Starting phenix.real_space_refine on Mon Sep 14 16:00:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6udo_20741/09_2026/6udo_20741.cif Found real_map, /net/cci-nas-00/data/ceres_data/6udo_20741/09_2026/6udo_20741.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6udo_20741/09_2026/6udo_20741.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6udo_20741/09_2026/6udo_20741.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6udo_20741/09_2026/6udo_20741.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6udo_20741/09_2026/6udo_20741.cif" model { file = "/net/cci-nas-00/data/ceres_data/6udo_20741/09_2026/6udo_20741.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6udo_20741/09_2026/6udo_20741.cif" } resolution = 3.21 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= 0.058 sd= 3.698 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 80 5.49 5 S 176 5.16 5 C 19544 2.51 5 N 5376 2.21 5 O 6216 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 88 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: 31392 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 3704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3704 Classifications: {'peptide': 487} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 469} Chain breaks: 1 Chain: "B" Number of atoms: 3704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3704 Classifications: {'peptide': 487} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 469} Chain breaks: 1 Chain: "C" Number of atoms: 3704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3704 Classifications: {'peptide': 487} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 469} Chain breaks: 1 Chain: "D" Number of atoms: 3704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3704 Classifications: {'peptide': 487} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 469} Chain breaks: 1 Chain: "E" Number of atoms: 3704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3704 Classifications: {'peptide': 487} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 469} Chain breaks: 1 Chain: "F" Number of atoms: 3704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3704 Classifications: {'peptide': 487} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 469} Chain breaks: 1 Chain: "G" Number of atoms: 3704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3704 Classifications: {'peptide': 487} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 469} Chain breaks: 1 Chain: "H" Number of atoms: 3704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3704 Classifications: {'peptide': 487} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 469} Chain breaks: 1 Chain: "I" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 102 Classifications: {'peptide': 14} Link IDs: {'PTRANS': 1, 'TRANS': 12} Chain: "J" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 102 Classifications: {'peptide': 14} Link IDs: {'PTRANS': 1, 'TRANS': 12} Chain: "K" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 102 Classifications: {'peptide': 14} Link IDs: {'PTRANS': 1, 'TRANS': 12} Chain: "L" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 102 Classifications: {'peptide': 14} Link IDs: {'PTRANS': 1, 'TRANS': 12} Chain: "M" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 102 Classifications: {'peptide': 14} Link IDs: {'PTRANS': 1, 'TRANS': 12} Chain: "N" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 102 Classifications: {'peptide': 14} Link IDs: {'PTRANS': 1, 'TRANS': 12} Chain: "O" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 102 Classifications: {'peptide': 14} Link IDs: {'PTRANS': 1, 'TRANS': 12} Chain: "P" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 102 Classifications: {'peptide': 14} Link IDs: {'PTRANS': 1, 'TRANS': 12} Chain: "A" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 118 Unusual residues: {'ATP': 1, 'GTP': 2} Classifications: {'RNAv2': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "B" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 118 Unusual residues: {'ATP': 1, 'GTP': 2} Classifications: {'RNAv2': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "C" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 118 Unusual residues: {'ATP': 1, 'GTP': 2} Classifications: {'RNAv2': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "D" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 118 Unusual residues: {'ATP': 1, 'GTP': 2} Classifications: {'RNAv2': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "E" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 118 Unusual residues: {'ATP': 1, 'GTP': 2} Classifications: {'RNAv2': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "F" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 118 Unusual residues: {'ATP': 1, 'GTP': 2} Classifications: {'RNAv2': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "G" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 118 Unusual residues: {'ATP': 1, 'GTP': 2} Classifications: {'RNAv2': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "H" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 118 Unusual residues: {'ATP': 1, 'GTP': 2} Classifications: {'RNAv2': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Time building chain proxies: 6.11, per 1000 atoms: 0.19 Number of scatterers: 31392 At special positions: 0 Unit cell: (149.597, 149.597, 118.19, 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 176 16.00 P 80 15.00 O 6216 8.00 N 5376 7.00 C 19544 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=8, symmetry=0 Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.51 Conformation dependent library (CDL) restraints added in 1.3 seconds 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7264 Finding SS restraints... Secondary structure from input PDB file: 152 helices and 44 sheets defined 36.7% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'A' and resid 19 through 24 Processing helix chain 'A' and resid 45 through 49 removed outlier: 3.533A pdb=" N GLN A 48 " --> pdb=" O THR A 45 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL A 49 " --> pdb=" O ALA A 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 45 through 49' Processing helix chain 'A' and resid 75 through 85 removed outlier: 3.770A pdb=" N THR A 85 " --> pdb=" O ALA A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 109 Processing helix chain 'A' and resid 126 through 138 removed outlier: 3.973A pdb=" N VAL A 130 " --> pdb=" O ARG A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 163 removed outlier: 3.598A pdb=" N ASP A 162 " --> pdb=" O SER A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 185 No H-bonds generated for 'chain 'A' and resid 183 through 185' Processing helix chain 'A' and resid 193 through 204 removed outlier: 3.511A pdb=" N ALA A 197 " --> pdb=" O THR A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 233 Processing helix chain 'A' and resid 255 through 267 removed outlier: 4.144A pdb=" N ARG A 259 " --> pdb=" O ASP A 255 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASP A 261 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 291 Processing helix chain 'A' and resid 307 through 315 removed outlier: 3.745A pdb=" N LYS A 311 " --> pdb=" O ALA A 307 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASN A 312 " --> pdb=" O ALA A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 336 removed outlier: 3.559A pdb=" N VAL A 336 " --> pdb=" O THR A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 355 Processing helix chain 'A' and resid 369 through 380 removed outlier: 3.837A pdb=" N ILE A 373 " --> pdb=" O ASN A 369 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY A 380 " --> pdb=" O ALA A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 472 Processing helix chain 'A' and resid 475 through 485 Processing helix chain 'A' and resid 496 through 502 removed outlier: 3.876A pdb=" N GLY A 502 " --> pdb=" O GLN A 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 24 Processing helix chain 'B' and resid 45 through 49 removed outlier: 3.533A pdb=" N GLN B 48 " --> pdb=" O THR B 45 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL B 49 " --> pdb=" O ALA B 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 45 through 49' Processing helix chain 'B' and resid 75 through 85 removed outlier: 3.770A pdb=" N THR B 85 " --> pdb=" O ALA B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 109 Processing helix chain 'B' and resid 126 through 138 removed outlier: 3.973A pdb=" N VAL B 130 " --> pdb=" O ARG B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 163 removed outlier: 3.598A pdb=" N ASP B 162 " --> pdb=" O SER B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 185 No H-bonds generated for 'chain 'B' and resid 183 through 185' Processing helix chain 'B' and resid 193 through 204 removed outlier: 3.511A pdb=" N ALA B 197 " --> pdb=" O THR B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 233 Processing helix chain 'B' and resid 255 through 267 removed outlier: 4.144A pdb=" N ARG B 259 " --> pdb=" O ASP B 255 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASP B 261 " --> pdb=" O LYS B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 291 Processing helix chain 'B' and resid 307 through 315 removed outlier: 3.745A pdb=" N LYS B 311 " --> pdb=" O ALA B 307 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASN B 312 " --> pdb=" O ALA B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 336 removed outlier: 3.559A pdb=" N VAL B 336 " --> pdb=" O THR B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 355 Processing helix chain 'B' and resid 369 through 380 removed outlier: 3.837A pdb=" N ILE B 373 " --> pdb=" O ASN B 369 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY B 380 " --> pdb=" O ALA B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 472 Processing helix chain 'B' and resid 475 through 485 Processing helix chain 'B' and resid 496 through 502 removed outlier: 3.875A pdb=" N GLY B 502 " --> pdb=" O GLN B 498 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 24 Processing helix chain 'C' and resid 45 through 49 removed outlier: 3.533A pdb=" N GLN C 48 " --> pdb=" O THR C 45 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL C 49 " --> pdb=" O ALA C 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 45 through 49' Processing helix chain 'C' and resid 75 through 85 removed outlier: 3.770A pdb=" N THR C 85 " --> pdb=" O ALA C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 109 Processing helix chain 'C' and resid 126 through 138 removed outlier: 3.973A pdb=" N VAL C 130 " --> pdb=" O ARG C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 163 removed outlier: 3.599A pdb=" N ASP C 162 " --> pdb=" O SER C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 185 No H-bonds generated for 'chain 'C' and resid 183 through 185' Processing helix chain 'C' and resid 193 through 204 removed outlier: 3.512A pdb=" N ALA C 197 " --> pdb=" O THR C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 233 Processing helix chain 'C' and resid 255 through 267 removed outlier: 4.144A pdb=" N ARG C 259 " --> pdb=" O ASP C 255 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASP C 261 " --> pdb=" O LYS C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 291 Processing helix chain 'C' and resid 307 through 315 removed outlier: 3.746A pdb=" N LYS C 311 " --> pdb=" O ALA C 307 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASN C 312 " --> pdb=" O ALA C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 336 removed outlier: 3.560A pdb=" N VAL C 336 " --> pdb=" O THR C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 355 Processing helix chain 'C' and resid 369 through 380 removed outlier: 3.836A pdb=" N ILE C 373 " --> pdb=" O ASN C 369 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY C 380 " --> pdb=" O ALA C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 456 through 472 Processing helix chain 'C' and resid 475 through 485 Processing helix chain 'C' and resid 496 through 502 removed outlier: 3.875A pdb=" N GLY C 502 " --> pdb=" O GLN C 498 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 24 Processing helix chain 'D' and resid 45 through 49 removed outlier: 3.534A pdb=" N GLN D 48 " --> pdb=" O THR D 45 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL D 49 " --> pdb=" O ALA D 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 45 through 49' Processing helix chain 'D' and resid 75 through 85 removed outlier: 3.769A pdb=" N THR D 85 " --> pdb=" O ALA D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 109 Processing helix chain 'D' and resid 126 through 138 removed outlier: 3.974A pdb=" N VAL D 130 " --> pdb=" O ARG D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 163 removed outlier: 3.598A pdb=" N ASP D 162 " --> pdb=" O SER D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 185 No H-bonds generated for 'chain 'D' and resid 183 through 185' Processing helix chain 'D' and resid 193 through 204 removed outlier: 3.512A pdb=" N ALA D 197 " --> pdb=" O THR D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 233 Processing helix chain 'D' and resid 255 through 267 removed outlier: 4.144A pdb=" N ARG D 259 " --> pdb=" O ASP D 255 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASP D 261 " --> pdb=" O LYS D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 291 Processing helix chain 'D' and resid 307 through 315 removed outlier: 3.746A pdb=" N LYS D 311 " --> pdb=" O ALA D 307 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASN D 312 " --> pdb=" O ALA D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 336 removed outlier: 3.560A pdb=" N VAL D 336 " --> pdb=" O THR D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 355 Processing helix chain 'D' and resid 369 through 380 removed outlier: 3.838A pdb=" N ILE D 373 " --> pdb=" O ASN D 369 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY D 380 " --> pdb=" O ALA D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 456 through 472 Processing helix chain 'D' and resid 475 through 485 Processing helix chain 'D' and resid 496 through 502 removed outlier: 3.875A pdb=" N GLY D 502 " --> pdb=" O GLN D 498 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 24 Processing helix chain 'E' and resid 45 through 49 removed outlier: 3.533A pdb=" N GLN E 48 " --> pdb=" O THR E 45 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL E 49 " --> pdb=" O ALA E 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 45 through 49' Processing helix chain 'E' and resid 75 through 85 removed outlier: 3.770A pdb=" N THR E 85 " --> pdb=" O ALA E 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 109 Processing helix chain 'E' and resid 126 through 138 removed outlier: 3.973A pdb=" N VAL E 130 " --> pdb=" O ARG E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 163 removed outlier: 3.598A pdb=" N ASP E 162 " --> pdb=" O SER E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 185 No H-bonds generated for 'chain 'E' and resid 183 through 185' Processing helix chain 'E' and resid 193 through 204 removed outlier: 3.510A pdb=" N ALA E 197 " --> pdb=" O THR E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 224 through 233 Processing helix chain 'E' and resid 255 through 267 removed outlier: 4.144A pdb=" N ARG E 259 " --> pdb=" O ASP E 255 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASP E 261 " --> pdb=" O LYS E 257 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 291 Processing helix chain 'E' and resid 307 through 315 removed outlier: 3.745A pdb=" N LYS E 311 " --> pdb=" O ALA E 307 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASN E 312 " --> pdb=" O ALA E 308 " (cutoff:3.500A) Processing helix chain 'E' and resid 332 through 336 removed outlier: 3.560A pdb=" N VAL E 336 " --> pdb=" O THR E 333 " (cutoff:3.500A) Processing helix chain 'E' and resid 342 through 355 Processing helix chain 'E' and resid 369 through 380 removed outlier: 3.837A pdb=" N ILE E 373 " --> pdb=" O ASN E 369 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY E 380 " --> pdb=" O ALA E 376 " (cutoff:3.500A) Processing helix chain 'E' and resid 456 through 472 Processing helix chain 'E' and resid 475 through 485 Processing helix chain 'E' and resid 496 through 502 removed outlier: 3.875A pdb=" N GLY E 502 " --> pdb=" O GLN E 498 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 24 Processing helix chain 'F' and resid 45 through 49 removed outlier: 3.533A pdb=" N GLN F 48 " --> pdb=" O THR F 45 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL F 49 " --> pdb=" O ALA F 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 45 through 49' Processing helix chain 'F' and resid 75 through 85 removed outlier: 3.771A pdb=" N THR F 85 " --> pdb=" O ALA F 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 109 Processing helix chain 'F' and resid 126 through 138 removed outlier: 3.972A pdb=" N VAL F 130 " --> pdb=" O ARG F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 163 removed outlier: 3.599A pdb=" N ASP F 162 " --> pdb=" O SER F 159 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 185 No H-bonds generated for 'chain 'F' and resid 183 through 185' Processing helix chain 'F' and resid 193 through 204 removed outlier: 3.511A pdb=" N ALA F 197 " --> pdb=" O THR F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 224 through 233 Processing helix chain 'F' and resid 255 through 267 removed outlier: 4.144A pdb=" N ARG F 259 " --> pdb=" O ASP F 255 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASP F 261 " --> pdb=" O LYS F 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 291 Processing helix chain 'F' and resid 307 through 315 removed outlier: 3.745A pdb=" N LYS F 311 " --> pdb=" O ALA F 307 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASN F 312 " --> pdb=" O ALA F 308 " (cutoff:3.500A) Processing helix chain 'F' and resid 332 through 336 removed outlier: 3.560A pdb=" N VAL F 336 " --> pdb=" O THR F 333 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 355 Processing helix chain 'F' and resid 369 through 380 removed outlier: 3.837A pdb=" N ILE F 373 " --> pdb=" O ASN F 369 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY F 380 " --> pdb=" O ALA F 376 " (cutoff:3.500A) Processing helix chain 'F' and resid 456 through 472 Processing helix chain 'F' and resid 475 through 485 Processing helix chain 'F' and resid 496 through 502 removed outlier: 3.876A pdb=" N GLY F 502 " --> pdb=" O GLN F 498 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 24 Processing helix chain 'G' and resid 45 through 49 removed outlier: 3.533A pdb=" N GLN G 48 " --> pdb=" O THR G 45 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL G 49 " --> pdb=" O ALA G 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 49' Processing helix chain 'G' and resid 75 through 85 removed outlier: 3.771A pdb=" N THR G 85 " --> pdb=" O ALA G 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 109 Processing helix chain 'G' and resid 126 through 138 removed outlier: 3.973A pdb=" N VAL G 130 " --> pdb=" O ARG G 126 " (cutoff:3.500A) Processing helix chain 'G' and resid 159 through 163 removed outlier: 3.598A pdb=" N ASP G 162 " --> pdb=" O SER G 159 " (cutoff:3.500A) Processing helix chain 'G' and resid 183 through 185 No H-bonds generated for 'chain 'G' and resid 183 through 185' Processing helix chain 'G' and resid 193 through 204 removed outlier: 3.511A pdb=" N ALA G 197 " --> pdb=" O THR G 193 " (cutoff:3.500A) Processing helix chain 'G' and resid 224 through 233 Processing helix chain 'G' and resid 255 through 267 removed outlier: 4.144A pdb=" N ARG G 259 " --> pdb=" O ASP G 255 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASP G 261 " --> pdb=" O LYS G 257 " (cutoff:3.500A) Processing helix chain 'G' and resid 280 through 291 Processing helix chain 'G' and resid 307 through 315 removed outlier: 3.745A pdb=" N LYS G 311 " --> pdb=" O ALA G 307 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASN G 312 " --> pdb=" O ALA G 308 " (cutoff:3.500A) Processing helix chain 'G' and resid 332 through 336 removed outlier: 3.561A pdb=" N VAL G 336 " --> pdb=" O THR G 333 " (cutoff:3.500A) Processing helix chain 'G' and resid 342 through 355 Processing helix chain 'G' and resid 369 through 380 removed outlier: 3.837A pdb=" N ILE G 373 " --> pdb=" O ASN G 369 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY G 380 " --> pdb=" O ALA G 376 " (cutoff:3.500A) Processing helix chain 'G' and resid 456 through 472 Processing helix chain 'G' and resid 475 through 485 Processing helix chain 'G' and resid 496 through 502 removed outlier: 3.876A pdb=" N GLY G 502 " --> pdb=" O GLN G 498 " (cutoff:3.500A) Processing helix chain 'H' and resid 19 through 24 Processing helix chain 'H' and resid 45 through 49 removed outlier: 3.533A pdb=" N GLN H 48 " --> pdb=" O THR H 45 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL H 49 " --> pdb=" O ALA H 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 45 through 49' Processing helix chain 'H' and resid 75 through 85 removed outlier: 3.770A pdb=" N THR H 85 " --> pdb=" O ALA H 81 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 109 Processing helix chain 'H' and resid 126 through 138 removed outlier: 3.972A pdb=" N VAL H 130 " --> pdb=" O ARG H 126 " (cutoff:3.500A) Processing helix chain 'H' and resid 159 through 163 removed outlier: 3.598A pdb=" N ASP H 162 " --> pdb=" O SER H 159 " (cutoff:3.500A) Processing helix chain 'H' and resid 183 through 185 No H-bonds generated for 'chain 'H' and resid 183 through 185' Processing helix chain 'H' and resid 193 through 204 removed outlier: 3.512A pdb=" N ALA H 197 " --> pdb=" O THR H 193 " (cutoff:3.500A) Processing helix chain 'H' and resid 224 through 233 Processing helix chain 'H' and resid 255 through 267 removed outlier: 4.144A pdb=" N ARG H 259 " --> pdb=" O ASP H 255 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASP H 261 " --> pdb=" O LYS H 257 " (cutoff:3.500A) Processing helix chain 'H' and resid 280 through 291 Processing helix chain 'H' and resid 307 through 315 removed outlier: 3.746A pdb=" N LYS H 311 " --> pdb=" O ALA H 307 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASN H 312 " --> pdb=" O ALA H 308 " (cutoff:3.500A) Processing helix chain 'H' and resid 332 through 336 removed outlier: 3.560A pdb=" N VAL H 336 " --> pdb=" O THR H 333 " (cutoff:3.500A) Processing helix chain 'H' and resid 342 through 355 Processing helix chain 'H' and resid 369 through 380 removed outlier: 3.837A pdb=" N ILE H 373 " --> pdb=" O ASN H 369 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY H 380 " --> pdb=" O ALA H 376 " (cutoff:3.500A) Processing helix chain 'H' and resid 456 through 472 Processing helix chain 'H' and resid 475 through 485 Processing helix chain 'H' and resid 496 through 502 removed outlier: 3.875A pdb=" N GLY H 502 " --> pdb=" O GLN H 498 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 6 removed outlier: 3.794A pdb=" N ILE I 6 " --> pdb=" O ALA I 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 2 through 6' Processing helix chain 'J' and resid 2 through 6 removed outlier: 3.794A pdb=" N ILE J 6 " --> pdb=" O ALA J 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 2 through 6' Processing helix chain 'K' and resid 2 through 6 removed outlier: 3.794A pdb=" N ILE K 6 " --> pdb=" O ALA K 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 2 through 6' Processing helix chain 'L' and resid 2 through 6 removed outlier: 3.794A pdb=" N ILE L 6 " --> pdb=" O ALA L 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 2 through 6' Processing helix chain 'M' and resid 2 through 6 removed outlier: 3.794A pdb=" N ILE M 6 " --> pdb=" O ALA M 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 2 through 6' Processing helix chain 'N' and resid 2 through 6 removed outlier: 3.794A pdb=" N ILE N 6 " --> pdb=" O ALA N 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 2 through 6' Processing helix chain 'O' and resid 2 through 6 removed outlier: 3.794A pdb=" N ILE O 6 " --> pdb=" O ALA O 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 2 through 6' Processing helix chain 'P' and resid 2 through 6 removed outlier: 3.794A pdb=" N ILE P 6 " --> pdb=" O ALA P 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 2 through 6' Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 37 Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 removed outlier: 3.507A pdb=" N SER A 53 " --> pdb=" O LEU A 61 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 65 through 67 removed outlier: 4.017A pdb=" N ILE A 88 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE A 90 " --> pdb=" O SER A 67 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N GLY A 89 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ALA A 249 " --> pdb=" O GLY A 89 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ILE A 91 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLY A 302 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL A 299 " --> pdb=" O ALA A 320 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N ARG A 322 " --> pdb=" O VAL A 299 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N GLY A 301 " --> pdb=" O ARG A 322 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL A 361 " --> pdb=" O THR A 383 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N MET A 385 " --> pdb=" O VAL A 361 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ALA A 363 " --> pdb=" O MET A 385 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL A 66 " --> pdb=" O MET A 386 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 142 through 145 removed outlier: 3.623A pdb=" N GLY A 156 " --> pdb=" O ILE A 144 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 188 through 189 removed outlier: 5.921A pdb=" N ALA A 188 " --> pdb=" O VAL A 212 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA A 220 " --> pdb=" O ILE A 211 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 400 through 403 removed outlier: 3.547A pdb=" N SER A 444 " --> pdb=" O GLU D 510 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER G 444 " --> pdb=" O GLU F 510 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 509 through 511 removed outlier: 3.546A pdb=" N SER B 444 " --> pdb=" O GLU A 510 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER F 444 " --> pdb=" O GLU E 510 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 35 through 37 Processing sheet with id=AA9, first strand: chain 'B' and resid 53 through 54 removed outlier: 3.507A pdb=" N SER B 53 " --> pdb=" O LEU B 61 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 65 through 67 removed outlier: 4.017A pdb=" N ILE B 88 " --> pdb=" O LEU B 65 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N PHE B 90 " --> pdb=" O SER B 67 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N GLY B 89 " --> pdb=" O GLY B 247 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ALA B 249 " --> pdb=" O GLY B 89 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ILE B 91 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLY B 302 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL B 299 " --> pdb=" O ALA B 320 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N ARG B 322 " --> pdb=" O VAL B 299 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLY B 301 " --> pdb=" O ARG B 322 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL B 361 " --> pdb=" O THR B 383 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N MET B 385 " --> pdb=" O VAL B 361 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ALA B 363 " --> pdb=" O MET B 385 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL B 66 " --> pdb=" O MET B 386 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 142 through 145 removed outlier: 3.624A pdb=" N GLY B 156 " --> pdb=" O ILE B 144 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 188 through 189 removed outlier: 5.921A pdb=" N ALA B 188 " --> pdb=" O VAL B 212 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA B 220 " --> pdb=" O ILE B 211 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 509 through 511 removed outlier: 3.549A pdb=" N SER C 444 " --> pdb=" O GLU B 510 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER E 444 " --> pdb=" O GLU H 510 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 35 through 37 Processing sheet with id=AB6, first strand: chain 'C' and resid 53 through 54 removed outlier: 3.508A pdb=" N SER C 53 " --> pdb=" O LEU C 61 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 65 through 67 removed outlier: 4.017A pdb=" N ILE C 88 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE C 90 " --> pdb=" O SER C 67 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N GLY C 89 " --> pdb=" O GLY C 247 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N ALA C 249 " --> pdb=" O GLY C 89 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ILE C 91 " --> pdb=" O ALA C 249 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLY C 302 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL C 299 " --> pdb=" O ALA C 320 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N ARG C 322 " --> pdb=" O VAL C 299 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N GLY C 301 " --> pdb=" O ARG C 322 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL C 361 " --> pdb=" O THR C 383 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N MET C 385 " --> pdb=" O VAL C 361 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ALA C 363 " --> pdb=" O MET C 385 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL C 66 " --> pdb=" O MET C 386 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 142 through 145 removed outlier: 3.623A pdb=" N GLY C 156 " --> pdb=" O ILE C 144 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 188 through 189 removed outlier: 5.921A pdb=" N ALA C 188 " --> pdb=" O VAL C 212 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA C 220 " --> pdb=" O ILE C 211 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 509 through 511 removed outlier: 3.580A pdb=" N SER D 444 " --> pdb=" O GLU C 510 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER H 444 " --> pdb=" O GLU G 510 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 35 through 37 Processing sheet with id=AC3, first strand: chain 'D' and resid 53 through 54 removed outlier: 3.508A pdb=" N SER D 53 " --> pdb=" O LEU D 61 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 65 through 67 removed outlier: 4.018A pdb=" N ILE D 88 " --> pdb=" O LEU D 65 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE D 90 " --> pdb=" O SER D 67 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N GLY D 89 " --> pdb=" O GLY D 247 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ALA D 249 " --> pdb=" O GLY D 89 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ILE D 91 " --> pdb=" O ALA D 249 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLY D 302 " --> pdb=" O LEU D 273 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL D 299 " --> pdb=" O ALA D 320 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N ARG D 322 " --> pdb=" O VAL D 299 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N GLY D 301 " --> pdb=" O ARG D 322 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL D 361 " --> pdb=" O THR D 383 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N MET D 385 " --> pdb=" O VAL D 361 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ALA D 363 " --> pdb=" O MET D 385 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL D 66 " --> pdb=" O MET D 386 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 142 through 145 removed outlier: 3.623A pdb=" N GLY D 156 " --> pdb=" O ILE D 144 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 188 through 189 removed outlier: 5.921A pdb=" N ALA D 188 " --> pdb=" O VAL D 212 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA D 220 " --> pdb=" O ILE D 211 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 35 through 37 Processing sheet with id=AC8, first strand: chain 'E' and resid 53 through 54 removed outlier: 3.507A pdb=" N SER E 53 " --> pdb=" O LEU E 61 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 65 through 67 removed outlier: 4.017A pdb=" N ILE E 88 " --> pdb=" O LEU E 65 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N PHE E 90 " --> pdb=" O SER E 67 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N GLY E 89 " --> pdb=" O GLY E 247 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ALA E 249 " --> pdb=" O GLY E 89 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE E 91 " --> pdb=" O ALA E 249 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLY E 302 " --> pdb=" O LEU E 273 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL E 299 " --> pdb=" O ALA E 320 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N ARG E 322 " --> pdb=" O VAL E 299 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLY E 301 " --> pdb=" O ARG E 322 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL E 361 " --> pdb=" O THR E 383 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N MET E 385 " --> pdb=" O VAL E 361 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ALA E 363 " --> pdb=" O MET E 385 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL E 66 " --> pdb=" O MET E 386 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 142 through 145 removed outlier: 3.623A pdb=" N GLY E 156 " --> pdb=" O ILE E 144 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 188 through 189 removed outlier: 5.921A pdb=" N ALA E 188 " --> pdb=" O VAL E 212 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA E 220 " --> pdb=" O ILE E 211 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 35 through 37 Processing sheet with id=AD4, first strand: chain 'F' and resid 53 through 54 removed outlier: 3.507A pdb=" N SER F 53 " --> pdb=" O LEU F 61 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 65 through 67 removed outlier: 4.018A pdb=" N ILE F 88 " --> pdb=" O LEU F 65 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE F 90 " --> pdb=" O SER F 67 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N GLY F 89 " --> pdb=" O GLY F 247 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ALA F 249 " --> pdb=" O GLY F 89 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ILE F 91 " --> pdb=" O ALA F 249 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLY F 302 " --> pdb=" O LEU F 273 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL F 299 " --> pdb=" O ALA F 320 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N ARG F 322 " --> pdb=" O VAL F 299 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N GLY F 301 " --> pdb=" O ARG F 322 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL F 361 " --> pdb=" O THR F 383 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N MET F 385 " --> pdb=" O VAL F 361 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ALA F 363 " --> pdb=" O MET F 385 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL F 66 " --> pdb=" O MET F 386 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 142 through 145 removed outlier: 3.623A pdb=" N GLY F 156 " --> pdb=" O ILE F 144 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 188 through 189 removed outlier: 5.920A pdb=" N ALA F 188 " --> pdb=" O VAL F 212 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA F 220 " --> pdb=" O ILE F 211 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 35 through 37 Processing sheet with id=AD9, first strand: chain 'G' and resid 53 through 54 removed outlier: 3.507A pdb=" N SER G 53 " --> pdb=" O LEU G 61 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 65 through 67 removed outlier: 4.018A pdb=" N ILE G 88 " --> pdb=" O LEU G 65 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE G 90 " --> pdb=" O SER G 67 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N GLY G 89 " --> pdb=" O GLY G 247 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ALA G 249 " --> pdb=" O GLY G 89 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE G 91 " --> pdb=" O ALA G 249 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLY G 302 " --> pdb=" O LEU G 273 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL G 299 " --> pdb=" O ALA G 320 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N ARG G 322 " --> pdb=" O VAL G 299 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLY G 301 " --> pdb=" O ARG G 322 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL G 361 " --> pdb=" O THR G 383 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N MET G 385 " --> pdb=" O VAL G 361 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ALA G 363 " --> pdb=" O MET G 385 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL G 66 " --> pdb=" O MET G 386 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 142 through 145 removed outlier: 3.623A pdb=" N GLY G 156 " --> pdb=" O ILE G 144 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 188 through 189 removed outlier: 5.921A pdb=" N ALA G 188 " --> pdb=" O VAL G 212 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA G 220 " --> pdb=" O ILE G 211 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 35 through 37 Processing sheet with id=AE5, first strand: chain 'H' and resid 53 through 54 removed outlier: 3.507A pdb=" N SER H 53 " --> pdb=" O LEU H 61 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 65 through 67 removed outlier: 4.017A pdb=" N ILE H 88 " --> pdb=" O LEU H 65 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N PHE H 90 " --> pdb=" O SER H 67 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N GLY H 89 " --> pdb=" O GLY H 247 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ALA H 249 " --> pdb=" O GLY H 89 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ILE H 91 " --> pdb=" O ALA H 249 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLY H 302 " --> pdb=" O LEU H 273 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL H 299 " --> pdb=" O ALA H 320 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N ARG H 322 " --> pdb=" O VAL H 299 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLY H 301 " --> pdb=" O ARG H 322 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL H 361 " --> pdb=" O THR H 383 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N MET H 385 " --> pdb=" O VAL H 361 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ALA H 363 " --> pdb=" O MET H 385 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL H 66 " --> pdb=" O MET H 386 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 142 through 145 removed outlier: 3.623A pdb=" N GLY H 156 " --> pdb=" O ILE H 144 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 188 through 189 removed outlier: 5.921A pdb=" N ALA H 188 " --> pdb=" O VAL H 212 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA H 220 " --> pdb=" O ILE H 211 " (cutoff:3.500A) 1032 hydrogen bonds defined for protein. 2952 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: 6.05 Time building geometry restraints manager: 3.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 5288 1.30 - 1.43: 7628 1.43 - 1.56: 18510 1.56 - 1.68: 206 1.68 - 1.81: 288 Bond restraints: 31920 Sorted by residual: bond pdb=" C2' GTP G 603 " pdb=" C3' GTP G 603 " ideal model delta sigma weight residual 1.524 1.231 0.293 2.00e-02 2.50e+03 2.15e+02 bond pdb=" C2' GTP E 603 " pdb=" C3' GTP E 603 " ideal model delta sigma weight residual 1.524 1.231 0.293 2.00e-02 2.50e+03 2.15e+02 bond pdb=" C2' GTP C 603 " pdb=" C3' GTP C 603 " ideal model delta sigma weight residual 1.524 1.231 0.293 2.00e-02 2.50e+03 2.15e+02 bond pdb=" C2' GTP A 603 " pdb=" C3' GTP A 603 " ideal model delta sigma weight residual 1.524 1.231 0.293 2.00e-02 2.50e+03 2.14e+02 bond pdb=" C2' GTP D 603 " pdb=" C3' GTP D 603 " ideal model delta sigma weight residual 1.524 1.231 0.293 2.00e-02 2.50e+03 2.14e+02 ... (remaining 31915 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.97: 42609 3.97 - 7.94: 567 7.94 - 11.90: 96 11.90 - 15.87: 8 15.87 - 19.84: 8 Bond angle restraints: 43288 Sorted by residual: angle pdb=" PB ATP F 604 " pdb=" O3B ATP F 604 " pdb=" PG ATP F 604 " ideal model delta sigma weight residual 139.87 120.03 19.84 1.00e+00 1.00e+00 3.94e+02 angle pdb=" PB ATP H 604 " pdb=" O3B ATP H 604 " pdb=" PG ATP H 604 " ideal model delta sigma weight residual 139.87 120.05 19.82 1.00e+00 1.00e+00 3.93e+02 angle pdb=" PB ATP A 604 " pdb=" O3B ATP A 604 " pdb=" PG ATP A 604 " ideal model delta sigma weight residual 139.87 120.05 19.82 1.00e+00 1.00e+00 3.93e+02 angle pdb=" PB ATP D 604 " pdb=" O3B ATP D 604 " pdb=" PG ATP D 604 " ideal model delta sigma weight residual 139.87 120.07 19.80 1.00e+00 1.00e+00 3.92e+02 angle pdb=" PB ATP G 604 " pdb=" O3B ATP G 604 " pdb=" PG ATP G 604 " ideal model delta sigma weight residual 139.87 120.07 19.80 1.00e+00 1.00e+00 3.92e+02 ... (remaining 43283 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.22: 18730 34.22 - 68.43: 290 68.43 - 102.65: 24 102.65 - 136.86: 8 136.86 - 171.08: 36 Dihedral angle restraints: 19088 sinusoidal: 7704 harmonic: 11384 Sorted by residual: dihedral pdb=" O2G GTP H 602 " pdb=" O3B GTP H 602 " pdb=" PG GTP H 602 " pdb=" PB GTP H 602 " ideal model delta sinusoidal sigma weight residual 177.30 6.22 171.08 1 2.00e+01 2.50e-03 4.77e+01 dihedral pdb=" O2G GTP D 602 " pdb=" O3B GTP D 602 " pdb=" PG GTP D 602 " pdb=" PB GTP D 602 " ideal model delta sinusoidal sigma weight residual 177.30 6.23 171.07 1 2.00e+01 2.50e-03 4.77e+01 dihedral pdb=" O2G GTP C 602 " pdb=" O3B GTP C 602 " pdb=" PG GTP C 602 " pdb=" PB GTP C 602 " ideal model delta sinusoidal sigma weight residual 177.30 6.24 171.06 1 2.00e+01 2.50e-03 4.77e+01 ... (remaining 19085 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 3293 0.056 - 0.113: 1361 0.113 - 0.169: 240 0.169 - 0.225: 18 0.225 - 0.282: 16 Chirality restraints: 4928 Sorted by residual: chirality pdb=" C2' IMP F 601 " pdb=" C1' IMP F 601 " pdb=" C3' IMP F 601 " pdb=" O2' IMP F 601 " both_signs ideal model delta sigma weight residual False -2.47 -2.75 0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" C2' IMP E 601 " pdb=" C1' IMP E 601 " pdb=" C3' IMP E 601 " pdb=" O2' IMP E 601 " both_signs ideal model delta sigma weight residual False -2.47 -2.75 0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" C2' IMP H 601 " pdb=" C1' IMP H 601 " pdb=" C3' IMP H 601 " pdb=" O2' IMP H 601 " both_signs ideal model delta sigma weight residual False -2.47 -2.75 0.28 2.00e-01 2.50e+01 1.97e+00 ... (remaining 4925 not shown) Planarity restraints: 5424 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN F 334 " -0.011 2.00e-02 2.50e+03 2.20e-02 4.83e+00 pdb=" CD GLN F 334 " 0.038 2.00e-02 2.50e+03 pdb=" OE1 GLN F 334 " -0.014 2.00e-02 2.50e+03 pdb=" NE2 GLN F 334 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN G 334 " -0.011 2.00e-02 2.50e+03 2.20e-02 4.83e+00 pdb=" CD GLN G 334 " 0.038 2.00e-02 2.50e+03 pdb=" OE1 GLN G 334 " -0.014 2.00e-02 2.50e+03 pdb=" NE2 GLN G 334 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 334 " 0.011 2.00e-02 2.50e+03 2.19e-02 4.81e+00 pdb=" CD GLN A 334 " -0.038 2.00e-02 2.50e+03 pdb=" OE1 GLN A 334 " 0.014 2.00e-02 2.50e+03 pdb=" NE2 GLN A 334 " 0.013 2.00e-02 2.50e+03 ... (remaining 5421 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 8722 2.81 - 3.33: 28092 3.33 - 3.85: 51643 3.85 - 4.38: 61731 4.38 - 4.90: 104651 Nonbonded interactions: 254839 Sorted by model distance: nonbonded pdb=" OG SER A 327 " pdb=" OE1 GLN A 343 " model vdw 2.284 3.040 nonbonded pdb=" OG SER E 327 " pdb=" OE1 GLN E 343 " model vdw 2.284 3.040 nonbonded pdb=" OG SER D 327 " pdb=" OE1 GLN D 343 " model vdw 2.285 3.040 nonbonded pdb=" OG SER F 327 " pdb=" OE1 GLN F 343 " model vdw 2.285 3.040 nonbonded pdb=" OG SER C 327 " pdb=" OE1 GLN C 343 " model vdw 2.285 3.040 ... (remaining 254834 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: 0.09 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' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } 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: 4.140 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: 0.570 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 26.460 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.090 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:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 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 : 0.014 0.293 31928 Z= 0.710 Angle : 1.248 19.841 43288 Z= 0.740 Chirality : 0.060 0.282 4928 Planarity : 0.006 0.046 5424 Dihedral : 15.559 171.080 11824 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 2.21 % Allowed : 5.15 % Favored : 92.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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: -4.03 (0.10), residues: 3960 helix: -3.27 (0.09), residues: 1312 sheet: -2.33 (0.18), residues: 544 loop : -2.33 (0.12), residues: 2104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 355 TYR 0.031 0.003 TYR F 484 PHE 0.015 0.003 PHE C 401 HIS 0.005 0.001 HIS B 504 Details of bonding type rmsd/Z covalent geometry : bond 0.01430 / 0.71 (31920) covalent geometry : angle 1.24827 / 0.74 (43288) hydrogen bonds : bond 0.20158 / 13.49 ( 1032) hydrogen bonds : angle 8.52875 / 5.85 ( 2952) Misc. bond : bond 0.00183 / 0.11 ( 8) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 888 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 816 time to evaluate : 1.020 Fit side-chains REVERT: A 105 ARG cc_start: 0.7351 (mtp-110) cc_final: 0.6953 (ttt-90) REVERT: A 149 ARG cc_start: 0.6430 (mpp-170) cc_final: 0.6197 (mpt180) REVERT: A 170 GLU cc_start: 0.2783 (OUTLIER) cc_final: 0.2321 (mp0) REVERT: A 203 ARG cc_start: 0.7818 (mpt90) cc_final: 0.7116 (mtm110) REVERT: A 228 LYS cc_start: 0.7796 (OUTLIER) cc_final: 0.7531 (ptmm) REVERT: A 232 ASP cc_start: 0.8604 (m-30) cc_final: 0.8360 (m-30) REVERT: A 235 LEU cc_start: 0.7734 (OUTLIER) cc_final: 0.6933 (pp) REVERT: A 410 LYS cc_start: 0.7570 (pttt) cc_final: 0.6363 (mmtt) REVERT: A 509 TYR cc_start: 0.8038 (p90) cc_final: 0.7683 (p90) REVERT: B 105 ARG cc_start: 0.7322 (mtp-110) cc_final: 0.6913 (ttt-90) REVERT: B 149 ARG cc_start: 0.6484 (mpp-170) cc_final: 0.6136 (mpt180) REVERT: B 170 GLU cc_start: 0.2801 (OUTLIER) cc_final: 0.2182 (mp0) REVERT: B 203 ARG cc_start: 0.7831 (mpt90) cc_final: 0.7033 (mtm110) REVERT: B 228 LYS cc_start: 0.7718 (OUTLIER) cc_final: 0.7446 (ptmm) REVERT: B 232 ASP cc_start: 0.8551 (m-30) cc_final: 0.8345 (m-30) REVERT: B 235 LEU cc_start: 0.7566 (OUTLIER) cc_final: 0.6708 (pp) REVERT: B 408 LEU cc_start: 0.6976 (OUTLIER) cc_final: 0.6721 (pp) REVERT: B 410 LYS cc_start: 0.7600 (pttt) cc_final: 0.6227 (mmtt) REVERT: B 509 TYR cc_start: 0.8074 (p90) cc_final: 0.7768 (p90) REVERT: C 13 VAL cc_start: 0.8678 (t) cc_final: 0.8437 (p) REVERT: C 105 ARG cc_start: 0.7364 (mtp-110) cc_final: 0.6973 (ttt-90) REVERT: C 149 ARG cc_start: 0.6465 (mpp-170) cc_final: 0.6263 (mpt180) REVERT: C 170 GLU cc_start: 0.2860 (OUTLIER) cc_final: 0.2377 (mp0) REVERT: C 203 ARG cc_start: 0.7823 (mpt90) cc_final: 0.7023 (mtm110) REVERT: C 228 LYS cc_start: 0.7756 (OUTLIER) cc_final: 0.7424 (ptmm) REVERT: C 232 ASP cc_start: 0.8600 (m-30) cc_final: 0.8330 (m-30) REVERT: C 235 LEU cc_start: 0.7728 (OUTLIER) cc_final: 0.6948 (pp) REVERT: C 408 LEU cc_start: 0.6845 (OUTLIER) cc_final: 0.6595 (pp) REVERT: C 410 LYS cc_start: 0.7638 (pttt) cc_final: 0.6331 (mmtt) REVERT: C 509 TYR cc_start: 0.8068 (p90) cc_final: 0.7687 (p90) REVERT: D 13 VAL cc_start: 0.8552 (t) cc_final: 0.8272 (p) REVERT: D 149 ARG cc_start: 0.6472 (mpp-170) cc_final: 0.6148 (mpt180) REVERT: D 170 GLU cc_start: 0.2645 (OUTLIER) cc_final: 0.2219 (mp0) REVERT: D 203 ARG cc_start: 0.7769 (mpt90) cc_final: 0.6930 (mtm110) REVERT: D 228 LYS cc_start: 0.7734 (OUTLIER) cc_final: 0.7502 (ptmm) REVERT: D 232 ASP cc_start: 0.8530 (m-30) cc_final: 0.8314 (m-30) REVERT: D 235 LEU cc_start: 0.7513 (OUTLIER) cc_final: 0.6668 (pp) REVERT: D 408 LEU cc_start: 0.6966 (OUTLIER) cc_final: 0.6704 (pp) REVERT: D 410 LYS cc_start: 0.7646 (pttt) cc_final: 0.6218 (mmtt) REVERT: D 509 TYR cc_start: 0.8094 (p90) cc_final: 0.7768 (p90) REVERT: E 105 ARG cc_start: 0.7340 (mtp-110) cc_final: 0.6909 (ttt-90) REVERT: E 170 GLU cc_start: 0.2708 (OUTLIER) cc_final: 0.2186 (mp0) REVERT: E 203 ARG cc_start: 0.7886 (mpt90) cc_final: 0.7159 (mtm110) REVERT: E 228 LYS cc_start: 0.7745 (OUTLIER) cc_final: 0.7425 (ptmm) REVERT: E 232 ASP cc_start: 0.8580 (m-30) cc_final: 0.8333 (m-30) REVERT: E 235 LEU cc_start: 0.7710 (OUTLIER) cc_final: 0.6899 (pp) REVERT: E 386 MET cc_start: 0.8472 (mtm) cc_final: 0.8214 (mtp) REVERT: E 408 LEU cc_start: 0.6787 (OUTLIER) cc_final: 0.6547 (pp) REVERT: E 410 LYS cc_start: 0.7557 (pttt) cc_final: 0.6356 (mmtt) REVERT: E 509 TYR cc_start: 0.8085 (p90) cc_final: 0.7689 (p90) REVERT: F 13 VAL cc_start: 0.8574 (t) cc_final: 0.8301 (p) REVERT: F 149 ARG cc_start: 0.6561 (mpp-170) cc_final: 0.6261 (mpt180) REVERT: F 170 GLU cc_start: 0.2675 (OUTLIER) cc_final: 0.2036 (mp0) REVERT: F 203 ARG cc_start: 0.7799 (mpt90) cc_final: 0.6969 (mtm110) REVERT: F 228 LYS cc_start: 0.7668 (OUTLIER) cc_final: 0.7381 (ptmm) REVERT: F 232 ASP cc_start: 0.8534 (m-30) cc_final: 0.8326 (m-30) REVERT: F 235 LEU cc_start: 0.7554 (OUTLIER) cc_final: 0.6676 (pp) REVERT: F 408 LEU cc_start: 0.6919 (OUTLIER) cc_final: 0.6669 (pp) REVERT: F 410 LYS cc_start: 0.7663 (pttt) cc_final: 0.6259 (mmtt) REVERT: F 509 TYR cc_start: 0.8097 (p90) cc_final: 0.7771 (p90) REVERT: G 149 ARG cc_start: 0.6461 (mpp-170) cc_final: 0.6217 (mpt180) REVERT: G 170 GLU cc_start: 0.2585 (OUTLIER) cc_final: 0.2064 (mp0) REVERT: G 203 ARG cc_start: 0.7798 (mpt90) cc_final: 0.7197 (mtp180) REVERT: G 228 LYS cc_start: 0.7732 (OUTLIER) cc_final: 0.7415 (ptmm) REVERT: G 232 ASP cc_start: 0.8563 (m-30) cc_final: 0.8308 (m-30) REVERT: G 235 LEU cc_start: 0.7703 (OUTLIER) cc_final: 0.6895 (pp) REVERT: G 410 LYS cc_start: 0.7576 (pttt) cc_final: 0.6346 (mmtt) REVERT: G 509 TYR cc_start: 0.8072 (p90) cc_final: 0.7667 (p90) REVERT: H 13 VAL cc_start: 0.8555 (t) cc_final: 0.8291 (p) REVERT: H 105 ARG cc_start: 0.7286 (mtp-110) cc_final: 0.6862 (ttt-90) REVERT: H 149 ARG cc_start: 0.6365 (mpp-170) cc_final: 0.6062 (mpt180) REVERT: H 170 GLU cc_start: 0.2727 (OUTLIER) cc_final: 0.2151 (mp0) REVERT: H 203 ARG cc_start: 0.7873 (mpt90) cc_final: 0.7034 (mtm110) REVERT: H 228 LYS cc_start: 0.7784 (OUTLIER) cc_final: 0.7506 (ptmm) REVERT: H 235 LEU cc_start: 0.7524 (OUTLIER) cc_final: 0.6695 (pp) REVERT: H 401 PHE cc_start: 0.7896 (p90) cc_final: 0.7521 (p90) REVERT: H 408 LEU cc_start: 0.6932 (OUTLIER) cc_final: 0.6727 (pp) REVERT: H 410 LYS cc_start: 0.7624 (pttt) cc_final: 0.6287 (mmtt) REVERT: H 509 TYR cc_start: 0.8078 (p90) cc_final: 0.7751 (p90) outliers start: 72 outliers final: 20 residues processed: 856 average time/residue: 0.1969 time to fit residues: 271.9017 Evaluate side-chains 600 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 550 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 228 LYS Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 228 LYS Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 254 GLU Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 228 LYS Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 254 GLU Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 228 LYS Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 254 GLU Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 170 GLU Chi-restraints excluded: chain E residue 228 LYS Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 254 GLU Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 170 GLU Chi-restraints excluded: chain F residue 228 LYS Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 254 GLU Chi-restraints excluded: chain F residue 408 LEU Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 170 GLU Chi-restraints excluded: chain G residue 228 LYS Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 254 GLU Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 170 GLU Chi-restraints excluded: chain H residue 228 LYS Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 254 GLU Chi-restraints excluded: chain H residue 408 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 197 optimal weight: 0.5980 chunk 388 optimal weight: 0.0570 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.2980 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 5.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 25 ASN A 48 GLN A 198 ASN A 253 HIS A 298 GLN ** A 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 GLN A 504 HIS A 507 HIS B 48 GLN B 198 ASN B 253 HIS B 298 GLN ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 GLN B 498 GLN B 504 HIS B 507 HIS C 48 GLN C 198 ASN C 253 HIS C 298 GLN ** C 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 368 GLN C 504 HIS C 507 HIS D 48 GLN D 112 GLN D 198 ASN D 253 HIS D 298 GLN ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 368 GLN D 498 GLN D 504 HIS D 507 HIS E 48 GLN E 198 ASN E 253 HIS E 298 GLN ** E 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 368 GLN E 504 HIS E 507 HIS F 48 GLN F 198 ASN F 253 HIS F 298 GLN ** F 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 368 GLN F 498 GLN F 504 HIS F 507 HIS G 48 GLN G 198 ASN G 253 HIS G 298 GLN ** G 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 368 GLN G 498 GLN G 504 HIS G 507 HIS H 48 GLN H 112 GLN H 198 ASN H 253 HIS H 298 GLN ** H 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 504 HIS H 507 HIS Total number of N/Q/H flips: 62 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.158430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.122377 restraints weight = 36156.294| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.43 r_work: 0.3255 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 31928 Z= 0.118 Angle : 0.605 6.968 43288 Z= 0.299 Chirality : 0.044 0.155 4928 Planarity : 0.004 0.041 5424 Dihedral : 18.239 175.315 4747 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.42 % Allowed : 10.97 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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: -2.70 (0.12), residues: 3960 helix: -1.46 (0.12), residues: 1336 sheet: -1.96 (0.19), residues: 544 loop : -1.94 (0.12), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 407 TYR 0.015 0.001 TYR H 353 PHE 0.006 0.001 PHE G 402 HIS 0.001 0.000 HIS B 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (31920) covalent geometry : angle 0.60529 / 0.30 (43288) hydrogen bonds : bond 0.03303 / 2.22 ( 1032) hydrogen bonds : angle 5.43773 / 3.73 ( 2952) Misc. bond : bond 0.00070 / 0.04 ( 8) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 685 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 606 time to evaluate : 1.201 Fit side-chains REVERT: A 105 ARG cc_start: 0.7355 (mtp-110) cc_final: 0.6749 (ttp80) REVERT: A 170 GLU cc_start: 0.3609 (OUTLIER) cc_final: 0.3022 (tp30) REVERT: A 203 ARG cc_start: 0.7759 (mpt90) cc_final: 0.7071 (mtp180) REVERT: A 232 ASP cc_start: 0.8789 (m-30) cc_final: 0.8329 (m-30) REVERT: A 235 LEU cc_start: 0.7759 (OUTLIER) cc_final: 0.6829 (pp) REVERT: A 257 LYS cc_start: 0.8133 (mtpt) cc_final: 0.7910 (mttt) REVERT: A 261 ASP cc_start: 0.8267 (t70) cc_final: 0.7446 (m-30) REVERT: A 330 ILE cc_start: 0.9207 (OUTLIER) cc_final: 0.8993 (pp) REVERT: A 351 SER cc_start: 0.8352 (t) cc_final: 0.7946 (m) REVERT: A 410 LYS cc_start: 0.7219 (pttt) cc_final: 0.5870 (mmtt) REVERT: A 487 GLU cc_start: 0.8601 (tt0) cc_final: 0.8345 (tt0) REVERT: A 509 TYR cc_start: 0.8052 (p90) cc_final: 0.7447 (p90) REVERT: B 105 ARG cc_start: 0.7327 (mtp-110) cc_final: 0.6778 (ttp80) REVERT: B 149 ARG cc_start: 0.5869 (mpp-170) cc_final: 0.5575 (mpt180) REVERT: B 170 GLU cc_start: 0.3377 (OUTLIER) cc_final: 0.2575 (tp30) REVERT: B 203 ARG cc_start: 0.7838 (mpt90) cc_final: 0.7089 (mtp180) REVERT: B 217 GLU cc_start: 0.6381 (OUTLIER) cc_final: 0.5823 (mm-30) REVERT: B 228 LYS cc_start: 0.7216 (ptmm) cc_final: 0.6933 (ptmm) REVERT: B 232 ASP cc_start: 0.8720 (m-30) cc_final: 0.8378 (m-30) REVERT: B 235 LEU cc_start: 0.7533 (OUTLIER) cc_final: 0.6553 (pp) REVERT: B 261 ASP cc_start: 0.8124 (t70) cc_final: 0.7268 (m-30) REVERT: B 327 SER cc_start: 0.8941 (p) cc_final: 0.8682 (t) REVERT: B 351 SER cc_start: 0.8444 (t) cc_final: 0.8041 (m) REVERT: B 410 LYS cc_start: 0.7333 (pttt) cc_final: 0.5928 (mmtt) REVERT: B 509 TYR cc_start: 0.8094 (p90) cc_final: 0.7529 (p90) REVERT: C 105 ARG cc_start: 0.7378 (mtp-110) cc_final: 0.6836 (ttp80) REVERT: C 149 ARG cc_start: 0.5891 (mpp-170) cc_final: 0.5605 (mpt180) REVERT: C 170 GLU cc_start: 0.3573 (OUTLIER) cc_final: 0.2598 (tp30) REVERT: C 203 ARG cc_start: 0.7665 (mpt90) cc_final: 0.6925 (mtp180) REVERT: C 232 ASP cc_start: 0.8717 (m-30) cc_final: 0.8235 (m-30) REVERT: C 235 LEU cc_start: 0.7709 (OUTLIER) cc_final: 0.6757 (pp) REVERT: C 257 LYS cc_start: 0.8228 (mtpt) cc_final: 0.8007 (mtmt) REVERT: C 261 ASP cc_start: 0.8286 (t70) cc_final: 0.7483 (m-30) REVERT: C 351 SER cc_start: 0.8408 (t) cc_final: 0.8015 (m) REVERT: C 410 LYS cc_start: 0.7366 (pttt) cc_final: 0.6061 (mmtt) REVERT: D 16 ASP cc_start: 0.8556 (t70) cc_final: 0.8165 (t0) REVERT: D 149 ARG cc_start: 0.5947 (mpp-170) cc_final: 0.5629 (mpt180) REVERT: D 165 PHE cc_start: 0.8418 (m-80) cc_final: 0.8198 (m-80) REVERT: D 170 GLU cc_start: 0.3448 (OUTLIER) cc_final: 0.2694 (tp30) REVERT: D 203 ARG cc_start: 0.7703 (mpt90) cc_final: 0.6916 (mtp180) REVERT: D 217 GLU cc_start: 0.6257 (OUTLIER) cc_final: 0.5864 (mm-30) REVERT: D 228 LYS cc_start: 0.7241 (ptmm) cc_final: 0.7020 (ptmm) REVERT: D 232 ASP cc_start: 0.8705 (m-30) cc_final: 0.8394 (m-30) REVERT: D 235 LEU cc_start: 0.7560 (OUTLIER) cc_final: 0.6569 (pp) REVERT: D 261 ASP cc_start: 0.8150 (t70) cc_final: 0.7263 (m-30) REVERT: D 327 SER cc_start: 0.8935 (p) cc_final: 0.8672 (t) REVERT: D 351 SER cc_start: 0.8430 (t) cc_final: 0.8030 (m) REVERT: D 410 LYS cc_start: 0.7451 (pttt) cc_final: 0.5999 (mmtt) REVERT: D 487 GLU cc_start: 0.8613 (tt0) cc_final: 0.8410 (tt0) REVERT: D 509 TYR cc_start: 0.8082 (p90) cc_final: 0.7471 (p90) REVERT: E 105 ARG cc_start: 0.7323 (mtp-110) cc_final: 0.6739 (ttp80) REVERT: E 149 ARG cc_start: 0.6118 (mpt180) cc_final: 0.5768 (mpt180) REVERT: E 170 GLU cc_start: 0.3364 (OUTLIER) cc_final: 0.2475 (tp30) REVERT: E 203 ARG cc_start: 0.7781 (mpt90) cc_final: 0.7076 (mtp180) REVERT: E 232 ASP cc_start: 0.8733 (m-30) cc_final: 0.8265 (m-30) REVERT: E 235 LEU cc_start: 0.7800 (OUTLIER) cc_final: 0.6822 (pp) REVERT: E 261 ASP cc_start: 0.8264 (t70) cc_final: 0.7453 (m-30) REVERT: E 351 SER cc_start: 0.8415 (t) cc_final: 0.8015 (m) REVERT: E 410 LYS cc_start: 0.7303 (pttt) cc_final: 0.6074 (mmtt) REVERT: F 149 ARG cc_start: 0.5913 (mpp-170) cc_final: 0.5599 (mpt180) REVERT: F 170 GLU cc_start: 0.3281 (OUTLIER) cc_final: 0.2653 (tp30) REVERT: F 196 GLU cc_start: 0.7375 (mp0) cc_final: 0.6937 (mt-10) REVERT: F 203 ARG cc_start: 0.7766 (mpt90) cc_final: 0.7006 (mtp180) REVERT: F 217 GLU cc_start: 0.6433 (OUTLIER) cc_final: 0.5895 (mm-30) REVERT: F 228 LYS cc_start: 0.7175 (ptmm) cc_final: 0.6948 (ptmm) REVERT: F 232 ASP cc_start: 0.8677 (m-30) cc_final: 0.8367 (m-30) REVERT: F 235 LEU cc_start: 0.7554 (OUTLIER) cc_final: 0.6589 (pp) REVERT: F 261 ASP cc_start: 0.8122 (t70) cc_final: 0.7241 (m-30) REVERT: F 327 SER cc_start: 0.8959 (p) cc_final: 0.8675 (t) REVERT: F 351 SER cc_start: 0.8427 (t) cc_final: 0.8035 (m) REVERT: F 408 LEU cc_start: 0.6914 (OUTLIER) cc_final: 0.6712 (pp) REVERT: F 410 LYS cc_start: 0.7420 (pttt) cc_final: 0.6009 (mmtt) REVERT: F 487 GLU cc_start: 0.8624 (tt0) cc_final: 0.8423 (tt0) REVERT: F 509 TYR cc_start: 0.8065 (p90) cc_final: 0.7469 (p90) REVERT: G 170 GLU cc_start: 0.3454 (OUTLIER) cc_final: 0.2879 (tp30) REVERT: G 203 ARG cc_start: 0.7712 (mpt90) cc_final: 0.7034 (mtp180) REVERT: G 232 ASP cc_start: 0.8709 (m-30) cc_final: 0.8239 (m-30) REVERT: G 235 LEU cc_start: 0.7712 (OUTLIER) cc_final: 0.6789 (pp) REVERT: G 257 LYS cc_start: 0.8086 (mtpt) cc_final: 0.7862 (mttt) REVERT: G 261 ASP cc_start: 0.8246 (t70) cc_final: 0.7425 (m-30) REVERT: G 351 SER cc_start: 0.8327 (t) cc_final: 0.7949 (m) REVERT: G 386 MET cc_start: 0.9248 (mtm) cc_final: 0.8982 (mtp) REVERT: G 410 LYS cc_start: 0.7262 (pttt) cc_final: 0.5952 (mmtt) REVERT: G 487 GLU cc_start: 0.8560 (tt0) cc_final: 0.8358 (tt0) REVERT: H 105 ARG cc_start: 0.7282 (mtp-110) cc_final: 0.6723 (ttp80) REVERT: H 149 ARG cc_start: 0.5802 (mpp-170) cc_final: 0.5529 (mpt180) REVERT: H 170 GLU cc_start: 0.3324 (OUTLIER) cc_final: 0.2460 (tp30) REVERT: H 196 GLU cc_start: 0.7481 (mp0) cc_final: 0.7029 (mt-10) REVERT: H 217 GLU cc_start: 0.6370 (OUTLIER) cc_final: 0.5830 (mm-30) REVERT: H 235 LEU cc_start: 0.7554 (OUTLIER) cc_final: 0.6562 (pp) REVERT: H 261 ASP cc_start: 0.8126 (t70) cc_final: 0.7232 (m-30) REVERT: H 327 SER cc_start: 0.8967 (p) cc_final: 0.8690 (t) REVERT: H 351 SER cc_start: 0.8414 (t) cc_final: 0.7998 (m) REVERT: H 410 LYS cc_start: 0.7406 (pttt) cc_final: 0.6057 (mmtt) REVERT: H 459 TYR cc_start: 0.8800 (t80) cc_final: 0.8572 (t80) REVERT: H 509 TYR cc_start: 0.8051 (p90) cc_final: 0.7451 (p90) REVERT: O 1 MET cc_start: 0.4694 (mtt) cc_final: 0.4338 (mmm) REVERT: O 5 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8157 (mp) REVERT: P 5 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8270 (mp) outliers start: 79 outliers final: 35 residues processed: 659 average time/residue: 0.1872 time to fit residues: 200.4646 Evaluate side-chains 564 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 505 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 280 SER Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 217 GLU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 170 GLU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 280 SER Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 329 SER Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 170 GLU Chi-restraints excluded: chain F residue 217 GLU Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 280 SER Chi-restraints excluded: chain F residue 408 LEU Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 170 GLU Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 280 SER Chi-restraints excluded: chain G residue 329 SER Chi-restraints excluded: chain G residue 496 SER Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 170 GLU Chi-restraints excluded: chain H residue 217 GLU Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 280 SER Chi-restraints excluded: chain O residue 5 LEU Chi-restraints excluded: chain P residue 5 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 223 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 263 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 306 optimal weight: 0.9980 chunk 133 optimal weight: 3.9990 chunk 265 optimal weight: 0.9990 chunk 174 optimal weight: 1.9990 chunk 77 optimal weight: 0.4980 chunk 317 optimal weight: 0.0570 chunk 346 optimal weight: 0.0470 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 243 GLN A 334 GLN B 243 GLN B 334 GLN C 243 GLN C 334 GLN D 112 GLN D 243 GLN D 334 GLN E 48 GLN E 243 GLN E 334 GLN F 243 GLN F 334 GLN G 243 GLN G 334 GLN H 112 GLN H 243 GLN H 334 GLN H 498 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.160541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.124466 restraints weight = 36153.428| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.42 r_work: 0.3259 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 31928 Z= 0.105 Angle : 0.559 6.826 43288 Z= 0.274 Chirality : 0.043 0.135 4928 Planarity : 0.004 0.039 5424 Dihedral : 17.456 177.408 4677 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.31 % Allowed : 11.64 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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: -1.81 (0.12), residues: 3960 helix: -0.35 (0.14), residues: 1328 sheet: -1.55 (0.21), residues: 544 loop : -1.66 (0.12), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 493 TYR 0.015 0.001 TYR E 509 PHE 0.009 0.001 PHE H 402 HIS 0.001 0.000 HIS A 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.10 (31920) covalent geometry : angle 0.55928 / 0.27 (43288) hydrogen bonds : bond 0.02676 / 1.79 ( 1032) hydrogen bonds : angle 4.81076 / 3.30 ( 2952) Misc. bond : bond 0.00025 / 0.02 ( 8) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 668 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 560 time to evaluate : 0.880 Fit side-chains REVERT: A 105 ARG cc_start: 0.7306 (mtp-110) cc_final: 0.6765 (ttp80) REVERT: A 149 ARG cc_start: 0.6002 (mpt180) cc_final: 0.5536 (mpt180) REVERT: A 170 GLU cc_start: 0.3655 (OUTLIER) cc_final: 0.2636 (tp30) REVERT: A 196 GLU cc_start: 0.7573 (mp0) cc_final: 0.7126 (mt-10) REVERT: A 203 ARG cc_start: 0.7753 (mpt90) cc_final: 0.6996 (mtp180) REVERT: A 232 ASP cc_start: 0.8643 (m-30) cc_final: 0.8234 (m-30) REVERT: A 235 LEU cc_start: 0.7576 (OUTLIER) cc_final: 0.6672 (pp) REVERT: A 257 LYS cc_start: 0.8059 (mtpt) cc_final: 0.7699 (mtmt) REVERT: A 261 ASP cc_start: 0.8318 (t70) cc_final: 0.7551 (m-30) REVERT: A 286 MET cc_start: 0.8741 (tpp) cc_final: 0.8121 (tpt) REVERT: A 330 ILE cc_start: 0.9241 (OUTLIER) cc_final: 0.8944 (pp) REVERT: A 351 SER cc_start: 0.8291 (t) cc_final: 0.7898 (m) REVERT: A 410 LYS cc_start: 0.7269 (pttt) cc_final: 0.5962 (mmtt) REVERT: A 509 TYR cc_start: 0.8180 (p90) cc_final: 0.7600 (p90) REVERT: B 105 ARG cc_start: 0.7278 (mtp-110) cc_final: 0.6743 (ttp80) REVERT: B 170 GLU cc_start: 0.3503 (OUTLIER) cc_final: 0.2449 (tp30) REVERT: B 196 GLU cc_start: 0.7597 (mp0) cc_final: 0.7155 (mt-10) REVERT: B 203 ARG cc_start: 0.7774 (mpt90) cc_final: 0.6844 (mtm110) REVERT: B 217 GLU cc_start: 0.6249 (OUTLIER) cc_final: 0.5830 (mm-30) REVERT: B 232 ASP cc_start: 0.8652 (m-30) cc_final: 0.8228 (m-30) REVERT: B 235 LEU cc_start: 0.7401 (OUTLIER) cc_final: 0.6428 (pp) REVERT: B 257 LYS cc_start: 0.8052 (OUTLIER) cc_final: 0.7798 (mttt) REVERT: B 261 ASP cc_start: 0.8233 (t70) cc_final: 0.7446 (m-30) REVERT: B 286 MET cc_start: 0.8762 (tpp) cc_final: 0.8229 (tpt) REVERT: B 351 SER cc_start: 0.8396 (t) cc_final: 0.8010 (m) REVERT: B 410 LYS cc_start: 0.7387 (pttt) cc_final: 0.6049 (mmtt) REVERT: B 411 TYR cc_start: 0.8161 (t80) cc_final: 0.7680 (t80) REVERT: B 509 TYR cc_start: 0.8184 (p90) cc_final: 0.7596 (p90) REVERT: C 13 VAL cc_start: 0.8545 (t) cc_final: 0.8237 (p) REVERT: C 105 ARG cc_start: 0.7328 (mtp-110) cc_final: 0.6796 (ttp80) REVERT: C 149 ARG cc_start: 0.5940 (mpp-170) cc_final: 0.5582 (mpt180) REVERT: C 170 GLU cc_start: 0.3924 (OUTLIER) cc_final: 0.2643 (tp30) REVERT: C 196 GLU cc_start: 0.7376 (mp0) cc_final: 0.6908 (mt-10) REVERT: C 203 ARG cc_start: 0.7729 (mpt90) cc_final: 0.6967 (mtp180) REVERT: C 232 ASP cc_start: 0.8567 (m-30) cc_final: 0.8144 (m-30) REVERT: C 235 LEU cc_start: 0.7582 (OUTLIER) cc_final: 0.6711 (pp) REVERT: C 261 ASP cc_start: 0.8325 (t0) cc_final: 0.7579 (m-30) REVERT: C 351 SER cc_start: 0.8336 (t) cc_final: 0.7955 (m) REVERT: C 410 LYS cc_start: 0.7285 (pttt) cc_final: 0.6050 (mmtt) REVERT: C 509 TYR cc_start: 0.8090 (p90) cc_final: 0.7749 (p90) REVERT: D 13 VAL cc_start: 0.8394 (t) cc_final: 0.8088 (p) REVERT: D 16 ASP cc_start: 0.8572 (t70) cc_final: 0.8312 (t0) REVERT: D 170 GLU cc_start: 0.3639 (OUTLIER) cc_final: 0.2560 (tp30) REVERT: D 196 GLU cc_start: 0.7520 (mp0) cc_final: 0.7058 (mt-10) REVERT: D 217 GLU cc_start: 0.6139 (OUTLIER) cc_final: 0.5761 (mm-30) REVERT: D 232 ASP cc_start: 0.8621 (m-30) cc_final: 0.8201 (m-30) REVERT: D 235 LEU cc_start: 0.7399 (OUTLIER) cc_final: 0.6462 (pp) REVERT: D 261 ASP cc_start: 0.8247 (t0) cc_final: 0.7445 (m-30) REVERT: D 286 MET cc_start: 0.8762 (tpp) cc_final: 0.8246 (tpt) REVERT: D 351 SER cc_start: 0.8446 (t) cc_final: 0.8058 (m) REVERT: D 410 LYS cc_start: 0.7361 (pttt) cc_final: 0.5963 (mmtt) REVERT: E 105 ARG cc_start: 0.7258 (mtp-110) cc_final: 0.6694 (ttp80) REVERT: E 149 ARG cc_start: 0.6157 (mpt180) cc_final: 0.5684 (mpt180) REVERT: E 170 GLU cc_start: 0.3706 (OUTLIER) cc_final: 0.2484 (tp30) REVERT: E 196 GLU cc_start: 0.7646 (mp0) cc_final: 0.7182 (mt-10) REVERT: E 203 ARG cc_start: 0.7847 (mpt90) cc_final: 0.6952 (mtm110) REVERT: E 232 ASP cc_start: 0.8597 (m-30) cc_final: 0.8174 (m-30) REVERT: E 235 LEU cc_start: 0.7613 (OUTLIER) cc_final: 0.6710 (pp) REVERT: E 261 ASP cc_start: 0.8324 (t70) cc_final: 0.7603 (m-30) REVERT: E 286 MET cc_start: 0.8794 (tpp) cc_final: 0.8214 (tpt) REVERT: E 351 SER cc_start: 0.8414 (t) cc_final: 0.8032 (m) REVERT: E 386 MET cc_start: 0.9230 (mtm) cc_final: 0.9019 (mtp) REVERT: E 410 LYS cc_start: 0.7357 (pttt) cc_final: 0.6160 (mmtt) REVERT: E 509 TYR cc_start: 0.8090 (p90) cc_final: 0.7745 (p90) REVERT: F 149 ARG cc_start: 0.5948 (mpp-170) cc_final: 0.5646 (mpt180) REVERT: F 170 GLU cc_start: 0.3382 (OUTLIER) cc_final: 0.2292 (tp30) REVERT: F 196 GLU cc_start: 0.7582 (mp0) cc_final: 0.7113 (mt-10) REVERT: F 217 GLU cc_start: 0.6364 (OUTLIER) cc_final: 0.5870 (tp30) REVERT: F 232 ASP cc_start: 0.8597 (m-30) cc_final: 0.8162 (m-30) REVERT: F 235 LEU cc_start: 0.7368 (OUTLIER) cc_final: 0.6384 (pp) REVERT: F 261 ASP cc_start: 0.8211 (t0) cc_final: 0.7431 (m-30) REVERT: F 286 MET cc_start: 0.8792 (tpp) cc_final: 0.8259 (tpt) REVERT: F 351 SER cc_start: 0.8404 (t) cc_final: 0.8022 (m) REVERT: F 410 LYS cc_start: 0.7461 (pttt) cc_final: 0.6188 (mmtt) REVERT: F 509 TYR cc_start: 0.8160 (p90) cc_final: 0.7560 (p90) REVERT: G 149 ARG cc_start: 0.6015 (mpt180) cc_final: 0.5571 (mpt180) REVERT: G 170 GLU cc_start: 0.3602 (OUTLIER) cc_final: 0.2545 (tp30) REVERT: G 196 GLU cc_start: 0.7566 (mp0) cc_final: 0.7092 (mt-10) REVERT: G 203 ARG cc_start: 0.7724 (mpt90) cc_final: 0.6991 (mtp180) REVERT: G 232 ASP cc_start: 0.8576 (m-30) cc_final: 0.8162 (m-30) REVERT: G 235 LEU cc_start: 0.7602 (OUTLIER) cc_final: 0.6739 (pp) REVERT: G 257 LYS cc_start: 0.8042 (mtpt) cc_final: 0.7672 (mtmt) REVERT: G 261 ASP cc_start: 0.8316 (t0) cc_final: 0.7572 (m-30) REVERT: G 286 MET cc_start: 0.8793 (tpp) cc_final: 0.8202 (tpt) REVERT: G 330 ILE cc_start: 0.9170 (OUTLIER) cc_final: 0.8942 (pp) REVERT: G 351 SER cc_start: 0.8305 (t) cc_final: 0.7942 (m) REVERT: G 410 LYS cc_start: 0.7274 (pttt) cc_final: 0.6005 (mmtt) REVERT: G 509 TYR cc_start: 0.8080 (p90) cc_final: 0.7739 (p90) REVERT: H 105 ARG cc_start: 0.7208 (mtp-110) cc_final: 0.6677 (ttp80) REVERT: H 149 ARG cc_start: 0.5851 (mpp-170) cc_final: 0.5596 (mpt180) REVERT: H 170 GLU cc_start: 0.3504 (OUTLIER) cc_final: 0.2533 (tp30) REVERT: H 196 GLU cc_start: 0.7695 (mp0) cc_final: 0.7230 (mt-10) REVERT: H 217 GLU cc_start: 0.6229 (OUTLIER) cc_final: 0.5744 (tp30) REVERT: H 235 LEU cc_start: 0.7361 (OUTLIER) cc_final: 0.6405 (pp) REVERT: H 261 ASP cc_start: 0.8213 (t0) cc_final: 0.7409 (m-30) REVERT: H 286 MET cc_start: 0.8714 (tpp) cc_final: 0.8208 (tpt) REVERT: H 351 SER cc_start: 0.8406 (t) cc_final: 0.8025 (m) REVERT: H 410 LYS cc_start: 0.7350 (pttt) cc_final: 0.5959 (mmtt) REVERT: H 509 TYR cc_start: 0.8145 (p90) cc_final: 0.7554 (p90) REVERT: J 5 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8285 (mp) REVERT: N 1 MET cc_start: 0.4660 (mtt) cc_final: 0.4259 (mmm) REVERT: N 5 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8368 (mp) outliers start: 108 outliers final: 63 residues processed: 640 average time/residue: 0.1809 time to fit residues: 190.4708 Evaluate side-chains 604 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 516 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 257 LYS Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 485 SER Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 280 SER Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 485 SER Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 217 GLU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 257 LYS Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 485 SER Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 170 GLU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 275 SER Chi-restraints excluded: chain E residue 280 SER Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 485 SER Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 170 GLU Chi-restraints excluded: chain F residue 217 GLU Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 275 SER Chi-restraints excluded: chain F residue 280 SER Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 485 SER Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 170 GLU Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 275 SER Chi-restraints excluded: chain G residue 280 SER Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 485 SER Chi-restraints excluded: chain G residue 496 SER Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 170 GLU Chi-restraints excluded: chain H residue 217 GLU Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 257 LYS Chi-restraints excluded: chain H residue 280 SER Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 339 CYS Chi-restraints excluded: chain H residue 485 SER Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain N residue 5 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 240 optimal weight: 6.9990 chunk 65 optimal weight: 6.9990 chunk 156 optimal weight: 3.9990 chunk 309 optimal weight: 3.9990 chunk 195 optimal weight: 0.7980 chunk 278 optimal weight: 0.9990 chunk 320 optimal weight: 2.9990 chunk 352 optimal weight: 0.1980 chunk 198 optimal weight: 4.9990 chunk 59 optimal weight: 6.9990 chunk 116 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 48 GLN A 334 GLN A 466 HIS B 334 GLN B 466 HIS ** C 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 GLN C 466 HIS D 334 GLN D 466 HIS E 48 GLN E 334 GLN E 466 HIS F 334 GLN F 466 HIS G 48 GLN G 334 GLN G 466 HIS ** H 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 466 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.151319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.115084 restraints weight = 36400.022| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.36 r_work: 0.3136 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 31928 Z= 0.204 Angle : 0.636 7.166 43288 Z= 0.313 Chirality : 0.047 0.144 4928 Planarity : 0.004 0.040 5424 Dihedral : 17.240 177.823 4675 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 4.66 % Allowed : 11.76 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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: -1.33 (0.13), residues: 3960 helix: 0.19 (0.15), residues: 1336 sheet: -1.47 (0.20), residues: 584 loop : -1.42 (0.13), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 493 TYR 0.018 0.002 TYR D 348 PHE 0.009 0.001 PHE G 24 HIS 0.002 0.000 HIS B 372 Details of bonding type rmsd/Z covalent geometry : bond 0.00500 / 0.20 (31920) covalent geometry : angle 0.63632 / 0.31 (43288) hydrogen bonds : bond 0.03312 / 2.23 ( 1032) hydrogen bonds : angle 4.77803 / 3.28 ( 2952) Misc. bond : bond 0.00083 / 0.05 ( 8) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 745 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 593 time to evaluate : 1.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 VAL cc_start: 0.8678 (t) cc_final: 0.8432 (p) REVERT: A 15 ASP cc_start: 0.8595 (t0) cc_final: 0.8239 (t70) REVERT: A 105 ARG cc_start: 0.7473 (mtp-110) cc_final: 0.6862 (ttp80) REVERT: A 170 GLU cc_start: 0.3914 (OUTLIER) cc_final: 0.2312 (tp30) REVERT: A 196 GLU cc_start: 0.7651 (mp0) cc_final: 0.7138 (mt-10) REVERT: A 203 ARG cc_start: 0.7922 (mpt90) cc_final: 0.7114 (mtm110) REVERT: A 232 ASP cc_start: 0.8498 (m-30) cc_final: 0.8020 (m-30) REVERT: A 235 LEU cc_start: 0.7763 (OUTLIER) cc_final: 0.6925 (pp) REVERT: A 286 MET cc_start: 0.8808 (tpp) cc_final: 0.8358 (tpt) REVERT: A 330 ILE cc_start: 0.9340 (OUTLIER) cc_final: 0.9033 (pp) REVERT: A 408 LEU cc_start: 0.7059 (OUTLIER) cc_final: 0.6646 (pp) REVERT: A 410 LYS cc_start: 0.7386 (pttt) cc_final: 0.6063 (mmtt) REVERT: B 13 VAL cc_start: 0.8605 (t) cc_final: 0.8381 (p) REVERT: B 105 ARG cc_start: 0.7489 (mtp-110) cc_final: 0.6887 (ttp80) REVERT: B 170 GLU cc_start: 0.3679 (OUTLIER) cc_final: 0.2226 (tp30) REVERT: B 196 GLU cc_start: 0.7645 (mp0) cc_final: 0.7139 (mt-10) REVERT: B 203 ARG cc_start: 0.7905 (mpt90) cc_final: 0.7012 (mtm110) REVERT: B 217 GLU cc_start: 0.6354 (OUTLIER) cc_final: 0.5954 (mm-30) REVERT: B 232 ASP cc_start: 0.8420 (m-30) cc_final: 0.7928 (m-30) REVERT: B 235 LEU cc_start: 0.7573 (OUTLIER) cc_final: 0.6654 (pp) REVERT: B 330 ILE cc_start: 0.9213 (OUTLIER) cc_final: 0.8988 (pp) REVERT: B 408 LEU cc_start: 0.7096 (OUTLIER) cc_final: 0.6653 (pp) REVERT: B 410 LYS cc_start: 0.7609 (pttt) cc_final: 0.6176 (mmtt) REVERT: C 13 VAL cc_start: 0.8750 (t) cc_final: 0.8491 (p) REVERT: C 105 ARG cc_start: 0.7530 (mtp-110) cc_final: 0.6922 (ttp80) REVERT: C 170 GLU cc_start: 0.3740 (OUTLIER) cc_final: 0.2085 (tp30) REVERT: C 196 GLU cc_start: 0.7650 (mp0) cc_final: 0.7125 (mt-10) REVERT: C 203 ARG cc_start: 0.7905 (mpt90) cc_final: 0.7009 (mtm110) REVERT: C 232 ASP cc_start: 0.8387 (m-30) cc_final: 0.7923 (m-30) REVERT: C 235 LEU cc_start: 0.7758 (OUTLIER) cc_final: 0.6918 (pp) REVERT: C 330 ILE cc_start: 0.9248 (OUTLIER) cc_final: 0.8990 (pp) REVERT: C 408 LEU cc_start: 0.6927 (OUTLIER) cc_final: 0.6533 (pp) REVERT: C 410 LYS cc_start: 0.7404 (pttt) cc_final: 0.6018 (mmtt) REVERT: D 13 VAL cc_start: 0.8653 (t) cc_final: 0.8391 (p) REVERT: D 15 ASP cc_start: 0.8644 (t0) cc_final: 0.8317 (t70) REVERT: D 170 GLU cc_start: 0.3820 (OUTLIER) cc_final: 0.2369 (tp30) REVERT: D 196 GLU cc_start: 0.7572 (mp0) cc_final: 0.7041 (mt-10) REVERT: D 217 GLU cc_start: 0.6342 (OUTLIER) cc_final: 0.5951 (mm-30) REVERT: D 232 ASP cc_start: 0.8354 (m-30) cc_final: 0.7852 (m-30) REVERT: D 235 LEU cc_start: 0.7545 (OUTLIER) cc_final: 0.6693 (pp) REVERT: D 330 ILE cc_start: 0.9245 (OUTLIER) cc_final: 0.9023 (pp) REVERT: D 410 LYS cc_start: 0.7493 (pttt) cc_final: 0.5972 (mmtt) REVERT: D 441 GLN cc_start: 0.8225 (mm-40) cc_final: 0.8014 (mm-40) REVERT: E 13 VAL cc_start: 0.8669 (t) cc_final: 0.8417 (p) REVERT: E 15 ASP cc_start: 0.8606 (t0) cc_final: 0.8259 (t70) REVERT: E 105 ARG cc_start: 0.7430 (mtp-110) cc_final: 0.6800 (ttp80) REVERT: E 170 GLU cc_start: 0.3701 (OUTLIER) cc_final: 0.2063 (tp30) REVERT: E 196 GLU cc_start: 0.7715 (mp0) cc_final: 0.7210 (mt-10) REVERT: E 203 ARG cc_start: 0.7963 (mpt90) cc_final: 0.7130 (mtm110) REVERT: E 232 ASP cc_start: 0.8418 (m-30) cc_final: 0.7904 (m-30) REVERT: E 235 LEU cc_start: 0.7758 (OUTLIER) cc_final: 0.6914 (pp) REVERT: E 286 MET cc_start: 0.8873 (tpp) cc_final: 0.8381 (tpt) REVERT: E 330 ILE cc_start: 0.9252 (OUTLIER) cc_final: 0.9020 (pp) REVERT: E 399 GLU cc_start: 0.6626 (OUTLIER) cc_final: 0.6419 (mm-30) REVERT: E 408 LEU cc_start: 0.6946 (OUTLIER) cc_final: 0.6515 (pp) REVERT: E 410 LYS cc_start: 0.7498 (pttt) cc_final: 0.6291 (mmtt) REVERT: F 13 VAL cc_start: 0.8648 (t) cc_final: 0.8408 (p) REVERT: F 15 ASP cc_start: 0.8660 (t0) cc_final: 0.8260 (t70) REVERT: F 170 GLU cc_start: 0.3473 (OUTLIER) cc_final: 0.2026 (tp30) REVERT: F 196 GLU cc_start: 0.7670 (mp0) cc_final: 0.7154 (mt-10) REVERT: F 217 GLU cc_start: 0.6392 (OUTLIER) cc_final: 0.5992 (mm-30) REVERT: F 232 ASP cc_start: 0.8362 (m-30) cc_final: 0.7887 (m-30) REVERT: F 235 LEU cc_start: 0.7565 (OUTLIER) cc_final: 0.6702 (pp) REVERT: F 309 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.8230 (pt0) REVERT: F 330 ILE cc_start: 0.9193 (OUTLIER) cc_final: 0.8987 (pp) REVERT: F 410 LYS cc_start: 0.7470 (pttt) cc_final: 0.5981 (mmtt) REVERT: G 13 VAL cc_start: 0.8671 (t) cc_final: 0.8424 (p) REVERT: G 15 ASP cc_start: 0.8649 (t0) cc_final: 0.8303 (t70) REVERT: G 170 GLU cc_start: 0.3781 (OUTLIER) cc_final: 0.2129 (tp30) REVERT: G 196 GLU cc_start: 0.7737 (mp0) cc_final: 0.7194 (mt-10) REVERT: G 203 ARG cc_start: 0.7960 (mpt90) cc_final: 0.7119 (mtm110) REVERT: G 232 ASP cc_start: 0.8455 (m-30) cc_final: 0.7971 (m-30) REVERT: G 235 LEU cc_start: 0.7674 (OUTLIER) cc_final: 0.6906 (pp) REVERT: G 286 MET cc_start: 0.8831 (tpp) cc_final: 0.8388 (tpt) REVERT: G 330 ILE cc_start: 0.9282 (OUTLIER) cc_final: 0.8976 (pp) REVERT: G 408 LEU cc_start: 0.7030 (OUTLIER) cc_final: 0.6621 (pp) REVERT: G 410 LYS cc_start: 0.7571 (pttt) cc_final: 0.6300 (mmtt) REVERT: H 13 VAL cc_start: 0.8638 (t) cc_final: 0.8414 (p) REVERT: H 105 ARG cc_start: 0.7414 (mtp-110) cc_final: 0.6812 (ttp80) REVERT: H 149 ARG cc_start: 0.6080 (mpp-170) cc_final: 0.5877 (mpt180) REVERT: H 170 GLU cc_start: 0.3840 (OUTLIER) cc_final: 0.2294 (tp30) REVERT: H 196 GLU cc_start: 0.7773 (mp0) cc_final: 0.7253 (mt-10) REVERT: H 217 GLU cc_start: 0.6289 (OUTLIER) cc_final: 0.5896 (mm-30) REVERT: H 235 LEU cc_start: 0.7576 (OUTLIER) cc_final: 0.6663 (pp) REVERT: H 286 MET cc_start: 0.8781 (tpp) cc_final: 0.8379 (tpt) REVERT: H 330 ILE cc_start: 0.9211 (OUTLIER) cc_final: 0.9000 (pp) REVERT: H 408 LEU cc_start: 0.7103 (OUTLIER) cc_final: 0.6618 (pp) REVERT: H 410 LYS cc_start: 0.7416 (pttt) cc_final: 0.6035 (mmtt) outliers start: 152 outliers final: 80 residues processed: 710 average time/residue: 0.1821 time to fit residues: 215.3162 Evaluate side-chains 653 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 537 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 339 CYS Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 485 SER Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 280 SER Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 485 SER Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 217 GLU Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 485 SER Chi-restraints excluded: chain D residue 496 SER Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 170 GLU Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 275 SER Chi-restraints excluded: chain E residue 280 SER Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 329 SER Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 339 CYS Chi-restraints excluded: chain E residue 399 GLU Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain E residue 485 SER Chi-restraints excluded: chain E residue 496 SER Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 170 GLU Chi-restraints excluded: chain F residue 217 GLU Chi-restraints excluded: chain F residue 225 THR Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 275 SER Chi-restraints excluded: chain F residue 280 SER Chi-restraints excluded: chain F residue 309 GLN Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 485 SER Chi-restraints excluded: chain F residue 496 SER Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 170 GLU Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 275 SER Chi-restraints excluded: chain G residue 280 SER Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 329 SER Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 339 CYS Chi-restraints excluded: chain G residue 408 LEU Chi-restraints excluded: chain G residue 485 SER Chi-restraints excluded: chain G residue 496 SER Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 170 GLU Chi-restraints excluded: chain H residue 217 GLU Chi-restraints excluded: chain H residue 225 THR Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 275 SER Chi-restraints excluded: chain H residue 280 SER Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 339 CYS Chi-restraints excluded: chain H residue 408 LEU Chi-restraints excluded: chain H residue 485 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 139 optimal weight: 0.6980 chunk 187 optimal weight: 0.9990 chunk 209 optimal weight: 6.9990 chunk 69 optimal weight: 0.6980 chunk 236 optimal weight: 2.9990 chunk 375 optimal weight: 3.9990 chunk 386 optimal weight: 0.9980 chunk 75 optimal weight: 0.7980 chunk 73 optimal weight: 3.9990 chunk 232 optimal weight: 4.9990 chunk 382 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 48 GLN ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 334 GLN B 309 GLN B 334 GLN ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 GLN ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 GLN E 48 GLN ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 334 GLN F 334 GLN G 48 GLN G 309 GLN G 334 GLN ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 334 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.154200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.118253 restraints weight = 36353.042| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.37 r_work: 0.3173 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 31928 Z= 0.127 Angle : 0.571 7.175 43288 Z= 0.278 Chirality : 0.044 0.152 4928 Planarity : 0.004 0.041 5424 Dihedral : 16.978 174.809 4671 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 3.71 % Allowed : 14.00 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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: -1.06 (0.13), residues: 3960 helix: 0.54 (0.15), residues: 1336 sheet: -1.35 (0.21), residues: 544 loop : -1.35 (0.13), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 136 TYR 0.023 0.001 TYR D 110 PHE 0.012 0.001 PHE D 401 HIS 0.002 0.000 HIS G 504 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (31920) covalent geometry : angle 0.57069 / 0.28 (43288) hydrogen bonds : bond 0.02683 / 1.78 ( 1032) hydrogen bonds : angle 4.58637 / 3.13 ( 2952) Misc. bond : bond 0.00013 / 0.01 ( 8) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 667 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 546 time to evaluate : 0.978 Fit side-chains REVERT: A 13 VAL cc_start: 0.8685 (t) cc_final: 0.8403 (p) REVERT: A 105 ARG cc_start: 0.7387 (mtp-110) cc_final: 0.6756 (ttp80) REVERT: A 170 GLU cc_start: 0.3798 (OUTLIER) cc_final: 0.2381 (tp30) REVERT: A 196 GLU cc_start: 0.7669 (mp0) cc_final: 0.7166 (mt-10) REVERT: A 203 ARG cc_start: 0.7907 (mpt90) cc_final: 0.7041 (mtm110) REVERT: A 232 ASP cc_start: 0.8492 (m-30) cc_final: 0.8042 (m-30) REVERT: A 235 LEU cc_start: 0.7597 (OUTLIER) cc_final: 0.6809 (pp) REVERT: A 286 MET cc_start: 0.8807 (tpp) cc_final: 0.8364 (tpt) REVERT: A 330 ILE cc_start: 0.9306 (OUTLIER) cc_final: 0.9014 (pp) REVERT: A 408 LEU cc_start: 0.6909 (OUTLIER) cc_final: 0.6473 (pp) REVERT: A 410 LYS cc_start: 0.7395 (pttt) cc_final: 0.6041 (mmtt) REVERT: B 13 VAL cc_start: 0.8652 (t) cc_final: 0.8393 (p) REVERT: B 105 ARG cc_start: 0.7411 (mtp-110) cc_final: 0.6800 (ttp80) REVERT: B 126 ARG cc_start: 0.4961 (mpt90) cc_final: 0.2061 (mtp180) REVERT: B 170 GLU cc_start: 0.3555 (OUTLIER) cc_final: 0.3317 (mp0) REVERT: B 196 GLU cc_start: 0.7678 (mp0) cc_final: 0.7210 (mt-10) REVERT: B 203 ARG cc_start: 0.7914 (mpt90) cc_final: 0.6963 (mtm110) REVERT: B 217 GLU cc_start: 0.6273 (OUTLIER) cc_final: 0.5856 (mm-30) REVERT: B 232 ASP cc_start: 0.8448 (m-30) cc_final: 0.8025 (m-30) REVERT: B 235 LEU cc_start: 0.7456 (OUTLIER) cc_final: 0.6597 (pp) REVERT: B 286 MET cc_start: 0.8798 (tpp) cc_final: 0.8345 (tpt) REVERT: B 330 ILE cc_start: 0.9218 (OUTLIER) cc_final: 0.8995 (pp) REVERT: B 410 LYS cc_start: 0.7408 (pttt) cc_final: 0.5917 (mmtt) REVERT: C 13 VAL cc_start: 0.8718 (t) cc_final: 0.8444 (p) REVERT: C 105 ARG cc_start: 0.7435 (mtp-110) cc_final: 0.6804 (ttp80) REVERT: C 170 GLU cc_start: 0.3526 (OUTLIER) cc_final: 0.2090 (tp30) REVERT: C 196 GLU cc_start: 0.7609 (mp0) cc_final: 0.7111 (mt-10) REVERT: C 203 ARG cc_start: 0.7833 (mpt90) cc_final: 0.6992 (mtm110) REVERT: C 217 GLU cc_start: 0.5999 (tp30) cc_final: 0.5712 (tp30) REVERT: C 228 LYS cc_start: 0.7711 (tttp) cc_final: 0.7354 (tttp) REVERT: C 232 ASP cc_start: 0.8444 (m-30) cc_final: 0.8001 (m-30) REVERT: C 235 LEU cc_start: 0.7557 (OUTLIER) cc_final: 0.6786 (pp) REVERT: C 286 MET cc_start: 0.8817 (tpp) cc_final: 0.8238 (tpt) REVERT: C 330 ILE cc_start: 0.9234 (OUTLIER) cc_final: 0.8991 (pp) REVERT: C 410 LYS cc_start: 0.7328 (pttt) cc_final: 0.5964 (mmtt) REVERT: D 13 VAL cc_start: 0.8601 (t) cc_final: 0.8319 (p) REVERT: D 15 ASP cc_start: 0.8675 (t0) cc_final: 0.8301 (t70) REVERT: D 126 ARG cc_start: 0.4984 (mpt90) cc_final: 0.2047 (mtp180) REVERT: D 170 GLU cc_start: 0.3525 (OUTLIER) cc_final: 0.3248 (mp0) REVERT: D 196 GLU cc_start: 0.7611 (mp0) cc_final: 0.7117 (mt-10) REVERT: D 217 GLU cc_start: 0.6193 (OUTLIER) cc_final: 0.5829 (mm-30) REVERT: D 232 ASP cc_start: 0.8390 (m-30) cc_final: 0.7952 (m-30) REVERT: D 235 LEU cc_start: 0.7392 (OUTLIER) cc_final: 0.6545 (pp) REVERT: D 330 ILE cc_start: 0.9250 (OUTLIER) cc_final: 0.9038 (pp) REVERT: D 408 LEU cc_start: 0.6952 (OUTLIER) cc_final: 0.6658 (pp) REVERT: D 410 LYS cc_start: 0.7447 (pttt) cc_final: 0.5954 (mmtt) REVERT: D 441 GLN cc_start: 0.8120 (mm-40) cc_final: 0.7920 (mm-40) REVERT: E 34 ASP cc_start: 0.8926 (OUTLIER) cc_final: 0.8706 (m-30) REVERT: E 105 ARG cc_start: 0.7367 (mtp-110) cc_final: 0.6733 (ttp80) REVERT: E 170 GLU cc_start: 0.3655 (OUTLIER) cc_final: 0.2157 (tp30) REVERT: E 196 GLU cc_start: 0.7755 (mp0) cc_final: 0.7266 (mt-10) REVERT: E 203 ARG cc_start: 0.7984 (mpt90) cc_final: 0.7166 (mtm110) REVERT: E 232 ASP cc_start: 0.8385 (m-30) cc_final: 0.7942 (m-30) REVERT: E 235 LEU cc_start: 0.7624 (OUTLIER) cc_final: 0.6828 (pp) REVERT: E 286 MET cc_start: 0.8819 (tpp) cc_final: 0.8384 (tpt) REVERT: E 330 ILE cc_start: 0.9236 (OUTLIER) cc_final: 0.9007 (pp) REVERT: E 410 LYS cc_start: 0.7356 (pttt) cc_final: 0.6136 (mmtt) REVERT: F 13 VAL cc_start: 0.8639 (t) cc_final: 0.8366 (p) REVERT: F 15 ASP cc_start: 0.8661 (t0) cc_final: 0.8252 (t70) REVERT: F 126 ARG cc_start: 0.4967 (mpt90) cc_final: 0.2072 (mtp180) REVERT: F 170 GLU cc_start: 0.3452 (OUTLIER) cc_final: 0.3175 (mp0) REVERT: F 196 GLU cc_start: 0.7740 (mp0) cc_final: 0.7228 (mt-10) REVERT: F 217 GLU cc_start: 0.6300 (OUTLIER) cc_final: 0.6084 (tp30) REVERT: F 232 ASP cc_start: 0.8354 (m-30) cc_final: 0.7926 (m-30) REVERT: F 235 LEU cc_start: 0.7414 (OUTLIER) cc_final: 0.6553 (pp) REVERT: F 410 LYS cc_start: 0.7369 (pttt) cc_final: 0.5938 (mmtt) REVERT: G 13 VAL cc_start: 0.8670 (t) cc_final: 0.8385 (p) REVERT: G 15 ASP cc_start: 0.8603 (t0) cc_final: 0.8293 (t70) REVERT: G 170 GLU cc_start: 0.3664 (OUTLIER) cc_final: 0.2203 (tp30) REVERT: G 196 GLU cc_start: 0.7679 (mp0) cc_final: 0.7162 (mt-10) REVERT: G 203 ARG cc_start: 0.7923 (mpt90) cc_final: 0.7121 (mtm110) REVERT: G 232 ASP cc_start: 0.8427 (m-30) cc_final: 0.7974 (m-30) REVERT: G 235 LEU cc_start: 0.7524 (OUTLIER) cc_final: 0.6767 (pp) REVERT: G 286 MET cc_start: 0.8797 (tpp) cc_final: 0.8365 (tpt) REVERT: G 330 ILE cc_start: 0.9259 (OUTLIER) cc_final: 0.8980 (pp) REVERT: G 408 LEU cc_start: 0.6894 (OUTLIER) cc_final: 0.6468 (pp) REVERT: G 410 LYS cc_start: 0.7367 (pttt) cc_final: 0.6053 (mmtt) REVERT: H 13 VAL cc_start: 0.8629 (t) cc_final: 0.8361 (p) REVERT: H 105 ARG cc_start: 0.7340 (mtp-110) cc_final: 0.6729 (ttp80) REVERT: H 170 GLU cc_start: 0.3648 (OUTLIER) cc_final: 0.2287 (tp30) REVERT: H 196 GLU cc_start: 0.7817 (mp0) cc_final: 0.7315 (mt-10) REVERT: H 199 GLU cc_start: 0.7929 (mm-30) cc_final: 0.7480 (mt-10) REVERT: H 217 GLU cc_start: 0.6156 (OUTLIER) cc_final: 0.5776 (mm-30) REVERT: H 235 LEU cc_start: 0.7432 (OUTLIER) cc_final: 0.6574 (pp) REVERT: H 286 MET cc_start: 0.8750 (tpp) cc_final: 0.8367 (tpt) REVERT: H 330 ILE cc_start: 0.9199 (OUTLIER) cc_final: 0.8982 (pp) REVERT: H 410 LYS cc_start: 0.7406 (pttt) cc_final: 0.5951 (mmtt) outliers start: 121 outliers final: 71 residues processed: 639 average time/residue: 0.1820 time to fit residues: 193.0136 Evaluate side-chains 624 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 522 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 331 CYS Chi-restraints excluded: chain B residue 485 SER Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 280 SER Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 485 SER Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 217 GLU Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 331 CYS Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 485 SER Chi-restraints excluded: chain D residue 496 SER Chi-restraints excluded: chain E residue 34 ASP Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 170 GLU Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 275 SER Chi-restraints excluded: chain E residue 280 SER Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 329 SER Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 496 SER Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 170 GLU Chi-restraints excluded: chain F residue 217 GLU Chi-restraints excluded: chain F residue 225 THR Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 275 SER Chi-restraints excluded: chain F residue 280 SER Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 331 CYS Chi-restraints excluded: chain F residue 485 SER Chi-restraints excluded: chain F residue 496 SER Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 170 GLU Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 275 SER Chi-restraints excluded: chain G residue 280 SER Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 408 LEU Chi-restraints excluded: chain G residue 485 SER Chi-restraints excluded: chain G residue 496 SER Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 170 GLU Chi-restraints excluded: chain H residue 217 GLU Chi-restraints excluded: chain H residue 225 THR Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 275 SER Chi-restraints excluded: chain H residue 280 SER Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 485 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 336 optimal weight: 0.0570 chunk 341 optimal weight: 2.9990 chunk 288 optimal weight: 6.9990 chunk 339 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 217 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 108 optimal weight: 2.9990 chunk 279 optimal weight: 0.9980 chunk 297 optimal weight: 0.8980 chunk 233 optimal weight: 8.9990 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 48 GLN ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 48 GLN B 112 GLN B 277 GLN B 309 GLN B 334 GLN C 112 GLN ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 GLN D 48 GLN ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 GLN E 48 GLN ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 309 GLN F 334 GLN G 48 GLN G 334 GLN ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 334 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.154868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.119012 restraints weight = 36086.099| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.35 r_work: 0.3184 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 31928 Z= 0.118 Angle : 0.556 7.054 43288 Z= 0.271 Chirality : 0.043 0.131 4928 Planarity : 0.004 0.040 5424 Dihedral : 16.882 174.762 4671 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 4.20 % Allowed : 14.55 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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: -0.84 (0.13), residues: 3960 helix: 0.76 (0.15), residues: 1336 sheet: -1.29 (0.22), residues: 544 loop : -1.23 (0.13), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 136 TYR 0.018 0.001 TYR B 110 PHE 0.010 0.001 PHE D 401 HIS 0.002 0.000 HIS B 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 (31920) covalent geometry : angle 0.55578 / 0.27 (43288) hydrogen bonds : bond 0.02586 / 1.72 ( 1032) hydrogen bonds : angle 4.44515 / 3.04 ( 2952) Misc. bond : bond 0.00013 / 0.01 ( 8) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 683 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 546 time to evaluate : 1.120 Fit side-chains REVERT: A 105 ARG cc_start: 0.7412 (mtp-110) cc_final: 0.6767 (ttp80) REVERT: A 170 GLU cc_start: 0.3806 (OUTLIER) cc_final: 0.2446 (tp30) REVERT: A 196 GLU cc_start: 0.7654 (mp0) cc_final: 0.7188 (mt-10) REVERT: A 199 GLU cc_start: 0.7758 (mm-30) cc_final: 0.7393 (mt-10) REVERT: A 232 ASP cc_start: 0.8516 (m-30) cc_final: 0.8141 (m-30) REVERT: A 235 LEU cc_start: 0.7564 (OUTLIER) cc_final: 0.6821 (pp) REVERT: A 330 ILE cc_start: 0.9330 (OUTLIER) cc_final: 0.9035 (pp) REVERT: A 408 LEU cc_start: 0.6915 (OUTLIER) cc_final: 0.6498 (pp) REVERT: A 410 LYS cc_start: 0.7430 (pttt) cc_final: 0.6071 (mmtt) REVERT: B 13 VAL cc_start: 0.8679 (t) cc_final: 0.8411 (p) REVERT: B 105 ARG cc_start: 0.7426 (mtp-110) cc_final: 0.6808 (ttp80) REVERT: B 126 ARG cc_start: 0.5018 (mpt90) cc_final: 0.2399 (mmm-85) REVERT: B 196 GLU cc_start: 0.7658 (mp0) cc_final: 0.7227 (mt-10) REVERT: B 199 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7489 (mt-10) REVERT: B 217 GLU cc_start: 0.6230 (OUTLIER) cc_final: 0.5845 (mm-30) REVERT: B 228 LYS cc_start: 0.7730 (tttp) cc_final: 0.7408 (tttp) REVERT: B 232 ASP cc_start: 0.8514 (m-30) cc_final: 0.8121 (m-30) REVERT: B 235 LEU cc_start: 0.7453 (OUTLIER) cc_final: 0.6632 (pp) REVERT: B 330 ILE cc_start: 0.9212 (OUTLIER) cc_final: 0.8985 (pp) REVERT: B 408 LEU cc_start: 0.6966 (OUTLIER) cc_final: 0.6593 (pp) REVERT: B 410 LYS cc_start: 0.7416 (pttt) cc_final: 0.5941 (mmtt) REVERT: C 13 VAL cc_start: 0.8741 (t) cc_final: 0.8475 (p) REVERT: C 105 ARG cc_start: 0.7459 (mtp-110) cc_final: 0.6802 (ttp80) REVERT: C 170 GLU cc_start: 0.3630 (OUTLIER) cc_final: 0.2260 (tp30) REVERT: C 196 GLU cc_start: 0.7567 (mp0) cc_final: 0.7106 (mt-10) REVERT: C 199 GLU cc_start: 0.7735 (mm-30) cc_final: 0.7340 (mt-10) REVERT: C 228 LYS cc_start: 0.7711 (tttp) cc_final: 0.7401 (tttp) REVERT: C 232 ASP cc_start: 0.8435 (m-30) cc_final: 0.8009 (m-30) REVERT: C 235 LEU cc_start: 0.7544 (OUTLIER) cc_final: 0.6801 (pp) REVERT: C 286 MET cc_start: 0.8821 (tpp) cc_final: 0.8313 (tpt) REVERT: C 330 ILE cc_start: 0.9252 (OUTLIER) cc_final: 0.9012 (pp) REVERT: C 408 LEU cc_start: 0.6898 (OUTLIER) cc_final: 0.6524 (pp) REVERT: C 410 LYS cc_start: 0.7374 (pttt) cc_final: 0.5998 (mmtt) REVERT: C 459 TYR cc_start: 0.8817 (t80) cc_final: 0.8479 (t80) REVERT: D 13 VAL cc_start: 0.8640 (t) cc_final: 0.8374 (p) REVERT: D 15 ASP cc_start: 0.8712 (t0) cc_final: 0.8300 (t70) REVERT: D 126 ARG cc_start: 0.5008 (mpt90) cc_final: 0.2383 (mmm-85) REVERT: D 196 GLU cc_start: 0.7582 (mp0) cc_final: 0.7138 (mt-10) REVERT: D 217 GLU cc_start: 0.6247 (OUTLIER) cc_final: 0.5746 (tp30) REVERT: D 232 ASP cc_start: 0.8463 (m-30) cc_final: 0.8067 (m-30) REVERT: D 235 LEU cc_start: 0.7412 (OUTLIER) cc_final: 0.6588 (pp) REVERT: D 330 ILE cc_start: 0.9270 (OUTLIER) cc_final: 0.9059 (pp) REVERT: D 408 LEU cc_start: 0.6988 (OUTLIER) cc_final: 0.6680 (pp) REVERT: D 410 LYS cc_start: 0.7443 (pttt) cc_final: 0.5942 (mmtt) REVERT: D 441 GLN cc_start: 0.8094 (mm-40) cc_final: 0.7893 (mm-40) REVERT: E 34 ASP cc_start: 0.8923 (OUTLIER) cc_final: 0.8673 (m-30) REVERT: E 105 ARG cc_start: 0.7390 (mtp-110) cc_final: 0.6730 (ttp80) REVERT: E 170 GLU cc_start: 0.3741 (OUTLIER) cc_final: 0.2377 (tp30) REVERT: E 196 GLU cc_start: 0.7742 (mp0) cc_final: 0.7297 (mt-10) REVERT: E 199 GLU cc_start: 0.7770 (mm-30) cc_final: 0.7307 (mt-10) REVERT: E 203 ARG cc_start: 0.7965 (mpt90) cc_final: 0.7129 (mtm110) REVERT: E 232 ASP cc_start: 0.8431 (m-30) cc_final: 0.8023 (m-30) REVERT: E 235 LEU cc_start: 0.7600 (OUTLIER) cc_final: 0.6818 (pp) REVERT: E 286 MET cc_start: 0.8849 (tpp) cc_final: 0.8410 (tpt) REVERT: E 330 ILE cc_start: 0.9230 (OUTLIER) cc_final: 0.9001 (pp) REVERT: E 408 LEU cc_start: 0.6813 (OUTLIER) cc_final: 0.6428 (pp) REVERT: E 410 LYS cc_start: 0.7297 (pttt) cc_final: 0.6075 (mmtt) REVERT: F 13 VAL cc_start: 0.8637 (t) cc_final: 0.8358 (p) REVERT: F 15 ASP cc_start: 0.8698 (t0) cc_final: 0.8311 (t70) REVERT: F 126 ARG cc_start: 0.5037 (mpt90) cc_final: 0.2448 (mmm-85) REVERT: F 196 GLU cc_start: 0.7748 (mp0) cc_final: 0.7220 (mt-10) REVERT: F 217 GLU cc_start: 0.6299 (OUTLIER) cc_final: 0.6073 (tp30) REVERT: F 228 LYS cc_start: 0.7682 (tttp) cc_final: 0.7353 (tttp) REVERT: F 232 ASP cc_start: 0.8381 (m-30) cc_final: 0.7984 (m-30) REVERT: F 235 LEU cc_start: 0.7420 (OUTLIER) cc_final: 0.6597 (pp) REVERT: F 408 LEU cc_start: 0.6962 (OUTLIER) cc_final: 0.6605 (pp) REVERT: F 410 LYS cc_start: 0.7359 (pttt) cc_final: 0.5950 (mmtt) REVERT: F 412 ARG cc_start: 0.8245 (ptp90) cc_final: 0.7885 (ptp90) REVERT: G 170 GLU cc_start: 0.3708 (OUTLIER) cc_final: 0.2337 (tp30) REVERT: G 196 GLU cc_start: 0.7652 (mp0) cc_final: 0.7170 (mt-10) REVERT: G 203 ARG cc_start: 0.7931 (mpt90) cc_final: 0.7088 (mtm110) REVERT: G 232 ASP cc_start: 0.8389 (m-30) cc_final: 0.7980 (m-30) REVERT: G 235 LEU cc_start: 0.7544 (OUTLIER) cc_final: 0.6803 (pp) REVERT: G 330 ILE cc_start: 0.9278 (OUTLIER) cc_final: 0.8922 (pp) REVERT: G 408 LEU cc_start: 0.6888 (OUTLIER) cc_final: 0.6470 (pp) REVERT: G 410 LYS cc_start: 0.7375 (pttt) cc_final: 0.6051 (mmtt) REVERT: H 13 VAL cc_start: 0.8643 (t) cc_final: 0.8369 (p) REVERT: H 105 ARG cc_start: 0.7340 (mtp-110) cc_final: 0.6713 (ttp80) REVERT: H 170 GLU cc_start: 0.3856 (OUTLIER) cc_final: 0.2506 (tp30) REVERT: H 196 GLU cc_start: 0.7838 (mp0) cc_final: 0.7309 (mt-10) REVERT: H 199 GLU cc_start: 0.7904 (mm-30) cc_final: 0.7476 (mt-10) REVERT: H 217 GLU cc_start: 0.6145 (OUTLIER) cc_final: 0.5643 (tp30) REVERT: H 235 LEU cc_start: 0.7394 (OUTLIER) cc_final: 0.6578 (pp) REVERT: H 330 ILE cc_start: 0.9196 (OUTLIER) cc_final: 0.8982 (pp) REVERT: H 408 LEU cc_start: 0.6971 (OUTLIER) cc_final: 0.6530 (pp) REVERT: H 410 LYS cc_start: 0.7382 (pttt) cc_final: 0.5983 (mmtt) outliers start: 137 outliers final: 85 residues processed: 654 average time/residue: 0.1808 time to fit residues: 196.0592 Evaluate side-chains 628 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 510 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 280 SER Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 485 SER Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 217 GLU Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 331 CYS Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 496 SER Chi-restraints excluded: chain E residue 34 ASP Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 170 GLU Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 275 SER Chi-restraints excluded: chain E residue 280 SER Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 329 SER Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 331 CYS Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain E residue 496 SER Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 217 GLU Chi-restraints excluded: chain F residue 225 THR Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 275 SER Chi-restraints excluded: chain F residue 280 SER Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 408 LEU Chi-restraints excluded: chain F residue 485 SER Chi-restraints excluded: chain F residue 496 SER Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 170 GLU Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 275 SER Chi-restraints excluded: chain G residue 280 SER Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 329 SER Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 331 CYS Chi-restraints excluded: chain G residue 408 LEU Chi-restraints excluded: chain G residue 496 SER Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 170 GLU Chi-restraints excluded: chain H residue 217 GLU Chi-restraints excluded: chain H residue 225 THR Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 275 SER Chi-restraints excluded: chain H residue 280 SER Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 331 CYS Chi-restraints excluded: chain H residue 408 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 168 optimal weight: 2.9990 chunk 296 optimal weight: 3.9990 chunk 6 optimal weight: 0.5980 chunk 271 optimal weight: 4.9990 chunk 360 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 264 optimal weight: 0.8980 chunk 335 optimal weight: 2.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 334 GLN B 48 GLN B 112 GLN C 48 GLN C 112 GLN ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 48 GLN ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 GLN E 112 GLN ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 48 GLN F 112 GLN F 334 GLN G 112 GLN G 498 GLN H 48 GLN H 112 GLN ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 334 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.148456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.112451 restraints weight = 36918.889| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 2.34 r_work: 0.3101 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 31928 Z= 0.243 Angle : 0.660 6.987 43288 Z= 0.326 Chirality : 0.048 0.155 4928 Planarity : 0.004 0.041 5424 Dihedral : 16.923 174.495 4662 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 4.07 % Allowed : 14.83 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.13), residues: 3960 helix: 0.53 (0.15), residues: 1336 sheet: -1.38 (0.22), residues: 504 loop : -1.25 (0.13), residues: 2120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 355 TYR 0.017 0.002 TYR B 110 PHE 0.008 0.001 PHE H 24 HIS 0.002 0.001 HIS G 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00603 / 0.24 (31920) covalent geometry : angle 0.65951 / 0.33 (43288) hydrogen bonds : bond 0.03526 / 2.36 ( 1032) hydrogen bonds : angle 4.76915 / 3.28 ( 2952) Misc. bond : bond 0.00059 / 0.03 ( 8) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 687 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 554 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: A 105 ARG cc_start: 0.7628 (mtp-110) cc_final: 0.6939 (ttp80) REVERT: A 170 GLU cc_start: 0.3758 (OUTLIER) cc_final: 0.2398 (tp30) REVERT: A 196 GLU cc_start: 0.7758 (mp0) cc_final: 0.7281 (mt-10) REVERT: A 232 ASP cc_start: 0.8358 (m-30) cc_final: 0.8128 (m-30) REVERT: A 235 LEU cc_start: 0.7625 (OUTLIER) cc_final: 0.6925 (pp) REVERT: A 286 MET cc_start: 0.8796 (tpp) cc_final: 0.8435 (tpt) REVERT: A 330 ILE cc_start: 0.9366 (OUTLIER) cc_final: 0.9050 (pp) REVERT: A 408 LEU cc_start: 0.7039 (OUTLIER) cc_final: 0.6582 (pp) REVERT: A 410 LYS cc_start: 0.7439 (pttt) cc_final: 0.6072 (mmtt) REVERT: B 13 VAL cc_start: 0.8763 (t) cc_final: 0.8495 (p) REVERT: B 105 ARG cc_start: 0.7603 (mtp-110) cc_final: 0.6873 (ttp80) REVERT: B 126 ARG cc_start: 0.5222 (mpt90) cc_final: 0.2148 (mtp85) REVERT: B 196 GLU cc_start: 0.7776 (mp0) cc_final: 0.7348 (mt-10) REVERT: B 217 GLU cc_start: 0.6340 (OUTLIER) cc_final: 0.5931 (mm-30) REVERT: B 232 ASP cc_start: 0.8296 (m-30) cc_final: 0.8085 (m-30) REVERT: B 235 LEU cc_start: 0.7541 (OUTLIER) cc_final: 0.6835 (pp) REVERT: B 286 MET cc_start: 0.8816 (tpp) cc_final: 0.8458 (tpt) REVERT: B 330 ILE cc_start: 0.9279 (OUTLIER) cc_final: 0.9053 (pp) REVERT: B 408 LEU cc_start: 0.7129 (OUTLIER) cc_final: 0.6662 (pp) REVERT: B 410 LYS cc_start: 0.7402 (pttt) cc_final: 0.5952 (mmtt) REVERT: C 105 ARG cc_start: 0.7639 (mtp-110) cc_final: 0.6900 (ttp80) REVERT: C 126 ARG cc_start: 0.5185 (mpt90) cc_final: 0.2376 (mtp180) REVERT: C 170 GLU cc_start: 0.3742 (OUTLIER) cc_final: 0.3412 (mp0) REVERT: C 196 GLU cc_start: 0.7700 (mp0) cc_final: 0.7226 (mt-10) REVERT: C 235 LEU cc_start: 0.7662 (OUTLIER) cc_final: 0.6966 (pp) REVERT: C 286 MET cc_start: 0.8853 (tpp) cc_final: 0.8372 (tpt) REVERT: C 330 ILE cc_start: 0.9315 (OUTLIER) cc_final: 0.9042 (pp) REVERT: C 408 LEU cc_start: 0.7062 (OUTLIER) cc_final: 0.6600 (pp) REVERT: C 410 LYS cc_start: 0.7470 (pttt) cc_final: 0.6071 (mmtt) REVERT: D 13 VAL cc_start: 0.8738 (t) cc_final: 0.8458 (p) REVERT: D 126 ARG cc_start: 0.5235 (mpt90) cc_final: 0.2102 (mtp85) REVERT: D 196 GLU cc_start: 0.7648 (mp0) cc_final: 0.7188 (mt-10) REVERT: D 217 GLU cc_start: 0.6425 (OUTLIER) cc_final: 0.6000 (mm-30) REVERT: D 232 ASP cc_start: 0.8274 (m-30) cc_final: 0.8056 (m-30) REVERT: D 235 LEU cc_start: 0.7470 (OUTLIER) cc_final: 0.6775 (pp) REVERT: D 286 MET cc_start: 0.8784 (tpp) cc_final: 0.8438 (tpt) REVERT: D 330 ILE cc_start: 0.9342 (OUTLIER) cc_final: 0.9083 (pp) REVERT: D 408 LEU cc_start: 0.7091 (OUTLIER) cc_final: 0.6687 (pp) REVERT: D 410 LYS cc_start: 0.7450 (pttt) cc_final: 0.5934 (mmtt) REVERT: D 441 GLN cc_start: 0.8283 (mm-40) cc_final: 0.8046 (mm-40) REVERT: E 170 GLU cc_start: 0.3563 (OUTLIER) cc_final: 0.2152 (tp30) REVERT: E 196 GLU cc_start: 0.7781 (mp0) cc_final: 0.7322 (mt-10) REVERT: E 203 ARG cc_start: 0.8091 (mpt90) cc_final: 0.7320 (mtm110) REVERT: E 235 LEU cc_start: 0.7621 (OUTLIER) cc_final: 0.6914 (pp) REVERT: E 286 MET cc_start: 0.8894 (tpp) cc_final: 0.8508 (tpt) REVERT: E 330 ILE cc_start: 0.9297 (OUTLIER) cc_final: 0.9060 (pp) REVERT: E 408 LEU cc_start: 0.6963 (OUTLIER) cc_final: 0.6506 (pp) REVERT: E 410 LYS cc_start: 0.7477 (pttt) cc_final: 0.6211 (mmtt) REVERT: F 13 VAL cc_start: 0.8707 (t) cc_final: 0.8414 (p) REVERT: F 126 ARG cc_start: 0.5169 (mpt90) cc_final: 0.2122 (mtp85) REVERT: F 196 GLU cc_start: 0.7791 (mp0) cc_final: 0.7300 (mt-10) REVERT: F 217 GLU cc_start: 0.6454 (OUTLIER) cc_final: 0.6233 (tp30) REVERT: F 232 ASP cc_start: 0.8243 (m-30) cc_final: 0.8027 (m-30) REVERT: F 235 LEU cc_start: 0.7512 (OUTLIER) cc_final: 0.6785 (pp) REVERT: F 286 MET cc_start: 0.8830 (tpp) cc_final: 0.8487 (tpt) REVERT: F 408 LEU cc_start: 0.7110 (OUTLIER) cc_final: 0.6669 (pp) REVERT: F 410 LYS cc_start: 0.7539 (pttt) cc_final: 0.6047 (mmtt) REVERT: G 170 GLU cc_start: 0.3552 (OUTLIER) cc_final: 0.2171 (tp30) REVERT: G 196 GLU cc_start: 0.7712 (mp0) cc_final: 0.7196 (mt-10) REVERT: G 203 ARG cc_start: 0.7945 (mpt90) cc_final: 0.7166 (mtm110) REVERT: G 232 ASP cc_start: 0.8323 (m-30) cc_final: 0.8091 (m-30) REVERT: G 235 LEU cc_start: 0.7614 (OUTLIER) cc_final: 0.6960 (pp) REVERT: G 286 MET cc_start: 0.8826 (tpp) cc_final: 0.8441 (tpt) REVERT: G 330 ILE cc_start: 0.9242 (OUTLIER) cc_final: 0.8946 (pp) REVERT: G 408 LEU cc_start: 0.7012 (OUTLIER) cc_final: 0.6579 (pp) REVERT: G 410 LYS cc_start: 0.7427 (pttt) cc_final: 0.6038 (mmtt) REVERT: H 13 VAL cc_start: 0.8711 (t) cc_final: 0.8447 (p) REVERT: H 170 GLU cc_start: 0.3925 (OUTLIER) cc_final: 0.2490 (tp30) REVERT: H 196 GLU cc_start: 0.7876 (mp0) cc_final: 0.7381 (mt-10) REVERT: H 217 GLU cc_start: 0.6375 (OUTLIER) cc_final: 0.5895 (tp30) REVERT: H 235 LEU cc_start: 0.7461 (OUTLIER) cc_final: 0.6716 (pp) REVERT: H 286 MET cc_start: 0.8728 (tpp) cc_final: 0.8436 (tpt) REVERT: H 330 ILE cc_start: 0.9282 (OUTLIER) cc_final: 0.9034 (pp) REVERT: H 408 LEU cc_start: 0.7128 (OUTLIER) cc_final: 0.6662 (pp) REVERT: H 410 LYS cc_start: 0.7419 (pttt) cc_final: 0.5976 (mmtt) outliers start: 133 outliers final: 95 residues processed: 651 average time/residue: 0.1787 time to fit residues: 193.0500 Evaluate side-chains 652 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 525 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 339 CYS Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 331 CYS Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain C residue 15 ASP Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 280 SER Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 485 SER Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 217 GLU Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 331 CYS Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 496 SER Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 170 GLU Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 275 SER Chi-restraints excluded: chain E residue 280 SER Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 329 SER Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 331 CYS Chi-restraints excluded: chain E residue 339 CYS Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain E residue 485 SER Chi-restraints excluded: chain E residue 496 SER Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 217 GLU Chi-restraints excluded: chain F residue 225 THR Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 275 SER Chi-restraints excluded: chain F residue 280 SER Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 331 CYS Chi-restraints excluded: chain F residue 408 LEU Chi-restraints excluded: chain F residue 485 SER Chi-restraints excluded: chain F residue 496 SER Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 170 GLU Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 275 SER Chi-restraints excluded: chain G residue 280 SER Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 329 SER Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 331 CYS Chi-restraints excluded: chain G residue 408 LEU Chi-restraints excluded: chain G residue 485 SER Chi-restraints excluded: chain G residue 496 SER Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 170 GLU Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 217 GLU Chi-restraints excluded: chain H residue 225 THR Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 275 SER Chi-restraints excluded: chain H residue 280 SER Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 331 CYS Chi-restraints excluded: chain H residue 408 LEU Chi-restraints excluded: chain O residue 7 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 357 optimal weight: 0.7980 chunk 288 optimal weight: 4.9990 chunk 180 optimal weight: 0.9990 chunk 165 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 224 optimal weight: 6.9990 chunk 387 optimal weight: 0.0170 chunk 349 optimal weight: 0.1980 chunk 72 optimal weight: 0.9990 chunk 194 optimal weight: 1.9990 overall best weight: 0.6022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 309 GLN A 334 GLN B 48 GLN B 334 GLN C 48 GLN C 309 GLN C 334 GLN D 48 GLN ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 GLN E 48 GLN E 309 GLN E 334 GLN F 48 GLN F 112 GLN F 202 GLN F 334 GLN G 334 GLN H 48 GLN ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 334 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.154068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.118254 restraints weight = 36449.396| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.34 r_work: 0.3177 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 31928 Z= 0.113 Angle : 0.562 6.759 43288 Z= 0.276 Chirality : 0.044 0.132 4928 Planarity : 0.004 0.064 5424 Dihedral : 16.783 173.542 4662 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.37 % Allowed : 16.27 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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: -0.75 (0.13), residues: 3960 helix: 0.88 (0.15), residues: 1328 sheet: -1.40 (0.22), residues: 544 loop : -1.15 (0.13), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG E 136 TYR 0.015 0.001 TYR D 509 PHE 0.009 0.001 PHE D 401 HIS 0.008 0.001 HIS E 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.11 (31920) covalent geometry : angle 0.56213 / 0.28 (43288) hydrogen bonds : bond 0.02583 / 1.71 ( 1032) hydrogen bonds : angle 4.45799 / 3.05 ( 2952) Misc. bond : bond 0.00012 / 0.01 ( 8) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 630 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 520 time to evaluate : 1.178 Fit side-chains REVERT: A 105 ARG cc_start: 0.7479 (mtp-110) cc_final: 0.6758 (ttp80) REVERT: A 170 GLU cc_start: 0.3925 (OUTLIER) cc_final: 0.2798 (tp30) REVERT: A 196 GLU cc_start: 0.7600 (mp0) cc_final: 0.7094 (mt-10) REVERT: A 199 GLU cc_start: 0.7640 (mm-30) cc_final: 0.7206 (mt-10) REVERT: A 232 ASP cc_start: 0.8341 (m-30) cc_final: 0.8112 (m-30) REVERT: A 235 LEU cc_start: 0.7407 (OUTLIER) cc_final: 0.6957 (pp) REVERT: A 330 ILE cc_start: 0.9342 (OUTLIER) cc_final: 0.9025 (pp) REVERT: A 408 LEU cc_start: 0.6876 (OUTLIER) cc_final: 0.6448 (pp) REVERT: A 410 LYS cc_start: 0.7356 (pttt) cc_final: 0.5992 (mmtt) REVERT: A 459 TYR cc_start: 0.8748 (t80) cc_final: 0.8411 (t80) REVERT: B 13 VAL cc_start: 0.8680 (t) cc_final: 0.8428 (p) REVERT: B 105 ARG cc_start: 0.7513 (mtp-110) cc_final: 0.6804 (ttp80) REVERT: B 126 ARG cc_start: 0.5143 (mpt90) cc_final: 0.2139 (mtp85) REVERT: B 196 GLU cc_start: 0.7717 (mp0) cc_final: 0.7261 (mt-10) REVERT: B 217 GLU cc_start: 0.6197 (OUTLIER) cc_final: 0.5703 (tp30) REVERT: B 232 ASP cc_start: 0.8318 (m-30) cc_final: 0.8111 (m-30) REVERT: B 235 LEU cc_start: 0.7342 (OUTLIER) cc_final: 0.6791 (pp) REVERT: B 330 ILE cc_start: 0.9237 (OUTLIER) cc_final: 0.9008 (pp) REVERT: B 408 LEU cc_start: 0.6921 (OUTLIER) cc_final: 0.6537 (pp) REVERT: B 410 LYS cc_start: 0.7381 (pttt) cc_final: 0.5887 (mmtt) REVERT: C 105 ARG cc_start: 0.7539 (mtp-110) cc_final: 0.6809 (ttp80) REVERT: C 126 ARG cc_start: 0.5089 (mpt90) cc_final: 0.2353 (mtp180) REVERT: C 196 GLU cc_start: 0.7578 (mp0) cc_final: 0.7083 (mt-10) REVERT: C 232 ASP cc_start: 0.8299 (m-30) cc_final: 0.8092 (m-30) REVERT: C 235 LEU cc_start: 0.7454 (OUTLIER) cc_final: 0.6995 (pp) REVERT: C 286 MET cc_start: 0.8778 (tpp) cc_final: 0.8293 (tpt) REVERT: C 330 ILE cc_start: 0.9265 (OUTLIER) cc_final: 0.9015 (pp) REVERT: C 408 LEU cc_start: 0.6841 (OUTLIER) cc_final: 0.6505 (pp) REVERT: C 410 LYS cc_start: 0.7347 (pttt) cc_final: 0.5955 (mmtt) REVERT: D 13 VAL cc_start: 0.8689 (t) cc_final: 0.8408 (p) REVERT: D 126 ARG cc_start: 0.5188 (mpt90) cc_final: 0.2167 (mtp85) REVERT: D 196 GLU cc_start: 0.7575 (mp0) cc_final: 0.7067 (mt-10) REVERT: D 217 GLU cc_start: 0.6251 (OUTLIER) cc_final: 0.5840 (mm-30) REVERT: D 232 ASP cc_start: 0.8290 (m-30) cc_final: 0.8086 (m-30) REVERT: D 235 LEU cc_start: 0.7318 (OUTLIER) cc_final: 0.6772 (pp) REVERT: D 319 ASP cc_start: 0.8355 (m-30) cc_final: 0.8100 (m-30) REVERT: D 330 ILE cc_start: 0.9288 (OUTLIER) cc_final: 0.9047 (pp) REVERT: D 408 LEU cc_start: 0.6860 (OUTLIER) cc_final: 0.6588 (pp) REVERT: D 410 LYS cc_start: 0.7394 (pttt) cc_final: 0.5884 (mmtt) REVERT: E 170 GLU cc_start: 0.3837 (OUTLIER) cc_final: 0.2686 (tp30) REVERT: E 196 GLU cc_start: 0.7655 (mp0) cc_final: 0.7143 (mt-10) REVERT: E 199 GLU cc_start: 0.7814 (mm-30) cc_final: 0.7287 (mt-10) REVERT: E 203 ARG cc_start: 0.7953 (mpt90) cc_final: 0.7133 (mtm110) REVERT: E 232 ASP cc_start: 0.8330 (m-30) cc_final: 0.8126 (m-30) REVERT: E 235 LEU cc_start: 0.7487 (OUTLIER) cc_final: 0.7013 (pp) REVERT: E 286 MET cc_start: 0.8815 (tpp) cc_final: 0.8414 (tpt) REVERT: E 330 ILE cc_start: 0.9262 (OUTLIER) cc_final: 0.8969 (pp) REVERT: E 408 LEU cc_start: 0.6752 (OUTLIER) cc_final: 0.6331 (pp) REVERT: E 410 LYS cc_start: 0.7298 (pttt) cc_final: 0.5983 (mmtt) REVERT: F 13 VAL cc_start: 0.8645 (t) cc_final: 0.8367 (p) REVERT: F 126 ARG cc_start: 0.5145 (mpt90) cc_final: 0.2188 (mtp85) REVERT: F 196 GLU cc_start: 0.7699 (mp0) cc_final: 0.7214 (mt-10) REVERT: F 199 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7394 (mt-10) REVERT: F 217 GLU cc_start: 0.6352 (OUTLIER) cc_final: 0.5955 (mm-30) REVERT: F 232 ASP cc_start: 0.8266 (m-30) cc_final: 0.8055 (m-30) REVERT: F 235 LEU cc_start: 0.7354 (OUTLIER) cc_final: 0.6808 (pp) REVERT: F 330 ILE cc_start: 0.9218 (OUTLIER) cc_final: 0.8982 (pp) REVERT: F 408 LEU cc_start: 0.6898 (OUTLIER) cc_final: 0.6588 (pp) REVERT: F 410 LYS cc_start: 0.7400 (pttt) cc_final: 0.5933 (mmtt) REVERT: G 170 GLU cc_start: 0.3799 (OUTLIER) cc_final: 0.2681 (tp30) REVERT: G 196 GLU cc_start: 0.7583 (mp0) cc_final: 0.7030 (mt-10) REVERT: G 199 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7210 (mt-10) REVERT: G 203 ARG cc_start: 0.7881 (mpt90) cc_final: 0.7015 (mtm110) REVERT: G 232 ASP cc_start: 0.8287 (m-30) cc_final: 0.8059 (m-30) REVERT: G 235 LEU cc_start: 0.7397 (OUTLIER) cc_final: 0.6985 (pp) REVERT: G 286 MET cc_start: 0.8782 (tpp) cc_final: 0.8422 (tpt) REVERT: G 330 ILE cc_start: 0.9223 (OUTLIER) cc_final: 0.8913 (pp) REVERT: G 408 LEU cc_start: 0.6825 (OUTLIER) cc_final: 0.6398 (pp) REVERT: G 410 LYS cc_start: 0.7370 (pttt) cc_final: 0.5989 (mmtt) REVERT: G 459 TYR cc_start: 0.8726 (t80) cc_final: 0.8447 (t80) REVERT: H 13 VAL cc_start: 0.8647 (t) cc_final: 0.8371 (p) REVERT: H 105 ARG cc_start: 0.7328 (mtp85) cc_final: 0.6589 (ttp80) REVERT: H 170 GLU cc_start: 0.3803 (OUTLIER) cc_final: 0.2776 (tp30) REVERT: H 196 GLU cc_start: 0.7790 (mp0) cc_final: 0.7308 (mt-10) REVERT: H 199 GLU cc_start: 0.7971 (mm-30) cc_final: 0.7473 (mt-10) REVERT: H 217 GLU cc_start: 0.6215 (OUTLIER) cc_final: 0.5735 (tp30) REVERT: H 235 LEU cc_start: 0.7344 (OUTLIER) cc_final: 0.6796 (pp) REVERT: H 286 MET cc_start: 0.8705 (tpp) cc_final: 0.8418 (tpt) REVERT: H 408 LEU cc_start: 0.6894 (OUTLIER) cc_final: 0.6509 (pp) REVERT: H 410 LYS cc_start: 0.7360 (pttt) cc_final: 0.5945 (mmtt) REVERT: H 412 ARG cc_start: 0.8334 (ptp90) cc_final: 0.7868 (ptp90) REVERT: H 459 TYR cc_start: 0.8751 (t80) cc_final: 0.8434 (t80) outliers start: 110 outliers final: 65 residues processed: 599 average time/residue: 0.1866 time to fit residues: 183.3775 Evaluate side-chains 594 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 498 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 114 PHE Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 255 ASP Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 331 CYS Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 280 SER Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 217 GLU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 331 CYS Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 496 SER Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 170 GLU Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 275 SER Chi-restraints excluded: chain E residue 280 SER Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain E residue 496 SER Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 217 GLU Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 275 SER Chi-restraints excluded: chain F residue 280 SER Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 408 LEU Chi-restraints excluded: chain F residue 496 SER Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 170 GLU Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 275 SER Chi-restraints excluded: chain G residue 280 SER Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 329 SER Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 331 CYS Chi-restraints excluded: chain G residue 408 LEU Chi-restraints excluded: chain G residue 496 SER Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 170 GLU Chi-restraints excluded: chain H residue 217 GLU Chi-restraints excluded: chain H residue 225 THR Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 275 SER Chi-restraints excluded: chain H residue 280 SER Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 331 CYS Chi-restraints excluded: chain H residue 408 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 142 optimal weight: 0.5980 chunk 251 optimal weight: 2.9990 chunk 279 optimal weight: 0.8980 chunk 280 optimal weight: 0.0670 chunk 348 optimal weight: 0.9980 chunk 158 optimal weight: 0.8980 chunk 382 optimal weight: 3.9990 chunk 355 optimal weight: 3.9990 chunk 243 optimal weight: 0.4980 chunk 96 optimal weight: 6.9990 chunk 84 optimal weight: 1.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 112 GLN A 309 GLN B 48 GLN B 112 GLN C 48 GLN C 112 GLN D 48 GLN D 112 GLN D 277 GLN ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 GLN E 48 GLN E 112 GLN F 48 GLN F 112 GLN G 112 GLN H 48 GLN H 112 GLN ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 334 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.154665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.118787 restraints weight = 36473.210| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.34 r_work: 0.3155 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.3251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 31928 Z= 0.111 Angle : 0.561 6.731 43288 Z= 0.274 Chirality : 0.043 0.137 4928 Planarity : 0.004 0.042 5424 Dihedral : 16.634 172.598 4656 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 3.00 % Allowed : 16.48 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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: -0.58 (0.14), residues: 3960 helix: 1.06 (0.15), residues: 1328 sheet: -1.32 (0.22), residues: 544 loop : -1.06 (0.14), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 136 TYR 0.018 0.001 TYR H 411 PHE 0.007 0.001 PHE D 401 HIS 0.001 0.000 HIS G 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.11 (31920) covalent geometry : angle 0.56145 / 0.27 (43288) hydrogen bonds : bond 0.02509 / 1.66 ( 1032) hydrogen bonds : angle 4.37130 / 2.99 ( 2952) Misc. bond : bond 0.00006 / 0.00 ( 8) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 605 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 507 time to evaluate : 1.148 Fit side-chains REVERT: A 105 ARG cc_start: 0.7463 (mtp-110) cc_final: 0.6730 (ttp80) REVERT: A 150 MET cc_start: 0.7838 (mmm) cc_final: 0.7528 (mmm) REVERT: A 170 GLU cc_start: 0.3841 (OUTLIER) cc_final: 0.2837 (tp30) REVERT: A 196 GLU cc_start: 0.7646 (mp0) cc_final: 0.7143 (mt-10) REVERT: A 199 GLU cc_start: 0.7626 (mm-30) cc_final: 0.7179 (mt-10) REVERT: A 232 ASP cc_start: 0.8328 (m-30) cc_final: 0.8105 (m-30) REVERT: A 235 LEU cc_start: 0.7304 (OUTLIER) cc_final: 0.6923 (pp) REVERT: A 330 ILE cc_start: 0.9333 (OUTLIER) cc_final: 0.9005 (pp) REVERT: A 408 LEU cc_start: 0.6802 (OUTLIER) cc_final: 0.6370 (pp) REVERT: A 410 LYS cc_start: 0.7320 (pttt) cc_final: 0.5971 (mmtt) REVERT: A 459 TYR cc_start: 0.8722 (t80) cc_final: 0.8387 (t80) REVERT: B 13 VAL cc_start: 0.8660 (t) cc_final: 0.8383 (p) REVERT: B 105 ARG cc_start: 0.7465 (mtp-110) cc_final: 0.6760 (ttp80) REVERT: B 126 ARG cc_start: 0.5105 (mpt90) cc_final: 0.2105 (mtp85) REVERT: B 196 GLU cc_start: 0.7737 (mp0) cc_final: 0.7299 (mt-10) REVERT: B 199 GLU cc_start: 0.7731 (mm-30) cc_final: 0.7407 (mt-10) REVERT: B 217 GLU cc_start: 0.6123 (OUTLIER) cc_final: 0.5614 (tp30) REVERT: B 232 ASP cc_start: 0.8300 (m-30) cc_final: 0.8100 (m-30) REVERT: B 235 LEU cc_start: 0.7280 (OUTLIER) cc_final: 0.6817 (pp) REVERT: B 330 ILE cc_start: 0.9204 (OUTLIER) cc_final: 0.8972 (pp) REVERT: B 408 LEU cc_start: 0.6861 (OUTLIER) cc_final: 0.6469 (pp) REVERT: B 410 LYS cc_start: 0.7369 (pttt) cc_final: 0.5874 (mmtt) REVERT: C 105 ARG cc_start: 0.7509 (mtp-110) cc_final: 0.6759 (ttp80) REVERT: C 196 GLU cc_start: 0.7638 (mp0) cc_final: 0.7173 (mt-10) REVERT: C 199 GLU cc_start: 0.7531 (mm-30) cc_final: 0.7208 (mt-10) REVERT: C 235 LEU cc_start: 0.7339 (OUTLIER) cc_final: 0.6952 (pp) REVERT: C 286 MET cc_start: 0.8729 (tpp) cc_final: 0.8286 (tpt) REVERT: C 330 ILE cc_start: 0.9227 (OUTLIER) cc_final: 0.8977 (pp) REVERT: C 399 GLU cc_start: 0.7209 (tp30) cc_final: 0.6650 (mm-30) REVERT: C 408 LEU cc_start: 0.6766 (OUTLIER) cc_final: 0.6409 (pp) REVERT: C 410 LYS cc_start: 0.7319 (pttt) cc_final: 0.5942 (mmtt) REVERT: D 13 VAL cc_start: 0.8658 (t) cc_final: 0.8375 (p) REVERT: D 126 ARG cc_start: 0.5168 (mpt90) cc_final: 0.2146 (mtp85) REVERT: D 196 GLU cc_start: 0.7576 (mp0) cc_final: 0.7083 (mt-10) REVERT: D 199 GLU cc_start: 0.7753 (mm-30) cc_final: 0.7263 (mt-10) REVERT: D 217 GLU cc_start: 0.6185 (OUTLIER) cc_final: 0.5673 (tp30) REVERT: D 232 ASP cc_start: 0.8283 (m-30) cc_final: 0.8083 (m-30) REVERT: D 235 LEU cc_start: 0.7214 (OUTLIER) cc_final: 0.6770 (pp) REVERT: D 319 ASP cc_start: 0.8342 (m-30) cc_final: 0.8102 (m-30) REVERT: D 330 ILE cc_start: 0.9234 (OUTLIER) cc_final: 0.8991 (pp) REVERT: D 408 LEU cc_start: 0.6862 (OUTLIER) cc_final: 0.6516 (pp) REVERT: D 410 LYS cc_start: 0.7365 (pttt) cc_final: 0.5855 (mmtt) REVERT: E 170 GLU cc_start: 0.3727 (OUTLIER) cc_final: 0.2636 (tp30) REVERT: E 196 GLU cc_start: 0.7697 (mp0) cc_final: 0.7198 (mt-10) REVERT: E 199 GLU cc_start: 0.7779 (mm-30) cc_final: 0.7199 (mt-10) REVERT: E 203 ARG cc_start: 0.7934 (mpt90) cc_final: 0.7118 (mtm110) REVERT: E 235 LEU cc_start: 0.7326 (OUTLIER) cc_final: 0.6949 (pp) REVERT: E 286 MET cc_start: 0.8761 (tpp) cc_final: 0.8387 (tpt) REVERT: E 399 GLU cc_start: 0.7017 (tp30) cc_final: 0.6550 (mm-30) REVERT: E 408 LEU cc_start: 0.6711 (OUTLIER) cc_final: 0.6303 (pp) REVERT: E 410 LYS cc_start: 0.7280 (pttt) cc_final: 0.5990 (mmtt) REVERT: F 13 VAL cc_start: 0.8631 (t) cc_final: 0.8344 (p) REVERT: F 126 ARG cc_start: 0.5197 (mpt90) cc_final: 0.2231 (mtp85) REVERT: F 196 GLU cc_start: 0.7735 (mp0) cc_final: 0.7254 (mt-10) REVERT: F 199 GLU cc_start: 0.7822 (mm-30) cc_final: 0.7329 (mt-10) REVERT: F 217 GLU cc_start: 0.6267 (OUTLIER) cc_final: 0.5771 (tp30) REVERT: F 232 ASP cc_start: 0.8251 (m-30) cc_final: 0.8047 (m-30) REVERT: F 235 LEU cc_start: 0.7252 (OUTLIER) cc_final: 0.6801 (pp) REVERT: F 330 ILE cc_start: 0.9200 (OUTLIER) cc_final: 0.8940 (pp) REVERT: F 408 LEU cc_start: 0.6851 (OUTLIER) cc_final: 0.6499 (pp) REVERT: F 410 LYS cc_start: 0.7366 (pttt) cc_final: 0.5908 (mmtt) REVERT: G 170 GLU cc_start: 0.3693 (OUTLIER) cc_final: 0.2631 (tp30) REVERT: G 196 GLU cc_start: 0.7589 (mp0) cc_final: 0.7048 (mt-10) REVERT: G 199 GLU cc_start: 0.7693 (mm-30) cc_final: 0.7165 (mt-10) REVERT: G 203 ARG cc_start: 0.7878 (mpt90) cc_final: 0.7007 (mtm110) REVERT: G 232 ASP cc_start: 0.8250 (m-30) cc_final: 0.8029 (m-30) REVERT: G 235 LEU cc_start: 0.7265 (OUTLIER) cc_final: 0.6938 (pp) REVERT: G 330 ILE cc_start: 0.9200 (OUTLIER) cc_final: 0.8876 (pp) REVERT: G 408 LEU cc_start: 0.6745 (OUTLIER) cc_final: 0.6333 (pp) REVERT: G 410 LYS cc_start: 0.7369 (pttt) cc_final: 0.5997 (mmtt) REVERT: G 459 TYR cc_start: 0.8700 (t80) cc_final: 0.8410 (t80) REVERT: H 13 VAL cc_start: 0.8616 (t) cc_final: 0.8343 (p) REVERT: H 105 ARG cc_start: 0.7273 (mtp85) cc_final: 0.6525 (ttp80) REVERT: H 170 GLU cc_start: 0.3769 (OUTLIER) cc_final: 0.2765 (tp30) REVERT: H 196 GLU cc_start: 0.7784 (mp0) cc_final: 0.7312 (mt-10) REVERT: H 199 GLU cc_start: 0.7912 (mm-30) cc_final: 0.7378 (mt-10) REVERT: H 217 GLU cc_start: 0.6143 (OUTLIER) cc_final: 0.5635 (tp30) REVERT: H 235 LEU cc_start: 0.7239 (OUTLIER) cc_final: 0.6805 (pp) REVERT: H 286 MET cc_start: 0.8650 (tpp) cc_final: 0.8372 (tpt) REVERT: H 319 ASP cc_start: 0.8289 (m-30) cc_final: 0.8027 (m-30) REVERT: H 330 ILE cc_start: 0.9160 (OUTLIER) cc_final: 0.8905 (pp) REVERT: H 408 LEU cc_start: 0.6832 (OUTLIER) cc_final: 0.6417 (pp) REVERT: H 410 LYS cc_start: 0.7314 (pttt) cc_final: 0.5909 (mmtt) outliers start: 98 outliers final: 65 residues processed: 582 average time/residue: 0.1752 time to fit residues: 169.5102 Evaluate side-chains 585 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 489 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 255 ASP Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 331 CYS Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 280 SER Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 217 GLU Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 331 CYS Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 496 SER Chi-restraints excluded: chain E residue 48 GLN Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 170 GLU Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 280 SER Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 217 GLU Chi-restraints excluded: chain F residue 225 THR Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 280 SER Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 331 CYS Chi-restraints excluded: chain F residue 408 LEU Chi-restraints excluded: chain F residue 496 SER Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 170 GLU Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 275 SER Chi-restraints excluded: chain G residue 280 SER Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 329 SER Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 331 CYS Chi-restraints excluded: chain G residue 408 LEU Chi-restraints excluded: chain G residue 496 SER Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 170 GLU Chi-restraints excluded: chain H residue 217 GLU Chi-restraints excluded: chain H residue 225 THR Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 280 SER Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 331 CYS Chi-restraints excluded: chain H residue 408 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 125 optimal weight: 3.9990 chunk 212 optimal weight: 7.9990 chunk 201 optimal weight: 0.8980 chunk 165 optimal weight: 2.9990 chunk 370 optimal weight: 2.9990 chunk 121 optimal weight: 4.9990 chunk 175 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 167 optimal weight: 5.9990 chunk 309 optimal weight: 4.9990 chunk 114 optimal weight: 0.9980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 112 GLN B 48 GLN B 112 GLN B 334 GLN C 112 GLN D 48 GLN D 112 GLN ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 GLN E 48 GLN E 112 GLN F 48 GLN F 112 GLN F 334 GLN G 112 GLN G 334 GLN H 48 GLN H 112 GLN ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.150594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.114333 restraints weight = 36583.432| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.35 r_work: 0.3100 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.3261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 31928 Z= 0.194 Angle : 0.625 6.919 43288 Z= 0.307 Chirality : 0.046 0.143 4928 Planarity : 0.004 0.041 5424 Dihedral : 16.725 172.685 4655 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 3.09 % Allowed : 16.27 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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: -0.71 (0.13), residues: 3960 helix: 0.84 (0.15), residues: 1336 sheet: -1.28 (0.23), residues: 504 loop : -1.11 (0.13), residues: 2120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 136 TYR 0.020 0.002 TYR H 411 PHE 0.007 0.001 PHE B 24 HIS 0.002 0.000 HIS B 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.19 (31920) covalent geometry : angle 0.62471 / 0.31 (43288) hydrogen bonds : bond 0.03155 / 2.12 ( 1032) hydrogen bonds : angle 4.54773 / 3.12 ( 2952) Misc. bond : bond 0.00043 / 0.02 ( 8) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 638 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 537 time to evaluate : 0.889 Fit side-chains REVERT: A 105 ARG cc_start: 0.7534 (mtp-110) cc_final: 0.6801 (ttp80) REVERT: A 170 GLU cc_start: 0.3929 (OUTLIER) cc_final: 0.2769 (tp30) REVERT: A 196 GLU cc_start: 0.7683 (mp0) cc_final: 0.7176 (mt-10) REVERT: A 199 GLU cc_start: 0.7703 (mm-30) cc_final: 0.7242 (mt-10) REVERT: A 232 ASP cc_start: 0.8328 (m-30) cc_final: 0.8108 (m-30) REVERT: A 235 LEU cc_start: 0.7473 (OUTLIER) cc_final: 0.6858 (pp) REVERT: A 330 ILE cc_start: 0.9343 (OUTLIER) cc_final: 0.9021 (pp) REVERT: A 408 LEU cc_start: 0.6895 (OUTLIER) cc_final: 0.6451 (pp) REVERT: A 410 LYS cc_start: 0.7341 (pttt) cc_final: 0.5968 (mmtt) REVERT: B 13 VAL cc_start: 0.8732 (t) cc_final: 0.8468 (p) REVERT: B 105 ARG cc_start: 0.7533 (mtp-110) cc_final: 0.6792 (ttp80) REVERT: B 126 ARG cc_start: 0.5284 (mpt90) cc_final: 0.2209 (mtp85) REVERT: B 196 GLU cc_start: 0.7733 (mp0) cc_final: 0.7273 (mt-10) REVERT: B 217 GLU cc_start: 0.6337 (OUTLIER) cc_final: 0.5822 (tp30) REVERT: B 232 ASP cc_start: 0.8293 (m-30) cc_final: 0.8085 (m-30) REVERT: B 235 LEU cc_start: 0.7347 (OUTLIER) cc_final: 0.6619 (pp) REVERT: B 286 MET cc_start: 0.8717 (tpp) cc_final: 0.8417 (tpt) REVERT: B 330 ILE cc_start: 0.9253 (OUTLIER) cc_final: 0.9019 (pp) REVERT: B 408 LEU cc_start: 0.6970 (OUTLIER) cc_final: 0.6525 (pp) REVERT: B 410 LYS cc_start: 0.7353 (pttt) cc_final: 0.5886 (mmtt) REVERT: C 105 ARG cc_start: 0.7555 (mtp-110) cc_final: 0.6777 (ttp80) REVERT: C 126 ARG cc_start: 0.5309 (mpt90) cc_final: 0.2419 (mtp180) REVERT: C 196 GLU cc_start: 0.7678 (mp0) cc_final: 0.7191 (mt-10) REVERT: C 235 LEU cc_start: 0.7445 (OUTLIER) cc_final: 0.6826 (pp) REVERT: C 286 MET cc_start: 0.8772 (tpp) cc_final: 0.8310 (tpt) REVERT: C 330 ILE cc_start: 0.9263 (OUTLIER) cc_final: 0.9003 (pp) REVERT: C 408 LEU cc_start: 0.6900 (OUTLIER) cc_final: 0.6458 (pp) REVERT: C 410 LYS cc_start: 0.7346 (pttt) cc_final: 0.5948 (mmtt) REVERT: D 13 VAL cc_start: 0.8727 (t) cc_final: 0.8457 (p) REVERT: D 126 ARG cc_start: 0.5302 (mpt90) cc_final: 0.2188 (mtp85) REVERT: D 196 GLU cc_start: 0.7592 (mp0) cc_final: 0.7100 (mt-10) REVERT: D 217 GLU cc_start: 0.6349 (OUTLIER) cc_final: 0.5850 (tp30) REVERT: D 232 ASP cc_start: 0.8218 (m-30) cc_final: 0.8011 (m-30) REVERT: D 235 LEU cc_start: 0.7383 (OUTLIER) cc_final: 0.6703 (pp) REVERT: D 330 ILE cc_start: 0.9296 (OUTLIER) cc_final: 0.9026 (pp) REVERT: D 408 LEU cc_start: 0.6963 (OUTLIER) cc_final: 0.6576 (pp) REVERT: D 410 LYS cc_start: 0.7411 (pttt) cc_final: 0.5889 (mmtt) REVERT: E 170 GLU cc_start: 0.3906 (OUTLIER) cc_final: 0.2652 (tp30) REVERT: E 196 GLU cc_start: 0.7738 (mp0) cc_final: 0.7248 (mt-10) REVERT: E 199 GLU cc_start: 0.7833 (mm-30) cc_final: 0.7265 (mt-10) REVERT: E 203 ARG cc_start: 0.8035 (mpt90) cc_final: 0.7192 (mtm110) REVERT: E 235 LEU cc_start: 0.7535 (OUTLIER) cc_final: 0.6929 (pp) REVERT: E 286 MET cc_start: 0.8809 (tpp) cc_final: 0.8427 (tpt) REVERT: E 330 ILE cc_start: 0.9227 (OUTLIER) cc_final: 0.8986 (pp) REVERT: E 408 LEU cc_start: 0.6802 (OUTLIER) cc_final: 0.6370 (pp) REVERT: E 410 LYS cc_start: 0.7280 (pttt) cc_final: 0.5992 (mmtt) REVERT: F 13 VAL cc_start: 0.8705 (t) cc_final: 0.8422 (p) REVERT: F 126 ARG cc_start: 0.5263 (mpt90) cc_final: 0.2195 (mtp85) REVERT: F 196 GLU cc_start: 0.7817 (mp0) cc_final: 0.7302 (mt-10) REVERT: F 217 GLU cc_start: 0.6348 (OUTLIER) cc_final: 0.5836 (tp30) REVERT: F 232 ASP cc_start: 0.8257 (m-30) cc_final: 0.8049 (m-30) REVERT: F 235 LEU cc_start: 0.7407 (OUTLIER) cc_final: 0.6754 (pp) REVERT: F 330 ILE cc_start: 0.9224 (OUTLIER) cc_final: 0.8957 (pp) REVERT: F 408 LEU cc_start: 0.6982 (OUTLIER) cc_final: 0.6565 (pp) REVERT: F 410 LYS cc_start: 0.7405 (pttt) cc_final: 0.5918 (mmtt) REVERT: G 150 MET cc_start: 0.7846 (mmm) cc_final: 0.7567 (mmm) REVERT: G 170 GLU cc_start: 0.3876 (OUTLIER) cc_final: 0.2676 (tp30) REVERT: G 196 GLU cc_start: 0.7677 (mp0) cc_final: 0.7143 (mt-10) REVERT: G 199 GLU cc_start: 0.7747 (mm-30) cc_final: 0.7182 (mt-10) REVERT: G 203 ARG cc_start: 0.7926 (mpt90) cc_final: 0.7053 (mtm110) REVERT: G 232 ASP cc_start: 0.8299 (m-30) cc_final: 0.8071 (m-30) REVERT: G 235 LEU cc_start: 0.7413 (OUTLIER) cc_final: 0.6872 (pp) REVERT: G 286 MET cc_start: 0.8746 (tpp) cc_final: 0.8424 (tpt) REVERT: G 330 ILE cc_start: 0.9229 (OUTLIER) cc_final: 0.8915 (pp) REVERT: G 408 LEU cc_start: 0.6903 (OUTLIER) cc_final: 0.6468 (pp) REVERT: G 410 LYS cc_start: 0.7357 (pttt) cc_final: 0.5992 (mmtt) REVERT: H 13 VAL cc_start: 0.8688 (t) cc_final: 0.8412 (p) REVERT: H 105 ARG cc_start: 0.7290 (mtp85) cc_final: 0.6558 (ttp80) REVERT: H 170 GLU cc_start: 0.3992 (OUTLIER) cc_final: 0.2880 (tp30) REVERT: H 196 GLU cc_start: 0.7875 (mp0) cc_final: 0.7370 (mt-10) REVERT: H 199 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7450 (mt-10) REVERT: H 217 GLU cc_start: 0.6305 (OUTLIER) cc_final: 0.5795 (tp30) REVERT: H 235 LEU cc_start: 0.7364 (OUTLIER) cc_final: 0.6685 (pp) REVERT: H 286 MET cc_start: 0.8676 (tpp) cc_final: 0.8407 (tpt) REVERT: H 330 ILE cc_start: 0.9221 (OUTLIER) cc_final: 0.8962 (pp) REVERT: H 408 LEU cc_start: 0.6968 (OUTLIER) cc_final: 0.6502 (pp) REVERT: H 410 LYS cc_start: 0.7414 (pttt) cc_final: 0.5945 (mmtt) outliers start: 101 outliers final: 68 residues processed: 613 average time/residue: 0.1790 time to fit residues: 182.0733 Evaluate side-chains 616 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 516 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 255 ASP Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 331 CYS Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 280 SER Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 217 GLU Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 331 CYS Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 496 SER Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 170 GLU Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 280 SER Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 331 CYS Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 217 GLU Chi-restraints excluded: chain F residue 225 THR Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 280 SER Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 331 CYS Chi-restraints excluded: chain F residue 408 LEU Chi-restraints excluded: chain F residue 496 SER Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 170 GLU Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 275 SER Chi-restraints excluded: chain G residue 280 SER Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 329 SER Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 331 CYS Chi-restraints excluded: chain G residue 408 LEU Chi-restraints excluded: chain G residue 496 SER Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 170 GLU Chi-restraints excluded: chain H residue 217 GLU Chi-restraints excluded: chain H residue 225 THR Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 275 SER Chi-restraints excluded: chain H residue 280 SER Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 331 CYS Chi-restraints excluded: chain H residue 408 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 267 optimal weight: 0.6980 chunk 292 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 chunk 389 optimal weight: 0.2980 chunk 368 optimal weight: 6.9990 chunk 296 optimal weight: 0.3980 chunk 135 optimal weight: 0.9980 chunk 158 optimal weight: 0.5980 chunk 79 optimal weight: 0.7980 chunk 216 optimal weight: 0.8980 chunk 17 optimal weight: 6.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 112 GLN A 334 GLN B 48 GLN B 112 GLN B 334 GLN C 48 GLN C 112 GLN C 334 GLN D 48 GLN D 112 GLN ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 GLN E 48 GLN E 112 GLN E 334 GLN F 48 GLN F 112 GLN F 334 GLN G 334 GLN H 48 GLN H 112 GLN ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 334 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.154340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.118401 restraints weight = 36531.981| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.36 r_work: 0.3178 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 31928 Z= 0.111 Angle : 0.569 6.787 43288 Z= 0.278 Chirality : 0.044 0.141 4928 Planarity : 0.004 0.044 5424 Dihedral : 16.669 172.080 4655 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 3.03 % Allowed : 16.88 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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: -0.54 (0.14), residues: 3960 helix: 1.09 (0.15), residues: 1328 sheet: -1.31 (0.22), residues: 544 loop : -1.03 (0.14), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 136 TYR 0.026 0.001 TYR G 110 PHE 0.009 0.001 PHE D 401 HIS 0.001 0.000 HIS F 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.11 (31920) covalent geometry : angle 0.56861 / 0.28 (43288) hydrogen bonds : bond 0.02525 / 1.68 ( 1032) hydrogen bonds : angle 4.40199 / 3.01 ( 2952) Misc. bond : bond 0.00014 / 0.01 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7954.81 seconds wall clock time: 136 minutes 55.67 seconds (8215.67 seconds total)