Starting phenix.real_space_refine on Mon May 19 01:35:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gvj_51636/05_2025/9gvj_51636.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gvj_51636/05_2025/9gvj_51636.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9gvj_51636/05_2025/9gvj_51636.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gvj_51636/05_2025/9gvj_51636.map" model { file = "/net/cci-nas-00/data/ceres_data/9gvj_51636/05_2025/9gvj_51636.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gvj_51636/05_2025/9gvj_51636.cif" } resolution = 2.91 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.001 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 6 9.91 5 Cu 2 5.60 5 S 250 5.16 5 C 10822 2.51 5 N 3010 2.21 5 O 3546 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 17636 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5230 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 690, 5197 Classifications: {'peptide': 690} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 3, 'PTRANS': 34, 'TRANS': 652} Chain breaks: 2 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 16 Conformer: "B" Number of residues, atoms: 690, 5197 Classifications: {'peptide': 690} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 3, 'PTRANS': 34, 'TRANS': 652} Chain breaks: 2 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 16 bond proxies already assigned to first conformer: 5277 Chain: "B" Number of atoms: 5219 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 688, 5184 Classifications: {'peptide': 688} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 3, 'PTRANS': 34, 'TRANS': 650} Chain breaks: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 688, 5184 Classifications: {'peptide': 688} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 3, 'PTRANS': 34, 'TRANS': 650} Chain breaks: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 5261 Chain: "C" Number of atoms: 3453 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 463, 3432 Classifications: {'peptide': 463} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 432} Chain breaks: 1 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Conformer: "B" Number of residues, atoms: 463, 3432 Classifications: {'peptide': 463} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 432} Chain breaks: 1 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 bond proxies already assigned to first conformer: 3494 Chain: "D" Number of atoms: 3465 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 463, 3436 Classifications: {'peptide': 463} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 432} Chain breaks: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Conformer: "B" Number of residues, atoms: 463, 3436 Classifications: {'peptide': 463} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 432} Chain breaks: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 bond proxies already assigned to first conformer: 3489 Chain: "A" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 45 Unusual residues: {' CA': 2, ' CU': 1, 'NAG': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 45 Unusual residues: {' CA': 2, ' CU': 1, 'NAG': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 64 Classifications: {'water': 64} Link IDs: {None: 63} Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 39 Classifications: {'water': 39} Link IDs: {None: 38} Chain: "C" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 45 Classifications: {'water': 45} Link IDs: {None: 44} Chain: "D" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AARG A 422 " occ=0.64 ... (20 atoms not shown) pdb=" NH2BARG A 422 " occ=0.36 residue: pdb=" N AARG B 422 " occ=0.71 ... (20 atoms not shown) pdb=" NH2BARG B 422 " occ=0.29 Time building chain proxies: 21.83, per 1000 atoms: 1.24 Number of scatterers: 17636 At special positions: 0 Unit cell: (127.751, 112.915, 155.774, 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) Cu 2 28.99 Ca 6 19.99 S 250 16.00 O 3546 8.00 N 3010 7.00 C 10822 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=107, symmetry=0 Simple disulfide: pdb=" SG CYS A 81 " - pdb=" SG CYS A 211 " distance=2.03 Simple disulfide: pdb=" SG CYS A 103 " - pdb=" SG CYS A 248 " distance=2.03 Simple disulfide: pdb=" SG CYS A 111 " - pdb=" SG CYS A 208 " distance=2.03 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 296 " distance=2.03 Simple disulfide: pdb=" SG CYS A 266 " - pdb=" SG CYS A 291 " distance=2.04 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 318 " distance=2.03 Simple disulfide: pdb=" SG CYS A 298 " - pdb=" SG CYS A 306 " distance=2.03 Simple disulfide: pdb=" SG CYS A 308 " - pdb=" SG CYS A 334 " distance=2.03 Simple disulfide: pdb=" SG CYS A 338 " - pdb=" SG CYS A 372 " distance=2.03 Simple disulfide: pdb=" SG CYS A 347 " - pdb=" SG CYS A 368 " distance=2.03 Simple disulfide: pdb=" SG CYS A 351 " - pdb=" SG CYS A 364 " distance=2.03 Simple disulfide: pdb=" SG CYS A 355 " - pdb=" SG CYS A 394 " distance=2.03 Simple disulfide: pdb=" SG CYS A 374 " - pdb=" SG CYS A 388 " distance=2.03 Simple disulfide: pdb=" SG CYS A 396 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 413 " - pdb=" SG CYS A 430 " distance=2.03 Simple disulfide: pdb=" SG CYS A 416 " - pdb=" SG CYS A 425 " distance=2.03 Simple disulfide: pdb=" SG CYS A 434 " - pdb=" SG CYS A 571 " distance=2.03 Simple disulfide: pdb=" SG CYS A 456 " - pdb=" SG CYS A 606 " distance=2.03 Simple disulfide: pdb=" SG CYS A 464 " - pdb=" SG CYS A 568 " distance=2.03 Simple disulfide: pdb=" SG CYS A 478 " - pdb=" SG CYS A 486 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 662 " distance=2.03 Simple disulfide: pdb=" SG CYS A 631 " - pdb=" SG CYS A 657 " distance=2.03 Simple disulfide: pdb=" SG CYS A 644 " - pdb=" SG CYS A 682 " distance=2.03 Simple disulfide: pdb=" SG CYS A 664 " - pdb=" SG CYS A 670 " distance=2.03 Simple disulfide: pdb=" SG CYS A 672 " - pdb=" SG CYS A 697 " distance=2.03 Simple disulfide: pdb=" SG CYS A 704 " - pdb=" SG CYS A 741 " distance=2.03 Simple disulfide: pdb=" SG CYS A 717 " - pdb=" SG CYS A 731 " distance=2.03 Simple disulfide: pdb=" SG CYS A 721 " - pdb=" SG CYS A 761 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 755 " distance=2.03 Simple disulfide: pdb=" SG CYS B 81 " - pdb=" SG CYS B 211 " distance=2.03 Simple disulfide: pdb=" SG CYS B 103 " - pdb=" SG CYS B 248 " distance=2.03 Simple disulfide: pdb=" SG CYS B 111 " - pdb=" SG CYS B 208 " distance=2.03 Simple disulfide: pdb=" SG CYS B 259 " - pdb=" SG CYS B 296 " distance=2.03 Simple disulfide: pdb=" SG CYS B 266 " - pdb=" SG CYS B 291 " distance=2.03 Simple disulfide: pdb=" SG CYS B 278 " - pdb=" SG CYS B 318 " distance=2.03 Simple disulfide: pdb=" SG CYS B 298 " - pdb=" SG CYS B 306 " distance=2.03 Simple disulfide: pdb=" SG CYS B 308 " - pdb=" SG CYS B 334 " distance=2.03 Simple disulfide: pdb=" SG CYS B 338 " - pdb=" SG CYS B 372 " distance=2.03 Simple disulfide: pdb=" SG CYS B 347 " - pdb=" SG CYS B 368 " distance=2.03 Simple disulfide: pdb=" SG CYS B 351 " - pdb=" SG CYS B 364 " distance=2.03 Simple disulfide: pdb=" SG CYS B 355 " - pdb=" SG CYS B 394 " distance=2.03 Simple disulfide: pdb=" SG CYS B 374 " - pdb=" SG CYS B 388 " distance=2.03 Simple disulfide: pdb=" SG CYS B 396 " - pdb=" SG CYS B 418 " distance=2.03 Simple disulfide: pdb=" SG CYS B 413 " - pdb=" SG CYS B 430 " distance=2.03 Simple disulfide: pdb=" SG CYS B 416 " - pdb=" SG CYS B 425 " distance=2.03 Simple disulfide: pdb=" SG CYS B 434 " - pdb=" SG CYS B 571 " distance=2.03 Simple disulfide: pdb=" SG CYS B 456 " - pdb=" SG CYS B 606 " distance=2.03 Simple disulfide: pdb=" SG CYS B 464 " - pdb=" SG CYS B 568 " distance=2.03 Simple disulfide: pdb=" SG CYS B 478 " - pdb=" SG CYS B 486 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 662 " distance=2.03 Simple disulfide: pdb=" SG CYS B 631 " - pdb=" SG CYS B 657 " distance=2.03 Simple disulfide: pdb=" SG CYS B 644 " - pdb=" SG CYS B 682 " distance=2.03 Simple disulfide: pdb=" SG CYS B 664 " - pdb=" SG CYS B 670 " distance=2.03 Simple disulfide: pdb=" SG CYS B 672 " - pdb=" SG CYS B 697 " distance=2.03 Simple disulfide: pdb=" SG CYS B 704 " - pdb=" SG CYS B 741 " distance=2.03 Simple disulfide: pdb=" SG CYS B 717 " - pdb=" SG CYS B 731 " distance=2.03 Simple disulfide: pdb=" SG CYS B 721 " - pdb=" SG CYS B 761 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 755 " distance=2.03 Simple disulfide: pdb=" SG CYS C 763 " - pdb=" SG CYS C 785 " distance=2.03 Simple disulfide: pdb=" SG CYS C 783 " - pdb=" SG CYS C 792 " distance=2.03 Simple disulfide: pdb=" SG CYS C 802 " - pdb=" SG CYS C 843 " distance=2.03 Simple disulfide: pdb=" SG CYS C 811 " - pdb=" SG CYS C 839 " distance=2.03 Simple disulfide: pdb=" SG CYS C 823 " - pdb=" SG CYS C 834 " distance=2.03 Simple disulfide: pdb=" SG CYS C 827 " - pdb=" SG CYS C 863 " distance=2.03 Simple disulfide: pdb=" SG CYS C 845 " - pdb=" SG CYS C 857 " distance=2.03 Simple disulfide: pdb=" SG CYS C 865 " - pdb=" SG CYS C 887 " distance=2.03 Simple disulfide: pdb=" SG CYS C 882 " - pdb=" SG CYS C 899 " distance=2.03 Simple disulfide: pdb=" SG CYS C 885 " - pdb=" SG CYS C 894 " distance=2.03 Simple disulfide: pdb=" SG CYS C 903 " - pdb=" SG CYS C1036 " distance=2.03 Simple disulfide: pdb=" SG CYS C 925 " - pdb=" SG CYS C1071 " distance=2.03 Simple disulfide: pdb=" SG CYS C 934 " - pdb=" SG CYS C1033 " distance=2.03 Simple disulfide: pdb=" SG CYS C 953 " - pdb=" SG CYS C 960 " distance=2.03 Simple disulfide: pdb=" SG CYS C1081 " - pdb=" SG CYS C1124 " distance=2.03 Simple disulfide: pdb=" SG CYS C1095 " - pdb=" SG CYS C1119 " distance=2.03 Simple disulfide: pdb=" SG CYS C1106 " - pdb=" SG CYS C1146 " distance=2.03 Simple disulfide: pdb=" SG CYS C1126 " - pdb=" SG CYS C1134 " distance=2.04 Simple disulfide: pdb=" SG CYS C1136 " - pdb=" SG CYS C1161 " distance=2.03 Simple disulfide: pdb=" SG CYS C1152 " - pdb=" SG CYS C1181 " distance=2.03 Simple disulfide: pdb=" SG CYS C1165 " - pdb=" SG CYS C1206 " distance=2.03 Simple disulfide: pdb=" SG CYS C1174 " - pdb=" SG CYS D1174 " distance=2.03 Simple disulfide: pdb=" SG CYS C1185 " - pdb=" SG CYS C1196 " distance=2.04 Simple disulfide: pdb=" SG CYS C1189 " - pdb=" SG CYS C1228 " distance=2.03 Simple disulfide: pdb=" SG CYS C1210 " - pdb=" SG CYS C1224 " distance=2.03 Simple disulfide: pdb=" SG CYS D 763 " - pdb=" SG CYS D 785 " distance=2.03 Simple disulfide: pdb=" SG CYS D 783 " - pdb=" SG CYS D 792 " distance=2.03 Simple disulfide: pdb=" SG CYS D 802 " - pdb=" SG CYS D 843 " distance=2.03 Simple disulfide: pdb=" SG CYS D 811 " - pdb=" SG CYS D 839 " distance=2.03 Simple disulfide: pdb=" SG CYS D 823 " - pdb=" SG CYS D 834 " distance=2.03 Simple disulfide: pdb=" SG CYS D 827 " - pdb=" SG CYS D 863 " distance=2.03 Simple disulfide: pdb=" SG CYS D 845 " - pdb=" SG CYS D 857 " distance=2.03 Simple disulfide: pdb=" SG CYS D 865 " - pdb=" SG CYS D 887 " distance=2.03 Simple disulfide: pdb=" SG CYS D 882 " - pdb=" SG CYS D 899 " distance=2.03 Simple disulfide: pdb=" SG CYS D 885 " - pdb=" SG CYS D 894 " distance=2.03 Simple disulfide: pdb=" SG CYS D 903 " - pdb=" SG CYS D1036 " distance=2.03 Simple disulfide: pdb=" SG CYS D 925 " - pdb=" SG CYS D1071 " distance=2.03 Simple disulfide: pdb=" SG CYS D 934 " - pdb=" SG CYS D1033 " distance=2.03 Simple disulfide: pdb=" SG CYS D 953 " - pdb=" SG CYS D 960 " distance=2.03 Simple disulfide: pdb=" SG CYS D1081 " - pdb=" SG CYS D1124 " distance=2.03 Simple disulfide: pdb=" SG CYS D1095 " - pdb=" SG CYS D1119 " distance=2.03 Simple disulfide: pdb=" SG CYS D1106 " - pdb=" SG CYS D1146 " distance=2.03 Simple disulfide: pdb=" SG CYS D1126 " - pdb=" SG CYS D1134 " distance=2.04 Simple disulfide: pdb=" SG CYS D1136 " - pdb=" SG CYS D1161 " distance=2.03 Simple disulfide: pdb=" SG CYS D1152 " - pdb=" SG CYS D1181 " distance=2.03 Simple disulfide: pdb=" SG CYS D1165 " - pdb=" SG CYS D1206 " distance=2.03 Simple disulfide: pdb=" SG CYS D1185 " - pdb=" SG CYS D1196 " distance=2.04 Simple disulfide: pdb=" SG CYS D1189 " - pdb=" SG CYS D1228 " distance=2.03 Simple disulfide: pdb=" SG CYS D1210 " - pdb=" SG CYS D1224 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1501 " - " ASN A 205 " " NAG A1502 " - " ASN A 524 " " NAG A1503 " - " ASN A 415 " " NAG B1501 " - " ASN B 205 " " NAG B1502 " - " ASN B 524 " " NAG B1503 " - " ASN B 415 " Time building additional restraints: 4.23 Conformation dependent library (CDL) restraints added in 4.5 seconds 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4246 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 40 sheets defined 21.9% alpha, 22.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.70 Creating SS restraints... Processing helix chain 'A' and resid 76 through 78 No H-bonds generated for 'chain 'A' and resid 76 through 78' Processing helix chain 'A' and resid 201 through 204 Processing helix chain 'A' and resid 231 through 238 Processing helix chain 'A' and resid 264 through 271 Processing helix chain 'A' and resid 284 through 297 Processing helix chain 'A' and resid 302 through 306 removed outlier: 3.518A pdb=" N CYS A 306 " --> pdb=" O LEU A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 321 Processing helix chain 'A' and resid 392 through 394 No H-bonds generated for 'chain 'A' and resid 392 through 394' Processing helix chain 'A' and resid 561 through 564 Processing helix chain 'A' and resid 578 through 583 removed outlier: 4.170A pdb=" N PHE A 582 " --> pdb=" O ALA A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 598 removed outlier: 3.513A pdb=" N PHE A 596 " --> pdb=" O THR A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 601 No H-bonds generated for 'chain 'A' and resid 599 through 601' Processing helix chain 'A' and resid 615 through 619 Processing helix chain 'A' and resid 620 through 632 Processing helix chain 'A' and resid 641 through 645 removed outlier: 3.695A pdb=" N HIS A 645 " --> pdb=" O GLY A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 664 Processing helix chain 'A' and resid 666 through 686 Processing helix chain 'A' and resid 698 through 703 removed outlier: 3.642A pdb=" N THR A 703 " --> pdb=" O PRO A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 727 Processing helix chain 'B' and resid 76 through 78 No H-bonds generated for 'chain 'B' and resid 76 through 78' Processing helix chain 'B' and resid 201 through 204 Processing helix chain 'B' and resid 231 through 239 Processing helix chain 'B' and resid 265 through 272 removed outlier: 3.838A pdb=" N LEU B 269 " --> pdb=" O ILE B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 280 removed outlier: 4.067A pdb=" N ALA B 280 " --> pdb=" O SER B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 298 Processing helix chain 'B' and resid 307 through 321 Processing helix chain 'B' and resid 360 through 364 removed outlier: 3.557A pdb=" N CYS B 364 " --> pdb=" O SER B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 394 No H-bonds generated for 'chain 'B' and resid 392 through 394' Processing helix chain 'B' and resid 561 through 564 Processing helix chain 'B' and resid 578 through 583 removed outlier: 4.089A pdb=" N PHE B 582 " --> pdb=" O ALA B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 599 removed outlier: 3.725A pdb=" N THR B 599 " --> pdb=" O ALA B 595 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 619 Processing helix chain 'B' and resid 620 through 632 Processing helix chain 'B' and resid 633 through 635 No H-bonds generated for 'chain 'B' and resid 633 through 635' Processing helix chain 'B' and resid 641 through 645 removed outlier: 3.629A pdb=" N HIS B 645 " --> pdb=" O GLY B 642 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 664 Processing helix chain 'B' and resid 666 through 685 Processing helix chain 'B' and resid 698 through 703 removed outlier: 3.866A pdb=" N THR B 702 " --> pdb=" O THR B 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 720 through 727 Processing helix chain 'C' and resid 859 through 863 Processing helix chain 'C' and resid 1026 through 1029 Processing helix chain 'C' and resid 1043 through 1047 removed outlier: 3.853A pdb=" N PHE C1047 " --> pdb=" O VAL C1044 " (cutoff:3.500A) Processing helix chain 'C' and resid 1057 through 1064 Processing helix chain 'C' and resid 1079 through 1084 Processing helix chain 'C' and resid 1084 through 1095 removed outlier: 3.700A pdb=" N LYS C1088 " --> pdb=" O ASN C1084 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N SER C1089 " --> pdb=" O PRO C1085 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N TRP C1090 " --> pdb=" O PHE C1086 " (cutoff:3.500A) Processing helix chain 'C' and resid 1096 through 1099 Processing helix chain 'C' and resid 1103 through 1107 Processing helix chain 'C' and resid 1112 through 1126 Processing helix chain 'C' and resid 1130 through 1149 removed outlier: 3.705A pdb=" N TYR C1142 " --> pdb=" O ALA C1138 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL C1149 " --> pdb=" O ALA C1145 " (cutoff:3.500A) Processing helix chain 'C' and resid 1164 through 1169 Processing helix chain 'D' and resid 810 through 814 removed outlier: 4.334A pdb=" N ASN D 813 " --> pdb=" O ASP D 810 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ALA D 814 " --> pdb=" O CYS D 811 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 810 through 814' Processing helix chain 'D' and resid 859 through 863 Processing helix chain 'D' and resid 1026 through 1029 removed outlier: 3.865A pdb=" N LYS D1029 " --> pdb=" O PRO D1026 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1026 through 1029' Processing helix chain 'D' and resid 1043 through 1048 removed outlier: 3.576A pdb=" N ASP D1046 " --> pdb=" O ALA D1043 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N PHE D1047 " --> pdb=" O VAL D1044 " (cutoff:3.500A) Processing helix chain 'D' and resid 1057 through 1064 Processing helix chain 'D' and resid 1079 through 1084 Processing helix chain 'D' and resid 1084 through 1096 removed outlier: 3.706A pdb=" N LYS D1088 " --> pdb=" O ASN D1084 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N SER D1089 " --> pdb=" O PRO D1085 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N TRP D1090 " --> pdb=" O PHE D1086 " (cutoff:3.500A) Processing helix chain 'D' and resid 1097 through 1104 removed outlier: 3.587A pdb=" N GLY D1100 " --> pdb=" O ILE D1097 " (cutoff:3.500A) Proline residue: D1101 - end of helix Processing helix chain 'D' and resid 1105 through 1109 removed outlier: 3.903A pdb=" N ALA D1108 " --> pdb=" O ALA D1105 " (cutoff:3.500A) Processing helix chain 'D' and resid 1112 through 1126 Processing helix chain 'D' and resid 1130 through 1149 removed outlier: 3.733A pdb=" N TYR D1142 " --> pdb=" O ALA D1138 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL D1149 " --> pdb=" O ALA D1145 " (cutoff:3.500A) Processing helix chain 'D' and resid 1164 through 1169 Processing sheet with id=AA1, first strand: chain 'A' and resid 68 through 70 removed outlier: 6.705A pdb=" N VAL A 69 " --> pdb=" O VAL C 982 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N SER C 961 " --> pdb=" O VAL C 951 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N VAL C 951 " --> pdb=" O SER C 961 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N PHE C 944 " --> pdb=" O GLN C 931 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N GLN C 931 " --> pdb=" O PHE C 944 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL C 946 " --> pdb=" O LEU C 929 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 98 Processing sheet with id=AA3, first strand: chain 'A' and resid 104 through 109 removed outlier: 6.530A pdb=" N ASN A 104 " --> pdb=" O ARG A 124 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N ARG A 124 " --> pdb=" O ASN A 104 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N VAL A 106 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEU A 122 " --> pdb=" O VAL A 106 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG A 135 " --> pdb=" O ARG A 123 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N SER A 125 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N LEU A 133 " --> pdb=" O SER A 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 343 through 348 removed outlier: 5.348A pdb=" N TYR A 344 " --> pdb=" O PHE A 373 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N PHE A 373 " --> pdb=" O TYR A 344 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N GLU A 346 " --> pdb=" O GLY A 371 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N GLY A 371 " --> pdb=" O GLU A 346 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 378 through 380 Processing sheet with id=AA6, first strand: chain 'A' and resid 397 through 398 Processing sheet with id=AA7, first strand: chain 'A' and resid 408 through 410 Processing sheet with id=AA8, first strand: chain 'A' and resid 449 through 451 removed outlier: 4.126A pdb=" N LEU A 543 " --> pdb=" O THR A 539 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL A 525 " --> pdb=" O ALA A 522 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 456 through 461 removed outlier: 6.663A pdb=" N VAL A 471 " --> pdb=" O LEU A 460 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N SER A 489 " --> pdb=" O GLU A 474 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ARG A 476 " --> pdb=" O LEU A 487 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N LEU A 487 " --> pdb=" O ARG A 476 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N VAL A 509 " --> pdb=" O THR A 516 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 709 through 714 removed outlier: 4.195A pdb=" N HIS A 713 " --> pdb=" O VAL A 738 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL A 738 " --> pdb=" O HIS A 713 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 748 through 750 removed outlier: 3.721A pdb=" N LYS A 754 " --> pdb=" O ASP A 750 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 69 through 70 removed outlier: 6.504A pdb=" N VAL B 69 " --> pdb=" O VAL D 982 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N SER D 961 " --> pdb=" O VAL D 951 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N VAL D 951 " --> pdb=" O SER D 961 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA D 963 " --> pdb=" O GLU D 949 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N PHE D 944 " --> pdb=" O GLN D 931 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N GLN D 931 " --> pdb=" O PHE D 944 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL D 946 " --> pdb=" O LEU D 929 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AB5, first strand: chain 'B' and resid 104 through 109 removed outlier: 6.586A pdb=" N ASN B 104 " --> pdb=" O ARG B 124 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N ARG B 124 " --> pdb=" O ASN B 104 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N VAL B 106 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N LEU B 122 " --> pdb=" O VAL B 106 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N SER B 125 " --> pdb=" O LEU B 133 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N LEU B 133 " --> pdb=" O SER B 125 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 343 through 348 removed outlier: 5.390A pdb=" N TYR B 344 " --> pdb=" O PHE B 373 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N PHE B 373 " --> pdb=" O TYR B 344 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N GLU B 346 " --> pdb=" O GLY B 371 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N GLY B 371 " --> pdb=" O GLU B 346 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 378 through 380 Processing sheet with id=AB8, first strand: chain 'B' and resid 397 through 398 Processing sheet with id=AB9, first strand: chain 'B' and resid 408 through 410 Processing sheet with id=AC1, first strand: chain 'B' and resid 449 through 451 removed outlier: 4.129A pdb=" N LEU B 543 " --> pdb=" O THR B 539 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 456 through 461 removed outlier: 5.085A pdb=" N SER B 457 " --> pdb=" O LEU B 475 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LEU B 475 " --> pdb=" O SER B 457 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N VAL B 459 " --> pdb=" O ALA B 473 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ALA B 473 " --> pdb=" O VAL B 459 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N SER B 489 " --> pdb=" O GLU B 474 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ARG B 476 " --> pdb=" O LEU B 487 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N LEU B 487 " --> pdb=" O ARG B 476 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 709 through 714 removed outlier: 4.120A pdb=" N HIS B 713 " --> pdb=" O VAL B 738 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N VAL B 738 " --> pdb=" O HIS B 713 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 748 through 749 Processing sheet with id=AC5, first strand: chain 'C' and resid 764 through 765 Processing sheet with id=AC6, first strand: chain 'C' and resid 775 through 778 Processing sheet with id=AC7, first strand: chain 'C' and resid 807 through 809 Processing sheet with id=AC8, first strand: chain 'C' and resid 850 through 851 Processing sheet with id=AC9, first strand: chain 'C' and resid 865 through 866 Processing sheet with id=AD1, first strand: chain 'C' and resid 877 through 880 Processing sheet with id=AD2, first strand: chain 'C' and resid 918 through 920 Processing sheet with id=AD3, first strand: chain 'C' and resid 1176 through 1179 Processing sheet with id=AD4, first strand: chain 'C' and resid 1216 through 1218 Processing sheet with id=AD5, first strand: chain 'D' and resid 764 through 765 Processing sheet with id=AD6, first strand: chain 'D' and resid 775 through 778 Processing sheet with id=AD7, first strand: chain 'D' and resid 807 through 809 Processing sheet with id=AD8, first strand: chain 'D' and resid 850 through 851 Processing sheet with id=AD9, first strand: chain 'D' and resid 865 through 867 Processing sheet with id=AE1, first strand: chain 'D' and resid 877 through 880 Processing sheet with id=AE2, first strand: chain 'D' and resid 918 through 920 Processing sheet with id=AE3, first strand: chain 'D' and resid 1176 through 1179 Processing sheet with id=AE4, first strand: chain 'D' and resid 1216 through 1218 654 hydrogen bonds defined for protein. 1610 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: 8.28 Time building geometry restraints manager: 5.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5855 1.34 - 1.46: 4115 1.46 - 1.58: 7617 1.58 - 1.70: 0 1.70 - 1.82: 284 Bond restraints: 17871 Sorted by residual: bond pdb=" C1 NAG B1503 " pdb=" O5 NAG B1503 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.41e+00 bond pdb=" C1 NAG A1503 " pdb=" O5 NAG A1503 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.32e+00 bond pdb=" C1 NAG B1502 " pdb=" O5 NAG B1502 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.19e+00 bond pdb=" C1 NAG A1502 " pdb=" O5 NAG A1502 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.17e+00 bond pdb=" C1 NAG B1501 " pdb=" O5 NAG B1501 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.93e+00 ... (remaining 17866 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.37: 23753 1.37 - 2.75: 438 2.75 - 4.12: 118 4.12 - 5.50: 16 5.50 - 6.87: 6 Bond angle restraints: 24331 Sorted by residual: angle pdb=" N ILE D 983 " pdb=" CA ILE D 983 " pdb=" C ILE D 983 " ideal model delta sigma weight residual 111.77 107.77 4.00 1.04e+00 9.25e-01 1.48e+01 angle pdb=" C ARG D1198 " pdb=" CA ARG D1198 " pdb=" CB ARG D1198 " ideal model delta sigma weight residual 115.89 111.07 4.82 1.32e+00 5.74e-01 1.33e+01 angle pdb=" N CYS D1185 " pdb=" CA CYS D1185 " pdb=" C CYS D1185 " ideal model delta sigma weight residual 110.44 114.27 -3.83 1.20e+00 6.94e-01 1.02e+01 angle pdb=" CA CYS B 486 " pdb=" CB CYS B 486 " pdb=" SG CYS B 486 " ideal model delta sigma weight residual 114.40 121.27 -6.87 2.30e+00 1.89e-01 8.93e+00 angle pdb=" CA CYS D1185 " pdb=" CB CYS D1185 " pdb=" SG CYS D1185 " ideal model delta sigma weight residual 114.40 120.22 -5.82 2.30e+00 1.89e-01 6.41e+00 ... (remaining 24326 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 9648 17.92 - 35.85: 1029 35.85 - 53.77: 310 53.77 - 71.69: 50 71.69 - 89.61: 24 Dihedral angle restraints: 11061 sinusoidal: 4419 harmonic: 6642 Sorted by residual: dihedral pdb=" CB CYS A 464 " pdb=" SG CYS A 464 " pdb=" SG CYS A 568 " pdb=" CB CYS A 568 " ideal model delta sinusoidal sigma weight residual -86.00 -175.61 89.61 1 1.00e+01 1.00e-02 9.54e+01 dihedral pdb=" CB CYS B 464 " pdb=" SG CYS B 464 " pdb=" SG CYS B 568 " pdb=" CB CYS B 568 " ideal model delta sinusoidal sigma weight residual 93.00 -179.12 -87.88 1 1.00e+01 1.00e-02 9.25e+01 dihedral pdb=" CB CYS B 111 " pdb=" SG CYS B 111 " pdb=" SG CYS B 208 " pdb=" CB CYS B 208 " ideal model delta sinusoidal sigma weight residual -86.00 -166.87 80.87 1 1.00e+01 1.00e-02 8.08e+01 ... (remaining 11058 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1926 0.040 - 0.080: 520 0.080 - 0.120: 247 0.120 - 0.160: 15 0.160 - 0.201: 1 Chirality restraints: 2709 Sorted by residual: chirality pdb=" CA CYS D1185 " pdb=" N CYS D1185 " pdb=" C CYS D1185 " pdb=" CB CYS D1185 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA ILE A 736 " pdb=" N ILE A 736 " pdb=" C ILE A 736 " pdb=" CB ILE A 736 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.88e-01 chirality pdb=" CA PRO B 705 " pdb=" N PRO B 705 " pdb=" C PRO B 705 " pdb=" CB PRO B 705 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.13 2.00e-01 2.50e+01 4.55e-01 ... (remaining 2706 not shown) Planarity restraints: 3223 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 815 " -0.032 5.00e-02 4.00e+02 4.93e-02 3.89e+00 pdb=" N PRO C 816 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO C 816 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 816 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 428 " 0.027 5.00e-02 4.00e+02 4.09e-02 2.68e+00 pdb=" N PRO A 429 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 429 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 429 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS B 704 " -0.024 5.00e-02 4.00e+02 3.59e-02 2.07e+00 pdb=" N PRO B 705 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO B 705 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 705 " -0.020 5.00e-02 4.00e+02 ... (remaining 3220 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 917 2.73 - 3.27: 16496 3.27 - 3.81: 29514 3.81 - 4.36: 36713 4.36 - 4.90: 63236 Nonbonded interactions: 146876 Sorted by model distance: nonbonded pdb=" NE2 HIS A 367 " pdb="CU CU A1506 " model vdw 2.184 2.320 nonbonded pdb=" NE2 HIS A 76 " pdb="CU CU A1506 " model vdw 2.184 2.320 nonbonded pdb=" OD1 ASN A 573 " pdb="CA CA A1505 " model vdw 2.187 2.510 nonbonded pdb=" OD1 ASP D1040 " pdb="CA CA D2000 " model vdw 2.196 2.510 nonbonded pdb=" O ILE A 577 " pdb="CA CA A1505 " model vdw 2.197 2.510 ... (remaining 146871 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 68 through 122 or resid 124 through 259 or resid 264 throu \ gh 266 or (resid 267 and (name N or name CA or name C or name O or name CB )) or \ resid 268 through 421 or resid 423 through 528 or resid 530 through 582 or resi \ d 584 through 756 or resid 758 through 762 or resid 1501 through 1506)) selection = (chain 'B' and (resid 68 through 122 or resid 124 through 299 or (resid 300 and \ (name N or name CA or name C or name O or name CB )) or resid 301 through 421 or \ resid 423 through 528 or resid 530 through 582 or resid 584 through 756 or resi \ d 758 through 762 or resid 1501 through 1506)) } ncs_group { reference = (chain 'C' and (resid 763 through 892 or resid 894 through 921 or resid 923 thro \ ugh 1113 or resid 1115 through 1200 or resid 1202 through 1228 or resid 2000)) selection = (chain 'D' and (resid 763 through 892 or resid 894 through 921 or resid 923 thro \ ugh 1113 or resid 1115 through 1197 or (resid 1198 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD )) or resid 1199 through 1200 or \ resid 1202 through 1228 or resid 2000)) } 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=0.29 max=1.00 mean=0.99 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: 20.040 Set stop_for_unknowns flag: 0.010 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: 0.820 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 59.050 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.120 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:12.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 17984 Z= 0.110 Angle : 0.519 6.875 24563 Z= 0.271 Chirality : 0.043 0.201 2709 Planarity : 0.004 0.049 3217 Dihedral : 15.911 88.743 6494 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.22 % Allowed : 20.68 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.18), residues: 2303 helix: 0.83 (0.27), residues: 352 sheet: 0.59 (0.25), residues: 444 loop : -0.05 (0.17), residues: 1507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 84 HIS 0.002 0.000 HIS C 777 PHE 0.011 0.001 PHE D 967 TYR 0.012 0.001 TYR B 176 ARG 0.008 0.000 ARG B 610 Details of bonding type rmsd link_NAG-ASN : bond 0.00245 ( 6) link_NAG-ASN : angle 2.49685 ( 18) hydrogen bonds : bond 0.13495 ( 654) hydrogen bonds : angle 5.90865 ( 1610) SS BOND : bond 0.00256 ( 107) SS BOND : angle 0.97227 ( 214) covalent geometry : bond 0.00239 (17871) covalent geometry : angle 0.50929 (24331) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 160 time to evaluate : 1.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 739 ASP cc_start: 0.8844 (p0) cc_final: 0.8630 (p0) REVERT: C 1223 GLN cc_start: 0.7742 (mt0) cc_final: 0.7108 (tp40) outliers start: 39 outliers final: 30 residues processed: 197 average time/residue: 1.1159 time to fit residues: 251.3908 Evaluate side-chains 175 residues out of total 1935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 145 time to evaluate : 1.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 517 GLN Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 732 SER Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 165 GLN Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 717 CYS Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 759 SER Chi-restraints excluded: chain C residue 943 SER Chi-restraints excluded: chain C residue 1157 THR Chi-restraints excluded: chain C residue 1186 LEU Chi-restraints excluded: chain D residue 877 THR Chi-restraints excluded: chain D residue 947 VAL Chi-restraints excluded: chain D residue 1219 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 193 optimal weight: 3.9990 chunk 173 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 117 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 179 optimal weight: 2.9990 chunk 69 optimal weight: 0.2980 chunk 109 optimal weight: 0.9980 chunk 133 optimal weight: 0.6980 chunk 207 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 GLN A 757 GLN B B 77 ASN B 426 GLN B 498 GLN C 922 ASN A C 997 GLN D 838 GLN D 922 ASN A D1147 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.133636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.098355 restraints weight = 64712.857| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 3.68 r_work: 0.2980 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3007 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3007 r_free = 0.3007 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3007 r_free = 0.3007 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3007 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.0565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17984 Z= 0.117 Angle : 0.523 7.092 24563 Z= 0.270 Chirality : 0.044 0.139 2709 Planarity : 0.004 0.046 3217 Dihedral : 5.752 61.736 2660 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.63 % Allowed : 19.49 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.18), residues: 2303 helix: 0.81 (0.27), residues: 364 sheet: 0.53 (0.25), residues: 443 loop : 0.06 (0.17), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D1090 HIS 0.004 0.001 HIS B 453 PHE 0.017 0.001 PHE B 597 TYR 0.012 0.001 TYR B 176 ARG 0.005 0.000 ARG B 610 Details of bonding type rmsd link_NAG-ASN : bond 0.00243 ( 6) link_NAG-ASN : angle 2.54298 ( 18) hydrogen bonds : bond 0.03458 ( 654) hydrogen bonds : angle 4.89218 ( 1610) SS BOND : bond 0.00272 ( 107) SS BOND : angle 1.00222 ( 214) covalent geometry : bond 0.00268 (17871) covalent geometry : angle 0.51219 (24331) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 157 time to evaluate : 2.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 GLN cc_start: 0.8086 (OUTLIER) cc_final: 0.7284 (mp-120) REVERT: A 750 ASP cc_start: 0.8219 (t70) cc_final: 0.7885 (p0) REVERT: C 1223 GLN cc_start: 0.7794 (mt0) cc_final: 0.7159 (tp40) REVERT: D 1223 GLN cc_start: 0.7425 (pp30) cc_final: 0.7061 (pm20) outliers start: 48 outliers final: 22 residues processed: 187 average time/residue: 1.1622 time to fit residues: 248.7632 Evaluate side-chains 169 residues out of total 1935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 146 time to evaluate : 1.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 GLN Chi-restraints excluded: chain A residue 306 CYS Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 717 CYS Chi-restraints excluded: chain A residue 731 CYS Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 233 MET Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 557 MET Chi-restraints excluded: chain B residue 717 CYS Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain C residue 789 LYS Chi-restraints excluded: chain C residue 877 THR Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1157 THR Chi-restraints excluded: chain D residue 769 MET Chi-restraints excluded: chain D residue 815 THR Chi-restraints excluded: chain D residue 877 THR Chi-restraints excluded: chain D residue 942 ASP Chi-restraints excluded: chain D residue 983 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 196 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 131 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 1 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 10 optimal weight: 0.0970 chunk 32 optimal weight: 4.9990 overall best weight: 1.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 554 GLN B 73 ASN B 77 ASN C 997 GLN D 838 GLN ** D 997 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.131312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.096195 restraints weight = 77011.174| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 3.74 r_work: 0.2922 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2947 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2947 r_free = 0.2947 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2947 r_free = 0.2947 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2947 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.0770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17984 Z= 0.185 Angle : 0.551 6.392 24563 Z= 0.284 Chirality : 0.046 0.138 2709 Planarity : 0.004 0.048 3217 Dihedral : 5.159 59.695 2627 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.63 % Allowed : 18.98 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.18), residues: 2303 helix: 0.65 (0.26), residues: 370 sheet: 0.31 (0.24), residues: 467 loop : 0.06 (0.17), residues: 1466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D1014 HIS 0.003 0.001 HIS B 453 PHE 0.021 0.001 PHE B 597 TYR 0.013 0.001 TYR B 515 ARG 0.006 0.000 ARG B 610 Details of bonding type rmsd link_NAG-ASN : bond 0.00193 ( 6) link_NAG-ASN : angle 2.53405 ( 18) hydrogen bonds : bond 0.03745 ( 654) hydrogen bonds : angle 4.85768 ( 1610) SS BOND : bond 0.00334 ( 107) SS BOND : angle 1.13889 ( 214) covalent geometry : bond 0.00440 (17871) covalent geometry : angle 0.53928 (24331) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 150 time to evaluate : 1.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 GLN cc_start: 0.8075 (OUTLIER) cc_final: 0.7406 (mp-120) REVERT: A 750 ASP cc_start: 0.8258 (t70) cc_final: 0.7818 (p0) REVERT: B 247 GLN cc_start: 0.8233 (OUTLIER) cc_final: 0.7417 (mm-40) REVERT: B 541 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8964 (mt) REVERT: B 717 CYS cc_start: 0.7973 (OUTLIER) cc_final: 0.7531 (m) REVERT: C 873 ARG cc_start: 0.7835 (mtm110) cc_final: 0.7508 (mtm110) REVERT: C 1223 GLN cc_start: 0.7823 (mt0) cc_final: 0.7171 (tp40) REVERT: D 1191 ASN cc_start: 0.7862 (t0) cc_final: 0.7638 (t0) REVERT: D 1223 GLN cc_start: 0.7447 (pp30) cc_final: 0.6978 (pm20) outliers start: 48 outliers final: 15 residues processed: 181 average time/residue: 1.1881 time to fit residues: 243.6684 Evaluate side-chains 166 residues out of total 1935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 147 time to evaluate : 1.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 247 GLN Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 306 CYS Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 717 CYS Chi-restraints excluded: chain A residue 731 CYS Chi-restraints excluded: chain B residue 233 MET Chi-restraints excluded: chain B residue 247 GLN Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 414 THR Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 717 CYS Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain C residue 877 THR Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 877 THR Chi-restraints excluded: chain D residue 942 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 86 optimal weight: 1.9990 chunk 156 optimal weight: 3.9990 chunk 116 optimal weight: 0.9980 chunk 110 optimal weight: 0.5980 chunk 223 optimal weight: 0.9990 chunk 175 optimal weight: 0.5980 chunk 26 optimal weight: 5.9990 chunk 70 optimal weight: 0.8980 chunk 188 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 226 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 997 GLN D 838 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.132742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.097981 restraints weight = 57519.872| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 3.39 r_work: 0.2990 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3013 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3013 r_free = 0.3013 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3013 r_free = 0.3013 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3013 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.0797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17984 Z= 0.116 Angle : 0.511 7.279 24563 Z= 0.263 Chirality : 0.044 0.163 2709 Planarity : 0.004 0.047 3217 Dihedral : 4.849 58.424 2622 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.32 % Allowed : 19.29 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.18), residues: 2303 helix: 0.76 (0.27), residues: 370 sheet: 0.38 (0.24), residues: 456 loop : 0.09 (0.17), residues: 1477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D1014 HIS 0.003 0.000 HIS B 453 PHE 0.016 0.001 PHE B 597 TYR 0.009 0.001 TYR A 287 ARG 0.007 0.000 ARG B 610 Details of bonding type rmsd link_NAG-ASN : bond 0.00196 ( 6) link_NAG-ASN : angle 2.41510 ( 18) hydrogen bonds : bond 0.03234 ( 654) hydrogen bonds : angle 4.68621 ( 1610) SS BOND : bond 0.00255 ( 107) SS BOND : angle 0.93814 ( 214) covalent geometry : bond 0.00274 (17871) covalent geometry : angle 0.50195 (24331) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 154 time to evaluate : 1.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 GLN cc_start: 0.8070 (OUTLIER) cc_final: 0.7408 (mp-120) REVERT: A 750 ASP cc_start: 0.8114 (t70) cc_final: 0.7892 (p0) REVERT: B 541 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8933 (mt) REVERT: C 838 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.7148 (pp30) REVERT: C 873 ARG cc_start: 0.7711 (mtm110) cc_final: 0.7467 (mtt90) REVERT: C 997 GLN cc_start: 0.8828 (OUTLIER) cc_final: 0.8410 (tp-100) REVERT: C 1223 GLN cc_start: 0.7786 (mt0) cc_final: 0.7164 (tp40) REVERT: D 1191 ASN cc_start: 0.7837 (t0) cc_final: 0.7558 (t0) REVERT: D 1223 GLN cc_start: 0.7422 (OUTLIER) cc_final: 0.6980 (pm20) outliers start: 42 outliers final: 18 residues processed: 179 average time/residue: 1.1876 time to fit residues: 242.1011 Evaluate side-chains 175 residues out of total 1935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 152 time to evaluate : 1.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 GLN Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 306 CYS Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 717 CYS Chi-restraints excluded: chain A residue 731 CYS Chi-restraints excluded: chain B residue 233 MET Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 414 THR Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain C residue 769 MET Chi-restraints excluded: chain C residue 789 LYS Chi-restraints excluded: chain C residue 807 VAL Chi-restraints excluded: chain C residue 838 GLN Chi-restraints excluded: chain C residue 877 THR Chi-restraints excluded: chain C residue 997 GLN Chi-restraints excluded: chain D residue 769 MET Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 877 THR Chi-restraints excluded: chain D residue 1223 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 15 optimal weight: 5.9990 chunk 39 optimal weight: 0.2980 chunk 98 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 181 optimal weight: 1.9990 chunk 223 optimal weight: 0.7980 chunk 112 optimal weight: 2.9990 chunk 225 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 201 optimal weight: 2.9990 chunk 120 optimal weight: 5.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 997 GLN D 838 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.131984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.096604 restraints weight = 76272.517| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 3.92 r_work: 0.2927 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2954 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2954 r_free = 0.2954 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2954 r_free = 0.2954 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2954 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.0872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 17984 Z= 0.153 Angle : 0.539 9.240 24563 Z= 0.276 Chirality : 0.045 0.165 2709 Planarity : 0.004 0.049 3217 Dihedral : 4.737 54.844 2621 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.27 % Allowed : 19.34 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.18), residues: 2303 helix: 0.76 (0.26), residues: 370 sheet: 0.27 (0.24), residues: 468 loop : 0.09 (0.17), residues: 1465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D1014 HIS 0.003 0.001 HIS B 453 PHE 0.018 0.001 PHE B 597 TYR 0.010 0.001 TYR A 287 ARG 0.007 0.000 ARG B 610 Details of bonding type rmsd link_NAG-ASN : bond 0.00195 ( 6) link_NAG-ASN : angle 2.39920 ( 18) hydrogen bonds : bond 0.03370 ( 654) hydrogen bonds : angle 4.70172 ( 1610) SS BOND : bond 0.00330 ( 107) SS BOND : angle 1.16312 ( 214) covalent geometry : bond 0.00364 (17871) covalent geometry : angle 0.52631 (24331) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 154 time to evaluate : 1.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 GLN cc_start: 0.8085 (OUTLIER) cc_final: 0.7416 (mp-120) REVERT: A 750 ASP cc_start: 0.8176 (t70) cc_final: 0.7941 (p0) REVERT: B 541 LEU cc_start: 0.9203 (OUTLIER) cc_final: 0.8958 (mt) REVERT: C 838 GLN cc_start: 0.8312 (OUTLIER) cc_final: 0.7210 (pp30) REVERT: C 873 ARG cc_start: 0.7846 (mtm110) cc_final: 0.7599 (mtt90) REVERT: C 1201 ARG cc_start: 0.7848 (mtp85) cc_final: 0.7145 (mmt-90) REVERT: C 1223 GLN cc_start: 0.7806 (mt0) cc_final: 0.7155 (tp40) REVERT: D 1191 ASN cc_start: 0.7879 (t0) cc_final: 0.7597 (t0) REVERT: D 1223 GLN cc_start: 0.7486 (OUTLIER) cc_final: 0.6958 (pm20) outliers start: 41 outliers final: 22 residues processed: 175 average time/residue: 1.1908 time to fit residues: 235.8325 Evaluate side-chains 176 residues out of total 1935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 150 time to evaluate : 1.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 247 GLN Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 306 CYS Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 717 CYS Chi-restraints excluded: chain A residue 731 CYS Chi-restraints excluded: chain B residue 233 MET Chi-restraints excluded: chain B residue 241 MET Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 414 THR Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain C residue 769 MET Chi-restraints excluded: chain C residue 789 LYS Chi-restraints excluded: chain C residue 807 VAL Chi-restraints excluded: chain C residue 838 GLN Chi-restraints excluded: chain C residue 877 THR Chi-restraints excluded: chain C residue 1186 LEU Chi-restraints excluded: chain D residue 769 MET Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 877 THR Chi-restraints excluded: chain D residue 942 ASP Chi-restraints excluded: chain D residue 1223 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 69 optimal weight: 9.9990 chunk 21 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 chunk 117 optimal weight: 2.9990 chunk 219 optimal weight: 4.9990 chunk 183 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 208 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 173 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 997 GLN D 838 GLN ** D 997 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.130472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.094847 restraints weight = 66419.083| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 3.67 r_work: 0.2928 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2951 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2951 r_free = 0.2951 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2951 r_free = 0.2951 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2951 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.1031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 17984 Z= 0.203 Angle : 0.571 10.341 24563 Z= 0.292 Chirality : 0.046 0.154 2709 Planarity : 0.004 0.052 3217 Dihedral : 4.807 38.840 2621 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.58 % Allowed : 19.24 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.18), residues: 2303 helix: 0.63 (0.26), residues: 370 sheet: 0.29 (0.24), residues: 471 loop : 0.04 (0.17), residues: 1462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D1014 HIS 0.003 0.001 HIS B 88 PHE 0.021 0.002 PHE B 597 TYR 0.014 0.002 TYR B 515 ARG 0.007 0.000 ARG B 610 Details of bonding type rmsd link_NAG-ASN : bond 0.00190 ( 6) link_NAG-ASN : angle 2.48775 ( 18) hydrogen bonds : bond 0.03723 ( 654) hydrogen bonds : angle 4.83964 ( 1610) SS BOND : bond 0.00370 ( 107) SS BOND : angle 1.21979 ( 214) covalent geometry : bond 0.00484 (17871) covalent geometry : angle 0.55759 (24331) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 146 time to evaluate : 1.853 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 247 GLN cc_start: 0.8094 (OUTLIER) cc_final: 0.7425 (mp-120) REVERT: A 750 ASP cc_start: 0.8218 (t70) cc_final: 0.7910 (p0) REVERT: B 247 GLN cc_start: 0.8228 (OUTLIER) cc_final: 0.7408 (mm-40) REVERT: B 541 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8961 (mt) REVERT: C 838 GLN cc_start: 0.8294 (OUTLIER) cc_final: 0.7236 (pp30) REVERT: C 1223 GLN cc_start: 0.7769 (mt0) cc_final: 0.7143 (tp40) REVERT: D 1191 ASN cc_start: 0.7951 (t0) cc_final: 0.7636 (t0) outliers start: 47 outliers final: 23 residues processed: 174 average time/residue: 1.1763 time to fit residues: 233.9269 Evaluate side-chains 173 residues out of total 1935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 146 time to evaluate : 1.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 247 GLN Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 306 CYS Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 717 CYS Chi-restraints excluded: chain A residue 731 CYS Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 233 MET Chi-restraints excluded: chain B residue 247 GLN Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 592 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain C residue 769 MET Chi-restraints excluded: chain C residue 789 LYS Chi-restraints excluded: chain C residue 807 VAL Chi-restraints excluded: chain C residue 838 GLN Chi-restraints excluded: chain C residue 877 THR Chi-restraints excluded: chain C residue 1157 THR Chi-restraints excluded: chain C residue 1185 CYS Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 877 THR Chi-restraints excluded: chain D residue 942 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 148 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 173 optimal weight: 2.9990 chunk 162 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 226 optimal weight: 1.9990 chunk 80 optimal weight: 0.5980 chunk 56 optimal weight: 4.9990 chunk 143 optimal weight: 5.9990 chunk 112 optimal weight: 0.4980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 517 GLN D 838 GLN ** D 997 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.131447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.096318 restraints weight = 82908.868| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 3.92 r_work: 0.2918 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2941 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2941 r_free = 0.2941 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2941 r_free = 0.2941 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2941 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.1002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17984 Z= 0.153 Angle : 0.541 9.370 24563 Z= 0.277 Chirality : 0.045 0.185 2709 Planarity : 0.004 0.051 3217 Dihedral : 4.657 38.387 2621 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.11 % Allowed : 19.96 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.18), residues: 2303 helix: 0.70 (0.26), residues: 370 sheet: 0.28 (0.24), residues: 470 loop : 0.07 (0.17), residues: 1463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D1014 HIS 0.003 0.001 HIS B 453 PHE 0.018 0.001 PHE B 597 TYR 0.010 0.001 TYR A 287 ARG 0.007 0.000 ARG B 610 Details of bonding type rmsd link_NAG-ASN : bond 0.00178 ( 6) link_NAG-ASN : angle 2.44976 ( 18) hydrogen bonds : bond 0.03405 ( 654) hydrogen bonds : angle 4.74904 ( 1610) SS BOND : bond 0.00311 ( 107) SS BOND : angle 1.09477 ( 214) covalent geometry : bond 0.00365 (17871) covalent geometry : angle 0.52962 (24331) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 158 time to evaluate : 1.987 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 247 GLN cc_start: 0.8139 (OUTLIER) cc_final: 0.7479 (mp-120) REVERT: A 750 ASP cc_start: 0.8165 (t70) cc_final: 0.7909 (p0) REVERT: B 247 GLN cc_start: 0.8222 (OUTLIER) cc_final: 0.7405 (mm-40) REVERT: B 294 ASP cc_start: 0.7870 (m-30) cc_final: 0.7520 (m-30) REVERT: B 541 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8964 (mt) REVERT: C 838 GLN cc_start: 0.8293 (OUTLIER) cc_final: 0.7222 (pp30) REVERT: C 873 ARG cc_start: 0.7790 (mtm-85) cc_final: 0.7579 (mtm110) REVERT: C 1223 GLN cc_start: 0.7782 (mt0) cc_final: 0.7152 (tp40) REVERT: D 1191 ASN cc_start: 0.7961 (t0) cc_final: 0.7617 (t0) REVERT: D 1223 GLN cc_start: 0.7373 (pp30) cc_final: 0.6904 (pm20) outliers start: 38 outliers final: 28 residues processed: 182 average time/residue: 1.0990 time to fit residues: 229.1495 Evaluate side-chains 181 residues out of total 1935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 149 time to evaluate : 1.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 247 GLN Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 306 CYS Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 717 CYS Chi-restraints excluded: chain A residue 731 CYS Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 233 MET Chi-restraints excluded: chain B residue 247 GLN Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 414 THR Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 592 THR Chi-restraints excluded: chain B residue 698 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain C residue 769 MET Chi-restraints excluded: chain C residue 789 LYS Chi-restraints excluded: chain C residue 807 VAL Chi-restraints excluded: chain C residue 838 GLN Chi-restraints excluded: chain C residue 877 THR Chi-restraints excluded: chain C residue 958 THR Chi-restraints excluded: chain C residue 1157 THR Chi-restraints excluded: chain C residue 1185 CYS Chi-restraints excluded: chain D residue 769 MET Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 815 THR Chi-restraints excluded: chain D residue 877 THR Chi-restraints excluded: chain D residue 942 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 76 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 18 optimal weight: 0.3980 chunk 21 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 218 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 838 GLN ** D 997 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 = 0.3627 r_free = 0.3627 target = 0.130867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.095373 restraints weight = 63330.315| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 3.67 r_work: 0.2934 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2960 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2960 r_free = 0.2960 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2960 r_free = 0.2960 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2960 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.1056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17984 Z= 0.178 Angle : 0.557 9.499 24563 Z= 0.285 Chirality : 0.046 0.181 2709 Planarity : 0.004 0.052 3217 Dihedral : 4.677 38.320 2621 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.22 % Allowed : 20.32 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.18), residues: 2303 helix: 0.67 (0.26), residues: 370 sheet: 0.26 (0.24), residues: 451 loop : 0.05 (0.17), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D1014 HIS 0.003 0.001 HIS B 88 PHE 0.020 0.001 PHE B 597 TYR 0.011 0.001 TYR A 287 ARG 0.008 0.000 ARG B 610 Details of bonding type rmsd link_NAG-ASN : bond 0.00178 ( 6) link_NAG-ASN : angle 2.47115 ( 18) hydrogen bonds : bond 0.03540 ( 654) hydrogen bonds : angle 4.78580 ( 1610) SS BOND : bond 0.00343 ( 107) SS BOND : angle 1.15421 ( 214) covalent geometry : bond 0.00424 (17871) covalent geometry : angle 0.54521 (24331) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 150 time to evaluate : 2.069 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 750 ASP cc_start: 0.8177 (t70) cc_final: 0.7922 (p0) REVERT: B 247 GLN cc_start: 0.8221 (OUTLIER) cc_final: 0.7422 (mm-40) REVERT: B 294 ASP cc_start: 0.7859 (m-30) cc_final: 0.7527 (m-30) REVERT: B 541 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8971 (mt) REVERT: C 838 GLN cc_start: 0.8301 (OUTLIER) cc_final: 0.7269 (pp30) REVERT: C 1223 GLN cc_start: 0.7765 (mt0) cc_final: 0.7138 (tp40) REVERT: D 858 ILE cc_start: 0.8373 (OUTLIER) cc_final: 0.7901 (pp) REVERT: D 1191 ASN cc_start: 0.7973 (t0) cc_final: 0.7637 (t0) REVERT: D 1223 GLN cc_start: 0.7379 (pp30) cc_final: 0.6872 (pm20) outliers start: 40 outliers final: 27 residues processed: 175 average time/residue: 1.1849 time to fit residues: 236.8965 Evaluate side-chains 179 residues out of total 1935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 148 time to evaluate : 2.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 306 CYS Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 717 CYS Chi-restraints excluded: chain A residue 731 CYS Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 233 MET Chi-restraints excluded: chain B residue 247 GLN Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 414 THR Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 592 THR Chi-restraints excluded: chain B residue 698 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain C residue 769 MET Chi-restraints excluded: chain C residue 789 LYS Chi-restraints excluded: chain C residue 807 VAL Chi-restraints excluded: chain C residue 838 GLN Chi-restraints excluded: chain C residue 877 THR Chi-restraints excluded: chain C residue 958 THR Chi-restraints excluded: chain C residue 1157 THR Chi-restraints excluded: chain D residue 769 MET Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 815 THR Chi-restraints excluded: chain D residue 858 ILE Chi-restraints excluded: chain D residue 877 THR Chi-restraints excluded: chain D residue 942 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 125 optimal weight: 0.9980 chunk 202 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 chunk 106 optimal weight: 0.8980 chunk 142 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 18 optimal weight: 0.0020 chunk 5 optimal weight: 1.9990 chunk 54 optimal weight: 0.4980 chunk 2 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 838 GLN ** D 997 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 = 0.3656 r_free = 0.3656 target = 0.133105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.097639 restraints weight = 62643.848| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 3.60 r_work: 0.2978 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3001 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3001 r_free = 0.3001 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3001 r_free = 0.3001 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3001 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.0991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17984 Z= 0.108 Angle : 0.513 7.987 24563 Z= 0.263 Chirality : 0.044 0.159 2709 Planarity : 0.004 0.049 3217 Dihedral : 4.404 37.477 2621 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.81 % Allowed : 20.63 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.18), residues: 2303 helix: 0.85 (0.27), residues: 370 sheet: 0.34 (0.24), residues: 469 loop : 0.12 (0.17), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D1014 HIS 0.002 0.000 HIS B 76 PHE 0.014 0.001 PHE B 597 TYR 0.011 0.001 TYR B 176 ARG 0.008 0.000 ARG B 610 Details of bonding type rmsd link_NAG-ASN : bond 0.00193 ( 6) link_NAG-ASN : angle 2.34061 ( 18) hydrogen bonds : bond 0.03057 ( 654) hydrogen bonds : angle 4.58755 ( 1610) SS BOND : bond 0.00267 ( 107) SS BOND : angle 0.94503 ( 214) covalent geometry : bond 0.00254 (17871) covalent geometry : angle 0.50345 (24331) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 160 time to evaluate : 1.844 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 294 ASP cc_start: 0.7776 (m-30) cc_final: 0.7407 (m-30) REVERT: B 541 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8942 (mt) REVERT: C 838 GLN cc_start: 0.8299 (OUTLIER) cc_final: 0.7203 (pp30) REVERT: C 1201 ARG cc_start: 0.7794 (mtp85) cc_final: 0.7126 (mmt-90) REVERT: C 1223 GLN cc_start: 0.7754 (mt0) cc_final: 0.7120 (tp40) REVERT: D 858 ILE cc_start: 0.8360 (OUTLIER) cc_final: 0.7884 (pp) REVERT: D 1191 ASN cc_start: 0.7977 (t0) cc_final: 0.7669 (t0) REVERT: D 1223 GLN cc_start: 0.7352 (pp30) cc_final: 0.6916 (pm20) outliers start: 32 outliers final: 26 residues processed: 179 average time/residue: 1.1330 time to fit residues: 232.6505 Evaluate side-chains 181 residues out of total 1935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 152 time to evaluate : 2.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 306 CYS Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 717 CYS Chi-restraints excluded: chain A residue 731 CYS Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 414 THR Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 592 THR Chi-restraints excluded: chain B residue 698 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain C residue 789 LYS Chi-restraints excluded: chain C residue 807 VAL Chi-restraints excluded: chain C residue 838 GLN Chi-restraints excluded: chain C residue 877 THR Chi-restraints excluded: chain C residue 958 THR Chi-restraints excluded: chain C residue 1157 THR Chi-restraints excluded: chain D residue 769 MET Chi-restraints excluded: chain D residue 815 THR Chi-restraints excluded: chain D residue 858 ILE Chi-restraints excluded: chain D residue 877 THR Chi-restraints excluded: chain D residue 942 ASP Chi-restraints excluded: chain D residue 980 VAL Chi-restraints excluded: chain D residue 983 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 92 optimal weight: 0.9990 chunk 9 optimal weight: 0.4980 chunk 91 optimal weight: 6.9990 chunk 100 optimal weight: 0.1980 chunk 26 optimal weight: 0.7980 chunk 150 optimal weight: 5.9990 chunk 125 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 129 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 838 GLN ** D 997 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 = 0.3658 r_free = 0.3658 target = 0.133263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.098173 restraints weight = 71968.566| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 3.74 r_work: 0.2953 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2978 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2978 r_free = 0.2978 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2978 r_free = 0.2978 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2978 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.1025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17984 Z= 0.106 Angle : 0.509 8.012 24563 Z= 0.261 Chirality : 0.044 0.147 2709 Planarity : 0.004 0.049 3217 Dihedral : 4.322 37.023 2621 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.60 % Allowed : 20.99 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.18), residues: 2303 helix: 0.89 (0.27), residues: 371 sheet: 0.39 (0.24), residues: 458 loop : 0.15 (0.17), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D1014 HIS 0.002 0.000 HIS B 453 PHE 0.013 0.001 PHE B 597 TYR 0.010 0.001 TYR B 287 ARG 0.008 0.000 ARG B 610 Details of bonding type rmsd link_NAG-ASN : bond 0.00189 ( 6) link_NAG-ASN : angle 2.29204 ( 18) hydrogen bonds : bond 0.03023 ( 654) hydrogen bonds : angle 4.53023 ( 1610) SS BOND : bond 0.00240 ( 107) SS BOND : angle 0.93845 ( 214) covalent geometry : bond 0.00251 (17871) covalent geometry : angle 0.50024 (24331) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 158 time to evaluate : 2.102 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 294 ASP cc_start: 0.7707 (m-30) cc_final: 0.7353 (m-30) REVERT: C 838 GLN cc_start: 0.8284 (OUTLIER) cc_final: 0.7188 (pp30) REVERT: C 1201 ARG cc_start: 0.7847 (mtp85) cc_final: 0.7150 (mmt-90) REVERT: C 1223 GLN cc_start: 0.7768 (mt0) cc_final: 0.7128 (tp40) REVERT: D 858 ILE cc_start: 0.8346 (OUTLIER) cc_final: 0.7991 (pp) REVERT: D 1191 ASN cc_start: 0.7938 (t0) cc_final: 0.7650 (t0) REVERT: D 1223 GLN cc_start: 0.7365 (pp30) cc_final: 0.6922 (pm20) outliers start: 28 outliers final: 21 residues processed: 171 average time/residue: 1.1505 time to fit residues: 224.5575 Evaluate side-chains 174 residues out of total 1935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 151 time to evaluate : 1.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 306 CYS Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 717 CYS Chi-restraints excluded: chain A residue 731 CYS Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 414 THR Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 557 MET Chi-restraints excluded: chain B residue 592 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain C residue 789 LYS Chi-restraints excluded: chain C residue 807 VAL Chi-restraints excluded: chain C residue 838 GLN Chi-restraints excluded: chain C residue 877 THR Chi-restraints excluded: chain C residue 958 THR Chi-restraints excluded: chain D residue 769 MET Chi-restraints excluded: chain D residue 815 THR Chi-restraints excluded: chain D residue 858 ILE Chi-restraints excluded: chain D residue 877 THR Chi-restraints excluded: chain D residue 942 ASP Chi-restraints excluded: chain D residue 983 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 32 optimal weight: 5.9990 chunk 139 optimal weight: 2.9990 chunk 177 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 209 optimal weight: 2.9990 chunk 182 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 133 optimal weight: 6.9990 chunk 105 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 997 GLN D 838 GLN ** D 997 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.129803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.094140 restraints weight = 71326.844| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 3.84 r_work: 0.2899 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2922 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2922 r_free = 0.2922 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2922 r_free = 0.2922 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2922 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.1186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 17984 Z= 0.247 Angle : 0.604 10.066 24563 Z= 0.308 Chirality : 0.048 0.167 2709 Planarity : 0.004 0.053 3217 Dihedral : 4.741 38.283 2621 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.65 % Allowed : 21.14 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.18), residues: 2303 helix: 0.61 (0.26), residues: 371 sheet: 0.23 (0.24), residues: 450 loop : 0.06 (0.17), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D1014 HIS 0.003 0.001 HIS B 88 PHE 0.023 0.002 PHE B 597 TYR 0.014 0.002 TYR B 515 ARG 0.008 0.000 ARG B 610 Details of bonding type rmsd link_NAG-ASN : bond 0.00189 ( 6) link_NAG-ASN : angle 2.50467 ( 18) hydrogen bonds : bond 0.03904 ( 654) hydrogen bonds : angle 4.85880 ( 1610) SS BOND : bond 0.00399 ( 107) SS BOND : angle 1.29532 ( 214) covalent geometry : bond 0.00592 (17871) covalent geometry : angle 0.59081 (24331) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11456.51 seconds wall clock time: 200 minutes 18.56 seconds (12018.56 seconds total)