Starting phenix.real_space_refine on Thu Jul 25 20:28:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u8o_42026/07_2024/8u8o_42026.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u8o_42026/07_2024/8u8o_42026.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u8o_42026/07_2024/8u8o_42026.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u8o_42026/07_2024/8u8o_42026.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u8o_42026/07_2024/8u8o_42026.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u8o_42026/07_2024/8u8o_42026.cif" } resolution = 2.4 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= 0.008 sd= 0.074 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 72 5.49 5 S 192 5.16 5 C 18760 2.51 5 N 5136 2.21 5 O 5920 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 43": "OD1" <-> "OD2" Residue "A GLU 75": "OE1" <-> "OE2" Residue "A ASP 77": "OD1" <-> "OD2" Residue "A PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 103": "OE1" <-> "OE2" Residue "A ASP 232": "OD1" <-> "OD2" Residue "A TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 335": "OE1" <-> "OE2" Residue "A GLU 395": "OE1" <-> "OE2" Residue "A TYR 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 477": "OD1" <-> "OD2" Residue "B ASP 43": "OD1" <-> "OD2" Residue "B GLU 75": "OE1" <-> "OE2" Residue "B ASP 77": "OD1" <-> "OD2" Residue "B PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 103": "OE1" <-> "OE2" Residue "B GLU 111": "OE1" <-> "OE2" Residue "B TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 335": "OE1" <-> "OE2" Residue "B GLU 395": "OE1" <-> "OE2" Residue "B TYR 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 477": "OD1" <-> "OD2" Residue "C TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 43": "OD1" <-> "OD2" Residue "C GLU 75": "OE1" <-> "OE2" Residue "C ASP 77": "OD1" <-> "OD2" Residue "C PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 103": "OE1" <-> "OE2" Residue "C GLU 111": "OE1" <-> "OE2" Residue "C TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 395": "OE1" <-> "OE2" Residue "C TYR 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 477": "OD1" <-> "OD2" Residue "D ASP 43": "OD1" <-> "OD2" Residue "D GLU 75": "OE1" <-> "OE2" Residue "D ASP 77": "OD1" <-> "OD2" Residue "D PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 103": "OE1" <-> "OE2" Residue "D GLU 111": "OE1" <-> "OE2" Residue "D TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 261": "OD1" <-> "OD2" Residue "D TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 395": "OE1" <-> "OE2" Residue "D TYR 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 477": "OD1" <-> "OD2" Residue "E ASP 43": "OD1" <-> "OD2" Residue "E GLU 75": "OE1" <-> "OE2" Residue "E ASP 77": "OD1" <-> "OD2" Residue "E PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 103": "OE1" <-> "OE2" Residue "E TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 335": "OE1" <-> "OE2" Residue "E GLU 395": "OE1" <-> "OE2" Residue "E TYR 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 477": "OD1" <-> "OD2" Residue "F TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 43": "OD1" <-> "OD2" Residue "F GLU 75": "OE1" <-> "OE2" Residue "F ASP 77": "OD1" <-> "OD2" Residue "F PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 103": "OE1" <-> "OE2" Residue "F TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 335": "OE1" <-> "OE2" Residue "F GLU 395": "OE1" <-> "OE2" Residue "F TYR 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 477": "OD1" <-> "OD2" Residue "G ASP 43": "OD1" <-> "OD2" Residue "G GLU 75": "OE1" <-> "OE2" Residue "G ASP 77": "OD1" <-> "OD2" Residue "G PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 103": "OE1" <-> "OE2" Residue "G GLU 111": "OE1" <-> "OE2" Residue "G TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 395": "OE1" <-> "OE2" Residue "G TYR 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 477": "OD1" <-> "OD2" Residue "H ASP 43": "OD1" <-> "OD2" Residue "H GLU 75": "OE1" <-> "OE2" Residue "H ASP 77": "OD1" <-> "OD2" Residue "H PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 103": "OE1" <-> "OE2" Residue "H ASP 232": "OD1" <-> "OD2" Residue "H TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 335": "OE1" <-> "OE2" Residue "H GLU 395": "OE1" <-> "OE2" Residue "H TYR 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 477": "OD1" <-> "OD2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 30080 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3631 Classifications: {'peptide': 482} Link IDs: {'PTRANS': 17, 'TRANS': 464} Chain breaks: 2 Chain: "B" Number of atoms: 3631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3631 Classifications: {'peptide': 482} Link IDs: {'PTRANS': 17, 'TRANS': 464} Chain breaks: 2 Chain: "C" Number of atoms: 3631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3631 Classifications: {'peptide': 482} Link IDs: {'PTRANS': 17, 'TRANS': 464} Chain breaks: 2 Chain: "D" Number of atoms: 3631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3631 Classifications: {'peptide': 482} Link IDs: {'PTRANS': 17, 'TRANS': 464} Chain breaks: 2 Chain: "E" Number of atoms: 3631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3631 Classifications: {'peptide': 482} Link IDs: {'PTRANS': 17, 'TRANS': 464} Chain breaks: 2 Chain: "F" Number of atoms: 3631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3631 Classifications: {'peptide': 482} Link IDs: {'PTRANS': 17, 'TRANS': 464} Chain breaks: 2 Chain: "G" Number of atoms: 3631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3631 Classifications: {'peptide': 482} Link IDs: {'PTRANS': 17, 'TRANS': 464} Chain breaks: 2 Chain: "H" Number of atoms: 3631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3631 Classifications: {'peptide': 482} Link IDs: {'PTRANS': 17, 'TRANS': 464} Chain breaks: 2 Chain: "A" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "B" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "C" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "D" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "E" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "F" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "G" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "H" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Time building chain proxies: 17.08, per 1000 atoms: 0.57 Number of scatterers: 30080 At special positions: 0 Unit cell: (159.327, 159.327, 134.037, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 192 16.00 P 72 15.00 O 5920 8.00 N 5136 7.00 C 18760 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.92 Conformation dependent library (CDL) restraints added in 6.0 seconds 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6944 Finding SS restraints... Secondary structure from input PDB file: 168 helices and 48 sheets defined 41.7% alpha, 13.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.36 Creating SS restraints... Processing helix chain 'A' and resid 19 through 24 Processing helix chain 'A' and resid 31 through 33 No H-bonds generated for 'chain 'A' and resid 31 through 33' Processing helix chain 'A' and resid 45 through 49 Processing helix chain 'A' and resid 75 through 86 Processing helix chain 'A' and resid 96 through 109 Processing helix chain 'A' and resid 126 through 138 Processing helix chain 'A' and resid 159 through 164 Processing helix chain 'A' and resid 183 through 185 No H-bonds generated for 'chain 'A' and resid 183 through 185' Processing helix chain 'A' and resid 193 through 205 Processing helix chain 'A' and resid 224 through 229 removed outlier: 3.630A pdb=" N LYS A 229 " --> pdb=" O THR A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 266 removed outlier: 3.601A pdb=" N ARG A 259 " --> pdb=" O ASP A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 294 Processing helix chain 'A' and resid 306 through 317 removed outlier: 3.736A pdb=" N ASN A 312 " --> pdb=" O ALA A 308 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU A 313 " --> pdb=" O GLN A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 338 Processing helix chain 'A' and resid 342 through 355 Processing helix chain 'A' and resid 356 through 358 No H-bonds generated for 'chain 'A' and resid 356 through 358' Processing helix chain 'A' and resid 369 through 379 Processing helix chain 'A' and resid 417 through 421 Processing helix chain 'A' and resid 452 through 472 Proline residue: A 458 - end of helix Processing helix chain 'A' and resid 475 through 486 Processing helix chain 'A' and resid 494 through 501 Processing helix chain 'B' and resid 19 through 24 Processing helix chain 'B' and resid 31 through 33 No H-bonds generated for 'chain 'B' and resid 31 through 33' Processing helix chain 'B' and resid 45 through 49 Processing helix chain 'B' and resid 75 through 86 Processing helix chain 'B' and resid 96 through 109 Processing helix chain 'B' and resid 126 through 138 Processing helix chain 'B' and resid 159 through 164 Processing helix chain 'B' and resid 183 through 185 No H-bonds generated for 'chain 'B' and resid 183 through 185' Processing helix chain 'B' and resid 193 through 205 Processing helix chain 'B' and resid 224 through 229 removed outlier: 3.638A pdb=" N LYS B 229 " --> pdb=" O THR B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 266 removed outlier: 3.602A pdb=" N ARG B 259 " --> pdb=" O ASP B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 294 Processing helix chain 'B' and resid 306 through 317 removed outlier: 3.737A pdb=" N ASN B 312 " --> pdb=" O ALA B 308 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU B 313 " --> pdb=" O GLN B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 338 Processing helix chain 'B' and resid 342 through 355 Processing helix chain 'B' and resid 356 through 358 No H-bonds generated for 'chain 'B' and resid 356 through 358' Processing helix chain 'B' and resid 369 through 379 Processing helix chain 'B' and resid 417 through 421 Processing helix chain 'B' and resid 452 through 472 Proline residue: B 458 - end of helix Processing helix chain 'B' and resid 475 through 486 Processing helix chain 'B' and resid 494 through 501 Processing helix chain 'C' and resid 19 through 24 Processing helix chain 'C' and resid 31 through 33 No H-bonds generated for 'chain 'C' and resid 31 through 33' Processing helix chain 'C' and resid 45 through 49 Processing helix chain 'C' and resid 75 through 86 Processing helix chain 'C' and resid 96 through 109 Processing helix chain 'C' and resid 126 through 138 Processing helix chain 'C' and resid 159 through 164 Processing helix chain 'C' and resid 183 through 185 No H-bonds generated for 'chain 'C' and resid 183 through 185' Processing helix chain 'C' and resid 193 through 205 Processing helix chain 'C' and resid 224 through 229 removed outlier: 3.633A pdb=" N LYS C 229 " --> pdb=" O THR C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 266 removed outlier: 3.612A pdb=" N ARG C 259 " --> pdb=" O ASP C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 294 Processing helix chain 'C' and resid 306 through 317 removed outlier: 3.738A pdb=" N ASN C 312 " --> pdb=" O ALA C 308 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU C 313 " --> pdb=" O GLN C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 338 Processing helix chain 'C' and resid 342 through 355 Processing helix chain 'C' and resid 356 through 358 No H-bonds generated for 'chain 'C' and resid 356 through 358' Processing helix chain 'C' and resid 369 through 379 Processing helix chain 'C' and resid 417 through 421 Processing helix chain 'C' and resid 452 through 472 Proline residue: C 458 - end of helix Processing helix chain 'C' and resid 475 through 486 Processing helix chain 'C' and resid 494 through 501 Processing helix chain 'D' and resid 19 through 24 Processing helix chain 'D' and resid 31 through 33 No H-bonds generated for 'chain 'D' and resid 31 through 33' Processing helix chain 'D' and resid 45 through 49 Processing helix chain 'D' and resid 75 through 86 Processing helix chain 'D' and resid 96 through 109 Processing helix chain 'D' and resid 126 through 138 Processing helix chain 'D' and resid 159 through 164 Processing helix chain 'D' and resid 183 through 185 No H-bonds generated for 'chain 'D' and resid 183 through 185' Processing helix chain 'D' and resid 193 through 205 Processing helix chain 'D' and resid 224 through 229 removed outlier: 3.629A pdb=" N LYS D 229 " --> pdb=" O THR D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 267 removed outlier: 3.589A pdb=" N ARG D 259 " --> pdb=" O ASP D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 294 Processing helix chain 'D' and resid 306 through 317 removed outlier: 3.737A pdb=" N ASN D 312 " --> pdb=" O ALA D 308 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU D 313 " --> pdb=" O GLN D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 338 Processing helix chain 'D' and resid 342 through 355 Processing helix chain 'D' and resid 356 through 358 No H-bonds generated for 'chain 'D' and resid 356 through 358' Processing helix chain 'D' and resid 369 through 379 Processing helix chain 'D' and resid 417 through 421 Processing helix chain 'D' and resid 452 through 472 Proline residue: D 458 - end of helix Processing helix chain 'D' and resid 475 through 486 Processing helix chain 'D' and resid 494 through 501 Processing helix chain 'E' and resid 19 through 24 Processing helix chain 'E' and resid 31 through 33 No H-bonds generated for 'chain 'E' and resid 31 through 33' Processing helix chain 'E' and resid 45 through 49 Processing helix chain 'E' and resid 75 through 86 Processing helix chain 'E' and resid 96 through 109 Processing helix chain 'E' and resid 126 through 138 Processing helix chain 'E' and resid 159 through 164 Processing helix chain 'E' and resid 183 through 185 No H-bonds generated for 'chain 'E' and resid 183 through 185' Processing helix chain 'E' and resid 193 through 205 Processing helix chain 'E' and resid 224 through 229 removed outlier: 3.638A pdb=" N LYS E 229 " --> pdb=" O THR E 225 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 266 removed outlier: 3.602A pdb=" N ARG E 259 " --> pdb=" O ASP E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 294 Processing helix chain 'E' and resid 306 through 317 removed outlier: 3.736A pdb=" N ASN E 312 " --> pdb=" O ALA E 308 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU E 313 " --> pdb=" O GLN E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 332 through 338 Processing helix chain 'E' and resid 342 through 355 Processing helix chain 'E' and resid 356 through 358 No H-bonds generated for 'chain 'E' and resid 356 through 358' Processing helix chain 'E' and resid 369 through 379 Processing helix chain 'E' and resid 417 through 421 Processing helix chain 'E' and resid 452 through 472 Proline residue: E 458 - end of helix Processing helix chain 'E' and resid 475 through 486 Processing helix chain 'E' and resid 494 through 501 Processing helix chain 'F' and resid 19 through 24 Processing helix chain 'F' and resid 31 through 33 No H-bonds generated for 'chain 'F' and resid 31 through 33' Processing helix chain 'F' and resid 45 through 49 Processing helix chain 'F' and resid 75 through 86 Processing helix chain 'F' and resid 96 through 109 Processing helix chain 'F' and resid 126 through 138 Processing helix chain 'F' and resid 159 through 164 Processing helix chain 'F' and resid 183 through 185 No H-bonds generated for 'chain 'F' and resid 183 through 185' Processing helix chain 'F' and resid 193 through 205 Processing helix chain 'F' and resid 224 through 229 removed outlier: 3.636A pdb=" N LYS F 229 " --> pdb=" O THR F 225 " (cutoff:3.500A) Processing helix chain 'F' and resid 255 through 266 removed outlier: 3.612A pdb=" N ARG F 259 " --> pdb=" O ASP F 255 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 294 Processing helix chain 'F' and resid 306 through 317 removed outlier: 3.737A pdb=" N ASN F 312 " --> pdb=" O ALA F 308 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU F 313 " --> pdb=" O GLN F 309 " (cutoff:3.500A) Processing helix chain 'F' and resid 332 through 338 Processing helix chain 'F' and resid 342 through 355 Processing helix chain 'F' and resid 356 through 358 No H-bonds generated for 'chain 'F' and resid 356 through 358' Processing helix chain 'F' and resid 369 through 379 Processing helix chain 'F' and resid 417 through 421 Processing helix chain 'F' and resid 452 through 472 Proline residue: F 458 - end of helix Processing helix chain 'F' and resid 475 through 486 Processing helix chain 'F' and resid 494 through 501 Processing helix chain 'G' and resid 19 through 24 Processing helix chain 'G' and resid 31 through 33 No H-bonds generated for 'chain 'G' and resid 31 through 33' Processing helix chain 'G' and resid 45 through 49 Processing helix chain 'G' and resid 75 through 86 Processing helix chain 'G' and resid 96 through 109 Processing helix chain 'G' and resid 126 through 138 Processing helix chain 'G' and resid 159 through 164 Processing helix chain 'G' and resid 183 through 185 No H-bonds generated for 'chain 'G' and resid 183 through 185' Processing helix chain 'G' and resid 193 through 205 Processing helix chain 'G' and resid 224 through 229 removed outlier: 3.634A pdb=" N LYS G 229 " --> pdb=" O THR G 225 " (cutoff:3.500A) Processing helix chain 'G' and resid 255 through 266 removed outlier: 3.594A pdb=" N ARG G 259 " --> pdb=" O ASP G 255 " (cutoff:3.500A) Processing helix chain 'G' and resid 280 through 294 Processing helix chain 'G' and resid 306 through 317 removed outlier: 3.736A pdb=" N ASN G 312 " --> pdb=" O ALA G 308 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU G 313 " --> pdb=" O GLN G 309 " (cutoff:3.500A) Processing helix chain 'G' and resid 332 through 338 Processing helix chain 'G' and resid 342 through 355 Processing helix chain 'G' and resid 356 through 358 No H-bonds generated for 'chain 'G' and resid 356 through 358' Processing helix chain 'G' and resid 369 through 379 Processing helix chain 'G' and resid 417 through 421 Processing helix chain 'G' and resid 452 through 472 Proline residue: G 458 - end of helix Processing helix chain 'G' and resid 475 through 486 Processing helix chain 'G' and resid 494 through 501 Processing helix chain 'H' and resid 19 through 24 Processing helix chain 'H' and resid 31 through 33 No H-bonds generated for 'chain 'H' and resid 31 through 33' Processing helix chain 'H' and resid 45 through 49 Processing helix chain 'H' and resid 75 through 86 Processing helix chain 'H' and resid 96 through 109 Processing helix chain 'H' and resid 126 through 138 Processing helix chain 'H' and resid 159 through 164 Processing helix chain 'H' and resid 183 through 185 No H-bonds generated for 'chain 'H' and resid 183 through 185' Processing helix chain 'H' and resid 193 through 205 Processing helix chain 'H' and resid 224 through 229 removed outlier: 3.634A pdb=" N LYS H 229 " --> pdb=" O THR H 225 " (cutoff:3.500A) Processing helix chain 'H' and resid 255 through 266 removed outlier: 3.595A pdb=" N ARG H 259 " --> pdb=" O ASP H 255 " (cutoff:3.500A) Processing helix chain 'H' and resid 280 through 294 Processing helix chain 'H' and resid 306 through 317 removed outlier: 3.736A pdb=" N ASN H 312 " --> pdb=" O ALA H 308 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU H 313 " --> pdb=" O GLN H 309 " (cutoff:3.500A) Processing helix chain 'H' and resid 332 through 338 Processing helix chain 'H' and resid 342 through 355 Processing helix chain 'H' and resid 356 through 358 No H-bonds generated for 'chain 'H' and resid 356 through 358' Processing helix chain 'H' and resid 369 through 379 Processing helix chain 'H' and resid 417 through 421 Processing helix chain 'H' and resid 452 through 472 Proline residue: H 458 - end of helix Processing helix chain 'H' and resid 475 through 486 Processing helix chain 'H' and resid 494 through 501 Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 37 Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'A' and resid 65 through 67 removed outlier: 3.630A pdb=" N ILE A 88 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE A 90 " --> pdb=" O SER A 67 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ALA A 248 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY A 302 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ASN A 303 " --> pdb=" O ARG A 322 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU A 321 " --> pdb=" O ILE A 362 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N ASP A 364 " --> pdb=" O LEU A 321 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N VAL A 323 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ILE A 361 " --> pdb=" O THR A 383 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N MET A 385 " --> pdb=" O ILE A 361 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ALA A 363 " --> pdb=" O MET A 385 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ILE A 66 " --> pdb=" O MET A 386 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 142 through 145 removed outlier: 3.652A pdb=" N ILE A 157 " --> pdb=" O THR A 180 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 188 through 189 removed outlier: 6.357A pdb=" N ALA A 188 " --> pdb=" O VAL A 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 401 through 402 removed outlier: 4.116A pdb=" N SER A 444 " --> pdb=" O THR D 510 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N SER D 508 " --> pdb=" O SER A 446 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 508 through 510 removed outlier: 3.940A pdb=" N SER A 508 " --> pdb=" O SER B 446 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N SER B 444 " --> pdb=" O THR A 510 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 35 through 37 Processing sheet with id=AA9, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AB1, first strand: chain 'B' and resid 65 through 67 removed outlier: 3.621A pdb=" N ILE B 88 " --> pdb=" O LEU B 65 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N PHE B 90 " --> pdb=" O SER B 67 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ALA B 248 " --> pdb=" O VAL B 272 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY B 302 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ASN B 303 " --> pdb=" O ARG B 322 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LEU B 321 " --> pdb=" O ILE B 362 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N ASP B 364 " --> pdb=" O LEU B 321 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N VAL B 323 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE B 361 " --> pdb=" O THR B 383 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N MET B 385 " --> pdb=" O ILE B 361 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ALA B 363 " --> pdb=" O MET B 385 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ILE B 66 " --> pdb=" O MET B 386 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 142 through 145 removed outlier: 3.652A pdb=" N ILE B 157 " --> pdb=" O THR B 180 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 188 through 189 removed outlier: 6.361A pdb=" N ALA B 188 " --> pdb=" O VAL B 212 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 508 through 510 removed outlier: 3.967A pdb=" N SER B 508 " --> pdb=" O SER C 446 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N SER C 444 " --> pdb=" O THR B 510 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 35 through 37 Processing sheet with id=AB6, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB7, first strand: chain 'C' and resid 65 through 67 removed outlier: 3.617A pdb=" N ILE C 88 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N PHE C 90 " --> pdb=" O SER C 67 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ALA C 248 " --> pdb=" O VAL C 272 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLY C 302 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ASN C 303 " --> pdb=" O ARG C 322 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N LEU C 321 " --> pdb=" O ILE C 362 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N ASP C 364 " --> pdb=" O LEU C 321 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N VAL C 323 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE C 361 " --> pdb=" O THR C 383 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N MET C 385 " --> pdb=" O ILE C 361 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ALA C 363 " --> pdb=" O MET C 385 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ILE C 66 " --> pdb=" O MET C 386 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 142 through 145 removed outlier: 3.653A pdb=" N ILE C 157 " --> pdb=" O THR C 180 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 188 through 189 removed outlier: 6.375A pdb=" N ALA C 188 " --> pdb=" O VAL C 212 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 508 through 510 removed outlier: 3.966A pdb=" N SER C 508 " --> pdb=" O SER D 446 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N SER D 444 " --> pdb=" O THR C 510 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 35 through 37 Processing sheet with id=AC3, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AC4, first strand: chain 'D' and resid 65 through 67 removed outlier: 3.631A pdb=" N ILE D 88 " --> pdb=" O LEU D 65 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE D 90 " --> pdb=" O SER D 67 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ALA D 248 " --> pdb=" O VAL D 272 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY D 302 " --> pdb=" O LEU D 273 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ASN D 303 " --> pdb=" O ARG D 322 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU D 321 " --> pdb=" O ILE D 362 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N ASP D 364 " --> pdb=" O LEU D 321 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N VAL D 323 " --> pdb=" O ASP D 364 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE D 361 " --> pdb=" O THR D 383 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N MET D 385 " --> pdb=" O ILE D 361 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ALA D 363 " --> pdb=" O MET D 385 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ILE D 66 " --> pdb=" O MET D 386 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 142 through 145 removed outlier: 3.652A pdb=" N ILE D 157 " --> pdb=" O THR D 180 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 188 through 189 removed outlier: 6.375A pdb=" N ALA D 188 " --> pdb=" O VAL D 212 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 35 through 37 Processing sheet with id=AC8, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AC9, first strand: chain 'E' and resid 65 through 67 removed outlier: 3.619A pdb=" N ILE E 88 " --> pdb=" O LEU E 65 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE E 90 " --> pdb=" O SER E 67 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ALA E 248 " --> pdb=" O VAL E 272 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY E 302 " --> pdb=" O LEU E 273 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASN E 303 " --> pdb=" O ARG E 322 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU E 321 " --> pdb=" O ILE E 362 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N ASP E 364 " --> pdb=" O LEU E 321 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N VAL E 323 " --> pdb=" O ASP E 364 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE E 361 " --> pdb=" O THR E 383 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N MET E 385 " --> pdb=" O ILE E 361 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ALA E 363 " --> pdb=" O MET E 385 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE E 66 " --> pdb=" O MET E 386 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 142 through 145 removed outlier: 3.651A pdb=" N ILE E 157 " --> pdb=" O THR E 180 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 188 through 189 removed outlier: 6.359A pdb=" N ALA E 188 " --> pdb=" O VAL E 212 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 401 through 402 removed outlier: 4.112A pdb=" N SER E 444 " --> pdb=" O THR H 510 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SER H 508 " --> pdb=" O SER E 446 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 508 through 510 removed outlier: 3.917A pdb=" N SER E 508 " --> pdb=" O SER F 446 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N SER F 444 " --> pdb=" O THR E 510 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 35 through 37 Processing sheet with id=AD6, first strand: chain 'F' and resid 53 through 54 Processing sheet with id=AD7, first strand: chain 'F' and resid 65 through 67 removed outlier: 3.620A pdb=" N ILE F 88 " --> pdb=" O LEU F 65 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE F 90 " --> pdb=" O SER F 67 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ALA F 248 " --> pdb=" O VAL F 272 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY F 302 " --> pdb=" O LEU F 273 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASN F 303 " --> pdb=" O ARG F 322 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU F 321 " --> pdb=" O ILE F 362 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N ASP F 364 " --> pdb=" O LEU F 321 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N VAL F 323 " --> pdb=" O ASP F 364 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE F 361 " --> pdb=" O THR F 383 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N MET F 385 " --> pdb=" O ILE F 361 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ALA F 363 " --> pdb=" O MET F 385 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE F 66 " --> pdb=" O MET F 386 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 142 through 145 removed outlier: 3.653A pdb=" N ILE F 157 " --> pdb=" O THR F 180 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 188 through 189 removed outlier: 6.370A pdb=" N ALA F 188 " --> pdb=" O VAL F 212 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 508 through 510 removed outlier: 3.902A pdb=" N SER F 508 " --> pdb=" O SER G 446 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N SER G 444 " --> pdb=" O THR F 510 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 35 through 37 Processing sheet with id=AE3, first strand: chain 'G' and resid 53 through 54 Processing sheet with id=AE4, first strand: chain 'G' and resid 65 through 67 removed outlier: 3.622A pdb=" N ILE G 88 " --> pdb=" O LEU G 65 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N PHE G 90 " --> pdb=" O SER G 67 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ALA G 248 " --> pdb=" O VAL G 272 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY G 302 " --> pdb=" O LEU G 273 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ASN G 303 " --> pdb=" O ARG G 322 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU G 321 " --> pdb=" O ILE G 362 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N ASP G 364 " --> pdb=" O LEU G 321 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N VAL G 323 " --> pdb=" O ASP G 364 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE G 361 " --> pdb=" O THR G 383 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N MET G 385 " --> pdb=" O ILE G 361 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ALA G 363 " --> pdb=" O MET G 385 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE G 66 " --> pdb=" O MET G 386 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 142 through 145 removed outlier: 3.653A pdb=" N ILE G 157 " --> pdb=" O THR G 180 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 188 through 189 removed outlier: 6.369A pdb=" N ALA G 188 " --> pdb=" O VAL G 212 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 508 through 510 removed outlier: 3.974A pdb=" N SER G 508 " --> pdb=" O SER H 446 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N SER H 444 " --> pdb=" O THR G 510 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 35 through 37 Processing sheet with id=AE9, first strand: chain 'H' and resid 53 through 54 Processing sheet with id=AF1, first strand: chain 'H' and resid 65 through 67 removed outlier: 3.631A pdb=" N ILE H 88 " --> pdb=" O LEU H 65 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE H 90 " --> pdb=" O SER H 67 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ALA H 248 " --> pdb=" O VAL H 272 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY H 302 " --> pdb=" O LEU H 273 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ASN H 303 " --> pdb=" O ARG H 322 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LEU H 321 " --> pdb=" O ILE H 362 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ASP H 364 " --> pdb=" O LEU H 321 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N VAL H 323 " --> pdb=" O ASP H 364 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ILE H 361 " --> pdb=" O THR H 383 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N MET H 385 " --> pdb=" O ILE H 361 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ALA H 363 " --> pdb=" O MET H 385 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ILE H 66 " --> pdb=" O MET H 386 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 142 through 145 removed outlier: 3.651A pdb=" N ILE H 157 " --> pdb=" O THR H 180 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 188 through 189 removed outlier: 6.374A pdb=" N ALA H 188 " --> pdb=" O VAL H 212 " (cutoff:3.500A) 1169 hydrogen bonds defined for protein. 3267 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: 11.68 Time building geometry restraints manager: 13.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 4969 1.30 - 1.43: 7402 1.43 - 1.56: 17765 1.56 - 1.69: 128 1.69 - 1.82: 328 Bond restraints: 30592 Sorted by residual: bond pdb=" C5 IMP A 603 " pdb=" C6 IMP A 603 " ideal model delta sigma weight residual 1.390 1.534 -0.144 2.00e-02 2.50e+03 5.18e+01 bond pdb=" C5 IMP H 603 " pdb=" C6 IMP H 603 " ideal model delta sigma weight residual 1.390 1.534 -0.144 2.00e-02 2.50e+03 5.18e+01 bond pdb=" C5 IMP D 603 " pdb=" C6 IMP D 603 " ideal model delta sigma weight residual 1.390 1.534 -0.144 2.00e-02 2.50e+03 5.16e+01 bond pdb=" C5 IMP E 603 " pdb=" C6 IMP E 603 " ideal model delta sigma weight residual 1.390 1.534 -0.144 2.00e-02 2.50e+03 5.16e+01 bond pdb=" C5 IMP G 603 " pdb=" C6 IMP G 603 " ideal model delta sigma weight residual 1.390 1.533 -0.143 2.00e-02 2.50e+03 5.15e+01 ... (remaining 30587 not shown) Histogram of bond angle deviations from ideal: 99.83 - 107.51: 1277 107.51 - 115.20: 18786 115.20 - 122.89: 18820 122.89 - 130.57: 2485 130.57 - 138.26: 168 Bond angle restraints: 41536 Sorted by residual: angle pdb=" PB ATP B 601 " pdb=" O3B ATP B 601 " pdb=" PG ATP B 601 " ideal model delta sigma weight residual 139.87 130.93 8.94 1.00e+00 1.00e+00 7.99e+01 angle pdb=" PB ATP C 601 " pdb=" O3B ATP C 601 " pdb=" PG ATP C 601 " ideal model delta sigma weight residual 139.87 131.00 8.87 1.00e+00 1.00e+00 7.86e+01 angle pdb=" PB ATP A 601 " pdb=" O3B ATP A 601 " pdb=" PG ATP A 601 " ideal model delta sigma weight residual 139.87 131.03 8.84 1.00e+00 1.00e+00 7.81e+01 angle pdb=" PB ATP D 601 " pdb=" O3B ATP D 601 " pdb=" PG ATP D 601 " ideal model delta sigma weight residual 139.87 131.06 8.81 1.00e+00 1.00e+00 7.77e+01 angle pdb=" PB ATP B 602 " pdb=" O3B ATP B 602 " pdb=" PG ATP B 602 " ideal model delta sigma weight residual 139.87 131.87 8.00 1.00e+00 1.00e+00 6.40e+01 ... (remaining 41531 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.18: 17766 31.18 - 62.37: 1042 62.37 - 93.55: 92 93.55 - 124.73: 0 124.73 - 155.92: 4 Dihedral angle restraints: 18904 sinusoidal: 8016 harmonic: 10888 Sorted by residual: dihedral pdb=" C5' IMP G 603 " pdb=" O5' IMP G 603 " pdb=" P IMP G 603 " pdb=" O2P IMP G 603 " ideal model delta sinusoidal sigma weight residual -168.07 -12.15 -155.92 1 2.00e+01 2.50e-03 4.59e+01 dihedral pdb=" C5' IMP H 603 " pdb=" O5' IMP H 603 " pdb=" P IMP H 603 " pdb=" O2P IMP H 603 " ideal model delta sinusoidal sigma weight residual -168.07 -12.17 -155.90 1 2.00e+01 2.50e-03 4.59e+01 dihedral pdb=" C5' IMP E 603 " pdb=" O5' IMP E 603 " pdb=" P IMP E 603 " pdb=" O2P IMP E 603 " ideal model delta sinusoidal sigma weight residual -168.07 -12.27 -155.80 1 2.00e+01 2.50e-03 4.59e+01 ... (remaining 18901 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 2650 0.030 - 0.060: 1280 0.060 - 0.090: 539 0.090 - 0.119: 291 0.119 - 0.149: 80 Chirality restraints: 4840 Sorted by residual: chirality pdb=" CA ILE C 439 " pdb=" N ILE C 439 " pdb=" C ILE C 439 " pdb=" CB ILE C 439 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.57e-01 chirality pdb=" CA ILE D 439 " pdb=" N ILE D 439 " pdb=" C ILE D 439 " pdb=" CB ILE D 439 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.31e-01 chirality pdb=" CA ILE F 439 " pdb=" N ILE F 439 " pdb=" C ILE F 439 " pdb=" CB ILE F 439 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.27e-01 ... (remaining 4837 not shown) Planarity restraints: 5160 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR G 63 " -0.032 5.00e-02 4.00e+02 4.86e-02 3.77e+00 pdb=" N PRO G 64 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO G 64 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO G 64 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 63 " 0.032 5.00e-02 4.00e+02 4.83e-02 3.74e+00 pdb=" N PRO C 64 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO C 64 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 64 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 63 " 0.032 5.00e-02 4.00e+02 4.83e-02 3.74e+00 pdb=" N PRO D 64 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO D 64 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 64 " 0.027 5.00e-02 4.00e+02 ... (remaining 5157 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 6185 2.79 - 3.31: 28229 3.31 - 3.84: 51888 3.84 - 4.37: 63870 4.37 - 4.90: 102765 Nonbonded interactions: 252937 Sorted by model distance: nonbonded pdb=" O ALA G 396 " pdb=" NZ LYS G 409 " model vdw 2.256 2.520 nonbonded pdb=" O ALA F 396 " pdb=" NZ LYS F 409 " model vdw 2.261 2.520 nonbonded pdb=" O ALA E 396 " pdb=" NZ LYS E 409 " model vdw 2.264 2.520 nonbonded pdb=" O ALA B 396 " pdb=" NZ LYS B 409 " model vdw 2.264 2.520 nonbonded pdb=" O ALA C 396 " pdb=" NZ LYS C 409 " model vdw 2.265 2.520 ... (remaining 252932 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.360 Check model and map are aligned: 0.240 Set scattering table: 0.290 Process input model: 82.130 Find NCS groups from input model: 2.050 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 100.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 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 : 0.006 0.144 30592 Z= 0.420 Angle : 0.783 8.941 41536 Z= 0.442 Chirality : 0.046 0.149 4840 Planarity : 0.005 0.049 5160 Dihedral : 18.028 155.916 11960 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.24 % Allowed : 12.15 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.12 (0.13), residues: 3808 helix: 0.80 (0.13), residues: 1464 sheet: 0.15 (0.25), residues: 448 loop : -0.44 (0.13), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 92 PHE 0.014 0.002 PHE C 357 TYR 0.012 0.002 TYR H 353 ARG 0.004 0.001 ARG B 57 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 894 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 855 time to evaluate : 3.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 11 residues processed: 875 average time/residue: 1.5179 time to fit residues: 1539.3987 Evaluate side-chains 664 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 653 time to evaluate : 3.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain D residue 361 ILE Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 361 ILE Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 361 ILE Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 361 ILE Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 361 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 324 optimal weight: 0.8980 chunk 291 optimal weight: 5.9990 chunk 161 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 chunk 196 optimal weight: 2.9990 chunk 155 optimal weight: 8.9990 chunk 300 optimal weight: 2.9990 chunk 116 optimal weight: 0.9980 chunk 183 optimal weight: 7.9990 chunk 224 optimal weight: 9.9990 chunk 348 optimal weight: 3.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 441 GLN ** B 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 GLN B 441 GLN ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 202 GLN C 441 GLN ** D 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 441 GLN ** E 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 230 ASN E 368 GLN E 441 GLN ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 202 GLN F 441 GLN ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 202 GLN G 368 GLN G 441 GLN ** H 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 441 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 30592 Z= 0.332 Angle : 0.610 6.433 41536 Z= 0.323 Chirality : 0.045 0.145 4840 Planarity : 0.004 0.042 5160 Dihedral : 12.836 171.553 5178 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.90 % Allowed : 16.33 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.54 (0.13), residues: 3808 helix: 1.32 (0.14), residues: 1464 sheet: 0.41 (0.25), residues: 448 loop : -0.38 (0.13), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS G 92 PHE 0.013 0.002 PHE D 114 TYR 0.013 0.002 TYR A 233 ARG 0.008 0.001 ARG E 356 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 764 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 673 time to evaluate : 3.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 487 GLU cc_start: 0.5987 (mm-30) cc_final: 0.3884 (mm-30) outliers start: 91 outliers final: 34 residues processed: 720 average time/residue: 1.5552 time to fit residues: 1290.4624 Evaluate side-chains 675 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 641 time to evaluate : 3.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 339 CYS Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 418 ASP Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 202 GLN Chi-restraints excluded: chain C residue 339 CYS Chi-restraints excluded: chain C residue 418 ASP Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 339 CYS Chi-restraints excluded: chain D residue 361 ILE Chi-restraints excluded: chain D residue 418 ASP Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 339 CYS Chi-restraints excluded: chain E residue 418 ASP Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 339 CYS Chi-restraints excluded: chain F residue 418 ASP Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 166 LEU Chi-restraints excluded: chain G residue 202 GLN Chi-restraints excluded: chain G residue 339 CYS Chi-restraints excluded: chain G residue 418 ASP Chi-restraints excluded: chain H residue 140 SER Chi-restraints excluded: chain H residue 339 CYS Chi-restraints excluded: chain H residue 418 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 193 optimal weight: 4.9990 chunk 108 optimal weight: 5.9990 chunk 290 optimal weight: 0.8980 chunk 237 optimal weight: 0.9980 chunk 96 optimal weight: 6.9990 chunk 349 optimal weight: 4.9990 chunk 377 optimal weight: 3.9990 chunk 311 optimal weight: 0.9990 chunk 346 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 280 optimal weight: 0.5980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 303 ASN A 368 GLN A 441 GLN ** B 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 GLN B 441 GLN ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 202 GLN C 368 GLN C 441 GLN ** D 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 368 GLN D 441 GLN ** E 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 202 GLN E 368 GLN E 441 GLN ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 441 GLN ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 202 GLN G 441 GLN ** H 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 441 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 30592 Z= 0.217 Angle : 0.525 5.582 41536 Z= 0.282 Chirality : 0.042 0.149 4840 Planarity : 0.004 0.039 5160 Dihedral : 12.260 173.773 5162 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.30 % Allowed : 17.83 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.87 (0.14), residues: 3808 helix: 1.67 (0.14), residues: 1472 sheet: 0.53 (0.25), residues: 432 loop : -0.23 (0.14), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS E 137 PHE 0.008 0.001 PHE D 114 TYR 0.011 0.001 TYR E 353 ARG 0.009 0.001 ARG A 203 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 726 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 654 time to evaluate : 3.711 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 203 ARG cc_start: 0.6136 (mtm-85) cc_final: 0.5799 (mtm110) REVERT: E 487 GLU cc_start: 0.5920 (mm-30) cc_final: 0.3939 (mm-30) REVERT: F 203 ARG cc_start: 0.6244 (mtm-85) cc_final: 0.5961 (mtm110) REVERT: F 487 GLU cc_start: 0.5851 (mm-30) cc_final: 0.3758 (mm-30) REVERT: G 487 GLU cc_start: 0.5916 (mm-30) cc_final: 0.3876 (mm-30) REVERT: H 487 GLU cc_start: 0.5845 (mm-30) cc_final: 0.5557 (mm-30) outliers start: 72 outliers final: 28 residues processed: 692 average time/residue: 1.5621 time to fit residues: 1248.3571 Evaluate side-chains 661 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 633 time to evaluate : 3.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 418 ASP Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 418 ASP Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 418 ASP Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 406 VAL Chi-restraints excluded: chain E residue 418 ASP Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 406 VAL Chi-restraints excluded: chain F residue 418 ASP Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 406 VAL Chi-restraints excluded: chain G residue 410 LYS Chi-restraints excluded: chain G residue 418 ASP Chi-restraints excluded: chain H residue 140 SER Chi-restraints excluded: chain H residue 406 VAL Chi-restraints excluded: chain H residue 418 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 345 optimal weight: 0.9990 chunk 262 optimal weight: 2.9990 chunk 181 optimal weight: 7.9990 chunk 38 optimal weight: 0.3980 chunk 166 optimal weight: 6.9990 chunk 234 optimal weight: 1.9990 chunk 350 optimal weight: 3.9990 chunk 371 optimal weight: 8.9990 chunk 183 optimal weight: 7.9990 chunk 332 optimal weight: 4.9990 chunk 100 optimal weight: 0.6980 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 303 ASN A 368 GLN A 441 GLN ** B 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 441 GLN ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 ASN D 441 GLN ** E 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 441 GLN ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 137 HIS ** F 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 441 GLN ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 137 HIS G 441 GLN ** H 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 441 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 30592 Z= 0.235 Angle : 0.544 6.824 41536 Z= 0.288 Chirality : 0.042 0.150 4840 Planarity : 0.004 0.041 5160 Dihedral : 11.615 137.030 5160 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.16 % Allowed : 18.08 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.98 (0.14), residues: 3808 helix: 1.79 (0.14), residues: 1472 sheet: 0.77 (0.29), residues: 352 loop : -0.20 (0.13), residues: 1984 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.016 0.001 HIS E 137 PHE 0.009 0.001 PHE D 114 TYR 0.011 0.001 TYR F 353 ARG 0.010 0.001 ARG G 203 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 743 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 644 time to evaluate : 3.274 Fit side-chains revert: symmetry clash REVERT: D 132 GLU cc_start: 0.4110 (tm-30) cc_final: 0.3698 (tm-30) REVERT: E 487 GLU cc_start: 0.5876 (mm-30) cc_final: 0.4003 (mm-30) REVERT: F 487 GLU cc_start: 0.5931 (mm-30) cc_final: 0.3786 (mm-30) REVERT: G 487 GLU cc_start: 0.5944 (mm-30) cc_final: 0.4057 (mm-30) REVERT: H 487 GLU cc_start: 0.5866 (mm-30) cc_final: 0.5299 (mm-30) outliers start: 99 outliers final: 53 residues processed: 696 average time/residue: 1.5176 time to fit residues: 1222.3384 Evaluate side-chains 680 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 627 time to evaluate : 3.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 339 CYS Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 418 ASP Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 335 GLU Chi-restraints excluded: chain C residue 339 CYS Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 418 ASP Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 418 ASP Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 335 GLU Chi-restraints excluded: chain E residue 339 CYS Chi-restraints excluded: chain E residue 361 ILE Chi-restraints excluded: chain E residue 406 VAL Chi-restraints excluded: chain E residue 418 ASP Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 335 GLU Chi-restraints excluded: chain F residue 339 CYS Chi-restraints excluded: chain F residue 406 VAL Chi-restraints excluded: chain F residue 418 ASP Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 159 THR Chi-restraints excluded: chain G residue 339 CYS Chi-restraints excluded: chain G residue 406 VAL Chi-restraints excluded: chain G residue 410 LYS Chi-restraints excluded: chain G residue 418 ASP Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 140 SER Chi-restraints excluded: chain H residue 339 CYS Chi-restraints excluded: chain H residue 406 VAL Chi-restraints excluded: chain H residue 418 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 309 optimal weight: 6.9990 chunk 210 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 276 optimal weight: 2.9990 chunk 153 optimal weight: 0.8980 chunk 316 optimal weight: 5.9990 chunk 256 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 189 optimal weight: 0.9990 chunk 333 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 303 ASN A 368 GLN A 441 GLN ** B 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 441 GLN ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 ASN D 441 GLN ** E 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 292 GLN E 441 GLN ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 441 GLN ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 441 GLN ** H 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 198 ASN ** H 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 441 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.3356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 30592 Z= 0.274 Angle : 0.564 6.026 41536 Z= 0.299 Chirality : 0.043 0.147 4840 Planarity : 0.004 0.041 5160 Dihedral : 11.338 90.851 5160 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.51 % Allowed : 19.16 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.93 (0.14), residues: 3808 helix: 1.72 (0.14), residues: 1472 sheet: 0.83 (0.29), residues: 352 loop : -0.23 (0.13), residues: 1984 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 137 PHE 0.010 0.002 PHE F 114 TYR 0.011 0.001 TYR E 353 ARG 0.011 0.001 ARG F 203 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 737 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 627 time to evaluate : 3.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 GLU cc_start: 0.4133 (tm-30) cc_final: 0.3485 (tm-30) REVERT: E 487 GLU cc_start: 0.5964 (mm-30) cc_final: 0.3918 (mm-30) REVERT: F 132 GLU cc_start: 0.4327 (tp30) cc_final: 0.3658 (tp30) REVERT: F 487 GLU cc_start: 0.6001 (mm-30) cc_final: 0.3821 (mm-30) REVERT: G 487 GLU cc_start: 0.6003 (mm-30) cc_final: 0.4093 (mm-30) REVERT: H 487 GLU cc_start: 0.5918 (mm-30) cc_final: 0.3939 (mm-30) outliers start: 110 outliers final: 54 residues processed: 688 average time/residue: 1.5062 time to fit residues: 1199.9291 Evaluate side-chains 664 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 610 time to evaluate : 3.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 339 CYS Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 418 ASP Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 335 GLU Chi-restraints excluded: chain C residue 339 CYS Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 418 ASP Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 339 CYS Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 418 ASP Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 339 CYS Chi-restraints excluded: chain E residue 361 ILE Chi-restraints excluded: chain E residue 406 VAL Chi-restraints excluded: chain E residue 418 ASP Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 339 CYS Chi-restraints excluded: chain F residue 406 VAL Chi-restraints excluded: chain F residue 418 ASP Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 159 THR Chi-restraints excluded: chain G residue 339 CYS Chi-restraints excluded: chain G residue 406 VAL Chi-restraints excluded: chain G residue 418 ASP Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 140 SER Chi-restraints excluded: chain H residue 339 CYS Chi-restraints excluded: chain H residue 361 ILE Chi-restraints excluded: chain H residue 406 VAL Chi-restraints excluded: chain H residue 418 ASP Chi-restraints excluded: chain H residue 455 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 124 optimal weight: 4.9990 chunk 334 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 217 optimal weight: 0.9980 chunk 91 optimal weight: 0.7980 chunk 371 optimal weight: 7.9990 chunk 308 optimal weight: 4.9990 chunk 172 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 122 optimal weight: 5.9990 chunk 195 optimal weight: 4.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 303 ASN A 441 GLN ** B 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 441 GLN ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 441 GLN ** D 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 ASN D 441 GLN ** E 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 441 GLN ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 198 ASN ** F 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 441 GLN ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 441 GLN ** H 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 441 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 30592 Z= 0.271 Angle : 0.577 7.396 41536 Z= 0.304 Chirality : 0.043 0.143 4840 Planarity : 0.004 0.044 5160 Dihedral : 11.240 85.323 5160 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.03 % Allowed : 20.54 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.93 (0.14), residues: 3808 helix: 1.72 (0.14), residues: 1472 sheet: 0.87 (0.29), residues: 352 loop : -0.24 (0.13), residues: 1984 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS E 137 PHE 0.010 0.002 PHE E 114 TYR 0.011 0.001 TYR H 353 ARG 0.012 0.001 ARG H 136 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 710 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 615 time to evaluate : 3.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 GLU cc_start: 0.4069 (tm-30) cc_final: 0.3825 (tm-30) REVERT: A 179 MET cc_start: 0.6733 (OUTLIER) cc_final: 0.6411 (ppp) REVERT: B 179 MET cc_start: 0.6711 (OUTLIER) cc_final: 0.6421 (ppp) REVERT: E 487 GLU cc_start: 0.5990 (mm-30) cc_final: 0.3854 (mm-30) REVERT: F 487 GLU cc_start: 0.6022 (mm-30) cc_final: 0.3919 (mm-30) REVERT: G 487 GLU cc_start: 0.6010 (mm-30) cc_final: 0.4078 (mm-30) REVERT: H 487 GLU cc_start: 0.5946 (mm-30) cc_final: 0.3875 (mm-30) outliers start: 95 outliers final: 54 residues processed: 666 average time/residue: 1.5353 time to fit residues: 1186.4079 Evaluate side-chains 670 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 614 time to evaluate : 3.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 339 CYS Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 418 ASP Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 335 GLU Chi-restraints excluded: chain C residue 339 CYS Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 418 ASP Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 339 CYS Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 418 ASP Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 339 CYS Chi-restraints excluded: chain E residue 361 ILE Chi-restraints excluded: chain E residue 418 ASP Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 339 CYS Chi-restraints excluded: chain F residue 406 VAL Chi-restraints excluded: chain F residue 418 ASP Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 159 THR Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 339 CYS Chi-restraints excluded: chain G residue 418 ASP Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 140 SER Chi-restraints excluded: chain H residue 339 CYS Chi-restraints excluded: chain H residue 361 ILE Chi-restraints excluded: chain H residue 418 ASP Chi-restraints excluded: chain H residue 455 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 358 optimal weight: 0.0070 chunk 41 optimal weight: 9.9990 chunk 211 optimal weight: 0.9990 chunk 271 optimal weight: 8.9990 chunk 210 optimal weight: 4.9990 chunk 312 optimal weight: 2.9990 chunk 207 optimal weight: 0.7980 chunk 370 optimal weight: 0.9990 chunk 231 optimal weight: 1.9990 chunk 225 optimal weight: 3.9990 chunk 170 optimal weight: 0.0770 overall best weight: 0.5760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 441 GLN ** B 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 441 GLN ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 ASN D 441 GLN ** E 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 441 GLN ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 441 GLN ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 441 GLN ** H 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 441 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.3639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 30592 Z= 0.167 Angle : 0.561 8.929 41536 Z= 0.293 Chirality : 0.041 0.149 4840 Planarity : 0.004 0.051 5160 Dihedral : 10.837 86.075 5160 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.36 % Allowed : 21.27 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.23 (0.14), residues: 3808 helix: 1.99 (0.14), residues: 1472 sheet: 1.37 (0.33), residues: 272 loop : -0.09 (0.13), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.000 HIS E 137 PHE 0.008 0.001 PHE E 139 TYR 0.010 0.001 TYR B 353 ARG 0.012 0.001 ARG F 203 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 726 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 652 time to evaluate : 3.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 MET cc_start: 0.6670 (OUTLIER) cc_final: 0.6335 (ppp) REVERT: B 179 MET cc_start: 0.6647 (OUTLIER) cc_final: 0.6308 (ppp) REVERT: E 487 GLU cc_start: 0.5901 (mm-30) cc_final: 0.3977 (mm-30) REVERT: F 487 GLU cc_start: 0.5935 (mm-30) cc_final: 0.3823 (mm-30) REVERT: G 487 GLU cc_start: 0.6089 (mm-30) cc_final: 0.4412 (mm-30) REVERT: H 487 GLU cc_start: 0.5800 (mm-30) cc_final: 0.4271 (mm-30) outliers start: 74 outliers final: 41 residues processed: 690 average time/residue: 1.5042 time to fit residues: 1201.2634 Evaluate side-chains 669 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 626 time to evaluate : 3.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 418 ASP Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 335 GLU Chi-restraints excluded: chain C residue 418 ASP Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 339 CYS Chi-restraints excluded: chain D residue 418 ASP Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 418 ASP Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 335 GLU Chi-restraints excluded: chain F residue 339 CYS Chi-restraints excluded: chain F residue 406 VAL Chi-restraints excluded: chain F residue 418 ASP Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 159 THR Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 406 VAL Chi-restraints excluded: chain G residue 418 ASP Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 140 SER Chi-restraints excluded: chain H residue 406 VAL Chi-restraints excluded: chain H residue 418 ASP Chi-restraints excluded: chain H residue 437 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 228 optimal weight: 2.9990 chunk 147 optimal weight: 0.8980 chunk 221 optimal weight: 3.9990 chunk 111 optimal weight: 6.9990 chunk 72 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 235 optimal weight: 0.9980 chunk 252 optimal weight: 0.7980 chunk 182 optimal weight: 1.9990 chunk 34 optimal weight: 0.3980 chunk 290 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 303 ASN A 441 GLN ** B 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 441 GLN ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 441 GLN ** E 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 441 GLN ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 441 GLN ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 441 GLN ** H 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 441 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.3725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 30592 Z= 0.203 Angle : 0.576 9.409 41536 Z= 0.301 Chirality : 0.042 0.148 4840 Planarity : 0.004 0.062 5160 Dihedral : 10.754 87.052 5160 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.30 % Allowed : 22.32 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.22 (0.14), residues: 3808 helix: 2.06 (0.14), residues: 1432 sheet: 0.94 (0.29), residues: 352 loop : -0.09 (0.13), residues: 2024 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.001 HIS E 137 PHE 0.007 0.001 PHE C 114 TYR 0.010 0.001 TYR B 353 ARG 0.015 0.001 ARG E 136 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 705 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 633 time to evaluate : 3.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 337 MET cc_start: 0.6995 (OUTLIER) cc_final: 0.5946 (mmt) REVERT: E 487 GLU cc_start: 0.5974 (mm-30) cc_final: 0.4465 (mm-30) REVERT: F 487 GLU cc_start: 0.5968 (mm-30) cc_final: 0.3756 (mm-30) REVERT: G 487 GLU cc_start: 0.6080 (mm-30) cc_final: 0.4500 (mm-30) REVERT: H 487 GLU cc_start: 0.5828 (mm-30) cc_final: 0.4265 (mm-30) outliers start: 72 outliers final: 49 residues processed: 671 average time/residue: 1.5231 time to fit residues: 1184.4788 Evaluate side-chains 669 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 619 time to evaluate : 3.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 418 ASP Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 335 GLU Chi-restraints excluded: chain C residue 339 CYS Chi-restraints excluded: chain C residue 418 ASP Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 339 CYS Chi-restraints excluded: chain D residue 418 ASP Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 337 MET Chi-restraints excluded: chain E residue 339 CYS Chi-restraints excluded: chain E residue 418 ASP Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 335 GLU Chi-restraints excluded: chain F residue 339 CYS Chi-restraints excluded: chain F residue 404 ASP Chi-restraints excluded: chain F residue 406 VAL Chi-restraints excluded: chain F residue 418 ASP Chi-restraints excluded: chain F residue 437 VAL Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 159 THR Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 406 VAL Chi-restraints excluded: chain G residue 418 ASP Chi-restraints excluded: chain G residue 510 THR Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 140 SER Chi-restraints excluded: chain H residue 406 VAL Chi-restraints excluded: chain H residue 418 ASP Chi-restraints excluded: chain H residue 437 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 336 optimal weight: 1.9990 chunk 354 optimal weight: 5.9990 chunk 323 optimal weight: 7.9990 chunk 344 optimal weight: 3.9990 chunk 207 optimal weight: 3.9990 chunk 150 optimal weight: 0.7980 chunk 270 optimal weight: 4.9990 chunk 105 optimal weight: 0.5980 chunk 311 optimal weight: 5.9990 chunk 326 optimal weight: 1.9990 chunk 343 optimal weight: 3.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 303 ASN A 441 GLN ** B 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 441 GLN ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 GLN ** D 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 441 GLN ** E 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 441 GLN ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 441 GLN ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 441 GLN ** H 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 441 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.3721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 30592 Z= 0.297 Angle : 0.635 9.823 41536 Z= 0.330 Chirality : 0.043 0.164 4840 Planarity : 0.005 0.061 5160 Dihedral : 11.041 87.193 5160 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.20 % Allowed : 22.45 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.01 (0.14), residues: 3808 helix: 1.86 (0.14), residues: 1432 sheet: 0.90 (0.28), residues: 352 loop : -0.21 (0.13), residues: 2024 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.014 0.001 HIS E 137 PHE 0.023 0.002 PHE G 401 TYR 0.012 0.001 TYR B 353 ARG 0.014 0.001 ARG A 203 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 688 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 619 time to evaluate : 3.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 487 GLU cc_start: 0.6037 (mm-30) cc_final: 0.4146 (mm-30) REVERT: F 132 GLU cc_start: 0.4138 (tp30) cc_final: 0.3506 (tp30) REVERT: F 487 GLU cc_start: 0.6033 (mm-30) cc_final: 0.3679 (mm-30) REVERT: G 487 GLU cc_start: 0.6085 (mm-30) cc_final: 0.4370 (mm-30) REVERT: H 487 GLU cc_start: 0.5964 (mm-30) cc_final: 0.4239 (mm-30) outliers start: 69 outliers final: 54 residues processed: 653 average time/residue: 1.5137 time to fit residues: 1144.2609 Evaluate side-chains 665 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 611 time to evaluate : 3.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 339 CYS Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 418 ASP Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 335 GLU Chi-restraints excluded: chain C residue 339 CYS Chi-restraints excluded: chain C residue 418 ASP Chi-restraints excluded: chain C residue 510 THR Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 339 CYS Chi-restraints excluded: chain D residue 418 ASP Chi-restraints excluded: chain E residue 132 GLU Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 339 CYS Chi-restraints excluded: chain E residue 406 VAL Chi-restraints excluded: chain E residue 418 ASP Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 339 CYS Chi-restraints excluded: chain F residue 404 ASP Chi-restraints excluded: chain F residue 406 VAL Chi-restraints excluded: chain F residue 418 ASP Chi-restraints excluded: chain F residue 437 VAL Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 159 THR Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 339 CYS Chi-restraints excluded: chain G residue 406 VAL Chi-restraints excluded: chain G residue 418 ASP Chi-restraints excluded: chain G residue 437 VAL Chi-restraints excluded: chain G residue 510 THR Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 140 SER Chi-restraints excluded: chain H residue 406 VAL Chi-restraints excluded: chain H residue 418 ASP Chi-restraints excluded: chain H residue 437 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 226 optimal weight: 0.7980 chunk 364 optimal weight: 4.9990 chunk 222 optimal weight: 0.8980 chunk 173 optimal weight: 1.9990 chunk 253 optimal weight: 3.9990 chunk 382 optimal weight: 2.9990 chunk 352 optimal weight: 0.0980 chunk 304 optimal weight: 0.0470 chunk 31 optimal weight: 7.9990 chunk 235 optimal weight: 1.9990 chunk 186 optimal weight: 3.9990 overall best weight: 0.7680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 303 ASN A 441 GLN ** B 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 441 GLN ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 441 GLN ** E 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 292 GLN E 441 GLN ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 441 GLN F 448 GLN ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 441 GLN ** H 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 441 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.3823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 30592 Z= 0.194 Angle : 0.614 10.643 41536 Z= 0.318 Chirality : 0.041 0.149 4840 Planarity : 0.005 0.064 5160 Dihedral : 10.807 88.151 5160 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.82 % Allowed : 23.31 % Favored : 74.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.13 (0.14), residues: 3808 helix: 1.98 (0.14), residues: 1432 sheet: 1.27 (0.31), residues: 272 loop : -0.16 (0.13), residues: 2104 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.001 HIS E 137 PHE 0.022 0.001 PHE G 401 TYR 0.010 0.001 TYR E 353 ARG 0.015 0.001 ARG A 203 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 685 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 628 time to evaluate : 3.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 MET cc_start: 0.6760 (OUTLIER) cc_final: 0.6369 (ppp) REVERT: B 150 MET cc_start: 0.6424 (mmt) cc_final: 0.6195 (mtt) REVERT: B 179 MET cc_start: 0.6573 (OUTLIER) cc_final: 0.6204 (ppp) REVERT: C 337 MET cc_start: 0.7076 (mmt) cc_final: 0.6086 (mmt) REVERT: E 487 GLU cc_start: 0.5923 (mm-30) cc_final: 0.4398 (mm-30) REVERT: F 487 GLU cc_start: 0.5991 (mm-30) cc_final: 0.3938 (mm-30) REVERT: G 487 GLU cc_start: 0.6021 (mm-30) cc_final: 0.4545 (mm-30) REVERT: H 487 GLU cc_start: 0.5861 (mm-30) cc_final: 0.4170 (mm-30) outliers start: 57 outliers final: 42 residues processed: 657 average time/residue: 1.5191 time to fit residues: 1157.5920 Evaluate side-chains 669 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 625 time to evaluate : 3.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 418 ASP Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 418 ASP Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 339 CYS Chi-restraints excluded: chain D residue 418 ASP Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 406 VAL Chi-restraints excluded: chain E residue 418 ASP Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 339 CYS Chi-restraints excluded: chain F residue 404 ASP Chi-restraints excluded: chain F residue 406 VAL Chi-restraints excluded: chain F residue 418 ASP Chi-restraints excluded: chain F residue 437 VAL Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 159 THR Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 406 VAL Chi-restraints excluded: chain G residue 418 ASP Chi-restraints excluded: chain G residue 437 VAL Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 140 SER Chi-restraints excluded: chain H residue 406 VAL Chi-restraints excluded: chain H residue 418 ASP Chi-restraints excluded: chain H residue 437 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 241 optimal weight: 0.0470 chunk 324 optimal weight: 0.0470 chunk 93 optimal weight: 0.0470 chunk 280 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 305 optimal weight: 5.9990 chunk 127 optimal weight: 7.9990 chunk 313 optimal weight: 0.8980 chunk 38 optimal weight: 6.9990 chunk 56 optimal weight: 3.9990 overall best weight: 0.4074 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 441 GLN ** B 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 441 GLN ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 GLN ** D 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 441 GLN ** E 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 441 GLN ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 441 GLN F 448 GLN ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 441 GLN ** H 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 441 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.090957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.080131 restraints weight = 54735.928| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 1.94 r_work: 0.3123 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.3948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 30592 Z= 0.176 Angle : 0.606 12.148 41536 Z= 0.313 Chirality : 0.041 0.339 4840 Planarity : 0.005 0.063 5160 Dihedral : 10.400 89.453 5160 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.43 % Allowed : 23.85 % Favored : 74.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.32 (0.14), residues: 3808 helix: 2.19 (0.15), residues: 1432 sheet: 1.27 (0.30), residues: 272 loop : -0.07 (0.13), residues: 2104 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.000 HIS E 137 PHE 0.023 0.001 PHE G 401 TYR 0.011 0.001 TYR A 353 ARG 0.016 0.001 ARG B 203 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16617.75 seconds wall clock time: 288 minutes 41.11 seconds (17321.11 seconds total)