 'A' and resid 781 through 793 removed outlier: 4.292A pdb=" N LYS A 790 " --> pdb=" O HIS A 786 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N THR A 791 " --> pdb=" O ARG A 787 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU A 792 " --> pdb=" O GLU A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 814 Processing helix chain 'A' and resid 815 through 819 Processing helix chain 'A' and resid 839 through 852 removed outlier: 3.510A pdb=" N MET A 852 " --> pdb=" O ASN A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 882 through 886 Processing helix chain 'A' and resid 894 through 902 removed outlier: 3.569A pdb=" N GLN A 899 " --> pdb=" O SER A 896 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ASP A 902 " --> pdb=" O GLN A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 915 Processing helix chain 'A' and resid 916 through 921 Processing helix chain 'A' and resid 928 through 931 Processing helix chain 'A' and resid 932 through 940 Processing helix chain 'A' and resid 940 through 953 removed outlier: 3.601A pdb=" N LEU A 944 " --> pdb=" O ASN A 940 " (cutoff:3.500A) Processing helix chain 'A' and resid 956 through 965 Processing helix chain 'A' and resid 975 through 980 Processing helix chain 'A' and resid 981 through 983 No H-bonds generated for 'chain 'A' and resid 981 through 983' Processing helix chain 'A' and resid 997 through 1002 removed outlier: 3.605A pdb=" N GLY A1001 " --> pdb=" O LEU A 997 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1018 removed outlier: 3.615A pdb=" N LEU A1009 " --> pdb=" O HIS A1005 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 44 removed outlier: 3.825A pdb=" N LEU B 20 " --> pdb=" O TRP B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 92 removed outlier: 3.894A pdb=" N LYS B 85 " --> pdb=" O MET B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 123 Processing helix chain 'B' and resid 136 through 160 removed outlier: 3.671A pdb=" N PHE B 148 " --> pdb=" O ALA B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 168 Processing helix chain 'B' and resid 169 through 188 removed outlier: 3.542A pdb=" N PHE B 173 " --> pdb=" O GLU B 169 " (cutoff:3.500A) Proline residue: B 180 - end of helix removed outlier: 3.546A pdb=" N ILE B 186 " --> pdb=" O SER B 182 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TYR B 187 " --> pdb=" O PHE B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 197 No H-bonds generated for 'chain 'B' and resid 195 through 197' Processing helix chain 'B' and resid 198 through 203 removed outlier: 4.185A pdb=" N ARG B 202 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU B 203 " --> pdb=" O ARG B 199 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 198 through 203' Processing helix chain 'B' and resid 205 through 213 Processing helix chain 'B' and resid 218 through 249 removed outlier: 4.751A pdb=" N LEU B 234 " --> pdb=" O SER B 230 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N THR B 237 " --> pdb=" O SER B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 254 Processing helix chain 'B' and resid 262 through 275 Processing helix chain 'B' and resid 286 through 303 removed outlier: 3.571A pdb=" N GLY B 302 " --> pdb=" O MET B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 317 Processing helix chain 'B' and resid 341 through 353 removed outlier: 3.682A pdb=" N ASP B 351 " --> pdb=" O ASN B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 383 Processing helix chain 'B' and resid 396 through 403 Processing helix chain 'B' and resid 421 through 440 Processing helix chain 'B' and resid 451 through 453 No H-bonds generated for 'chain 'B' and resid 451 through 453' Processing helix chain 'B' and resid 454 through 461 removed outlier: 3.918A pdb=" N LEU B 458 " --> pdb=" O ASN B 454 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN B 460 " --> pdb=" O ALA B 456 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE B 461 " --> pdb=" O TYR B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 489 removed outlier: 3.523A pdb=" N LEU B 488 " --> pdb=" O ALA B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 500 removed outlier: 3.752A pdb=" N ASN B 498 " --> pdb=" O THR B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 524 removed outlier: 3.817A pdb=" N MET B 524 " --> pdb=" O ARG B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 536 Processing helix chain 'B' and resid 539 through 550 Processing helix chain 'B' and resid 592 through 597 Processing helix chain 'B' and resid 597 through 602 Processing helix chain 'B' and resid 603 through 607 Processing helix chain 'B' and resid 612 through 616 Processing helix chain 'B' and resid 721 through 725 Processing helix chain 'B' and resid 728 through 735 Processing helix chain 'B' and resid 756 through 761 Processing helix chain 'B' and resid 762 through 765 removed outlier: 3.713A pdb=" N ALA B 765 " --> pdb=" O PRO B 762 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 762 through 765' Processing helix chain 'B' and resid 769 through 773 Processing helix chain 'B' and resid 781 through 793 removed outlier: 4.292A pdb=" N LYS B 790 " --> pdb=" O HIS B 786 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N THR B 791 " --> pdb=" O ARG B 787 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU B 792 " --> pdb=" O GLU B 788 " (cutoff:3.500A) Processing helix chain 'B' and resid 807 through 814 Processing helix chain 'B' and resid 815 through 819 Processing helix chain 'B' and resid 839 through 852 removed outlier: 3.510A pdb=" N MET B 852 " --> pdb=" O ASN B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 882 through 886 Processing helix chain 'B' and resid 894 through 902 removed outlier: 3.569A pdb=" N GLN B 899 " --> pdb=" O SER B 896 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ASP B 902 " --> pdb=" O GLN B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 915 Processing helix chain 'B' and resid 916 through 921 Processing helix chain 'B' and resid 928 through 931 Processing helix chain 'B' and resid 932 through 940 Processing helix chain 'B' and resid 940 through 953 removed outlier: 3.600A pdb=" N LEU B 944 " --> pdb=" O ASN B 940 " (cutoff:3.500A) Processing helix chain 'B' and resid 956 through 965 Processing helix chain 'B' and resid 975 through 980 Processing helix chain 'B' and resid 981 through 983 No H-bonds generated for 'chain 'B' and resid 981 through 983' Processing helix chain 'B' and resid 997 through 1002 removed outlier: 3.606A pdb=" N GLY B1001 " --> pdb=" O LEU B 997 " (cutoff:3.500A) Processing helix chain 'B' and resid 1005 through 1018 removed outlier: 3.614A pdb=" N LEU B1009 " --> pdb=" O HIS B1005 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 44 removed outlier: 3.826A pdb=" N LEU C 20 " --> pdb=" O TRP C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 92 removed outlier: 3.895A pdb=" N LYS C 85 " --> pdb=" O MET C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 123 Processing helix chain 'C' and resid 136 through 160 removed outlier: 3.670A pdb=" N PHE C 148 " --> pdb=" O ALA C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 168 Processing helix chain 'C' and resid 169 through 188 removed outlier: 3.542A pdb=" N PHE C 173 " --> pdb=" O GLU C 169 " (cutoff:3.500A) Proline residue: C 180 - end of helix removed outlier: 3.546A pdb=" N ILE C 186 " --> pdb=" O SER C 182 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR C 187 " --> pdb=" O PHE C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 198 through 203 removed outlier: 4.186A pdb=" N ARG C 202 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU C 203 " --> pdb=" O ARG C 199 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 198 through 203' Processing helix chain 'C' and resid 205 through 213 Processing helix chain 'C' and resid 218 through 249 removed outlier: 4.750A pdb=" N LEU C 234 " --> pdb=" O SER C 230 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N THR C 237 " --> pdb=" O SER C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 254 Processing helix chain 'C' and resid 262 through 275 Processing helix chain 'C' and resid 286 through 303 removed outlier: 3.571A pdb=" N GLY C 302 " --> pdb=" O MET C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 317 Processing helix chain 'C' and resid 341 through 353 removed outlier: 3.681A pdb=" N ASP C 351 " --> pdb=" O ASN C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 383 Processing helix chain 'C' and resid 396 through 403 Processing helix chain 'C' and resid 421 through 440 Processing helix chain 'C' and resid 451 through 453 No H-bonds generated for 'chain 'C' and resid 451 through 453' Processing helix chain 'C' and resid 454 through 461 removed outlier: 3.918A pdb=" N LEU C 458 " --> pdb=" O ASN C 454 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN C 460 " --> pdb=" O ALA C 456 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE C 461 " --> pdb=" O TYR C 457 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 489 removed outlier: 3.522A pdb=" N LEU C 488 " --> pdb=" O ALA C 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 491 through 500 removed outlier: 3.753A pdb=" N ASN C 498 " --> pdb=" O THR C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 512 through 524 removed outlier: 3.818A pdb=" N MET C 524 " --> pdb=" O ARG C 520 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 536 Processing helix chain 'C' and resid 539 through 550 Processing helix chain 'C' and resid 592 through 597 Processing helix chain 'C' and resid 597 through 602 Processing helix chain 'C' and resid 603 through 607 Processing helix chain 'C' and resid 612 through 616 Processing helix chain 'C' and resid 721 through 725 Processing helix chain 'C' and resid 728 through 735 Processing helix chain 'C' and resid 756 through 761 Processing helix chain 'C' and resid 762 through 765 removed outlier: 3.714A pdb=" N ALA C 765 " --> pdb=" O PRO C 762 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 762 through 765' Processing helix chain 'C' and resid 769 through 773 Processing helix chain 'C' and resid 781 through 793 removed outlier: 4.291A pdb=" N LYS C 790 " --> pdb=" O HIS C 786 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N THR C 791 " --> pdb=" O ARG C 787 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU C 792 " --> pdb=" O GLU C 788 " (cutoff:3.500A) Processing helix chain 'C' and resid 807 through 814 Processing helix chain 'C' and resid 815 through 819 Processing helix chain 'C' and resid 839 through 852 removed outlier: 3.508A pdb=" N MET C 852 " --> pdb=" O ASN C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 882 through 886 Processing helix chain 'C' and resid 894 through 902 removed outlier: 3.569A pdb=" N GLN C 899 " --> pdb=" O SER C 896 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ASP C 902 " --> pdb=" O GLN C 899 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 915 Processing helix chain 'C' and resid 916 through 921 Processing helix chain 'C' and resid 928 through 931 Processing helix chain 'C' and resid 932 through 940 Processing helix chain 'C' and resid 940 through 953 removed outlier: 3.601A pdb=" N LEU C 944 " --> pdb=" O ASN C 940 " (cutoff:3.500A) Processing helix chain 'C' and resid 956 through 965 Processing helix chain 'C' and resid 975 through 980 Processing helix chain 'C' and resid 981 through 983 No H-bonds generated for 'chain 'C' and resid 981 through 983' Processing helix chain 'C' and resid 997 through 1002 removed outlier: 3.606A pdb=" N GLY C1001 " --> pdb=" O LEU C 997 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1018 removed outlier: 3.615A pdb=" N LEU C1009 " --> pdb=" O HIS C1005 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 44 removed outlier: 3.826A pdb=" N LEU D 20 " --> pdb=" O TRP D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 92 removed outlier: 3.896A pdb=" N LYS D 85 " --> pdb=" O MET D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 123 Processing helix chain 'D' and resid 136 through 160 removed outlier: 3.670A pdb=" N PHE D 148 " --> pdb=" O ALA D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 168 Processing helix chain 'D' and resid 169 through 188 removed outlier: 3.542A pdb=" N PHE D 173 " --> pdb=" O GLU D 169 " (cutoff:3.500A) Proline residue: D 180 - end of helix removed outlier: 3.546A pdb=" N ILE D 186 " --> pdb=" O SER D 182 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR D 187 " --> pdb=" O PHE D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 197 No H-bonds generated for 'chain 'D' and resid 195 through 197' Processing helix chain 'D' and resid 198 through 203 removed outlier: 4.186A pdb=" N ARG D 202 " --> pdb=" O LEU D 198 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU D 203 " --> pdb=" O ARG D 199 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 198 through 203' Processing helix chain 'D' and resid 205 through 213 Processing helix chain 'D' and resid 218 through 249 removed outlier: 4.751A pdb=" N LEU D 234 " --> pdb=" O SER D 230 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N THR D 237 " --> pdb=" O SER D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 254 Processing helix chain 'D' and resid 262 through 275 Processing helix chain 'D' and resid 286 through 303 removed outlier: 3.571A pdb=" N GLY D 302 " --> pdb=" O MET D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 317 Processing helix chain 'D' and resid 341 through 353 removed outlier: 3.682A pdb=" N ASP D 351 " --> pdb=" O ASN D 347 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 383 Processing helix chain 'D' and resid 396 through 403 Processing helix chain 'D' and resid 421 through 440 Processing helix chain 'D' and resid 451 through 453 No H-bonds generated for 'chain 'D' and resid 451 through 453' Processing helix chain 'D' and resid 454 through 461 removed outlier: 3.918A pdb=" N LEU D 458 " --> pdb=" O ASN D 454 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN D 460 " --> pdb=" O ALA D 456 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE D 461 " --> pdb=" O TYR D 457 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 489 removed outlier: 3.524A pdb=" N LEU D 488 " --> pdb=" O ALA D 484 " (cutoff:3.500A) Processing helix chain 'D' and resid 491 through 500 removed outlier: 3.754A pdb=" N ASN D 498 " --> pdb=" O THR D 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 512 through 524 removed outlier: 3.817A pdb=" N MET D 524 " --> pdb=" O ARG D 520 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 536 Processing helix chain 'D' and resid 539 through 550 Processing helix chain 'D' and resid 592 through 597 Processing helix chain 'D' and resid 597 through 602 Processing helix chain 'D' and resid 603 through 607 Processing helix chain 'D' and resid 612 through 616 Processing helix chain 'D' and resid 721 through 725 Processing helix chain 'D' and resid 728 through 735 Processing helix chain 'D' and resid 756 through 761 Processing helix chain 'D' and resid 762 through 765 removed outlier: 3.713A pdb=" N ALA D 765 " --> pdb=" O PRO D 762 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 762 through 765' Processing helix chain 'D' and resid 769 through 773 Processing helix chain 'D' and resid 781 through 793 removed outlier: 4.292A pdb=" N LYS D 790 " --> pdb=" O HIS D 786 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N THR D 791 " --> pdb=" O ARG D 787 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU D 792 " --> pdb=" O GLU D 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 807 through 814 Processing helix chain 'D' and resid 815 through 819 Processing helix chain 'D' and resid 839 through 852 removed outlier: 3.508A pdb=" N MET D 852 " --> pdb=" O ASN D 848 " (cutoff:3.500A) Processing helix chain 'D' and resid 882 through 886 Processing helix chain 'D' and resid 894 through 902 removed outlier: 3.570A pdb=" N GLN D 899 " --> pdb=" O SER D 896 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ASP D 902 " --> pdb=" O GLN D 899 " (cutoff:3.500A) Processing helix chain 'D' and resid 912 through 915 Processing helix chain 'D' and resid 916 through 921 Processing helix chain 'D' and resid 928 through 931 Processing helix chain 'D' and resid 932 through 940 Processing helix chain 'D' and resid 940 through 953 removed outlier: 3.601A pdb=" N LEU D 944 " --> pdb=" O ASN D 940 " (cutoff:3.500A) Processing helix chain 'D' and resid 956 through 965 Processing helix chain 'D' and resid 975 through 980 Processing helix chain 'D' and resid 981 through 983 No H-bonds generated for 'chain 'D' and resid 981 through 983' Processing helix chain 'D' and resid 997 through 1002 removed outlier: 3.605A pdb=" N GLY D1001 " --> pdb=" O LEU D 997 " (cutoff:3.500A) Processing helix chain 'D' and resid 1005 through 1018 removed outlier: 3.615A pdb=" N LEU D1009 " --> pdb=" O HIS D1005 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 128 through 129 Processing sheet with id=AA2, first strand: chain 'A' and resid 387 through 391 removed outlier: 6.427A pdb=" N VAL A 334 " --> pdb=" O VAL A 365 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N LEU A 367 " --> pdb=" O VAL A 334 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N VAL A 336 " --> pdb=" O LEU A 367 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N HIS A 333 " --> pdb=" O ALA A 410 " (cutoff:3.500A) removed outlier: 8.538A pdb=" N LEU A 412 " --> pdb=" O HIS A 333 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N VAL A 335 " --> pdb=" O LEU A 412 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N LEU A 414 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N CYS A 337 " --> pdb=" O LEU A 414 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N CYS A 411 " --> pdb=" O ILE A 446 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N GLN A 448 " --> pdb=" O CYS A 411 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N VAL A 413 " --> pdb=" O GLN A 448 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 525 through 530 removed outlier: 6.906A pdb=" N GLN A 585 " --> pdb=" O ILE A 558 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ILE A 558 " --> pdb=" O GLN A 585 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N PHE A 587 " --> pdb=" O LEU A 556 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 798 through 802 removed outlier: 6.582A pdb=" N THR A 776 " --> pdb=" O SER A 799 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N LEU A 801 " --> pdb=" O THR A 776 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ILE A 778 " --> pdb=" O LEU A 801 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N VAL A 741 " --> pdb=" O ILE A 777 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N VAL A 779 " --> pdb=" O VAL A 741 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N VAL A 743 " --> pdb=" O VAL A 779 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N VAL A 742 " --> pdb=" O VAL A 823 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N VAL A 825 " --> pdb=" O VAL A 742 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N CYS A 744 " --> pdb=" O VAL A 825 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N SER A 826 " --> pdb=" O GLU A 891 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 986 through 991 removed outlier: 3.570A pdb=" N GLN A1058 " --> pdb=" O TYR A1025 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLY A1023 " --> pdb=" O TYR A1060 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N LEU A1062 " --> pdb=" O CYS A1021 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N CYS A1021 " --> pdb=" O LEU A1062 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 128 through 129 Processing sheet with id=AA7, first strand: chain 'B' and resid 387 through 391 removed outlier: 6.427A pdb=" N VAL B 334 " --> pdb=" O VAL B 365 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N LEU B 367 " --> pdb=" O VAL B 334 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N VAL B 336 " --> pdb=" O LEU B 367 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N HIS B 333 " --> pdb=" O ALA B 410 " (cutoff:3.500A) removed outlier: 8.537A pdb=" N LEU B 412 " --> pdb=" O HIS B 333 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL B 335 " --> pdb=" O LEU B 412 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N LEU B 414 " --> pdb=" O VAL B 335 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N CYS B 337 " --> pdb=" O LEU B 414 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N CYS B 411 " --> pdb=" O ILE B 446 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N GLN B 448 " --> pdb=" O CYS B 411 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N VAL B 413 " --> pdb=" O GLN B 448 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 525 through 530 removed outlier: 6.906A pdb=" N GLN B 585 " --> pdb=" O ILE B 558 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ILE B 558 " --> pdb=" O GLN B 585 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N PHE B 587 " --> pdb=" O LEU B 556 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 798 through 802 removed outlier: 6.582A pdb=" N THR B 776 " --> pdb=" O SER B 799 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N LEU B 801 " --> pdb=" O THR B 776 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ILE B 778 " --> pdb=" O LEU B 801 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N VAL B 741 " --> pdb=" O ILE B 777 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N VAL B 779 " --> pdb=" O VAL B 741 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N VAL B 743 " --> pdb=" O VAL B 779 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N VAL B 742 " --> pdb=" O VAL B 823 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N VAL B 825 " --> pdb=" O VAL B 742 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N CYS B 744 " --> pdb=" O VAL B 825 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N SER B 826 " --> pdb=" O GLU B 891 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 986 through 991 removed outlier: 3.797A pdb=" N GLY B1023 " --> pdb=" O TYR B1060 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N LEU B1062 " --> pdb=" O CYS B1021 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N CYS B1021 " --> pdb=" O LEU B1062 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 128 through 129 Processing sheet with id=AB3, first strand: chain 'C' and resid 387 through 391 removed outlier: 6.426A pdb=" N VAL C 334 " --> pdb=" O VAL C 365 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N LEU C 367 " --> pdb=" O VAL C 334 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N VAL C 336 " --> pdb=" O LEU C 367 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N HIS C 333 " --> pdb=" O ALA C 410 " (cutoff:3.500A) removed outlier: 8.537A pdb=" N LEU C 412 " --> pdb=" O HIS C 333 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N VAL C 335 " --> pdb=" O LEU C 412 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N LEU C 414 " --> pdb=" O VAL C 335 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N CYS C 337 " --> pdb=" O LEU C 414 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N CYS C 411 " --> pdb=" O ILE C 446 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N GLN C 448 " --> pdb=" O CYS C 411 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N VAL C 413 " --> pdb=" O GLN C 448 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 525 through 530 removed outlier: 6.906A pdb=" N GLN C 585 " --> pdb=" O ILE C 558 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ILE C 558 " --> pdb=" O GLN C 585 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N PHE C 587 " --> pdb=" O LEU C 556 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 798 through 802 removed outlier: 6.583A pdb=" N THR C 776 " --> pdb=" O SER C 799 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N LEU C 801 " --> pdb=" O THR C 776 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ILE C 778 " --> pdb=" O LEU C 801 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N VAL C 741 " --> pdb=" O ILE C 777 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N VAL C 779 " --> pdb=" O VAL C 741 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N VAL C 743 " --> pdb=" O VAL C 779 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N VAL C 742 " --> pdb=" O VAL C 823 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N VAL C 825 " --> pdb=" O VAL C 742 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N CYS C 744 " --> pdb=" O VAL C 825 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N SER C 826 " --> pdb=" O GLU C 891 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 986 through 991 removed outlier: 3.799A pdb=" N GLY C1023 " --> pdb=" O TYR C1060 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N LEU C1062 " --> pdb=" O CYS C1021 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N CYS C1021 " --> pdb=" O LEU C1062 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 128 through 129 Processing sheet with id=AB8, first strand: chain 'D' and resid 387 through 391 removed outlier: 6.426A pdb=" N VAL D 334 " --> pdb=" O VAL D 365 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N LEU D 367 " --> pdb=" O VAL D 334 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N VAL D 336 " --> pdb=" O LEU D 367 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N HIS D 333 " --> pdb=" O ALA D 410 " (cutoff:3.500A) removed outlier: 8.539A pdb=" N LEU D 412 " --> pdb=" O HIS D 333 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL D 335 " --> pdb=" O LEU D 412 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N LEU D 414 " --> pdb=" O VAL D 335 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N CYS D 337 " --> pdb=" O LEU D 414 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N CYS D 411 " --> pdb=" O ILE D 446 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N GLN D 448 " --> pdb=" O CYS D 411 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N VAL D 413 " --> pdb=" O GLN D 448 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 525 through 530 removed outlier: 6.906A pdb=" N GLN D 585 " --> pdb=" O ILE D 558 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ILE D 558 " --> pdb=" O GLN D 585 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N PHE D 587 " --> pdb=" O LEU D 556 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 798 through 802 removed outlier: 6.582A pdb=" N THR D 776 " --> pdb=" O SER D 799 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N LEU D 801 " --> pdb=" O THR D 776 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ILE D 778 " --> pdb=" O LEU D 801 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N VAL D 741 " --> pdb=" O ILE D 777 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N VAL D 779 " --> pdb=" O VAL D 741 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N VAL D 743 " --> pdb=" O VAL D 779 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N VAL D 742 " --> pdb=" O VAL D 823 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N VAL D 825 " --> pdb=" O VAL D 742 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N CYS D 744 " --> pdb=" O VAL D 825 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N SER D 826 " --> pdb=" O GLU D 891 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 986 through 991 removed outlier: 3.569A pdb=" N GLN D1058 " --> pdb=" O TYR D1025 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLY D1023 " --> pdb=" O TYR D1060 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N LEU D1062 " --> pdb=" O CYS D1021 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N CYS D1021 " --> pdb=" O LEU D1062 " (cutoff:3.500A) 1362 hydrogen bonds defined for protein. 3744 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: 3.09 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: 5362 1.32 - 1.44: 7675 1.44 - 1.57: 15791 1.57 - 1.69: 0 1.69 - 1.82: 260 Bond restraints: 29088 Sorted by residual: bond pdb=" N GLU A 477 " pdb=" CA GLU A 477 " ideal model delta sigma weight residual 1.459 1.368 0.091 1.21e-02 6.83e+03 5.63e+01 bond pdb=" N GLU B 477 " pdb=" CA GLU B 477 " ideal model delta sigma weight residual 1.459 1.368 0.091 1.21e-02 6.83e+03 5.63e+01 bond pdb=" N GLU D 477 " pdb=" CA GLU D 477 " ideal model delta sigma weight residual 1.459 1.369 0.090 1.21e-02 6.83e+03 5.48e+01 bond pdb=" N GLU C 477 " pdb=" CA GLU C 477 " ideal model delta sigma weight residual 1.459 1.370 0.089 1.21e-02 6.83e+03 5.41e+01 bond pdb=" N GLN B 485 " pdb=" CA GLN B 485 " ideal model delta sigma weight residual 1.459 1.377 0.082 1.25e-02 6.40e+03 4.26e+01 ... (remaining 29083 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 30731 2.01 - 4.02: 7822 4.02 - 6.02: 835 6.02 - 8.03: 112 8.03 - 10.04: 32 Bond angle restraints: 39532 Sorted by residual: angle pdb=" C ASN C1046 " pdb=" N PRO C1047 " pdb=" CA PRO C1047 " ideal model delta sigma weight residual 119.66 113.38 6.28 7.20e-01 1.93e+00 7.61e+01 angle pdb=" C ALA A 476 " pdb=" N GLU A 477 " pdb=" CA GLU A 477 " ideal model delta sigma weight residual 120.28 129.52 -9.24 1.34e+00 5.57e-01 4.76e+01 angle pdb=" C ALA D 476 " pdb=" N GLU D 477 " pdb=" CA GLU D 477 " ideal model delta sigma weight residual 120.28 129.50 -9.22 1.34e+00 5.57e-01 4.74e+01 angle pdb=" C ALA C 476 " pdb=" N GLU C 477 " pdb=" CA GLU C 477 " ideal model delta sigma weight residual 120.28 129.50 -9.22 1.34e+00 5.57e-01 4.74e+01 angle pdb=" C ALA B 476 " pdb=" N GLU B 477 " pdb=" CA GLU B 477 " ideal model delta sigma weight residual 120.28 129.48 -9.20 1.34e+00 5.57e-01 4.72e+01 ... (remaining 39527 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 15935 17.78 - 35.55: 916 35.55 - 53.33: 182 53.33 - 71.10: 35 71.10 - 88.88: 32 Dihedral angle restraints: 17100 sinusoidal: 6608 harmonic: 10492 Sorted by residual: dihedral pdb=" CA LEU D 193 " pdb=" C LEU D 193 " pdb=" N GLY D 194 " pdb=" CA GLY D 194 " ideal model delta harmonic sigma weight residual 180.00 151.66 28.34 0 5.00e+00 4.00e-02 3.21e+01 dihedral pdb=" CA LEU A 193 " pdb=" C LEU A 193 " pdb=" N GLY A 194 " pdb=" CA GLY A 194 " ideal model delta harmonic sigma weight residual 180.00 151.71 28.29 0 5.00e+00 4.00e-02 3.20e+01 dihedral pdb=" CA LEU C 193 " pdb=" C LEU C 193 " pdb=" N GLY C 194 " pdb=" CA GLY C 194 " ideal model delta harmonic sigma weight residual 180.00 151.72 28.28 0 5.00e+00 4.00e-02 3.20e+01 ... (remaining 17097 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.141: 3997 0.141 - 0.282: 430 0.282 - 0.423: 41 0.423 - 0.564: 16 0.564 - 0.705: 12 Chirality restraints: 4496 Sorted by residual: chirality pdb=" CA GLN A 989 " pdb=" N GLN A 989 " pdb=" C GLN A 989 " pdb=" CB GLN A 989 " both_signs ideal model delta sigma weight residual False 2.51 1.81 0.71 2.00e-01 2.50e+01 1.24e+01 chirality pdb=" CA GLN C 989 " pdb=" N GLN C 989 " pdb=" C GLN C 989 " pdb=" CB GLN C 989 " both_signs ideal model delta sigma weight residual False 2.51 1.81 0.70 2.00e-01 2.50e+01 1.24e+01 chirality pdb=" CA GLN D 989 " pdb=" N GLN D 989 " pdb=" C GLN D 989 " pdb=" CB GLN D 989 " both_signs ideal model delta sigma weight residual False 2.51 1.81 0.70 2.00e-01 2.50e+01 1.24e+01 ... (remaining 4493 not shown) Planarity restraints: 5004 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 264 " 0.117 2.00e-02 2.50e+03 6.01e-02 9.04e+01 pdb=" CG TRP B 264 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 TRP B 264 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP B 264 " -0.059 2.00e-02 2.50e+03 pdb=" NE1 TRP B 264 " -0.035 2.00e-02 2.50e+03 pdb=" CE2 TRP B 264 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP B 264 " -0.087 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 264 " 0.063 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 264 " -0.017 2.00e-02 2.50e+03 pdb=" CH2 TRP B 264 " 0.069 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 264 " 0.118 2.00e-02 2.50e+03 6.01e-02 9.02e+01 pdb=" CG TRP A 264 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 TRP A 264 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP A 264 " -0.059 2.00e-02 2.50e+03 pdb=" NE1 TRP A 264 " -0.034 2.00e-02 2.50e+03 pdb=" CE2 TRP A 264 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP A 264 " -0.086 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 264 " 0.063 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 264 " -0.017 2.00e-02 2.50e+03 pdb=" CH2 TRP A 264 " 0.069 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 264 " -0.118 2.00e-02 2.50e+03 6.00e-02 9.01e+01 pdb=" CG TRP D 264 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 TRP D 264 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP D 264 " 0.060 2.00e-02 2.50e+03 pdb=" NE1 TRP D 264 " 0.034 2.00e-02 2.50e+03 pdb=" CE2 TRP D 264 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP D 264 " 0.086 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 264 " -0.063 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 264 " 0.017 2.00e-02 2.50e+03 pdb=" CH2 TRP D 264 " -0.068 2.00e-02 2.50e+03 ... (remaining 5001 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.83: 8393 2.83 - 3.41: 33559 3.41 - 3.98: 54177 3.98 - 4.56: 75403 4.56 - 5.14: 112129 Nonbonded interactions: 283661 Sorted by model distance: nonbonded pdb=" O GLY C 278 " pdb=" K K C1101 " model vdw 2.251 3.590 nonbonded pdb=" OD2 ASP B 356 " pdb="CA CA B1101 " model vdw 2.279 3.250 nonbonded pdb=" OD2 ASP D 356 " pdb="CA CA D1101 " model vdw 2.279 3.250 nonbonded pdb=" OD2 ASP A 356 " pdb="CA CA A1101 " model vdw 2.279 3.250 nonbonded pdb=" OD2 ASP C 356 " pdb="CA CA C1103 " model vdw 2.279 3.250 ... (remaining 283656 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 14 through 1065) selection = (chain 'B' and resid 14 through 1065) selection = (chain 'C' and resid 14 through 1065) selection = (chain 'D' and resid 14 through 1065) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 24.100 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 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 : 0.015 0.125 29088 Z= 0.944 Angle : 1.727 10.039 39532 Z= 1.152 Chirality : 0.100 0.705 4496 Planarity : 0.012 0.108 5004 Dihedral : 12.831 88.876 10316 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.62 % Favored : 95.29 % Rotamer: Outliers : 0.78 % Allowed : 4.60 % Favored : 94.61 % Cbeta Deviations : 0.35 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.13), residues: 3548 helix: -1.55 (0.10), residues: 1724 sheet: 0.15 (0.25), residues: 392 loop : -0.51 (0.17), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 190 TYR 0.094 0.012 TYR A 527 PHE 0.111 0.013 PHE A 500 TRP 0.121 0.020 TRP C 16 HIS 0.008 0.002 HIS B 786 Details of bonding type rmsd/Z covalent geometry : bond 0.01456 / 0.94 (29088) covalent geometry : angle 1.72733 / 1.15 (39532) hydrogen bonds : bond 0.19911 / 12.93 ( 1362) hydrogen bonds : angle 7.95402 / 5.69 ( 3744) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 989 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 965 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.8116 (m-80) cc_final: 0.7877 (m-80) REVERT: A 82 THR cc_start: 0.7861 (m) cc_final: 0.7644 (m) REVERT: A 246 GLU cc_start: 0.8952 (mm-30) cc_final: 0.8670 (mm-30) REVERT: A 250 ASP cc_start: 0.8653 (m-30) cc_final: 0.8417 (m-30) REVERT: A 257 ASN cc_start: 0.8719 (t0) cc_final: 0.8410 (t0) REVERT: A 300 PHE cc_start: 0.8347 (m-80) cc_final: 0.8053 (m-80) REVERT: A 317 LYS cc_start: 0.8730 (mmtm) cc_final: 0.8505 (mmtm) REVERT: A 318 ARG cc_start: 0.8453 (ptm160) cc_final: 0.8152 (ptm-80) REVERT: A 347 ASN cc_start: 0.9262 (m-40) cc_final: 0.9056 (m-40) REVERT: A 369 LYS cc_start: 0.9457 (tptp) cc_final: 0.9213 (tptp) REVERT: A 388 GLU cc_start: 0.8065 (mp0) cc_final: 0.7094 (mp0) REVERT: A 401 GLU cc_start: 0.8668 (tm-30) cc_final: 0.8410 (tm-30) REVERT: A 409 ASP cc_start: 0.8976 (t0) cc_final: 0.8552 (t0) REVERT: A 547 CYS cc_start: 0.9370 (m) cc_final: 0.8714 (m) REVERT: A 559 GLU cc_start: 0.8337 (tp30) cc_final: 0.8129 (tp30) REVERT: A 595 GLU cc_start: 0.8899 (mm-30) cc_final: 0.8631 (mm-30) REVERT: A 891 GLU cc_start: 0.8858 (tm-30) cc_final: 0.8497 (tm-30) REVERT: A 940 ASN cc_start: 0.8205 (OUTLIER) cc_final: 0.7614 (p0) REVERT: A 958 GLU cc_start: 0.8414 (mp0) cc_final: 0.8016 (mp0) REVERT: B 82 THR cc_start: 0.7846 (m) cc_final: 0.7613 (m) REVERT: B 171 PHE cc_start: 0.8639 (m-10) cc_final: 0.8425 (m-80) REVERT: B 246 GLU cc_start: 0.8983 (mm-30) cc_final: 0.8593 (mm-30) REVERT: B 250 ASP cc_start: 0.8777 (m-30) cc_final: 0.8418 (m-30) REVERT: B 252 PHE cc_start: 0.9035 (m-80) cc_final: 0.8718 (m-80) REVERT: B 271 MET cc_start: 0.9388 (tpp) cc_final: 0.9066 (tpp) REVERT: B 300 PHE cc_start: 0.8264 (m-80) cc_final: 0.7937 (m-80) REVERT: B 318 ARG cc_start: 0.8418 (ptm160) cc_final: 0.8118 (ptm-80) REVERT: B 347 ASN cc_start: 0.9286 (m-40) cc_final: 0.9052 (m110) REVERT: B 369 LYS cc_start: 0.9460 (tptp) cc_final: 0.9196 (tptp) REVERT: B 388 GLU cc_start: 0.8047 (mp0) cc_final: 0.7047 (mp0) REVERT: B 401 GLU cc_start: 0.8705 (tm-30) cc_final: 0.8430 (tm-30) REVERT: B 409 ASP cc_start: 0.8954 (t0) cc_final: 0.8530 (t0) REVERT: B 492 PHE cc_start: 0.9181 (t80) cc_final: 0.8870 (t80) REVERT: B 547 CYS cc_start: 0.9382 (m) cc_final: 0.8727 (m) REVERT: B 595 GLU cc_start: 0.8895 (mm-30) cc_final: 0.8545 (mm-30) REVERT: B 772 GLU cc_start: 0.9084 (pt0) cc_final: 0.8856 (pt0) REVERT: B 891 GLU cc_start: 0.8945 (tm-30) cc_final: 0.8564 (tm-30) REVERT: B 940 ASN cc_start: 0.8305 (OUTLIER) cc_final: 0.7738 (p0) REVERT: B 958 GLU cc_start: 0.8415 (mp0) cc_final: 0.7979 (mp0) REVERT: C 82 THR cc_start: 0.7959 (m) cc_final: 0.7731 (m) REVERT: C 169 GLU cc_start: 0.7924 (tp30) cc_final: 0.7660 (tp30) REVERT: C 246 GLU cc_start: 0.8990 (mm-30) cc_final: 0.8687 (mm-30) REVERT: C 250 ASP cc_start: 0.8783 (m-30) cc_final: 0.8510 (m-30) REVERT: C 252 PHE cc_start: 0.9029 (m-80) cc_final: 0.8720 (m-80) REVERT: C 271 MET cc_start: 0.9407 (tpp) cc_final: 0.9099 (tpp) REVERT: C 300 PHE cc_start: 0.8281 (m-80) cc_final: 0.7961 (m-80) REVERT: C 310 GLU cc_start: 0.7154 (tt0) cc_final: 0.6280 (mp0) REVERT: C 313 GLU cc_start: 0.8366 (tt0) cc_final: 0.8148 (tm-30) REVERT: C 317 LYS cc_start: 0.8720 (mmtm) cc_final: 0.8454 (mmtm) REVERT: C 318 ARG cc_start: 0.8459 (ptm160) cc_final: 0.8162 (ptm-80) REVERT: C 331 LYS cc_start: 0.9343 (mmmm) cc_final: 0.9130 (mmmm) REVERT: C 347 ASN cc_start: 0.9268 (m-40) cc_final: 0.9063 (m-40) REVERT: C 369 LYS cc_start: 0.9451 (tptp) cc_final: 0.9187 (tptp) REVERT: C 388 GLU cc_start: 0.8073 (mp0) cc_final: 0.7069 (mp0) REVERT: C 401 GLU cc_start: 0.8702 (tm-30) cc_final: 0.8439 (tm-30) REVERT: C 409 ASP cc_start: 0.8979 (t0) cc_final: 0.8752 (t0) REVERT: C 492 PHE cc_start: 0.9199 (t80) cc_final: 0.8941 (t80) REVERT: C 547 CYS cc_start: 0.9378 (m) cc_final: 0.8750 (m) REVERT: C 595 GLU cc_start: 0.8895 (mm-30) cc_final: 0.8591 (mm-30) REVERT: C 891 GLU cc_start: 0.8934 (tm-30) cc_final: 0.8538 (tm-30) REVERT: C 940 ASN cc_start: 0.8346 (OUTLIER) cc_final: 0.7782 (p0) REVERT: C 961 GLN cc_start: 0.9140 (mm-40) cc_final: 0.8937 (mt0) REVERT: D 82 THR cc_start: 0.7842 (m) cc_final: 0.7621 (m) REVERT: D 246 GLU cc_start: 0.8986 (mm-30) cc_final: 0.8628 (mm-30) REVERT: D 250 ASP cc_start: 0.8762 (m-30) cc_final: 0.8394 (m-30) REVERT: D 252 PHE cc_start: 0.9011 (m-80) cc_final: 0.8521 (m-80) REVERT: D 271 MET cc_start: 0.9419 (tpp) cc_final: 0.9213 (tpp) REVERT: D 300 PHE cc_start: 0.8304 (m-80) cc_final: 0.7964 (m-80) REVERT: D 310 GLU cc_start: 0.7149 (tt0) cc_final: 0.6770 (mm-30) REVERT: D 313 GLU cc_start: 0.8386 (tt0) cc_final: 0.8063 (tm-30) REVERT: D 317 LYS cc_start: 0.8706 (mmtm) cc_final: 0.8405 (mmtm) REVERT: D 318 ARG cc_start: 0.8446 (ptm160) cc_final: 0.8197 (ptm-80) REVERT: D 347 ASN cc_start: 0.9285 (m-40) cc_final: 0.9050 (m110) REVERT: D 369 LYS cc_start: 0.9437 (tptp) cc_final: 0.9162 (tptp) REVERT: D 384 PHE cc_start: 0.8928 (p90) cc_final: 0.8629 (p90) REVERT: D 388 GLU cc_start: 0.7985 (mp0) cc_final: 0.6965 (mp0) REVERT: D 401 GLU cc_start: 0.8713 (tm-30) cc_final: 0.8425 (tm-30) REVERT: D 409 ASP cc_start: 0.8960 (t0) cc_final: 0.8726 (t0) REVERT: D 492 PHE cc_start: 0.9191 (t80) cc_final: 0.8959 (t80) REVERT: D 547 CYS cc_start: 0.9360 (m) cc_final: 0.8712 (m) REVERT: D 595 GLU cc_start: 0.8917 (mm-30) cc_final: 0.8559 (mm-30) REVERT: D 843 ILE cc_start: 0.9508 (mp) cc_final: 0.9240 (mp) REVERT: D 846 SER cc_start: 0.9719 (t) cc_final: 0.9156 (p) REVERT: D 891 GLU cc_start: 0.8977 (tm-30) cc_final: 0.8537 (tm-30) REVERT: D 940 ASN cc_start: 0.8457 (OUTLIER) cc_final: 0.7916 (p0) REVERT: D 961 GLN cc_start: 0.9114 (mm-40) cc_final: 0.8906 (mt0) outliers start: 24 outliers final: 2 residues processed: 979 average time/residue: 0.1784 time to fit residues: 275.1236 Evaluate side-chains 772 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 766 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 940 ASN Chi-restraints excluded: chain B residue 940 ASN Chi-restraints excluded: chain C residue 940 ASN Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 940 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 10.0000 chunk 298 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 161 ASN A 214 ASN A 398 ASN ** A 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 460 ASN A 536 ASN B 161 ASN B 214 ASN B 383 HIS B 398 ASN ** B 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 460 ASN B 536 ASN C 161 ASN C 214 ASN ** C 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 460 ASN C 536 ASN D 161 ASN D 214 ASN ** D 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 460 ASN D 536 ASN D 582 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.126351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.092101 restraints weight = 47671.304| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 3.33 r_work: 0.2810 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 29088 Z= 0.155 Angle : 0.642 8.517 39532 Z= 0.342 Chirality : 0.043 0.178 4496 Planarity : 0.004 0.037 5004 Dihedral : 5.357 27.035 3878 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.86 % Allowed : 10.12 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.14), residues: 3548 helix: 0.40 (0.12), residues: 1724 sheet: -0.38 (0.24), residues: 440 loop : 0.06 (0.17), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 970 TYR 0.021 0.002 TYR A 176 PHE 0.019 0.002 PHE B 154 TRP 0.016 0.002 TRP D 514 HIS 0.003 0.001 HIS A 769 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.16 (29088) covalent geometry : angle 0.64205 / 0.34 (39532) hydrogen bonds : bond 0.05107 / 3.31 ( 1362) hydrogen bonds : angle 5.30402 / 3.70 ( 3744) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 893 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 836 time to evaluate : 1.119 Fit side-chains revert: symmetry clash REVERT: A 250 ASP cc_start: 0.8486 (m-30) cc_final: 0.8053 (m-30) REVERT: A 252 PHE cc_start: 0.8777 (m-80) cc_final: 0.8441 (m-80) REVERT: A 257 ASN cc_start: 0.8955 (t0) cc_final: 0.8131 (t0) REVERT: A 318 ARG cc_start: 0.8465 (ptm160) cc_final: 0.8232 (ptm-80) REVERT: A 401 GLU cc_start: 0.9047 (tm-30) cc_final: 0.8755 (tm-30) REVERT: A 409 ASP cc_start: 0.9236 (t0) cc_final: 0.8908 (t0) REVERT: A 547 CYS cc_start: 0.9199 (m) cc_final: 0.8802 (m) REVERT: A 559 GLU cc_start: 0.8015 (tp30) cc_final: 0.7790 (tp30) REVERT: A 591 GLU cc_start: 0.8417 (tp30) cc_final: 0.8055 (tp30) REVERT: A 891 GLU cc_start: 0.8734 (tm-30) cc_final: 0.8348 (tm-30) REVERT: A 989 GLN cc_start: 0.8906 (mt0) cc_final: 0.8638 (mt0) REVERT: A 1046 ASN cc_start: 0.9397 (t0) cc_final: 0.8962 (t0) REVERT: B 250 ASP cc_start: 0.8569 (m-30) cc_final: 0.8280 (m-30) REVERT: B 252 PHE cc_start: 0.8977 (m-80) cc_final: 0.8655 (m-80) REVERT: B 274 MET cc_start: 0.9299 (mtm) cc_final: 0.9092 (mtp) REVERT: B 318 ARG cc_start: 0.8393 (ptm160) cc_final: 0.8185 (ptm-80) REVERT: B 401 GLU cc_start: 0.9058 (tm-30) cc_final: 0.8764 (tm-30) REVERT: B 409 ASP cc_start: 0.9221 (t0) cc_final: 0.8936 (t0) REVERT: B 506 LYS cc_start: 0.9127 (mmmm) cc_final: 0.8918 (mmmm) REVERT: B 547 CYS cc_start: 0.9186 (m) cc_final: 0.8837 (m) REVERT: B 591 GLU cc_start: 0.8456 (tp30) cc_final: 0.8053 (tp30) REVERT: B 772 GLU cc_start: 0.9145 (pt0) cc_final: 0.8924 (pt0) REVERT: B 891 GLU cc_start: 0.8773 (tm-30) cc_final: 0.8305 (tm-30) REVERT: B 958 GLU cc_start: 0.8737 (mp0) cc_final: 0.8533 (mp0) REVERT: B 989 GLN cc_start: 0.8974 (mt0) cc_final: 0.8771 (mt0) REVERT: B 1046 ASN cc_start: 0.9378 (t0) cc_final: 0.8951 (t0) REVERT: C 199 ARG cc_start: 0.9230 (mmp80) cc_final: 0.8974 (mmp80) REVERT: C 250 ASP cc_start: 0.8501 (m-30) cc_final: 0.8212 (m-30) REVERT: C 252 PHE cc_start: 0.8979 (m-80) cc_final: 0.8682 (m-80) REVERT: C 271 MET cc_start: 0.9421 (tpp) cc_final: 0.9087 (tpp) REVERT: C 318 ARG cc_start: 0.8425 (ptm160) cc_final: 0.8200 (ptm-80) REVERT: C 401 GLU cc_start: 0.9078 (tm-30) cc_final: 0.8780 (tm-30) REVERT: C 409 ASP cc_start: 0.9207 (t0) cc_final: 0.8726 (t0) REVERT: C 486 SER cc_start: 0.9738 (t) cc_final: 0.9495 (t) REVERT: C 547 CYS cc_start: 0.9246 (m) cc_final: 0.8905 (m) REVERT: C 591 GLU cc_start: 0.8422 (tp30) cc_final: 0.8032 (tp30) REVERT: C 891 GLU cc_start: 0.8757 (tm-30) cc_final: 0.8284 (tm-30) REVERT: C 989 GLN cc_start: 0.8969 (mt0) cc_final: 0.8744 (mt0) REVERT: D 199 ARG cc_start: 0.9236 (mmp80) cc_final: 0.8973 (mmp80) REVERT: D 246 GLU cc_start: 0.9170 (mm-30) cc_final: 0.8826 (mm-30) REVERT: D 250 ASP cc_start: 0.8474 (m-30) cc_final: 0.8183 (m-30) REVERT: D 252 PHE cc_start: 0.8965 (m-80) cc_final: 0.8633 (m-80) REVERT: D 271 MET cc_start: 0.9429 (tpp) cc_final: 0.9087 (tpp) REVERT: D 318 ARG cc_start: 0.8468 (ptm160) cc_final: 0.8233 (ptm-80) REVERT: D 384 PHE cc_start: 0.8973 (p90) cc_final: 0.8624 (p90) REVERT: D 401 GLU cc_start: 0.9062 (tm-30) cc_final: 0.8726 (tm-30) REVERT: D 409 ASP cc_start: 0.9197 (t0) cc_final: 0.8824 (t0) REVERT: D 486 SER cc_start: 0.9736 (t) cc_final: 0.9519 (t) REVERT: D 547 CYS cc_start: 0.9195 (m) cc_final: 0.8874 (m) REVERT: D 591 GLU cc_start: 0.8475 (tp30) cc_final: 0.8068 (tp30) REVERT: D 713 MET cc_start: 0.9399 (mmm) cc_final: 0.8680 (mmm) REVERT: D 945 THR cc_start: 0.9322 (m) cc_final: 0.9091 (t) REVERT: D 989 GLN cc_start: 0.8986 (mt0) cc_final: 0.8733 (mt0) REVERT: D 1046 ASN cc_start: 0.9387 (t0) cc_final: 0.8982 (t0) outliers start: 57 outliers final: 20 residues processed: 864 average time/residue: 0.1690 time to fit residues: 233.7943 Evaluate side-chains 734 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 714 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 SER Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 947 ILE Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 709 ASP Chi-restraints excluded: chain B residue 947 ILE Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 311 ILE Chi-restraints excluded: chain C residue 709 ASP Chi-restraints excluded: chain C residue 947 ILE Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 248 SER Chi-restraints excluded: chain D residue 311 ILE Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain D residue 709 ASP Chi-restraints excluded: chain D residue 927 VAL Chi-restraints excluded: chain D residue 947 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 150 optimal weight: 0.8980 chunk 3 optimal weight: 5.9990 chunk 341 optimal weight: 0.3980 chunk 166 optimal weight: 6.9990 chunk 15 optimal weight: 0.9980 chunk 61 optimal weight: 7.9990 chunk 53 optimal weight: 6.9990 chunk 27 optimal weight: 8.9990 chunk 280 optimal weight: 0.9990 chunk 100 optimal weight: 7.9990 chunk 118 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 214 ASN A 438 ASN A 453 HIS B 214 ASN B 438 ASN C 214 ASN C 438 ASN C 453 HIS C 582 ASN D 214 ASN D 438 ASN D 453 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.126907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.092589 restraints weight = 47628.679| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 3.33 r_work: 0.2823 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 29088 Z= 0.129 Angle : 0.581 8.670 39532 Z= 0.303 Chirality : 0.041 0.170 4496 Planarity : 0.004 0.041 5004 Dihedral : 4.806 24.169 3869 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.51 % Allowed : 12.66 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.14), residues: 3548 helix: 0.98 (0.13), residues: 1728 sheet: -0.51 (0.25), residues: 440 loop : 0.34 (0.18), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 970 TYR 0.030 0.001 TYR B 176 PHE 0.023 0.002 PHE D 148 TRP 0.016 0.002 TRP A 87 HIS 0.003 0.000 HIS B 453 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (29088) covalent geometry : angle 0.58140 / 0.30 (39532) hydrogen bonds : bond 0.04231 / 2.75 ( 1362) hydrogen bonds : angle 4.92776 / 3.43 ( 3744) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 835 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 758 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 TYR cc_start: 0.8446 (m-80) cc_final: 0.8203 (m-80) REVERT: A 199 ARG cc_start: 0.9153 (mmp80) cc_final: 0.8896 (mmp80) REVERT: A 250 ASP cc_start: 0.8447 (m-30) cc_final: 0.8094 (m-30) REVERT: A 252 PHE cc_start: 0.8773 (m-80) cc_final: 0.8541 (m-80) REVERT: A 257 ASN cc_start: 0.8894 (t0) cc_final: 0.8156 (t0) REVERT: A 271 MET cc_start: 0.9487 (tpt) cc_final: 0.9243 (tpp) REVERT: A 317 LYS cc_start: 0.8765 (OUTLIER) cc_final: 0.8542 (mmmm) REVERT: A 401 GLU cc_start: 0.9069 (tm-30) cc_final: 0.8726 (tm-30) REVERT: A 409 ASP cc_start: 0.9260 (t0) cc_final: 0.9004 (t0) REVERT: A 502 MET cc_start: 0.9255 (mmp) cc_final: 0.8682 (mmp) REVERT: A 527 TYR cc_start: 0.8969 (m-80) cc_final: 0.8586 (m-80) REVERT: A 547 CYS cc_start: 0.9163 (m) cc_final: 0.8806 (m) REVERT: A 559 GLU cc_start: 0.7818 (tp30) cc_final: 0.7580 (tp30) REVERT: A 591 GLU cc_start: 0.8476 (tp30) cc_final: 0.8088 (tp30) REVERT: A 595 GLU cc_start: 0.9219 (mm-30) cc_final: 0.8651 (mm-30) REVERT: A 891 GLU cc_start: 0.8722 (tm-30) cc_final: 0.8245 (tm-30) REVERT: A 1046 ASN cc_start: 0.9398 (t0) cc_final: 0.8831 (t0) REVERT: B 148 PHE cc_start: 0.8983 (t80) cc_final: 0.8737 (t80) REVERT: B 202 ARG cc_start: 0.9059 (tpp-160) cc_final: 0.8857 (tpp80) REVERT: B 246 GLU cc_start: 0.9171 (mm-30) cc_final: 0.8805 (mm-30) REVERT: B 250 ASP cc_start: 0.8474 (m-30) cc_final: 0.8235 (m-30) REVERT: B 252 PHE cc_start: 0.8949 (m-80) cc_final: 0.8705 (m-80) REVERT: B 271 MET cc_start: 0.9461 (tpt) cc_final: 0.9191 (tpp) REVERT: B 401 GLU cc_start: 0.9081 (tm-30) cc_final: 0.8742 (tm-30) REVERT: B 451 GLN cc_start: 0.9213 (OUTLIER) cc_final: 0.9010 (mt0) REVERT: B 506 LYS cc_start: 0.9184 (mmmm) cc_final: 0.8857 (mmmm) REVERT: B 547 CYS cc_start: 0.9145 (m) cc_final: 0.8797 (m) REVERT: B 595 GLU cc_start: 0.9193 (mm-30) cc_final: 0.8618 (mm-30) REVERT: B 713 MET cc_start: 0.9413 (mmm) cc_final: 0.8675 (mmm) REVERT: B 1008 GLU cc_start: 0.8981 (OUTLIER) cc_final: 0.8736 (mt-10) REVERT: B 1046 ASN cc_start: 0.9402 (t0) cc_final: 0.8828 (t0) REVERT: C 246 GLU cc_start: 0.9138 (mm-30) cc_final: 0.8818 (mm-30) REVERT: C 250 ASP cc_start: 0.8511 (m-30) cc_final: 0.8260 (m-30) REVERT: C 252 PHE cc_start: 0.8971 (m-80) cc_final: 0.8744 (m-80) REVERT: C 271 MET cc_start: 0.9417 (tpp) cc_final: 0.9176 (tpp) REVERT: C 401 GLU cc_start: 0.9100 (tm-30) cc_final: 0.8762 (tm-30) REVERT: C 409 ASP cc_start: 0.9244 (t0) cc_final: 0.8983 (t0) REVERT: C 547 CYS cc_start: 0.9207 (m) cc_final: 0.8876 (m) REVERT: C 591 GLU cc_start: 0.8487 (tp30) cc_final: 0.8082 (tp30) REVERT: C 891 GLU cc_start: 0.8767 (tm-30) cc_final: 0.8270 (tm-30) REVERT: D 176 TYR cc_start: 0.8422 (m-80) cc_final: 0.8203 (m-80) REVERT: D 246 GLU cc_start: 0.9175 (mm-30) cc_final: 0.8880 (mm-30) REVERT: D 250 ASP cc_start: 0.8383 (m-30) cc_final: 0.8118 (m-30) REVERT: D 252 PHE cc_start: 0.8921 (m-80) cc_final: 0.8655 (m-80) REVERT: D 271 MET cc_start: 0.9405 (tpp) cc_final: 0.9169 (tpp) REVERT: D 384 PHE cc_start: 0.8989 (OUTLIER) cc_final: 0.8664 (p90) REVERT: D 401 GLU cc_start: 0.9077 (tm-30) cc_final: 0.8738 (tm-30) REVERT: D 409 ASP cc_start: 0.9235 (t0) cc_final: 0.8988 (t0) REVERT: D 547 CYS cc_start: 0.9175 (m) cc_final: 0.8875 (m) REVERT: D 1046 ASN cc_start: 0.9386 (t0) cc_final: 0.8880 (t0) outliers start: 77 outliers final: 44 residues processed: 790 average time/residue: 0.1655 time to fit residues: 208.8961 Evaluate side-chains 748 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 700 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 317 LYS Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 848 ASN Chi-restraints excluded: chain A residue 945 THR Chi-restraints excluded: chain A residue 947 ILE Chi-restraints excluded: chain A residue 1063 THR Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 451 GLN Chi-restraints excluded: chain B residue 709 ASP Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 906 ASP Chi-restraints excluded: chain B residue 945 THR Chi-restraints excluded: chain B residue 947 ILE Chi-restraints excluded: chain B residue 1008 GLU Chi-restraints excluded: chain B residue 1063 THR Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 311 ILE Chi-restraints excluded: chain C residue 360 VAL Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 709 ASP Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 906 ASP Chi-restraints excluded: chain C residue 945 THR Chi-restraints excluded: chain C residue 947 ILE Chi-restraints excluded: chain C residue 1063 THR Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 111 ILE Chi-restraints excluded: chain D residue 248 SER Chi-restraints excluded: chain D residue 311 ILE Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 384 PHE Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain D residue 709 ASP Chi-restraints excluded: chain D residue 790 LYS Chi-restraints excluded: chain D residue 906 ASP Chi-restraints excluded: chain D residue 927 VAL Chi-restraints excluded: chain D residue 947 ILE Chi-restraints excluded: chain D residue 1063 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 89 optimal weight: 20.0000 chunk 230 optimal weight: 0.9990 chunk 234 optimal weight: 2.9990 chunk 315 optimal weight: 6.9990 chunk 80 optimal weight: 9.9990 chunk 329 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 275 optimal weight: 0.7980 chunk 100 optimal weight: 9.9990 chunk 115 optimal weight: 0.7980 chunk 222 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 214 ASN A 416 ASN A 429 ASN A 961 GLN B 416 ASN B 429 ASN C 214 ASN C 416 ASN C 429 ASN D 214 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.126604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.091760 restraints weight = 47427.194| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 3.34 r_work: 0.2807 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 29088 Z= 0.140 Angle : 0.553 7.035 39532 Z= 0.288 Chirality : 0.041 0.196 4496 Planarity : 0.004 0.039 5004 Dihedral : 4.541 25.448 3868 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.51 % Allowed : 13.74 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.15), residues: 3548 helix: 1.20 (0.13), residues: 1728 sheet: -0.58 (0.25), residues: 440 loop : 0.41 (0.18), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 970 TYR 0.037 0.001 TYR B 176 PHE 0.023 0.001 PHE A 148 TRP 0.013 0.001 TRP A 80 HIS 0.002 0.000 HIS B 453 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (29088) covalent geometry : angle 0.55278 / 0.29 (39532) hydrogen bonds : bond 0.03918 / 2.56 ( 1362) hydrogen bonds : angle 4.78872 / 3.34 ( 3744) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 794 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 717 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 ASP cc_start: 0.8382 (m-30) cc_final: 0.8038 (m-30) REVERT: A 257 ASN cc_start: 0.8864 (t0) cc_final: 0.8172 (t0) REVERT: A 317 LYS cc_start: 0.8687 (OUTLIER) cc_final: 0.8307 (mppt) REVERT: A 401 GLU cc_start: 0.9097 (tm-30) cc_final: 0.8767 (tm-30) REVERT: A 409 ASP cc_start: 0.9311 (t0) cc_final: 0.9032 (t0) REVERT: A 506 LYS cc_start: 0.9278 (mmmm) cc_final: 0.8942 (mmmm) REVERT: A 559 GLU cc_start: 0.7706 (tp30) cc_final: 0.7477 (tp30) REVERT: A 595 GLU cc_start: 0.9198 (mm-30) cc_final: 0.8556 (mm-30) REVERT: A 945 THR cc_start: 0.9473 (OUTLIER) cc_final: 0.9241 (t) REVERT: A 1046 ASN cc_start: 0.9376 (t0) cc_final: 0.8778 (t0) REVERT: B 246 GLU cc_start: 0.9124 (mm-30) cc_final: 0.8813 (mm-30) REVERT: B 250 ASP cc_start: 0.8381 (m-30) cc_final: 0.8146 (m-30) REVERT: B 271 MET cc_start: 0.9452 (tpt) cc_final: 0.9216 (tpp) REVERT: B 356 ASP cc_start: 0.8713 (m-30) cc_final: 0.8425 (m-30) REVERT: B 401 GLU cc_start: 0.9107 (tm-30) cc_final: 0.8776 (tm-30) REVERT: B 451 GLN cc_start: 0.9221 (OUTLIER) cc_final: 0.8849 (mt0) REVERT: B 506 LYS cc_start: 0.9209 (mmmm) cc_final: 0.8893 (mmmm) REVERT: B 591 GLU cc_start: 0.8503 (tp30) cc_final: 0.8252 (tp30) REVERT: B 595 GLU cc_start: 0.9164 (mm-30) cc_final: 0.8518 (mm-30) REVERT: B 945 THR cc_start: 0.9571 (OUTLIER) cc_final: 0.9334 (t) REVERT: B 1008 GLU cc_start: 0.8923 (OUTLIER) cc_final: 0.8679 (mt-10) REVERT: B 1046 ASN cc_start: 0.9417 (t0) cc_final: 0.8930 (t0) REVERT: C 246 GLU cc_start: 0.9123 (mm-30) cc_final: 0.8856 (mm-30) REVERT: C 250 ASP cc_start: 0.8410 (m-30) cc_final: 0.8169 (m-30) REVERT: C 271 MET cc_start: 0.9452 (tpp) cc_final: 0.9236 (tpp) REVERT: C 356 ASP cc_start: 0.8781 (m-30) cc_final: 0.8560 (m-30) REVERT: C 401 GLU cc_start: 0.9108 (tm-30) cc_final: 0.8778 (tm-30) REVERT: C 409 ASP cc_start: 0.9242 (t0) cc_final: 0.8968 (t0) REVERT: C 506 LYS cc_start: 0.9247 (mmmm) cc_final: 0.8780 (mmmm) REVERT: C 547 CYS cc_start: 0.9216 (m) cc_final: 0.8907 (m) REVERT: C 591 GLU cc_start: 0.8631 (tp30) cc_final: 0.8329 (tp30) REVERT: C 595 GLU cc_start: 0.9184 (mm-30) cc_final: 0.8497 (mm-30) REVERT: C 945 THR cc_start: 0.9521 (OUTLIER) cc_final: 0.9285 (t) REVERT: D 199 ARG cc_start: 0.9150 (mmp80) cc_final: 0.8866 (mmp80) REVERT: D 250 ASP cc_start: 0.8302 (m-30) cc_final: 0.8027 (m-30) REVERT: D 384 PHE cc_start: 0.9135 (OUTLIER) cc_final: 0.8795 (p90) REVERT: D 401 GLU cc_start: 0.9101 (tm-30) cc_final: 0.8766 (tm-30) REVERT: D 409 ASP cc_start: 0.9274 (t0) cc_final: 0.8985 (t0) REVERT: D 547 CYS cc_start: 0.9138 (m) cc_final: 0.8823 (m) REVERT: D 595 GLU cc_start: 0.9179 (mm-30) cc_final: 0.8508 (mm-30) REVERT: D 615 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.8044 (pt0) REVERT: D 1046 ASN cc_start: 0.9391 (t0) cc_final: 0.8750 (t0) outliers start: 77 outliers final: 50 residues processed: 745 average time/residue: 0.1678 time to fit residues: 199.2192 Evaluate side-chains 737 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 679 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 230 SER Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 317 LYS Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 945 THR Chi-restraints excluded: chain A residue 947 ILE Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 451 GLN Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 906 ASP Chi-restraints excluded: chain B residue 927 VAL Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 945 THR Chi-restraints excluded: chain B residue 947 ILE Chi-restraints excluded: chain B residue 1008 GLU Chi-restraints excluded: chain B residue 1043 VAL Chi-restraints excluded: chain B residue 1063 THR Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 311 ILE Chi-restraints excluded: chain C residue 360 VAL Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 906 ASP Chi-restraints excluded: chain C residue 927 VAL Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 945 THR Chi-restraints excluded: chain C residue 947 ILE Chi-restraints excluded: chain D residue 111 ILE Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 248 SER Chi-restraints excluded: chain D residue 311 ILE Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 384 PHE Chi-restraints excluded: chain D residue 394 VAL Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain D residue 615 GLN Chi-restraints excluded: chain D residue 790 LYS Chi-restraints excluded: chain D residue 906 ASP Chi-restraints excluded: chain D residue 927 VAL Chi-restraints excluded: chain D residue 947 ILE Chi-restraints excluded: chain D residue 1063 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 346 optimal weight: 5.9990 chunk 289 optimal weight: 1.9990 chunk 138 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 157 optimal weight: 0.0980 chunk 214 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 chunk 81 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 231 optimal weight: 7.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 429 ASN ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 429 ASN B 897 ASN C 429 ASN C 897 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.126918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.091997 restraints weight = 47417.451| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 3.34 r_work: 0.2814 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.3254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 29088 Z= 0.131 Angle : 0.538 6.267 39532 Z= 0.281 Chirality : 0.041 0.172 4496 Planarity : 0.004 0.039 5004 Dihedral : 4.395 26.071 3868 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.42 % Allowed : 15.18 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.15), residues: 3548 helix: 1.23 (0.13), residues: 1740 sheet: -0.57 (0.25), residues: 440 loop : 0.55 (0.18), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 970 TYR 0.047 0.001 TYR B 176 PHE 0.021 0.001 PHE C 148 TRP 0.014 0.001 TRP B 16 HIS 0.003 0.000 HIS A 453 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (29088) covalent geometry : angle 0.53835 / 0.28 (39532) hydrogen bonds : bond 0.03690 / 2.41 ( 1362) hydrogen bonds : angle 4.70097 / 3.28 ( 3744) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 786 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 712 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 TYR cc_start: 0.8393 (m-80) cc_final: 0.8180 (m-80) REVERT: A 250 ASP cc_start: 0.8365 (m-30) cc_final: 0.8081 (m-30) REVERT: A 257 ASN cc_start: 0.8853 (t0) cc_final: 0.8204 (t0) REVERT: A 317 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.8340 (mppt) REVERT: A 401 GLU cc_start: 0.9122 (tm-30) cc_final: 0.8800 (tm-30) REVERT: A 409 ASP cc_start: 0.9280 (t0) cc_final: 0.8998 (t0) REVERT: A 506 LYS cc_start: 0.9271 (mmmm) cc_final: 0.8939 (mmmm) REVERT: A 559 GLU cc_start: 0.7693 (tp30) cc_final: 0.7466 (tp30) REVERT: A 595 GLU cc_start: 0.9162 (mm-30) cc_final: 0.8517 (mm-30) REVERT: A 945 THR cc_start: 0.9454 (OUTLIER) cc_final: 0.9220 (t) REVERT: A 1046 ASN cc_start: 0.9372 (t0) cc_final: 0.8785 (t0) REVERT: B 246 GLU cc_start: 0.9105 (mm-30) cc_final: 0.8825 (mm-30) REVERT: B 250 ASP cc_start: 0.8344 (m-30) cc_final: 0.8076 (m-30) REVERT: B 271 MET cc_start: 0.9454 (tpt) cc_final: 0.9238 (tpp) REVERT: B 401 GLU cc_start: 0.9119 (tm-30) cc_final: 0.8797 (tm-30) REVERT: B 451 GLN cc_start: 0.9215 (OUTLIER) cc_final: 0.8797 (mt0) REVERT: B 506 LYS cc_start: 0.9233 (mmmm) cc_final: 0.8914 (mmmm) REVERT: B 595 GLU cc_start: 0.9130 (mm-30) cc_final: 0.8479 (mm-30) REVERT: B 945 THR cc_start: 0.9576 (OUTLIER) cc_final: 0.9337 (t) REVERT: B 1008 GLU cc_start: 0.8938 (OUTLIER) cc_final: 0.8697 (mt-10) REVERT: B 1046 ASN cc_start: 0.9413 (t0) cc_final: 0.9019 (t0) REVERT: C 246 GLU cc_start: 0.9093 (mm-30) cc_final: 0.8826 (mm-30) REVERT: C 250 ASP cc_start: 0.8372 (m-30) cc_final: 0.8110 (m-30) REVERT: C 355 LYS cc_start: 0.9393 (ptpp) cc_final: 0.9151 (pttm) REVERT: C 401 GLU cc_start: 0.9109 (tm-30) cc_final: 0.8792 (tm-30) REVERT: C 409 ASP cc_start: 0.9244 (t0) cc_final: 0.8963 (t0) REVERT: C 506 LYS cc_start: 0.9266 (mmmm) cc_final: 0.8793 (mmmm) REVERT: C 524 MET cc_start: 0.8745 (mtp) cc_final: 0.8463 (mtp) REVERT: C 547 CYS cc_start: 0.9137 (m) cc_final: 0.8787 (m) REVERT: C 594 GLU cc_start: 0.8670 (mp0) cc_final: 0.8355 (mp0) REVERT: C 595 GLU cc_start: 0.9175 (mm-30) cc_final: 0.8526 (mm-30) REVERT: C 945 THR cc_start: 0.9527 (OUTLIER) cc_final: 0.9318 (t) REVERT: C 1046 ASN cc_start: 0.9337 (t0) cc_final: 0.8917 (t0) REVERT: D 173 PHE cc_start: 0.8782 (OUTLIER) cc_final: 0.8412 (m-80) REVERT: D 356 ASP cc_start: 0.8563 (m-30) cc_final: 0.8267 (m-30) REVERT: D 384 PHE cc_start: 0.9138 (OUTLIER) cc_final: 0.8827 (p90) REVERT: D 401 GLU cc_start: 0.9107 (tm-30) cc_final: 0.8794 (tm-30) REVERT: D 409 ASP cc_start: 0.9271 (t0) cc_final: 0.8977 (t0) REVERT: D 506 LYS cc_start: 0.9232 (mmmm) cc_final: 0.8895 (mmmm) REVERT: D 547 CYS cc_start: 0.9151 (m) cc_final: 0.8834 (m) REVERT: D 591 GLU cc_start: 0.8534 (tp30) cc_final: 0.8253 (tp30) REVERT: D 595 GLU cc_start: 0.9207 (mm-30) cc_final: 0.8526 (mm-30) REVERT: D 1046 ASN cc_start: 0.9384 (t0) cc_final: 0.8860 (t0) outliers start: 74 outliers final: 53 residues processed: 737 average time/residue: 0.1654 time to fit residues: 195.8524 Evaluate side-chains 745 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 684 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 317 LYS Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 906 ASP Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 945 THR Chi-restraints excluded: chain A residue 947 ILE Chi-restraints excluded: chain A residue 1063 THR Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 451 GLN Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 597 LYS Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 906 ASP Chi-restraints excluded: chain B residue 927 VAL Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 945 THR Chi-restraints excluded: chain B residue 947 ILE Chi-restraints excluded: chain B residue 1008 GLU Chi-restraints excluded: chain B residue 1063 THR Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 311 ILE Chi-restraints excluded: chain C residue 360 VAL Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 906 ASP Chi-restraints excluded: chain C residue 927 VAL Chi-restraints excluded: chain C residue 945 THR Chi-restraints excluded: chain C residue 947 ILE Chi-restraints excluded: chain C residue 1063 THR Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 111 ILE Chi-restraints excluded: chain D residue 150 MET Chi-restraints excluded: chain D residue 173 PHE Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 311 ILE Chi-restraints excluded: chain D residue 384 PHE Chi-restraints excluded: chain D residue 394 VAL Chi-restraints excluded: chain D residue 597 LYS Chi-restraints excluded: chain D residue 790 LYS Chi-restraints excluded: chain D residue 906 ASP Chi-restraints excluded: chain D residue 927 VAL Chi-restraints excluded: chain D residue 947 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 301 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 chunk 309 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 254 optimal weight: 3.9990 chunk 225 optimal weight: 4.9990 chunk 351 optimal weight: 8.9990 chunk 52 optimal weight: 0.0970 chunk 281 optimal weight: 3.9990 chunk 79 optimal weight: 0.8980 overall best weight: 2.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 429 ASN A 989 GLN B 214 ASN B 429 ASN C 214 ASN C 429 ASN D 416 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.120242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.085319 restraints weight = 48007.363| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 3.33 r_work: 0.2713 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 29088 Z= 0.199 Angle : 0.572 10.915 39532 Z= 0.297 Chirality : 0.042 0.188 4496 Planarity : 0.004 0.041 5004 Dihedral : 4.407 26.364 3868 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.94 % Allowed : 15.67 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.14), residues: 3548 helix: 1.24 (0.13), residues: 1740 sheet: -0.35 (0.27), residues: 396 loop : 0.43 (0.17), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 970 TYR 0.045 0.002 TYR C 176 PHE 0.019 0.001 PHE D 148 TRP 0.015 0.001 TRP C 16 HIS 0.003 0.001 HIS B 453 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.20 (29088) covalent geometry : angle 0.57242 / 0.30 (39532) hydrogen bonds : bond 0.03986 / 2.60 ( 1362) hydrogen bonds : angle 4.80256 / 3.37 ( 3744) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 818 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 728 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 PHE cc_start: 0.8750 (OUTLIER) cc_final: 0.8419 (m-80) REVERT: A 250 ASP cc_start: 0.8337 (m-30) cc_final: 0.8005 (m-30) REVERT: A 257 ASN cc_start: 0.8812 (t0) cc_final: 0.8112 (t0) REVERT: A 317 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.8308 (mppt) REVERT: A 401 GLU cc_start: 0.9150 (tm-30) cc_final: 0.8862 (tm-30) REVERT: A 492 PHE cc_start: 0.9134 (t80) cc_final: 0.8895 (t80) REVERT: A 506 LYS cc_start: 0.9340 (mmmm) cc_final: 0.9048 (mmmm) REVERT: A 559 GLU cc_start: 0.7630 (tp30) cc_final: 0.7419 (tp30) REVERT: A 591 GLU cc_start: 0.8680 (tp30) cc_final: 0.8355 (tp30) REVERT: A 595 GLU cc_start: 0.9160 (mm-30) cc_final: 0.8510 (mm-30) REVERT: A 758 ASN cc_start: 0.9444 (m-40) cc_final: 0.9114 (m-40) REVERT: A 945 THR cc_start: 0.9475 (OUTLIER) cc_final: 0.9262 (t) REVERT: A 1046 ASN cc_start: 0.9424 (t0) cc_final: 0.8822 (t0) REVERT: B 246 GLU cc_start: 0.9231 (mm-30) cc_final: 0.8946 (mm-30) REVERT: B 271 MET cc_start: 0.9497 (tpt) cc_final: 0.9257 (tpp) REVERT: B 401 GLU cc_start: 0.9162 (tm-30) cc_final: 0.8873 (tm-30) REVERT: B 451 GLN cc_start: 0.9237 (OUTLIER) cc_final: 0.8811 (mt0) REVERT: B 492 PHE cc_start: 0.9123 (t80) cc_final: 0.8881 (t80) REVERT: B 502 MET cc_start: 0.9233 (mmp) cc_final: 0.8957 (mmp) REVERT: B 506 LYS cc_start: 0.9296 (mmmm) cc_final: 0.8956 (mmmm) REVERT: B 591 GLU cc_start: 0.8592 (tp30) cc_final: 0.8299 (tp30) REVERT: B 594 GLU cc_start: 0.8840 (mp0) cc_final: 0.8443 (mp0) REVERT: B 595 GLU cc_start: 0.9185 (mm-30) cc_final: 0.8549 (mm-30) REVERT: B 945 THR cc_start: 0.9537 (OUTLIER) cc_final: 0.9327 (t) REVERT: B 1008 GLU cc_start: 0.8967 (OUTLIER) cc_final: 0.8762 (mt-10) REVERT: B 1046 ASN cc_start: 0.9445 (t0) cc_final: 0.8806 (t0) REVERT: C 246 GLU cc_start: 0.9256 (mm-30) cc_final: 0.8973 (mm-30) REVERT: C 317 LYS cc_start: 0.8682 (mmmm) cc_final: 0.8297 (mtmt) REVERT: C 401 GLU cc_start: 0.9155 (tm-30) cc_final: 0.8839 (tm-30) REVERT: C 409 ASP cc_start: 0.9275 (t0) cc_final: 0.8949 (t0) REVERT: C 492 PHE cc_start: 0.9136 (t80) cc_final: 0.8912 (t80) REVERT: C 506 LYS cc_start: 0.9327 (mmmm) cc_final: 0.8868 (mmmm) REVERT: C 547 CYS cc_start: 0.9226 (m) cc_final: 0.8890 (m) REVERT: C 591 GLU cc_start: 0.8550 (tp30) cc_final: 0.8243 (tp30) REVERT: C 594 GLU cc_start: 0.8739 (mp0) cc_final: 0.8365 (mp0) REVERT: C 595 GLU cc_start: 0.9211 (mm-30) cc_final: 0.8534 (mm-30) REVERT: C 945 THR cc_start: 0.9491 (OUTLIER) cc_final: 0.9280 (t) REVERT: C 1046 ASN cc_start: 0.9389 (t0) cc_final: 0.8910 (t0) REVERT: D 173 PHE cc_start: 0.8757 (OUTLIER) cc_final: 0.8415 (m-80) REVERT: D 176 TYR cc_start: 0.8316 (m-80) cc_final: 0.8025 (m-80) REVERT: D 257 ASN cc_start: 0.8748 (t0) cc_final: 0.8214 (t0) REVERT: D 356 ASP cc_start: 0.8709 (m-30) cc_final: 0.8481 (m-30) REVERT: D 384 PHE cc_start: 0.9206 (OUTLIER) cc_final: 0.8921 (p90) REVERT: D 401 GLU cc_start: 0.9158 (tm-30) cc_final: 0.8839 (tm-30) REVERT: D 409 ASP cc_start: 0.9275 (t0) cc_final: 0.8960 (t0) REVERT: D 506 LYS cc_start: 0.9334 (mmmm) cc_final: 0.9019 (mmmm) REVERT: D 594 GLU cc_start: 0.8807 (mp0) cc_final: 0.8451 (mp0) REVERT: D 595 GLU cc_start: 0.9208 (mm-30) cc_final: 0.8540 (mm-30) REVERT: D 615 GLN cc_start: 0.8394 (OUTLIER) cc_final: 0.7981 (pt0) REVERT: D 1046 ASN cc_start: 0.9428 (t0) cc_final: 0.8764 (t0) outliers start: 90 outliers final: 61 residues processed: 757 average time/residue: 0.1662 time to fit residues: 202.7459 Evaluate side-chains 772 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 701 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 173 PHE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 230 SER Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 317 LYS Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 547 CYS Chi-restraints excluded: chain A residue 597 LYS Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 906 ASP Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 945 THR Chi-restraints excluded: chain A residue 947 ILE Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 451 GLN Chi-restraints excluded: chain B residue 547 CYS Chi-restraints excluded: chain B residue 597 LYS Chi-restraints excluded: chain B residue 709 ASP Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 906 ASP Chi-restraints excluded: chain B residue 927 VAL Chi-restraints excluded: chain B residue 945 THR Chi-restraints excluded: chain B residue 947 ILE Chi-restraints excluded: chain B residue 1008 GLU Chi-restraints excluded: chain B residue 1014 LEU Chi-restraints excluded: chain B residue 1043 VAL Chi-restraints excluded: chain B residue 1063 THR Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 311 ILE Chi-restraints excluded: chain C residue 326 LYS Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 486 SER Chi-restraints excluded: chain C residue 709 ASP Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 906 ASP Chi-restraints excluded: chain C residue 927 VAL Chi-restraints excluded: chain C residue 945 THR Chi-restraints excluded: chain C residue 947 ILE Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 111 ILE Chi-restraints excluded: chain D residue 173 PHE Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 248 SER Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 311 ILE Chi-restraints excluded: chain D residue 384 PHE Chi-restraints excluded: chain D residue 394 VAL Chi-restraints excluded: chain D residue 486 SER Chi-restraints excluded: chain D residue 597 LYS Chi-restraints excluded: chain D residue 615 GLN Chi-restraints excluded: chain D residue 709 ASP Chi-restraints excluded: chain D residue 790 LYS Chi-restraints excluded: chain D residue 906 ASP Chi-restraints excluded: chain D residue 927 VAL Chi-restraints excluded: chain D residue 947 ILE Chi-restraints excluded: chain D residue 1063 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 215 optimal weight: 0.9990 chunk 176 optimal weight: 3.9990 chunk 255 optimal weight: 0.9990 chunk 271 optimal weight: 7.9990 chunk 22 optimal weight: 0.7980 chunk 280 optimal weight: 4.9990 chunk 96 optimal weight: 0.5980 chunk 253 optimal weight: 0.2980 chunk 310 optimal weight: 0.6980 chunk 312 optimal weight: 0.9980 chunk 198 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 214 ASN A 429 ASN B 429 ASN C 429 ASN ** C1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 ASN ** D 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 897 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.127869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.092768 restraints weight = 47166.967| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 3.36 r_work: 0.2826 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.3569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.069 29088 Z= 0.111 Angle : 0.547 9.397 39532 Z= 0.282 Chirality : 0.040 0.163 4496 Planarity : 0.004 0.049 5004 Dihedral : 4.280 27.032 3868 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.51 % Allowed : 16.91 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.15), residues: 3548 helix: 1.34 (0.13), residues: 1740 sheet: -0.30 (0.27), residues: 404 loop : 0.48 (0.17), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 970 TYR 0.050 0.001 TYR A 176 PHE 0.024 0.001 PHE C 148 TRP 0.016 0.001 TRP B 16 HIS 0.003 0.000 HIS D 453 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (29088) covalent geometry : angle 0.54683 / 0.28 (39532) hydrogen bonds : bond 0.03464 / 2.26 ( 1362) hydrogen bonds : angle 4.63747 / 3.25 ( 3744) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 824 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 747 time to evaluate : 1.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 TYR cc_start: 0.8369 (m-80) cc_final: 0.8116 (m-80) REVERT: A 250 ASP cc_start: 0.8337 (m-30) cc_final: 0.8043 (m-30) REVERT: A 257 ASN cc_start: 0.8792 (t0) cc_final: 0.8156 (t0) REVERT: A 317 LYS cc_start: 0.8648 (OUTLIER) cc_final: 0.8383 (mtmm) REVERT: A 388 GLU cc_start: 0.8273 (mp0) cc_final: 0.7763 (mp0) REVERT: A 401 GLU cc_start: 0.9127 (tm-30) cc_final: 0.8819 (tm-30) REVERT: A 506 LYS cc_start: 0.9281 (mmmm) cc_final: 0.8995 (mmmm) REVERT: A 594 GLU cc_start: 0.8762 (mp0) cc_final: 0.8367 (mp0) REVERT: A 595 GLU cc_start: 0.9190 (mm-30) cc_final: 0.8603 (mm-30) REVERT: A 758 ASN cc_start: 0.9402 (m-40) cc_final: 0.9060 (m-40) REVERT: A 970 ARG cc_start: 0.8392 (mtm110) cc_final: 0.8155 (mtm110) REVERT: A 1046 ASN cc_start: 0.9352 (t0) cc_final: 0.8778 (t0) REVERT: B 257 ASN cc_start: 0.8692 (t0) cc_final: 0.8222 (t0) REVERT: B 388 GLU cc_start: 0.8257 (mp0) cc_final: 0.7746 (mp0) REVERT: B 401 GLU cc_start: 0.9130 (tm-30) cc_final: 0.8817 (tm-30) REVERT: B 591 GLU cc_start: 0.8526 (tp30) cc_final: 0.8258 (tp30) REVERT: B 594 GLU cc_start: 0.8833 (mp0) cc_final: 0.8462 (mp0) REVERT: B 595 GLU cc_start: 0.9189 (mm-30) cc_final: 0.8584 (mm-30) REVERT: B 758 ASN cc_start: 0.9369 (m-40) cc_final: 0.9013 (m-40) REVERT: B 1008 GLU cc_start: 0.8951 (OUTLIER) cc_final: 0.8730 (mt-10) REVERT: B 1046 ASN cc_start: 0.9407 (t0) cc_final: 0.9026 (t0) REVERT: C 257 ASN cc_start: 0.8683 (t0) cc_final: 0.8242 (t0) REVERT: C 401 GLU cc_start: 0.9135 (tm-30) cc_final: 0.8827 (tm-30) REVERT: C 594 GLU cc_start: 0.8730 (mp0) cc_final: 0.8438 (mp0) REVERT: C 595 GLU cc_start: 0.9183 (mm-30) cc_final: 0.8576 (mm-30) REVERT: C 758 ASN cc_start: 0.9392 (m-40) cc_final: 0.9049 (m-40) REVERT: C 986 ARG cc_start: 0.8201 (OUTLIER) cc_final: 0.7696 (ttp-110) REVERT: D 176 TYR cc_start: 0.8331 (m-80) cc_final: 0.8044 (m-80) REVERT: D 257 ASN cc_start: 0.8653 (t0) cc_final: 0.8252 (t0) REVERT: D 355 LYS cc_start: 0.9382 (pttm) cc_final: 0.9129 (pttp) REVERT: D 356 ASP cc_start: 0.8399 (m-30) cc_final: 0.8195 (m-30) REVERT: D 384 PHE cc_start: 0.9145 (OUTLIER) cc_final: 0.8864 (p90) REVERT: D 401 GLU cc_start: 0.9116 (tm-30) cc_final: 0.8813 (tm-30) REVERT: D 409 ASP cc_start: 0.9260 (t0) cc_final: 0.8973 (t0) REVERT: D 425 GLU cc_start: 0.8650 (tp30) cc_final: 0.8200 (tp30) REVERT: D 594 GLU cc_start: 0.8792 (mp0) cc_final: 0.8425 (mp0) REVERT: D 595 GLU cc_start: 0.9227 (mm-30) cc_final: 0.8623 (mm-30) REVERT: D 615 GLN cc_start: 0.8457 (OUTLIER) cc_final: 0.8094 (pt0) REVERT: D 758 ASN cc_start: 0.9400 (m-40) cc_final: 0.9050 (m-40) REVERT: D 1046 ASN cc_start: 0.9373 (t0) cc_final: 0.8857 (t0) outliers start: 77 outliers final: 51 residues processed: 771 average time/residue: 0.1660 time to fit residues: 205.8511 Evaluate side-chains 770 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 714 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 317 LYS Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 547 CYS Chi-restraints excluded: chain A residue 597 LYS Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 906 ASP Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 947 ILE Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 547 CYS Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 906 ASP Chi-restraints excluded: chain B residue 927 VAL Chi-restraints excluded: chain B residue 947 ILE Chi-restraints excluded: chain B residue 1008 GLU Chi-restraints excluded: chain B residue 1063 THR Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 107 PHE Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 311 ILE Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 486 SER Chi-restraints excluded: chain C residue 597 LYS Chi-restraints excluded: chain C residue 906 ASP Chi-restraints excluded: chain C residue 927 VAL Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 947 ILE Chi-restraints excluded: chain C residue 986 ARG Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 111 ILE Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 311 ILE Chi-restraints excluded: chain D residue 384 PHE Chi-restraints excluded: chain D residue 394 VAL Chi-restraints excluded: chain D residue 486 SER Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain D residue 597 LYS Chi-restraints excluded: chain D residue 615 GLN Chi-restraints excluded: chain D residue 790 LYS Chi-restraints excluded: chain D residue 906 ASP Chi-restraints excluded: chain D residue 927 VAL Chi-restraints excluded: chain D residue 947 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 316 optimal weight: 0.9990 chunk 242 optimal weight: 6.9990 chunk 264 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 chunk 33 optimal weight: 7.9990 chunk 340 optimal weight: 0.9990 chunk 303 optimal weight: 0.9990 chunk 11 optimal weight: 9.9990 chunk 22 optimal weight: 0.9990 chunk 323 optimal weight: 2.9990 chunk 304 optimal weight: 5.9990 overall best weight: 0.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 429 ASN B 214 ASN B 429 ASN C 429 ASN ** C 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 140 GLN D 347 ASN ** D 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.127363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.092318 restraints weight = 47379.974| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 3.36 r_work: 0.2821 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.3678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 29088 Z= 0.126 Angle : 0.554 8.716 39532 Z= 0.287 Chirality : 0.041 0.164 4496 Planarity : 0.004 0.053 5004 Dihedral : 4.218 26.397 3868 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.06 % Allowed : 18.37 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.15), residues: 3548 helix: 1.35 (0.13), residues: 1744 sheet: -0.28 (0.28), residues: 404 loop : 0.52 (0.17), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 970 TYR 0.048 0.001 TYR B 176 PHE 0.024 0.001 PHE D 148 TRP 0.034 0.001 TRP D 16 HIS 0.002 0.000 HIS B 453 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (29088) covalent geometry : angle 0.55372 / 0.29 (39532) hydrogen bonds : bond 0.03508 / 2.28 ( 1362) hydrogen bonds : angle 4.65878 / 3.27 ( 3744) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 782 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 719 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 TYR cc_start: 0.8395 (m-80) cc_final: 0.8183 (m-80) REVERT: A 204 MET cc_start: 0.9138 (mtp) cc_final: 0.8803 (mtp) REVERT: A 250 ASP cc_start: 0.8289 (m-30) cc_final: 0.8011 (m-30) REVERT: A 257 ASN cc_start: 0.8788 (t0) cc_final: 0.8158 (t0) REVERT: A 388 GLU cc_start: 0.8303 (mp0) cc_final: 0.7800 (mp0) REVERT: A 401 GLU cc_start: 0.9136 (tm-30) cc_final: 0.8856 (tm-30) REVERT: A 506 LYS cc_start: 0.9285 (mmmm) cc_final: 0.9001 (mmmm) REVERT: A 591 GLU cc_start: 0.8480 (tp30) cc_final: 0.8192 (tp30) REVERT: A 594 GLU cc_start: 0.8789 (mp0) cc_final: 0.8392 (mp0) REVERT: A 595 GLU cc_start: 0.9175 (mm-30) cc_final: 0.8581 (mm-30) REVERT: A 758 ASN cc_start: 0.9407 (m-40) cc_final: 0.9058 (m-40) REVERT: A 986 ARG cc_start: 0.8199 (OUTLIER) cc_final: 0.7663 (ttp-110) REVERT: A 1046 ASN cc_start: 0.9366 (t0) cc_final: 0.8736 (t0) REVERT: B 257 ASN cc_start: 0.8712 (t0) cc_final: 0.8312 (t0) REVERT: B 401 GLU cc_start: 0.9138 (tm-30) cc_final: 0.8857 (tm-30) REVERT: B 451 GLN cc_start: 0.9169 (OUTLIER) cc_final: 0.8795 (mt0) REVERT: B 594 GLU cc_start: 0.8810 (mp0) cc_final: 0.8459 (mp0) REVERT: B 595 GLU cc_start: 0.9199 (mm-30) cc_final: 0.8613 (mm-30) REVERT: B 757 ARG cc_start: 0.9220 (ptm-80) cc_final: 0.8514 (ptm-80) REVERT: B 758 ASN cc_start: 0.9391 (m-40) cc_final: 0.9080 (m-40) REVERT: B 1008 GLU cc_start: 0.8949 (OUTLIER) cc_final: 0.8743 (mt-10) REVERT: B 1046 ASN cc_start: 0.9429 (t0) cc_final: 0.8793 (t0) REVERT: C 139 GLN cc_start: 0.9233 (tt0) cc_final: 0.8851 (mt0) REVERT: C 257 ASN cc_start: 0.8697 (t0) cc_final: 0.8301 (t0) REVERT: C 388 GLU cc_start: 0.8329 (mp0) cc_final: 0.7839 (mp0) REVERT: C 401 GLU cc_start: 0.9142 (tm-30) cc_final: 0.8836 (tm-30) REVERT: C 594 GLU cc_start: 0.8729 (mp0) cc_final: 0.8456 (mp0) REVERT: C 595 GLU cc_start: 0.9224 (mm-30) cc_final: 0.8581 (mm-30) REVERT: C 758 ASN cc_start: 0.9392 (m-40) cc_final: 0.9026 (m-40) REVERT: C 986 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.7712 (ttp-110) REVERT: D 176 TYR cc_start: 0.8296 (m-80) cc_final: 0.8088 (m-80) REVERT: D 202 ARG cc_start: 0.9212 (tpp-160) cc_final: 0.8988 (ttm-80) REVERT: D 257 ASN cc_start: 0.8663 (t0) cc_final: 0.8280 (t0) REVERT: D 355 LYS cc_start: 0.9419 (pttm) cc_final: 0.9151 (pttp) REVERT: D 384 PHE cc_start: 0.9164 (OUTLIER) cc_final: 0.8889 (p90) REVERT: D 401 GLU cc_start: 0.9131 (tm-30) cc_final: 0.8828 (tm-30) REVERT: D 409 ASP cc_start: 0.9258 (t0) cc_final: 0.8972 (t0) REVERT: D 425 GLU cc_start: 0.8706 (tp30) cc_final: 0.8240 (tp30) REVERT: D 594 GLU cc_start: 0.8790 (mp0) cc_final: 0.8432 (mp0) REVERT: D 595 GLU cc_start: 0.9224 (mm-30) cc_final: 0.8609 (mm-30) REVERT: D 615 GLN cc_start: 0.8469 (OUTLIER) cc_final: 0.8117 (pt0) REVERT: D 758 ASN cc_start: 0.9401 (m-40) cc_final: 0.9075 (m-40) REVERT: D 1046 ASN cc_start: 0.9386 (t0) cc_final: 0.8827 (t0) outliers start: 63 outliers final: 48 residues processed: 734 average time/residue: 0.1752 time to fit residues: 206.6506 Evaluate side-chains 751 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 697 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 547 CYS Chi-restraints excluded: chain A residue 597 LYS Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 947 ILE Chi-restraints excluded: chain A residue 986 ARG Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 451 GLN Chi-restraints excluded: chain B residue 547 CYS Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 927 VAL Chi-restraints excluded: chain B residue 947 ILE Chi-restraints excluded: chain B residue 1008 GLU Chi-restraints excluded: chain B residue 1063 THR Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 311 ILE Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 486 SER Chi-restraints excluded: chain C residue 597 LYS Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 927 VAL Chi-restraints excluded: chain C residue 947 ILE Chi-restraints excluded: chain C residue 986 ARG Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 111 ILE Chi-restraints excluded: chain D residue 250 ASP Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 311 ILE Chi-restraints excluded: chain D residue 384 PHE Chi-restraints excluded: chain D residue 394 VAL Chi-restraints excluded: chain D residue 486 SER Chi-restraints excluded: chain D residue 597 LYS Chi-restraints excluded: chain D residue 615 GLN Chi-restraints excluded: chain D residue 790 LYS Chi-restraints excluded: chain D residue 927 VAL Chi-restraints excluded: chain D residue 947 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 62 optimal weight: 0.6980 chunk 68 optimal weight: 0.3980 chunk 199 optimal weight: 0.0270 chunk 296 optimal weight: 0.0870 chunk 270 optimal weight: 10.0000 chunk 287 optimal weight: 0.0870 chunk 202 optimal weight: 0.0470 chunk 293 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 chunk 283 optimal weight: 6.9990 chunk 143 optimal weight: 7.9990 overall best weight: 0.1292 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 214 ASN A 429 ASN B 429 ASN B 536 ASN C 214 ASN C 429 ASN ** C 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 ASN ** D 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.129950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.094997 restraints weight = 47248.086| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 3.40 r_work: 0.2871 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.3899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 29088 Z= 0.109 Angle : 0.559 9.880 39532 Z= 0.284 Chirality : 0.040 0.177 4496 Planarity : 0.004 0.053 5004 Dihedral : 4.114 26.871 3868 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.50 % Allowed : 19.48 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.15), residues: 3548 helix: 1.32 (0.13), residues: 1768 sheet: 0.06 (0.28), residues: 408 loop : 0.42 (0.17), residues: 1372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 970 TYR 0.046 0.001 TYR B 176 PHE 0.030 0.001 PHE B 148 TRP 0.033 0.001 TRP C 16 HIS 0.002 0.000 HIS B 740 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 (29088) covalent geometry : angle 0.55921 / 0.28 (39532) hydrogen bonds : bond 0.03240 / 2.12 ( 1362) hydrogen bonds : angle 4.56836 / 3.21 ( 3744) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 815 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 769 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 MET cc_start: 0.9071 (mtp) cc_final: 0.8804 (mtp) REVERT: A 250 ASP cc_start: 0.8390 (m-30) cc_final: 0.8140 (m-30) REVERT: A 257 ASN cc_start: 0.8771 (t0) cc_final: 0.8180 (t0) REVERT: A 401 GLU cc_start: 0.9138 (tm-30) cc_final: 0.8827 (tm-30) REVERT: A 463 SER cc_start: 0.8884 (m) cc_final: 0.8659 (t) REVERT: A 506 LYS cc_start: 0.9277 (mmmm) cc_final: 0.8974 (mmmm) REVERT: A 594 GLU cc_start: 0.8753 (mp0) cc_final: 0.8411 (mp0) REVERT: A 595 GLU cc_start: 0.9152 (mm-30) cc_final: 0.8947 (mm-30) REVERT: A 758 ASN cc_start: 0.9390 (m-40) cc_final: 0.9078 (m-40) REVERT: A 782 LEU cc_start: 0.9471 (tp) cc_final: 0.9108 (tt) REVERT: A 891 GLU cc_start: 0.8697 (tm-30) cc_final: 0.8232 (tm-30) REVERT: A 970 ARG cc_start: 0.8421 (mtm110) cc_final: 0.8188 (mtm110) REVERT: A 986 ARG cc_start: 0.8092 (OUTLIER) cc_final: 0.7554 (ttp-110) REVERT: A 1046 ASN cc_start: 0.9318 (t0) cc_final: 0.8688 (t0) REVERT: B 257 ASN cc_start: 0.8742 (t0) cc_final: 0.8357 (t0) REVERT: B 401 GLU cc_start: 0.9130 (tm-30) cc_final: 0.8811 (tm-30) REVERT: B 463 SER cc_start: 0.8904 (m) cc_final: 0.8638 (t) REVERT: B 591 GLU cc_start: 0.8549 (tp30) cc_final: 0.8279 (tp30) REVERT: B 594 GLU cc_start: 0.8774 (mp0) cc_final: 0.8462 (mp0) REVERT: B 757 ARG cc_start: 0.9214 (ptm-80) cc_final: 0.8516 (ptm-80) REVERT: B 758 ASN cc_start: 0.9363 (m-40) cc_final: 0.9044 (m-40) REVERT: B 782 LEU cc_start: 0.9477 (tp) cc_final: 0.9122 (tt) REVERT: B 1046 ASN cc_start: 0.9396 (t0) cc_final: 0.8977 (t0) REVERT: C 148 PHE cc_start: 0.9014 (t80) cc_final: 0.8773 (t80) REVERT: C 192 TRP cc_start: 0.8541 (t60) cc_final: 0.8325 (t60) REVERT: C 257 ASN cc_start: 0.8719 (t0) cc_final: 0.8342 (t0) REVERT: C 401 GLU cc_start: 0.9136 (tm-30) cc_final: 0.8822 (tm-30) REVERT: C 463 SER cc_start: 0.8908 (m) cc_final: 0.8638 (t) REVERT: C 503 ARG cc_start: 0.8986 (mtt-85) cc_final: 0.8716 (mtt-85) REVERT: C 594 GLU cc_start: 0.8724 (mp0) cc_final: 0.8451 (mp0) REVERT: C 595 GLU cc_start: 0.9203 (mm-30) cc_final: 0.9002 (mm-30) REVERT: C 758 ASN cc_start: 0.9386 (m-40) cc_final: 0.9049 (m-40) REVERT: C 782 LEU cc_start: 0.9460 (tp) cc_final: 0.8939 (tt) REVERT: C 986 ARG cc_start: 0.8150 (OUTLIER) cc_final: 0.7637 (ttp-110) REVERT: D 176 TYR cc_start: 0.8326 (m-80) cc_final: 0.8111 (m-80) REVERT: D 202 ARG cc_start: 0.9201 (tpp-160) cc_final: 0.8952 (ttm-80) REVERT: D 257 ASN cc_start: 0.8720 (t0) cc_final: 0.8337 (t0) REVERT: D 384 PHE cc_start: 0.9103 (OUTLIER) cc_final: 0.8839 (p90) REVERT: D 401 GLU cc_start: 0.9141 (tm-30) cc_final: 0.8835 (tm-30) REVERT: D 425 GLU cc_start: 0.8629 (tp30) cc_final: 0.8181 (tp30) REVERT: D 463 SER cc_start: 0.8919 (m) cc_final: 0.8676 (t) REVERT: D 594 GLU cc_start: 0.8713 (mp0) cc_final: 0.8376 (mp0) REVERT: D 595 GLU cc_start: 0.9172 (mm-30) cc_final: 0.8948 (mm-30) REVERT: D 615 GLN cc_start: 0.8469 (OUTLIER) cc_final: 0.8135 (pt0) REVERT: D 758 ASN cc_start: 0.9396 (m-40) cc_final: 0.9059 (m-40) REVERT: D 782 LEU cc_start: 0.9471 (tp) cc_final: 0.9111 (tt) REVERT: D 1046 ASN cc_start: 0.9337 (t0) cc_final: 0.8767 (t0) outliers start: 46 outliers final: 33 residues processed: 785 average time/residue: 0.1799 time to fit residues: 227.7940 Evaluate side-chains 765 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 728 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 947 ILE Chi-restraints excluded: chain A residue 986 ARG Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 547 CYS Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 927 VAL Chi-restraints excluded: chain B residue 947 ILE Chi-restraints excluded: chain B residue 1063 THR Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 486 SER Chi-restraints excluded: chain C residue 927 VAL Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 947 ILE Chi-restraints excluded: chain C residue 986 ARG Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 111 ILE Chi-restraints excluded: chain D residue 150 MET Chi-restraints excluded: chain D residue 250 ASP Chi-restraints excluded: chain D residue 311 ILE Chi-restraints excluded: chain D residue 384 PHE Chi-restraints excluded: chain D residue 394 VAL Chi-restraints excluded: chain D residue 486 SER Chi-restraints excluded: chain D residue 615 GLN Chi-restraints excluded: chain D residue 927 VAL Chi-restraints excluded: chain D residue 947 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 2 optimal weight: 10.0000 chunk 22 optimal weight: 2.9990 chunk 60 optimal weight: 0.4980 chunk 68 optimal weight: 1.9990 chunk 177 optimal weight: 0.4980 chunk 164 optimal weight: 0.5980 chunk 285 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 232 optimal weight: 5.9990 chunk 318 optimal weight: 8.9990 chunk 179 optimal weight: 9.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 214 ASN B 140 GLN B 214 ASN C 140 GLN ** C 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 451 GLN ** 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 = 0.3560 r_free = 0.3560 target = 0.128335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.093481 restraints weight = 47301.620| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 3.37 r_work: 0.2833 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.3895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 29088 Z= 0.130 Angle : 0.576 10.331 39532 Z= 0.293 Chirality : 0.041 0.169 4496 Planarity : 0.004 0.061 5004 Dihedral : 4.080 25.236 3868 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.31 % Allowed : 20.86 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.15), residues: 3548 helix: 1.43 (0.13), residues: 1744 sheet: -0.14 (0.28), residues: 396 loop : 0.52 (0.17), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 970 TYR 0.047 0.001 TYR B 176 PHE 0.031 0.001 PHE C 148 TRP 0.037 0.001 TRP D 16 HIS 0.002 0.000 HIS B 453 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (29088) covalent geometry : angle 0.57596 / 0.29 (39532) hydrogen bonds : bond 0.03443 / 2.26 ( 1362) hydrogen bonds : angle 4.64045 / 3.26 ( 3744) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 776 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 736 time to evaluate : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 PHE cc_start: 0.8505 (m-80) cc_final: 0.8186 (m-80) REVERT: A 202 ARG cc_start: 0.9151 (tpp-160) cc_final: 0.8951 (tpp-160) REVERT: A 204 MET cc_start: 0.9101 (mtp) cc_final: 0.8829 (mtp) REVERT: A 250 ASP cc_start: 0.8321 (m-30) cc_final: 0.8074 (m-30) REVERT: A 257 ASN cc_start: 0.8778 (t0) cc_final: 0.8194 (t0) REVERT: A 401 GLU cc_start: 0.9137 (tm-30) cc_final: 0.8832 (tm-30) REVERT: A 463 SER cc_start: 0.8865 (m) cc_final: 0.8656 (t) REVERT: A 506 LYS cc_start: 0.9283 (mmmm) cc_final: 0.8982 (mmmm) REVERT: A 594 GLU cc_start: 0.8793 (mp0) cc_final: 0.8443 (mp0) REVERT: A 595 GLU cc_start: 0.9134 (mm-30) cc_final: 0.8930 (mm-30) REVERT: A 758 ASN cc_start: 0.9400 (m-40) cc_final: 0.9097 (m-40) REVERT: A 891 GLU cc_start: 0.8692 (tm-30) cc_final: 0.8240 (tm-30) REVERT: A 970 ARG cc_start: 0.8415 (mtm110) cc_final: 0.8191 (mtm110) REVERT: A 986 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.7582 (ttp-110) REVERT: A 1046 ASN cc_start: 0.9360 (t0) cc_final: 0.8715 (t0) REVERT: B 202 ARG cc_start: 0.9090 (tpp-160) cc_final: 0.8889 (ttm-80) REVERT: B 257 ASN cc_start: 0.8710 (t0) cc_final: 0.8333 (t0) REVERT: B 401 GLU cc_start: 0.9125 (tm-30) cc_final: 0.8820 (tm-30) REVERT: B 463 SER cc_start: 0.8874 (m) cc_final: 0.8619 (t) REVERT: B 591 GLU cc_start: 0.8487 (tp30) cc_final: 0.8209 (tp30) REVERT: B 594 GLU cc_start: 0.8813 (mp0) cc_final: 0.8493 (mp0) REVERT: B 757 ARG cc_start: 0.9225 (ptm-80) cc_final: 0.8516 (ptm-80) REVERT: B 758 ASN cc_start: 0.9382 (m-40) cc_final: 0.9076 (m-40) REVERT: B 1046 ASN cc_start: 0.9407 (t0) cc_final: 0.8776 (t0) REVERT: C 171 PHE cc_start: 0.8536 (m-80) cc_final: 0.8153 (m-80) REVERT: C 202 ARG cc_start: 0.9102 (tpp-160) cc_final: 0.8776 (tpp80) REVERT: C 257 ASN cc_start: 0.8696 (t0) cc_final: 0.8322 (t0) REVERT: C 401 GLU cc_start: 0.9154 (tm-30) cc_final: 0.8846 (tm-30) REVERT: C 463 SER cc_start: 0.8825 (m) cc_final: 0.8604 (t) REVERT: C 503 ARG cc_start: 0.9041 (mtt-85) cc_final: 0.8767 (mtt-85) REVERT: C 594 GLU cc_start: 0.8722 (mp0) cc_final: 0.8471 (mp0) REVERT: C 595 GLU cc_start: 0.9223 (mm-30) cc_final: 0.9006 (mm-30) REVERT: C 758 ASN cc_start: 0.9386 (m-40) cc_final: 0.9053 (m-40) REVERT: C 986 ARG cc_start: 0.8201 (OUTLIER) cc_final: 0.7698 (ttp-110) REVERT: D 176 TYR cc_start: 0.8337 (m-80) cc_final: 0.8130 (m-80) REVERT: D 202 ARG cc_start: 0.9214 (tpp-160) cc_final: 0.8933 (ttm-80) REVERT: D 257 ASN cc_start: 0.8705 (t0) cc_final: 0.8326 (t0) REVERT: D 384 PHE cc_start: 0.9152 (OUTLIER) cc_final: 0.8890 (p90) REVERT: D 401 GLU cc_start: 0.9147 (tm-30) cc_final: 0.8851 (tm-30) REVERT: D 463 SER cc_start: 0.8840 (m) cc_final: 0.8637 (t) REVERT: D 594 GLU cc_start: 0.8757 (mp0) cc_final: 0.8441 (mp0) REVERT: D 595 GLU cc_start: 0.9163 (mm-30) cc_final: 0.8934 (mm-30) REVERT: D 615 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.8067 (pt0) REVERT: D 758 ASN cc_start: 0.9396 (m-40) cc_final: 0.9065 (m-40) REVERT: D 1046 ASN cc_start: 0.9391 (t0) cc_final: 0.8771 (t0) outliers start: 40 outliers final: 34 residues processed: 746 average time/residue: 0.1717 time to fit residues: 206.1291 Evaluate side-chains 763 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 725 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 947 ILE Chi-restraints excluded: chain A residue 986 ARG Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 547 CYS Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 927 VAL Chi-restraints excluded: chain B residue 947 ILE Chi-restraints excluded: chain B residue 1063 THR Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 107 PHE Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 927 VAL Chi-restraints excluded: chain C residue 947 ILE Chi-restraints excluded: chain C residue 986 ARG Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 111 ILE Chi-restraints excluded: chain D residue 150 MET Chi-restraints excluded: chain D residue 250 ASP Chi-restraints excluded: chain D residue 311 ILE Chi-restraints excluded: chain D residue 384 PHE Chi-restraints excluded: chain D residue 394 VAL Chi-restraints excluded: chain D residue 615 GLN Chi-restraints excluded: chain D residue 927 VAL Chi-restraints excluded: chain D residue 947 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 241 optimal weight: 0.4980 chunk 87 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 110 optimal weight: 0.9980 chunk 315 optimal weight: 8.9990 chunk 62 optimal weight: 0.7980 chunk 169 optimal weight: 10.0000 chunk 309 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 158 optimal weight: 7.9990 chunk 281 optimal weight: 7.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 ASN ** C 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 ASN D 438 ASN ** D 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.128450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.093316 restraints weight = 47436.291| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 3.38 r_work: 0.2833 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.3935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 29088 Z= 0.133 Angle : 0.581 9.761 39532 Z= 0.294 Chirality : 0.041 0.188 4496 Planarity : 0.004 0.061 5004 Dihedral : 4.072 26.114 3868 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.37 % Allowed : 21.28 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.15), residues: 3548 helix: 1.42 (0.13), residues: 1744 sheet: -0.09 (0.28), residues: 392 loop : 0.46 (0.17), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 970 TYR 0.051 0.001 TYR A 176 PHE 0.038 0.001 PHE B 148 TRP 0.037 0.001 TRP D 16 HIS 0.002 0.000 HIS B 440 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 (29088) covalent geometry : angle 0.58127 / 0.29 (39532) hydrogen bonds : bond 0.03463 / 2.28 ( 1362) hydrogen bonds : angle 4.64660 / 3.27 ( 3744) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6397.08 seconds wall clock time: 110 minutes 20.86 seconds (6620.86 seconds total)