Starting phenix.real_space_refine on Mon Aug 25 23:50:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yr2_34043/08_2025/7yr2_34043.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yr2_34043/08_2025/7yr2_34043.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yr2_34043/08_2025/7yr2_34043.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yr2_34043/08_2025/7yr2_34043.map" model { file = "/net/cci-nas-00/data/ceres_data/7yr2_34043/08_2025/7yr2_34043.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yr2_34043/08_2025/7yr2_34043.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.033 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 Zn 1 6.06 5 S 140 5.16 5 Cl 1 4.86 5 C 20008 2.51 5 N 5142 2.21 5 O 6200 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 61 residue(s): 0.06s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31492 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 4870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569} Chain: "D" Number of atoms: 8535 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1097, 8530 Classifications: {'peptide': 1097} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 58, 'TRANS': 1038} Chain breaks: 2 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 59 Planarities with less than four sites: {'ARG:plan': 4, 'TYR:plan': 1, 'TRP:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 42 Conformer: "B" Number of residues, atoms: 1097, 8530 Classifications: {'peptide': 1097} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 58, 'TRANS': 1038} Chain breaks: 2 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 59 Planarities with less than four sites: {'ARG:plan': 4, 'TYR:plan': 1, 'TRP:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 42 bond proxies already assigned to first conformer: 8729 Chain: "E" Number of atoms: 8540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1097, 8540 Classifications: {'peptide': 1097} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 58, 'TRANS': 1038} Chain breaks: 2 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 48 Planarities with less than four sites: {'ARG:plan': 4, 'TYR:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "C" Number of atoms: 8536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1097, 8536 Classifications: {'peptide': 1097} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 58, 'TRANS': 1038} Chain breaks: 2 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 53 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 1, 'TYR:plan': 1, 'TRP:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 58 Unusual residues: {' CL': 1, ' ZN': 1, 'NAG': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "D" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Chain: "E" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Chain: "C" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Chain: "A" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 71 Classifications: {'water': 71} Link IDs: {None: 70} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG D 78 " occ=0.51 ... (8 atoms not shown) pdb=" CB BARG D 78 " occ=0.49 Time building chain proxies: 10.41, per 1000 atoms: 0.33 Number of scatterers: 31492 At special positions: 0 Unit cell: (156, 173.68, 237.12, 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) Zn 1 29.99 Cl 1 17.00 S 140 16.00 O 6200 8.00 N 5142 7.00 C 20008 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 166 " distance=2.03 Simple disulfide: pdb=" SG CYS D 291 " - pdb=" SG CYS D 301 " distance=2.03 Simple disulfide: pdb=" SG CYS D 336 " - pdb=" SG CYS D 361 " distance=2.02 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.03 Simple disulfide: pdb=" SG CYS D 391 " - pdb=" SG CYS D 525 " distance=2.03 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 617 " - pdb=" SG CYS D 649 " distance=2.03 Simple disulfide: pdb=" SG CYS D 662 " - pdb=" SG CYS D 671 " distance=2.03 Simple disulfide: pdb=" SG CYS D 738 " - pdb=" SG CYS D 760 " distance=2.03 Simple disulfide: pdb=" SG CYS D 743 " - pdb=" SG CYS D 749 " distance=2.03 Simple disulfide: pdb=" SG CYS D1032 " - pdb=" SG CYS D1043 " distance=2.03 Simple disulfide: pdb=" SG CYS D1082 " - pdb=" SG CYS D1126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 166 " distance=2.03 Simple disulfide: pdb=" SG CYS E 291 " - pdb=" SG CYS E 301 " distance=2.03 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.03 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 Simple disulfide: pdb=" SG CYS E 617 " - pdb=" SG CYS E 649 " distance=2.03 Simple disulfide: pdb=" SG CYS E 662 " - pdb=" SG CYS E 671 " distance=2.03 Simple disulfide: pdb=" SG CYS E 738 " - pdb=" SG CYS E 760 " distance=2.03 Simple disulfide: pdb=" SG CYS E 743 " - pdb=" SG CYS E 749 " distance=2.03 Simple disulfide: pdb=" SG CYS E1032 " - pdb=" SG CYS E1043 " distance=2.03 Simple disulfide: pdb=" SG CYS E1082 " - pdb=" SG CYS E1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " NAG-ASN " NAG A 903 " - " ASN A 546 " " NAG A 904 " - " ASN A 90 " " NAG A 905 " - " ASN A 322 " " NAG A 906 " - " ASN A 53 " " NAG B 1 " - " ASN D 717 " " NAG C1301 " - " ASN C 61 " " NAG C1311 " - " ASN C 616 " " NAG C1313 " - " ASN C 709 " " NAG C1315 " - " ASN C1134 " " NAG D1301 " - " ASN D 61 " " NAG D1302 " - " ASN D 74 " " NAG D1303 " - " ASN D 122 " " NAG D1304 " - " ASN D 149 " " NAG D1305 " - " ASN D 165 " " NAG D1306 " - " ASN D 234 " " NAG D1307 " - " ASN D 282 " " NAG D1308 " - " ASN D 331 " " NAG D1310 " - " ASN D 603 " " NAG D1311 " - " ASN D 616 " " NAG D1312 " - " ASN D 657 " " NAG D1313 " - " ASN D 709 " " NAG E1301 " - " ASN E 61 " " NAG E1302 " - " ASN E 74 " " NAG E1303 " - " ASN E 122 " " NAG E1304 " - " ASN E 149 " " NAG E1305 " - " ASN E 165 " " NAG E1306 " - " ASN E 234 " " NAG E1307 " - " ASN E 282 " " NAG E1308 " - " ASN E 331 " " NAG E1309 " - " ASN E 343 " " NAG E1310 " - " ASN E 603 " " NAG E1311 " - " ASN E 616 " " NAG E1312 " - " ASN E 657 " " NAG E1313 " - " ASN E 709 " " NAG E1314 " - " ASN E1098 " " NAG E1315 " - " ASN E1134 " " NAG F 1 " - " ASN D 801 " " NAG G 1 " - " ASN D1074 " " NAG H 1 " - " ASN E 717 " " NAG I 1 " - " ASN E 801 " " NAG J 1 " - " ASN E1074 " " NAG K 1 " - " ASN C 717 " " NAG L 1 " - " ASN C 801 " " NAG M 1 " - " ASN C1074 " Time building additional restraints: 2.79 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 1.2 microseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 901 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 374 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 378 " 7742 Ramachandran restraints generated. 3871 Oldfield, 0 Emsley, 3871 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7294 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 53 sheets defined 27.6% alpha, 14.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 4.270A pdb=" N ASP A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 81 Processing helix chain 'A' and resid 92 through 101 removed outlier: 3.799A pdb=" N GLN A 96 " --> pdb=" O THR A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 108 removed outlier: 3.841A pdb=" N VAL A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU A 108 " --> pdb=" O SER A 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 104 through 108' Processing helix chain 'A' and resid 109 through 129 Processing helix chain 'A' and resid 146 through 155 removed outlier: 3.576A pdb=" N ASN A 154 " --> pdb=" O GLU A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 194 removed outlier: 3.692A pdb=" N LYS A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N GLN A 175 " --> pdb=" O GLU A 171 " (cutoff:3.500A) Proline residue: A 178 - end of helix Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 218 through 252 removed outlier: 3.701A pdb=" N ILE A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLU A 232 " --> pdb=" O HIS A 228 " (cutoff:3.500A) Proline residue: A 235 - end of helix Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 293 through 301 Processing helix chain 'A' and resid 303 through 318 Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.744A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 384 Processing helix chain 'A' and resid 399 through 413 Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 431 through 446 Processing helix chain 'A' and resid 448 through 466 removed outlier: 4.391A pdb=" N PHE A 452 " --> pdb=" O GLY A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 484 Processing helix chain 'A' and resid 498 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 512 through 533 removed outlier: 4.119A pdb=" N TYR A 516 " --> pdb=" O PHE A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.542A pdb=" N GLY A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 4.487A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL A 574 " --> pdb=" O LEU A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 599 Proline residue: A 590 - end of helix Processing helix chain 'D' and resid 294 through 303 Processing helix chain 'D' and resid 337 through 343 removed outlier: 4.052A pdb=" N VAL D 341 " --> pdb=" O PRO D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 371 Processing helix chain 'D' and resid 417 through 422 Processing helix chain 'D' and resid 737 through 742 Processing helix chain 'D' and resid 746 through 754 removed outlier: 3.808A pdb=" N LEU D 752 " --> pdb=" O GLU D 748 " (cutoff:3.500A) Processing helix chain 'D' and resid 755 through 757 No H-bonds generated for 'chain 'D' and resid 755 through 757' Processing helix chain 'D' and resid 760 through 783 removed outlier: 3.513A pdb=" N ASP D 775 " --> pdb=" O ALA D 771 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N PHE D 782 " --> pdb=" O THR D 778 " (cutoff:3.500A) Processing helix chain 'D' and resid 816 through 826 Processing helix chain 'D' and resid 869 through 884 removed outlier: 3.624A pdb=" N THR D 883 " --> pdb=" O ALA D 879 " (cutoff:3.500A) Processing helix chain 'D' and resid 886 through 890 Processing helix chain 'D' and resid 897 through 908 Processing helix chain 'D' and resid 913 through 918 Processing helix chain 'D' and resid 919 through 941 removed outlier: 4.555A pdb=" N GLN D 935 " --> pdb=" O ILE D 931 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ASP D 936 " --> pdb=" O GLY D 932 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR D 941 " --> pdb=" O SER D 937 " (cutoff:3.500A) Processing helix chain 'D' and resid 945 through 965 removed outlier: 3.610A pdb=" N GLN D 965 " --> pdb=" O THR D 961 " (cutoff:3.500A) Processing helix chain 'D' and resid 976 through 983 Processing helix chain 'D' and resid 985 through 1033 removed outlier: 4.336A pdb=" N VAL D 991 " --> pdb=" O PRO D 987 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG D 995 " --> pdb=" O VAL D 991 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU D 996 " --> pdb=" O GLN D 992 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLN D1002 " --> pdb=" O THR D 998 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 303 removed outlier: 3.533A pdb=" N LEU E 303 " --> pdb=" O THR E 299 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 343 Processing helix chain 'E' and resid 405 through 410 removed outlier: 4.499A pdb=" N SER E 408 " --> pdb=" O ASN E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 422 removed outlier: 3.558A pdb=" N TYR E 421 " --> pdb=" O ASN E 417 " (cutoff:3.500A) Processing helix chain 'E' and resid 737 through 742 Processing helix chain 'E' and resid 746 through 755 Processing helix chain 'E' and resid 759 through 783 removed outlier: 3.668A pdb=" N LEU E 763 " --> pdb=" O PHE E 759 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR E 778 " --> pdb=" O GLN E 774 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLN E 779 " --> pdb=" O ASP E 775 " (cutoff:3.500A) Processing helix chain 'E' and resid 816 through 826 Processing helix chain 'E' and resid 851 through 855 removed outlier: 3.569A pdb=" N PHE E 855 " --> pdb=" O ALA E 852 " (cutoff:3.500A) Processing helix chain 'E' and resid 869 through 884 Processing helix chain 'E' and resid 886 through 890 Processing helix chain 'E' and resid 897 through 908 Processing helix chain 'E' and resid 912 through 941 removed outlier: 4.401A pdb=" N LEU E 916 " --> pdb=" O THR E 912 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N LYS E 921 " --> pdb=" O TYR E 917 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEU E 922 " --> pdb=" O GLU E 918 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLN E 935 " --> pdb=" O ILE E 931 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASP E 936 " --> pdb=" O GLY E 932 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR E 941 " --> pdb=" O SER E 937 " (cutoff:3.500A) Processing helix chain 'E' and resid 945 through 965 removed outlier: 3.552A pdb=" N ASN E 955 " --> pdb=" O VAL E 951 " (cutoff:3.500A) Processing helix chain 'E' and resid 976 through 984 Processing helix chain 'E' and resid 985 through 1032 removed outlier: 4.541A pdb=" N VAL E 991 " --> pdb=" O PRO E 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 366 through 371 removed outlier: 3.668A pdb=" N TYR C 369 " --> pdb=" O SER C 366 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN C 370 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.718A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 737 through 742 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.765A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 760 through 783 removed outlier: 3.604A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLN C 779 " --> pdb=" O ASP C 775 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 850 through 854 Processing helix chain 'C' and resid 869 through 884 Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.512A pdb=" N ALA C 890 " --> pdb=" O THR C 887 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.637A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 941 removed outlier: 6.998A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.526A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 981 removed outlier: 3.775A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.096A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 262 through 263 removed outlier: 5.945A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 350 Processing sheet with id=AA3, first strand: chain 'D' and resid 26 through 30 removed outlier: 4.346A pdb=" N TYR D 265 " --> pdb=" O PHE D 65 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 42 through 43 removed outlier: 3.848A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 50 through 55 removed outlier: 3.747A pdb=" N ASP D 287 " --> pdb=" O LYS D 278 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 84 through 85 Processing sheet with id=AA7, first strand: chain 'D' and resid 311 through 318 removed outlier: 7.565A pdb=" N VAL D 595 " --> pdb=" O THR D 315 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N ASN D 317 " --> pdb=" O GLY D 593 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N GLY D 593 " --> pdb=" O ASN D 317 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLY D 594 " --> pdb=" O GLN D 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 325 through 326 removed outlier: 3.620A pdb=" N ASN D 542 " --> pdb=" O ILE D 326 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL D 539 " --> pdb=" O GLY D 550 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 356 through 358 Processing sheet with id=AB1, first strand: chain 'D' and resid 361 through 362 removed outlier: 6.632A pdb=" N CYS D 361 " --> pdb=" O CYS D 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'D' and resid 452 through 454 removed outlier: 4.042A pdb=" N TYR D 453 " --> pdb=" O GLN D 493 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 575 through 577 Processing sheet with id=AB4, first strand: chain 'D' and resid 654 through 655 removed outlier: 5.642A pdb=" N GLU D 654 " --> pdb=" O ALA D 694 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N THR D 696 " --> pdb=" O GLU D 654 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER D 691 " --> pdb=" O GLN D 675 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE D 670 " --> pdb=" O ILE D 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 702 through 704 Processing sheet with id=AB6, first strand: chain 'D' and resid 711 through 715 removed outlier: 3.550A pdb=" N LYS D1073 " --> pdb=" O ILE D 714 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 718 through 728 removed outlier: 7.324A pdb=" N GLY D1059 " --> pdb=" O SER D1055 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N SER D1055 " --> pdb=" O GLY D1059 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL D1061 " --> pdb=" O PRO D1053 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N LEU D1063 " --> pdb=" O SER D1051 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N SER D1051 " --> pdb=" O LEU D1063 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N VAL D1065 " --> pdb=" O LEU D1049 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 733 through 735 removed outlier: 4.395A pdb=" N LYS D 733 " --> pdb=" O LEU D 861 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 787 through 788 Processing sheet with id=AC1, first strand: chain 'D' and resid 1088 through 1090 Processing sheet with id=AC2, first strand: chain 'E' and resid 28 through 30 removed outlier: 3.528A pdb=" N THR E 63 " --> pdb=" O VAL E 267 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL E 267 " --> pdb=" O THR E 63 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TYR E 91 " --> pdb=" O GLY E 268 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR E 208 " --> pdb=" O LEU E 189 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TYR E 204 " --> pdb=" O VAL E 193 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 50 through 55 removed outlier: 4.240A pdb=" N ASP E 287 " --> pdb=" O LYS E 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 168 through 169 removed outlier: 3.821A pdb=" N PHE E 168 " --> pdb=" O VAL E 130 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N PHE E 106 " --> pdb=" O LEU E 117 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 311 through 319 removed outlier: 7.093A pdb=" N VAL E 595 " --> pdb=" O THR E 315 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ASN E 317 " --> pdb=" O GLY E 593 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N GLY E 593 " --> pdb=" O ASN E 317 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 325 through 326 Processing sheet with id=AC7, first strand: chain 'E' and resid 354 through 358 removed outlier: 4.167A pdb=" N VAL E 395 " --> pdb=" O ILE E 358 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 361 through 362 removed outlier: 6.352A pdb=" N CYS E 361 " --> pdb=" O CYS E 525 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'E' and resid 565 through 566 removed outlier: 7.099A pdb=" N PHE E 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'E' and resid 654 through 655 removed outlier: 5.732A pdb=" N GLU E 654 " --> pdb=" O ALA E 694 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N THR E 696 " --> pdb=" O GLU E 654 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ILE E 670 " --> pdb=" O ILE E 666 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 702 through 704 removed outlier: 3.736A pdb=" N LYS C 790 " --> pdb=" O ASN E 703 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 711 through 715 Processing sheet with id=AD5, first strand: chain 'E' and resid 718 through 727 removed outlier: 7.073A pdb=" N GLY E1059 " --> pdb=" O SER E1055 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N SER E1055 " --> pdb=" O GLY E1059 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL E1061 " --> pdb=" O PRO E1053 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N LEU E1063 " --> pdb=" O SER E1051 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N SER E1051 " --> pdb=" O LEU E1063 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL E1065 " --> pdb=" O LEU E1049 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 733 through 735 removed outlier: 4.377A pdb=" N LYS E 733 " --> pdb=" O LEU E 861 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 1081 through 1082 Processing sheet with id=AD8, first strand: chain 'E' and resid 1094 through 1097 Processing sheet with id=AD9, first strand: chain 'C' and resid 26 through 30 removed outlier: 3.509A pdb=" N SER C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N SER C 94 " --> pdb=" O ARG C 190 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 50 through 55 removed outlier: 3.806A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 168 through 169 removed outlier: 3.943A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL C 130 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 201 through 202 removed outlier: 3.781A pdb=" N LEU C 229 " --> pdb=" O PHE C 201 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.323A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 324 through 326 removed outlier: 7.692A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.656A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE C 543 " --> pdb=" O LEU C 546 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.043A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.366A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE9, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.763A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 659 through 660 removed outlier: 4.489A pdb=" N TYR C 660 " --> pdb=" O THR C 696 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 674 through 675 Processing sheet with id=AF3, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AF4, first strand: chain 'C' and resid 718 through 728 removed outlier: 7.012A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF6, first strand: chain 'C' and resid 1081 through 1082 Processing sheet with id=AF7, first strand: chain 'C' and resid 1089 through 1090 Processing sheet with id=AF8, first strand: chain 'C' and resid 1094 through 1097 1073 hydrogen bonds defined for protein. 2991 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.96 Time building geometry restraints manager: 3.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.89 - 1.08: 1 1.08 - 1.27: 5101 1.27 - 1.46: 12806 1.46 - 1.65: 14076 1.65 - 1.85: 189 Bond restraints: 32173 Sorted by residual: bond pdb=" CG PRO A 321 " pdb=" CD PRO A 321 " ideal model delta sigma weight residual 1.503 0.890 0.613 3.40e-02 8.65e+02 3.25e+02 bond pdb=" N PRO A 321 " pdb=" CD PRO A 321 " ideal model delta sigma weight residual 1.473 1.606 -0.133 1.40e-02 5.10e+03 9.02e+01 bond pdb=" CB PRO A 321 " pdb=" CG PRO A 321 " ideal model delta sigma weight residual 1.492 1.846 -0.354 5.00e-02 4.00e+02 5.00e+01 bond pdb=" N PRO A 321 " pdb=" CA PRO A 321 " ideal model delta sigma weight residual 1.466 1.404 0.063 1.17e-02 7.31e+03 2.86e+01 bond pdb=" C1 NAG E1303 " pdb=" O5 NAG E1303 " ideal model delta sigma weight residual 1.406 1.475 -0.069 2.00e-02 2.50e+03 1.19e+01 ... (remaining 32168 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.86: 43738 4.86 - 9.72: 60 9.72 - 14.57: 4 14.57 - 19.43: 1 19.43 - 24.29: 2 Bond angle restraints: 43805 Sorted by residual: angle pdb=" N PRO A 321 " pdb=" CD PRO A 321 " pdb=" CG PRO A 321 " ideal model delta sigma weight residual 103.20 78.91 24.29 1.50e+00 4.44e-01 2.62e+02 angle pdb=" CA PRO A 321 " pdb=" N PRO A 321 " pdb=" CD PRO A 321 " ideal model delta sigma weight residual 112.00 94.34 17.66 1.40e+00 5.10e-01 1.59e+02 angle pdb=" N ASN D 331 " pdb=" CA ASN D 331 " pdb=" C ASN D 331 " ideal model delta sigma weight residual 111.71 97.76 13.95 1.15e+00 7.56e-01 1.47e+02 angle pdb=" CA PRO A 321 " pdb=" CB PRO A 321 " pdb=" CG PRO A 321 " ideal model delta sigma weight residual 104.50 84.26 20.24 1.90e+00 2.77e-01 1.14e+02 angle pdb=" N PRO D 330 " pdb=" CA PRO D 330 " pdb=" C PRO D 330 " ideal model delta sigma weight residual 112.47 125.47 -13.00 2.06e+00 2.36e-01 3.98e+01 ... (remaining 43800 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.93: 18852 24.93 - 49.85: 957 49.85 - 74.78: 154 74.78 - 99.71: 33 99.71 - 124.63: 4 Dihedral angle restraints: 20000 sinusoidal: 8651 harmonic: 11349 Sorted by residual: dihedral pdb=" CB CYS D 738 " pdb=" SG CYS D 738 " pdb=" SG CYS D 760 " pdb=" CB CYS D 760 " ideal model delta sinusoidal sigma weight residual 93.00 -178.79 -88.21 1 1.00e+01 1.00e-02 9.30e+01 dihedral pdb=" CB CYS E 662 " pdb=" SG CYS E 662 " pdb=" SG CYS E 671 " pdb=" CB CYS E 671 " ideal model delta sinusoidal sigma weight residual -86.00 -2.86 -83.14 1 1.00e+01 1.00e-02 8.45e+01 dihedral pdb=" CB CYS C 336 " pdb=" SG CYS C 336 " pdb=" SG CYS C 361 " pdb=" CB CYS C 361 " ideal model delta sinusoidal sigma weight residual 93.00 21.16 71.84 1 1.00e+01 1.00e-02 6.61e+01 ... (remaining 19997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 4699 0.090 - 0.181: 363 0.181 - 0.271: 8 0.271 - 0.362: 4 0.362 - 0.452: 5 Chirality restraints: 5079 Sorted by residual: chirality pdb=" C1 NAG D1301 " pdb=" ND2 ASN D 61 " pdb=" C2 NAG D1301 " pdb=" O5 NAG D1301 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-01 2.50e+01 5.12e+00 chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN E 801 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 4.00e+00 chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN D 801 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.52e+00 ... (remaining 5076 not shown) Planarity restraints: 5639 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 320 " -0.112 5.00e-02 4.00e+02 1.52e-01 3.68e+01 pdb=" N PRO A 321 " 0.261 5.00e-02 4.00e+02 pdb=" CA PRO A 321 " -0.078 5.00e-02 4.00e+02 pdb=" CD PRO A 321 " -0.071 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG D 328 " 0.025 2.00e-02 2.50e+03 5.01e-02 2.51e+01 pdb=" C ARG D 328 " -0.087 2.00e-02 2.50e+03 pdb=" O ARG D 328 " 0.033 2.00e-02 2.50e+03 pdb=" N PHE D 329 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 122 " 0.006 2.00e-02 2.50e+03 3.23e-02 1.30e+01 pdb=" CG ASN D 122 " -0.042 2.00e-02 2.50e+03 pdb=" OD1 ASN D 122 " 0.038 2.00e-02 2.50e+03 pdb=" ND2 ASN D 122 " -0.033 2.00e-02 2.50e+03 pdb=" C1 NAG D1303 " 0.030 2.00e-02 2.50e+03 ... (remaining 5636 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 580 2.66 - 3.22: 29861 3.22 - 3.78: 47600 3.78 - 4.34: 64075 4.34 - 4.90: 105860 Nonbonded interactions: 247976 Sorted by model distance: nonbonded pdb=" OD2 ASP D 737 " pdb=" ND2 ASN C 317 " model vdw 2.101 3.120 nonbonded pdb=" O THR D 393 " pdb=" OG1 THR D 523 " model vdw 2.153 3.040 nonbonded pdb=" OD1 ASN C 122 " pdb=" N ALA C 123 " model vdw 2.156 3.120 nonbonded pdb=" OG SER D 116 " pdb=" O CYS D 131 " model vdw 2.161 3.040 nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A 901 " model vdw 2.168 2.230 ... (remaining 247971 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 'B' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' } ncs_group { reference = (chain 'C' and (resid 25 through 77 or resid 79 through 189 or (resid 190 and (n \ ame N or name CA or name C or name O or name CB )) or resid 191 through 194 or ( \ resid 195 and (name N or name CA or name C or name O or name CB )) or resid 196 \ through 327 or (resid 328 through 329 and (name N or name CA or name C or name O \ or name CB )) or resid 330 through 1315)) selection = (chain 'D' and (resid 25 through 77 or resid 79 through 95 or (resid 96 and (nam \ e N or name CA or name C or name O or name CB )) or resid 97 through 189 or (res \ id 190 and (name N or name CA or name C or name O or name CB )) or resid 191 thr \ ough 346 or (resid 347 through 348 and (name N or name CA or name C or name O or \ name CB )) or resid 349 through 1315)) selection = (chain 'E' and (resid 25 through 77 or resid 79 through 95 or (resid 96 and (nam \ e N or name CA or name C or name O or name CB )) or resid 97 through 194 or (res \ id 195 and (name N or name CA or name C or name O or name CB )) or resid 196 thr \ ough 327 or (resid 328 through 329 and (name N or name CA or name C or name O or \ name CB )) or resid 330 through 346 or (resid 347 through 348 and (name N or na \ me CA or name C or name O or name CB )) or resid 349 through 1315)) } 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=0.49 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: 1.980 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: 0.720 Check model and map are aligned: 0.120 Set scattering table: 0.130 Process input model: 33.370 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 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 : 0.005 0.613 32267 Z= 0.217 Angle : 0.714 24.290 44042 Z= 0.374 Chirality : 0.048 0.452 5079 Planarity : 0.005 0.152 5595 Dihedral : 14.563 124.632 12589 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.03 % Favored : 92.79 % Rotamer: Outliers : 0.03 % Allowed : 0.30 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.35 (0.13), residues: 3871 helix: 0.83 (0.17), residues: 1008 sheet: -0.60 (0.20), residues: 592 loop : -1.87 (0.12), residues: 2271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D1107 TYR 0.032 0.001 TYR C 495 PHE 0.019 0.001 PHE C 490 TRP 0.041 0.002 TRP A 271 HIS 0.008 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00538 (32173) covalent geometry : angle 0.68665 (43805) SS BOND : bond 0.00290 ( 39) SS BOND : angle 1.34334 ( 78) hydrogen bonds : bond 0.16894 ( 1073) hydrogen bonds : angle 7.20685 ( 2991) metal coordination : bond 0.00017 ( 2) link_BETA1-4 : bond 0.00551 ( 9) link_BETA1-4 : angle 3.29716 ( 27) link_NAG-ASN : bond 0.00736 ( 44) link_NAG-ASN : angle 3.23239 ( 132) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7742 Ramachandran restraints generated. 3871 Oldfield, 0 Emsley, 3871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7742 Ramachandran restraints generated. 3871 Oldfield, 0 Emsley, 3871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 3400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 321 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.4352 (ppp) cc_final: 0.2022 (ttt) REVERT: A 249 MET cc_start: 0.1329 (tmm) cc_final: 0.0828 (tmm) REVERT: A 360 MET cc_start: -0.1243 (tpt) cc_final: -0.2029 (ptt) REVERT: A 480 MET cc_start: 0.0779 (mtt) cc_final: 0.0453 (mtt) REVERT: D 578 ASP cc_start: 0.5818 (t0) cc_final: 0.5539 (t0) REVERT: D 950 ASP cc_start: 0.7306 (m-30) cc_final: 0.6965 (m-30) REVERT: E 389 ASP cc_start: 0.7465 (p0) cc_final: 0.7254 (p0) REVERT: E 867 ASP cc_start: 0.7597 (m-30) cc_final: 0.7117 (m-30) REVERT: C 574 ASP cc_start: 0.8257 (t70) cc_final: 0.7493 (t0) REVERT: C 950 ASP cc_start: 0.7682 (m-30) cc_final: 0.7399 (m-30) outliers start: 1 outliers final: 0 residues processed: 321 average time/residue: 0.1850 time to fit residues: 102.3110 Evaluate side-chains 226 residues out of total 3400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 0.5980 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 0.0670 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 0.0670 overall best weight: 0.4256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN A 154 ASN ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 542 ASN D 607 GLN E 450 ASN ** E 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 949 GLN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1071 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.201311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.134607 restraints weight = 50932.973| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 3.62 r_work: 0.3555 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3561 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3561 r_free = 0.3561 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3561 r_free = 0.3561 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3561 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.0963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 32267 Z= 0.119 Angle : 0.624 14.400 44042 Z= 0.310 Chirality : 0.045 0.248 5079 Planarity : 0.004 0.060 5595 Dihedral : 8.229 112.266 5580 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.24 % Favored : 92.71 % Rotamer: Outliers : 0.92 % Allowed : 6.37 % Favored : 92.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % 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 aren not related in a simple way. whole: -1.15 (0.13), residues: 3871 helix: 0.99 (0.17), residues: 1010 sheet: -0.67 (0.20), residues: 583 loop : -1.68 (0.13), residues: 2278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 161 TYR 0.023 0.001 TYR D1138 PHE 0.029 0.001 PHE D 541 TRP 0.030 0.002 TRP A 271 HIS 0.008 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00255 (32173) covalent geometry : angle 0.59718 (43805) SS BOND : bond 0.00215 ( 39) SS BOND : angle 1.21005 ( 78) hydrogen bonds : bond 0.04140 ( 1073) hydrogen bonds : angle 5.70171 ( 2991) metal coordination : bond 0.00135 ( 2) link_BETA1-4 : bond 0.00828 ( 9) link_BETA1-4 : angle 2.97494 ( 27) link_NAG-ASN : bond 0.00485 ( 44) link_NAG-ASN : angle 3.00147 ( 132) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7742 Ramachandran restraints generated. 3871 Oldfield, 0 Emsley, 3871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7742 Ramachandran restraints generated. 3871 Oldfield, 0 Emsley, 3871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 3400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 276 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.4112 (ppp) cc_final: 0.3161 (ttt) REVERT: A 323 MET cc_start: -0.1648 (mmm) cc_final: -0.2426 (mtm) REVERT: A 360 MET cc_start: -0.0587 (tpt) cc_final: -0.1241 (ptt) REVERT: D 902 MET cc_start: 0.8787 (tpp) cc_final: 0.8481 (mmt) REVERT: E 389 ASP cc_start: 0.7926 (p0) cc_final: 0.7662 (p0) REVERT: E 585 LEU cc_start: 0.8298 (pp) cc_final: 0.8062 (pp) REVERT: E 723 THR cc_start: 0.9034 (t) cc_final: 0.8769 (p) REVERT: C 26 GLN cc_start: 0.7745 (tm-30) cc_final: 0.7089 (tm-30) REVERT: C 462 LYS cc_start: 0.8450 (mttp) cc_final: 0.8239 (mmmt) REVERT: C 574 ASP cc_start: 0.8509 (t70) cc_final: 0.7702 (t0) REVERT: C 950 ASP cc_start: 0.8366 (m-30) cc_final: 0.8057 (m-30) outliers start: 31 outliers final: 15 residues processed: 300 average time/residue: 0.1709 time to fit residues: 88.3878 Evaluate side-chains 251 residues out of total 3400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 236 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain E residue 359 SER Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 660 TYR Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1097 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 20 optimal weight: 20.0000 chunk 68 optimal weight: 0.8980 chunk 121 optimal weight: 0.7980 chunk 114 optimal weight: 0.0010 chunk 195 optimal weight: 0.8980 chunk 188 optimal weight: 8.9990 chunk 168 optimal weight: 20.0000 chunk 26 optimal weight: 3.9990 chunk 211 optimal weight: 0.0970 chunk 163 optimal weight: 0.5980 chunk 299 optimal weight: 6.9990 overall best weight: 0.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 321 GLN D 542 ASN D 607 GLN ** E 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 ASN C 394 ASN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 ASN C 505 HIS ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.201479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.136667 restraints weight = 50920.490| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 3.77 r_work: 0.3535 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3542 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3542 r_free = 0.3542 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3542 r_free = 0.3542 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3542 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 32267 Z= 0.110 Angle : 0.590 16.439 44042 Z= 0.290 Chirality : 0.046 0.821 5079 Planarity : 0.004 0.059 5595 Dihedral : 7.303 110.449 5580 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.93 % Favored : 93.02 % Rotamer: Outliers : 1.22 % Allowed : 8.65 % Favored : 90.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % 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 aren not related in a simple way. whole: -1.07 (0.13), residues: 3871 helix: 1.12 (0.17), residues: 1011 sheet: -0.53 (0.20), residues: 591 loop : -1.70 (0.13), residues: 2269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 457 TYR 0.021 0.001 TYR C 265 PHE 0.019 0.001 PHE D 541 TRP 0.033 0.001 TRP A 271 HIS 0.008 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00239 (32173) covalent geometry : angle 0.56528 (43805) SS BOND : bond 0.00218 ( 39) SS BOND : angle 1.17475 ( 78) hydrogen bonds : bond 0.03724 ( 1073) hydrogen bonds : angle 5.29061 ( 2991) metal coordination : bond 0.00291 ( 2) link_BETA1-4 : bond 0.00659 ( 9) link_BETA1-4 : angle 2.68868 ( 27) link_NAG-ASN : bond 0.00605 ( 44) link_NAG-ASN : angle 2.78025 ( 132) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7742 Ramachandran restraints generated. 3871 Oldfield, 0 Emsley, 3871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7742 Ramachandran restraints generated. 3871 Oldfield, 0 Emsley, 3871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 3400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 266 time to evaluate : 1.157 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.4151 (ppp) cc_final: 0.3152 (ttt) REVERT: A 360 MET cc_start: -0.0686 (tpt) cc_final: -0.1396 (ptt) REVERT: D 206 LYS cc_start: 0.6520 (pttm) cc_final: 0.6124 (mtmt) REVERT: D 542 ASN cc_start: 0.7072 (t0) cc_final: 0.6446 (t0) REVERT: D 902 MET cc_start: 0.8835 (tpp) cc_final: 0.8470 (mmt) REVERT: E 389 ASP cc_start: 0.7956 (p0) cc_final: 0.7685 (p0) REVERT: E 420 ASP cc_start: 0.8351 (OUTLIER) cc_final: 0.8027 (t0) REVERT: E 585 LEU cc_start: 0.8285 (pp) cc_final: 0.8051 (pp) REVERT: E 988 GLU cc_start: 0.7434 (mp0) cc_final: 0.7231 (mp0) REVERT: C 26 GLN cc_start: 0.7728 (tm-30) cc_final: 0.7331 (tm-30) REVERT: C 950 ASP cc_start: 0.8397 (m-30) cc_final: 0.8090 (m-30) outliers start: 41 outliers final: 24 residues processed: 296 average time/residue: 0.1815 time to fit residues: 92.3482 Evaluate side-chains 267 residues out of total 3400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 242 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain E residue 420 ASP Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 515 PHE Chi-restraints excluded: chain E residue 660 TYR Chi-restraints excluded: chain E residue 666 ILE Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1098 ASN Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 123 optimal weight: 0.9990 chunk 179 optimal weight: 0.4980 chunk 265 optimal weight: 0.6980 chunk 12 optimal weight: 20.0000 chunk 30 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 chunk 186 optimal weight: 6.9990 chunk 278 optimal weight: 0.8980 chunk 312 optimal weight: 0.0870 chunk 63 optimal weight: 4.9990 chunk 332 optimal weight: 5.9990 overall best weight: 0.6360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 239 GLN ** E 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 658 ASN E1005 GLN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 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 = 0.4463 r_free = 0.4463 target = 0.199917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.135120 restraints weight = 50993.227| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 3.14 r_work: 0.3554 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3563 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3563 r_free = 0.3563 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3563 r_free = 0.3563 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3563 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 32267 Z= 0.110 Angle : 0.573 11.153 44042 Z= 0.282 Chirality : 0.045 0.656 5079 Planarity : 0.004 0.060 5595 Dihedral : 6.856 108.043 5580 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.06 % Favored : 92.92 % Rotamer: Outliers : 1.30 % Allowed : 9.99 % Favored : 88.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % 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 aren not related in a simple way. whole: -1.03 (0.13), residues: 3871 helix: 1.22 (0.17), residues: 1011 sheet: -0.56 (0.20), residues: 611 loop : -1.70 (0.13), residues: 2249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 273 TYR 0.020 0.001 TYR C 265 PHE 0.034 0.001 PHE C 855 TRP 0.033 0.001 TRP A 271 HIS 0.008 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00244 (32173) covalent geometry : angle 0.55130 (43805) SS BOND : bond 0.00226 ( 39) SS BOND : angle 1.15637 ( 78) hydrogen bonds : bond 0.03499 ( 1073) hydrogen bonds : angle 5.08654 ( 2991) metal coordination : bond 0.00136 ( 2) link_BETA1-4 : bond 0.00607 ( 9) link_BETA1-4 : angle 2.50489 ( 27) link_NAG-ASN : bond 0.00384 ( 44) link_NAG-ASN : angle 2.58160 ( 132) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7742 Ramachandran restraints generated. 3871 Oldfield, 0 Emsley, 3871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7742 Ramachandran restraints generated. 3871 Oldfield, 0 Emsley, 3871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 3400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 256 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.4062 (ppp) cc_final: 0.2627 (mtt) REVERT: A 360 MET cc_start: -0.1097 (tpt) cc_final: -0.1970 (ptt) REVERT: D 206 LYS cc_start: 0.6432 (pttm) cc_final: 0.6178 (mtmt) REVERT: D 542 ASN cc_start: 0.7057 (t0) cc_final: 0.6434 (t0) REVERT: D 902 MET cc_start: 0.8806 (tpp) cc_final: 0.8453 (mmt) REVERT: D 950 ASP cc_start: 0.8082 (m-30) cc_final: 0.7460 (m-30) REVERT: E 389 ASP cc_start: 0.7919 (p0) cc_final: 0.7634 (p0) REVERT: E 451 TYR cc_start: 0.4201 (m-10) cc_final: 0.3799 (m-10) REVERT: E 585 LEU cc_start: 0.8326 (pp) cc_final: 0.8090 (pp) REVERT: E 737 ASP cc_start: 0.8001 (t0) cc_final: 0.7800 (t0) REVERT: E 740 MET cc_start: 0.8661 (ttp) cc_final: 0.8334 (tpp) REVERT: E 988 GLU cc_start: 0.7483 (mp0) cc_final: 0.7256 (mp0) REVERT: C 26 GLN cc_start: 0.7639 (tm-30) cc_final: 0.7222 (tm-30) REVERT: C 462 LYS cc_start: 0.8486 (mmmt) cc_final: 0.8172 (mttp) REVERT: C 867 ASP cc_start: 0.8037 (t0) cc_final: 0.7785 (t0) REVERT: C 950 ASP cc_start: 0.8346 (m-30) cc_final: 0.8040 (m-30) outliers start: 44 outliers final: 32 residues processed: 284 average time/residue: 0.1904 time to fit residues: 91.8176 Evaluate side-chains 270 residues out of total 3400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 238 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 869 MET Chi-restraints excluded: chain D residue 1122 VAL Chi-restraints excluded: chain E residue 280 ASN Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain E residue 511 VAL Chi-restraints excluded: chain E residue 515 PHE Chi-restraints excluded: chain E residue 660 TYR Chi-restraints excluded: chain E residue 666 ILE Chi-restraints excluded: chain E residue 1005 GLN Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1098 ASN Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 244 optimal weight: 4.9990 chunk 291 optimal weight: 5.9990 chunk 210 optimal weight: 0.2980 chunk 26 optimal weight: 0.9980 chunk 118 optimal weight: 1.9990 chunk 225 optimal weight: 0.8980 chunk 347 optimal weight: 0.9990 chunk 220 optimal weight: 10.0000 chunk 293 optimal weight: 7.9990 chunk 370 optimal weight: 4.9990 chunk 120 optimal weight: 4.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 607 GLN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1005 GLN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.198616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.133521 restraints weight = 51183.274| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 3.12 r_work: 0.3538 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3545 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3545 r_free = 0.3545 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3545 r_free = 0.3545 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3545 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 32267 Z= 0.125 Angle : 0.570 9.649 44042 Z= 0.282 Chirality : 0.044 0.362 5079 Planarity : 0.004 0.061 5595 Dihedral : 6.603 106.306 5580 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.08 % Favored : 92.89 % Rotamer: Outliers : 1.75 % Allowed : 10.67 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % 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 aren not related in a simple way. whole: -1.02 (0.13), residues: 3871 helix: 1.25 (0.17), residues: 1011 sheet: -0.63 (0.20), residues: 599 loop : -1.68 (0.13), residues: 2261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 457 TYR 0.021 0.001 TYR C 265 PHE 0.023 0.001 PHE C 855 TRP 0.032 0.001 TRP A 271 HIS 0.007 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00289 (32173) covalent geometry : angle 0.55045 (43805) SS BOND : bond 0.00246 ( 39) SS BOND : angle 1.19593 ( 78) hydrogen bonds : bond 0.03449 ( 1073) hydrogen bonds : angle 5.01049 ( 2991) metal coordination : bond 0.00177 ( 2) link_BETA1-4 : bond 0.00577 ( 9) link_BETA1-4 : angle 2.42352 ( 27) link_NAG-ASN : bond 0.00373 ( 44) link_NAG-ASN : angle 2.38595 ( 132) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7742 Ramachandran restraints generated. 3871 Oldfield, 0 Emsley, 3871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7742 Ramachandran restraints generated. 3871 Oldfield, 0 Emsley, 3871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 3400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 245 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.3991 (ppp) cc_final: 0.2556 (mtt) REVERT: A 323 MET cc_start: -0.0954 (mmm) cc_final: -0.1170 (mmm) REVERT: A 360 MET cc_start: -0.1443 (tpt) cc_final: -0.2378 (ptt) REVERT: D 206 LYS cc_start: 0.6635 (pttm) cc_final: 0.6331 (mtmt) REVERT: D 542 ASN cc_start: 0.7199 (t0) cc_final: 0.6584 (t0) REVERT: D 902 MET cc_start: 0.8834 (tpp) cc_final: 0.8433 (mmt) REVERT: E 389 ASP cc_start: 0.7984 (p0) cc_final: 0.7687 (p0) REVERT: E 451 TYR cc_start: 0.4478 (m-10) cc_final: 0.4105 (m-10) REVERT: E 585 LEU cc_start: 0.8375 (pp) cc_final: 0.8083 (pp) REVERT: E 697 MET cc_start: 0.8448 (ptm) cc_final: 0.8180 (ptp) REVERT: E 737 ASP cc_start: 0.8102 (t0) cc_final: 0.7873 (t0) REVERT: E 740 MET cc_start: 0.8717 (ttp) cc_final: 0.8350 (tpp) REVERT: E 988 GLU cc_start: 0.7515 (mp0) cc_final: 0.7259 (mp0) REVERT: E 1005 GLN cc_start: 0.8573 (OUTLIER) cc_final: 0.8235 (mm-40) REVERT: C 26 GLN cc_start: 0.7644 (tm-30) cc_final: 0.7231 (tm-30) REVERT: C 456 PHE cc_start: 0.8322 (m-80) cc_final: 0.8008 (m-80) REVERT: C 740 MET cc_start: 0.8678 (OUTLIER) cc_final: 0.8456 (ttt) REVERT: C 787 GLN cc_start: 0.8433 (mp10) cc_final: 0.8205 (mt0) REVERT: C 867 ASP cc_start: 0.8056 (t0) cc_final: 0.7849 (t0) REVERT: C 950 ASP cc_start: 0.8363 (m-30) cc_final: 0.8050 (m-30) outliers start: 59 outliers final: 40 residues processed: 285 average time/residue: 0.1674 time to fit residues: 82.0284 Evaluate side-chains 279 residues out of total 3400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 237 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 869 MET Chi-restraints excluded: chain D residue 1122 VAL Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain E residue 511 VAL Chi-restraints excluded: chain E residue 515 PHE Chi-restraints excluded: chain E residue 660 TYR Chi-restraints excluded: chain E residue 666 ILE Chi-restraints excluded: chain E residue 869 MET Chi-restraints excluded: chain E residue 1005 GLN Chi-restraints excluded: chain E residue 1097 SER Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1098 ASN Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 381 optimal weight: 0.8980 chunk 145 optimal weight: 0.7980 chunk 210 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 371 optimal weight: 2.9990 chunk 282 optimal weight: 5.9990 chunk 253 optimal weight: 0.7980 chunk 364 optimal weight: 2.9990 chunk 174 optimal weight: 0.8980 chunk 340 optimal weight: 7.9990 chunk 6 optimal weight: 9.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 607 GLN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.198565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.133403 restraints weight = 51020.293| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 3.14 r_work: 0.3534 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3543 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3543 r_free = 0.3543 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3543 r_free = 0.3543 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3543 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 32267 Z= 0.116 Angle : 0.565 9.778 44042 Z= 0.280 Chirality : 0.044 0.264 5079 Planarity : 0.004 0.061 5595 Dihedral : 6.367 104.000 5580 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.42 % Favored : 92.55 % Rotamer: Outliers : 1.75 % Allowed : 11.44 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % 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 aren not related in a simple way. whole: -1.00 (0.13), residues: 3871 helix: 1.35 (0.17), residues: 1003 sheet: -0.62 (0.19), residues: 618 loop : -1.70 (0.13), residues: 2250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 273 TYR 0.021 0.001 TYR C 265 PHE 0.021 0.001 PHE C 855 TRP 0.037 0.001 TRP A 271 HIS 0.007 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00265 (32173) covalent geometry : angle 0.54708 (43805) SS BOND : bond 0.00232 ( 39) SS BOND : angle 1.15192 ( 78) hydrogen bonds : bond 0.03364 ( 1073) hydrogen bonds : angle 4.92199 ( 2991) metal coordination : bond 0.00166 ( 2) link_BETA1-4 : bond 0.00584 ( 9) link_BETA1-4 : angle 2.36801 ( 27) link_NAG-ASN : bond 0.00369 ( 44) link_NAG-ASN : angle 2.31161 ( 132) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7742 Ramachandran restraints generated. 3871 Oldfield, 0 Emsley, 3871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7742 Ramachandran restraints generated. 3871 Oldfield, 0 Emsley, 3871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 3400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 247 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.3993 (ppp) cc_final: 0.2713 (mtt) REVERT: A 360 MET cc_start: -0.1785 (tpt) cc_final: -0.2553 (ptt) REVERT: D 190 ARG cc_start: 0.5813 (ttt90) cc_final: 0.5441 (ttm-80) REVERT: D 206 LYS cc_start: 0.6604 (pttm) cc_final: 0.6345 (mtmt) REVERT: D 542 ASN cc_start: 0.7010 (t0) cc_final: 0.6475 (t0) REVERT: D 902 MET cc_start: 0.8842 (tpp) cc_final: 0.8428 (mmt) REVERT: D 950 ASP cc_start: 0.8170 (m-30) cc_final: 0.7571 (m-30) REVERT: E 41 LYS cc_start: 0.7713 (tptp) cc_final: 0.7508 (tptm) REVERT: E 389 ASP cc_start: 0.7926 (p0) cc_final: 0.7623 (p0) REVERT: E 451 TYR cc_start: 0.4828 (m-10) cc_final: 0.4510 (m-10) REVERT: E 585 LEU cc_start: 0.8390 (pp) cc_final: 0.8088 (pp) REVERT: E 697 MET cc_start: 0.8439 (ptm) cc_final: 0.8233 (ptp) REVERT: E 988 GLU cc_start: 0.7475 (mp0) cc_final: 0.7216 (mp0) REVERT: C 26 GLN cc_start: 0.7628 (tm-30) cc_final: 0.7224 (tm-30) REVERT: C 177 MET cc_start: 0.3799 (OUTLIER) cc_final: 0.3467 (tpp) REVERT: C 740 MET cc_start: 0.8717 (OUTLIER) cc_final: 0.8510 (ttt) REVERT: C 787 GLN cc_start: 0.8440 (mp10) cc_final: 0.8178 (mt0) REVERT: C 950 ASP cc_start: 0.8367 (m-30) cc_final: 0.8051 (m-30) outliers start: 59 outliers final: 46 residues processed: 288 average time/residue: 0.1692 time to fit residues: 83.4753 Evaluate side-chains 287 residues out of total 3400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 239 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 869 MET Chi-restraints excluded: chain D residue 1097 SER Chi-restraints excluded: chain D residue 1122 VAL Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain E residue 511 VAL Chi-restraints excluded: chain E residue 515 PHE Chi-restraints excluded: chain E residue 660 TYR Chi-restraints excluded: chain E residue 666 ILE Chi-restraints excluded: chain E residue 869 MET Chi-restraints excluded: chain E residue 1097 SER Chi-restraints excluded: chain E residue 1109 PHE Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 467 ASP Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1098 ASN Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 61.1309 > 50: distance: 19 - 23: 12.527 distance: 23 - 24: 12.863 distance: 24 - 25: 21.283 distance: 24 - 27: 6.818 distance: 25 - 26: 26.872 distance: 25 - 32: 22.236 distance: 27 - 28: 24.218 distance: 28 - 29: 19.950 distance: 29 - 30: 5.736 distance: 29 - 31: 25.862 distance: 32 - 33: 10.494 distance: 32 - 161: 17.394 distance: 33 - 34: 10.680 distance: 33 - 36: 7.832 distance: 34 - 35: 34.277 distance: 34 - 39: 18.157 distance: 36 - 37: 24.211 distance: 36 - 38: 42.514 distance: 39 - 40: 20.832 distance: 40 - 41: 36.534 distance: 40 - 43: 13.907 distance: 41 - 42: 24.614 distance: 41 - 45: 26.848 distance: 43 - 44: 17.322 distance: 45 - 46: 19.347 distance: 46 - 47: 29.051 distance: 46 - 49: 26.156 distance: 47 - 48: 22.365 distance: 47 - 53: 23.751 distance: 49 - 50: 17.898 distance: 50 - 51: 43.407 distance: 50 - 52: 12.071 distance: 53 - 54: 9.478 distance: 54 - 55: 18.654 distance: 54 - 57: 17.665 distance: 55 - 56: 16.129 distance: 55 - 64: 8.963 distance: 57 - 58: 15.177 distance: 58 - 59: 10.532 distance: 58 - 60: 23.048 distance: 59 - 61: 20.999 distance: 60 - 62: 17.777 distance: 61 - 63: 22.717 distance: 62 - 63: 24.821 distance: 65 - 66: 15.076 distance: 65 - 68: 14.453 distance: 66 - 67: 11.838 distance: 66 - 75: 4.351 distance: 68 - 69: 9.377 distance: 69 - 70: 8.600 distance: 70 - 71: 6.634 distance: 71 - 72: 6.887 distance: 72 - 73: 5.464 distance: 72 - 74: 5.513 distance: 75 - 76: 23.625 distance: 76 - 77: 44.257 distance: 76 - 79: 42.184 distance: 77 - 78: 44.297 distance: 77 - 82: 26.956 distance: 79 - 80: 15.931 distance: 79 - 81: 18.395 distance: 82 - 83: 9.949 distance: 83 - 84: 36.880 distance: 83 - 86: 26.995 distance: 84 - 85: 12.964 distance: 84 - 91: 7.887 distance: 86 - 87: 21.456 distance: 87 - 88: 29.475 distance: 88 - 89: 26.647 distance: 88 - 90: 9.436 distance: 91 - 92: 16.234 distance: 91 - 97: 13.659 distance: 92 - 93: 26.607 distance: 92 - 95: 37.237 distance: 93 - 98: 28.707 distance: 95 - 96: 18.496 distance: 96 - 97: 49.237 distance: 98 - 99: 15.350 distance: 99 - 100: 24.268 distance: 99 - 102: 36.238 distance: 100 - 101: 9.599 distance: 100 - 105: 29.739 distance: 102 - 103: 9.786 distance: 102 - 104: 36.156