Starting phenix.real_space_refine on Mon Sep 14 12:06:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7res_24438/09_2026/7res_24438.cif Found real_map, /net/cci-nas-00/data/ceres_data/7res_24438/09_2026/7res_24438.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7res_24438/09_2026/7res_24438.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7res_24438/09_2026/7res_24438.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7res_24438/09_2026/7res_24438.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7res_24438/09_2026/7res_24438.map" model { file = "/net/cci-nas-00/data/ceres_data/7res_24438/09_2026/7res_24438.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7res_24438/09_2026/7res_24438.cif" } resolution = 3.05 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.256 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 184 5.16 5 C 18768 2.51 5 N 5152 2.21 5 O 5912 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 275 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 30088 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3632 Classifications: {'peptide': 482} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 463} Chain breaks: 3 Chain: "B" Number of atoms: 3632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3632 Classifications: {'peptide': 482} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 463} Chain breaks: 3 Chain: "C" Number of atoms: 3632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3632 Classifications: {'peptide': 482} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 463} Chain breaks: 3 Chain: "D" Number of atoms: 3632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3632 Classifications: {'peptide': 482} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 463} Chain breaks: 3 Chain: "E" Number of atoms: 3632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3632 Classifications: {'peptide': 482} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 463} Chain breaks: 3 Chain: "F" Number of atoms: 3632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3632 Classifications: {'peptide': 482} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 463} Chain breaks: 3 Chain: "G" Number of atoms: 3632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3632 Classifications: {'peptide': 482} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 463} Chain breaks: 3 Chain: "H" Number of atoms: 3632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3632 Classifications: {'peptide': 482} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 463} Chain breaks: 3 Chain: "A" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNAv2': 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: {'RNAv2': 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: {'RNAv2': 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: {'RNAv2': 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: {'RNAv2': 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: {'RNAv2': 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: {'RNAv2': 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: {'RNAv2': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Time building chain proxies: 6.75, per 1000 atoms: 0.22 Number of scatterers: 30088 At special positions: 0 Unit cell: (135.45, 136.5, 142.8, 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 184 16.00 P 72 15.00 O 5912 8.00 N 5152 7.00 C 18768 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.09 Conformation dependent library (CDL) restraints added in 1.7 seconds 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6912 Finding SS restraints... Secondary structure from input PDB file: 160 helices and 32 sheets defined 40.1% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 19 through 24 removed outlier: 3.512A pdb=" N PHE A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) 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 removed outlier: 3.630A pdb=" N VAL A 49 " --> pdb=" O ALA A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 86 Processing helix chain 'A' and resid 96 through 109 Processing helix chain 'A' and resid 127 through 137 removed outlier: 3.953A pdb=" N LEU A 131 " --> pdb=" O VAL A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 163 Processing helix chain 'A' and resid 193 through 205 Processing helix chain 'A' and resid 224 through 230 removed outlier: 3.525A pdb=" N LYS A 229 " --> pdb=" O THR A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 266 removed outlier: 3.617A 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 Processing helix chain 'A' and resid 333 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 removed outlier: 3.608A pdb=" N VAL A 373 " --> pdb=" O THR A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 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 485 Processing helix chain 'A' and resid 494 through 502 Processing helix chain 'B' and resid 19 through 24 removed outlier: 3.518A pdb=" N PHE B 24 " --> pdb=" O ALA B 20 " (cutoff:3.500A) 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 removed outlier: 3.562A pdb=" N VAL B 49 " --> pdb=" O ALA B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 85 Processing helix chain 'B' and resid 96 through 109 Processing helix chain 'B' and resid 127 through 137 removed outlier: 3.886A pdb=" N LEU B 131 " --> pdb=" O VAL B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 163 Processing helix chain 'B' and resid 193 through 205 Processing helix chain 'B' and resid 224 through 228 Processing helix chain 'B' and resid 255 through 266 removed outlier: 3.645A 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 Processing helix chain 'B' and resid 333 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 removed outlier: 3.616A pdb=" N VAL B 373 " --> pdb=" O THR B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 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 485 Processing helix chain 'B' and resid 494 through 502 Processing helix chain 'C' and resid 19 through 24 removed outlier: 3.503A pdb=" N PHE C 24 " --> pdb=" O ALA C 20 " (cutoff:3.500A) 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 removed outlier: 3.636A pdb=" N VAL C 49 " --> pdb=" O ALA C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 85 Processing helix chain 'C' and resid 96 through 109 Processing helix chain 'C' and resid 127 through 137 removed outlier: 3.918A pdb=" N LEU C 131 " --> pdb=" O VAL C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 163 Processing helix chain 'C' and resid 193 through 205 Processing helix chain 'C' and resid 224 through 228 Processing helix chain 'C' and resid 255 through 266 removed outlier: 3.638A 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 Processing helix chain 'C' and resid 333 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 removed outlier: 3.608A pdb=" N VAL C 373 " --> pdb=" O THR C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 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 485 Processing helix chain 'C' and resid 494 through 502 Processing helix chain 'D' and resid 19 through 24 removed outlier: 3.515A pdb=" N PHE D 24 " --> pdb=" O ALA D 20 " (cutoff:3.500A) 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 removed outlier: 3.623A pdb=" N VAL D 49 " --> pdb=" O ALA D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 85 Processing helix chain 'D' and resid 96 through 109 Processing helix chain 'D' and resid 127 through 137 removed outlier: 3.911A pdb=" N LEU D 131 " --> pdb=" O VAL D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 163 Processing helix chain 'D' and resid 193 through 205 Processing helix chain 'D' and resid 224 through 228 Processing helix chain 'D' and resid 255 through 266 removed outlier: 3.656A 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 Processing helix chain 'D' and resid 333 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 removed outlier: 3.610A pdb=" N VAL D 373 " --> pdb=" O THR D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 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 485 Processing helix chain 'D' and resid 494 through 502 Processing helix chain 'E' and resid 19 through 24 removed outlier: 3.502A pdb=" N PHE E 24 " --> pdb=" O ALA E 20 " (cutoff:3.500A) 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 removed outlier: 3.594A pdb=" N VAL E 49 " --> pdb=" O ALA E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 75 through 85 Processing helix chain 'E' and resid 96 through 109 Processing helix chain 'E' and resid 127 through 137 removed outlier: 3.901A pdb=" N LEU E 131 " --> pdb=" O VAL E 127 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 163 Processing helix chain 'E' and resid 193 through 205 Processing helix chain 'E' and resid 224 through 228 Processing helix chain 'E' and resid 255 through 266 removed outlier: 3.661A 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 Processing helix chain 'E' and resid 333 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 removed outlier: 3.612A pdb=" N VAL E 373 " --> pdb=" O THR E 369 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 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 485 Processing helix chain 'E' and resid 494 through 502 Processing helix chain 'F' and resid 19 through 24 removed outlier: 3.507A pdb=" N PHE F 24 " --> pdb=" O ALA F 20 " (cutoff:3.500A) 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 removed outlier: 3.620A pdb=" N VAL F 49 " --> pdb=" O ALA F 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 85 Processing helix chain 'F' and resid 96 through 109 Processing helix chain 'F' and resid 127 through 137 removed outlier: 3.797A pdb=" N LEU F 131 " --> pdb=" O VAL F 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 163 Processing helix chain 'F' and resid 193 through 205 Processing helix chain 'F' and resid 224 through 228 Processing helix chain 'F' and resid 255 through 266 removed outlier: 3.661A 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 Processing helix chain 'F' and resid 333 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 removed outlier: 3.607A pdb=" N VAL F 373 " --> pdb=" O THR F 369 " (cutoff:3.500A) Processing helix chain 'F' and resid 416 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 485 Processing helix chain 'F' and resid 494 through 502 Processing helix chain 'G' and resid 19 through 24 removed outlier: 3.511A pdb=" N PHE G 24 " --> pdb=" O ALA G 20 " (cutoff:3.500A) 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 removed outlier: 3.703A pdb=" N VAL G 49 " --> pdb=" O ALA G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 75 through 85 Processing helix chain 'G' and resid 96 through 109 Processing helix chain 'G' and resid 127 through 137 removed outlier: 3.816A pdb=" N LEU G 131 " --> pdb=" O VAL G 127 " (cutoff:3.500A) Processing helix chain 'G' and resid 159 through 163 Processing helix chain 'G' and resid 193 through 205 Processing helix chain 'G' and resid 224 through 228 Processing helix chain 'G' and resid 255 through 266 removed outlier: 3.647A 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 Processing helix chain 'G' and resid 333 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 removed outlier: 3.614A pdb=" N VAL G 373 " --> pdb=" O THR G 369 " (cutoff:3.500A) Processing helix chain 'G' and resid 416 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 485 Processing helix chain 'G' and resid 494 through 502 Processing helix chain 'H' and resid 19 through 24 removed outlier: 3.511A pdb=" N PHE H 24 " --> pdb=" O ALA H 20 " (cutoff:3.500A) 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 removed outlier: 3.657A pdb=" N VAL H 49 " --> pdb=" O ALA H 46 " (cutoff:3.500A) Processing helix chain 'H' and resid 75 through 85 Processing helix chain 'H' and resid 96 through 109 Processing helix chain 'H' and resid 127 through 137 removed outlier: 3.939A pdb=" N LEU H 131 " --> pdb=" O VAL H 127 " (cutoff:3.500A) Processing helix chain 'H' and resid 159 through 163 Processing helix chain 'H' and resid 193 through 205 Processing helix chain 'H' and resid 224 through 228 Processing helix chain 'H' and resid 255 through 266 removed outlier: 3.606A 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 Processing helix chain 'H' and resid 333 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 removed outlier: 3.616A pdb=" N VAL H 373 " --> pdb=" O THR H 369 " (cutoff:3.500A) Processing helix chain 'H' and resid 416 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 485 Processing helix chain 'H' and resid 494 through 502 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 65 through 67 removed outlier: 3.526A pdb=" N ILE A 88 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE A 90 " --> pdb=" O SER A 67 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ILE A 271 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N GLY A 302 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N LEU A 273 " --> pdb=" O GLY A 302 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N VAL A 304 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ASN A 303 " --> pdb=" O ARG A 322 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N LEU A 321 " --> pdb=" O ILE A 362 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N ASP A 364 " --> pdb=" O LEU A 321 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N VAL A 323 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ILE A 66 " --> pdb=" O MET A 386 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 208 through 211 removed outlier: 3.733A pdb=" N ALA A 220 " --> pdb=" O ILE A 211 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 401 through 403 removed outlier: 3.661A pdb=" N SER A 403 " --> pdb=" O VAL A 406 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER A 444 " --> pdb=" O GLU D 510 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER D 508 " --> pdb=" O SER A 446 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 508 through 510 removed outlier: 3.827A pdb=" N SER A 508 " --> pdb=" O SER B 446 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER B 444 " --> pdb=" O GLU A 510 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER B 403 " --> pdb=" O VAL B 406 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 35 through 37 Processing sheet with id=AA7, first strand: chain 'B' and resid 65 through 67 removed outlier: 3.525A pdb=" N ILE B 88 " --> pdb=" O LEU B 65 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE B 90 " --> pdb=" O SER B 67 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ILE B 271 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N GLY B 302 " --> pdb=" O ILE B 271 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N LEU B 273 " --> pdb=" O GLY B 302 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N VAL B 304 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ASN B 303 " --> pdb=" O ARG B 322 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N LEU B 321 " --> pdb=" O ILE B 362 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N ASP B 364 " --> pdb=" O LEU B 321 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N VAL B 323 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ILE B 66 " --> pdb=" O MET B 386 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 208 through 211 removed outlier: 3.794A pdb=" N ALA B 220 " --> pdb=" O ILE B 211 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 508 through 510 removed outlier: 3.813A pdb=" N SER B 508 " --> pdb=" O SER C 446 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER C 444 " --> pdb=" O GLU B 510 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER C 403 " --> pdb=" O VAL C 406 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 35 through 37 Processing sheet with id=AB2, first strand: chain 'C' and resid 65 through 67 removed outlier: 3.525A pdb=" N ILE C 88 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE C 90 " --> pdb=" O SER C 67 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ILE C 271 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N GLY C 302 " --> pdb=" O ILE C 271 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N LEU C 273 " --> pdb=" O GLY C 302 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N VAL C 304 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASN C 303 " --> pdb=" O ARG C 322 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N LEU C 321 " --> pdb=" O ILE C 362 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N ASP C 364 " --> pdb=" O LEU C 321 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N VAL C 323 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ILE C 66 " --> pdb=" O MET C 386 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 208 through 211 removed outlier: 3.816A pdb=" N ALA C 220 " --> pdb=" O ILE C 211 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 508 through 510 removed outlier: 3.829A pdb=" N SER C 508 " --> pdb=" O SER D 446 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER D 444 " --> pdb=" O GLU C 510 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER D 403 " --> pdb=" O VAL D 406 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 35 through 37 Processing sheet with id=AB6, first strand: chain 'D' and resid 65 through 67 removed outlier: 3.524A pdb=" N ILE D 88 " --> pdb=" O LEU D 65 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE D 90 " --> pdb=" O SER D 67 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ILE D 271 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N GLY D 302 " --> pdb=" O ILE D 271 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N LEU D 273 " --> pdb=" O GLY D 302 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N VAL D 304 " --> pdb=" O LEU D 273 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ASN D 303 " --> pdb=" O ARG D 322 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N LEU D 321 " --> pdb=" O ILE D 362 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N ASP D 364 " --> pdb=" O LEU D 321 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N VAL D 323 " --> pdb=" O ASP D 364 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE D 66 " --> pdb=" O MET D 386 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 208 through 211 removed outlier: 3.818A pdb=" N ALA D 220 " --> pdb=" O ILE D 211 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 35 through 37 Processing sheet with id=AB9, first strand: chain 'E' and resid 65 through 67 removed outlier: 3.528A pdb=" N ILE E 88 " --> pdb=" O LEU E 65 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE E 90 " --> pdb=" O SER E 67 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ILE E 271 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N GLY E 302 " --> pdb=" O ILE E 271 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N LEU E 273 " --> pdb=" O GLY E 302 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N VAL E 304 " --> pdb=" O LEU E 273 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ASN E 303 " --> pdb=" O ARG E 322 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N LEU E 321 " --> pdb=" O ILE E 362 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N ASP E 364 " --> pdb=" O LEU E 321 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N VAL E 323 " --> pdb=" O ASP E 364 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ILE E 66 " --> pdb=" O MET E 386 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 208 through 211 removed outlier: 3.699A pdb=" N ALA E 220 " --> pdb=" O ILE E 211 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 401 through 403 removed outlier: 3.628A pdb=" N SER E 403 " --> pdb=" O VAL E 406 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER E 444 " --> pdb=" O GLU H 510 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N SER H 508 " --> pdb=" O SER E 446 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 508 through 510 removed outlier: 3.801A pdb=" N SER E 508 " --> pdb=" O SER F 446 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER F 444 " --> pdb=" O GLU E 510 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER F 403 " --> pdb=" O VAL F 406 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 35 through 37 Processing sheet with id=AC5, first strand: chain 'F' and resid 65 through 67 removed outlier: 3.526A pdb=" N ILE F 88 " --> pdb=" O LEU F 65 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE F 90 " --> pdb=" O SER F 67 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ILE F 271 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N GLY F 302 " --> pdb=" O ILE F 271 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N LEU F 273 " --> pdb=" O GLY F 302 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N VAL F 304 " --> pdb=" O LEU F 273 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASN F 303 " --> pdb=" O ARG F 322 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N LEU F 321 " --> pdb=" O ILE F 362 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N ASP F 364 " --> pdb=" O LEU F 321 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N VAL F 323 " --> pdb=" O ASP F 364 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE F 66 " --> pdb=" O MET F 386 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 208 through 211 removed outlier: 3.829A pdb=" N ALA F 220 " --> pdb=" O ILE F 211 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 508 through 510 removed outlier: 3.812A pdb=" N SER F 508 " --> pdb=" O SER G 446 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER G 444 " --> pdb=" O GLU F 510 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER G 403 " --> pdb=" O VAL G 406 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 35 through 37 Processing sheet with id=AC9, first strand: chain 'G' and resid 65 through 67 removed outlier: 3.525A pdb=" N ILE G 88 " --> pdb=" O LEU G 65 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE G 90 " --> pdb=" O SER G 67 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ILE G 271 " --> pdb=" O ILE G 300 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N GLY G 302 " --> pdb=" O ILE G 271 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N LEU G 273 " --> pdb=" O GLY G 302 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N VAL G 304 " --> pdb=" O LEU G 273 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ASN G 303 " --> pdb=" O ARG G 322 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N LEU G 321 " --> pdb=" O ILE G 362 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N ASP G 364 " --> pdb=" O LEU G 321 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N VAL G 323 " --> pdb=" O ASP G 364 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ILE G 66 " --> pdb=" O MET G 386 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 208 through 211 removed outlier: 3.813A pdb=" N ALA G 220 " --> pdb=" O ILE G 211 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 508 through 510 removed outlier: 3.827A pdb=" N SER G 508 " --> pdb=" O SER H 446 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER H 444 " --> pdb=" O GLU G 510 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER H 403 " --> pdb=" O VAL H 406 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 35 through 37 Processing sheet with id=AD4, first strand: chain 'H' and resid 65 through 67 removed outlier: 3.530A pdb=" N ILE H 88 " --> pdb=" O LEU H 65 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N PHE H 90 " --> pdb=" O SER H 67 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ILE H 271 " --> pdb=" O ILE H 300 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N GLY H 302 " --> pdb=" O ILE H 271 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N LEU H 273 " --> pdb=" O GLY H 302 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N VAL H 304 " --> pdb=" O LEU H 273 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASN H 303 " --> pdb=" O ARG H 322 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N LEU H 321 " --> pdb=" O ILE H 362 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N ASP H 364 " --> pdb=" O LEU H 321 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N VAL H 323 " --> pdb=" O ASP H 364 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ILE H 66 " --> pdb=" O MET H 386 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 208 through 211 removed outlier: 3.698A pdb=" N ALA H 220 " --> pdb=" O ILE H 211 " (cutoff:3.500A) 1090 hydrogen bonds defined for protein. 3078 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: 6.91 Time building geometry restraints manager: 4.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.26: 4987 1.26 - 1.40: 6918 1.40 - 1.53: 17690 1.53 - 1.67: 669 1.67 - 1.81: 328 Bond restraints: 30592 Sorted by residual: bond pdb=" C2' ATP B 601 " pdb=" C3' ATP B 601 " ideal model delta sigma weight residual 1.531 1.241 0.290 1.20e-02 6.94e+03 5.84e+02 bond pdb=" C2' ATP E 601 " pdb=" C3' ATP E 601 " ideal model delta sigma weight residual 1.531 1.241 0.290 1.20e-02 6.94e+03 5.83e+02 bond pdb=" C2' ATP G 601 " pdb=" C3' ATP G 601 " ideal model delta sigma weight residual 1.531 1.242 0.289 1.20e-02 6.94e+03 5.81e+02 bond pdb=" C2' ATP H 601 " pdb=" C3' ATP H 601 " ideal model delta sigma weight residual 1.531 1.242 0.289 1.20e-02 6.94e+03 5.79e+02 bond pdb=" C2' ATP F 601 " pdb=" C3' ATP F 601 " ideal model delta sigma weight residual 1.531 1.242 0.289 1.20e-02 6.94e+03 5.79e+02 ... (remaining 30587 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.53: 40937 4.53 - 9.05: 398 9.05 - 13.58: 57 13.58 - 18.11: 59 18.11 - 22.64: 45 Bond angle restraints: 41496 Sorted by residual: angle pdb=" PB ATP G 601 " pdb=" O3B ATP G 601 " pdb=" PG ATP G 601 " ideal model delta sigma weight residual 139.87 117.23 22.64 1.00e+00 1.00e+00 5.12e+02 angle pdb=" PB ATP A 601 " pdb=" O3B ATP A 601 " pdb=" PG ATP A 601 " ideal model delta sigma weight residual 139.87 117.68 22.19 1.00e+00 1.00e+00 4.93e+02 angle pdb=" PB ATP C 602 " pdb=" O3B ATP C 602 " pdb=" PG ATP C 602 " ideal model delta sigma weight residual 139.87 117.81 22.06 1.00e+00 1.00e+00 4.87e+02 angle pdb=" PB ATP H 601 " pdb=" O3B ATP H 601 " pdb=" PG ATP H 601 " ideal model delta sigma weight residual 139.87 118.19 21.68 1.00e+00 1.00e+00 4.70e+02 angle pdb=" PB ATP F 601 " pdb=" O3B ATP F 601 " pdb=" PG ATP F 601 " ideal model delta sigma weight residual 139.87 118.27 21.60 1.00e+00 1.00e+00 4.66e+02 ... (remaining 41491 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.92: 17329 32.92 - 65.84: 556 65.84 - 98.76: 114 98.76 - 131.68: 0 131.68 - 164.60: 1 Dihedral angle restraints: 18000 sinusoidal: 7144 harmonic: 10856 Sorted by residual: 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 -3.47 -164.60 1 2.00e+01 2.50e-03 4.71e+01 dihedral pdb=" N THR A 10 " pdb=" C THR A 10 " pdb=" CA THR A 10 " pdb=" CB THR A 10 " ideal model delta harmonic sigma weight residual 123.40 140.08 -16.68 0 2.50e+00 1.60e-01 4.45e+01 dihedral pdb=" C THR A 10 " pdb=" N THR A 10 " pdb=" CA THR A 10 " pdb=" CB THR A 10 " ideal model delta harmonic sigma weight residual -122.00 -136.36 14.36 0 2.50e+00 1.60e-01 3.30e+01 ... (remaining 17997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.136: 4722 0.136 - 0.273: 46 0.273 - 0.409: 30 0.409 - 0.545: 0 0.545 - 0.682: 2 Chirality restraints: 4800 Sorted by residual: chirality pdb=" CA THR A 10 " pdb=" N THR A 10 " pdb=" C THR A 10 " pdb=" CB THR A 10 " both_signs ideal model delta sigma weight residual False 2.53 1.84 0.68 2.00e-01 2.50e+01 1.16e+01 chirality pdb=" CA TYR E 12 " pdb=" N TYR E 12 " pdb=" C TYR E 12 " pdb=" CB TYR E 12 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.61 2.00e-01 2.50e+01 9.16e+00 chirality pdb=" C3B NAD H 604 " pdb=" C2B NAD H 604 " pdb=" C4B NAD H 604 " pdb=" O3B NAD H 604 " both_signs ideal model delta sigma weight residual False -2.71 -2.34 -0.37 2.00e-01 2.50e+01 3.44e+00 ... (remaining 4797 not shown) Planarity restraints: 5160 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR E 12 " 0.033 2.00e-02 2.50e+03 6.47e-02 4.19e+01 pdb=" C TYR E 12 " -0.112 2.00e-02 2.50e+03 pdb=" O TYR E 12 " 0.043 2.00e-02 2.50e+03 pdb=" N VAL E 13 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 12 " -0.010 2.00e-02 2.50e+03 3.27e-02 2.14e+01 pdb=" CG TYR E 12 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TYR E 12 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TYR E 12 " -0.050 2.00e-02 2.50e+03 pdb=" CE1 TYR E 12 " -0.051 2.00e-02 2.50e+03 pdb=" CE2 TYR E 12 " 0.022 2.00e-02 2.50e+03 pdb=" CZ TYR E 12 " 0.008 2.00e-02 2.50e+03 pdb=" OH TYR E 12 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 8 " -0.009 2.00e-02 2.50e+03 1.83e-02 3.35e+00 pdb=" C GLY A 8 " 0.032 2.00e-02 2.50e+03 pdb=" O GLY A 8 " -0.012 2.00e-02 2.50e+03 pdb=" N GLY A 9 " -0.011 2.00e-02 2.50e+03 ... (remaining 5157 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 1601 2.70 - 3.25: 30769 3.25 - 3.80: 51427 3.80 - 4.35: 68032 4.35 - 4.90: 110806 Nonbonded interactions: 262635 Sorted by model distance: nonbonded pdb=" OD1 ASP C 364 " pdb=" O3' IMP C 603 " model vdw 2.150 3.040 nonbonded pdb=" OD1 ASP F 226 " pdb=" O3' ATP F 602 " model vdw 2.188 3.040 nonbonded pdb=" O ALA D 396 " pdb=" NZ LYS D 409 " model vdw 2.188 3.120 nonbonded pdb=" O2' ATP C 601 " pdb=" O3' ATP C 601 " model vdw 2.188 2.432 nonbonded pdb=" O ALA A 396 " pdb=" NZ LYS A 409 " model vdw 2.189 3.120 ... (remaining 262630 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 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: 2.680 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: 0.040 Extract box with map and model: 0.530 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 29.950 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.100 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:1.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 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 : 0.018 0.901 30593 Z= 1.173 Angle : 1.407 22.637 41496 Z= 0.941 Chirality : 0.060 0.682 4800 Planarity : 0.004 0.065 5160 Dihedral : 16.616 164.597 11088 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.99 % Favored : 92.96 % Rotamer: Outliers : 4.87 % Allowed : 10.42 % Favored : 84.71 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.02 (0.12), residues: 3792 helix: -1.31 (0.12), residues: 1416 sheet: -1.25 (0.23), residues: 352 loop : -2.74 (0.12), residues: 2024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 203 TYR 0.051 0.002 TYR E 12 PHE 0.010 0.002 PHE H 99 HIS 0.004 0.001 HIS E 466 Details of bonding type rmsd/Z covalent geometry : bond 0.01698 / 1.05 (30592) covalent geometry : angle 1.40712 / 0.94 (41496) hydrogen bonds : bond 0.16453 / 11.41 ( 1090) hydrogen bonds : angle 7.36953 / 5.17 ( 3078) Misc. bond : bond 0.90091 / 56.31 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 755 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 603 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 ILE cc_start: 0.9119 (OUTLIER) cc_final: 0.8634 (mm) REVERT: A 146 GLU cc_start: 0.6688 (OUTLIER) cc_final: 0.5503 (pp20) REVERT: A 224 ARG cc_start: 0.8439 (ttt90) cc_final: 0.8225 (ttt-90) REVERT: A 312 ASN cc_start: 0.9057 (m-40) cc_final: 0.8754 (m-40) REVERT: A 355 ARG cc_start: 0.8640 (OUTLIER) cc_final: 0.8135 (ptt-90) REVERT: A 441 GLN cc_start: 0.8501 (mt0) cc_final: 0.8233 (mt0) REVERT: A 449 ASP cc_start: 0.7538 (t70) cc_final: 0.6824 (t70) REVERT: B 161 ARG cc_start: 0.8445 (mtt180) cc_final: 0.8208 (mtt180) REVERT: B 312 ASN cc_start: 0.9073 (m-40) cc_final: 0.8798 (m-40) REVERT: B 355 ARG cc_start: 0.8611 (OUTLIER) cc_final: 0.8178 (ptt-90) REVERT: B 395 GLU cc_start: 0.7751 (mp0) cc_final: 0.7531 (mp0) REVERT: B 441 GLN cc_start: 0.8460 (mt0) cc_final: 0.8230 (mt0) REVERT: B 448 GLN cc_start: 0.7453 (tt0) cc_final: 0.7240 (tt0) REVERT: B 449 ASP cc_start: 0.7522 (t70) cc_final: 0.7116 (t70) REVERT: C 224 ARG cc_start: 0.8353 (ttt90) cc_final: 0.8138 (ttt-90) REVERT: C 312 ASN cc_start: 0.9050 (m-40) cc_final: 0.8745 (m-40) REVERT: C 355 ARG cc_start: 0.8610 (OUTLIER) cc_final: 0.8030 (ptt-90) REVERT: D 91 ILE cc_start: 0.9110 (OUTLIER) cc_final: 0.8630 (mm) REVERT: D 146 GLU cc_start: 0.6573 (OUTLIER) cc_final: 0.5379 (pp20) REVERT: D 161 ARG cc_start: 0.8693 (mtt180) cc_final: 0.8485 (mtt180) REVERT: D 224 ARG cc_start: 0.8393 (ttt90) cc_final: 0.8163 (ttt-90) REVERT: D 312 ASN cc_start: 0.9101 (m-40) cc_final: 0.8760 (m-40) REVERT: D 355 ARG cc_start: 0.8608 (OUTLIER) cc_final: 0.7925 (ptt-90) REVERT: D 395 GLU cc_start: 0.7759 (mp0) cc_final: 0.7504 (mp0) REVERT: D 441 GLN cc_start: 0.8479 (mt0) cc_final: 0.8199 (mt0) REVERT: D 449 ASP cc_start: 0.7545 (t70) cc_final: 0.6855 (t70) REVERT: E 146 GLU cc_start: 0.6659 (OUTLIER) cc_final: 0.5518 (pp20) REVERT: E 179 MET cc_start: 0.5193 (mtt) cc_final: 0.4979 (mtm) REVERT: E 224 ARG cc_start: 0.8328 (ttt90) cc_final: 0.8112 (ttt-90) REVERT: E 312 ASN cc_start: 0.9057 (m-40) cc_final: 0.8757 (m-40) REVERT: E 355 ARG cc_start: 0.8605 (OUTLIER) cc_final: 0.7979 (ptt-90) REVERT: E 395 GLU cc_start: 0.7778 (mp0) cc_final: 0.7555 (mp0) REVERT: E 449 ASP cc_start: 0.7523 (t70) cc_final: 0.7085 (t70) REVERT: F 91 ILE cc_start: 0.9110 (OUTLIER) cc_final: 0.8617 (mm) REVERT: F 146 GLU cc_start: 0.5911 (OUTLIER) cc_final: 0.4605 (pp20) REVERT: F 161 ARG cc_start: 0.8535 (mtt180) cc_final: 0.8323 (mtt180) REVERT: F 224 ARG cc_start: 0.8332 (ttt90) cc_final: 0.8131 (ttt-90) REVERT: F 229 LYS cc_start: 0.8194 (ptpt) cc_final: 0.7964 (ptpp) REVERT: F 312 ASN cc_start: 0.9066 (m-40) cc_final: 0.8781 (m-40) REVERT: F 355 ARG cc_start: 0.8609 (OUTLIER) cc_final: 0.8042 (ptt-90) REVERT: F 395 GLU cc_start: 0.7751 (mp0) cc_final: 0.7527 (mp0) REVERT: G 91 ILE cc_start: 0.9115 (OUTLIER) cc_final: 0.8629 (mm) REVERT: G 146 GLU cc_start: 0.7275 (OUTLIER) cc_final: 0.6050 (pp20) REVERT: G 179 MET cc_start: 0.3655 (mtt) cc_final: 0.2840 (mpp) REVERT: G 224 ARG cc_start: 0.8371 (ttt90) cc_final: 0.8134 (ttt-90) REVERT: G 312 ASN cc_start: 0.9079 (m-40) cc_final: 0.8726 (m-40) REVERT: G 355 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.8047 (ptt-90) REVERT: G 441 GLN cc_start: 0.8431 (mt0) cc_final: 0.8154 (mt0) REVERT: G 449 ASP cc_start: 0.7506 (t70) cc_final: 0.7012 (t70) REVERT: H 91 ILE cc_start: 0.9105 (OUTLIER) cc_final: 0.8616 (mm) REVERT: H 312 ASN cc_start: 0.9092 (m-40) cc_final: 0.8795 (m-40) REVERT: H 355 ARG cc_start: 0.8635 (OUTLIER) cc_final: 0.8092 (ptt-90) REVERT: H 395 GLU cc_start: 0.7789 (mp0) cc_final: 0.7570 (mp0) REVERT: H 441 GLN cc_start: 0.8484 (mt0) cc_final: 0.8206 (mt0) REVERT: H 449 ASP cc_start: 0.7528 (t70) cc_final: 0.7106 (t70) outliers start: 152 outliers final: 108 residues processed: 735 average time/residue: 0.1918 time to fit residues: 223.2637 Evaluate side-chains 689 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 563 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 452 SER Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 93 HIS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 146 GLU Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 146 GLU Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 206 LYS Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 355 ARG Chi-restraints excluded: chain D residue 361 ILE Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 452 SER Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 146 GLU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 206 LYS Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 355 ARG Chi-restraints excluded: chain E residue 361 ILE Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 452 SER Chi-restraints excluded: chain F residue 53 SER Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 146 GLU Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 206 LYS Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 355 ARG Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain G residue 53 SER Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 91 ILE Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 146 GLU Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 283 GLN Chi-restraints excluded: chain G residue 355 ARG Chi-restraints excluded: chain G residue 361 ILE Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 452 SER Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 146 GLU Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 180 THR Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 206 LYS Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 355 ARG Chi-restraints excluded: chain H residue 361 ILE Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 452 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 112 GLN A 277 GLN A 303 ASN A 454 GLN A 498 GLN B 112 GLN B 277 GLN B 498 GLN C 112 GLN C 277 GLN C 303 ASN C 498 GLN D 112 GLN D 277 GLN D 454 GLN D 498 GLN ** E 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 112 GLN E 277 GLN E 498 GLN F 112 GLN F 277 GLN F 454 GLN F 498 GLN G 112 GLN G 277 GLN G 303 ASN G 498 GLN H 112 GLN H 277 GLN H 454 GLN H 498 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.151761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.105289 restraints weight = 33951.290| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 1.95 r_work: 0.2845 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.1186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 30593 Z= 0.152 Angle : 0.584 9.090 41496 Z= 0.300 Chirality : 0.043 0.143 4800 Planarity : 0.004 0.101 5160 Dihedral : 11.702 162.990 4511 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 3.08 % Allowed : 15.64 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.13), residues: 3792 helix: 0.21 (0.14), residues: 1424 sheet: -0.76 (0.26), residues: 272 loop : -2.09 (0.12), residues: 2096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 203 TYR 0.015 0.001 TYR G 400 PHE 0.015 0.001 PHE E 401 HIS 0.004 0.001 HIS E 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (30592) covalent geometry : angle 0.58407 / 0.30 (41496) hydrogen bonds : bond 0.03603 / 2.41 ( 1090) hydrogen bonds : angle 5.38684 / 3.79 ( 3078) Misc. bond : bond 0.00157 / 0.10 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 745 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 649 time to evaluate : 1.052 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: A 134 LYS cc_start: 0.7854 (tptt) cc_final: 0.7573 (tppt) REVERT: A 229 LYS cc_start: 0.8088 (ptpp) cc_final: 0.7869 (ptpp) REVERT: A 312 ASN cc_start: 0.9255 (m-40) cc_final: 0.9009 (m-40) REVERT: A 449 ASP cc_start: 0.7806 (t70) cc_final: 0.7296 (t70) REVERT: B 91 ILE cc_start: 0.8966 (mm) cc_final: 0.8560 (mm) REVERT: B 134 LYS cc_start: 0.7896 (tptt) cc_final: 0.7564 (tppt) REVERT: B 202 GLN cc_start: 0.8405 (tt0) cc_final: 0.8097 (mm-40) REVERT: B 312 ASN cc_start: 0.9251 (m-40) cc_final: 0.9003 (m-40) REVERT: B 395 GLU cc_start: 0.8133 (mp0) cc_final: 0.7870 (mp0) REVERT: B 411 TYR cc_start: 0.8907 (t80) cc_final: 0.8702 (t80) REVERT: B 449 ASP cc_start: 0.7895 (t70) cc_final: 0.7232 (t70) REVERT: B 455 LYS cc_start: 0.8148 (ptpp) cc_final: 0.7906 (ptpp) REVERT: C 135 MET cc_start: 0.8271 (mpp) cc_final: 0.7717 (mpp) REVERT: C 202 GLN cc_start: 0.8435 (tt0) cc_final: 0.8041 (mt0) REVERT: C 312 ASN cc_start: 0.9232 (m-40) cc_final: 0.8965 (m-40) REVERT: C 400 TYR cc_start: 0.7696 (m-80) cc_final: 0.7191 (m-80) REVERT: C 449 ASP cc_start: 0.8027 (t0) cc_final: 0.7761 (t70) REVERT: D 134 LYS cc_start: 0.7934 (tptt) cc_final: 0.7692 (tppt) REVERT: D 202 GLN cc_start: 0.8439 (tt0) cc_final: 0.8047 (mt0) REVERT: D 312 ASN cc_start: 0.9278 (m-40) cc_final: 0.8994 (m-40) REVERT: D 395 GLU cc_start: 0.8151 (mp0) cc_final: 0.7860 (mp0) REVERT: D 411 TYR cc_start: 0.8872 (t80) cc_final: 0.8573 (t80) REVERT: D 412 ARG cc_start: 0.8244 (ptt180) cc_final: 0.8031 (ptt180) REVERT: D 449 ASP cc_start: 0.7766 (t70) cc_final: 0.7384 (t70) REVERT: E 91 ILE cc_start: 0.8955 (mm) cc_final: 0.8550 (mm) REVERT: E 134 LYS cc_start: 0.7983 (tptt) cc_final: 0.7685 (tppt) REVERT: E 243 GLN cc_start: 0.8070 (mp10) cc_final: 0.7708 (mp10) REVERT: E 312 ASN cc_start: 0.9243 (m-40) cc_final: 0.8982 (m-40) REVERT: E 395 GLU cc_start: 0.8080 (mp0) cc_final: 0.7845 (mp0) REVERT: E 400 TYR cc_start: 0.7802 (m-80) cc_final: 0.7128 (m-80) REVERT: E 448 GLN cc_start: 0.7599 (tt0) cc_final: 0.7345 (tt0) REVERT: E 449 ASP cc_start: 0.7884 (t70) cc_final: 0.7227 (t70) REVERT: F 243 GLN cc_start: 0.8120 (mp10) cc_final: 0.7234 (mp-120) REVERT: F 274 ASP cc_start: 0.8796 (t0) cc_final: 0.8508 (t0) REVERT: F 312 ASN cc_start: 0.9225 (m-40) cc_final: 0.8969 (m-40) REVERT: F 395 GLU cc_start: 0.8061 (mp0) cc_final: 0.7799 (mp0) REVERT: G 179 MET cc_start: 0.3996 (mtt) cc_final: 0.3250 (mpp) REVERT: G 231 ARG cc_start: 0.8594 (ptp90) cc_final: 0.8362 (mtm110) REVERT: G 312 ASN cc_start: 0.9271 (m-40) cc_final: 0.8960 (m-40) REVERT: G 395 GLU cc_start: 0.8160 (mp0) cc_final: 0.7865 (mp0) REVERT: G 412 ARG cc_start: 0.8261 (ptt180) cc_final: 0.8026 (ptt180) REVERT: H 231 ARG cc_start: 0.8709 (ptp90) cc_final: 0.8479 (mtm180) REVERT: H 312 ASN cc_start: 0.9279 (m-40) cc_final: 0.9035 (m-40) REVERT: H 395 GLU cc_start: 0.8047 (mp0) cc_final: 0.7794 (mp0) REVERT: H 411 TYR cc_start: 0.8862 (t80) cc_final: 0.8565 (t80) REVERT: H 441 GLN cc_start: 0.8498 (mt0) cc_final: 0.8288 (mt0) outliers start: 96 outliers final: 68 residues processed: 725 average time/residue: 0.1946 time to fit residues: 222.6938 Evaluate side-chains 676 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 608 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 283 GLN Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain C residue 93 HIS Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 283 GLN Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 452 SER Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 206 LYS Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 283 GLN Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 206 LYS Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 283 GLN Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 206 LYS Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 283 GLN Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 452 SER Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 206 LYS Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 283 GLN Chi-restraints excluded: chain H residue 383 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 314 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 175 optimal weight: 3.9990 chunk 137 optimal weight: 9.9990 chunk 364 optimal weight: 0.9980 chunk 202 optimal weight: 4.9990 chunk 269 optimal weight: 1.9990 chunk 123 optimal weight: 0.0060 chunk 241 optimal weight: 1.9990 chunk 112 optimal weight: 7.9990 overall best weight: 1.1400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 334 GLN B 334 GLN C 334 GLN D 303 ASN D 334 GLN ** E 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 334 GLN F 303 ASN F 334 GLN G 334 GLN H 303 ASN H 334 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.151367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.106783 restraints weight = 34126.078| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 2.05 r_work: 0.2866 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2728 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 30593 Z= 0.172 Angle : 0.561 8.473 41496 Z= 0.285 Chirality : 0.043 0.143 4800 Planarity : 0.004 0.045 5160 Dihedral : 10.525 154.733 4379 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 3.49 % Allowed : 16.89 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.13), residues: 3792 helix: 0.79 (0.14), residues: 1424 sheet: -0.37 (0.26), residues: 288 loop : -1.76 (0.13), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 231 TYR 0.013 0.001 TYR G 400 PHE 0.013 0.001 PHE C 401 HIS 0.004 0.001 HIS E 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 (30592) covalent geometry : angle 0.56145 / 0.29 (41496) hydrogen bonds : bond 0.03554 / 2.37 ( 1090) hydrogen bonds : angle 5.08220 / 3.57 ( 3078) Misc. bond : bond 0.00126 / 0.08 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 711 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 602 time to evaluate : 1.087 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: A 202 GLN cc_start: 0.8360 (tt0) cc_final: 0.8100 (mm-40) REVERT: A 229 LYS cc_start: 0.8100 (ptpp) cc_final: 0.7831 (ptpp) REVERT: A 243 GLN cc_start: 0.7895 (mp-120) cc_final: 0.7604 (mp10) REVERT: A 312 ASN cc_start: 0.9223 (m-40) cc_final: 0.8947 (m-40) REVERT: A 441 GLN cc_start: 0.8503 (mt0) cc_final: 0.8232 (mt0) REVERT: B 134 LYS cc_start: 0.7829 (tptt) cc_final: 0.7472 (tppt) REVERT: B 243 GLN cc_start: 0.7758 (mp-120) cc_final: 0.7504 (mp10) REVERT: B 312 ASN cc_start: 0.9221 (m-40) cc_final: 0.8981 (m-40) REVERT: B 395 GLU cc_start: 0.8111 (mp0) cc_final: 0.7818 (mp0) REVERT: B 441 GLN cc_start: 0.8456 (mt0) cc_final: 0.8168 (mt0) REVERT: B 449 ASP cc_start: 0.7870 (t70) cc_final: 0.7350 (t70) REVERT: C 135 MET cc_start: 0.8341 (mpp) cc_final: 0.7936 (mpp) REVERT: C 202 GLN cc_start: 0.8474 (tt0) cc_final: 0.8261 (tt0) REVERT: C 243 GLN cc_start: 0.7799 (mp-120) cc_final: 0.7546 (mp10) REVERT: C 286 MET cc_start: 0.8822 (tpp) cc_final: 0.8618 (tpp) REVERT: C 312 ASN cc_start: 0.9201 (m-40) cc_final: 0.8914 (m-40) REVERT: C 330 ILE cc_start: 0.9004 (OUTLIER) cc_final: 0.8794 (pp) REVERT: C 441 GLN cc_start: 0.8474 (mt0) cc_final: 0.8209 (mt0) REVERT: C 449 ASP cc_start: 0.7819 (t0) cc_final: 0.7612 (t70) REVERT: D 184 GLU cc_start: 0.1937 (OUTLIER) cc_final: 0.0024 (tp30) REVERT: D 243 GLN cc_start: 0.7799 (mp-120) cc_final: 0.7552 (mp10) REVERT: D 312 ASN cc_start: 0.9251 (m-40) cc_final: 0.8949 (m-40) REVERT: D 395 GLU cc_start: 0.8078 (mp0) cc_final: 0.7730 (mp0) REVERT: D 412 ARG cc_start: 0.8112 (ptt180) cc_final: 0.7887 (ptt180) REVERT: D 441 GLN cc_start: 0.8508 (mt0) cc_final: 0.8213 (mt0) REVERT: D 449 ASP cc_start: 0.7865 (t70) cc_final: 0.7334 (t70) REVERT: D 455 LYS cc_start: 0.7935 (ptpp) cc_final: 0.7693 (ptpp) REVERT: E 91 ILE cc_start: 0.8926 (mm) cc_final: 0.8466 (mm) REVERT: E 134 LYS cc_start: 0.7915 (tptt) cc_final: 0.7635 (tppt) REVERT: E 243 GLN cc_start: 0.7986 (mp10) cc_final: 0.7739 (mp-120) REVERT: E 312 ASN cc_start: 0.9204 (m-40) cc_final: 0.8953 (m-40) REVERT: E 395 GLU cc_start: 0.8058 (mp0) cc_final: 0.7750 (mp0) REVERT: E 441 GLN cc_start: 0.8482 (mt0) cc_final: 0.8176 (mt0) REVERT: E 449 ASP cc_start: 0.7906 (t70) cc_final: 0.7239 (t0) REVERT: F 206 LYS cc_start: 0.8270 (OUTLIER) cc_final: 0.6979 (mtmm) REVERT: F 243 GLN cc_start: 0.8071 (mp10) cc_final: 0.7795 (mp-120) REVERT: F 274 ASP cc_start: 0.8762 (t0) cc_final: 0.8451 (t0) REVERT: F 312 ASN cc_start: 0.9211 (m-40) cc_final: 0.8935 (m-40) REVERT: F 395 GLU cc_start: 0.8052 (mp0) cc_final: 0.7722 (mp0) REVERT: F 400 TYR cc_start: 0.7577 (m-80) cc_final: 0.7056 (m-80) REVERT: F 441 GLN cc_start: 0.8497 (mt0) cc_final: 0.8184 (mt0) REVERT: F 449 ASP cc_start: 0.7838 (t0) cc_final: 0.7475 (t0) REVERT: G 135 MET cc_start: 0.8197 (mpp) cc_final: 0.7840 (mpp) REVERT: G 179 MET cc_start: 0.3902 (mtt) cc_final: 0.3212 (mpp) REVERT: G 231 ARG cc_start: 0.8608 (ptp90) cc_final: 0.8369 (mtm110) REVERT: G 243 GLN cc_start: 0.7842 (mp-120) cc_final: 0.7597 (mp10) REVERT: G 312 ASN cc_start: 0.9216 (m-40) cc_final: 0.8897 (m-40) REVERT: G 395 GLU cc_start: 0.8114 (mp0) cc_final: 0.7795 (mp0) REVERT: G 412 ARG cc_start: 0.8182 (ptt180) cc_final: 0.7941 (ptt180) REVERT: G 441 GLN cc_start: 0.8470 (mt0) cc_final: 0.8181 (mt0) REVERT: H 225 THR cc_start: 0.8304 (m) cc_final: 0.7826 (p) REVERT: H 231 ARG cc_start: 0.8750 (ptp90) cc_final: 0.8488 (mtm180) REVERT: H 243 GLN cc_start: 0.7784 (mp-120) cc_final: 0.7525 (mp10) REVERT: H 312 ASN cc_start: 0.9243 (m-40) cc_final: 0.8946 (m-40) REVERT: H 395 GLU cc_start: 0.8068 (mp0) cc_final: 0.7767 (mp0) REVERT: H 412 ARG cc_start: 0.8072 (ptt180) cc_final: 0.7868 (ptt180) REVERT: H 441 GLN cc_start: 0.8407 (mt0) cc_final: 0.8150 (mt0) outliers start: 109 outliers final: 94 residues processed: 678 average time/residue: 0.1884 time to fit residues: 202.2079 Evaluate side-chains 690 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 593 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 283 GLN Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 93 HIS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 283 GLN Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 452 SER Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 206 LYS Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 283 GLN Chi-restraints excluded: chain D residue 361 ILE Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 448 GLN Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 206 LYS Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 283 GLN Chi-restraints excluded: chain E residue 361 ILE Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 206 LYS Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 283 GLN Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 452 SER Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 361 ILE Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 448 GLN Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 206 LYS Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 283 GLN Chi-restraints excluded: chain H residue 361 ILE Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 448 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 148 optimal weight: 4.9990 chunk 163 optimal weight: 1.9990 chunk 111 optimal weight: 0.0970 chunk 46 optimal weight: 0.6980 chunk 298 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 32 optimal weight: 0.5980 chunk 358 optimal weight: 1.9990 chunk 254 optimal weight: 8.9990 chunk 278 optimal weight: 6.9990 chunk 119 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.152802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.108510 restraints weight = 33818.764| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 2.07 r_work: 0.2865 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 30593 Z= 0.161 Angle : 0.540 8.448 41496 Z= 0.275 Chirality : 0.043 0.141 4800 Planarity : 0.004 0.041 5160 Dihedral : 10.266 147.978 4369 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 4.71 % Allowed : 16.89 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.14), residues: 3792 helix: 1.01 (0.14), residues: 1432 sheet: -0.22 (0.26), residues: 288 loop : -1.56 (0.14), residues: 2072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 231 TYR 0.013 0.001 TYR E 400 PHE 0.013 0.001 PHE F 401 HIS 0.004 0.001 HIS E 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (30592) covalent geometry : angle 0.53999 / 0.27 (41496) hydrogen bonds : bond 0.03324 / 2.21 ( 1090) hydrogen bonds : angle 4.92729 / 3.46 ( 3078) Misc. bond : bond 0.00089 / 0.06 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 767 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 620 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 LYS cc_start: 0.7753 (tptt) cc_final: 0.7539 (tppt) REVERT: A 229 LYS cc_start: 0.8120 (ptpp) cc_final: 0.7855 (ptpp) REVERT: A 312 ASN cc_start: 0.9233 (m-40) cc_final: 0.8916 (m-40) REVERT: A 330 ILE cc_start: 0.9014 (OUTLIER) cc_final: 0.8810 (pp) REVERT: A 441 GLN cc_start: 0.8439 (mt0) cc_final: 0.8175 (mt0) REVERT: A 455 LYS cc_start: 0.7923 (ptpp) cc_final: 0.7626 (ptpp) REVERT: A 476 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.9015 (mt) REVERT: B 312 ASN cc_start: 0.9214 (m-40) cc_final: 0.8959 (m-40) REVERT: B 395 GLU cc_start: 0.8109 (mp0) cc_final: 0.7802 (mp0) REVERT: B 441 GLN cc_start: 0.8406 (mt0) cc_final: 0.8124 (mt0) REVERT: B 449 ASP cc_start: 0.7911 (t70) cc_final: 0.7374 (t70) REVERT: C 135 MET cc_start: 0.8334 (mpp) cc_final: 0.7891 (mpp) REVERT: C 182 ARG cc_start: 0.6987 (mmm-85) cc_final: 0.6481 (mmm160) REVERT: C 286 MET cc_start: 0.8847 (tpp) cc_final: 0.8613 (tpp) REVERT: C 312 ASN cc_start: 0.9216 (m-40) cc_final: 0.8921 (m-40) REVERT: C 400 TYR cc_start: 0.7562 (m-80) cc_final: 0.7232 (m-80) REVERT: C 412 ARG cc_start: 0.8101 (ptt180) cc_final: 0.7880 (ptt180) REVERT: C 441 GLN cc_start: 0.8398 (mt0) cc_final: 0.8132 (mt0) REVERT: D 134 LYS cc_start: 0.7833 (tptt) cc_final: 0.7554 (tppt) REVERT: D 161 ARG cc_start: 0.8486 (mtt180) cc_final: 0.8165 (mtt180) REVERT: D 184 GLU cc_start: 0.1886 (OUTLIER) cc_final: 0.0034 (tp30) REVERT: D 202 GLN cc_start: 0.8393 (tt0) cc_final: 0.8010 (mt0) REVERT: D 312 ASN cc_start: 0.9237 (m-40) cc_final: 0.8906 (m-40) REVERT: D 395 GLU cc_start: 0.8084 (mp0) cc_final: 0.7723 (mp0) REVERT: D 412 ARG cc_start: 0.8111 (ptt180) cc_final: 0.7871 (ptt180) REVERT: D 441 GLN cc_start: 0.8410 (mt0) cc_final: 0.8129 (mt0) REVERT: D 449 ASP cc_start: 0.7844 (t70) cc_final: 0.7374 (t70) REVERT: E 78 MET cc_start: 0.8956 (tpp) cc_final: 0.8651 (tpp) REVERT: E 134 LYS cc_start: 0.7842 (tptt) cc_final: 0.7558 (tppt) REVERT: E 243 GLN cc_start: 0.7984 (mp10) cc_final: 0.7688 (mp-120) REVERT: E 312 ASN cc_start: 0.9226 (m-40) cc_final: 0.8933 (m-40) REVERT: E 330 ILE cc_start: 0.9022 (OUTLIER) cc_final: 0.8797 (pp) REVERT: E 395 GLU cc_start: 0.8055 (mp0) cc_final: 0.7699 (mp0) REVERT: E 441 GLN cc_start: 0.8397 (mt0) cc_final: 0.8103 (mt0) REVERT: E 449 ASP cc_start: 0.7853 (t70) cc_final: 0.7319 (t70) REVERT: F 184 GLU cc_start: 0.4980 (OUTLIER) cc_final: 0.4069 (tp30) REVERT: F 206 LYS cc_start: 0.8134 (OUTLIER) cc_final: 0.6982 (mtmm) REVERT: F 231 ARG cc_start: 0.8260 (mtm110) cc_final: 0.7934 (mtm180) REVERT: F 243 GLN cc_start: 0.8074 (mp10) cc_final: 0.7744 (mp-120) REVERT: F 312 ASN cc_start: 0.9224 (m-40) cc_final: 0.8909 (m-40) REVERT: F 330 ILE cc_start: 0.9022 (OUTLIER) cc_final: 0.8790 (pp) REVERT: F 395 GLU cc_start: 0.8070 (mp0) cc_final: 0.7749 (mp0) REVERT: F 400 TYR cc_start: 0.7570 (m-80) cc_final: 0.7151 (m-80) REVERT: F 412 ARG cc_start: 0.8046 (ptt180) cc_final: 0.7840 (ptt180) REVERT: F 441 GLN cc_start: 0.8408 (mt0) cc_final: 0.8084 (mt0) REVERT: F 449 ASP cc_start: 0.7780 (t0) cc_final: 0.7556 (t70) REVERT: F 476 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.9012 (mt) REVERT: G 135 MET cc_start: 0.8241 (mpp) cc_final: 0.7779 (mpp) REVERT: G 179 MET cc_start: 0.3735 (mtt) cc_final: 0.3002 (mpp) REVERT: G 286 MET cc_start: 0.8852 (tpp) cc_final: 0.8646 (tpp) REVERT: G 312 ASN cc_start: 0.9202 (m-40) cc_final: 0.8851 (m-40) REVERT: G 330 ILE cc_start: 0.9011 (OUTLIER) cc_final: 0.8795 (pp) REVERT: G 395 GLU cc_start: 0.8093 (mp0) cc_final: 0.7752 (mp0) REVERT: G 441 GLN cc_start: 0.8382 (mt0) cc_final: 0.8092 (mt0) REVERT: G 449 ASP cc_start: 0.7879 (t70) cc_final: 0.7445 (t70) REVERT: G 455 LYS cc_start: 0.7964 (ptpp) cc_final: 0.7724 (ptpp) REVERT: H 134 LYS cc_start: 0.7798 (tptt) cc_final: 0.7461 (tppt) REVERT: H 182 ARG cc_start: 0.6751 (mmm-85) cc_final: 0.6512 (mmm-85) REVERT: H 202 GLN cc_start: 0.8345 (tt0) cc_final: 0.8027 (mm-40) REVERT: H 225 THR cc_start: 0.8216 (m) cc_final: 0.7761 (p) REVERT: H 231 ARG cc_start: 0.8761 (ptp90) cc_final: 0.8500 (mtm180) REVERT: H 243 GLN cc_start: 0.7765 (mp-120) cc_final: 0.6975 (mp-120) REVERT: H 312 ASN cc_start: 0.9241 (m-40) cc_final: 0.8929 (m-40) REVERT: H 330 ILE cc_start: 0.9037 (OUTLIER) cc_final: 0.8802 (pp) REVERT: H 395 GLU cc_start: 0.8076 (mp0) cc_final: 0.7768 (mp0) REVERT: H 441 GLN cc_start: 0.8345 (mt0) cc_final: 0.8110 (mt0) outliers start: 147 outliers final: 115 residues processed: 725 average time/residue: 0.1854 time to fit residues: 214.8121 Evaluate side-chains 727 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 602 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 448 GLN Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 283 GLN Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 93 HIS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 283 GLN Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 452 SER Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 206 LYS Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 283 GLN Chi-restraints excluded: chain D residue 361 ILE Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 448 GLN Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 206 LYS Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 283 GLN Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 361 ILE Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 77 ASP Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 184 GLU Chi-restraints excluded: chain F residue 206 LYS Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 283 GLN Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 452 SER Chi-restraints excluded: chain F residue 476 LEU Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 147 THR Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 287 VAL Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 361 ILE Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 448 GLN Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 77 ASP Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 206 LYS Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 283 GLN Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 361 ILE Chi-restraints excluded: chain H residue 383 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 82 optimal weight: 2.9990 chunk 298 optimal weight: 4.9990 chunk 315 optimal weight: 0.7980 chunk 87 optimal weight: 5.9990 chunk 146 optimal weight: 1.9990 chunk 291 optimal weight: 2.9990 chunk 65 optimal weight: 9.9990 chunk 205 optimal weight: 5.9990 chunk 321 optimal weight: 1.9990 chunk 193 optimal weight: 0.9990 chunk 115 optimal weight: 0.1980 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 303 ASN E 93 HIS E 303 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.153341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.105606 restraints weight = 33767.537| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 1.96 r_work: 0.2849 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 30593 Z= 0.172 Angle : 0.541 8.185 41496 Z= 0.275 Chirality : 0.043 0.145 4800 Planarity : 0.004 0.043 5160 Dihedral : 10.026 133.595 4366 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 4.90 % Allowed : 17.79 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.14), residues: 3792 helix: 1.10 (0.14), residues: 1432 sheet: 0.01 (0.27), residues: 272 loop : -1.43 (0.14), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 231 TYR 0.012 0.001 TYR F 348 PHE 0.007 0.001 PHE A 99 HIS 0.004 0.001 HIS E 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 (30592) covalent geometry : angle 0.54100 / 0.27 (41496) hydrogen bonds : bond 0.03331 / 2.21 ( 1090) hydrogen bonds : angle 4.88578 / 3.43 ( 3078) Misc. bond : bond 0.00096 / 0.06 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 761 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 608 time to evaluate : 1.144 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: A 202 GLN cc_start: 0.8387 (tt0) cc_final: 0.8165 (mm-40) REVERT: A 229 LYS cc_start: 0.8077 (ptpp) cc_final: 0.7776 (ptpp) REVERT: A 231 ARG cc_start: 0.8076 (mtm180) cc_final: 0.7827 (mtm180) REVERT: A 243 GLN cc_start: 0.7948 (mp-120) cc_final: 0.7741 (mp10) REVERT: A 312 ASN cc_start: 0.9263 (m-40) cc_final: 0.8945 (m-40) REVERT: A 441 GLN cc_start: 0.8448 (mt0) cc_final: 0.8211 (mt0) REVERT: A 449 ASP cc_start: 0.7880 (t70) cc_final: 0.7369 (t70) REVERT: A 476 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.9004 (mp) REVERT: B 134 LYS cc_start: 0.7952 (tptt) cc_final: 0.7718 (tppt) REVERT: B 312 ASN cc_start: 0.9266 (m-40) cc_final: 0.8988 (m-40) REVERT: B 395 GLU cc_start: 0.8148 (mp0) cc_final: 0.7847 (mp0) REVERT: B 441 GLN cc_start: 0.8431 (mt0) cc_final: 0.8185 (mt0) REVERT: B 449 ASP cc_start: 0.7935 (t70) cc_final: 0.7452 (t70) REVERT: C 182 ARG cc_start: 0.7063 (mmm-85) cc_final: 0.6506 (mmm160) REVERT: C 202 GLN cc_start: 0.8395 (tt0) cc_final: 0.8189 (mm-40) REVERT: C 243 GLN cc_start: 0.7853 (mp-120) cc_final: 0.7651 (mp10) REVERT: C 286 MET cc_start: 0.8906 (tpp) cc_final: 0.8676 (tpp) REVERT: C 312 ASN cc_start: 0.9249 (m-40) cc_final: 0.8943 (m-40) REVERT: C 441 GLN cc_start: 0.8392 (mt0) cc_final: 0.8149 (mt0) REVERT: C 449 ASP cc_start: 0.7584 (t0) cc_final: 0.7286 (t70) REVERT: D 134 LYS cc_start: 0.7821 (tptt) cc_final: 0.7562 (tppt) REVERT: D 184 GLU cc_start: 0.2020 (OUTLIER) cc_final: 0.0105 (tp30) REVERT: D 312 ASN cc_start: 0.9255 (m-40) cc_final: 0.8931 (m-40) REVERT: D 395 GLU cc_start: 0.8145 (mp0) cc_final: 0.7791 (mp0) REVERT: D 441 GLN cc_start: 0.8460 (mt0) cc_final: 0.8216 (mt0) REVERT: D 449 ASP cc_start: 0.7895 (t70) cc_final: 0.7474 (t70) REVERT: E 243 GLN cc_start: 0.8077 (mp10) cc_final: 0.7219 (mp10) REVERT: E 286 MET cc_start: 0.8954 (tpp) cc_final: 0.8685 (tpp) REVERT: E 312 ASN cc_start: 0.9266 (m-40) cc_final: 0.8964 (m-40) REVERT: E 330 ILE cc_start: 0.9049 (OUTLIER) cc_final: 0.8847 (pp) REVERT: E 395 GLU cc_start: 0.8122 (mp0) cc_final: 0.7812 (mp0) REVERT: E 441 GLN cc_start: 0.8411 (mt0) cc_final: 0.8136 (mt0) REVERT: E 448 GLN cc_start: 0.7646 (tt0) cc_final: 0.7397 (tt0) REVERT: E 449 ASP cc_start: 0.7878 (t70) cc_final: 0.7378 (t0) REVERT: F 184 GLU cc_start: 0.4962 (OUTLIER) cc_final: 0.3926 (tp30) REVERT: F 206 LYS cc_start: 0.8260 (OUTLIER) cc_final: 0.7186 (mtmm) REVERT: F 231 ARG cc_start: 0.8288 (mtm110) cc_final: 0.7974 (mtm180) REVERT: F 243 GLN cc_start: 0.8111 (mp10) cc_final: 0.7868 (mp10) REVERT: F 312 ASN cc_start: 0.9236 (m-40) cc_final: 0.8932 (m-40) REVERT: F 395 GLU cc_start: 0.8114 (mp0) cc_final: 0.7804 (mp0) REVERT: F 400 TYR cc_start: 0.7619 (m-80) cc_final: 0.7178 (m-80) REVERT: F 412 ARG cc_start: 0.8134 (ptt180) cc_final: 0.7906 (ptt180) REVERT: F 441 GLN cc_start: 0.8463 (mt0) cc_final: 0.8187 (mt0) REVERT: F 449 ASP cc_start: 0.7728 (t0) cc_final: 0.7504 (t70) REVERT: F 476 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.8964 (mp) REVERT: G 135 MET cc_start: 0.8299 (mpp) cc_final: 0.7859 (mpp) REVERT: G 179 MET cc_start: 0.3770 (mtt) cc_final: 0.3036 (mpp) REVERT: G 286 MET cc_start: 0.8946 (tpp) cc_final: 0.8709 (tpp) REVERT: G 312 ASN cc_start: 0.9246 (m-40) cc_final: 0.8904 (m-40) REVERT: G 395 GLU cc_start: 0.8148 (mp0) cc_final: 0.7830 (mp0) REVERT: G 412 ARG cc_start: 0.8153 (ptt180) cc_final: 0.7944 (ptt180) REVERT: G 441 GLN cc_start: 0.8412 (mt0) cc_final: 0.8144 (mt0) REVERT: G 449 ASP cc_start: 0.7914 (t70) cc_final: 0.7387 (t70) REVERT: G 455 LYS cc_start: 0.8030 (ptpp) cc_final: 0.7806 (ptpp) REVERT: H 225 THR cc_start: 0.8140 (m) cc_final: 0.7630 (p) REVERT: H 231 ARG cc_start: 0.8766 (ptp90) cc_final: 0.8528 (mtm180) REVERT: H 243 GLN cc_start: 0.7901 (mp-120) cc_final: 0.7196 (mp-120) REVERT: H 312 ASN cc_start: 0.9247 (m-40) cc_final: 0.8931 (m-40) REVERT: H 395 GLU cc_start: 0.8115 (mp0) cc_final: 0.7822 (mp0) REVERT: H 412 ARG cc_start: 0.8129 (ptt180) cc_final: 0.7917 (ptt180) REVERT: H 449 ASP cc_start: 0.7890 (t70) cc_final: 0.7329 (t70) outliers start: 153 outliers final: 123 residues processed: 721 average time/residue: 0.1920 time to fit residues: 221.1018 Evaluate side-chains 728 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 599 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 448 GLN Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 283 GLN Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 93 HIS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 283 GLN Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 452 SER Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 206 LYS Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 283 GLN Chi-restraints excluded: chain D residue 361 ILE Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 448 GLN Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 206 LYS Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 283 GLN Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 361 ILE Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 184 GLU Chi-restraints excluded: chain F residue 206 LYS Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 283 GLN Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 452 SER Chi-restraints excluded: chain F residue 476 LEU Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 147 THR Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 283 GLN Chi-restraints excluded: chain G residue 287 VAL Chi-restraints excluded: chain G residue 361 ILE Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 448 GLN Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 206 LYS Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 283 GLN Chi-restraints excluded: chain H residue 361 ILE Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 448 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 345 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 226 optimal weight: 0.6980 chunk 262 optimal weight: 5.9990 chunk 97 optimal weight: 0.8980 chunk 181 optimal weight: 0.7980 chunk 66 optimal weight: 8.9990 chunk 149 optimal weight: 0.9990 chunk 164 optimal weight: 0.7980 chunk 113 optimal weight: 7.9990 chunk 303 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.153322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.107872 restraints weight = 33812.148| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 2.16 r_work: 0.2884 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 30593 Z= 0.135 Angle : 0.523 8.182 41496 Z= 0.265 Chirality : 0.042 0.149 4800 Planarity : 0.004 0.040 5160 Dihedral : 9.754 119.737 4366 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 4.07 % Allowed : 18.88 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.14), residues: 3792 helix: 1.01 (0.14), residues: 1480 sheet: 0.15 (0.27), residues: 272 loop : -1.33 (0.14), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 231 TYR 0.012 0.001 TYR G 400 PHE 0.015 0.001 PHE F 401 HIS 0.002 0.000 HIS D 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (30592) covalent geometry : angle 0.52348 / 0.27 (41496) hydrogen bonds : bond 0.03037 / 2.02 ( 1090) hydrogen bonds : angle 4.75030 / 3.33 ( 3078) Misc. bond : bond 0.00075 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 741 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 614 time to evaluate : 0.975 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: A 134 LYS cc_start: 0.7786 (tptt) cc_final: 0.7561 (tppt) REVERT: A 202 GLN cc_start: 0.8355 (tt0) cc_final: 0.8105 (mm-40) REVERT: A 225 THR cc_start: 0.8269 (m) cc_final: 0.8039 (m) REVERT: A 231 ARG cc_start: 0.8088 (mtm180) cc_final: 0.7846 (mtm180) REVERT: A 243 GLN cc_start: 0.7931 (mp-120) cc_final: 0.7682 (mp10) REVERT: A 312 ASN cc_start: 0.9235 (m-40) cc_final: 0.8957 (m-40) REVERT: A 449 ASP cc_start: 0.7881 (t70) cc_final: 0.7258 (t70) REVERT: A 455 LYS cc_start: 0.7982 (ptpp) cc_final: 0.7701 (ptpp) REVERT: B 134 LYS cc_start: 0.7845 (tptt) cc_final: 0.7549 (tppt) REVERT: B 206 LYS cc_start: 0.8057 (OUTLIER) cc_final: 0.7491 (mttm) REVERT: B 265 GLN cc_start: 0.8156 (mm-40) cc_final: 0.7914 (mm-40) REVERT: B 286 MET cc_start: 0.8860 (tpp) cc_final: 0.8584 (tpp) REVERT: B 312 ASN cc_start: 0.9237 (m-40) cc_final: 0.8961 (m-40) REVERT: B 337 MET cc_start: 0.8980 (mmm) cc_final: 0.8306 (mtt) REVERT: B 395 GLU cc_start: 0.8142 (mp0) cc_final: 0.7844 (mp0) REVERT: B 441 GLN cc_start: 0.8370 (mt0) cc_final: 0.7814 (mt0) REVERT: B 449 ASP cc_start: 0.7957 (t70) cc_final: 0.7734 (t0) REVERT: C 135 MET cc_start: 0.8297 (mpp) cc_final: 0.7841 (mpp) REVERT: C 182 ARG cc_start: 0.6972 (mmm-85) cc_final: 0.6570 (mmm160) REVERT: C 184 GLU cc_start: 0.4750 (OUTLIER) cc_final: 0.4220 (tp30) REVERT: C 202 GLN cc_start: 0.8381 (tt0) cc_final: 0.8004 (mt0) REVERT: C 206 LYS cc_start: 0.8128 (OUTLIER) cc_final: 0.7676 (mttm) REVERT: C 243 GLN cc_start: 0.7742 (mp-120) cc_final: 0.7505 (mp10) REVERT: C 286 MET cc_start: 0.8880 (tpp) cc_final: 0.8630 (tpp) REVERT: C 312 ASN cc_start: 0.9224 (m-40) cc_final: 0.8924 (m-40) REVERT: C 449 ASP cc_start: 0.7596 (t0) cc_final: 0.7331 (t70) REVERT: D 114 PHE cc_start: 0.8299 (m-10) cc_final: 0.8066 (m-10) REVERT: D 161 ARG cc_start: 0.8447 (mtt180) cc_final: 0.7970 (mtt180) REVERT: D 184 GLU cc_start: 0.1829 (OUTLIER) cc_final: 0.0130 (tp30) REVERT: D 312 ASN cc_start: 0.9235 (m-40) cc_final: 0.8936 (m-40) REVERT: D 395 GLU cc_start: 0.8145 (mp0) cc_final: 0.7799 (mp0) REVERT: D 449 ASP cc_start: 0.7917 (t70) cc_final: 0.7416 (t70) REVERT: E 134 LYS cc_start: 0.7885 (tppt) cc_final: 0.7533 (tppt) REVERT: E 205 LYS cc_start: 0.8801 (mmtp) cc_final: 0.8239 (mmtp) REVERT: E 206 LYS cc_start: 0.8120 (OUTLIER) cc_final: 0.7283 (mttm) REVERT: E 243 GLN cc_start: 0.8037 (mp10) cc_final: 0.7254 (mp10) REVERT: E 312 ASN cc_start: 0.9241 (m-40) cc_final: 0.8948 (m-40) REVERT: E 395 GLU cc_start: 0.8116 (mp0) cc_final: 0.7811 (mp0) REVERT: E 441 GLN cc_start: 0.8394 (mt0) cc_final: 0.8177 (mt0) REVERT: E 448 GLN cc_start: 0.7635 (tt0) cc_final: 0.7398 (tt0) REVERT: E 449 ASP cc_start: 0.7887 (t70) cc_final: 0.7377 (t0) REVERT: F 184 GLU cc_start: 0.4838 (OUTLIER) cc_final: 0.3919 (tp30) REVERT: F 206 LYS cc_start: 0.8268 (OUTLIER) cc_final: 0.7197 (mtmm) REVERT: F 231 ARG cc_start: 0.8282 (mtm110) cc_final: 0.7962 (mtm180) REVERT: F 243 GLN cc_start: 0.8073 (mp10) cc_final: 0.7825 (mp10) REVERT: F 312 ASN cc_start: 0.9218 (m-40) cc_final: 0.8904 (m-40) REVERT: F 395 GLU cc_start: 0.8099 (mp0) cc_final: 0.7776 (mp0) REVERT: F 400 TYR cc_start: 0.7586 (m-80) cc_final: 0.7154 (m-80) REVERT: F 441 GLN cc_start: 0.8422 (mt0) cc_final: 0.8143 (mt0) REVERT: F 449 ASP cc_start: 0.7689 (t0) cc_final: 0.7445 (t70) REVERT: G 135 MET cc_start: 0.8301 (OUTLIER) cc_final: 0.7984 (mpp) REVERT: G 179 MET cc_start: 0.3744 (mtt) cc_final: 0.3077 (mpp) REVERT: G 243 GLN cc_start: 0.7874 (mp10) cc_final: 0.7625 (mp-120) REVERT: G 277 GLN cc_start: 0.9247 (OUTLIER) cc_final: 0.7573 (tm-30) REVERT: G 286 MET cc_start: 0.8905 (tpp) cc_final: 0.8646 (tpp) REVERT: G 312 ASN cc_start: 0.9225 (m-40) cc_final: 0.8908 (m-40) REVERT: G 395 GLU cc_start: 0.8144 (mp0) cc_final: 0.7828 (mp0) REVERT: G 441 GLN cc_start: 0.8390 (mt0) cc_final: 0.8190 (mt0) REVERT: G 449 ASP cc_start: 0.7874 (t70) cc_final: 0.7464 (t70) REVERT: G 455 LYS cc_start: 0.7988 (ptpp) cc_final: 0.7787 (ptpp) REVERT: H 202 GLN cc_start: 0.8291 (tt0) cc_final: 0.8001 (mm-40) REVERT: H 206 LYS cc_start: 0.7897 (OUTLIER) cc_final: 0.7660 (mttm) REVERT: H 225 THR cc_start: 0.7988 (m) cc_final: 0.7571 (p) REVERT: H 231 ARG cc_start: 0.8788 (ptp90) cc_final: 0.8535 (mtm180) REVERT: H 243 GLN cc_start: 0.7736 (mp-120) cc_final: 0.7010 (mp-120) REVERT: H 286 MET cc_start: 0.8903 (tpp) cc_final: 0.8687 (tpp) REVERT: H 312 ASN cc_start: 0.9231 (m-40) cc_final: 0.8931 (m-40) REVERT: H 337 MET cc_start: 0.8749 (mmm) cc_final: 0.8337 (mtt) REVERT: H 395 GLU cc_start: 0.8107 (mp0) cc_final: 0.7807 (mp0) REVERT: H 400 TYR cc_start: 0.7618 (m-80) cc_final: 0.6891 (m-80) REVERT: H 449 ASP cc_start: 0.7896 (t70) cc_final: 0.7249 (t70) outliers start: 127 outliers final: 105 residues processed: 706 average time/residue: 0.1936 time to fit residues: 216.7532 Evaluate side-chains 718 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 603 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 448 GLN Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 283 GLN Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 93 HIS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 184 GLU Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 283 GLN Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 452 SER Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 206 LYS Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 283 GLN Chi-restraints excluded: chain D residue 361 ILE Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 206 LYS Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 283 GLN Chi-restraints excluded: chain E residue 361 ILE Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 184 GLU Chi-restraints excluded: chain F residue 206 LYS Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 283 GLN Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 452 SER Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 135 MET Chi-restraints excluded: chain G residue 147 THR Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 287 VAL Chi-restraints excluded: chain G residue 361 ILE Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 448 GLN Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 206 LYS Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 283 GLN Chi-restraints excluded: chain H residue 361 ILE Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 448 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 292 optimal weight: 3.9990 chunk 343 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 282 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 106 optimal weight: 0.6980 chunk 68 optimal weight: 4.9990 chunk 279 optimal weight: 5.9990 chunk 380 optimal weight: 3.9990 chunk 313 optimal weight: 0.5980 chunk 145 optimal weight: 0.1980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 441 GLN ** C 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.153690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.106289 restraints weight = 33682.508| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 1.95 r_work: 0.2864 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 30593 Z= 0.159 Angle : 0.537 8.046 41496 Z= 0.272 Chirality : 0.043 0.151 4800 Planarity : 0.004 0.045 5160 Dihedral : 9.637 111.382 4365 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 4.13 % Allowed : 19.62 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.14), residues: 3792 helix: 1.03 (0.14), residues: 1480 sheet: 0.13 (0.27), residues: 272 loop : -1.27 (0.14), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 231 TYR 0.012 0.001 TYR G 400 PHE 0.006 0.001 PHE E 99 HIS 0.002 0.001 HIS E 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 (30592) covalent geometry : angle 0.53746 / 0.27 (41496) hydrogen bonds : bond 0.03176 / 2.11 ( 1090) hydrogen bonds : angle 4.76593 / 3.34 ( 3078) Misc. bond : bond 0.00096 / 0.06 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 735 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 606 time to evaluate : 1.108 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: A 134 LYS cc_start: 0.7798 (tptt) cc_final: 0.7577 (tppt) REVERT: A 225 THR cc_start: 0.8269 (m) cc_final: 0.8051 (m) REVERT: A 231 ARG cc_start: 0.8097 (mtm180) cc_final: 0.7875 (mtm180) REVERT: A 243 GLN cc_start: 0.7970 (mp-120) cc_final: 0.7675 (mp-120) REVERT: A 286 MET cc_start: 0.8891 (tpp) cc_final: 0.8658 (tpp) REVERT: A 312 ASN cc_start: 0.9249 (m-40) cc_final: 0.8929 (m-40) REVERT: A 449 ASP cc_start: 0.7879 (t70) cc_final: 0.7372 (t70) REVERT: A 455 LYS cc_start: 0.8015 (ptpp) cc_final: 0.7736 (ptpp) REVERT: A 470 ASP cc_start: 0.8970 (m-30) cc_final: 0.8718 (m-30) REVERT: A 476 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.8996 (mp) REVERT: B 134 LYS cc_start: 0.7882 (tptt) cc_final: 0.7611 (tppt) REVERT: B 243 GLN cc_start: 0.7932 (mp10) cc_final: 0.7703 (mp-120) REVERT: B 265 GLN cc_start: 0.8162 (mm-40) cc_final: 0.7906 (mm-40) REVERT: B 286 MET cc_start: 0.8920 (tpp) cc_final: 0.8625 (tpp) REVERT: B 312 ASN cc_start: 0.9257 (m-40) cc_final: 0.8956 (m-40) REVERT: B 395 GLU cc_start: 0.8165 (mp0) cc_final: 0.7875 (mp0) REVERT: B 441 GLN cc_start: 0.8393 (mt0) cc_final: 0.8154 (mt0) REVERT: B 449 ASP cc_start: 0.7944 (t70) cc_final: 0.7479 (t70) REVERT: C 182 ARG cc_start: 0.6995 (mmm-85) cc_final: 0.6570 (mmm160) REVERT: C 184 GLU cc_start: 0.4820 (OUTLIER) cc_final: 0.4258 (tp30) REVERT: C 202 GLN cc_start: 0.8399 (tt0) cc_final: 0.7984 (mt0) REVERT: C 243 GLN cc_start: 0.7795 (mp-120) cc_final: 0.7126 (mp10) REVERT: C 286 MET cc_start: 0.8927 (tpp) cc_final: 0.8659 (tpp) REVERT: C 312 ASN cc_start: 0.9244 (m-40) cc_final: 0.8944 (m-40) REVERT: C 449 ASP cc_start: 0.7654 (t0) cc_final: 0.7383 (t70) REVERT: D 16 ASP cc_start: 0.8234 (m-30) cc_final: 0.7977 (m-30) REVERT: D 184 GLU cc_start: 0.1889 (OUTLIER) cc_final: 0.0181 (tp30) REVERT: D 206 LYS cc_start: 0.7829 (OUTLIER) cc_final: 0.7422 (mttm) REVERT: D 243 GLN cc_start: 0.7904 (mp10) cc_final: 0.7680 (mp-120) REVERT: D 312 ASN cc_start: 0.9245 (m-40) cc_final: 0.8958 (m-40) REVERT: D 395 GLU cc_start: 0.8175 (mp0) cc_final: 0.7829 (mp0) REVERT: D 438 LYS cc_start: 0.8488 (mmmt) cc_final: 0.8125 (mmmm) REVERT: D 449 ASP cc_start: 0.7912 (t70) cc_final: 0.7499 (t70) REVERT: E 134 LYS cc_start: 0.7909 (tppt) cc_final: 0.7634 (tppt) REVERT: E 205 LYS cc_start: 0.8840 (mmtp) cc_final: 0.8336 (mmtp) REVERT: E 206 LYS cc_start: 0.8065 (OUTLIER) cc_final: 0.7561 (mttm) REVERT: E 243 GLN cc_start: 0.8064 (mp10) cc_final: 0.7297 (mp10) REVERT: E 312 ASN cc_start: 0.9260 (m-40) cc_final: 0.8954 (m-40) REVERT: E 395 GLU cc_start: 0.8142 (mp0) cc_final: 0.7844 (mp0) REVERT: E 448 GLN cc_start: 0.7673 (tt0) cc_final: 0.7437 (tt0) REVERT: F 184 GLU cc_start: 0.4934 (OUTLIER) cc_final: 0.3949 (tp30) REVERT: F 202 GLN cc_start: 0.8406 (tt0) cc_final: 0.8098 (mm-40) REVERT: F 206 LYS cc_start: 0.8206 (OUTLIER) cc_final: 0.7206 (mtmm) REVERT: F 231 ARG cc_start: 0.8273 (mtm110) cc_final: 0.7963 (mtm180) REVERT: F 243 GLN cc_start: 0.8090 (mp10) cc_final: 0.7837 (mp10) REVERT: F 312 ASN cc_start: 0.9230 (m-40) cc_final: 0.8910 (m-40) REVERT: F 395 GLU cc_start: 0.8126 (mp0) cc_final: 0.7806 (mp0) REVERT: F 441 GLN cc_start: 0.8405 (mt0) cc_final: 0.8143 (mt0) REVERT: F 449 ASP cc_start: 0.7699 (t0) cc_final: 0.7454 (t70) REVERT: F 476 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.8984 (mp) REVERT: G 135 MET cc_start: 0.8313 (OUTLIER) cc_final: 0.8000 (mpp) REVERT: G 179 MET cc_start: 0.3811 (mtt) cc_final: 0.3173 (mpp) REVERT: G 286 MET cc_start: 0.8941 (tpp) cc_final: 0.8690 (tpp) REVERT: G 312 ASN cc_start: 0.9240 (m-40) cc_final: 0.8937 (m-40) REVERT: G 395 GLU cc_start: 0.8180 (mp0) cc_final: 0.7866 (mp0) REVERT: G 449 ASP cc_start: 0.7902 (t70) cc_final: 0.7498 (t70) REVERT: H 16 ASP cc_start: 0.8229 (m-30) cc_final: 0.7983 (m-30) REVERT: H 202 GLN cc_start: 0.8310 (tt0) cc_final: 0.8015 (mm-40) REVERT: H 206 LYS cc_start: 0.7898 (OUTLIER) cc_final: 0.7509 (mttm) REVERT: H 225 THR cc_start: 0.8036 (m) cc_final: 0.7597 (p) REVERT: H 231 ARG cc_start: 0.8769 (ptp90) cc_final: 0.8481 (mtm180) REVERT: H 243 GLN cc_start: 0.7769 (mp-120) cc_final: 0.7075 (mp-120) REVERT: H 312 ASN cc_start: 0.9251 (m-40) cc_final: 0.8943 (m-40) REVERT: H 337 MET cc_start: 0.8807 (mmm) cc_final: 0.8320 (mtt) REVERT: H 395 GLU cc_start: 0.8127 (mp0) cc_final: 0.7840 (mp0) REVERT: H 449 ASP cc_start: 0.7917 (t70) cc_final: 0.7292 (t70) outliers start: 129 outliers final: 111 residues processed: 701 average time/residue: 0.1855 time to fit residues: 206.4871 Evaluate side-chains 711 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 590 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 448 GLN Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 283 GLN Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 93 HIS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 184 GLU Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 283 GLN Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 452 SER Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 206 LYS Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 283 GLN Chi-restraints excluded: chain D residue 361 ILE Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 448 GLN Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 206 LYS Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 283 GLN Chi-restraints excluded: chain E residue 361 ILE Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 452 SER Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 184 GLU Chi-restraints excluded: chain F residue 206 LYS Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 283 GLN Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 452 SER Chi-restraints excluded: chain F residue 476 LEU Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 135 MET Chi-restraints excluded: chain G residue 147 THR Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 287 VAL Chi-restraints excluded: chain G residue 361 ILE Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 448 GLN Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 206 LYS Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 283 GLN Chi-restraints excluded: chain H residue 361 ILE Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 448 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 137 optimal weight: 10.0000 chunk 380 optimal weight: 3.9990 chunk 260 optimal weight: 7.9990 chunk 334 optimal weight: 1.9990 chunk 305 optimal weight: 9.9990 chunk 117 optimal weight: 0.0270 chunk 161 optimal weight: 0.3980 chunk 344 optimal weight: 2.9990 chunk 343 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 317 optimal weight: 1.9990 overall best weight: 1.0242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.154790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.107774 restraints weight = 33761.235| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 1.96 r_work: 0.2867 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2726 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 30593 Z= 0.154 Angle : 0.537 8.035 41496 Z= 0.272 Chirality : 0.043 0.148 4800 Planarity : 0.004 0.049 5160 Dihedral : 9.447 104.332 4357 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 4.20 % Allowed : 19.87 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.14), residues: 3792 helix: 1.06 (0.14), residues: 1472 sheet: -0.61 (0.25), residues: 352 loop : -1.30 (0.14), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 231 TYR 0.012 0.001 TYR F 400 PHE 0.015 0.001 PHE H 401 HIS 0.002 0.001 HIS E 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 (30592) covalent geometry : angle 0.53740 / 0.27 (41496) hydrogen bonds : bond 0.03139 / 2.09 ( 1090) hydrogen bonds : angle 4.75282 / 3.33 ( 3078) Misc. bond : bond 0.00092 / 0.06 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 733 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 602 time to evaluate : 1.137 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: A 134 LYS cc_start: 0.7749 (tptt) cc_final: 0.7529 (tppt) REVERT: A 231 ARG cc_start: 0.8106 (mtm180) cc_final: 0.7882 (mtm180) REVERT: A 243 GLN cc_start: 0.7975 (mp-120) cc_final: 0.7664 (mp-120) REVERT: A 286 MET cc_start: 0.8868 (tpp) cc_final: 0.8624 (tpp) REVERT: A 312 ASN cc_start: 0.9245 (m-40) cc_final: 0.8923 (m-40) REVERT: A 420 MET cc_start: 0.6933 (mtt) cc_final: 0.6570 (mtt) REVERT: A 449 ASP cc_start: 0.7872 (t70) cc_final: 0.7287 (t70) REVERT: A 455 LYS cc_start: 0.8012 (ptpp) cc_final: 0.7749 (ptpp) REVERT: A 470 ASP cc_start: 0.8976 (m-30) cc_final: 0.8728 (m-30) REVERT: A 476 LEU cc_start: 0.9245 (OUTLIER) cc_final: 0.9037 (mt) REVERT: B 134 LYS cc_start: 0.7878 (tptt) cc_final: 0.7591 (tppt) REVERT: B 265 GLN cc_start: 0.8247 (mm-40) cc_final: 0.8023 (mm-40) REVERT: B 312 ASN cc_start: 0.9255 (m-40) cc_final: 0.8950 (m-40) REVERT: B 395 GLU cc_start: 0.8173 (mp0) cc_final: 0.7870 (mp0) REVERT: B 421 GLU cc_start: 0.7260 (mt-10) cc_final: 0.6957 (mt-10) REVERT: B 441 GLN cc_start: 0.8365 (mt0) cc_final: 0.8119 (mt0) REVERT: B 449 ASP cc_start: 0.7941 (t70) cc_final: 0.7422 (t70) REVERT: C 135 MET cc_start: 0.8276 (OUTLIER) cc_final: 0.7907 (mpp) REVERT: C 182 ARG cc_start: 0.6990 (mmm-85) cc_final: 0.6440 (mmm160) REVERT: C 243 GLN cc_start: 0.7770 (mp-120) cc_final: 0.7108 (mp10) REVERT: C 286 MET cc_start: 0.8916 (tpp) cc_final: 0.8648 (tpp) REVERT: C 312 ASN cc_start: 0.9245 (m-40) cc_final: 0.8943 (m-40) REVERT: C 449 ASP cc_start: 0.7647 (t0) cc_final: 0.7372 (t70) REVERT: D 184 GLU cc_start: 0.2156 (OUTLIER) cc_final: 0.0196 (tp30) REVERT: D 286 MET cc_start: 0.8966 (tpp) cc_final: 0.8696 (tpp) REVERT: D 312 ASN cc_start: 0.9245 (m-40) cc_final: 0.8960 (m-40) REVERT: D 395 GLU cc_start: 0.8167 (mp0) cc_final: 0.7822 (mp0) REVERT: D 421 GLU cc_start: 0.7340 (mm-30) cc_final: 0.7069 (pt0) REVERT: D 438 LYS cc_start: 0.8485 (mmmt) cc_final: 0.8114 (mmmm) REVERT: D 449 ASP cc_start: 0.7929 (t70) cc_final: 0.7483 (t70) REVERT: E 134 LYS cc_start: 0.7804 (tppt) cc_final: 0.7513 (tppt) REVERT: E 205 LYS cc_start: 0.8862 (mmtp) cc_final: 0.8390 (mmtp) REVERT: E 312 ASN cc_start: 0.9265 (m-40) cc_final: 0.8979 (m-40) REVERT: E 395 GLU cc_start: 0.8152 (mp0) cc_final: 0.7851 (mp0) REVERT: E 448 GLN cc_start: 0.7686 (tt0) cc_final: 0.7449 (tt0) REVERT: F 184 GLU cc_start: 0.4942 (OUTLIER) cc_final: 0.4167 (tp30) REVERT: F 206 LYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7175 (mtmm) REVERT: F 231 ARG cc_start: 0.8251 (mtm110) cc_final: 0.7937 (mtm180) REVERT: F 243 GLN cc_start: 0.8083 (mp10) cc_final: 0.7823 (mp10) REVERT: F 312 ASN cc_start: 0.9232 (m-40) cc_final: 0.8908 (m-40) REVERT: F 395 GLU cc_start: 0.8131 (mp0) cc_final: 0.7806 (mp0) REVERT: F 441 GLN cc_start: 0.8376 (mt0) cc_final: 0.8110 (mt0) REVERT: F 476 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.9033 (mt) REVERT: G 135 MET cc_start: 0.8351 (OUTLIER) cc_final: 0.8028 (mpp) REVERT: G 179 MET cc_start: 0.3740 (mtt) cc_final: 0.3156 (mpp) REVERT: G 243 GLN cc_start: 0.7930 (mp10) cc_final: 0.7718 (mp-120) REVERT: G 286 MET cc_start: 0.8929 (tpp) cc_final: 0.8677 (tpp) REVERT: G 312 ASN cc_start: 0.9240 (m-40) cc_final: 0.8938 (m-40) REVERT: G 395 GLU cc_start: 0.8176 (mp0) cc_final: 0.7852 (mp0) REVERT: G 449 ASP cc_start: 0.7917 (t70) cc_final: 0.7512 (t70) REVERT: H 202 GLN cc_start: 0.8300 (tt0) cc_final: 0.8065 (mm-40) REVERT: H 206 LYS cc_start: 0.7735 (OUTLIER) cc_final: 0.7362 (mttm) REVERT: H 225 THR cc_start: 0.7998 (m) cc_final: 0.7572 (p) REVERT: H 231 ARG cc_start: 0.8780 (ptp90) cc_final: 0.8492 (mtm180) REVERT: H 243 GLN cc_start: 0.7762 (mp-120) cc_final: 0.7114 (mp-120) REVERT: H 286 MET cc_start: 0.8929 (tpp) cc_final: 0.8684 (tpp) REVERT: H 312 ASN cc_start: 0.9252 (m-40) cc_final: 0.8965 (m-40) REVERT: H 337 MET cc_start: 0.8857 (mmm) cc_final: 0.8364 (mtt) REVERT: H 395 GLU cc_start: 0.8132 (mp0) cc_final: 0.7834 (mp0) REVERT: H 449 ASP cc_start: 0.7914 (t70) cc_final: 0.7408 (t0) outliers start: 131 outliers final: 119 residues processed: 696 average time/residue: 0.1951 time to fit residues: 215.8374 Evaluate side-chains 717 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 590 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 448 GLN Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 283 GLN Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 93 HIS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 135 MET Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 283 GLN Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 452 SER Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 283 GLN Chi-restraints excluded: chain D residue 361 ILE Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 448 GLN Chi-restraints excluded: chain D residue 452 SER Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 206 LYS Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 283 GLN Chi-restraints excluded: chain E residue 361 ILE Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 452 SER Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 184 GLU Chi-restraints excluded: chain F residue 206 LYS Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 283 GLN Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 452 SER Chi-restraints excluded: chain F residue 476 LEU Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 135 MET Chi-restraints excluded: chain G residue 147 THR Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 287 VAL Chi-restraints excluded: chain G residue 361 ILE Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 448 GLN Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 160 SER Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 206 LYS Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 283 GLN Chi-restraints excluded: chain H residue 361 ILE Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 448 GLN Chi-restraints excluded: chain H residue 452 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 164 optimal weight: 5.9990 chunk 155 optimal weight: 6.9990 chunk 180 optimal weight: 0.0060 chunk 377 optimal weight: 9.9990 chunk 216 optimal weight: 0.7980 chunk 166 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 63 optimal weight: 0.0870 chunk 261 optimal weight: 2.9990 chunk 363 optimal weight: 0.0070 chunk 223 optimal weight: 0.8980 overall best weight: 0.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 HIS B 93 HIS C 441 GLN D 93 HIS D 441 GLN E 441 GLN G 93 HIS ** G 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.156746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.111628 restraints weight = 33611.098| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 2.12 r_work: 0.2940 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 30593 Z= 0.098 Angle : 0.508 7.989 41496 Z= 0.256 Chirality : 0.042 0.147 4800 Planarity : 0.004 0.035 5160 Dihedral : 9.094 85.594 4353 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 3.24 % Allowed : 20.74 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.14), residues: 3792 helix: 1.17 (0.14), residues: 1472 sheet: -0.54 (0.25), residues: 368 loop : -1.25 (0.15), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 203 TYR 0.011 0.001 TYR F 353 PHE 0.006 0.001 PHE A 24 HIS 0.002 0.000 HIS D 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 (30592) covalent geometry : angle 0.50846 / 0.26 (41496) hydrogen bonds : bond 0.02715 / 1.81 ( 1090) hydrogen bonds : angle 4.58671 / 3.21 ( 3078) Misc. bond : bond 0.00047 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 738 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 637 time to evaluate : 1.095 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: A 47 ASP cc_start: 0.8643 (m-30) cc_final: 0.8219 (m-30) REVERT: A 134 LYS cc_start: 0.7733 (tptt) cc_final: 0.7495 (tppt) REVERT: A 206 LYS cc_start: 0.7960 (OUTLIER) cc_final: 0.7438 (mttm) REVERT: A 231 ARG cc_start: 0.8106 (mtm180) cc_final: 0.7884 (mtm180) REVERT: A 277 GLN cc_start: 0.9174 (OUTLIER) cc_final: 0.8033 (tm-30) REVERT: A 312 ASN cc_start: 0.9176 (m-40) cc_final: 0.8885 (m-40) REVERT: A 337 MET cc_start: 0.8759 (mmm) cc_final: 0.8317 (mtt) REVERT: A 420 MET cc_start: 0.6814 (mtt) cc_final: 0.6286 (mtt) REVERT: A 441 GLN cc_start: 0.8083 (mt0) cc_final: 0.7708 (mt0) REVERT: A 449 ASP cc_start: 0.7776 (t70) cc_final: 0.7342 (t70) REVERT: A 455 LYS cc_start: 0.7958 (ptpp) cc_final: 0.7711 (ptpp) REVERT: B 103 GLU cc_start: 0.8633 (tp30) cc_final: 0.8423 (mm-30) REVERT: B 134 LYS cc_start: 0.7852 (tptt) cc_final: 0.7540 (tppt) REVERT: B 205 LYS cc_start: 0.8849 (mmtp) cc_final: 0.8594 (mmtp) REVERT: B 277 GLN cc_start: 0.9181 (OUTLIER) cc_final: 0.8018 (tm-30) REVERT: B 312 ASN cc_start: 0.9174 (m-40) cc_final: 0.8906 (m-40) REVERT: B 395 GLU cc_start: 0.8158 (mp0) cc_final: 0.7901 (mp0) REVERT: B 400 TYR cc_start: 0.7680 (m-80) cc_final: 0.7004 (m-80) REVERT: B 449 ASP cc_start: 0.7930 (t70) cc_final: 0.7467 (t70) REVERT: C 135 MET cc_start: 0.8304 (OUTLIER) cc_final: 0.7931 (mpp) REVERT: C 182 ARG cc_start: 0.6965 (mmm-85) cc_final: 0.6564 (mmm160) REVERT: C 184 GLU cc_start: 0.4792 (OUTLIER) cc_final: 0.4347 (tp30) REVERT: C 243 GLN cc_start: 0.7774 (mp-120) cc_final: 0.7130 (mp10) REVERT: C 277 GLN cc_start: 0.9187 (OUTLIER) cc_final: 0.7961 (tm-30) REVERT: C 286 MET cc_start: 0.8894 (tpp) cc_final: 0.8552 (tpp) REVERT: C 312 ASN cc_start: 0.9164 (m-40) cc_final: 0.8897 (m-40) REVERT: C 441 GLN cc_start: 0.8099 (mt0) cc_final: 0.7869 (mt0) REVERT: C 449 ASP cc_start: 0.7631 (t0) cc_final: 0.7431 (t70) REVERT: D 103 GLU cc_start: 0.8644 (tp30) cc_final: 0.8434 (mm-30) REVERT: D 134 LYS cc_start: 0.7835 (tptt) cc_final: 0.7573 (tppt) REVERT: D 184 GLU cc_start: 0.1869 (OUTLIER) cc_final: 0.0705 (mm-30) REVERT: D 205 LYS cc_start: 0.8852 (mmtp) cc_final: 0.8600 (mmtp) REVERT: D 277 GLN cc_start: 0.9171 (OUTLIER) cc_final: 0.7937 (tm-30) REVERT: D 286 MET cc_start: 0.8941 (tpp) cc_final: 0.8660 (tpp) REVERT: D 312 ASN cc_start: 0.9161 (m-40) cc_final: 0.8865 (m-40) REVERT: D 395 GLU cc_start: 0.8167 (mp0) cc_final: 0.7872 (mp0) REVERT: D 421 GLU cc_start: 0.7407 (mm-30) cc_final: 0.7110 (pt0) REVERT: D 438 LYS cc_start: 0.8479 (mmmt) cc_final: 0.8101 (mmmm) REVERT: D 441 GLN cc_start: 0.8032 (mt0) cc_final: 0.7757 (mt0) REVERT: D 449 ASP cc_start: 0.7759 (t70) cc_final: 0.7396 (t70) REVERT: E 134 LYS cc_start: 0.7845 (tppt) cc_final: 0.7558 (tppt) REVERT: E 205 LYS cc_start: 0.8850 (mmtp) cc_final: 0.8321 (mmtp) REVERT: E 206 LYS cc_start: 0.7924 (OUTLIER) cc_final: 0.7633 (mttm) REVERT: E 277 GLN cc_start: 0.9145 (OUTLIER) cc_final: 0.7865 (tm-30) REVERT: E 286 MET cc_start: 0.8889 (tpp) cc_final: 0.8602 (tpp) REVERT: E 312 ASN cc_start: 0.9195 (m-40) cc_final: 0.8936 (m-40) REVERT: E 395 GLU cc_start: 0.8124 (mp0) cc_final: 0.7854 (mp0) REVERT: E 441 GLN cc_start: 0.8139 (mt0) cc_final: 0.7740 (mt0) REVERT: E 448 GLN cc_start: 0.7649 (tt0) cc_final: 0.7437 (tt0) REVERT: F 103 GLU cc_start: 0.8637 (tp30) cc_final: 0.8412 (mm-30) REVERT: F 184 GLU cc_start: 0.5175 (OUTLIER) cc_final: 0.4181 (tp30) REVERT: F 202 GLN cc_start: 0.8310 (tt0) cc_final: 0.7968 (mm-40) REVERT: F 231 ARG cc_start: 0.8244 (mtm110) cc_final: 0.7938 (mtm180) REVERT: F 243 GLN cc_start: 0.8077 (mp10) cc_final: 0.7811 (mp10) REVERT: F 277 GLN cc_start: 0.9160 (OUTLIER) cc_final: 0.7779 (tm-30) REVERT: F 312 ASN cc_start: 0.9173 (m-40) cc_final: 0.8898 (m-40) REVERT: F 395 GLU cc_start: 0.8153 (mp0) cc_final: 0.7886 (mp0) REVERT: G 103 GLU cc_start: 0.8595 (tp30) cc_final: 0.8377 (mm-30) REVERT: G 135 MET cc_start: 0.8344 (OUTLIER) cc_final: 0.8019 (mpp) REVERT: G 179 MET cc_start: 0.3603 (mtt) cc_final: 0.3156 (mpp) REVERT: G 205 LYS cc_start: 0.8822 (mmtp) cc_final: 0.8609 (mmtp) REVERT: G 277 GLN cc_start: 0.9192 (OUTLIER) cc_final: 0.8166 (tm-30) REVERT: G 286 MET cc_start: 0.8923 (tpp) cc_final: 0.8609 (tpp) REVERT: G 312 ASN cc_start: 0.9160 (m-40) cc_final: 0.8854 (m-40) REVERT: G 395 GLU cc_start: 0.8175 (mp0) cc_final: 0.7901 (mp0) REVERT: G 400 TYR cc_start: 0.7726 (m-80) cc_final: 0.7137 (m-80) REVERT: G 441 GLN cc_start: 0.8085 (mt0) cc_final: 0.7759 (mt0) REVERT: G 449 ASP cc_start: 0.7816 (t70) cc_final: 0.7441 (t70) REVERT: H 103 GLU cc_start: 0.8617 (tp30) cc_final: 0.8410 (mm-30) REVERT: H 202 GLN cc_start: 0.8274 (tt0) cc_final: 0.8041 (mm-40) REVERT: H 225 THR cc_start: 0.7950 (m) cc_final: 0.7507 (p) REVERT: H 231 ARG cc_start: 0.8802 (ptp90) cc_final: 0.8490 (mtm180) REVERT: H 243 GLN cc_start: 0.7755 (mp-120) cc_final: 0.7087 (mp10) REVERT: H 277 GLN cc_start: 0.9171 (OUTLIER) cc_final: 0.7955 (tm-30) REVERT: H 286 MET cc_start: 0.8901 (tpp) cc_final: 0.8657 (tpp) REVERT: H 312 ASN cc_start: 0.9197 (m-40) cc_final: 0.8919 (m-40) REVERT: H 337 MET cc_start: 0.8730 (mmm) cc_final: 0.8291 (mtt) REVERT: H 395 GLU cc_start: 0.8123 (mp0) cc_final: 0.7870 (mp0) REVERT: H 400 TYR cc_start: 0.7679 (m-80) cc_final: 0.7066 (m-80) REVERT: H 449 ASP cc_start: 0.7855 (t70) cc_final: 0.7352 (t70) outliers start: 101 outliers final: 75 residues processed: 709 average time/residue: 0.1901 time to fit residues: 216.4745 Evaluate side-chains 708 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 618 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 93 HIS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 283 GLN Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 93 HIS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 135 MET Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 184 GLU Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 283 GLN Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 93 HIS Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 283 GLN Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 206 LYS Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 283 GLN Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 184 GLU Chi-restraints excluded: chain F residue 206 LYS Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 283 GLN Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 93 HIS Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 135 MET Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 287 VAL Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 448 GLN Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 283 GLN Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 448 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 143 optimal weight: 0.0370 chunk 20 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 167 optimal weight: 4.9990 chunk 363 optimal weight: 0.4980 chunk 300 optimal weight: 9.9990 chunk 134 optimal weight: 7.9990 chunk 130 optimal weight: 2.9990 chunk 259 optimal weight: 0.9990 chunk 118 optimal weight: 0.8980 chunk 172 optimal weight: 0.0970 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 HIS B 93 HIS ** B 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 93 HIS E 198 ASN F 198 ASN ** F 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 93 HIS ** G 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.157327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.111600 restraints weight = 33377.498| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 2.32 r_work: 0.2915 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 30593 Z= 0.109 Angle : 0.518 8.043 41496 Z= 0.262 Chirality : 0.042 0.149 4800 Planarity : 0.003 0.031 5160 Dihedral : 8.932 83.818 4345 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 3.11 % Allowed : 20.90 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.14), residues: 3792 helix: 1.39 (0.14), residues: 1424 sheet: -0.55 (0.25), residues: 368 loop : -1.18 (0.14), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 412 TYR 0.012 0.001 TYR F 400 PHE 0.031 0.001 PHE C 99 HIS 0.005 0.000 HIS B 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (30592) covalent geometry : angle 0.51776 / 0.26 (41496) hydrogen bonds : bond 0.02783 / 1.86 ( 1090) hydrogen bonds : angle 4.59943 / 3.22 ( 3078) Misc. bond : bond 0.00069 / 0.04 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 718 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 621 time to evaluate : 1.080 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: A 134 LYS cc_start: 0.7740 (tptt) cc_final: 0.7532 (tppt) REVERT: A 206 LYS cc_start: 0.7920 (OUTLIER) cc_final: 0.7238 (mtmm) REVERT: A 225 THR cc_start: 0.8109 (m) cc_final: 0.7655 (p) REVERT: A 231 ARG cc_start: 0.8130 (mtm180) cc_final: 0.7912 (mtm180) REVERT: A 243 GLN cc_start: 0.7972 (mp-120) cc_final: 0.7619 (mp-120) REVERT: A 277 GLN cc_start: 0.9181 (OUTLIER) cc_final: 0.8142 (tm-30) REVERT: A 312 ASN cc_start: 0.9185 (m-40) cc_final: 0.8893 (m-40) REVERT: A 337 MET cc_start: 0.8806 (mmm) cc_final: 0.8358 (mtt) REVERT: A 420 MET cc_start: 0.6845 (mtt) cc_final: 0.6316 (mtt) REVERT: A 441 GLN cc_start: 0.8113 (mt0) cc_final: 0.7729 (mt0) REVERT: A 449 ASP cc_start: 0.7817 (t70) cc_final: 0.7365 (t70) REVERT: A 455 LYS cc_start: 0.7961 (ptpp) cc_final: 0.7722 (ptpp) REVERT: B 205 LYS cc_start: 0.8879 (mmtp) cc_final: 0.8678 (mttm) REVERT: B 277 GLN cc_start: 0.9205 (OUTLIER) cc_final: 0.8027 (tm-30) REVERT: B 312 ASN cc_start: 0.9188 (m-40) cc_final: 0.8933 (m-40) REVERT: B 337 MET cc_start: 0.8840 (mmm) cc_final: 0.8266 (mtt) REVERT: B 395 GLU cc_start: 0.8153 (mp0) cc_final: 0.7895 (mp0) REVERT: B 400 TYR cc_start: 0.7690 (m-80) cc_final: 0.7058 (m-80) REVERT: B 441 GLN cc_start: 0.8319 (mt0) cc_final: 0.7877 (mt0) REVERT: B 449 ASP cc_start: 0.7979 (t70) cc_final: 0.7484 (t0) REVERT: C 135 MET cc_start: 0.8342 (OUTLIER) cc_final: 0.7958 (mpp) REVERT: C 182 ARG cc_start: 0.6952 (mmm-85) cc_final: 0.6545 (mmm160) REVERT: C 184 GLU cc_start: 0.4877 (OUTLIER) cc_final: 0.4266 (tp30) REVERT: C 225 THR cc_start: 0.7777 (m) cc_final: 0.7364 (p) REVERT: C 243 GLN cc_start: 0.7775 (mp-120) cc_final: 0.7133 (mp10) REVERT: C 277 GLN cc_start: 0.9207 (OUTLIER) cc_final: 0.8030 (tm-30) REVERT: C 286 MET cc_start: 0.8909 (tpp) cc_final: 0.8608 (tpp) REVERT: C 312 ASN cc_start: 0.9183 (m-40) cc_final: 0.8904 (m-40) REVERT: C 441 GLN cc_start: 0.8154 (mt0) cc_final: 0.7884 (mt0) REVERT: C 449 ASP cc_start: 0.7682 (t0) cc_final: 0.7478 (t70) REVERT: D 134 LYS cc_start: 0.7840 (tptt) cc_final: 0.7584 (tppt) REVERT: D 184 GLU cc_start: 0.1924 (OUTLIER) cc_final: 0.0483 (tp30) REVERT: D 205 LYS cc_start: 0.8862 (mmtp) cc_final: 0.8565 (mmtp) REVERT: D 277 GLN cc_start: 0.9217 (OUTLIER) cc_final: 0.8029 (tm-30) REVERT: D 286 MET cc_start: 0.8970 (tpp) cc_final: 0.8695 (tpp) REVERT: D 312 ASN cc_start: 0.9182 (m-40) cc_final: 0.8892 (m-40) REVERT: D 395 GLU cc_start: 0.8093 (mp0) cc_final: 0.7806 (mp0) REVERT: D 449 ASP cc_start: 0.7892 (t70) cc_final: 0.7501 (t70) REVERT: E 206 LYS cc_start: 0.7958 (OUTLIER) cc_final: 0.7716 (mttm) REVERT: E 277 GLN cc_start: 0.9192 (OUTLIER) cc_final: 0.7968 (tm-30) REVERT: E 286 MET cc_start: 0.8907 (tpp) cc_final: 0.8616 (tpp) REVERT: E 312 ASN cc_start: 0.9213 (m-40) cc_final: 0.8961 (m-40) REVERT: E 395 GLU cc_start: 0.8068 (mp0) cc_final: 0.7786 (mp0) REVERT: E 441 GLN cc_start: 0.8195 (mt0) cc_final: 0.7791 (mt0) REVERT: F 103 GLU cc_start: 0.8658 (tp30) cc_final: 0.8434 (mm-30) REVERT: F 184 GLU cc_start: 0.5258 (OUTLIER) cc_final: 0.4230 (tp30) REVERT: F 202 GLN cc_start: 0.8309 (tt0) cc_final: 0.7953 (mm-40) REVERT: F 205 LYS cc_start: 0.8931 (mmtp) cc_final: 0.8664 (mmtp) REVERT: F 206 LYS cc_start: 0.8060 (OUTLIER) cc_final: 0.7121 (mtmm) REVERT: F 231 ARG cc_start: 0.8256 (mtm110) cc_final: 0.7969 (mtm180) REVERT: F 243 GLN cc_start: 0.8087 (mp10) cc_final: 0.7820 (mp10) REVERT: F 277 GLN cc_start: 0.9166 (OUTLIER) cc_final: 0.7891 (tm-30) REVERT: F 312 ASN cc_start: 0.9193 (m-40) cc_final: 0.8933 (m-40) REVERT: F 337 MET cc_start: 0.8903 (mmm) cc_final: 0.8356 (mtt) REVERT: F 395 GLU cc_start: 0.8085 (mp0) cc_final: 0.7779 (mp0) REVERT: F 441 GLN cc_start: 0.8337 (mt0) cc_final: 0.7985 (mt0) REVERT: G 103 GLU cc_start: 0.8605 (tp30) cc_final: 0.8391 (mm-30) REVERT: G 135 MET cc_start: 0.8352 (OUTLIER) cc_final: 0.8024 (mpp) REVERT: G 179 MET cc_start: 0.3641 (mtt) cc_final: 0.3184 (mpp) REVERT: G 205 LYS cc_start: 0.8837 (mmtp) cc_final: 0.8627 (mmtp) REVERT: G 277 GLN cc_start: 0.9189 (OUTLIER) cc_final: 0.8133 (tm-30) REVERT: G 286 MET cc_start: 0.8929 (tpp) cc_final: 0.8607 (tpp) REVERT: G 312 ASN cc_start: 0.9174 (m-40) cc_final: 0.8854 (m-40) REVERT: G 337 MET cc_start: 0.8847 (mmm) cc_final: 0.8315 (mtt) REVERT: G 395 GLU cc_start: 0.8103 (mp0) cc_final: 0.7811 (mp0) REVERT: G 400 TYR cc_start: 0.7730 (m-80) cc_final: 0.7127 (m-80) REVERT: G 441 GLN cc_start: 0.8133 (mt0) cc_final: 0.7582 (mt0) REVERT: G 449 ASP cc_start: 0.7874 (t70) cc_final: 0.7468 (t70) REVERT: H 78 MET cc_start: 0.8766 (tpp) cc_final: 0.8306 (tpp) REVERT: H 225 THR cc_start: 0.7981 (m) cc_final: 0.7531 (p) REVERT: H 231 ARG cc_start: 0.8810 (ptp90) cc_final: 0.8498 (mtm180) REVERT: H 243 GLN cc_start: 0.7768 (mp-120) cc_final: 0.7132 (mp10) REVERT: H 277 GLN cc_start: 0.9178 (OUTLIER) cc_final: 0.7971 (tm-30) REVERT: H 312 ASN cc_start: 0.9199 (m-40) cc_final: 0.8923 (m-40) REVERT: H 337 MET cc_start: 0.8749 (mmm) cc_final: 0.8290 (mtt) REVERT: H 395 GLU cc_start: 0.8169 (mp0) cc_final: 0.7881 (mp0) REVERT: H 400 TYR cc_start: 0.7743 (m-80) cc_final: 0.7088 (m-80) REVERT: H 449 ASP cc_start: 0.7821 (t70) cc_final: 0.7372 (t70) outliers start: 97 outliers final: 74 residues processed: 689 average time/residue: 0.1911 time to fit residues: 210.8162 Evaluate side-chains 694 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 604 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 283 GLN Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 93 HIS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 135 MET Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 184 GLU Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 283 GLN Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 283 GLN Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 206 LYS Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 283 GLN Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 184 GLU Chi-restraints excluded: chain F residue 206 LYS Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 283 GLN Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 135 MET Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 287 VAL Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 448 GLN Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 283 GLN Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 448 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 121 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 chunk 147 optimal weight: 0.6980 chunk 40 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 100 optimal weight: 0.8980 chunk 71 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 143 optimal weight: 0.5980 chunk 255 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 HIS B 93 HIS ** B 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 202 GLN D 93 HIS F 93 HIS ** F 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 93 HIS G 202 GLN ** G 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.156919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.111295 restraints weight = 33764.118| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 2.14 r_work: 0.2894 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 30593 Z= 0.137 Angle : 0.534 7.975 41496 Z= 0.271 Chirality : 0.043 0.211 4800 Planarity : 0.004 0.033 5160 Dihedral : 8.905 84.737 4345 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 3.37 % Allowed : 20.96 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.14), residues: 3792 helix: 1.32 (0.14), residues: 1424 sheet: -0.55 (0.25), residues: 352 loop : -1.14 (0.14), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 412 TYR 0.016 0.001 TYR F 400 PHE 0.028 0.001 PHE B 99 HIS 0.004 0.001 HIS B 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (30592) covalent geometry : angle 0.53405 / 0.27 (41496) hydrogen bonds : bond 0.02982 / 1.99 ( 1090) hydrogen bonds : angle 4.65432 / 3.26 ( 3078) Misc. bond : bond 0.00096 / 0.06 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8906.85 seconds wall clock time: 153 minutes 9.83 seconds (9189.83 seconds total)