Starting phenix.real_space_refine on Tue Mar 19 11:17:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gao_29902/03_2024/8gao_29902_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gao_29902/03_2024/8gao_29902.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gao_29902/03_2024/8gao_29902.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gao_29902/03_2024/8gao_29902.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gao_29902/03_2024/8gao_29902_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gao_29902/03_2024/8gao_29902_updated.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.050 sd= 0.387 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 41 5.49 5 Mg 5 5.21 5 S 132 5.16 5 C 15149 2.51 5 N 4000 2.21 5 O 4659 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 159": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 23987 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3424 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 12, 'TRANS': 419} Chain: "B" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3424 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 12, 'TRANS': 419} Chain: "C" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3424 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 12, 'TRANS': 419} Chain: "D" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3424 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 12, 'TRANS': 419} Chain: "E" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3424 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 12, 'TRANS': 419} Chain: "F" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3424 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 12, 'TRANS': 419} Chain: "G" Number of atoms: 2781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2781 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 24, 'TRANS': 314} Chain: "M" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 240 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Chain: "P" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 117 Unusual residues: {'GTP': 1} Classifications: {'RNA': 4, 'undetermined': 1} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 2} Link IDs: {'rna3p': 3, None: 1} Not linked: pdbres="GTP P 1 " pdbres=" C P 2 " Chain: "T" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 144 Classifications: {'DNA': 7} Link IDs: {'rna3p': 6} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 20839 SG CYS G 37 50.110 92.436 69.765 1.00234.26 S ATOM 20859 SG CYS G 40 46.540 91.001 70.356 1.00251.45 S ATOM 21058 SG CYS G 65 49.027 90.884 73.007 1.00220.03 S ATOM 21084 SG CYS G 68 49.610 88.675 69.955 1.00211.90 S Time building chain proxies: 12.58, per 1000 atoms: 0.52 Number of scatterers: 23987 At special positions: 0 Unit cell: (140.973, 137.886, 143.031, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 132 16.00 P 41 15.00 Mg 5 11.99 O 4659 8.00 N 4000 7.00 C 15149 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 10.85 Conformation dependent library (CDL) restraints added in 4.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN G 401 " pdb="ZN ZN G 401 " - pdb=" SG CYS G 65 " pdb="ZN ZN G 401 " - pdb=" SG CYS G 40 " pdb="ZN ZN G 401 " - pdb=" SG CYS G 37 " pdb="ZN ZN G 401 " - pdb=" SG CYS G 68 " Number of angles added : 6 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5562 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 132 helices and 16 sheets defined 46.0% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.65 Creating SS restraints... Processing helix chain 'A' and resid 2 through 10 Processing helix chain 'A' and resid 14 through 22 Proline residue: A 21 - end of helix Processing helix chain 'A' and resid 25 through 27 No H-bonds generated for 'chain 'A' and resid 25 through 27' Processing helix chain 'A' and resid 32 through 46 Processing helix chain 'A' and resid 53 through 61 Processing helix chain 'A' and resid 67 through 78 Processing helix chain 'A' and resid 87 through 117 Processing helix chain 'A' and resid 131 through 142 Proline residue: A 135 - end of helix removed outlier: 3.835A pdb=" N MET A 138 " --> pdb=" O PRO A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 167 Processing helix chain 'A' and resid 177 through 183 Processing helix chain 'A' and resid 203 through 216 removed outlier: 3.551A pdb=" N LEU A 207 " --> pdb=" O LYS A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 241 Processing helix chain 'A' and resid 246 through 251 Processing helix chain 'A' and resid 256 through 268 Processing helix chain 'A' and resid 287 through 300 Processing helix chain 'A' and resid 329 through 346 Processing helix chain 'A' and resid 358 through 362 Processing helix chain 'A' and resid 376 through 380 removed outlier: 3.541A pdb=" N THR A 380 " --> pdb=" O GLY A 376 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 376 through 380' Processing helix chain 'A' and resid 391 through 395 Processing helix chain 'B' and resid 2 through 10 Processing helix chain 'B' and resid 13 through 22 Proline residue: B 21 - end of helix Processing helix chain 'B' and resid 25 through 27 No H-bonds generated for 'chain 'B' and resid 25 through 27' Processing helix chain 'B' and resid 32 through 47 Processing helix chain 'B' and resid 53 through 57 Processing helix chain 'B' and resid 67 through 79 Processing helix chain 'B' and resid 89 through 118 Processing helix chain 'B' and resid 132 through 142 Proline residue: B 135 - end of helix Processing helix chain 'B' and resid 158 through 167 Processing helix chain 'B' and resid 177 through 182 Processing helix chain 'B' and resid 205 through 216 Processing helix chain 'B' and resid 230 through 241 removed outlier: 3.813A pdb=" N ALA B 234 " --> pdb=" O GLU B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 251 removed outlier: 3.534A pdb=" N ASP B 250 " --> pdb=" O LEU B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 268 Processing helix chain 'B' and resid 287 through 300 Processing helix chain 'B' and resid 328 through 346 Processing helix chain 'B' and resid 358 through 360 No H-bonds generated for 'chain 'B' and resid 358 through 360' Processing helix chain 'B' and resid 368 through 370 No H-bonds generated for 'chain 'B' and resid 368 through 370' Processing helix chain 'B' and resid 377 through 380 No H-bonds generated for 'chain 'B' and resid 377 through 380' Processing helix chain 'B' and resid 392 through 395 No H-bonds generated for 'chain 'B' and resid 392 through 395' Processing helix chain 'C' and resid 2 through 10 Processing helix chain 'C' and resid 14 through 19 Processing helix chain 'C' and resid 25 through 27 No H-bonds generated for 'chain 'C' and resid 25 through 27' Processing helix chain 'C' and resid 32 through 46 Processing helix chain 'C' and resid 53 through 62 Processing helix chain 'C' and resid 67 through 76 removed outlier: 3.827A pdb=" N GLY C 72 " --> pdb=" O THR C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 118 Processing helix chain 'C' and resid 131 through 142 Proline residue: C 135 - end of helix Processing helix chain 'C' and resid 163 through 166 No H-bonds generated for 'chain 'C' and resid 163 through 166' Processing helix chain 'C' and resid 177 through 183 Processing helix chain 'C' and resid 203 through 216 Processing helix chain 'C' and resid 230 through 241 removed outlier: 3.870A pdb=" N ASN C 240 " --> pdb=" O ARG C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 250 Processing helix chain 'C' and resid 256 through 268 Processing helix chain 'C' and resid 287 through 299 Processing helix chain 'C' and resid 328 through 346 Processing helix chain 'C' and resid 358 through 360 No H-bonds generated for 'chain 'C' and resid 358 through 360' Processing helix chain 'C' and resid 368 through 370 No H-bonds generated for 'chain 'C' and resid 368 through 370' Processing helix chain 'C' and resid 376 through 380 Processing helix chain 'C' and resid 391 through 396 removed outlier: 3.728A pdb=" N ALA C 396 " --> pdb=" O GLU C 392 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 10 Processing helix chain 'D' and resid 13 through 19 Processing helix chain 'D' and resid 25 through 27 No H-bonds generated for 'chain 'D' and resid 25 through 27' Processing helix chain 'D' and resid 32 through 47 Processing helix chain 'D' and resid 53 through 61 Processing helix chain 'D' and resid 67 through 79 Processing helix chain 'D' and resid 87 through 117 Processing helix chain 'D' and resid 131 through 142 Proline residue: D 135 - end of helix Processing helix chain 'D' and resid 159 through 164 removed outlier: 4.026A pdb=" N SER D 164 " --> pdb=" O ALA D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 183 Processing helix chain 'D' and resid 203 through 216 Processing helix chain 'D' and resid 230 through 242 Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 256 through 268 Processing helix chain 'D' and resid 287 through 300 Processing helix chain 'D' and resid 328 through 346 Processing helix chain 'D' and resid 358 through 360 No H-bonds generated for 'chain 'D' and resid 358 through 360' Processing helix chain 'D' and resid 368 through 370 No H-bonds generated for 'chain 'D' and resid 368 through 370' Processing helix chain 'D' and resid 377 through 380 No H-bonds generated for 'chain 'D' and resid 377 through 380' Processing helix chain 'D' and resid 391 through 396 Processing helix chain 'E' and resid 2 through 10 Processing helix chain 'E' and resid 13 through 19 Processing helix chain 'E' and resid 25 through 27 No H-bonds generated for 'chain 'E' and resid 25 through 27' Processing helix chain 'E' and resid 32 through 46 Processing helix chain 'E' and resid 53 through 62 Processing helix chain 'E' and resid 67 through 78 Processing helix chain 'E' and resid 87 through 118 Processing helix chain 'E' and resid 131 through 142 Proline residue: E 135 - end of helix removed outlier: 3.914A pdb=" N GLN E 140 " --> pdb=" O ILE E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 158 through 166 Processing helix chain 'E' and resid 168 through 170 No H-bonds generated for 'chain 'E' and resid 168 through 170' Processing helix chain 'E' and resid 177 through 183 Processing helix chain 'E' and resid 203 through 216 Processing helix chain 'E' and resid 230 through 241 Processing helix chain 'E' and resid 246 through 251 removed outlier: 3.516A pdb=" N ASP E 250 " --> pdb=" O LEU E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 256 through 268 Processing helix chain 'E' and resid 287 through 300 Processing helix chain 'E' and resid 328 through 346 Processing helix chain 'E' and resid 358 through 360 No H-bonds generated for 'chain 'E' and resid 358 through 360' Processing helix chain 'E' and resid 377 through 380 No H-bonds generated for 'chain 'E' and resid 377 through 380' Processing helix chain 'E' and resid 391 through 396 Processing helix chain 'F' and resid 2 through 10 Processing helix chain 'F' and resid 14 through 22 Proline residue: F 21 - end of helix Processing helix chain 'F' and resid 25 through 27 No H-bonds generated for 'chain 'F' and resid 25 through 27' Processing helix chain 'F' and resid 32 through 47 Processing helix chain 'F' and resid 53 through 61 Processing helix chain 'F' and resid 67 through 79 Processing helix chain 'F' and resid 89 through 118 Processing helix chain 'F' and resid 131 through 143 Proline residue: F 135 - end of helix removed outlier: 3.856A pdb=" N ALA F 141 " --> pdb=" O MET F 138 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU F 142 " --> pdb=" O ARG F 139 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 166 Processing helix chain 'F' and resid 177 through 183 Processing helix chain 'F' and resid 203 through 216 Processing helix chain 'F' and resid 230 through 242 Processing helix chain 'F' and resid 246 through 251 Processing helix chain 'F' and resid 256 through 267 Processing helix chain 'F' and resid 287 through 299 Processing helix chain 'F' and resid 313 through 315 No H-bonds generated for 'chain 'F' and resid 313 through 315' Processing helix chain 'F' and resid 328 through 346 Processing helix chain 'F' and resid 368 through 370 No H-bonds generated for 'chain 'F' and resid 368 through 370' Processing helix chain 'F' and resid 377 through 380 No H-bonds generated for 'chain 'F' and resid 377 through 380' Processing helix chain 'G' and resid 5 through 16 Processing helix chain 'G' and resid 74 through 81 Processing helix chain 'G' and resid 83 through 98 removed outlier: 3.831A pdb=" N ARG G 94 " --> pdb=" O ILE G 90 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY G 98 " --> pdb=" O ARG G 94 " (cutoff:3.500A) Processing helix chain 'G' and resid 127 through 129 No H-bonds generated for 'chain 'G' and resid 127 through 129' Processing helix chain 'G' and resid 135 through 143 Processing helix chain 'G' and resid 147 through 152 removed outlier: 3.996A pdb=" N LYS G 151 " --> pdb=" O ASP G 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 159 through 166 Processing helix chain 'G' and resid 222 through 224 No H-bonds generated for 'chain 'G' and resid 222 through 224' Processing helix chain 'G' and resid 236 through 241 removed outlier: 3.632A pdb=" N PHE G 241 " --> pdb=" O ILE G 237 " (cutoff:3.500A) Processing helix chain 'G' and resid 275 through 286 Processing helix chain 'G' and resid 294 through 296 No H-bonds generated for 'chain 'G' and resid 294 through 296' Processing helix chain 'G' and resid 304 through 310 Processing helix chain 'G' and resid 315 through 324 Processing helix chain 'G' and resid 329 through 340 Processing sheet with id= A, first strand: chain 'A' and resid 416 through 419 removed outlier: 6.599A pdb=" N MET A 384 " --> pdb=" O ILE A 404 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ALA A 353 " --> pdb=" O VAL A 310 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS A 278 " --> pdb=" O TYR A 223 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 420 through 422 Processing sheet with id= C, first strand: chain 'B' and resid 383 through 386 removed outlier: 3.727A pdb=" N PHE B 383 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU B 350 " --> pdb=" O ASN B 193 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N LEU B 195 " --> pdb=" O LEU B 350 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N THR B 352 " --> pdb=" O LEU B 195 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ALA B 353 " --> pdb=" O VAL B 310 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 420 through 422 Processing sheet with id= E, first strand: chain 'C' and resid 402 through 406 removed outlier: 6.400A pdb=" N MET C 384 " --> pdb=" O ILE C 404 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE C 383 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU C 350 " --> pdb=" O ASN C 193 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N LEU C 195 " --> pdb=" O LEU C 350 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N THR C 352 " --> pdb=" O LEU C 195 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N ALA C 197 " --> pdb=" O THR C 352 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N ALA C 354 " --> pdb=" O ALA C 197 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA C 353 " --> pdb=" O VAL C 310 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 419 through 422 Processing sheet with id= G, first strand: chain 'D' and resid 349 through 354 removed outlier: 6.306A pdb=" N THR D 191 " --> pdb=" O LEU D 350 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N THR D 352 " --> pdb=" O THR D 191 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ASN D 193 " --> pdb=" O THR D 352 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N ALA D 354 " --> pdb=" O ASN D 193 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N LEU D 195 " --> pdb=" O ALA D 354 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N PHE D 383 " --> pdb=" O VAL D 194 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N MET D 196 " --> pdb=" O PHE D 383 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N LEU D 385 " --> pdb=" O MET D 196 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ALA D 386 " --> pdb=" O GLN D 403 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N GLN D 403 " --> pdb=" O ALA D 386 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ILE D 388 " --> pdb=" O ILE D 401 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N ILE D 401 " --> pdb=" O ILE D 388 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 220 through 225 removed outlier: 6.489A pdb=" N ARG D 274 " --> pdb=" O VAL D 221 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N TYR D 223 " --> pdb=" O ARG D 274 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ILE D 276 " --> pdb=" O TYR D 223 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N SER D 225 " --> pdb=" O ILE D 276 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LYS D 278 " --> pdb=" O SER D 225 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'D' and resid 420 through 422 Processing sheet with id= J, first strand: chain 'E' and resid 416 through 418 removed outlier: 6.522A pdb=" N MET E 384 " --> pdb=" O ILE E 404 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE E 383 " --> pdb=" O LEU E 192 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LEU E 350 " --> pdb=" O ASN E 193 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N LEU E 195 " --> pdb=" O LEU E 350 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N THR E 352 " --> pdb=" O LEU E 195 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N ALA E 197 " --> pdb=" O THR E 352 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N ALA E 354 " --> pdb=" O ALA E 197 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA E 353 " --> pdb=" O VAL E 310 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ARG E 274 " --> pdb=" O VAL E 221 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N TYR E 223 " --> pdb=" O ARG E 274 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ILE E 276 " --> pdb=" O TYR E 223 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N SER E 225 " --> pdb=" O ILE E 276 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N LYS E 278 " --> pdb=" O SER E 225 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 350 through 352 removed outlier: 6.104A pdb=" N PHE F 383 " --> pdb=" O VAL F 194 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 275 through 279 removed outlier: 6.624A pdb=" N VAL F 221 " --> pdb=" O ILE F 276 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N LYS F 278 " --> pdb=" O VAL F 221 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N TYR F 223 " --> pdb=" O LYS F 278 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ILE F 307 " --> pdb=" O LEU F 222 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N ILE F 224 " --> pdb=" O ILE F 307 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ILE F 309 " --> pdb=" O ILE F 224 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'F' and resid 419 through 422 Processing sheet with id= N, first strand: chain 'G' and resid 23 through 27 Processing sheet with id= O, first strand: chain 'G' and resid 124 through 126 Processing sheet with id= P, first strand: chain 'G' and resid 264 through 266 removed outlier: 6.294A pdb=" N VAL G 230 " --> pdb=" O VAL G 265 " (cutoff:3.500A) 946 hydrogen bonds defined for protein. 2673 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: 7.25 Time building geometry restraints manager: 11.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 7692 1.36 - 1.50: 6603 1.50 - 1.65: 9986 1.65 - 1.80: 141 1.80 - 1.95: 88 Bond restraints: 24510 Sorted by residual: bond pdb=" N VAL A 221 " pdb=" CA VAL A 221 " ideal model delta sigma weight residual 1.457 1.494 -0.038 1.15e-02 7.56e+03 1.07e+01 bond pdb=" N GLU E 188 " pdb=" CA GLU E 188 " ideal model delta sigma weight residual 1.454 1.492 -0.038 1.23e-02 6.61e+03 9.61e+00 bond pdb=" N ILE A 224 " pdb=" CA ILE A 224 " ideal model delta sigma weight residual 1.461 1.492 -0.031 1.08e-02 8.57e+03 8.35e+00 bond pdb=" N VAL D 199 " pdb=" CA VAL D 199 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.20e-02 6.94e+03 8.16e+00 bond pdb=" N LEU E 192 " pdb=" CA LEU E 192 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.22e-02 6.72e+03 7.63e+00 ... (remaining 24505 not shown) Histogram of bond angle deviations from ideal: 99.46 - 106.37: 749 106.37 - 113.28: 13499 113.28 - 120.19: 8619 120.19 - 127.09: 10065 127.09 - 134.00: 331 Bond angle restraints: 33263 Sorted by residual: angle pdb=" N LEU A 207 " pdb=" CA LEU A 207 " pdb=" C LEU A 207 " ideal model delta sigma weight residual 111.28 104.72 6.56 1.09e+00 8.42e-01 3.62e+01 angle pdb=" N PRO A 378 " pdb=" CA PRO A 378 " pdb=" C PRO A 378 " ideal model delta sigma weight residual 113.53 106.29 7.24 1.39e+00 5.18e-01 2.72e+01 angle pdb=" N VAL D 201 " pdb=" CA VAL D 201 " pdb=" C VAL D 201 " ideal model delta sigma weight residual 112.29 107.86 4.43 9.40e-01 1.13e+00 2.22e+01 angle pdb=" N LEU A 210 " pdb=" CA LEU A 210 " pdb=" C LEU A 210 " ideal model delta sigma weight residual 111.11 106.32 4.79 1.20e+00 6.94e-01 1.59e+01 angle pdb=" PB GTP P 1 " pdb=" O3B GTP P 1 " pdb=" PG GTP P 1 " ideal model delta sigma weight residual 120.50 131.87 -11.37 3.00e+00 1.11e-01 1.44e+01 ... (remaining 33258 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.94: 14580 35.94 - 71.87: 233 71.87 - 107.81: 8 107.81 - 143.75: 0 143.75 - 179.68: 3 Dihedral angle restraints: 14824 sinusoidal: 6212 harmonic: 8612 Sorted by residual: dihedral pdb=" O1A AGS F 501 " pdb=" O3A AGS F 501 " pdb=" PA AGS F 501 " pdb=" PB AGS F 501 " ideal model delta sinusoidal sigma weight residual -67.73 111.95 -179.68 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O1B AGS B 501 " pdb=" O3B AGS B 501 " pdb=" PB AGS B 501 " pdb=" PG AGS B 501 " ideal model delta sinusoidal sigma weight residual 68.91 -86.76 155.67 1 3.00e+01 1.11e-03 2.04e+01 dihedral pdb=" C5' GTP P 1 " pdb=" O5' GTP P 1 " pdb=" PA GTP P 1 " pdb=" O3A GTP P 1 " ideal model delta sinusoidal sigma weight residual 69.27 143.57 -74.30 1 2.00e+01 2.50e-03 1.75e+01 ... (remaining 14821 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 2803 0.042 - 0.083: 643 0.083 - 0.125: 220 0.125 - 0.167: 27 0.167 - 0.209: 4 Chirality restraints: 3697 Sorted by residual: chirality pdb=" CA VAL E 244 " pdb=" N VAL E 244 " pdb=" C VAL E 244 " pdb=" CB VAL E 244 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA ILE F 321 " pdb=" N ILE F 321 " pdb=" C ILE F 321 " pdb=" CB ILE F 321 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 8.21e-01 chirality pdb=" CA LEU A 210 " pdb=" N LEU A 210 " pdb=" C LEU A 210 " pdb=" CB LEU A 210 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.85e-01 ... (remaining 3694 not shown) Planarity restraints: 4105 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA E 187 " -0.015 2.00e-02 2.50e+03 2.91e-02 8.45e+00 pdb=" C ALA E 187 " 0.050 2.00e-02 2.50e+03 pdb=" O ALA E 187 " -0.019 2.00e-02 2.50e+03 pdb=" N GLU E 188 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS F 316 " -0.010 2.00e-02 2.50e+03 1.91e-02 3.65e+00 pdb=" C CYS F 316 " 0.033 2.00e-02 2.50e+03 pdb=" O CYS F 316 " -0.013 2.00e-02 2.50e+03 pdb=" N LYS F 317 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 377 " -0.010 2.00e-02 2.50e+03 1.89e-02 3.58e+00 pdb=" C LEU A 377 " 0.033 2.00e-02 2.50e+03 pdb=" O LEU A 377 " -0.012 2.00e-02 2.50e+03 pdb=" N PRO A 378 " -0.011 2.00e-02 2.50e+03 ... (remaining 4102 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 250 2.52 - 3.11: 18931 3.11 - 3.71: 39461 3.71 - 4.30: 55823 4.30 - 4.90: 90418 Nonbonded interactions: 204883 Sorted by model distance: nonbonded pdb=" O2A AGS F 501 " pdb="MG MG F 502 " model vdw 1.924 2.170 nonbonded pdb=" O3B AGS B 501 " pdb="MG MG B 502 " model vdw 1.932 2.170 nonbonded pdb=" O3G AGS F 501 " pdb="MG MG F 502 " model vdw 1.934 2.170 nonbonded pdb=" O3G AGS C 501 " pdb="MG MG C 502 " model vdw 1.938 2.170 nonbonded pdb=" O3G AGS E 501 " pdb="MG MG E 502 " model vdw 1.980 2.170 ... (remaining 204878 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 1 through 432) selection = (chain 'C' and resid 1 through 432) selection = (chain 'D' and resid 1 through 432) selection = (chain 'E' and resid 1 through 432) selection = (chain 'F' and resid 1 through 432) } 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 group one per residue 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: 0.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 3.340 Check model and map are aligned: 0.330 Set scattering table: 0.180 Process input model: 70.320 Find NCS groups from input model: 1.720 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 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 : 0.003 0.049 24510 Z= 0.205 Angle : 0.592 11.371 33263 Z= 0.355 Chirality : 0.041 0.209 3697 Planarity : 0.003 0.044 4105 Dihedral : 12.626 179.685 9262 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 3.47 % Allowed : 7.64 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.16), residues: 2917 helix: 1.46 (0.14), residues: 1419 sheet: -1.24 (0.27), residues: 357 loop : -1.09 (0.19), residues: 1141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 162 HIS 0.003 0.001 HIS C 8 PHE 0.012 0.001 PHE D 65 TYR 0.012 0.001 TYR E 15 ARG 0.003 0.000 ARG E 236 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1378 residues out of total 2539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 1290 time to evaluate : 2.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7706 (mm-30) REVERT: A 11 PHE cc_start: 0.8133 (m-80) cc_final: 0.7601 (m-80) REVERT: A 19 VAL cc_start: 0.8366 (m) cc_final: 0.7944 (p) REVERT: A 66 THR cc_start: 0.8833 (p) cc_final: 0.8597 (p) REVERT: A 73 VAL cc_start: 0.8295 (t) cc_final: 0.7456 (p) REVERT: A 79 LYS cc_start: 0.8501 (ttmt) cc_final: 0.7760 (ttmt) REVERT: A 85 GLU cc_start: 0.7720 (mm-30) cc_final: 0.7075 (mm-30) REVERT: A 103 MET cc_start: 0.8244 (mmm) cc_final: 0.7990 (mmm) REVERT: A 104 PHE cc_start: 0.8251 (t80) cc_final: 0.7571 (t80) REVERT: A 113 ILE cc_start: 0.8724 (mt) cc_final: 0.8194 (mt) REVERT: A 123 LYS cc_start: 0.8020 (mmmm) cc_final: 0.7709 (mmmm) REVERT: A 131 VAL cc_start: 0.9071 (t) cc_final: 0.8825 (m) REVERT: A 136 ASP cc_start: 0.7389 (m-30) cc_final: 0.7169 (m-30) REVERT: A 163 LEU cc_start: 0.8984 (tp) cc_final: 0.8782 (tt) REVERT: A 164 SER cc_start: 0.8927 (m) cc_final: 0.8687 (t) REVERT: A 165 TYR cc_start: 0.8497 (m-10) cc_final: 0.8222 (m-10) REVERT: A 174 PHE cc_start: 0.8449 (m-80) cc_final: 0.8136 (m-10) REVERT: A 191 THR cc_start: 0.8949 (p) cc_final: 0.8682 (p) REVERT: A 214 TYR cc_start: 0.9045 (m-10) cc_final: 0.8523 (m-10) REVERT: A 223 TYR cc_start: 0.8071 (t80) cc_final: 0.7776 (t80) REVERT: A 224 ILE cc_start: 0.8288 (mt) cc_final: 0.7833 (mt) REVERT: A 235 LYS cc_start: 0.8291 (ttpt) cc_final: 0.7938 (ttpt) REVERT: A 241 MET cc_start: 0.8216 (mmm) cc_final: 0.7728 (mmm) REVERT: A 255 SER cc_start: 0.8355 (p) cc_final: 0.7369 (p) REVERT: A 265 LYS cc_start: 0.8484 (ttpp) cc_final: 0.8244 (ttpp) REVERT: A 312 TYR cc_start: 0.6557 (t80) cc_final: 0.6027 (t80) REVERT: A 316 CYS cc_start: 0.8081 (m) cc_final: 0.7490 (m) REVERT: A 342 LEU cc_start: 0.8205 (tp) cc_final: 0.7287 (tp) REVERT: A 403 GLN cc_start: 0.7578 (tt0) cc_final: 0.7354 (tt0) REVERT: A 408 TYR cc_start: 0.8731 (m-80) cc_final: 0.8514 (m-80) REVERT: A 416 LYS cc_start: 0.8748 (mptt) cc_final: 0.8486 (mptt) REVERT: A 423 LYS cc_start: 0.8562 (mmmm) cc_final: 0.8311 (mmmm) REVERT: B 3 GLU cc_start: 0.7653 (tt0) cc_final: 0.7066 (tt0) REVERT: B 8 HIS cc_start: 0.8300 (m90) cc_final: 0.7749 (m90) REVERT: B 47 TYR cc_start: 0.8572 (m-80) cc_final: 0.7820 (m-10) REVERT: B 70 TYR cc_start: 0.8353 (t80) cc_final: 0.8030 (t80) REVERT: B 79 LYS cc_start: 0.8739 (ttmm) cc_final: 0.8134 (ttmm) REVERT: B 92 LYS cc_start: 0.8500 (mmtt) cc_final: 0.8156 (mmtt) REVERT: B 101 ARG cc_start: 0.8481 (mmm160) cc_final: 0.8277 (tpp-160) REVERT: B 103 MET cc_start: 0.7772 (mmm) cc_final: 0.7558 (mmm) REVERT: B 155 MET cc_start: 0.7612 (tpp) cc_final: 0.7129 (tpp) REVERT: B 159 GLU cc_start: 0.7751 (mm-30) cc_final: 0.7485 (mm-30) REVERT: B 161 ARG cc_start: 0.8530 (ttm110) cc_final: 0.8230 (ttp-110) REVERT: B 175 LYS cc_start: 0.7306 (OUTLIER) cc_final: 0.7056 (ttpp) REVERT: B 192 LEU cc_start: 0.8796 (tp) cc_final: 0.8591 (tt) REVERT: B 196 MET cc_start: 0.6887 (mtm) cc_final: 0.6381 (ptp) REVERT: B 213 ASP cc_start: 0.7889 (m-30) cc_final: 0.7629 (m-30) REVERT: B 226 MET cc_start: 0.8432 (mmm) cc_final: 0.7961 (mmp) REVERT: B 231 GLU cc_start: 0.8015 (mm-30) cc_final: 0.7801 (mm-30) REVERT: B 243 ASP cc_start: 0.7076 (t0) cc_final: 0.6720 (t0) REVERT: B 245 SER cc_start: 0.8913 (t) cc_final: 0.8442 (p) REVERT: B 265 LYS cc_start: 0.8802 (ttmt) cc_final: 0.8550 (ttmt) REVERT: B 271 THR cc_start: 0.8171 (OUTLIER) cc_final: 0.7551 (t) REVERT: B 300 LYS cc_start: 0.8052 (mtpt) cc_final: 0.7665 (mtpt) REVERT: B 318 SER cc_start: 0.7871 (m) cc_final: 0.7529 (t) REVERT: B 324 TYR cc_start: 0.7557 (t80) cc_final: 0.7319 (t80) REVERT: B 325 SER cc_start: 0.7663 (OUTLIER) cc_final: 0.7238 (p) REVERT: B 345 GLU cc_start: 0.7912 (tt0) cc_final: 0.7673 (tt0) REVERT: B 392 GLU cc_start: 0.7172 (tm-30) cc_final: 0.6833 (tm-30) REVERT: B 403 GLN cc_start: 0.7434 (tt0) cc_final: 0.7095 (tt0) REVERT: B 413 LYS cc_start: 0.8507 (tppt) cc_final: 0.8136 (tppt) REVERT: C 22 TYR cc_start: 0.8779 (m-80) cc_final: 0.8569 (m-10) REVERT: C 26 GLU cc_start: 0.7532 (pt0) cc_final: 0.7278 (pt0) REVERT: C 39 LEU cc_start: 0.8864 (mt) cc_final: 0.8518 (mt) REVERT: C 41 LYS cc_start: 0.8523 (tttt) cc_final: 0.8127 (tttt) REVERT: C 80 LEU cc_start: 0.7835 (mt) cc_final: 0.7582 (mp) REVERT: C 109 LYS cc_start: 0.8730 (tptt) cc_final: 0.8497 (tptt) REVERT: C 114 GLN cc_start: 0.8117 (mt0) cc_final: 0.7681 (mt0) REVERT: C 149 TYR cc_start: 0.7083 (m-10) cc_final: 0.6804 (m-10) REVERT: C 167 ASN cc_start: 0.8305 (p0) cc_final: 0.7853 (p0) REVERT: C 180 ASN cc_start: 0.8598 (m-40) cc_final: 0.8380 (m-40) REVERT: C 181 LYS cc_start: 0.8627 (ttpp) cc_final: 0.8023 (ttpp) REVERT: C 200 ASN cc_start: 0.7231 (OUTLIER) cc_final: 0.6484 (t160) REVERT: C 226 MET cc_start: 0.7847 (mmt) cc_final: 0.7602 (mmt) REVERT: C 240 ASN cc_start: 0.8067 (t0) cc_final: 0.7607 (t0) REVERT: C 241 MET cc_start: 0.8096 (mmm) cc_final: 0.7644 (mmm) REVERT: C 255 SER cc_start: 0.8313 (m) cc_final: 0.7957 (p) REVERT: C 263 MET cc_start: 0.7325 (mmm) cc_final: 0.6955 (mmm) REVERT: C 272 LEU cc_start: 0.9012 (tp) cc_final: 0.8797 (tt) REVERT: C 280 TYR cc_start: 0.8934 (m-80) cc_final: 0.8618 (m-80) REVERT: C 292 SER cc_start: 0.8802 (m) cc_final: 0.8429 (t) REVERT: C 294 LEU cc_start: 0.9206 (mt) cc_final: 0.8968 (mt) REVERT: C 322 ARG cc_start: 0.7094 (ttp-110) cc_final: 0.6867 (ttp-110) REVERT: C 331 THR cc_start: 0.8178 (m) cc_final: 0.7911 (t) REVERT: C 345 GLU cc_start: 0.7859 (tt0) cc_final: 0.7482 (tt0) REVERT: C 402 LYS cc_start: 0.7986 (pttt) cc_final: 0.7679 (ptmt) REVERT: C 416 LYS cc_start: 0.8189 (mttt) cc_final: 0.7987 (mttt) REVERT: D 11 PHE cc_start: 0.7663 (m-80) cc_final: 0.7078 (m-10) REVERT: D 19 VAL cc_start: 0.8683 (m) cc_final: 0.8091 (p) REVERT: D 40 ILE cc_start: 0.9249 (mt) cc_final: 0.9039 (mm) REVERT: D 41 LYS cc_start: 0.8533 (ttpp) cc_final: 0.8096 (ttmm) REVERT: D 47 TYR cc_start: 0.8899 (m-80) cc_final: 0.8239 (m-80) REVERT: D 54 ASN cc_start: 0.8315 (m-40) cc_final: 0.8093 (m110) REVERT: D 89 TRP cc_start: 0.8047 (t60) cc_final: 0.7466 (t60) REVERT: D 93 GLU cc_start: 0.7839 (mm-30) cc_final: 0.7173 (mm-30) REVERT: D 103 MET cc_start: 0.8158 (mmm) cc_final: 0.7310 (mmm) REVERT: D 109 LYS cc_start: 0.8561 (tttp) cc_final: 0.8206 (ttmm) REVERT: D 111 ILE cc_start: 0.8320 (mt) cc_final: 0.8053 (mt) REVERT: D 118 GLU cc_start: 0.7396 (tp30) cc_final: 0.6830 (tp30) REVERT: D 128 MET cc_start: 0.8694 (tpp) cc_final: 0.8350 (tpp) REVERT: D 143 SER cc_start: 0.8913 (m) cc_final: 0.7972 (t) REVERT: D 153 ASP cc_start: 0.7711 (t0) cc_final: 0.7419 (t0) REVERT: D 154 TRP cc_start: 0.8644 (t60) cc_final: 0.8319 (t60) REVERT: D 159 GLU cc_start: 0.6776 (mm-30) cc_final: 0.6268 (tp30) REVERT: D 189 THR cc_start: 0.8617 (p) cc_final: 0.7374 (p) REVERT: D 192 LEU cc_start: 0.9168 (tp) cc_final: 0.8951 (tp) REVERT: D 226 MET cc_start: 0.7759 (mmm) cc_final: 0.7032 (mmm) REVERT: D 237 ILE cc_start: 0.8894 (mm) cc_final: 0.8419 (mm) REVERT: D 263 MET cc_start: 0.7999 (mmm) cc_final: 0.7530 (mmm) REVERT: D 264 GLU cc_start: 0.8356 (mm-30) cc_final: 0.8125 (mm-30) REVERT: D 267 ARG cc_start: 0.8009 (ttm110) cc_final: 0.7573 (ttm-80) REVERT: D 280 TYR cc_start: 0.8401 (m-80) cc_final: 0.8075 (m-80) REVERT: D 324 TYR cc_start: 0.7427 (m-80) cc_final: 0.7142 (m-80) REVERT: D 326 GLU cc_start: 0.7622 (mm-30) cc_final: 0.7368 (mm-30) REVERT: D 347 GLU cc_start: 0.7136 (tp30) cc_final: 0.6712 (tp30) REVERT: D 392 GLU cc_start: 0.7163 (tp30) cc_final: 0.6820 (tp30) REVERT: D 393 LEU cc_start: 0.8343 (mt) cc_final: 0.8050 (mm) REVERT: D 412 ASN cc_start: 0.8017 (m-40) cc_final: 0.7793 (m-40) REVERT: D 414 TRP cc_start: 0.8324 (m-90) cc_final: 0.8048 (m100) REVERT: D 425 ASN cc_start: 0.8433 (m110) cc_final: 0.8055 (m-40) REVERT: E 4 ILE cc_start: 0.8944 (mt) cc_final: 0.8669 (mt) REVERT: E 35 ASN cc_start: 0.8008 (m-40) cc_final: 0.7416 (m-40) REVERT: E 38 LYS cc_start: 0.8723 (mtpt) cc_final: 0.8459 (mtpt) REVERT: E 39 LEU cc_start: 0.8766 (mt) cc_final: 0.8460 (mt) REVERT: E 104 PHE cc_start: 0.8585 (t80) cc_final: 0.8071 (t80) REVERT: E 127 LYS cc_start: 0.8477 (ttmt) cc_final: 0.8250 (ttmt) REVERT: E 144 ILE cc_start: 0.7499 (OUTLIER) cc_final: 0.7277 (tt) REVERT: E 158 TYR cc_start: 0.6134 (p90) cc_final: 0.5245 (p90) REVERT: E 216 GLN cc_start: 0.7671 (mt0) cc_final: 0.7393 (mt0) REVERT: E 237 ILE cc_start: 0.8656 (mt) cc_final: 0.8413 (mt) REVERT: E 241 MET cc_start: 0.8023 (mmm) cc_final: 0.7707 (mmm) REVERT: E 242 LEU cc_start: 0.9025 (mp) cc_final: 0.8655 (mp) REVERT: E 245 SER cc_start: 0.8932 (t) cc_final: 0.8465 (p) REVERT: E 259 TYR cc_start: 0.9061 (t80) cc_final: 0.8530 (t80) REVERT: E 260 LYS cc_start: 0.8795 (OUTLIER) cc_final: 0.8318 (tmmm) REVERT: E 263 MET cc_start: 0.8110 (mmm) cc_final: 0.7573 (tpp) REVERT: E 271 THR cc_start: 0.9139 (p) cc_final: 0.8767 (t) REVERT: E 292 SER cc_start: 0.8575 (m) cc_final: 0.8371 (t) REVERT: E 326 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7573 (mt-10) REVERT: E 329 TYR cc_start: 0.6873 (t80) cc_final: 0.6560 (t80) REVERT: E 365 ASP cc_start: 0.6248 (m-30) cc_final: 0.5998 (m-30) REVERT: F 5 ILE cc_start: 0.9191 (mt) cc_final: 0.8979 (mt) REVERT: F 15 TYR cc_start: 0.7884 (t80) cc_final: 0.7305 (t80) REVERT: F 18 LYS cc_start: 0.8014 (tppp) cc_final: 0.7686 (tppp) REVERT: F 26 GLU cc_start: 0.7449 (mm-30) cc_final: 0.7242 (mm-30) REVERT: F 34 LYS cc_start: 0.8989 (ttmt) cc_final: 0.8459 (ttmm) REVERT: F 43 HIS cc_start: 0.8694 (t-90) cc_final: 0.8225 (t-90) REVERT: F 60 LEU cc_start: 0.8815 (tp) cc_final: 0.8395 (tp) REVERT: F 61 GLU cc_start: 0.7472 (mm-30) cc_final: 0.6511 (mm-30) REVERT: F 95 GLU cc_start: 0.7526 (tt0) cc_final: 0.7055 (tt0) REVERT: F 100 GLN cc_start: 0.8088 (mt0) cc_final: 0.7853 (mt0) REVERT: F 111 ILE cc_start: 0.8521 (mt) cc_final: 0.8301 (mm) REVERT: F 115 THR cc_start: 0.8728 (m) cc_final: 0.8138 (p) REVERT: F 119 LEU cc_start: 0.8491 (mt) cc_final: 0.8246 (mt) REVERT: F 146 PHE cc_start: 0.8275 (m-10) cc_final: 0.7490 (m-10) REVERT: F 157 ASP cc_start: 0.8504 (m-30) cc_final: 0.7878 (m-30) REVERT: F 166 MET cc_start: 0.8072 (ptm) cc_final: 0.7608 (tmm) REVERT: F 183 THR cc_start: 0.8136 (p) cc_final: 0.7710 (t) REVERT: F 200 ASN cc_start: 0.6997 (t0) cc_final: 0.6007 (t0) REVERT: F 237 ILE cc_start: 0.8896 (mm) cc_final: 0.7570 (mt) REVERT: F 256 TYR cc_start: 0.7558 (t80) cc_final: 0.7072 (t80) REVERT: F 263 MET cc_start: 0.7728 (mmm) cc_final: 0.7439 (tpp) REVERT: F 267 ARG cc_start: 0.7387 (ttm-80) cc_final: 0.6831 (ttm170) REVERT: F 275 LEU cc_start: 0.8864 (tp) cc_final: 0.8483 (tt) REVERT: F 291 ARG cc_start: 0.7731 (mtt90) cc_final: 0.7185 (mtt90) REVERT: F 296 GLU cc_start: 0.7420 (pt0) cc_final: 0.7209 (pt0) REVERT: F 329 TYR cc_start: 0.8045 (t80) cc_final: 0.7678 (t80) REVERT: F 340 ARG cc_start: 0.8858 (ttt-90) cc_final: 0.8633 (ttt-90) REVERT: F 345 GLU cc_start: 0.7935 (tt0) cc_final: 0.7334 (tt0) REVERT: F 419 MET cc_start: 0.3589 (mmp) cc_final: 0.3195 (tpt) REVERT: F 421 VAL cc_start: 0.7885 (t) cc_final: 0.7651 (p) REVERT: G 4 ILE cc_start: 0.9098 (mm) cc_final: 0.8819 (mm) REVERT: G 11 PHE cc_start: 0.8687 (m-80) cc_final: 0.8415 (m-80) REVERT: G 19 LEU cc_start: 0.8717 (mt) cc_final: 0.8388 (tt) REVERT: G 21 LYS cc_start: 0.8286 (mmtt) cc_final: 0.7614 (mmtp) REVERT: G 35 PHE cc_start: 0.8475 (p90) cc_final: 0.8214 (p90) REVERT: G 46 ASP cc_start: 0.8997 (OUTLIER) cc_final: 0.8255 (m-30) REVERT: G 47 GLN cc_start: 0.7793 (mt0) cc_final: 0.6225 (pt0) REVERT: G 77 TYR cc_start: 0.9066 (t80) cc_final: 0.8467 (t80) REVERT: G 80 GLU cc_start: 0.8777 (mm-30) cc_final: 0.8452 (mm-30) REVERT: G 81 PHE cc_start: 0.8774 (m-80) cc_final: 0.8555 (m-80) REVERT: G 84 ASP cc_start: 0.9403 (p0) cc_final: 0.9072 (p0) REVERT: G 85 LEU cc_start: 0.9518 (mt) cc_final: 0.8966 (mm) REVERT: G 91 PHE cc_start: 0.9182 (t80) cc_final: 0.8529 (t80) REVERT: G 93 ILE cc_start: 0.9315 (tt) cc_final: 0.8938 (tt) REVERT: G 94 ARG cc_start: 0.8307 (tpt170) cc_final: 0.7959 (tpp80) REVERT: G 95 LYS cc_start: 0.9328 (tttt) cc_final: 0.8627 (mtpp) REVERT: G 97 LYS cc_start: 0.8504 (tptm) cc_final: 0.8263 (mptm) REVERT: G 100 SER cc_start: 0.8467 (p) cc_final: 0.7849 (p) REVERT: G 194 PHE cc_start: 0.7795 (p90) cc_final: 0.7509 (p90) REVERT: G 210 ILE cc_start: 0.8876 (mm) cc_final: 0.8656 (mp) REVERT: G 231 TYR cc_start: 0.8867 (m-80) cc_final: 0.8516 (m-80) REVERT: G 238 ASP cc_start: 0.9241 (m-30) cc_final: 0.8544 (m-30) REVERT: G 243 GLU cc_start: 0.9412 (mp0) cc_final: 0.9185 (mp0) REVERT: G 263 ARG cc_start: 0.7843 (ptt180) cc_final: 0.7432 (ptt180) REVERT: G 265 VAL cc_start: 0.9017 (t) cc_final: 0.8125 (t) REVERT: G 266 TRP cc_start: 0.8438 (m100) cc_final: 0.7658 (m100) REVERT: G 295 ASP cc_start: 0.7469 (p0) cc_final: 0.5551 (p0) REVERT: G 304 VAL cc_start: 0.9264 (OUTLIER) cc_final: 0.9020 (p) REVERT: G 305 ASN cc_start: 0.9068 (t0) cc_final: 0.8679 (t0) REVERT: G 307 MET cc_start: 0.9407 (mmt) cc_final: 0.8892 (mmm) REVERT: G 309 ARG cc_start: 0.8732 (mtp180) cc_final: 0.8502 (mtp180) REVERT: G 310 LYS cc_start: 0.9309 (mttt) cc_final: 0.8914 (mmtm) REVERT: G 317 GLN cc_start: 0.9428 (mt0) cc_final: 0.9190 (mt0) REVERT: G 334 MET cc_start: 0.8127 (tpp) cc_final: 0.7567 (tpp) outliers start: 88 outliers final: 29 residues processed: 1336 average time/residue: 0.3965 time to fit residues: 784.5053 Evaluate side-chains 1161 residues out of total 2539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 1124 time to evaluate : 2.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 246 optimal weight: 7.9990 chunk 221 optimal weight: 8.9990 chunk 122 optimal weight: 10.0000 chunk 75 optimal weight: 7.9990 chunk 149 optimal weight: 0.9980 chunk 118 optimal weight: 0.0010 chunk 228 optimal weight: 0.0170 chunk 88 optimal weight: 5.9990 chunk 139 optimal weight: 4.9990 chunk 170 optimal weight: 5.9990 chunk 265 optimal weight: 10.0000 overall best weight: 2.4028 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 ASN A 100 GLN A 116 ASN A 193 ASN A 219 HIS A 240 ASN A 295 ASN B 114 GLN C 45 ASN ** C 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 HIS D 422 GLN F 48 HIS F 62 ASN F 105 ASN ** F 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 216 GLN F 288 ASN ** F 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 24510 Z= 0.281 Angle : 0.602 8.818 33263 Z= 0.313 Chirality : 0.044 0.220 3697 Planarity : 0.004 0.052 4105 Dihedral : 11.519 176.438 3510 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 17.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 0.08 % Allowed : 3.35 % Favored : 96.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.16), residues: 2917 helix: 1.31 (0.14), residues: 1410 sheet: -1.22 (0.27), residues: 359 loop : -1.13 (0.19), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 20 HIS 0.012 0.001 HIS G 274 PHE 0.035 0.002 PHE G 293 TYR 0.031 0.002 TYR G 54 ARG 0.007 0.001 ARG E 139 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1200 residues out of total 2539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1198 time to evaluate : 2.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8237 (tpp) cc_final: 0.7754 (tpp) REVERT: A 11 PHE cc_start: 0.7963 (m-80) cc_final: 0.7638 (m-10) REVERT: A 19 VAL cc_start: 0.8371 (m) cc_final: 0.7957 (p) REVERT: A 42 SER cc_start: 0.8279 (m) cc_final: 0.8059 (p) REVERT: A 47 TYR cc_start: 0.6157 (m-80) cc_final: 0.5878 (m-80) REVERT: A 60 LEU cc_start: 0.9119 (tp) cc_final: 0.8835 (tp) REVERT: A 66 THR cc_start: 0.8777 (p) cc_final: 0.8347 (p) REVERT: A 73 VAL cc_start: 0.8470 (t) cc_final: 0.8008 (t) REVERT: A 79 LYS cc_start: 0.8545 (ttmt) cc_final: 0.7940 (ttmt) REVERT: A 96 LYS cc_start: 0.8603 (mtmt) cc_final: 0.8332 (mtmt) REVERT: A 103 MET cc_start: 0.8313 (mmm) cc_final: 0.8054 (tpp) REVERT: A 104 PHE cc_start: 0.8382 (t80) cc_final: 0.8169 (t80) REVERT: A 113 ILE cc_start: 0.8857 (mt) cc_final: 0.8595 (mt) REVERT: A 123 LYS cc_start: 0.8159 (mmmm) cc_final: 0.7830 (mmmm) REVERT: A 131 VAL cc_start: 0.9059 (t) cc_final: 0.8836 (m) REVERT: A 136 ASP cc_start: 0.7333 (m-30) cc_final: 0.7089 (m-30) REVERT: A 163 LEU cc_start: 0.9030 (tp) cc_final: 0.8807 (tt) REVERT: A 164 SER cc_start: 0.9038 (m) cc_final: 0.8764 (t) REVERT: A 165 TYR cc_start: 0.8600 (m-10) cc_final: 0.8208 (m-10) REVERT: A 168 LYS cc_start: 0.8722 (mmmm) cc_final: 0.8489 (mmtm) REVERT: A 171 LYS cc_start: 0.8219 (mmtp) cc_final: 0.7794 (mmtp) REVERT: A 174 PHE cc_start: 0.8465 (m-80) cc_final: 0.8228 (m-80) REVERT: A 203 LYS cc_start: 0.7221 (pttm) cc_final: 0.6890 (pttm) REVERT: A 207 LEU cc_start: 0.8401 (mt) cc_final: 0.8121 (mm) REVERT: A 214 TYR cc_start: 0.8778 (m-80) cc_final: 0.8092 (m-10) REVERT: A 224 ILE cc_start: 0.8229 (mt) cc_final: 0.8009 (mt) REVERT: A 235 LYS cc_start: 0.8380 (ttpt) cc_final: 0.7994 (ttpt) REVERT: A 241 MET cc_start: 0.8153 (mmm) cc_final: 0.7691 (mmm) REVERT: A 265 LYS cc_start: 0.8444 (ttpp) cc_final: 0.8140 (ttpp) REVERT: A 267 ARG cc_start: 0.6373 (ttm-80) cc_final: 0.5040 (ttm-80) REVERT: A 278 LYS cc_start: 0.9001 (tptm) cc_final: 0.8581 (tptm) REVERT: A 291 ARG cc_start: 0.7791 (mtt-85) cc_final: 0.7588 (ttm110) REVERT: A 316 CYS cc_start: 0.8062 (m) cc_final: 0.7754 (m) REVERT: A 385 LEU cc_start: 0.8622 (mt) cc_final: 0.8390 (mt) REVERT: A 401 ILE cc_start: 0.7746 (mm) cc_final: 0.7537 (pt) REVERT: A 408 TYR cc_start: 0.8684 (m-80) cc_final: 0.8468 (m-80) REVERT: A 415 ASN cc_start: 0.7828 (t0) cc_final: 0.7480 (t0) REVERT: A 426 GLN cc_start: 0.7361 (mt0) cc_final: 0.7011 (mt0) REVERT: B 8 HIS cc_start: 0.8235 (m90) cc_final: 0.7525 (m90) REVERT: B 26 GLU cc_start: 0.7283 (mt-10) cc_final: 0.7011 (mt-10) REVERT: B 145 SER cc_start: 0.8353 (p) cc_final: 0.7977 (p) REVERT: B 147 ASP cc_start: 0.7315 (m-30) cc_final: 0.7044 (m-30) REVERT: B 159 GLU cc_start: 0.7831 (mm-30) cc_final: 0.7558 (mm-30) REVERT: B 161 ARG cc_start: 0.8483 (ttm110) cc_final: 0.8281 (ttp-110) REVERT: B 203 LYS cc_start: 0.8067 (ttpp) cc_final: 0.7682 (ttmt) REVERT: B 243 ASP cc_start: 0.7265 (t0) cc_final: 0.6895 (t0) REVERT: B 245 SER cc_start: 0.8912 (t) cc_final: 0.8407 (p) REVERT: B 265 LYS cc_start: 0.8803 (ttmt) cc_final: 0.8412 (ttmt) REVERT: B 318 SER cc_start: 0.8124 (m) cc_final: 0.7429 (t) REVERT: B 345 GLU cc_start: 0.8021 (tt0) cc_final: 0.7819 (tt0) REVERT: B 370 ASP cc_start: 0.6891 (m-30) cc_final: 0.6355 (m-30) REVERT: B 392 GLU cc_start: 0.7313 (tm-30) cc_final: 0.6948 (tm-30) REVERT: B 413 LYS cc_start: 0.8464 (tppt) cc_final: 0.8187 (tppt) REVERT: C 39 LEU cc_start: 0.8784 (mt) cc_final: 0.8374 (mt) REVERT: C 41 LYS cc_start: 0.8444 (tttt) cc_final: 0.8237 (tttt) REVERT: C 85 GLU cc_start: 0.8087 (mm-30) cc_final: 0.7850 (mm-30) REVERT: C 114 GLN cc_start: 0.8192 (mt0) cc_final: 0.7565 (mt0) REVERT: C 118 GLU cc_start: 0.7449 (mt-10) cc_final: 0.7152 (mt-10) REVERT: C 140 GLN cc_start: 0.7969 (tm-30) cc_final: 0.7724 (tm-30) REVERT: C 149 TYR cc_start: 0.7084 (m-10) cc_final: 0.6776 (m-10) REVERT: C 155 MET cc_start: 0.7658 (tpt) cc_final: 0.7336 (tpt) REVERT: C 167 ASN cc_start: 0.8394 (p0) cc_final: 0.7997 (p0) REVERT: C 180 ASN cc_start: 0.8682 (m-40) cc_final: 0.8478 (m-40) REVERT: C 241 MET cc_start: 0.8172 (mmm) cc_final: 0.7640 (mmm) REVERT: C 263 MET cc_start: 0.7339 (mmm) cc_final: 0.6951 (mmm) REVERT: C 269 LYS cc_start: 0.7695 (mmtp) cc_final: 0.7482 (mttm) REVERT: C 272 LEU cc_start: 0.8985 (tp) cc_final: 0.8783 (tt) REVERT: C 280 TYR cc_start: 0.8670 (m-80) cc_final: 0.8109 (m-80) REVERT: C 292 SER cc_start: 0.8794 (m) cc_final: 0.8421 (t) REVERT: C 293 LEU cc_start: 0.8895 (tp) cc_final: 0.8445 (tp) REVERT: C 315 ILE cc_start: 0.8601 (pt) cc_final: 0.8385 (pt) REVERT: C 318 SER cc_start: 0.8025 (t) cc_final: 0.7742 (p) REVERT: C 331 THR cc_start: 0.8283 (m) cc_final: 0.8059 (t) REVERT: C 345 GLU cc_start: 0.7824 (tt0) cc_final: 0.7607 (tt0) REVERT: C 393 LEU cc_start: 0.8510 (mt) cc_final: 0.8226 (mt) REVERT: D 1 MET cc_start: 0.8407 (ppp) cc_final: 0.7722 (ppp) REVERT: D 40 ILE cc_start: 0.9314 (mt) cc_final: 0.9082 (mm) REVERT: D 41 LYS cc_start: 0.8599 (ttpp) cc_final: 0.8149 (ttmm) REVERT: D 47 TYR cc_start: 0.9021 (m-80) cc_final: 0.8259 (m-80) REVERT: D 66 THR cc_start: 0.7814 (p) cc_final: 0.7483 (p) REVERT: D 89 TRP cc_start: 0.7907 (t60) cc_final: 0.7110 (t60) REVERT: D 93 GLU cc_start: 0.7818 (mm-30) cc_final: 0.7062 (mm-30) REVERT: D 96 LYS cc_start: 0.8358 (ttpp) cc_final: 0.7923 (ttpp) REVERT: D 103 MET cc_start: 0.8185 (mmm) cc_final: 0.7380 (mmm) REVERT: D 109 LYS cc_start: 0.8596 (tttp) cc_final: 0.8234 (ttmm) REVERT: D 118 GLU cc_start: 0.7549 (tp30) cc_final: 0.6897 (tp30) REVERT: D 128 MET cc_start: 0.8663 (tpp) cc_final: 0.8251 (tpp) REVERT: D 143 SER cc_start: 0.8919 (m) cc_final: 0.8061 (t) REVERT: D 147 ASP cc_start: 0.7568 (p0) cc_final: 0.7275 (p0) REVERT: D 153 ASP cc_start: 0.7857 (t0) cc_final: 0.7552 (t0) REVERT: D 154 TRP cc_start: 0.8628 (t60) cc_final: 0.8258 (t60) REVERT: D 155 MET cc_start: 0.7671 (tpt) cc_final: 0.6841 (tpt) REVERT: D 177 ARG cc_start: 0.7936 (mtm110) cc_final: 0.7697 (ptp90) REVERT: D 181 LYS cc_start: 0.9067 (ttpt) cc_final: 0.8758 (ttpt) REVERT: D 189 THR cc_start: 0.8644 (p) cc_final: 0.7170 (p) REVERT: D 223 TYR cc_start: 0.8053 (t80) cc_final: 0.7813 (t80) REVERT: D 226 MET cc_start: 0.7753 (mmm) cc_final: 0.7245 (mmm) REVERT: D 263 MET cc_start: 0.8072 (mmm) cc_final: 0.7746 (mmm) REVERT: D 278 LYS cc_start: 0.8800 (tptp) cc_final: 0.8278 (tppt) REVERT: D 280 TYR cc_start: 0.8398 (m-80) cc_final: 0.7888 (m-80) REVERT: D 312 TYR cc_start: 0.5104 (t80) cc_final: 0.4524 (t80) REVERT: D 324 TYR cc_start: 0.7494 (m-80) cc_final: 0.7150 (m-80) REVERT: D 326 GLU cc_start: 0.7774 (mm-30) cc_final: 0.7411 (mm-30) REVERT: D 329 TYR cc_start: 0.6421 (t80) cc_final: 0.5781 (t80) REVERT: D 333 LYS cc_start: 0.8507 (ttmt) cc_final: 0.8085 (ttmt) REVERT: D 338 GLU cc_start: 0.7209 (mt-10) cc_final: 0.6962 (mt-10) REVERT: D 347 GLU cc_start: 0.7149 (tp30) cc_final: 0.6549 (tp30) REVERT: D 391 GLU cc_start: 0.7705 (tt0) cc_final: 0.7497 (tt0) REVERT: D 392 GLU cc_start: 0.7388 (tp30) cc_final: 0.7176 (tp30) REVERT: D 393 LEU cc_start: 0.8227 (mt) cc_final: 0.7982 (mm) REVERT: D 412 ASN cc_start: 0.7985 (m-40) cc_final: 0.7771 (m-40) REVERT: D 414 TRP cc_start: 0.8353 (m-90) cc_final: 0.8104 (m100) REVERT: D 416 LYS cc_start: 0.8460 (mppt) cc_final: 0.7851 (mppt) REVERT: E 1 MET cc_start: 0.7496 (ptm) cc_final: 0.6583 (ptm) REVERT: E 4 ILE cc_start: 0.8948 (mt) cc_final: 0.8727 (mt) REVERT: E 18 LYS cc_start: 0.9179 (tppt) cc_final: 0.8967 (tppt) REVERT: E 25 SER cc_start: 0.9035 (m) cc_final: 0.8768 (m) REVERT: E 34 LYS cc_start: 0.8314 (tttp) cc_final: 0.7889 (tttp) REVERT: E 38 LYS cc_start: 0.8684 (mtpt) cc_final: 0.8410 (mtpt) REVERT: E 47 TYR cc_start: 0.6278 (t80) cc_final: 0.6043 (t80) REVERT: E 79 LYS cc_start: 0.7931 (mtmt) cc_final: 0.7649 (mtmt) REVERT: E 85 GLU cc_start: 0.7438 (mp0) cc_final: 0.7117 (mp0) REVERT: E 93 GLU cc_start: 0.8054 (tp30) cc_final: 0.7457 (tp30) REVERT: E 111 ILE cc_start: 0.9175 (mm) cc_final: 0.8691 (mm) REVERT: E 113 ILE cc_start: 0.8786 (mm) cc_final: 0.7852 (mm) REVERT: E 126 LYS cc_start: 0.8613 (ptpt) cc_final: 0.8392 (ptpt) REVERT: E 155 MET cc_start: 0.7918 (tpp) cc_final: 0.7454 (tpp) REVERT: E 158 TYR cc_start: 0.6263 (p90) cc_final: 0.5963 (p90) REVERT: E 216 GLN cc_start: 0.7799 (mt0) cc_final: 0.7466 (mt0) REVERT: E 226 MET cc_start: 0.5724 (mmm) cc_final: 0.5279 (mmm) REVERT: E 237 ILE cc_start: 0.8583 (mt) cc_final: 0.8319 (mt) REVERT: E 241 MET cc_start: 0.7889 (mmm) cc_final: 0.7688 (mmm) REVERT: E 242 LEU cc_start: 0.9100 (mp) cc_final: 0.8815 (mp) REVERT: E 245 SER cc_start: 0.8898 (t) cc_final: 0.8507 (p) REVERT: E 247 ASP cc_start: 0.8249 (p0) cc_final: 0.7443 (p0) REVERT: E 248 ASP cc_start: 0.8190 (m-30) cc_final: 0.7285 (m-30) REVERT: E 259 TYR cc_start: 0.9056 (t80) cc_final: 0.8597 (t80) REVERT: E 263 MET cc_start: 0.8310 (mmm) cc_final: 0.7766 (tpp) REVERT: E 271 THR cc_start: 0.9163 (p) cc_final: 0.8843 (t) REVERT: E 326 GLU cc_start: 0.7829 (mt-10) cc_final: 0.7589 (mt-10) REVERT: E 329 TYR cc_start: 0.6791 (t80) cc_final: 0.6525 (t80) REVERT: E 333 LYS cc_start: 0.8226 (tttp) cc_final: 0.7873 (tttp) REVERT: E 419 MET cc_start: 0.7374 (tpp) cc_final: 0.7085 (tpp) REVERT: F 34 LYS cc_start: 0.9065 (ttmt) cc_final: 0.8467 (ttmm) REVERT: F 38 LYS cc_start: 0.8799 (mmtp) cc_final: 0.8509 (mmtp) REVERT: F 43 HIS cc_start: 0.8815 (t-90) cc_final: 0.8359 (t-90) REVERT: F 60 LEU cc_start: 0.8778 (tp) cc_final: 0.8416 (tp) REVERT: F 61 GLU cc_start: 0.7346 (mm-30) cc_final: 0.6927 (mm-30) REVERT: F 96 LYS cc_start: 0.8654 (ttpp) cc_final: 0.8112 (ttpp) REVERT: F 111 ILE cc_start: 0.8682 (mt) cc_final: 0.8389 (mm) REVERT: F 115 THR cc_start: 0.8782 (m) cc_final: 0.8281 (p) REVERT: F 116 ASN cc_start: 0.8660 (t0) cc_final: 0.8265 (t0) REVERT: F 119 LEU cc_start: 0.8552 (mt) cc_final: 0.8282 (mt) REVERT: F 123 LYS cc_start: 0.8662 (tptt) cc_final: 0.8420 (tptt) REVERT: F 155 MET cc_start: 0.6541 (tpp) cc_final: 0.5390 (tpp) REVERT: F 157 ASP cc_start: 0.8573 (m-30) cc_final: 0.7392 (m-30) REVERT: F 158 TYR cc_start: 0.7005 (p90) cc_final: 0.6327 (p90) REVERT: F 167 ASN cc_start: 0.8339 (m110) cc_final: 0.8128 (m-40) REVERT: F 183 THR cc_start: 0.8163 (p) cc_final: 0.7686 (t) REVERT: F 200 ASN cc_start: 0.6890 (t0) cc_final: 0.6543 (t0) REVERT: F 235 LYS cc_start: 0.8374 (ttpt) cc_final: 0.7964 (tttm) REVERT: F 237 ILE cc_start: 0.8847 (mm) cc_final: 0.7129 (mt) REVERT: F 256 TYR cc_start: 0.7520 (t80) cc_final: 0.6491 (t80) REVERT: F 280 TYR cc_start: 0.8268 (m-80) cc_final: 0.7919 (m-80) REVERT: F 291 ARG cc_start: 0.8148 (mtt90) cc_final: 0.7553 (mtt90) REVERT: F 329 TYR cc_start: 0.8014 (t80) cc_final: 0.7596 (t80) REVERT: F 345 GLU cc_start: 0.7454 (tt0) cc_final: 0.7146 (tt0) REVERT: G 4 ILE cc_start: 0.9144 (mm) cc_final: 0.8741 (mm) REVERT: G 8 ASP cc_start: 0.8913 (m-30) cc_final: 0.8466 (m-30) REVERT: G 19 LEU cc_start: 0.8788 (mt) cc_final: 0.8436 (tt) REVERT: G 63 ILE cc_start: 0.9062 (mt) cc_final: 0.8849 (mt) REVERT: G 74 ILE cc_start: 0.9172 (tp) cc_final: 0.8836 (tp) REVERT: G 77 TYR cc_start: 0.9110 (t80) cc_final: 0.8508 (t80) REVERT: G 78 LEU cc_start: 0.9524 (mt) cc_final: 0.9308 (mt) REVERT: G 80 GLU cc_start: 0.8791 (mm-30) cc_final: 0.8450 (mm-30) REVERT: G 81 PHE cc_start: 0.8824 (m-80) cc_final: 0.8539 (m-80) REVERT: G 82 GLU cc_start: 0.9013 (mm-30) cc_final: 0.8631 (mm-30) REVERT: G 85 LEU cc_start: 0.9428 (mt) cc_final: 0.9114 (mm) REVERT: G 89 TYR cc_start: 0.8603 (t80) cc_final: 0.8093 (t80) REVERT: G 92 GLU cc_start: 0.8888 (tp30) cc_final: 0.7327 (tp30) REVERT: G 95 LYS cc_start: 0.9313 (tttt) cc_final: 0.8824 (ttpp) REVERT: G 96 GLU cc_start: 0.8869 (mm-30) cc_final: 0.7968 (mm-30) REVERT: G 97 LYS cc_start: 0.8602 (tptm) cc_final: 0.8340 (mptm) REVERT: G 100 SER cc_start: 0.8152 (p) cc_final: 0.7372 (p) REVERT: G 151 LYS cc_start: 0.9249 (ptpp) cc_final: 0.8750 (pttm) REVERT: G 158 GLU cc_start: 0.9136 (mt-10) cc_final: 0.8874 (mp0) REVERT: G 177 GLU cc_start: 0.9188 (mt-10) cc_final: 0.8799 (tm-30) REVERT: G 194 PHE cc_start: 0.7937 (p90) cc_final: 0.7660 (p90) REVERT: G 210 ILE cc_start: 0.8907 (mm) cc_final: 0.8637 (mp) REVERT: G 224 ARG cc_start: 0.9028 (ptp-110) cc_final: 0.8807 (ptp-110) REVERT: G 231 TYR cc_start: 0.8860 (m-80) cc_final: 0.8223 (m-80) REVERT: G 238 ASP cc_start: 0.9249 (m-30) cc_final: 0.8784 (m-30) REVERT: G 240 LEU cc_start: 0.9269 (mt) cc_final: 0.9006 (mt) REVERT: G 241 PHE cc_start: 0.8127 (m-80) cc_final: 0.7817 (m-80) REVERT: G 242 ILE cc_start: 0.9091 (mp) cc_final: 0.8652 (tp) REVERT: G 266 TRP cc_start: 0.8584 (m100) cc_final: 0.7649 (m100) REVERT: G 281 MET cc_start: 0.9042 (mmt) cc_final: 0.8765 (mpp) REVERT: G 290 ARG cc_start: 0.7783 (mtm-85) cc_final: 0.7478 (mtm110) REVERT: G 303 ASP cc_start: 0.9161 (p0) cc_final: 0.8920 (p0) REVERT: G 306 ASP cc_start: 0.8920 (t70) cc_final: 0.8653 (t0) REVERT: G 319 MET cc_start: 0.9146 (mpp) cc_final: 0.8918 (mmt) REVERT: G 328 GLN cc_start: 0.7395 (tp40) cc_final: 0.7123 (tp40) REVERT: G 334 MET cc_start: 0.8103 (tpp) cc_final: 0.7533 (tpp) REVERT: G 335 ARG cc_start: 0.8444 (mtm180) cc_final: 0.8190 (mtm180) outliers start: 2 outliers final: 0 residues processed: 1199 average time/residue: 0.4045 time to fit residues: 723.2974 Evaluate side-chains 1088 residues out of total 2539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1088 time to evaluate : 2.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 147 optimal weight: 5.9990 chunk 82 optimal weight: 5.9990 chunk 220 optimal weight: 0.9980 chunk 180 optimal weight: 0.0470 chunk 73 optimal weight: 0.8980 chunk 265 optimal weight: 2.9990 chunk 286 optimal weight: 4.9990 chunk 236 optimal weight: 9.9990 chunk 263 optimal weight: 20.0000 chunk 90 optimal weight: 0.0970 chunk 213 optimal weight: 6.9990 overall best weight: 1.0078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN A 116 ASN A 180 ASN A 193 ASN A 219 HIS A 240 ASN A 403 GLN B 403 GLN ** C 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 114 GLN D 422 GLN F 48 HIS ** F 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 325 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 24510 Z= 0.197 Angle : 0.559 8.856 33263 Z= 0.291 Chirality : 0.042 0.277 3697 Planarity : 0.004 0.052 4105 Dihedral : 11.165 168.584 3510 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 16.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 0.08 % Allowed : 2.56 % Favored : 97.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.16), residues: 2917 helix: 1.37 (0.14), residues: 1413 sheet: -1.11 (0.27), residues: 366 loop : -1.15 (0.19), residues: 1138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP F 89 HIS 0.008 0.001 HIS B 43 PHE 0.027 0.002 PHE A 417 TYR 0.027 0.001 TYR B 165 ARG 0.008 0.001 ARG F 236 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1168 residues out of total 2539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1166 time to evaluate : 2.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 VAL cc_start: 0.8363 (m) cc_final: 0.8088 (p) REVERT: A 26 GLU cc_start: 0.7403 (pm20) cc_final: 0.6917 (pm20) REVERT: A 35 ASN cc_start: 0.8050 (m-40) cc_final: 0.7804 (m-40) REVERT: A 47 TYR cc_start: 0.6121 (m-80) cc_final: 0.5868 (m-80) REVERT: A 60 LEU cc_start: 0.9101 (tp) cc_final: 0.8833 (tp) REVERT: A 66 THR cc_start: 0.8733 (p) cc_final: 0.8285 (p) REVERT: A 73 VAL cc_start: 0.8444 (t) cc_final: 0.7727 (p) REVERT: A 83 SER cc_start: 0.8474 (m) cc_final: 0.8103 (m) REVERT: A 85 GLU cc_start: 0.7557 (mm-30) cc_final: 0.7229 (mm-30) REVERT: A 113 ILE cc_start: 0.8824 (mt) cc_final: 0.8544 (mt) REVERT: A 123 LYS cc_start: 0.8124 (mmmm) cc_final: 0.7890 (mmmm) REVERT: A 131 VAL cc_start: 0.9041 (t) cc_final: 0.8755 (m) REVERT: A 146 PHE cc_start: 0.8203 (m-10) cc_final: 0.7835 (m-10) REVERT: A 148 SER cc_start: 0.7966 (t) cc_final: 0.7757 (t) REVERT: A 163 LEU cc_start: 0.8949 (tp) cc_final: 0.8682 (mp) REVERT: A 164 SER cc_start: 0.9015 (m) cc_final: 0.8776 (t) REVERT: A 165 TYR cc_start: 0.8615 (m-10) cc_final: 0.8284 (m-10) REVERT: A 168 LYS cc_start: 0.8615 (mmmm) cc_final: 0.8399 (mmtm) REVERT: A 171 LYS cc_start: 0.8145 (mmtp) cc_final: 0.7793 (mmtp) REVERT: A 174 PHE cc_start: 0.8507 (m-80) cc_final: 0.8261 (m-80) REVERT: A 196 MET cc_start: 0.7298 (mmt) cc_final: 0.7014 (mmt) REVERT: A 207 LEU cc_start: 0.8209 (mt) cc_final: 0.7966 (mm) REVERT: A 213 ASP cc_start: 0.7693 (m-30) cc_final: 0.7246 (m-30) REVERT: A 214 TYR cc_start: 0.8676 (m-80) cc_final: 0.7954 (m-10) REVERT: A 224 ILE cc_start: 0.8245 (mt) cc_final: 0.8033 (mt) REVERT: A 235 LYS cc_start: 0.8340 (ttpt) cc_final: 0.7923 (ttpt) REVERT: A 241 MET cc_start: 0.8162 (mmm) cc_final: 0.7667 (mmm) REVERT: A 255 SER cc_start: 0.8110 (p) cc_final: 0.7607 (p) REVERT: A 260 LYS cc_start: 0.8609 (mmmm) cc_final: 0.8080 (mmmm) REVERT: A 265 LYS cc_start: 0.8369 (ttpp) cc_final: 0.8086 (ttpp) REVERT: A 267 ARG cc_start: 0.6525 (ttm-80) cc_final: 0.6005 (ttm-80) REVERT: A 278 LYS cc_start: 0.8870 (tptm) cc_final: 0.8254 (tptm) REVERT: A 313 LEU cc_start: 0.7093 (tt) cc_final: 0.6872 (tt) REVERT: A 316 CYS cc_start: 0.8060 (m) cc_final: 0.7608 (m) REVERT: A 347 GLU cc_start: 0.7687 (mm-30) cc_final: 0.7475 (mt-10) REVERT: A 408 TYR cc_start: 0.8483 (m-80) cc_final: 0.8224 (m-80) REVERT: B 3 GLU cc_start: 0.7566 (tt0) cc_final: 0.7334 (tt0) REVERT: B 8 HIS cc_start: 0.8103 (m90) cc_final: 0.7563 (m90) REVERT: B 75 THR cc_start: 0.9006 (p) cc_final: 0.8636 (t) REVERT: B 145 SER cc_start: 0.8566 (p) cc_final: 0.7793 (p) REVERT: B 147 ASP cc_start: 0.7350 (m-30) cc_final: 0.7029 (m-30) REVERT: B 171 LYS cc_start: 0.8201 (mmmm) cc_final: 0.7992 (mmmm) REVERT: B 194 VAL cc_start: 0.8889 (t) cc_final: 0.8397 (t) REVERT: B 203 LYS cc_start: 0.8118 (ttpp) cc_final: 0.7734 (ttpp) REVERT: B 236 ARG cc_start: 0.7656 (ttm110) cc_final: 0.7021 (ttm110) REVERT: B 243 ASP cc_start: 0.7173 (t0) cc_final: 0.6841 (t0) REVERT: B 245 SER cc_start: 0.8798 (t) cc_final: 0.8386 (p) REVERT: B 279 GLN cc_start: 0.8579 (tt0) cc_final: 0.8339 (tt0) REVERT: B 301 LYS cc_start: 0.8834 (mttp) cc_final: 0.8569 (mttp) REVERT: B 318 SER cc_start: 0.8095 (m) cc_final: 0.7469 (t) REVERT: B 337 GLU cc_start: 0.7641 (mt-10) cc_final: 0.7387 (mt-10) REVERT: B 352 THR cc_start: 0.8395 (t) cc_final: 0.8086 (m) REVERT: B 370 ASP cc_start: 0.6646 (m-30) cc_final: 0.6400 (m-30) REVERT: B 392 GLU cc_start: 0.7302 (tm-30) cc_final: 0.6962 (tm-30) REVERT: B 413 LYS cc_start: 0.8161 (tppt) cc_final: 0.7907 (tppt) REVERT: B 427 LYS cc_start: 0.7991 (tttm) cc_final: 0.7696 (tttm) REVERT: C 13 GLN cc_start: 0.8147 (tp40) cc_final: 0.7882 (tp40) REVERT: C 26 GLU cc_start: 0.7546 (pt0) cc_final: 0.7201 (pt0) REVERT: C 39 LEU cc_start: 0.8649 (mt) cc_final: 0.8300 (mt) REVERT: C 41 LYS cc_start: 0.8459 (tttt) cc_final: 0.8254 (tttt) REVERT: C 85 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7806 (mm-30) REVERT: C 140 GLN cc_start: 0.8007 (tm-30) cc_final: 0.7741 (tm-30) REVERT: C 149 TYR cc_start: 0.6976 (m-10) cc_final: 0.6744 (m-80) REVERT: C 154 TRP cc_start: 0.8517 (t60) cc_final: 0.8184 (t60) REVERT: C 166 MET cc_start: 0.7257 (tpt) cc_final: 0.6591 (tpt) REVERT: C 167 ASN cc_start: 0.8188 (p0) cc_final: 0.7607 (p0) REVERT: C 178 ILE cc_start: 0.8367 (tp) cc_final: 0.7759 (mm) REVERT: C 181 LYS cc_start: 0.8533 (ttpp) cc_final: 0.7872 (ttpp) REVERT: C 184 LYS cc_start: 0.8637 (mtmm) cc_final: 0.8411 (mtmm) REVERT: C 196 MET cc_start: 0.7851 (ptp) cc_final: 0.7644 (ptp) REVERT: C 203 LYS cc_start: 0.8209 (mtmm) cc_final: 0.7876 (mtmm) REVERT: C 241 MET cc_start: 0.8156 (mmm) cc_final: 0.7633 (mmm) REVERT: C 263 MET cc_start: 0.7367 (mmm) cc_final: 0.7083 (mmm) REVERT: C 276 ILE cc_start: 0.9184 (mm) cc_final: 0.8982 (mm) REVERT: C 292 SER cc_start: 0.8797 (m) cc_final: 0.8410 (t) REVERT: C 295 ASN cc_start: 0.7935 (t0) cc_final: 0.7664 (t0) REVERT: C 331 THR cc_start: 0.8331 (m) cc_final: 0.7996 (t) REVERT: C 419 MET cc_start: 0.7202 (tpp) cc_final: 0.6911 (ttm) REVERT: D 1 MET cc_start: 0.8359 (ppp) cc_final: 0.7724 (ppp) REVERT: D 40 ILE cc_start: 0.9315 (mt) cc_final: 0.9063 (mm) REVERT: D 41 LYS cc_start: 0.8553 (ttpp) cc_final: 0.8052 (ttmm) REVERT: D 47 TYR cc_start: 0.9036 (m-80) cc_final: 0.8321 (m-80) REVERT: D 89 TRP cc_start: 0.7803 (t60) cc_final: 0.7509 (t60) REVERT: D 93 GLU cc_start: 0.7716 (mm-30) cc_final: 0.7244 (mm-30) REVERT: D 96 LYS cc_start: 0.8323 (ttpp) cc_final: 0.7864 (ttpp) REVERT: D 103 MET cc_start: 0.8187 (mmm) cc_final: 0.7288 (mmm) REVERT: D 109 LYS cc_start: 0.8547 (tttp) cc_final: 0.8198 (ttmm) REVERT: D 118 GLU cc_start: 0.7322 (tp30) cc_final: 0.6917 (tp30) REVERT: D 128 MET cc_start: 0.8634 (tpp) cc_final: 0.8394 (tpp) REVERT: D 143 SER cc_start: 0.8835 (m) cc_final: 0.7987 (t) REVERT: D 147 ASP cc_start: 0.7529 (p0) cc_final: 0.7220 (p0) REVERT: D 153 ASP cc_start: 0.7817 (t0) cc_final: 0.7575 (t0) REVERT: D 154 TRP cc_start: 0.8621 (t60) cc_final: 0.8367 (t60) REVERT: D 155 MET cc_start: 0.7660 (tpt) cc_final: 0.6853 (tpt) REVERT: D 189 THR cc_start: 0.8678 (p) cc_final: 0.6971 (p) REVERT: D 226 MET cc_start: 0.7715 (mmm) cc_final: 0.6940 (mmm) REVERT: D 237 ILE cc_start: 0.8391 (mm) cc_final: 0.7992 (tp) REVERT: D 241 MET cc_start: 0.7830 (mtm) cc_final: 0.6239 (mtm) REVERT: D 280 TYR cc_start: 0.8370 (m-80) cc_final: 0.7952 (m-80) REVERT: D 293 LEU cc_start: 0.8310 (tp) cc_final: 0.8095 (tp) REVERT: D 324 TYR cc_start: 0.7407 (m-80) cc_final: 0.7136 (m-80) REVERT: D 326 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7391 (mm-30) REVERT: D 338 GLU cc_start: 0.7167 (mt-10) cc_final: 0.6953 (mt-10) REVERT: D 347 GLU cc_start: 0.7223 (tp30) cc_final: 0.6556 (tp30) REVERT: D 392 GLU cc_start: 0.7344 (tp30) cc_final: 0.6989 (tp30) REVERT: E 1 MET cc_start: 0.7315 (ptm) cc_final: 0.6927 (ptm) REVERT: E 18 LYS cc_start: 0.9131 (tppt) cc_final: 0.8896 (tppt) REVERT: E 34 LYS cc_start: 0.8255 (tttp) cc_final: 0.7903 (tttp) REVERT: E 39 LEU cc_start: 0.8584 (mt) cc_final: 0.8284 (mt) REVERT: E 41 LYS cc_start: 0.8388 (ttpt) cc_final: 0.8073 (ttpt) REVERT: E 79 LYS cc_start: 0.7898 (mtmt) cc_final: 0.7614 (mtmt) REVERT: E 85 GLU cc_start: 0.7306 (mp0) cc_final: 0.7064 (mp0) REVERT: E 93 GLU cc_start: 0.8061 (tp30) cc_final: 0.7669 (tp30) REVERT: E 95 GLU cc_start: 0.8157 (tt0) cc_final: 0.7714 (tt0) REVERT: E 139 ARG cc_start: 0.7551 (ttp80) cc_final: 0.7162 (ttp80) REVERT: E 146 PHE cc_start: 0.7487 (m-10) cc_final: 0.7168 (m-10) REVERT: E 226 MET cc_start: 0.5567 (mmm) cc_final: 0.5320 (mmp) REVERT: E 241 MET cc_start: 0.7836 (mmm) cc_final: 0.7605 (mmm) REVERT: E 242 LEU cc_start: 0.9144 (mp) cc_final: 0.8779 (mp) REVERT: E 245 SER cc_start: 0.8821 (t) cc_final: 0.8444 (p) REVERT: E 247 ASP cc_start: 0.8067 (p0) cc_final: 0.7118 (p0) REVERT: E 248 ASP cc_start: 0.8126 (m-30) cc_final: 0.7068 (m-30) REVERT: E 259 TYR cc_start: 0.9082 (t80) cc_final: 0.8562 (t80) REVERT: E 263 MET cc_start: 0.8350 (mmm) cc_final: 0.7778 (tpp) REVERT: E 267 ARG cc_start: 0.8415 (tpp80) cc_final: 0.7735 (tpp80) REVERT: E 271 THR cc_start: 0.9175 (p) cc_final: 0.8852 (t) REVERT: E 301 LYS cc_start: 0.7851 (ptpp) cc_final: 0.7474 (ptpp) REVERT: E 326 GLU cc_start: 0.7750 (mt-10) cc_final: 0.7529 (mt-10) REVERT: E 329 TYR cc_start: 0.6794 (t80) cc_final: 0.6555 (t80) REVERT: E 333 LYS cc_start: 0.8154 (tttp) cc_final: 0.7769 (tttp) REVERT: E 416 LYS cc_start: 0.8106 (mttp) cc_final: 0.7766 (mttp) REVERT: F 22 TYR cc_start: 0.8373 (m-80) cc_final: 0.7829 (m-10) REVERT: F 34 LYS cc_start: 0.9020 (ttmt) cc_final: 0.8433 (ttmm) REVERT: F 41 LYS cc_start: 0.8897 (tttp) cc_final: 0.8115 (tppp) REVERT: F 43 HIS cc_start: 0.8766 (t-90) cc_final: 0.8282 (t-90) REVERT: F 60 LEU cc_start: 0.8780 (tp) cc_final: 0.8453 (tp) REVERT: F 61 GLU cc_start: 0.7378 (mm-30) cc_final: 0.6855 (mm-30) REVERT: F 62 ASN cc_start: 0.7916 (t0) cc_final: 0.7685 (t0) REVERT: F 82 ASP cc_start: 0.7327 (t0) cc_final: 0.7053 (t0) REVERT: F 96 LYS cc_start: 0.8617 (ttpp) cc_final: 0.8128 (ttpp) REVERT: F 115 THR cc_start: 0.8756 (m) cc_final: 0.8211 (p) REVERT: F 116 ASN cc_start: 0.8574 (t0) cc_final: 0.7998 (t0) REVERT: F 119 LEU cc_start: 0.8523 (mt) cc_final: 0.8184 (mt) REVERT: F 156 ASP cc_start: 0.8099 (t0) cc_final: 0.7860 (t0) REVERT: F 158 TYR cc_start: 0.7148 (p90) cc_final: 0.6899 (p90) REVERT: F 183 THR cc_start: 0.8180 (p) cc_final: 0.7726 (t) REVERT: F 275 LEU cc_start: 0.8798 (tp) cc_final: 0.8560 (tp) REVERT: F 280 TYR cc_start: 0.8262 (m-80) cc_final: 0.7907 (m-80) REVERT: F 291 ARG cc_start: 0.8150 (mtt90) cc_final: 0.7313 (mtt90) REVERT: F 296 GLU cc_start: 0.7463 (pt0) cc_final: 0.7207 (pt0) REVERT: F 329 TYR cc_start: 0.8063 (t80) cc_final: 0.7735 (t80) REVERT: F 404 ILE cc_start: 0.8325 (mt) cc_final: 0.7953 (mt) REVERT: G 4 ILE cc_start: 0.9037 (mm) cc_final: 0.8006 (mm) REVERT: G 8 ASP cc_start: 0.8921 (m-30) cc_final: 0.8505 (m-30) REVERT: G 19 LEU cc_start: 0.8726 (mt) cc_final: 0.8435 (tt) REVERT: G 77 TYR cc_start: 0.9088 (t80) cc_final: 0.8511 (t80) REVERT: G 80 GLU cc_start: 0.8772 (mm-30) cc_final: 0.8448 (mm-30) REVERT: G 81 PHE cc_start: 0.8729 (m-80) cc_final: 0.8478 (m-80) REVERT: G 89 TYR cc_start: 0.8605 (t80) cc_final: 0.8146 (t80) REVERT: G 91 PHE cc_start: 0.9248 (t80) cc_final: 0.8583 (t80) REVERT: G 92 GLU cc_start: 0.8822 (tp30) cc_final: 0.8523 (tp30) REVERT: G 93 ILE cc_start: 0.9321 (tt) cc_final: 0.8999 (tt) REVERT: G 96 GLU cc_start: 0.8669 (mm-30) cc_final: 0.8317 (pp20) REVERT: G 97 LYS cc_start: 0.8563 (tppp) cc_final: 0.8250 (tppp) REVERT: G 100 SER cc_start: 0.8196 (p) cc_final: 0.7260 (p) REVERT: G 137 ILE cc_start: 0.9405 (mm) cc_final: 0.9108 (mm) REVERT: G 158 GLU cc_start: 0.9189 (mt-10) cc_final: 0.8988 (mp0) REVERT: G 177 GLU cc_start: 0.9158 (mt-10) cc_final: 0.8754 (tm-30) REVERT: G 194 PHE cc_start: 0.7833 (p90) cc_final: 0.7493 (p90) REVERT: G 210 ILE cc_start: 0.8870 (mm) cc_final: 0.8614 (mp) REVERT: G 231 TYR cc_start: 0.8808 (m-80) cc_final: 0.8396 (m-80) REVERT: G 238 ASP cc_start: 0.9261 (m-30) cc_final: 0.8759 (m-30) REVERT: G 240 LEU cc_start: 0.9286 (mt) cc_final: 0.9027 (mt) REVERT: G 242 ILE cc_start: 0.9204 (mp) cc_final: 0.8764 (tp) REVERT: G 266 TRP cc_start: 0.8453 (m100) cc_final: 0.7953 (m100) REVERT: G 277 THR cc_start: 0.9411 (m) cc_final: 0.8968 (t) REVERT: G 279 LYS cc_start: 0.9300 (mtmm) cc_final: 0.9099 (mttm) REVERT: G 281 MET cc_start: 0.8969 (mmt) cc_final: 0.8736 (mmt) REVERT: G 283 LYS cc_start: 0.9318 (pttm) cc_final: 0.8998 (pttm) REVERT: G 285 VAL cc_start: 0.9293 (p) cc_final: 0.8709 (p) REVERT: G 305 ASN cc_start: 0.9077 (t0) cc_final: 0.8769 (t0) REVERT: G 306 ASP cc_start: 0.8998 (t70) cc_final: 0.8685 (t0) REVERT: G 307 MET cc_start: 0.9245 (mmt) cc_final: 0.8687 (mmm) REVERT: G 314 THR cc_start: 0.9221 (p) cc_final: 0.8969 (t) REVERT: G 328 GLN cc_start: 0.7645 (tp40) cc_final: 0.7388 (tp40) REVERT: G 330 LEU cc_start: 0.9088 (mt) cc_final: 0.8648 (mt) REVERT: G 333 LYS cc_start: 0.9173 (mmtt) cc_final: 0.8690 (mmtt) outliers start: 2 outliers final: 0 residues processed: 1166 average time/residue: 0.4182 time to fit residues: 727.0695 Evaluate side-chains 1072 residues out of total 2539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1072 time to evaluate : 3.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 262 optimal weight: 0.1980 chunk 199 optimal weight: 0.4980 chunk 137 optimal weight: 5.9990 chunk 29 optimal weight: 9.9990 chunk 126 optimal weight: 0.9980 chunk 178 optimal weight: 9.9990 chunk 266 optimal weight: 0.8980 chunk 282 optimal weight: 40.0000 chunk 139 optimal weight: 0.9990 chunk 252 optimal weight: 10.0000 chunk 76 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 GLN A 116 ASN A 193 ASN A 219 HIS A 240 ASN ** A 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 GLN ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 398 GLN ** C 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 114 GLN D 219 HIS D 422 GLN ** D 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 48 HIS ** F 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.3042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24510 Z= 0.179 Angle : 0.560 9.554 33263 Z= 0.291 Chirality : 0.042 0.234 3697 Planarity : 0.004 0.054 4105 Dihedral : 10.978 163.162 3510 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 15.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.16), residues: 2917 helix: 1.39 (0.14), residues: 1410 sheet: -1.12 (0.26), residues: 390 loop : -1.20 (0.18), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP G 294 HIS 0.007 0.001 HIS D 219 PHE 0.021 0.002 PHE G 91 TYR 0.036 0.001 TYR B 165 ARG 0.012 0.001 ARG C 236 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1164 residues out of total 2539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1164 time to evaluate : 2.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 PHE cc_start: 0.7973 (m-10) cc_final: 0.7733 (m-10) REVERT: A 19 VAL cc_start: 0.8441 (m) cc_final: 0.8132 (p) REVERT: A 26 GLU cc_start: 0.7377 (pm20) cc_final: 0.6868 (pm20) REVERT: A 60 LEU cc_start: 0.9071 (tp) cc_final: 0.8801 (tp) REVERT: A 66 THR cc_start: 0.8701 (p) cc_final: 0.8290 (p) REVERT: A 73 VAL cc_start: 0.8415 (t) cc_final: 0.7735 (p) REVERT: A 104 PHE cc_start: 0.8343 (t80) cc_final: 0.7673 (t80) REVERT: A 123 LYS cc_start: 0.8064 (mmmm) cc_final: 0.7700 (mmmm) REVERT: A 128 MET cc_start: 0.8082 (tpt) cc_final: 0.7815 (tpt) REVERT: A 131 VAL cc_start: 0.8996 (t) cc_final: 0.8716 (m) REVERT: A 146 PHE cc_start: 0.8221 (m-10) cc_final: 0.7940 (m-10) REVERT: A 163 LEU cc_start: 0.8949 (tp) cc_final: 0.8711 (mp) REVERT: A 188 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7698 (mt-10) REVERT: A 196 MET cc_start: 0.7357 (mmt) cc_final: 0.6996 (mmt) REVERT: A 213 ASP cc_start: 0.7711 (m-30) cc_final: 0.7273 (m-30) REVERT: A 214 TYR cc_start: 0.8768 (m-80) cc_final: 0.8231 (m-80) REVERT: A 224 ILE cc_start: 0.8294 (mt) cc_final: 0.7988 (mt) REVERT: A 235 LYS cc_start: 0.8252 (ttpt) cc_final: 0.7825 (ttpt) REVERT: A 241 MET cc_start: 0.8152 (mmm) cc_final: 0.7595 (mmm) REVERT: A 248 ASP cc_start: 0.7613 (m-30) cc_final: 0.7119 (m-30) REVERT: A 255 SER cc_start: 0.8063 (p) cc_final: 0.7606 (p) REVERT: A 260 LYS cc_start: 0.8652 (mmmm) cc_final: 0.8119 (mmmm) REVERT: A 265 LYS cc_start: 0.8396 (ttpp) cc_final: 0.8113 (ttpp) REVERT: A 278 LYS cc_start: 0.8961 (tptm) cc_final: 0.8358 (tptm) REVERT: A 316 CYS cc_start: 0.8008 (m) cc_final: 0.7702 (m) REVERT: A 347 GLU cc_start: 0.7608 (mm-30) cc_final: 0.7280 (mm-30) REVERT: A 423 LYS cc_start: 0.8466 (mmmm) cc_final: 0.8253 (mmmm) REVERT: A 426 GLN cc_start: 0.7685 (mt0) cc_final: 0.7412 (mt0) REVERT: B 15 TYR cc_start: 0.8216 (t80) cc_final: 0.7987 (t80) REVERT: B 26 GLU cc_start: 0.6702 (mp0) cc_final: 0.6260 (mp0) REVERT: B 41 LYS cc_start: 0.8967 (ttmt) cc_final: 0.8728 (ttmt) REVERT: B 43 HIS cc_start: 0.8724 (t-170) cc_final: 0.8399 (t-170) REVERT: B 47 TYR cc_start: 0.8650 (m-80) cc_final: 0.8121 (m-10) REVERT: B 94 THR cc_start: 0.8906 (m) cc_final: 0.8693 (m) REVERT: B 145 SER cc_start: 0.8612 (p) cc_final: 0.7825 (p) REVERT: B 147 ASP cc_start: 0.7341 (m-30) cc_final: 0.6994 (m-30) REVERT: B 155 MET cc_start: 0.7859 (tpp) cc_final: 0.7546 (tpp) REVERT: B 194 VAL cc_start: 0.8732 (t) cc_final: 0.8231 (t) REVERT: B 203 LYS cc_start: 0.8102 (ttpp) cc_final: 0.7617 (ttmt) REVERT: B 228 MET cc_start: 0.7827 (mtm) cc_final: 0.7096 (mtm) REVERT: B 236 ARG cc_start: 0.7732 (ttm110) cc_final: 0.7015 (ttm110) REVERT: B 243 ASP cc_start: 0.7075 (t0) cc_final: 0.6801 (t0) REVERT: B 245 SER cc_start: 0.8906 (t) cc_final: 0.8525 (p) REVERT: B 258 GLU cc_start: 0.7938 (pt0) cc_final: 0.7714 (pt0) REVERT: B 260 LYS cc_start: 0.8759 (tttp) cc_final: 0.8540 (tttm) REVERT: B 263 MET cc_start: 0.7882 (mmm) cc_final: 0.7129 (mmm) REVERT: B 288 ASN cc_start: 0.8450 (m-40) cc_final: 0.8116 (m-40) REVERT: B 318 SER cc_start: 0.8097 (m) cc_final: 0.7468 (t) REVERT: B 352 THR cc_start: 0.8339 (t) cc_final: 0.8034 (m) REVERT: B 392 GLU cc_start: 0.7243 (tm-30) cc_final: 0.6954 (tm-30) REVERT: B 403 GLN cc_start: 0.7247 (tt0) cc_final: 0.6836 (pt0) REVERT: B 413 LYS cc_start: 0.8149 (tppt) cc_final: 0.7202 (tppt) REVERT: B 414 TRP cc_start: 0.7036 (m-90) cc_final: 0.6565 (m-90) REVERT: C 3 GLU cc_start: 0.8140 (mm-30) cc_final: 0.7913 (mm-30) REVERT: C 13 GLN cc_start: 0.8089 (tp40) cc_final: 0.7821 (tp40) REVERT: C 26 GLU cc_start: 0.7478 (pt0) cc_final: 0.7263 (pt0) REVERT: C 39 LEU cc_start: 0.8472 (mt) cc_final: 0.8152 (mt) REVERT: C 41 LYS cc_start: 0.8476 (tttt) cc_final: 0.8226 (tttt) REVERT: C 85 GLU cc_start: 0.8075 (mm-30) cc_final: 0.7809 (mm-30) REVERT: C 113 ILE cc_start: 0.8600 (pt) cc_final: 0.8317 (pt) REVERT: C 140 GLN cc_start: 0.7923 (tm-30) cc_final: 0.7633 (tm-30) REVERT: C 166 MET cc_start: 0.7183 (tpt) cc_final: 0.6930 (tpt) REVERT: C 167 ASN cc_start: 0.8114 (p0) cc_final: 0.7860 (p0) REVERT: C 178 ILE cc_start: 0.8354 (tp) cc_final: 0.7902 (mm) REVERT: C 184 LYS cc_start: 0.8569 (mtmm) cc_final: 0.8337 (mtmm) REVERT: C 203 LYS cc_start: 0.8107 (mtmm) cc_final: 0.7840 (mtmm) REVERT: C 237 ILE cc_start: 0.8592 (mm) cc_final: 0.7990 (mm) REVERT: C 241 MET cc_start: 0.8158 (mmm) cc_final: 0.7613 (mmm) REVERT: C 263 MET cc_start: 0.7328 (mmm) cc_final: 0.7049 (mmm) REVERT: C 280 TYR cc_start: 0.8382 (m-80) cc_final: 0.8056 (m-80) REVERT: C 292 SER cc_start: 0.8742 (m) cc_final: 0.8353 (t) REVERT: C 293 LEU cc_start: 0.8812 (tp) cc_final: 0.8426 (tp) REVERT: C 295 ASN cc_start: 0.7990 (t0) cc_final: 0.7633 (t0) REVERT: C 315 ILE cc_start: 0.8364 (pt) cc_final: 0.8150 (pt) REVERT: C 318 SER cc_start: 0.7957 (p) cc_final: 0.7744 (p) REVERT: C 322 ARG cc_start: 0.6769 (ptt-90) cc_final: 0.6550 (ptt-90) REVERT: C 331 THR cc_start: 0.8277 (m) cc_final: 0.8022 (t) REVERT: C 335 ILE cc_start: 0.8581 (mt) cc_final: 0.8327 (tp) REVERT: C 342 LEU cc_start: 0.8760 (tp) cc_final: 0.8483 (tp) REVERT: C 345 GLU cc_start: 0.7658 (tt0) cc_final: 0.7386 (tt0) REVERT: D 40 ILE cc_start: 0.9297 (mt) cc_final: 0.9038 (mm) REVERT: D 41 LYS cc_start: 0.8544 (ttpp) cc_final: 0.8098 (ttmm) REVERT: D 47 TYR cc_start: 0.9000 (m-80) cc_final: 0.8709 (m-80) REVERT: D 62 ASN cc_start: 0.8221 (t0) cc_final: 0.8020 (t0) REVERT: D 67 GLU cc_start: 0.7778 (tm-30) cc_final: 0.7476 (tm-30) REVERT: D 89 TRP cc_start: 0.7739 (t60) cc_final: 0.7523 (t60) REVERT: D 93 GLU cc_start: 0.7679 (mm-30) cc_final: 0.6997 (mm-30) REVERT: D 96 LYS cc_start: 0.8365 (ttpp) cc_final: 0.7978 (ttpp) REVERT: D 109 LYS cc_start: 0.8538 (tttp) cc_final: 0.8168 (ttmm) REVERT: D 118 GLU cc_start: 0.7323 (tp30) cc_final: 0.7017 (tp30) REVERT: D 127 LYS cc_start: 0.7872 (ptpp) cc_final: 0.7537 (ptpp) REVERT: D 128 MET cc_start: 0.8625 (tpp) cc_final: 0.8364 (tpp) REVERT: D 147 ASP cc_start: 0.7534 (p0) cc_final: 0.7113 (p0) REVERT: D 153 ASP cc_start: 0.7752 (t0) cc_final: 0.7525 (t0) REVERT: D 154 TRP cc_start: 0.8563 (t60) cc_final: 0.8345 (t60) REVERT: D 155 MET cc_start: 0.7692 (tpt) cc_final: 0.7121 (tpt) REVERT: D 181 LYS cc_start: 0.9225 (tmmt) cc_final: 0.8873 (ttpp) REVERT: D 189 THR cc_start: 0.8593 (p) cc_final: 0.6765 (p) REVERT: D 226 MET cc_start: 0.7653 (mmm) cc_final: 0.7026 (mmm) REVERT: D 263 MET cc_start: 0.7977 (mmm) cc_final: 0.7685 (mmm) REVERT: D 276 ILE cc_start: 0.9024 (mt) cc_final: 0.8592 (mt) REVERT: D 280 TYR cc_start: 0.8367 (m-80) cc_final: 0.8031 (m-80) REVERT: D 293 LEU cc_start: 0.8398 (tp) cc_final: 0.8174 (tp) REVERT: D 296 GLU cc_start: 0.7122 (pt0) cc_final: 0.6824 (pt0) REVERT: D 303 PHE cc_start: 0.8262 (t80) cc_final: 0.7955 (t80) REVERT: D 324 TYR cc_start: 0.7324 (m-80) cc_final: 0.7054 (m-80) REVERT: D 326 GLU cc_start: 0.7696 (mm-30) cc_final: 0.7362 (mm-30) REVERT: D 338 GLU cc_start: 0.7217 (mt-10) cc_final: 0.6958 (mt-10) REVERT: D 347 GLU cc_start: 0.7200 (tp30) cc_final: 0.6589 (tp30) REVERT: D 392 GLU cc_start: 0.7325 (tp30) cc_final: 0.6862 (tp30) REVERT: E 34 LYS cc_start: 0.8293 (tttp) cc_final: 0.8050 (tttp) REVERT: E 35 ASN cc_start: 0.8004 (m-40) cc_final: 0.7444 (m-40) REVERT: E 39 LEU cc_start: 0.8508 (mt) cc_final: 0.8221 (mt) REVERT: E 95 GLU cc_start: 0.8158 (tt0) cc_final: 0.7665 (tt0) REVERT: E 96 LYS cc_start: 0.8466 (tttp) cc_final: 0.8232 (tttp) REVERT: E 103 MET cc_start: 0.8019 (mmp) cc_final: 0.7622 (mmt) REVERT: E 146 PHE cc_start: 0.7548 (m-10) cc_final: 0.7075 (m-10) REVERT: E 155 MET cc_start: 0.7881 (tpp) cc_final: 0.7148 (tpp) REVERT: E 241 MET cc_start: 0.7771 (mmm) cc_final: 0.7506 (mmm) REVERT: E 242 LEU cc_start: 0.9113 (mp) cc_final: 0.8712 (mp) REVERT: E 245 SER cc_start: 0.8814 (t) cc_final: 0.8605 (p) REVERT: E 247 ASP cc_start: 0.7895 (p0) cc_final: 0.7278 (p0) REVERT: E 259 TYR cc_start: 0.9069 (t80) cc_final: 0.8580 (t80) REVERT: E 263 MET cc_start: 0.8394 (mmm) cc_final: 0.7831 (tpp) REVERT: E 265 LYS cc_start: 0.8870 (mtmt) cc_final: 0.8647 (mtmt) REVERT: E 271 THR cc_start: 0.9162 (p) cc_final: 0.8819 (t) REVERT: E 293 LEU cc_start: 0.8857 (tp) cc_final: 0.8642 (tp) REVERT: E 296 GLU cc_start: 0.7421 (mt-10) cc_final: 0.7134 (mt-10) REVERT: E 301 LYS cc_start: 0.7832 (ptpp) cc_final: 0.7354 (ptpp) REVERT: E 333 LYS cc_start: 0.8176 (tttp) cc_final: 0.7717 (tttp) REVERT: F 5 ILE cc_start: 0.9123 (mt) cc_final: 0.8906 (mt) REVERT: F 15 TYR cc_start: 0.8237 (t80) cc_final: 0.7317 (t80) REVERT: F 18 LYS cc_start: 0.8044 (tppp) cc_final: 0.7702 (tppp) REVERT: F 22 TYR cc_start: 0.8205 (m-80) cc_final: 0.7985 (m-10) REVERT: F 34 LYS cc_start: 0.9049 (ttmt) cc_final: 0.8360 (ttmm) REVERT: F 38 LYS cc_start: 0.8768 (mmtp) cc_final: 0.8442 (mmtp) REVERT: F 41 LYS cc_start: 0.8850 (tttp) cc_final: 0.8336 (tppp) REVERT: F 43 HIS cc_start: 0.8774 (t-90) cc_final: 0.8274 (t-90) REVERT: F 60 LEU cc_start: 0.8762 (tp) cc_final: 0.8507 (tp) REVERT: F 61 GLU cc_start: 0.7346 (mm-30) cc_final: 0.6899 (mm-30) REVERT: F 62 ASN cc_start: 0.7880 (t0) cc_final: 0.7592 (t0) REVERT: F 82 ASP cc_start: 0.7302 (t0) cc_final: 0.7050 (t0) REVERT: F 90 LEU cc_start: 0.8009 (mm) cc_final: 0.7548 (mm) REVERT: F 96 LYS cc_start: 0.8588 (ttpp) cc_final: 0.8218 (ttpp) REVERT: F 115 THR cc_start: 0.8771 (m) cc_final: 0.8232 (p) REVERT: F 119 LEU cc_start: 0.8494 (mt) cc_final: 0.8150 (mt) REVERT: F 183 THR cc_start: 0.8142 (p) cc_final: 0.7760 (t) REVERT: F 280 TYR cc_start: 0.8329 (m-80) cc_final: 0.8073 (m-80) REVERT: F 296 GLU cc_start: 0.7487 (pt0) cc_final: 0.7246 (pt0) REVERT: F 301 LYS cc_start: 0.7902 (mmmm) cc_final: 0.7640 (mmmm) REVERT: F 329 TYR cc_start: 0.8059 (t80) cc_final: 0.7816 (t80) REVERT: G 4 ILE cc_start: 0.9039 (mm) cc_final: 0.8763 (mm) REVERT: G 8 ASP cc_start: 0.8824 (m-30) cc_final: 0.8397 (m-30) REVERT: G 19 LEU cc_start: 0.8723 (mt) cc_final: 0.8473 (tt) REVERT: G 74 ILE cc_start: 0.9012 (tp) cc_final: 0.8772 (tp) REVERT: G 77 TYR cc_start: 0.9080 (t80) cc_final: 0.8537 (t80) REVERT: G 80 GLU cc_start: 0.8751 (mm-30) cc_final: 0.8450 (mm-30) REVERT: G 81 PHE cc_start: 0.8711 (m-80) cc_final: 0.8470 (m-80) REVERT: G 82 GLU cc_start: 0.9176 (mm-30) cc_final: 0.8588 (tp30) REVERT: G 85 LEU cc_start: 0.9376 (mm) cc_final: 0.8983 (mm) REVERT: G 89 TYR cc_start: 0.8551 (t80) cc_final: 0.8007 (t80) REVERT: G 91 PHE cc_start: 0.9153 (t80) cc_final: 0.8721 (t80) REVERT: G 92 GLU cc_start: 0.8635 (tp30) cc_final: 0.8404 (tp30) REVERT: G 95 LYS cc_start: 0.8865 (mtmm) cc_final: 0.8148 (mtpp) REVERT: G 96 GLU cc_start: 0.8637 (mm-30) cc_final: 0.8157 (mm-30) REVERT: G 97 LYS cc_start: 0.8759 (tppp) cc_final: 0.8321 (mtmt) REVERT: G 100 SER cc_start: 0.8164 (p) cc_final: 0.7209 (p) REVERT: G 137 ILE cc_start: 0.9207 (mm) cc_final: 0.8964 (mm) REVERT: G 147 LYS cc_start: 0.9251 (mmtm) cc_final: 0.8699 (mmmt) REVERT: G 158 GLU cc_start: 0.9287 (mt-10) cc_final: 0.9067 (mp0) REVERT: G 186 ASN cc_start: 0.9191 (p0) cc_final: 0.8971 (p0) REVERT: G 190 LYS cc_start: 0.9293 (mmmt) cc_final: 0.8928 (tptp) REVERT: G 194 PHE cc_start: 0.7808 (p90) cc_final: 0.7480 (p90) REVERT: G 210 ILE cc_start: 0.8852 (mm) cc_final: 0.8628 (mp) REVERT: G 224 ARG cc_start: 0.9071 (ptp-110) cc_final: 0.8626 (ptp-170) REVERT: G 238 ASP cc_start: 0.9282 (m-30) cc_final: 0.8722 (m-30) REVERT: G 240 LEU cc_start: 0.9348 (mt) cc_final: 0.9085 (mt) REVERT: G 242 ILE cc_start: 0.9232 (mp) cc_final: 0.8894 (tp) REVERT: G 260 PHE cc_start: 0.8559 (m-80) cc_final: 0.8316 (m-10) REVERT: G 266 TRP cc_start: 0.8632 (m100) cc_final: 0.7743 (m100) REVERT: G 277 THR cc_start: 0.9491 (m) cc_final: 0.8804 (t) REVERT: G 279 LYS cc_start: 0.9308 (mtmm) cc_final: 0.9079 (mttm) REVERT: G 281 MET cc_start: 0.8974 (mmt) cc_final: 0.8762 (mmt) REVERT: G 283 LYS cc_start: 0.9296 (pttm) cc_final: 0.9079 (pttm) REVERT: G 295 ASP cc_start: 0.8669 (p0) cc_final: 0.8150 (p0) REVERT: G 296 LYS cc_start: 0.8874 (mmmt) cc_final: 0.8494 (mmmt) REVERT: G 306 ASP cc_start: 0.8990 (t70) cc_final: 0.8688 (t0) REVERT: G 307 MET cc_start: 0.9178 (mmt) cc_final: 0.8731 (mmm) REVERT: G 314 THR cc_start: 0.9211 (p) cc_final: 0.8944 (t) REVERT: G 322 MET cc_start: 0.9138 (mtm) cc_final: 0.8781 (mtp) REVERT: G 328 GLN cc_start: 0.7862 (tp40) cc_final: 0.7572 (tp40) REVERT: G 333 LYS cc_start: 0.9184 (mmtt) cc_final: 0.8733 (tppt) outliers start: 0 outliers final: 0 residues processed: 1164 average time/residue: 0.3975 time to fit residues: 685.5791 Evaluate side-chains 1080 residues out of total 2539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1080 time to evaluate : 2.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 235 optimal weight: 7.9990 chunk 160 optimal weight: 0.9990 chunk 4 optimal weight: 9.9990 chunk 210 optimal weight: 7.9990 chunk 116 optimal weight: 3.9990 chunk 240 optimal weight: 2.9990 chunk 195 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 144 optimal weight: 6.9990 chunk 253 optimal weight: 0.9990 chunk 71 optimal weight: 7.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 116 ASN A 193 ASN A 219 HIS A 240 ASN A 295 ASN ** A 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 35 ASN B 99 GLN B 105 ASN ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 426 GLN D 100 GLN D 219 HIS D 403 GLN ** F 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.3271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 24510 Z= 0.237 Angle : 0.571 8.138 33263 Z= 0.300 Chirality : 0.043 0.238 3697 Planarity : 0.004 0.055 4105 Dihedral : 10.935 157.218 3510 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 16.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.16), residues: 2917 helix: 1.36 (0.14), residues: 1412 sheet: -1.15 (0.26), residues: 397 loop : -1.21 (0.18), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP G 294 HIS 0.006 0.001 HIS D 219 PHE 0.018 0.002 PHE A 383 TYR 0.038 0.002 TYR G 54 ARG 0.010 0.001 ARG F 236 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1145 residues out of total 2539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1145 time to evaluate : 2.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 PHE cc_start: 0.7951 (m-10) cc_final: 0.7586 (m-10) REVERT: A 19 VAL cc_start: 0.8402 (m) cc_final: 0.8031 (p) REVERT: A 26 GLU cc_start: 0.7425 (pm20) cc_final: 0.6973 (pm20) REVERT: A 66 THR cc_start: 0.8736 (p) cc_final: 0.8335 (p) REVERT: A 73 VAL cc_start: 0.8451 (t) cc_final: 0.7793 (p) REVERT: A 104 PHE cc_start: 0.8404 (t80) cc_final: 0.7703 (t80) REVERT: A 123 LYS cc_start: 0.8085 (mmmm) cc_final: 0.7800 (mmmm) REVERT: A 163 LEU cc_start: 0.8953 (tp) cc_final: 0.8753 (tt) REVERT: A 170 ARG cc_start: 0.8338 (mtp85) cc_final: 0.8074 (mtp85) REVERT: A 171 LYS cc_start: 0.8112 (mmtp) cc_final: 0.7796 (mmtp) REVERT: A 188 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7611 (mt-10) REVERT: A 196 MET cc_start: 0.7438 (mmt) cc_final: 0.7053 (mmt) REVERT: A 203 LYS cc_start: 0.7405 (pttm) cc_final: 0.7012 (pttm) REVERT: A 213 ASP cc_start: 0.7778 (m-30) cc_final: 0.7333 (m-30) REVERT: A 214 TYR cc_start: 0.8812 (m-80) cc_final: 0.8357 (m-10) REVERT: A 224 ILE cc_start: 0.8243 (mt) cc_final: 0.7941 (mt) REVERT: A 235 LYS cc_start: 0.8250 (ttpt) cc_final: 0.7847 (ttpt) REVERT: A 241 MET cc_start: 0.8204 (mmm) cc_final: 0.7684 (mmm) REVERT: A 248 ASP cc_start: 0.7654 (m-30) cc_final: 0.7205 (m-30) REVERT: A 265 LYS cc_start: 0.8408 (ttpp) cc_final: 0.8014 (ttpp) REVERT: A 278 LYS cc_start: 0.8939 (tptm) cc_final: 0.8320 (tptm) REVERT: A 313 LEU cc_start: 0.7009 (tt) cc_final: 0.6727 (tt) REVERT: A 316 CYS cc_start: 0.8054 (m) cc_final: 0.7816 (m) REVERT: A 342 LEU cc_start: 0.8261 (tp) cc_final: 0.7693 (tp) REVERT: A 423 LYS cc_start: 0.8440 (mmmm) cc_final: 0.8212 (mmmm) REVERT: A 426 GLN cc_start: 0.7672 (mt0) cc_final: 0.7405 (mt0) REVERT: B 8 HIS cc_start: 0.8013 (m90) cc_final: 0.7024 (m90) REVERT: B 26 GLU cc_start: 0.6865 (mp0) cc_final: 0.6105 (mp0) REVERT: B 47 TYR cc_start: 0.8674 (m-80) cc_final: 0.8167 (m-80) REVERT: B 67 GLU cc_start: 0.7346 (tp30) cc_final: 0.7082 (tp30) REVERT: B 79 LYS cc_start: 0.8669 (ttmm) cc_final: 0.8294 (ttmm) REVERT: B 114 GLN cc_start: 0.8842 (mt0) cc_final: 0.8578 (mt0) REVERT: B 115 THR cc_start: 0.9421 (p) cc_final: 0.8630 (p) REVERT: B 145 SER cc_start: 0.8639 (p) cc_final: 0.7814 (p) REVERT: B 147 ASP cc_start: 0.7372 (m-30) cc_final: 0.7075 (m-30) REVERT: B 155 MET cc_start: 0.8043 (tpp) cc_final: 0.7434 (tpp) REVERT: B 171 LYS cc_start: 0.8196 (mmmm) cc_final: 0.7908 (mmmm) REVERT: B 184 LYS cc_start: 0.8446 (mmtm) cc_final: 0.8139 (mmmt) REVERT: B 243 ASP cc_start: 0.7215 (t0) cc_final: 0.6783 (t0) REVERT: B 245 SER cc_start: 0.8875 (t) cc_final: 0.8536 (p) REVERT: B 262 LYS cc_start: 0.8860 (mtmm) cc_final: 0.8495 (mtpp) REVERT: B 263 MET cc_start: 0.7990 (mmm) cc_final: 0.7216 (mmm) REVERT: B 265 LYS cc_start: 0.8620 (ttpp) cc_final: 0.8392 (ttpp) REVERT: B 288 ASN cc_start: 0.8477 (m-40) cc_final: 0.8086 (m-40) REVERT: B 318 SER cc_start: 0.8102 (m) cc_final: 0.7475 (t) REVERT: B 352 THR cc_start: 0.8372 (t) cc_final: 0.8115 (m) REVERT: B 392 GLU cc_start: 0.7328 (tm-30) cc_final: 0.7029 (tm-30) REVERT: B 403 GLN cc_start: 0.7250 (tt0) cc_final: 0.6885 (pt0) REVERT: B 413 LYS cc_start: 0.8257 (tppt) cc_final: 0.7484 (tppt) REVERT: B 414 TRP cc_start: 0.7133 (m-90) cc_final: 0.6681 (m-90) REVERT: C 3 GLU cc_start: 0.8255 (mm-30) cc_final: 0.8050 (mm-30) REVERT: C 13 GLN cc_start: 0.8119 (tp40) cc_final: 0.7881 (tp40) REVERT: C 39 LEU cc_start: 0.8521 (mt) cc_final: 0.8226 (mt) REVERT: C 77 ILE cc_start: 0.8777 (tp) cc_final: 0.8565 (tp) REVERT: C 85 GLU cc_start: 0.8127 (mm-30) cc_final: 0.7833 (mm-30) REVERT: C 113 ILE cc_start: 0.8644 (pt) cc_final: 0.8316 (pt) REVERT: C 140 GLN cc_start: 0.7901 (tm-30) cc_final: 0.7589 (tm-30) REVERT: C 166 MET cc_start: 0.7260 (tpt) cc_final: 0.6630 (tpt) REVERT: C 167 ASN cc_start: 0.8178 (p0) cc_final: 0.7679 (p0) REVERT: C 178 ILE cc_start: 0.8162 (tp) cc_final: 0.7647 (mm) REVERT: C 184 LYS cc_start: 0.8605 (mtmm) cc_final: 0.8328 (mtmm) REVERT: C 203 LYS cc_start: 0.8207 (mtmm) cc_final: 0.7835 (mtmm) REVERT: C 241 MET cc_start: 0.8213 (mmm) cc_final: 0.7783 (mmm) REVERT: C 263 MET cc_start: 0.7298 (mmm) cc_final: 0.6954 (mmm) REVERT: C 276 ILE cc_start: 0.9143 (mm) cc_final: 0.8929 (mm) REVERT: C 292 SER cc_start: 0.8791 (m) cc_final: 0.8342 (t) REVERT: C 295 ASN cc_start: 0.8007 (t0) cc_final: 0.7718 (t0) REVERT: C 315 ILE cc_start: 0.8469 (pt) cc_final: 0.8094 (pt) REVERT: C 318 SER cc_start: 0.7937 (p) cc_final: 0.7558 (p) REVERT: C 331 THR cc_start: 0.8300 (m) cc_final: 0.8068 (t) REVERT: C 335 ILE cc_start: 0.8594 (mt) cc_final: 0.8291 (tp) REVERT: C 345 GLU cc_start: 0.7755 (tt0) cc_final: 0.7391 (tt0) REVERT: D 15 TYR cc_start: 0.7957 (t80) cc_final: 0.7316 (t80) REVERT: D 38 LYS cc_start: 0.8867 (mttm) cc_final: 0.8649 (mttm) REVERT: D 40 ILE cc_start: 0.9328 (mt) cc_final: 0.9071 (mm) REVERT: D 41 LYS cc_start: 0.8578 (ttpp) cc_final: 0.8082 (ttmm) REVERT: D 47 TYR cc_start: 0.8921 (m-80) cc_final: 0.8643 (m-80) REVERT: D 62 ASN cc_start: 0.8296 (t0) cc_final: 0.8089 (t0) REVERT: D 67 GLU cc_start: 0.7789 (tm-30) cc_final: 0.7476 (tm-30) REVERT: D 96 LYS cc_start: 0.8412 (ttpp) cc_final: 0.8059 (ttpp) REVERT: D 118 GLU cc_start: 0.7235 (tp30) cc_final: 0.7025 (tp30) REVERT: D 127 LYS cc_start: 0.7917 (ptpp) cc_final: 0.7716 (ptpp) REVERT: D 147 ASP cc_start: 0.7610 (p0) cc_final: 0.7143 (p0) REVERT: D 153 ASP cc_start: 0.7712 (t0) cc_final: 0.7431 (t0) REVERT: D 154 TRP cc_start: 0.8581 (t60) cc_final: 0.8358 (t60) REVERT: D 155 MET cc_start: 0.7713 (tpt) cc_final: 0.7227 (tpt) REVERT: D 189 THR cc_start: 0.8628 (p) cc_final: 0.6684 (p) REVERT: D 223 TYR cc_start: 0.8674 (t80) cc_final: 0.8120 (t80) REVERT: D 226 MET cc_start: 0.7707 (mmm) cc_final: 0.7045 (mmm) REVERT: D 276 ILE cc_start: 0.9097 (mt) cc_final: 0.8724 (mt) REVERT: D 278 LYS cc_start: 0.8750 (tptp) cc_final: 0.8245 (tptp) REVERT: D 280 TYR cc_start: 0.8425 (m-80) cc_final: 0.7978 (m-80) REVERT: D 293 LEU cc_start: 0.8446 (tp) cc_final: 0.8212 (tp) REVERT: D 296 GLU cc_start: 0.7220 (pt0) cc_final: 0.6519 (pt0) REVERT: D 324 TYR cc_start: 0.7415 (m-80) cc_final: 0.7156 (m-80) REVERT: D 326 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7350 (mm-30) REVERT: D 333 LYS cc_start: 0.8329 (ttmt) cc_final: 0.8013 (ttmt) REVERT: D 338 GLU cc_start: 0.7272 (mt-10) cc_final: 0.6966 (mt-10) REVERT: D 347 GLU cc_start: 0.7312 (tp30) cc_final: 0.6651 (tp30) REVERT: D 426 GLN cc_start: 0.7981 (tp-100) cc_final: 0.7497 (tp-100) REVERT: E 23 MET cc_start: 0.8381 (mmt) cc_final: 0.8091 (mmt) REVERT: E 34 LYS cc_start: 0.8392 (tttp) cc_final: 0.8110 (tttp) REVERT: E 35 ASN cc_start: 0.8122 (m-40) cc_final: 0.7768 (m-40) REVERT: E 39 LEU cc_start: 0.8555 (mt) cc_final: 0.8235 (mt) REVERT: E 41 LYS cc_start: 0.8370 (ttpt) cc_final: 0.8163 (ttpt) REVERT: E 93 GLU cc_start: 0.8026 (tp30) cc_final: 0.7667 (tp30) REVERT: E 103 MET cc_start: 0.7975 (mmp) cc_final: 0.7648 (mmp) REVERT: E 139 ARG cc_start: 0.7533 (ttp80) cc_final: 0.7185 (ttp80) REVERT: E 177 ARG cc_start: 0.7505 (mtt90) cc_final: 0.7289 (mtt90) REVERT: E 178 ILE cc_start: 0.8475 (tp) cc_final: 0.7757 (mm) REVERT: E 241 MET cc_start: 0.7786 (mmm) cc_final: 0.7454 (mmm) REVERT: E 242 LEU cc_start: 0.9128 (mp) cc_final: 0.8829 (mp) REVERT: E 247 ASP cc_start: 0.7845 (p0) cc_final: 0.7576 (p0) REVERT: E 248 ASP cc_start: 0.8035 (m-30) cc_final: 0.7429 (m-30) REVERT: E 263 MET cc_start: 0.8393 (mmm) cc_final: 0.7883 (tpp) REVERT: E 265 LYS cc_start: 0.8885 (mtmt) cc_final: 0.8585 (mtmt) REVERT: E 271 THR cc_start: 0.9159 (p) cc_final: 0.8724 (t) REVERT: E 301 LYS cc_start: 0.7865 (ptpp) cc_final: 0.7461 (ptpp) REVERT: E 326 GLU cc_start: 0.7612 (pt0) cc_final: 0.7402 (pt0) REVERT: E 333 LYS cc_start: 0.8103 (tttp) cc_final: 0.7774 (tttp) REVERT: F 22 TYR cc_start: 0.8317 (m-80) cc_final: 0.7942 (m-10) REVERT: F 34 LYS cc_start: 0.9029 (ttmt) cc_final: 0.8356 (ttmm) REVERT: F 41 LYS cc_start: 0.8871 (tttp) cc_final: 0.8338 (tppp) REVERT: F 43 HIS cc_start: 0.8805 (t-90) cc_final: 0.8321 (t-90) REVERT: F 60 LEU cc_start: 0.8816 (tp) cc_final: 0.8539 (tp) REVERT: F 61 GLU cc_start: 0.7449 (mm-30) cc_final: 0.6987 (mm-30) REVERT: F 62 ASN cc_start: 0.7882 (t0) cc_final: 0.7581 (t0) REVERT: F 82 ASP cc_start: 0.7355 (t0) cc_final: 0.7090 (t0) REVERT: F 96 LYS cc_start: 0.8629 (ttpp) cc_final: 0.8205 (ttpp) REVERT: F 115 THR cc_start: 0.8778 (m) cc_final: 0.8203 (p) REVERT: F 119 LEU cc_start: 0.8488 (mt) cc_final: 0.8174 (mt) REVERT: F 123 LYS cc_start: 0.8456 (tppt) cc_final: 0.8165 (tppt) REVERT: F 155 MET cc_start: 0.6381 (tpp) cc_final: 0.6010 (tpp) REVERT: F 183 THR cc_start: 0.8307 (p) cc_final: 0.7854 (t) REVERT: F 296 GLU cc_start: 0.7526 (pt0) cc_final: 0.7301 (pt0) REVERT: F 340 ARG cc_start: 0.8823 (ttt-90) cc_final: 0.8510 (tpt-90) REVERT: G 8 ASP cc_start: 0.8931 (m-30) cc_final: 0.8436 (m-30) REVERT: G 19 LEU cc_start: 0.8783 (mt) cc_final: 0.8501 (tt) REVERT: G 54 TYR cc_start: 0.8589 (t80) cc_final: 0.8274 (t80) REVERT: G 77 TYR cc_start: 0.9101 (t80) cc_final: 0.8659 (t80) REVERT: G 80 GLU cc_start: 0.8789 (mm-30) cc_final: 0.8434 (mm-30) REVERT: G 81 PHE cc_start: 0.8727 (m-80) cc_final: 0.8444 (m-80) REVERT: G 82 GLU cc_start: 0.9206 (mm-30) cc_final: 0.8729 (mm-30) REVERT: G 85 LEU cc_start: 0.9388 (mm) cc_final: 0.9059 (mm) REVERT: G 89 TYR cc_start: 0.8609 (t80) cc_final: 0.7846 (t80) REVERT: G 91 PHE cc_start: 0.9141 (t80) cc_final: 0.8784 (t80) REVERT: G 92 GLU cc_start: 0.8682 (tp30) cc_final: 0.8362 (tp30) REVERT: G 93 ILE cc_start: 0.9383 (tt) cc_final: 0.9133 (pt) REVERT: G 95 LYS cc_start: 0.8827 (mtmm) cc_final: 0.8195 (mtpp) REVERT: G 96 GLU cc_start: 0.8675 (mm-30) cc_final: 0.8115 (mm-30) REVERT: G 100 SER cc_start: 0.8094 (p) cc_final: 0.7170 (p) REVERT: G 147 LYS cc_start: 0.9188 (mmtm) cc_final: 0.8677 (mmmt) REVERT: G 152 TYR cc_start: 0.8471 (m-80) cc_final: 0.8261 (m-80) REVERT: G 158 GLU cc_start: 0.9356 (mt-10) cc_final: 0.9010 (mp0) REVERT: G 177 GLU cc_start: 0.9183 (mt-10) cc_final: 0.8770 (tm-30) REVERT: G 186 ASN cc_start: 0.9159 (p0) cc_final: 0.8952 (p0) REVERT: G 190 LYS cc_start: 0.9311 (mmmt) cc_final: 0.8961 (tptp) REVERT: G 224 ARG cc_start: 0.9014 (ptp-110) cc_final: 0.8544 (ptp-170) REVERT: G 231 TYR cc_start: 0.8818 (m-80) cc_final: 0.8491 (m-80) REVERT: G 238 ASP cc_start: 0.9191 (m-30) cc_final: 0.8597 (m-30) REVERT: G 240 LEU cc_start: 0.9342 (mt) cc_final: 0.9095 (mt) REVERT: G 260 PHE cc_start: 0.8610 (m-80) cc_final: 0.8409 (m-10) REVERT: G 266 TRP cc_start: 0.8708 (m100) cc_final: 0.7875 (m100) REVERT: G 277 THR cc_start: 0.9498 (m) cc_final: 0.8773 (t) REVERT: G 279 LYS cc_start: 0.9297 (mtmm) cc_final: 0.9061 (mttm) REVERT: G 283 LYS cc_start: 0.9357 (pttm) cc_final: 0.9038 (pttm) REVERT: G 306 ASP cc_start: 0.8989 (t70) cc_final: 0.8708 (t0) REVERT: G 307 MET cc_start: 0.9186 (mmt) cc_final: 0.8745 (mmm) REVERT: G 314 THR cc_start: 0.9229 (p) cc_final: 0.8958 (t) REVERT: G 322 MET cc_start: 0.9108 (mtm) cc_final: 0.8840 (mtp) REVERT: G 323 LYS cc_start: 0.9391 (pttm) cc_final: 0.9166 (pttm) REVERT: G 328 GLN cc_start: 0.7961 (tp40) cc_final: 0.7657 (tp40) REVERT: G 330 LEU cc_start: 0.8944 (mt) cc_final: 0.8499 (mt) REVERT: G 331 MET cc_start: 0.8155 (mmp) cc_final: 0.7855 (mmm) REVERT: G 333 LYS cc_start: 0.9178 (mmtt) cc_final: 0.8659 (mmtt) outliers start: 0 outliers final: 0 residues processed: 1145 average time/residue: 0.3954 time to fit residues: 669.5197 Evaluate side-chains 1076 residues out of total 2539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1076 time to evaluate : 2.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 94 optimal weight: 0.9980 chunk 254 optimal weight: 7.9990 chunk 55 optimal weight: 5.9990 chunk 165 optimal weight: 4.9990 chunk 69 optimal weight: 0.7980 chunk 282 optimal weight: 40.0000 chunk 234 optimal weight: 8.9990 chunk 130 optimal weight: 3.9990 chunk 23 optimal weight: 9.9990 chunk 93 optimal weight: 0.9980 chunk 148 optimal weight: 5.9990 overall best weight: 2.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN A 116 ASN A 219 HIS A 240 ASN ** A 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 GLN ** C 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 GLN D 114 GLN D 219 HIS D 422 GLN ** F 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 274 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 24510 Z= 0.259 Angle : 0.605 11.194 33263 Z= 0.314 Chirality : 0.043 0.277 3697 Planarity : 0.004 0.062 4105 Dihedral : 10.902 156.556 3510 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 17.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.16), residues: 2917 helix: 1.27 (0.14), residues: 1414 sheet: -1.18 (0.26), residues: 392 loop : -1.17 (0.18), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP F 89 HIS 0.014 0.001 HIS G 274 PHE 0.019 0.002 PHE A 383 TYR 0.031 0.002 TYR B 165 ARG 0.020 0.001 ARG G 309 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1131 residues out of total 2539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1131 time to evaluate : 2.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 PHE cc_start: 0.7995 (m-80) cc_final: 0.7619 (m-10) REVERT: A 19 VAL cc_start: 0.8374 (m) cc_final: 0.7994 (p) REVERT: A 26 GLU cc_start: 0.7535 (pm20) cc_final: 0.6970 (pm20) REVERT: A 73 VAL cc_start: 0.8454 (t) cc_final: 0.7947 (p) REVERT: A 79 LYS cc_start: 0.8838 (ttpt) cc_final: 0.8532 (ttpt) REVERT: A 85 GLU cc_start: 0.7597 (mm-30) cc_final: 0.7382 (mm-30) REVERT: A 104 PHE cc_start: 0.8456 (t80) cc_final: 0.7796 (t80) REVERT: A 123 LYS cc_start: 0.8105 (mmmm) cc_final: 0.7857 (mmmm) REVERT: A 128 MET cc_start: 0.8172 (tpt) cc_final: 0.7913 (tpt) REVERT: A 148 SER cc_start: 0.7927 (t) cc_final: 0.7725 (t) REVERT: A 163 LEU cc_start: 0.8982 (tp) cc_final: 0.8699 (tt) REVERT: A 171 LYS cc_start: 0.8099 (mmtp) cc_final: 0.7820 (mmtp) REVERT: A 196 MET cc_start: 0.7493 (mmt) cc_final: 0.7079 (mmt) REVERT: A 203 LYS cc_start: 0.7591 (pttm) cc_final: 0.7112 (pttm) REVERT: A 213 ASP cc_start: 0.7790 (m-30) cc_final: 0.7325 (m-30) REVERT: A 214 TYR cc_start: 0.8830 (m-80) cc_final: 0.8381 (m-10) REVERT: A 235 LYS cc_start: 0.8242 (ttpt) cc_final: 0.7877 (ttpt) REVERT: A 241 MET cc_start: 0.8204 (mmm) cc_final: 0.7652 (mmm) REVERT: A 248 ASP cc_start: 0.7744 (m-30) cc_final: 0.7237 (m-30) REVERT: A 265 LYS cc_start: 0.8367 (ttpp) cc_final: 0.8060 (ttpp) REVERT: A 278 LYS cc_start: 0.8896 (tptm) cc_final: 0.8438 (tptm) REVERT: A 313 LEU cc_start: 0.7104 (tt) cc_final: 0.6888 (tt) REVERT: A 316 CYS cc_start: 0.8187 (m) cc_final: 0.7881 (m) REVERT: A 342 LEU cc_start: 0.8226 (tp) cc_final: 0.7814 (tp) REVERT: A 426 GLN cc_start: 0.7661 (mt0) cc_final: 0.7333 (mt0) REVERT: B 8 HIS cc_start: 0.8127 (m90) cc_final: 0.7127 (m90) REVERT: B 41 LYS cc_start: 0.8944 (ttmt) cc_final: 0.8646 (ttmt) REVERT: B 47 TYR cc_start: 0.8639 (m-80) cc_final: 0.8231 (m-80) REVERT: B 67 GLU cc_start: 0.7369 (tp30) cc_final: 0.7107 (tp30) REVERT: B 79 LYS cc_start: 0.8759 (ttmm) cc_final: 0.8362 (ttmm) REVERT: B 109 LYS cc_start: 0.8690 (tptp) cc_final: 0.8333 (tptp) REVERT: B 138 MET cc_start: 0.8002 (mmm) cc_final: 0.7614 (mmm) REVERT: B 145 SER cc_start: 0.8619 (p) cc_final: 0.7807 (p) REVERT: B 147 ASP cc_start: 0.7301 (m-30) cc_final: 0.6975 (m-30) REVERT: B 155 MET cc_start: 0.7862 (tpp) cc_final: 0.7638 (tpp) REVERT: B 166 MET cc_start: 0.7709 (ppp) cc_final: 0.7448 (ppp) REVERT: B 167 ASN cc_start: 0.8396 (m110) cc_final: 0.8185 (m-40) REVERT: B 184 LYS cc_start: 0.8453 (mmtm) cc_final: 0.8214 (mmmt) REVERT: B 194 VAL cc_start: 0.8749 (t) cc_final: 0.8336 (t) REVERT: B 243 ASP cc_start: 0.7200 (t0) cc_final: 0.6757 (t0) REVERT: B 245 SER cc_start: 0.8934 (t) cc_final: 0.8565 (p) REVERT: B 260 LYS cc_start: 0.8789 (tttp) cc_final: 0.8540 (tttp) REVERT: B 262 LYS cc_start: 0.8834 (mtmm) cc_final: 0.8504 (mtpp) REVERT: B 265 LYS cc_start: 0.8633 (ttpp) cc_final: 0.8309 (ttpp) REVERT: B 288 ASN cc_start: 0.8465 (m-40) cc_final: 0.8073 (m-40) REVERT: B 298 LYS cc_start: 0.8548 (ttmt) cc_final: 0.8110 (ttmt) REVERT: B 318 SER cc_start: 0.8051 (m) cc_final: 0.7496 (t) REVERT: B 352 THR cc_start: 0.8461 (t) cc_final: 0.8163 (m) REVERT: B 370 ASP cc_start: 0.6983 (m-30) cc_final: 0.6607 (m-30) REVERT: B 384 MET cc_start: 0.8544 (mmm) cc_final: 0.8333 (mmt) REVERT: B 392 GLU cc_start: 0.7412 (tm-30) cc_final: 0.7116 (tm-30) REVERT: B 403 GLN cc_start: 0.7333 (tt0) cc_final: 0.6936 (pt0) REVERT: B 413 LYS cc_start: 0.8308 (tppt) cc_final: 0.7707 (tppt) REVERT: B 414 TRP cc_start: 0.7187 (m-90) cc_final: 0.6723 (m-90) REVERT: B 419 MET cc_start: 0.4764 (tpp) cc_final: 0.4261 (ttm) REVERT: C 13 GLN cc_start: 0.8131 (tp40) cc_final: 0.7916 (tp40) REVERT: C 41 LYS cc_start: 0.8565 (mtpp) cc_final: 0.8017 (mtpp) REVERT: C 56 LEU cc_start: 0.8690 (mm) cc_final: 0.8052 (mm) REVERT: C 85 GLU cc_start: 0.8160 (mm-30) cc_final: 0.7837 (mm-30) REVERT: C 109 LYS cc_start: 0.9003 (tppt) cc_final: 0.8606 (mmmm) REVERT: C 140 GLN cc_start: 0.7942 (tm-30) cc_final: 0.7693 (tm-30) REVERT: C 166 MET cc_start: 0.7310 (tpt) cc_final: 0.6904 (tpt) REVERT: C 167 ASN cc_start: 0.8218 (p0) cc_final: 0.7972 (p0) REVERT: C 178 ILE cc_start: 0.8341 (tp) cc_final: 0.7870 (mm) REVERT: C 184 LYS cc_start: 0.8633 (mtmm) cc_final: 0.8342 (mtmm) REVERT: C 203 LYS cc_start: 0.8180 (mtmm) cc_final: 0.7800 (mtmm) REVERT: C 241 MET cc_start: 0.8273 (mmm) cc_final: 0.7847 (mmm) REVERT: C 263 MET cc_start: 0.7309 (mmm) cc_final: 0.6973 (mmm) REVERT: C 271 THR cc_start: 0.8762 (p) cc_final: 0.8551 (p) REVERT: C 292 SER cc_start: 0.8798 (m) cc_final: 0.8370 (t) REVERT: C 295 ASN cc_start: 0.8026 (t0) cc_final: 0.7646 (t0) REVERT: C 315 ILE cc_start: 0.8502 (pt) cc_final: 0.8261 (pt) REVERT: C 318 SER cc_start: 0.7963 (p) cc_final: 0.7550 (p) REVERT: C 322 ARG cc_start: 0.6882 (ptt90) cc_final: 0.6488 (ptt90) REVERT: C 331 THR cc_start: 0.8283 (m) cc_final: 0.8052 (t) REVERT: C 335 ILE cc_start: 0.8625 (mt) cc_final: 0.8303 (tp) REVERT: C 345 GLU cc_start: 0.7714 (tt0) cc_final: 0.7419 (tt0) REVERT: D 15 TYR cc_start: 0.7902 (t80) cc_final: 0.7227 (t80) REVERT: D 40 ILE cc_start: 0.9333 (mt) cc_final: 0.9068 (mm) REVERT: D 41 LYS cc_start: 0.8539 (ttpp) cc_final: 0.8095 (ttmm) REVERT: D 46 GLU cc_start: 0.8103 (tt0) cc_final: 0.7696 (tt0) REVERT: D 47 TYR cc_start: 0.8901 (m-80) cc_final: 0.8001 (m-80) REVERT: D 93 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7319 (mm-30) REVERT: D 96 LYS cc_start: 0.8516 (ttpp) cc_final: 0.7922 (ttpp) REVERT: D 108 SER cc_start: 0.8527 (m) cc_final: 0.8282 (t) REVERT: D 109 LYS cc_start: 0.8565 (ttmm) cc_final: 0.8236 (ttmm) REVERT: D 118 GLU cc_start: 0.7350 (tp30) cc_final: 0.6939 (tp30) REVERT: D 127 LYS cc_start: 0.7902 (ptpp) cc_final: 0.7637 (ptpp) REVERT: D 139 ARG cc_start: 0.7825 (ptp-110) cc_final: 0.7602 (ptp-110) REVERT: D 147 ASP cc_start: 0.7619 (p0) cc_final: 0.7203 (p0) REVERT: D 153 ASP cc_start: 0.7668 (t0) cc_final: 0.7431 (t0) REVERT: D 155 MET cc_start: 0.7701 (tpt) cc_final: 0.7273 (tpt) REVERT: D 205 LEU cc_start: 0.8489 (tp) cc_final: 0.8256 (tp) REVERT: D 223 TYR cc_start: 0.8711 (t80) cc_final: 0.8095 (t80) REVERT: D 226 MET cc_start: 0.7717 (mmm) cc_final: 0.7033 (mmm) REVERT: D 243 ASP cc_start: 0.7945 (m-30) cc_final: 0.7716 (m-30) REVERT: D 263 MET cc_start: 0.7990 (mmm) cc_final: 0.7755 (mmm) REVERT: D 280 TYR cc_start: 0.8484 (m-80) cc_final: 0.8141 (m-80) REVERT: D 293 LEU cc_start: 0.8454 (tp) cc_final: 0.8203 (tp) REVERT: D 296 GLU cc_start: 0.7263 (pt0) cc_final: 0.6366 (pt0) REVERT: D 324 TYR cc_start: 0.7494 (m-80) cc_final: 0.7230 (m-80) REVERT: D 326 GLU cc_start: 0.7753 (mm-30) cc_final: 0.7367 (mm-30) REVERT: D 329 TYR cc_start: 0.6424 (t80) cc_final: 0.5843 (t80) REVERT: D 333 LYS cc_start: 0.8362 (ttmt) cc_final: 0.8085 (ttmt) REVERT: D 426 GLN cc_start: 0.7870 (tp-100) cc_final: 0.7479 (tp-100) REVERT: E 23 MET cc_start: 0.8447 (mmt) cc_final: 0.8153 (mmt) REVERT: E 24 ASP cc_start: 0.7316 (t0) cc_final: 0.7053 (t0) REVERT: E 25 SER cc_start: 0.8900 (m) cc_final: 0.8618 (m) REVERT: E 34 LYS cc_start: 0.8401 (tttp) cc_final: 0.7947 (tttp) REVERT: E 35 ASN cc_start: 0.8187 (m-40) cc_final: 0.7730 (m-40) REVERT: E 39 LEU cc_start: 0.8553 (mt) cc_final: 0.8295 (mt) REVERT: E 47 TYR cc_start: 0.6393 (t80) cc_final: 0.6180 (t80) REVERT: E 73 VAL cc_start: 0.8619 (t) cc_final: 0.8250 (p) REVERT: E 104 PHE cc_start: 0.8765 (t80) cc_final: 0.8544 (t80) REVERT: E 177 ARG cc_start: 0.7617 (mtt90) cc_final: 0.7403 (mtt90) REVERT: E 241 MET cc_start: 0.7787 (mmm) cc_final: 0.7539 (mmm) REVERT: E 242 LEU cc_start: 0.9139 (mp) cc_final: 0.8830 (mm) REVERT: E 259 TYR cc_start: 0.9076 (t80) cc_final: 0.8470 (t80) REVERT: E 263 MET cc_start: 0.8399 (mmm) cc_final: 0.7835 (tpp) REVERT: E 271 THR cc_start: 0.9141 (p) cc_final: 0.8768 (t) REVERT: E 298 LYS cc_start: 0.8469 (ttmt) cc_final: 0.8235 (mtmt) REVERT: E 301 LYS cc_start: 0.7892 (ptpp) cc_final: 0.7510 (ptpp) REVERT: E 310 VAL cc_start: 0.6948 (t) cc_final: 0.6726 (t) REVERT: E 326 GLU cc_start: 0.7621 (pt0) cc_final: 0.7392 (pt0) REVERT: E 333 LYS cc_start: 0.8117 (tttp) cc_final: 0.7786 (tttp) REVERT: E 423 LYS cc_start: 0.8847 (mtpp) cc_final: 0.8618 (mtpp) REVERT: F 18 LYS cc_start: 0.8183 (tppp) cc_final: 0.7791 (tppp) REVERT: F 22 TYR cc_start: 0.8260 (m-80) cc_final: 0.7963 (m-10) REVERT: F 34 LYS cc_start: 0.9013 (ttmt) cc_final: 0.8694 (ttmm) REVERT: F 43 HIS cc_start: 0.8816 (t-90) cc_final: 0.8299 (t-90) REVERT: F 60 LEU cc_start: 0.8836 (tp) cc_final: 0.8561 (tp) REVERT: F 61 GLU cc_start: 0.7437 (mm-30) cc_final: 0.7077 (mm-30) REVERT: F 62 ASN cc_start: 0.7867 (t0) cc_final: 0.7486 (t0) REVERT: F 82 ASP cc_start: 0.7423 (t0) cc_final: 0.7163 (t0) REVERT: F 96 LYS cc_start: 0.8674 (ttpp) cc_final: 0.8407 (ttpp) REVERT: F 115 THR cc_start: 0.8801 (m) cc_final: 0.8308 (p) REVERT: F 119 LEU cc_start: 0.8526 (mt) cc_final: 0.8217 (mt) REVERT: F 123 LYS cc_start: 0.8470 (tppt) cc_final: 0.8180 (tppt) REVERT: F 155 MET cc_start: 0.6570 (tpp) cc_final: 0.6006 (tpp) REVERT: F 158 TYR cc_start: 0.7386 (p90) cc_final: 0.7108 (p90) REVERT: F 183 THR cc_start: 0.8211 (p) cc_final: 0.7870 (t) REVERT: F 231 GLU cc_start: 0.8070 (mp0) cc_final: 0.7858 (mp0) REVERT: F 258 GLU cc_start: 0.7564 (mt-10) cc_final: 0.7344 (mt-10) REVERT: F 340 ARG cc_start: 0.8802 (ttt-90) cc_final: 0.8554 (ttt90) REVERT: F 404 ILE cc_start: 0.8247 (mt) cc_final: 0.7828 (mt) REVERT: F 418 LEU cc_start: 0.7714 (mp) cc_final: 0.7310 (pp) REVERT: G 7 ILE cc_start: 0.9457 (pt) cc_final: 0.9064 (tp) REVERT: G 8 ASP cc_start: 0.8904 (m-30) cc_final: 0.8579 (m-30) REVERT: G 77 TYR cc_start: 0.9120 (t80) cc_final: 0.8624 (t80) REVERT: G 80 GLU cc_start: 0.8780 (mm-30) cc_final: 0.8505 (mm-30) REVERT: G 81 PHE cc_start: 0.8742 (m-80) cc_final: 0.8450 (m-80) REVERT: G 82 GLU cc_start: 0.9239 (mm-30) cc_final: 0.8817 (mm-30) REVERT: G 89 TYR cc_start: 0.8620 (t80) cc_final: 0.7984 (t80) REVERT: G 91 PHE cc_start: 0.9165 (t80) cc_final: 0.8824 (t80) REVERT: G 93 ILE cc_start: 0.9364 (tt) cc_final: 0.9155 (pt) REVERT: G 95 LYS cc_start: 0.8865 (mtmm) cc_final: 0.8103 (mtpp) REVERT: G 96 GLU cc_start: 0.8744 (mm-30) cc_final: 0.8365 (pp20) REVERT: G 97 LYS cc_start: 0.8906 (mttt) cc_final: 0.8673 (mttt) REVERT: G 100 SER cc_start: 0.8084 (p) cc_final: 0.7142 (p) REVERT: G 137 ILE cc_start: 0.9428 (mm) cc_final: 0.9211 (mm) REVERT: G 147 LYS cc_start: 0.9226 (mmtm) cc_final: 0.8704 (mmmt) REVERT: G 152 TYR cc_start: 0.8460 (m-80) cc_final: 0.8238 (m-80) REVERT: G 157 THR cc_start: 0.8888 (p) cc_final: 0.8325 (p) REVERT: G 158 GLU cc_start: 0.9293 (mt-10) cc_final: 0.8887 (mp0) REVERT: G 177 GLU cc_start: 0.9090 (mt-10) cc_final: 0.8763 (pt0) REVERT: G 194 PHE cc_start: 0.7931 (p90) cc_final: 0.7729 (p90) REVERT: G 224 ARG cc_start: 0.9043 (ptp-110) cc_final: 0.8579 (ptp-170) REVERT: G 231 TYR cc_start: 0.8813 (m-80) cc_final: 0.8513 (m-80) REVERT: G 238 ASP cc_start: 0.9195 (m-30) cc_final: 0.8604 (m-30) REVERT: G 240 LEU cc_start: 0.9393 (mt) cc_final: 0.9117 (mt) REVERT: G 241 PHE cc_start: 0.8154 (m-80) cc_final: 0.7797 (m-80) REVERT: G 242 ILE cc_start: 0.9204 (mp) cc_final: 0.8777 (tp) REVERT: G 243 GLU cc_start: 0.9257 (mp0) cc_final: 0.9051 (pm20) REVERT: G 266 TRP cc_start: 0.8680 (m100) cc_final: 0.7835 (m100) REVERT: G 283 LYS cc_start: 0.9327 (pttm) cc_final: 0.9096 (pttm) REVERT: G 295 ASP cc_start: 0.8742 (p0) cc_final: 0.8217 (p0) REVERT: G 296 LYS cc_start: 0.8764 (mmmt) cc_final: 0.8518 (mmmt) REVERT: G 306 ASP cc_start: 0.8953 (t70) cc_final: 0.8566 (t70) REVERT: G 307 MET cc_start: 0.9080 (mmt) cc_final: 0.8612 (mmt) REVERT: G 314 THR cc_start: 0.9208 (p) cc_final: 0.8943 (t) REVERT: G 318 ILE cc_start: 0.9664 (mt) cc_final: 0.9441 (mt) REVERT: G 319 MET cc_start: 0.9216 (mpp) cc_final: 0.8936 (mmt) REVERT: G 323 LYS cc_start: 0.9410 (pttm) cc_final: 0.9162 (pttm) REVERT: G 328 GLN cc_start: 0.8002 (tp40) cc_final: 0.7592 (tp40) REVERT: G 333 LYS cc_start: 0.9172 (mmtt) cc_final: 0.8637 (mmtt) REVERT: G 334 MET cc_start: 0.8931 (ptp) cc_final: 0.8472 (tmm) outliers start: 0 outliers final: 0 residues processed: 1131 average time/residue: 0.4092 time to fit residues: 682.4833 Evaluate side-chains 1079 residues out of total 2539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1079 time to evaluate : 3.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 272 optimal weight: 0.7980 chunk 31 optimal weight: 6.9990 chunk 160 optimal weight: 0.6980 chunk 206 optimal weight: 8.9990 chunk 159 optimal weight: 5.9990 chunk 237 optimal weight: 5.9990 chunk 157 optimal weight: 8.9990 chunk 281 optimal weight: 0.5980 chunk 176 optimal weight: 1.9990 chunk 171 optimal weight: 4.9990 chunk 129 optimal weight: 10.0000 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 116 ASN A 219 HIS A 220 ASN A 240 ASN ** A 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 GLN B 219 HIS ** C 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 412 ASN D 62 ASN D 100 GLN D 114 GLN D 219 HIS D 403 GLN D 422 GLN ** F 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 288 ASN ** G 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.3675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 24510 Z= 0.230 Angle : 0.622 13.182 33263 Z= 0.318 Chirality : 0.043 0.243 3697 Planarity : 0.004 0.052 4105 Dihedral : 10.837 156.999 3510 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 17.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 0.04 % Allowed : 0.95 % Favored : 99.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.16), residues: 2917 helix: 1.17 (0.14), residues: 1422 sheet: -1.06 (0.27), residues: 393 loop : -1.22 (0.18), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP G 294 HIS 0.010 0.001 HIS G 274 PHE 0.019 0.002 PHE E 28 TYR 0.036 0.002 TYR G 54 ARG 0.018 0.001 ARG G 280 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1129 residues out of total 2539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1128 time to evaluate : 2.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7236 (tpp) cc_final: 0.6992 (tpt) REVERT: A 11 PHE cc_start: 0.8008 (m-80) cc_final: 0.7630 (m-10) REVERT: A 19 VAL cc_start: 0.8348 (m) cc_final: 0.8094 (p) REVERT: A 26 GLU cc_start: 0.7528 (pm20) cc_final: 0.6993 (pm20) REVERT: A 73 VAL cc_start: 0.8495 (t) cc_final: 0.8028 (p) REVERT: A 79 LYS cc_start: 0.8791 (ttpt) cc_final: 0.8440 (ttpt) REVERT: A 85 GLU cc_start: 0.7606 (mm-30) cc_final: 0.7397 (mm-30) REVERT: A 123 LYS cc_start: 0.8107 (mmmm) cc_final: 0.7867 (mmmm) REVERT: A 128 MET cc_start: 0.8089 (tpt) cc_final: 0.7797 (tpt) REVERT: A 163 LEU cc_start: 0.8995 (tp) cc_final: 0.8724 (tt) REVERT: A 171 LYS cc_start: 0.8061 (mmtp) cc_final: 0.7829 (mmtp) REVERT: A 196 MET cc_start: 0.7389 (mmt) cc_final: 0.7036 (mmt) REVERT: A 203 LYS cc_start: 0.7642 (pttm) cc_final: 0.7122 (pttm) REVERT: A 213 ASP cc_start: 0.7776 (m-30) cc_final: 0.7331 (m-30) REVERT: A 214 TYR cc_start: 0.8898 (m-80) cc_final: 0.8554 (m-10) REVERT: A 235 LYS cc_start: 0.8165 (ttpt) cc_final: 0.7879 (ttpt) REVERT: A 241 MET cc_start: 0.8115 (mmm) cc_final: 0.7591 (mmm) REVERT: A 248 ASP cc_start: 0.7674 (m-30) cc_final: 0.7126 (m-30) REVERT: A 265 LYS cc_start: 0.8359 (ttpp) cc_final: 0.8156 (ttpp) REVERT: A 316 CYS cc_start: 0.8163 (m) cc_final: 0.7928 (m) REVERT: A 342 LEU cc_start: 0.8233 (tp) cc_final: 0.7902 (tp) REVERT: A 411 LYS cc_start: 0.7164 (ttmm) cc_final: 0.6871 (ttmm) REVERT: A 423 LYS cc_start: 0.8430 (mmmm) cc_final: 0.8127 (mmmm) REVERT: A 426 GLN cc_start: 0.7674 (mt0) cc_final: 0.7362 (mt0) REVERT: B 8 HIS cc_start: 0.8148 (m90) cc_final: 0.6960 (m90) REVERT: B 41 LYS cc_start: 0.8920 (ttmt) cc_final: 0.8639 (ttmt) REVERT: B 67 GLU cc_start: 0.7392 (tp30) cc_final: 0.7142 (tp30) REVERT: B 79 LYS cc_start: 0.8729 (ttmm) cc_final: 0.8218 (ttmm) REVERT: B 109 LYS cc_start: 0.8648 (tptp) cc_final: 0.8239 (mmmm) REVERT: B 118 GLU cc_start: 0.7592 (tt0) cc_final: 0.7137 (tt0) REVERT: B 138 MET cc_start: 0.8056 (mmm) cc_final: 0.7714 (mmm) REVERT: B 145 SER cc_start: 0.8668 (p) cc_final: 0.7832 (p) REVERT: B 147 ASP cc_start: 0.7406 (m-30) cc_final: 0.7071 (m-30) REVERT: B 155 MET cc_start: 0.8010 (tpp) cc_final: 0.7603 (tpp) REVERT: B 163 LEU cc_start: 0.9000 (mm) cc_final: 0.8715 (mm) REVERT: B 184 LYS cc_start: 0.8425 (mmtm) cc_final: 0.8205 (mmmt) REVERT: B 194 VAL cc_start: 0.8749 (t) cc_final: 0.8358 (t) REVERT: B 243 ASP cc_start: 0.7149 (t0) cc_final: 0.6808 (t0) REVERT: B 245 SER cc_start: 0.8947 (t) cc_final: 0.8561 (p) REVERT: B 260 LYS cc_start: 0.8730 (tttp) cc_final: 0.8491 (tttm) REVERT: B 262 LYS cc_start: 0.8891 (mtmm) cc_final: 0.8537 (mtpp) REVERT: B 265 LYS cc_start: 0.8644 (ttpp) cc_final: 0.8327 (ttpp) REVERT: B 279 GLN cc_start: 0.8560 (tt0) cc_final: 0.8315 (tt0) REVERT: B 288 ASN cc_start: 0.8409 (m-40) cc_final: 0.8179 (m-40) REVERT: B 318 SER cc_start: 0.8075 (m) cc_final: 0.7412 (t) REVERT: B 342 LEU cc_start: 0.8896 (tp) cc_final: 0.8653 (tp) REVERT: B 345 GLU cc_start: 0.8057 (tt0) cc_final: 0.7747 (tt0) REVERT: B 370 ASP cc_start: 0.6966 (m-30) cc_final: 0.6636 (m-30) REVERT: B 384 MET cc_start: 0.8514 (mmm) cc_final: 0.8267 (mmt) REVERT: B 392 GLU cc_start: 0.7413 (tm-30) cc_final: 0.7141 (tm-30) REVERT: B 403 GLN cc_start: 0.7257 (tt0) cc_final: 0.6938 (pt0) REVERT: B 413 LYS cc_start: 0.8226 (tppt) cc_final: 0.8014 (tppt) REVERT: B 419 MET cc_start: 0.4814 (tpp) cc_final: 0.4484 (ttm) REVERT: B 427 LYS cc_start: 0.8043 (tttm) cc_final: 0.7821 (tttm) REVERT: C 13 GLN cc_start: 0.8048 (tp40) cc_final: 0.7784 (tp40) REVERT: C 20 TRP cc_start: 0.8790 (t-100) cc_final: 0.8550 (t-100) REVERT: C 41 LYS cc_start: 0.8585 (mtpp) cc_final: 0.8068 (mtpp) REVERT: C 85 GLU cc_start: 0.8161 (mm-30) cc_final: 0.7799 (mm-30) REVERT: C 96 LYS cc_start: 0.8511 (mttt) cc_final: 0.8293 (mttt) REVERT: C 101 ARG cc_start: 0.8248 (mmm-85) cc_final: 0.7972 (mmm-85) REVERT: C 109 LYS cc_start: 0.8997 (tppt) cc_final: 0.8567 (mmmm) REVERT: C 140 GLN cc_start: 0.7891 (tm-30) cc_final: 0.7648 (tm-30) REVERT: C 166 MET cc_start: 0.7294 (tpt) cc_final: 0.6678 (tpt) REVERT: C 167 ASN cc_start: 0.8217 (p0) cc_final: 0.7754 (p0) REVERT: C 184 LYS cc_start: 0.8588 (mtmm) cc_final: 0.8351 (mtmm) REVERT: C 203 LYS cc_start: 0.8262 (mtmm) cc_final: 0.7885 (mtmm) REVERT: C 241 MET cc_start: 0.8240 (mmm) cc_final: 0.7735 (mmm) REVERT: C 263 MET cc_start: 0.7280 (mmm) cc_final: 0.6960 (mmm) REVERT: C 280 TYR cc_start: 0.8424 (m-80) cc_final: 0.8154 (m-80) REVERT: C 292 SER cc_start: 0.8800 (m) cc_final: 0.8308 (t) REVERT: C 293 LEU cc_start: 0.9005 (tp) cc_final: 0.8621 (tp) REVERT: C 315 ILE cc_start: 0.8447 (pt) cc_final: 0.8100 (pt) REVERT: C 318 SER cc_start: 0.7949 (p) cc_final: 0.7496 (p) REVERT: C 322 ARG cc_start: 0.6834 (ptt90) cc_final: 0.6607 (ptt90) REVERT: C 331 THR cc_start: 0.8289 (m) cc_final: 0.8022 (t) REVERT: C 335 ILE cc_start: 0.8620 (mt) cc_final: 0.8319 (tp) REVERT: C 345 GLU cc_start: 0.7706 (tt0) cc_final: 0.7421 (tt0) REVERT: D 40 ILE cc_start: 0.9336 (mt) cc_final: 0.9087 (mm) REVERT: D 41 LYS cc_start: 0.8544 (ttpp) cc_final: 0.8158 (ttpp) REVERT: D 46 GLU cc_start: 0.8068 (tt0) cc_final: 0.7705 (tt0) REVERT: D 47 TYR cc_start: 0.8839 (m-80) cc_final: 0.8014 (m-80) REVERT: D 93 GLU cc_start: 0.7745 (mm-30) cc_final: 0.7543 (mm-30) REVERT: D 96 LYS cc_start: 0.8540 (ttpp) cc_final: 0.8306 (ttpp) REVERT: D 109 LYS cc_start: 0.8552 (ttmm) cc_final: 0.8254 (ttmm) REVERT: D 118 GLU cc_start: 0.7221 (tp30) cc_final: 0.6778 (tp30) REVERT: D 126 LYS cc_start: 0.8793 (tptt) cc_final: 0.8567 (tptt) REVERT: D 127 LYS cc_start: 0.7807 (ptpp) cc_final: 0.7559 (ptpp) REVERT: D 139 ARG cc_start: 0.7917 (ptp-110) cc_final: 0.7703 (ptp-110) REVERT: D 147 ASP cc_start: 0.7608 (p0) cc_final: 0.7195 (p0) REVERT: D 153 ASP cc_start: 0.7682 (t0) cc_final: 0.7431 (t0) REVERT: D 155 MET cc_start: 0.7588 (tpt) cc_final: 0.7245 (tpt) REVERT: D 189 THR cc_start: 0.8625 (p) cc_final: 0.8033 (p) REVERT: D 223 TYR cc_start: 0.8772 (t80) cc_final: 0.8093 (t80) REVERT: D 226 MET cc_start: 0.7698 (mmm) cc_final: 0.7044 (mmm) REVERT: D 263 MET cc_start: 0.7994 (mmm) cc_final: 0.7737 (mmm) REVERT: D 276 ILE cc_start: 0.8956 (mt) cc_final: 0.8631 (mt) REVERT: D 280 TYR cc_start: 0.8466 (m-80) cc_final: 0.8200 (m-80) REVERT: D 296 GLU cc_start: 0.7227 (pt0) cc_final: 0.6482 (pt0) REVERT: D 324 TYR cc_start: 0.7507 (m-80) cc_final: 0.7212 (m-80) REVERT: D 326 GLU cc_start: 0.7728 (mm-30) cc_final: 0.7332 (mm-30) REVERT: D 338 GLU cc_start: 0.7269 (mt-10) cc_final: 0.7022 (mt-10) REVERT: D 403 GLN cc_start: 0.8236 (tt0) cc_final: 0.8026 (tt0) REVERT: D 413 LYS cc_start: 0.8340 (mppt) cc_final: 0.8059 (mppt) REVERT: D 416 LYS cc_start: 0.8386 (mppt) cc_final: 0.8120 (mppt) REVERT: E 23 MET cc_start: 0.8460 (mmt) cc_final: 0.8220 (mmt) REVERT: E 25 SER cc_start: 0.8889 (m) cc_final: 0.8634 (m) REVERT: E 34 LYS cc_start: 0.8333 (tttp) cc_final: 0.8022 (tttp) REVERT: E 39 LEU cc_start: 0.8587 (mt) cc_final: 0.8283 (mt) REVERT: E 47 TYR cc_start: 0.6398 (t80) cc_final: 0.6187 (t80) REVERT: E 79 LYS cc_start: 0.8111 (mttt) cc_final: 0.7846 (tttt) REVERT: E 103 MET cc_start: 0.8093 (mmp) cc_final: 0.7732 (mmt) REVERT: E 178 ILE cc_start: 0.8457 (mm) cc_final: 0.7911 (mm) REVERT: E 241 MET cc_start: 0.7751 (mmm) cc_final: 0.7520 (mmm) REVERT: E 259 TYR cc_start: 0.9035 (t80) cc_final: 0.8512 (t80) REVERT: E 263 MET cc_start: 0.8376 (mmm) cc_final: 0.7730 (tpp) REVERT: E 265 LYS cc_start: 0.8909 (mtmt) cc_final: 0.8625 (mtmt) REVERT: E 271 THR cc_start: 0.9132 (p) cc_final: 0.8776 (t) REVERT: E 301 LYS cc_start: 0.7878 (ptpp) cc_final: 0.7469 (ptpp) REVERT: E 326 GLU cc_start: 0.7575 (pt0) cc_final: 0.7341 (pt0) REVERT: E 333 LYS cc_start: 0.8091 (tttp) cc_final: 0.7757 (tttp) REVERT: E 423 LYS cc_start: 0.8913 (mtpp) cc_final: 0.8587 (mtpp) REVERT: F 18 LYS cc_start: 0.8163 (tppp) cc_final: 0.7926 (tppp) REVERT: F 22 TYR cc_start: 0.8205 (m-80) cc_final: 0.7941 (m-10) REVERT: F 34 LYS cc_start: 0.9055 (ttmt) cc_final: 0.8720 (ttmm) REVERT: F 43 HIS cc_start: 0.8767 (t-90) cc_final: 0.8287 (t-90) REVERT: F 60 LEU cc_start: 0.8847 (tp) cc_final: 0.8607 (tp) REVERT: F 61 GLU cc_start: 0.7447 (mm-30) cc_final: 0.7058 (mm-30) REVERT: F 62 ASN cc_start: 0.7839 (t0) cc_final: 0.7480 (t0) REVERT: F 82 ASP cc_start: 0.7420 (t0) cc_final: 0.7156 (t0) REVERT: F 96 LYS cc_start: 0.8655 (ttpp) cc_final: 0.8386 (ttpp) REVERT: F 115 THR cc_start: 0.8792 (m) cc_final: 0.8264 (p) REVERT: F 119 LEU cc_start: 0.8551 (mt) cc_final: 0.8217 (mt) REVERT: F 123 LYS cc_start: 0.8489 (tppt) cc_final: 0.8212 (tppt) REVERT: F 155 MET cc_start: 0.6542 (tpp) cc_final: 0.5966 (tpp) REVERT: F 158 TYR cc_start: 0.7456 (p90) cc_final: 0.7140 (p90) REVERT: F 183 THR cc_start: 0.8177 (p) cc_final: 0.7846 (t) REVERT: F 231 GLU cc_start: 0.8020 (mp0) cc_final: 0.7634 (mp0) REVERT: F 258 GLU cc_start: 0.7503 (mt-10) cc_final: 0.7244 (mt-10) REVERT: F 265 LYS cc_start: 0.8634 (mmmt) cc_final: 0.8261 (mmmt) REVERT: F 280 TYR cc_start: 0.8384 (m-80) cc_final: 0.8146 (m-80) REVERT: F 296 GLU cc_start: 0.7704 (pt0) cc_final: 0.7478 (pt0) REVERT: F 329 TYR cc_start: 0.7714 (t80) cc_final: 0.7302 (t80) REVERT: F 333 LYS cc_start: 0.8893 (ttpt) cc_final: 0.8434 (ttpt) REVERT: G 7 ILE cc_start: 0.9445 (pt) cc_final: 0.9045 (tp) REVERT: G 8 ASP cc_start: 0.8986 (m-30) cc_final: 0.8655 (m-30) REVERT: G 77 TYR cc_start: 0.9134 (t80) cc_final: 0.8630 (t80) REVERT: G 80 GLU cc_start: 0.8800 (mm-30) cc_final: 0.8477 (mm-30) REVERT: G 81 PHE cc_start: 0.8702 (m-80) cc_final: 0.8425 (m-80) REVERT: G 89 TYR cc_start: 0.8638 (t80) cc_final: 0.8062 (t80) REVERT: G 91 PHE cc_start: 0.9145 (t80) cc_final: 0.8773 (t80) REVERT: G 93 ILE cc_start: 0.9333 (tt) cc_final: 0.9055 (pt) REVERT: G 96 GLU cc_start: 0.8789 (mm-30) cc_final: 0.8455 (pp20) REVERT: G 97 LYS cc_start: 0.8823 (mttt) cc_final: 0.8481 (mttt) REVERT: G 100 SER cc_start: 0.8104 (p) cc_final: 0.7266 (p) REVERT: G 137 ILE cc_start: 0.9447 (mm) cc_final: 0.9229 (mm) REVERT: G 147 LYS cc_start: 0.9246 (mmtm) cc_final: 0.8696 (mmmt) REVERT: G 152 TYR cc_start: 0.8483 (m-80) cc_final: 0.8270 (m-80) REVERT: G 157 THR cc_start: 0.8877 (p) cc_final: 0.8289 (p) REVERT: G 158 GLU cc_start: 0.9268 (mt-10) cc_final: 0.8846 (mp0) REVERT: G 177 GLU cc_start: 0.9036 (mt-10) cc_final: 0.8717 (pt0) REVERT: G 186 ASN cc_start: 0.9129 (p0) cc_final: 0.8855 (p0) REVERT: G 190 LYS cc_start: 0.9306 (mmmt) cc_final: 0.8933 (tptp) REVERT: G 224 ARG cc_start: 0.9021 (ptp-110) cc_final: 0.8605 (ptp-170) REVERT: G 231 TYR cc_start: 0.8871 (m-80) cc_final: 0.8436 (m-80) REVERT: G 238 ASP cc_start: 0.9160 (m-30) cc_final: 0.8565 (m-30) REVERT: G 240 LEU cc_start: 0.9376 (mt) cc_final: 0.9136 (mt) REVERT: G 241 PHE cc_start: 0.8156 (m-80) cc_final: 0.7701 (m-80) REVERT: G 242 ILE cc_start: 0.9203 (mp) cc_final: 0.8778 (tp) REVERT: G 243 GLU cc_start: 0.9241 (mp0) cc_final: 0.9027 (pm20) REVERT: G 266 TRP cc_start: 0.8608 (m100) cc_final: 0.7809 (m100) REVERT: G 283 LYS cc_start: 0.9257 (pttm) cc_final: 0.9048 (pttm) REVERT: G 295 ASP cc_start: 0.8704 (p0) cc_final: 0.8362 (p0) REVERT: G 306 ASP cc_start: 0.8954 (t70) cc_final: 0.8582 (t70) REVERT: G 307 MET cc_start: 0.9215 (mmt) cc_final: 0.8636 (mmt) REVERT: G 314 THR cc_start: 0.9202 (p) cc_final: 0.8968 (t) REVERT: G 319 MET cc_start: 0.9241 (mpp) cc_final: 0.8846 (mpp) REVERT: G 323 LYS cc_start: 0.9335 (pttm) cc_final: 0.9099 (pttm) REVERT: G 328 GLN cc_start: 0.7987 (tp40) cc_final: 0.7620 (tp40) REVERT: G 333 LYS cc_start: 0.9182 (mmtt) cc_final: 0.8641 (mmtt) REVERT: G 334 MET cc_start: 0.8888 (ptp) cc_final: 0.8372 (tmm) outliers start: 1 outliers final: 0 residues processed: 1129 average time/residue: 0.4050 time to fit residues: 676.6257 Evaluate side-chains 1074 residues out of total 2539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1074 time to evaluate : 2.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 174 optimal weight: 5.9990 chunk 112 optimal weight: 2.9990 chunk 168 optimal weight: 10.0000 chunk 84 optimal weight: 0.1980 chunk 55 optimal weight: 0.0970 chunk 54 optimal weight: 0.9990 chunk 178 optimal weight: 4.9990 chunk 191 optimal weight: 6.9990 chunk 139 optimal weight: 6.9990 chunk 26 optimal weight: 9.9990 chunk 221 optimal weight: 6.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN A 220 ASN A 240 ASN A 295 ASN ** A 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 35 ASN B 99 GLN ** C 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 GLN D 114 GLN ** D 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 422 GLN ** F 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.3857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 24510 Z= 0.232 Angle : 0.613 9.604 33263 Z= 0.316 Chirality : 0.043 0.225 3697 Planarity : 0.004 0.054 4105 Dihedral : 10.806 158.724 3510 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 17.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.16), residues: 2917 helix: 1.16 (0.14), residues: 1409 sheet: -1.18 (0.27), residues: 390 loop : -1.24 (0.18), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP F 154 HIS 0.006 0.001 HIS B 8 PHE 0.023 0.002 PHE A 16 TYR 0.032 0.002 TYR G 54 ARG 0.012 0.001 ARG G 280 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1118 residues out of total 2539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1118 time to evaluate : 2.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7078 (tpp) cc_final: 0.6871 (tpt) REVERT: A 11 PHE cc_start: 0.8045 (m-80) cc_final: 0.7687 (m-10) REVERT: A 19 VAL cc_start: 0.8466 (m) cc_final: 0.8082 (p) REVERT: A 26 GLU cc_start: 0.7475 (pm20) cc_final: 0.6971 (pm20) REVERT: A 73 VAL cc_start: 0.8492 (t) cc_final: 0.8020 (p) REVERT: A 79 LYS cc_start: 0.8811 (ttpt) cc_final: 0.8378 (ttpt) REVERT: A 113 ILE cc_start: 0.8921 (mt) cc_final: 0.8699 (mt) REVERT: A 123 LYS cc_start: 0.8157 (mmmm) cc_final: 0.7908 (mmmm) REVERT: A 146 PHE cc_start: 0.8148 (m-10) cc_final: 0.7715 (m-80) REVERT: A 148 SER cc_start: 0.7862 (t) cc_final: 0.7621 (t) REVERT: A 163 LEU cc_start: 0.9045 (tp) cc_final: 0.8677 (tt) REVERT: A 171 LYS cc_start: 0.8087 (mmtp) cc_final: 0.7868 (mmtp) REVERT: A 196 MET cc_start: 0.7460 (mmt) cc_final: 0.7019 (mmt) REVERT: A 203 LYS cc_start: 0.7629 (pttm) cc_final: 0.7136 (pttm) REVERT: A 213 ASP cc_start: 0.7784 (m-30) cc_final: 0.7326 (m-30) REVERT: A 214 TYR cc_start: 0.8925 (m-80) cc_final: 0.8633 (m-80) REVERT: A 235 LYS cc_start: 0.8148 (ttpt) cc_final: 0.7844 (ttpt) REVERT: A 241 MET cc_start: 0.8151 (mmm) cc_final: 0.7572 (mmm) REVERT: A 248 ASP cc_start: 0.7661 (m-30) cc_final: 0.7148 (m-30) REVERT: A 265 LYS cc_start: 0.8319 (ttpp) cc_final: 0.8001 (ttpp) REVERT: A 316 CYS cc_start: 0.8079 (m) cc_final: 0.7845 (m) REVERT: A 345 GLU cc_start: 0.7153 (pp20) cc_final: 0.6950 (pp20) REVERT: A 411 LYS cc_start: 0.6955 (ttmm) cc_final: 0.6751 (ttmm) REVERT: A 423 LYS cc_start: 0.8429 (mmmm) cc_final: 0.8106 (mmmm) REVERT: A 426 GLN cc_start: 0.7649 (mt0) cc_final: 0.7280 (mt0) REVERT: B 4 ILE cc_start: 0.8930 (tp) cc_final: 0.8702 (tp) REVERT: B 34 LYS cc_start: 0.8664 (tttm) cc_final: 0.8417 (ttpt) REVERT: B 41 LYS cc_start: 0.8929 (ttmt) cc_final: 0.8648 (ttmt) REVERT: B 67 GLU cc_start: 0.7371 (tp30) cc_final: 0.7132 (tp30) REVERT: B 75 THR cc_start: 0.9162 (p) cc_final: 0.8772 (t) REVERT: B 79 LYS cc_start: 0.8718 (ttmm) cc_final: 0.8297 (ttmm) REVERT: B 109 LYS cc_start: 0.8662 (tptp) cc_final: 0.8275 (mmmm) REVERT: B 118 GLU cc_start: 0.7616 (tt0) cc_final: 0.7119 (tt0) REVERT: B 145 SER cc_start: 0.8672 (p) cc_final: 0.7862 (p) REVERT: B 147 ASP cc_start: 0.7323 (m-30) cc_final: 0.6969 (m-30) REVERT: B 155 MET cc_start: 0.8014 (tpp) cc_final: 0.7649 (tpp) REVERT: B 166 MET cc_start: 0.7633 (ppp) cc_final: 0.7433 (ppp) REVERT: B 194 VAL cc_start: 0.8740 (t) cc_final: 0.8358 (t) REVERT: B 235 LYS cc_start: 0.8577 (ttpt) cc_final: 0.8335 (ttpt) REVERT: B 243 ASP cc_start: 0.7180 (t0) cc_final: 0.6748 (t0) REVERT: B 245 SER cc_start: 0.8948 (t) cc_final: 0.8581 (p) REVERT: B 260 LYS cc_start: 0.8758 (tttp) cc_final: 0.8493 (tttm) REVERT: B 262 LYS cc_start: 0.8910 (mtmm) cc_final: 0.8553 (mtpp) REVERT: B 265 LYS cc_start: 0.8595 (ttpp) cc_final: 0.8323 (ttpp) REVERT: B 279 GLN cc_start: 0.8547 (tt0) cc_final: 0.8326 (tt0) REVERT: B 288 ASN cc_start: 0.8442 (m-40) cc_final: 0.8182 (m-40) REVERT: B 298 LYS cc_start: 0.8539 (ttmt) cc_final: 0.8197 (ttmt) REVERT: B 300 LYS cc_start: 0.7632 (mtpp) cc_final: 0.7371 (mtpp) REVERT: B 316 CYS cc_start: 0.8110 (m) cc_final: 0.7525 (m) REVERT: B 318 SER cc_start: 0.8060 (m) cc_final: 0.7417 (t) REVERT: B 345 GLU cc_start: 0.8018 (tt0) cc_final: 0.7761 (tt0) REVERT: B 384 MET cc_start: 0.8501 (mmm) cc_final: 0.8258 (mmt) REVERT: B 392 GLU cc_start: 0.7378 (tm-30) cc_final: 0.7123 (tm-30) REVERT: B 403 GLN cc_start: 0.7401 (tt0) cc_final: 0.6987 (pt0) REVERT: B 413 LYS cc_start: 0.8482 (tppt) cc_final: 0.8124 (tppt) REVERT: B 414 TRP cc_start: 0.7881 (m100) cc_final: 0.7557 (m100) REVERT: B 419 MET cc_start: 0.4542 (tpp) cc_final: 0.3981 (ttm) REVERT: C 20 TRP cc_start: 0.8889 (t-100) cc_final: 0.8659 (t-100) REVERT: C 26 GLU cc_start: 0.7543 (pt0) cc_final: 0.7303 (pt0) REVERT: C 41 LYS cc_start: 0.8581 (mtpp) cc_final: 0.8296 (mtpp) REVERT: C 85 GLU cc_start: 0.8138 (mm-30) cc_final: 0.7810 (mm-30) REVERT: C 92 LYS cc_start: 0.8526 (tptm) cc_final: 0.8312 (tptm) REVERT: C 96 LYS cc_start: 0.8498 (mttt) cc_final: 0.8155 (mttt) REVERT: C 101 ARG cc_start: 0.8310 (mmm-85) cc_final: 0.8034 (mmm-85) REVERT: C 109 LYS cc_start: 0.8999 (tppt) cc_final: 0.8539 (mmmm) REVERT: C 140 GLN cc_start: 0.7877 (tm-30) cc_final: 0.7644 (tm-30) REVERT: C 166 MET cc_start: 0.7287 (tpt) cc_final: 0.6576 (tpt) REVERT: C 167 ASN cc_start: 0.8234 (p0) cc_final: 0.7637 (p0) REVERT: C 178 ILE cc_start: 0.8347 (tp) cc_final: 0.7892 (mm) REVERT: C 184 LYS cc_start: 0.8622 (mtmm) cc_final: 0.8331 (mtmm) REVERT: C 203 LYS cc_start: 0.8244 (mtmm) cc_final: 0.7306 (mtmm) REVERT: C 240 ASN cc_start: 0.8053 (t0) cc_final: 0.7634 (t0) REVERT: C 241 MET cc_start: 0.8237 (mmm) cc_final: 0.7741 (mmm) REVERT: C 263 MET cc_start: 0.7269 (mmm) cc_final: 0.6901 (mmm) REVERT: C 288 ASN cc_start: 0.8641 (m-40) cc_final: 0.8228 (m110) REVERT: C 292 SER cc_start: 0.8788 (m) cc_final: 0.8310 (t) REVERT: C 293 LEU cc_start: 0.8951 (tp) cc_final: 0.8515 (tp) REVERT: C 312 TYR cc_start: 0.7032 (t80) cc_final: 0.6577 (t80) REVERT: C 318 SER cc_start: 0.7937 (p) cc_final: 0.7439 (p) REVERT: C 331 THR cc_start: 0.8273 (m) cc_final: 0.8019 (t) REVERT: C 335 ILE cc_start: 0.8615 (mt) cc_final: 0.8327 (tp) REVERT: C 345 GLU cc_start: 0.7738 (tt0) cc_final: 0.7457 (tt0) REVERT: C 355 GLN cc_start: 0.7020 (mm-40) cc_final: 0.6405 (mm-40) REVERT: C 410 ASP cc_start: 0.7876 (t0) cc_final: 0.7643 (t0) REVERT: D 40 ILE cc_start: 0.9320 (mt) cc_final: 0.9060 (mm) REVERT: D 41 LYS cc_start: 0.8506 (ttpp) cc_final: 0.7988 (ttpp) REVERT: D 46 GLU cc_start: 0.8090 (tt0) cc_final: 0.7697 (tt0) REVERT: D 47 TYR cc_start: 0.8857 (m-80) cc_final: 0.7957 (m-80) REVERT: D 93 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7376 (mm-30) REVERT: D 96 LYS cc_start: 0.8547 (ttpp) cc_final: 0.8006 (ttpp) REVERT: D 109 LYS cc_start: 0.8607 (ttmm) cc_final: 0.8249 (ttmm) REVERT: D 118 GLU cc_start: 0.7222 (tp30) cc_final: 0.6755 (tp30) REVERT: D 127 LYS cc_start: 0.7797 (ptpp) cc_final: 0.7567 (ptpp) REVERT: D 128 MET cc_start: 0.8662 (tpp) cc_final: 0.8414 (tpp) REVERT: D 143 SER cc_start: 0.8971 (m) cc_final: 0.8205 (t) REVERT: D 147 ASP cc_start: 0.7580 (p0) cc_final: 0.7217 (p0) REVERT: D 155 MET cc_start: 0.7585 (tpt) cc_final: 0.7013 (tpt) REVERT: D 194 VAL cc_start: 0.8177 (t) cc_final: 0.7630 (t) REVERT: D 223 TYR cc_start: 0.8896 (t80) cc_final: 0.7535 (t80) REVERT: D 226 MET cc_start: 0.7705 (mmm) cc_final: 0.7079 (mmm) REVERT: D 263 MET cc_start: 0.8004 (mmm) cc_final: 0.7761 (mmm) REVERT: D 276 ILE cc_start: 0.8963 (mt) cc_final: 0.8571 (mt) REVERT: D 280 TYR cc_start: 0.8387 (m-80) cc_final: 0.8048 (m-80) REVERT: D 296 GLU cc_start: 0.7306 (pt0) cc_final: 0.6581 (pt0) REVERT: D 324 TYR cc_start: 0.7512 (m-80) cc_final: 0.7202 (m-80) REVERT: D 326 GLU cc_start: 0.7701 (mm-30) cc_final: 0.7280 (mm-30) REVERT: D 338 GLU cc_start: 0.7282 (mt-10) cc_final: 0.7042 (mt-10) REVERT: D 377 LEU cc_start: 0.8599 (tp) cc_final: 0.8394 (tp) REVERT: D 416 LYS cc_start: 0.8348 (mppt) cc_final: 0.8085 (mppt) REVERT: E 23 MET cc_start: 0.8439 (mmt) cc_final: 0.8230 (mmt) REVERT: E 34 LYS cc_start: 0.8316 (tttp) cc_final: 0.7902 (tttp) REVERT: E 35 ASN cc_start: 0.8072 (m-40) cc_final: 0.7786 (m-40) REVERT: E 39 LEU cc_start: 0.8585 (mt) cc_final: 0.8313 (mt) REVERT: E 47 TYR cc_start: 0.6396 (t80) cc_final: 0.6183 (t80) REVERT: E 79 LYS cc_start: 0.8091 (mttt) cc_final: 0.7790 (tttt) REVERT: E 103 MET cc_start: 0.8075 (mmp) cc_final: 0.7869 (mmp) REVERT: E 109 LYS cc_start: 0.8532 (tptt) cc_final: 0.8278 (tptt) REVERT: E 140 GLN cc_start: 0.8035 (pp30) cc_final: 0.7780 (pp30) REVERT: E 168 LYS cc_start: 0.7699 (mmpt) cc_final: 0.7492 (mmpt) REVERT: E 175 LYS cc_start: 0.7906 (tptp) cc_final: 0.7513 (tptp) REVERT: E 241 MET cc_start: 0.7739 (mmm) cc_final: 0.7494 (mmm) REVERT: E 259 TYR cc_start: 0.9047 (t80) cc_final: 0.8574 (t80) REVERT: E 265 LYS cc_start: 0.8923 (mtmt) cc_final: 0.8511 (mtmt) REVERT: E 271 THR cc_start: 0.9137 (p) cc_final: 0.8765 (t) REVERT: E 296 GLU cc_start: 0.7644 (pt0) cc_final: 0.7381 (pt0) REVERT: E 301 LYS cc_start: 0.7935 (ptpp) cc_final: 0.7490 (ptpp) REVERT: E 326 GLU cc_start: 0.7554 (pt0) cc_final: 0.7216 (pt0) REVERT: F 22 TYR cc_start: 0.8189 (m-80) cc_final: 0.7923 (m-10) REVERT: F 34 LYS cc_start: 0.9028 (ttmt) cc_final: 0.8398 (ttmm) REVERT: F 43 HIS cc_start: 0.8791 (t-90) cc_final: 0.8310 (t-90) REVERT: F 60 LEU cc_start: 0.8850 (tp) cc_final: 0.8610 (tp) REVERT: F 61 GLU cc_start: 0.7454 (mm-30) cc_final: 0.7116 (mm-30) REVERT: F 62 ASN cc_start: 0.7858 (t0) cc_final: 0.7464 (t0) REVERT: F 82 ASP cc_start: 0.7472 (t0) cc_final: 0.7232 (t0) REVERT: F 96 LYS cc_start: 0.8734 (ttpp) cc_final: 0.8223 (ttpp) REVERT: F 115 THR cc_start: 0.8806 (m) cc_final: 0.8252 (p) REVERT: F 119 LEU cc_start: 0.8564 (mt) cc_final: 0.8246 (mt) REVERT: F 123 LYS cc_start: 0.8492 (tppt) cc_final: 0.8175 (tppt) REVERT: F 155 MET cc_start: 0.6510 (tpp) cc_final: 0.5977 (tpp) REVERT: F 158 TYR cc_start: 0.7534 (p90) cc_final: 0.7190 (p90) REVERT: F 183 THR cc_start: 0.8188 (p) cc_final: 0.7862 (t) REVERT: F 231 GLU cc_start: 0.8054 (mp0) cc_final: 0.7508 (mp0) REVERT: F 241 MET cc_start: 0.7021 (tpt) cc_final: 0.6799 (tpt) REVERT: F 329 TYR cc_start: 0.7682 (t80) cc_final: 0.7198 (t80) REVERT: F 333 LYS cc_start: 0.8867 (ttpt) cc_final: 0.8449 (ttpt) REVERT: F 404 ILE cc_start: 0.8097 (mt) cc_final: 0.7661 (mt) REVERT: F 418 LEU cc_start: 0.7750 (mp) cc_final: 0.7362 (pp) REVERT: F 419 MET cc_start: 0.4753 (tpt) cc_final: 0.4491 (tpt) REVERT: G 7 ILE cc_start: 0.9462 (pt) cc_final: 0.9048 (tp) REVERT: G 8 ASP cc_start: 0.8948 (m-30) cc_final: 0.8675 (m-30) REVERT: G 19 LEU cc_start: 0.8738 (mt) cc_final: 0.8420 (tt) REVERT: G 77 TYR cc_start: 0.9126 (t80) cc_final: 0.8639 (t80) REVERT: G 81 PHE cc_start: 0.8679 (m-80) cc_final: 0.8423 (m-80) REVERT: G 87 ARG cc_start: 0.8698 (tpp-160) cc_final: 0.8451 (tpp-160) REVERT: G 89 TYR cc_start: 0.8613 (t80) cc_final: 0.8074 (t80) REVERT: G 91 PHE cc_start: 0.9136 (t80) cc_final: 0.8755 (t80) REVERT: G 93 ILE cc_start: 0.9330 (tt) cc_final: 0.8993 (pt) REVERT: G 96 GLU cc_start: 0.8831 (mm-30) cc_final: 0.8449 (pp20) REVERT: G 97 LYS cc_start: 0.8876 (mttt) cc_final: 0.8411 (mttt) REVERT: G 100 SER cc_start: 0.8073 (p) cc_final: 0.7282 (p) REVERT: G 137 ILE cc_start: 0.9445 (mm) cc_final: 0.9235 (mm) REVERT: G 147 LYS cc_start: 0.9253 (mmtm) cc_final: 0.8706 (mmmt) REVERT: G 157 THR cc_start: 0.8867 (p) cc_final: 0.8659 (p) REVERT: G 158 GLU cc_start: 0.9273 (mt-10) cc_final: 0.9006 (mp0) REVERT: G 186 ASN cc_start: 0.9167 (p0) cc_final: 0.8945 (p0) REVERT: G 224 ARG cc_start: 0.8997 (ptp-110) cc_final: 0.8601 (ptp-170) REVERT: G 231 TYR cc_start: 0.8778 (m-80) cc_final: 0.8446 (m-80) REVERT: G 238 ASP cc_start: 0.9120 (m-30) cc_final: 0.8518 (m-30) REVERT: G 240 LEU cc_start: 0.9405 (mt) cc_final: 0.9156 (mt) REVERT: G 241 PHE cc_start: 0.8131 (m-80) cc_final: 0.7853 (m-80) REVERT: G 242 ILE cc_start: 0.9311 (mp) cc_final: 0.8797 (tp) REVERT: G 260 PHE cc_start: 0.8670 (m-80) cc_final: 0.8372 (m-10) REVERT: G 266 TRP cc_start: 0.8597 (m100) cc_final: 0.7905 (m100) REVERT: G 291 VAL cc_start: 0.8312 (t) cc_final: 0.7289 (t) REVERT: G 293 PHE cc_start: 0.7535 (m-80) cc_final: 0.7321 (m-10) REVERT: G 306 ASP cc_start: 0.8937 (t70) cc_final: 0.8607 (t70) REVERT: G 307 MET cc_start: 0.9174 (mmt) cc_final: 0.8683 (mmt) REVERT: G 314 THR cc_start: 0.9196 (p) cc_final: 0.8955 (t) REVERT: G 319 MET cc_start: 0.9071 (mpp) cc_final: 0.8810 (mmt) REVERT: G 322 MET cc_start: 0.8977 (mtm) cc_final: 0.8672 (ptp) REVERT: G 323 LYS cc_start: 0.9358 (pttm) cc_final: 0.9046 (pttm) REVERT: G 328 GLN cc_start: 0.8158 (tp40) cc_final: 0.7808 (tp40) REVERT: G 333 LYS cc_start: 0.9229 (mmtt) cc_final: 0.8654 (mmtt) REVERT: G 334 MET cc_start: 0.8975 (ptp) cc_final: 0.8441 (tmm) outliers start: 0 outliers final: 0 residues processed: 1118 average time/residue: 0.3956 time to fit residues: 655.2462 Evaluate side-chains 1060 residues out of total 2539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1060 time to evaluate : 2.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 256 optimal weight: 0.9990 chunk 269 optimal weight: 1.9990 chunk 245 optimal weight: 4.9990 chunk 262 optimal weight: 30.0000 chunk 157 optimal weight: 9.9990 chunk 114 optimal weight: 4.9990 chunk 205 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 236 optimal weight: 7.9990 chunk 248 optimal weight: 0.9990 chunk 261 optimal weight: 8.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 116 ASN A 193 ASN A 220 ASN A 240 ASN ** A 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 GLN D 114 GLN ** D 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 422 GLN E 398 GLN F 48 HIS ** F 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 422 GLN ** G 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.4017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 24510 Z= 0.230 Angle : 0.633 9.529 33263 Z= 0.324 Chirality : 0.043 0.252 3697 Planarity : 0.004 0.061 4105 Dihedral : 10.775 159.307 3510 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 17.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.16), residues: 2917 helix: 1.12 (0.14), residues: 1421 sheet: -1.17 (0.27), residues: 381 loop : -1.22 (0.18), residues: 1115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP G 294 HIS 0.008 0.001 HIS F 87 PHE 0.019 0.002 PHE E 146 TYR 0.032 0.002 TYR A 47 ARG 0.027 0.001 ARG G 280 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1117 residues out of total 2539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1117 time to evaluate : 2.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 PHE cc_start: 0.8062 (m-80) cc_final: 0.7710 (m-10) REVERT: A 19 VAL cc_start: 0.8449 (m) cc_final: 0.8064 (p) REVERT: A 26 GLU cc_start: 0.7448 (pm20) cc_final: 0.6901 (pm20) REVERT: A 39 LEU cc_start: 0.8826 (mt) cc_final: 0.8615 (mt) REVERT: A 61 GLU cc_start: 0.6416 (tm-30) cc_final: 0.6027 (tm-30) REVERT: A 73 VAL cc_start: 0.8513 (t) cc_final: 0.8088 (p) REVERT: A 79 LYS cc_start: 0.8820 (ttpt) cc_final: 0.8380 (ttpt) REVERT: A 95 GLU cc_start: 0.8829 (tt0) cc_final: 0.7789 (tt0) REVERT: A 123 LYS cc_start: 0.8184 (mmmm) cc_final: 0.7936 (mmmm) REVERT: A 128 MET cc_start: 0.8160 (tpt) cc_final: 0.7813 (tpt) REVERT: A 146 PHE cc_start: 0.8227 (m-10) cc_final: 0.7603 (m-80) REVERT: A 163 LEU cc_start: 0.8958 (tp) cc_final: 0.8719 (tt) REVERT: A 171 LYS cc_start: 0.8073 (mmtp) cc_final: 0.7795 (mmtp) REVERT: A 184 LYS cc_start: 0.8043 (mmtm) cc_final: 0.7794 (mmtm) REVERT: A 196 MET cc_start: 0.7356 (mmt) cc_final: 0.6996 (mmt) REVERT: A 203 LYS cc_start: 0.7662 (pttm) cc_final: 0.7102 (pttm) REVERT: A 213 ASP cc_start: 0.7818 (m-30) cc_final: 0.7315 (m-30) REVERT: A 214 TYR cc_start: 0.8881 (m-80) cc_final: 0.8599 (m-80) REVERT: A 224 ILE cc_start: 0.8231 (mt) cc_final: 0.8027 (mt) REVERT: A 235 LYS cc_start: 0.8010 (ttpt) cc_final: 0.7724 (ttpt) REVERT: A 241 MET cc_start: 0.7996 (mmm) cc_final: 0.7475 (mmm) REVERT: A 245 SER cc_start: 0.7305 (t) cc_final: 0.6426 (t) REVERT: A 248 ASP cc_start: 0.7661 (m-30) cc_final: 0.7004 (m-30) REVERT: A 260 LYS cc_start: 0.8673 (mmmm) cc_final: 0.8267 (mmmm) REVERT: A 265 LYS cc_start: 0.8347 (ttpp) cc_final: 0.7915 (ttpp) REVERT: A 268 GLU cc_start: 0.7465 (mt-10) cc_final: 0.7238 (mt-10) REVERT: A 278 LYS cc_start: 0.8952 (tptm) cc_final: 0.8394 (tptm) REVERT: A 316 CYS cc_start: 0.8141 (m) cc_final: 0.7846 (m) REVERT: A 411 LYS cc_start: 0.6956 (ttmm) cc_final: 0.6693 (ttmm) REVERT: A 423 LYS cc_start: 0.8425 (mmmm) cc_final: 0.8104 (mmmm) REVERT: A 426 GLN cc_start: 0.7687 (mt0) cc_final: 0.7280 (mt0) REVERT: B 4 ILE cc_start: 0.8918 (tp) cc_final: 0.8622 (tp) REVERT: B 13 GLN cc_start: 0.8023 (tp40) cc_final: 0.7431 (tp40) REVERT: B 34 LYS cc_start: 0.8676 (tttm) cc_final: 0.8418 (ttpt) REVERT: B 41 LYS cc_start: 0.8961 (ttmt) cc_final: 0.8623 (ttmt) REVERT: B 46 GLU cc_start: 0.7330 (tt0) cc_final: 0.6965 (tt0) REVERT: B 47 TYR cc_start: 0.8597 (m-80) cc_final: 0.7184 (m-80) REVERT: B 67 GLU cc_start: 0.7408 (tp30) cc_final: 0.7174 (tp30) REVERT: B 75 THR cc_start: 0.9165 (p) cc_final: 0.8854 (t) REVERT: B 79 LYS cc_start: 0.8723 (ttmm) cc_final: 0.8443 (ttmm) REVERT: B 109 LYS cc_start: 0.8687 (tptp) cc_final: 0.8342 (tptp) REVERT: B 118 GLU cc_start: 0.7632 (tt0) cc_final: 0.7171 (tt0) REVERT: B 138 MET cc_start: 0.7792 (mmm) cc_final: 0.7437 (mmm) REVERT: B 145 SER cc_start: 0.8624 (p) cc_final: 0.7746 (p) REVERT: B 147 ASP cc_start: 0.7316 (m-30) cc_final: 0.6982 (m-30) REVERT: B 155 MET cc_start: 0.8057 (tpp) cc_final: 0.7633 (tpp) REVERT: B 166 MET cc_start: 0.7691 (ppp) cc_final: 0.7454 (ppp) REVERT: B 184 LYS cc_start: 0.8396 (mmtm) cc_final: 0.8089 (mmmt) REVERT: B 194 VAL cc_start: 0.8728 (t) cc_final: 0.8377 (t) REVERT: B 243 ASP cc_start: 0.7131 (t0) cc_final: 0.6745 (t0) REVERT: B 245 SER cc_start: 0.8930 (t) cc_final: 0.8594 (p) REVERT: B 260 LYS cc_start: 0.8770 (tttp) cc_final: 0.8484 (tttm) REVERT: B 262 LYS cc_start: 0.8911 (mtmm) cc_final: 0.8513 (mtpp) REVERT: B 265 LYS cc_start: 0.8623 (ttpp) cc_final: 0.8082 (ttpp) REVERT: B 269 LYS cc_start: 0.8046 (mtmm) cc_final: 0.7312 (mtmm) REVERT: B 279 GLN cc_start: 0.8541 (tt0) cc_final: 0.8316 (tt0) REVERT: B 288 ASN cc_start: 0.8404 (m-40) cc_final: 0.8039 (m-40) REVERT: B 298 LYS cc_start: 0.8465 (ttmt) cc_final: 0.7979 (ttmt) REVERT: B 318 SER cc_start: 0.8085 (m) cc_final: 0.7442 (t) REVERT: B 342 LEU cc_start: 0.8853 (tp) cc_final: 0.8651 (tp) REVERT: B 345 GLU cc_start: 0.8034 (tt0) cc_final: 0.7687 (tt0) REVERT: B 384 MET cc_start: 0.8500 (mmm) cc_final: 0.8239 (mmt) REVERT: B 392 GLU cc_start: 0.7433 (tm-30) cc_final: 0.7192 (tm-30) REVERT: B 403 GLN cc_start: 0.7334 (tt0) cc_final: 0.6943 (pt0) REVERT: B 413 LYS cc_start: 0.8450 (tppt) cc_final: 0.8133 (tppt) REVERT: B 419 MET cc_start: 0.4401 (tpp) cc_final: 0.3692 (ttt) REVERT: B 427 LYS cc_start: 0.8093 (tttm) cc_final: 0.7867 (ttmm) REVERT: C 41 LYS cc_start: 0.8566 (mtpp) cc_final: 0.8057 (mtpp) REVERT: C 85 GLU cc_start: 0.8116 (mm-30) cc_final: 0.7751 (mm-30) REVERT: C 96 LYS cc_start: 0.8521 (mttt) cc_final: 0.8106 (mttt) REVERT: C 109 LYS cc_start: 0.8995 (tppt) cc_final: 0.8533 (mmmm) REVERT: C 140 GLN cc_start: 0.7848 (tm-30) cc_final: 0.7604 (tm-30) REVERT: C 166 MET cc_start: 0.7282 (tpt) cc_final: 0.6748 (tpt) REVERT: C 167 ASN cc_start: 0.8222 (p0) cc_final: 0.7762 (p0) REVERT: C 178 ILE cc_start: 0.8232 (tp) cc_final: 0.7726 (mm) REVERT: C 184 LYS cc_start: 0.8588 (mtmm) cc_final: 0.8328 (mtmm) REVERT: C 196 MET cc_start: 0.7925 (ptm) cc_final: 0.7703 (ptp) REVERT: C 203 LYS cc_start: 0.8281 (mtmm) cc_final: 0.7326 (mtmm) REVERT: C 240 ASN cc_start: 0.7876 (t0) cc_final: 0.7627 (t0) REVERT: C 241 MET cc_start: 0.8201 (mmm) cc_final: 0.7711 (mmm) REVERT: C 263 MET cc_start: 0.7220 (mmm) cc_final: 0.6955 (mmm) REVERT: C 288 ASN cc_start: 0.8579 (m-40) cc_final: 0.8258 (m110) REVERT: C 292 SER cc_start: 0.8793 (m) cc_final: 0.8373 (t) REVERT: C 295 ASN cc_start: 0.8075 (t0) cc_final: 0.7831 (t0) REVERT: C 312 TYR cc_start: 0.7114 (t80) cc_final: 0.6747 (t80) REVERT: C 318 SER cc_start: 0.7956 (p) cc_final: 0.7363 (p) REVERT: C 331 THR cc_start: 0.8277 (m) cc_final: 0.8022 (t) REVERT: C 335 ILE cc_start: 0.8670 (mt) cc_final: 0.8348 (tp) REVERT: C 345 GLU cc_start: 0.7714 (tt0) cc_final: 0.7443 (tt0) REVERT: C 355 GLN cc_start: 0.7136 (mm-40) cc_final: 0.6307 (mm-40) REVERT: D 40 ILE cc_start: 0.9304 (mt) cc_final: 0.9055 (mm) REVERT: D 41 LYS cc_start: 0.8576 (ttpp) cc_final: 0.8136 (ttmm) REVERT: D 47 TYR cc_start: 0.8837 (m-80) cc_final: 0.8604 (m-80) REVERT: D 93 GLU cc_start: 0.7787 (mm-30) cc_final: 0.7397 (mm-30) REVERT: D 96 LYS cc_start: 0.8560 (ttpp) cc_final: 0.8011 (ttpp) REVERT: D 109 LYS cc_start: 0.8594 (ttmm) cc_final: 0.8221 (ttmm) REVERT: D 118 GLU cc_start: 0.7232 (tp30) cc_final: 0.6827 (tp30) REVERT: D 126 LYS cc_start: 0.8761 (tptt) cc_final: 0.8510 (tptt) REVERT: D 127 LYS cc_start: 0.7825 (ptpp) cc_final: 0.7594 (ptpp) REVERT: D 139 ARG cc_start: 0.7871 (ptp-110) cc_final: 0.7562 (ptp-110) REVERT: D 143 SER cc_start: 0.8963 (m) cc_final: 0.8272 (t) REVERT: D 147 ASP cc_start: 0.7564 (p0) cc_final: 0.7228 (p0) REVERT: D 155 MET cc_start: 0.7587 (tpt) cc_final: 0.7209 (tpt) REVERT: D 296 GLU cc_start: 0.7296 (pt0) cc_final: 0.6424 (pt0) REVERT: D 324 TYR cc_start: 0.7512 (m-80) cc_final: 0.7189 (m-80) REVERT: D 326 GLU cc_start: 0.7675 (mm-30) cc_final: 0.7285 (mm-30) REVERT: D 329 TYR cc_start: 0.6207 (t80) cc_final: 0.5693 (t80) REVERT: D 333 LYS cc_start: 0.8267 (ttmt) cc_final: 0.8047 (ttmt) REVERT: D 338 GLU cc_start: 0.7297 (mt-10) cc_final: 0.7033 (mt-10) REVERT: D 416 LYS cc_start: 0.8393 (mppt) cc_final: 0.8116 (mppt) REVERT: E 26 GLU cc_start: 0.7035 (mp0) cc_final: 0.6666 (mp0) REVERT: E 34 LYS cc_start: 0.8315 (tttp) cc_final: 0.7872 (tttp) REVERT: E 35 ASN cc_start: 0.8089 (m-40) cc_final: 0.7776 (m-40) REVERT: E 39 LEU cc_start: 0.8591 (mt) cc_final: 0.8273 (mt) REVERT: E 47 TYR cc_start: 0.6472 (t80) cc_final: 0.6267 (t80) REVERT: E 79 LYS cc_start: 0.8067 (mttt) cc_final: 0.7825 (tttt) REVERT: E 95 GLU cc_start: 0.8200 (tt0) cc_final: 0.7545 (tt0) REVERT: E 103 MET cc_start: 0.8082 (mmp) cc_final: 0.7849 (mmp) REVERT: E 109 LYS cc_start: 0.8523 (tptt) cc_final: 0.8298 (tptt) REVERT: E 139 ARG cc_start: 0.7361 (ttp80) cc_final: 0.6871 (ttp80) REVERT: E 140 GLN cc_start: 0.8005 (pp30) cc_final: 0.7804 (pp30) REVERT: E 146 PHE cc_start: 0.7427 (m-10) cc_final: 0.6768 (m-10) REVERT: E 168 LYS cc_start: 0.7692 (mmpt) cc_final: 0.7433 (mmpt) REVERT: E 175 LYS cc_start: 0.7781 (tptp) cc_final: 0.7455 (tptp) REVERT: E 241 MET cc_start: 0.7683 (mmm) cc_final: 0.7352 (mmm) REVERT: E 259 TYR cc_start: 0.8969 (t80) cc_final: 0.8521 (t80) REVERT: E 263 MET cc_start: 0.8007 (tpp) cc_final: 0.7623 (tpp) REVERT: E 265 LYS cc_start: 0.8891 (mtmt) cc_final: 0.8640 (mtmt) REVERT: E 271 THR cc_start: 0.9132 (p) cc_final: 0.8748 (t) REVERT: E 296 GLU cc_start: 0.7651 (pt0) cc_final: 0.7398 (pt0) REVERT: E 301 LYS cc_start: 0.7922 (ptpp) cc_final: 0.7364 (ptpp) REVERT: E 326 GLU cc_start: 0.7556 (pt0) cc_final: 0.7225 (pt0) REVERT: F 18 LYS cc_start: 0.8338 (tppt) cc_final: 0.8081 (tppt) REVERT: F 22 TYR cc_start: 0.8140 (m-80) cc_final: 0.7896 (m-10) REVERT: F 34 LYS cc_start: 0.9045 (ttmt) cc_final: 0.8725 (ttmm) REVERT: F 43 HIS cc_start: 0.8797 (t-90) cc_final: 0.8307 (t-90) REVERT: F 60 LEU cc_start: 0.8842 (tp) cc_final: 0.8619 (tp) REVERT: F 61 GLU cc_start: 0.7471 (mm-30) cc_final: 0.7132 (mm-30) REVERT: F 62 ASN cc_start: 0.7799 (t0) cc_final: 0.7407 (t0) REVERT: F 82 ASP cc_start: 0.7496 (t0) cc_final: 0.7275 (t0) REVERT: F 96 LYS cc_start: 0.8616 (ttpp) cc_final: 0.8371 (ttpp) REVERT: F 115 THR cc_start: 0.8811 (m) cc_final: 0.8270 (p) REVERT: F 119 LEU cc_start: 0.8546 (mt) cc_final: 0.8201 (mt) REVERT: F 123 LYS cc_start: 0.8502 (tppt) cc_final: 0.8173 (tppt) REVERT: F 155 MET cc_start: 0.6657 (tpp) cc_final: 0.5989 (tpp) REVERT: F 158 TYR cc_start: 0.7532 (p90) cc_final: 0.7108 (p90) REVERT: F 183 THR cc_start: 0.8195 (p) cc_final: 0.7844 (t) REVERT: F 231 GLU cc_start: 0.8054 (mp0) cc_final: 0.7490 (mp0) REVERT: F 329 TYR cc_start: 0.7721 (t80) cc_final: 0.7158 (t80) REVERT: F 333 LYS cc_start: 0.8853 (ttpt) cc_final: 0.8471 (ttpt) REVERT: F 384 MET cc_start: 0.7532 (mtp) cc_final: 0.7224 (mtp) REVERT: F 418 LEU cc_start: 0.7732 (mp) cc_final: 0.7286 (pp) REVERT: F 419 MET cc_start: 0.4702 (tpt) cc_final: 0.4432 (tpt) REVERT: G 7 ILE cc_start: 0.9455 (pt) cc_final: 0.9064 (tp) REVERT: G 8 ASP cc_start: 0.8973 (m-30) cc_final: 0.8679 (m-30) REVERT: G 19 LEU cc_start: 0.8721 (mt) cc_final: 0.8385 (tt) REVERT: G 77 TYR cc_start: 0.9152 (t80) cc_final: 0.8722 (t80) REVERT: G 80 GLU cc_start: 0.8466 (mm-30) cc_final: 0.8224 (mm-30) REVERT: G 81 PHE cc_start: 0.8697 (m-80) cc_final: 0.8421 (m-80) REVERT: G 82 GLU cc_start: 0.9168 (mm-30) cc_final: 0.8647 (tp30) REVERT: G 85 LEU cc_start: 0.9251 (mm) cc_final: 0.8753 (mm) REVERT: G 87 ARG cc_start: 0.8679 (tpp-160) cc_final: 0.8345 (tpp-160) REVERT: G 89 TYR cc_start: 0.8621 (t80) cc_final: 0.8090 (t80) REVERT: G 91 PHE cc_start: 0.9169 (t80) cc_final: 0.8891 (t80) REVERT: G 93 ILE cc_start: 0.9342 (tt) cc_final: 0.8966 (pt) REVERT: G 96 GLU cc_start: 0.8830 (mm-30) cc_final: 0.8589 (pp20) REVERT: G 97 LYS cc_start: 0.8801 (mttt) cc_final: 0.8330 (mttt) REVERT: G 100 SER cc_start: 0.8062 (p) cc_final: 0.7306 (p) REVERT: G 137 ILE cc_start: 0.9442 (mm) cc_final: 0.9234 (mm) REVERT: G 147 LYS cc_start: 0.9252 (mmtm) cc_final: 0.8696 (mmmt) REVERT: G 158 GLU cc_start: 0.9280 (mt-10) cc_final: 0.9033 (mp0) REVERT: G 186 ASN cc_start: 0.9167 (p0) cc_final: 0.8887 (p0) REVERT: G 190 LYS cc_start: 0.9301 (mmmt) cc_final: 0.8914 (tptp) REVERT: G 224 ARG cc_start: 0.8968 (ptp-110) cc_final: 0.8593 (ptp-170) REVERT: G 231 TYR cc_start: 0.8800 (m-80) cc_final: 0.8581 (m-80) REVERT: G 238 ASP cc_start: 0.9124 (m-30) cc_final: 0.8488 (m-30) REVERT: G 240 LEU cc_start: 0.9403 (mt) cc_final: 0.9178 (mt) REVERT: G 241 PHE cc_start: 0.8101 (m-80) cc_final: 0.7890 (m-80) REVERT: G 260 PHE cc_start: 0.8664 (m-80) cc_final: 0.8392 (m-80) REVERT: G 266 TRP cc_start: 0.8553 (m100) cc_final: 0.7806 (m100) REVERT: G 279 LYS cc_start: 0.9306 (ptpp) cc_final: 0.8986 (ptpp) REVERT: G 283 LYS cc_start: 0.9059 (pttm) cc_final: 0.8698 (pttt) REVERT: G 306 ASP cc_start: 0.8914 (t70) cc_final: 0.8589 (t70) REVERT: G 307 MET cc_start: 0.9257 (mmt) cc_final: 0.8668 (mmt) REVERT: G 314 THR cc_start: 0.9198 (p) cc_final: 0.8757 (t) REVERT: G 322 MET cc_start: 0.9037 (mtm) cc_final: 0.8781 (ptp) REVERT: G 323 LYS cc_start: 0.9308 (pttm) cc_final: 0.9064 (pttm) REVERT: G 328 GLN cc_start: 0.8150 (tp40) cc_final: 0.7805 (tp40) REVERT: G 333 LYS cc_start: 0.9224 (mmtt) cc_final: 0.8697 (mmtt) REVERT: G 334 MET cc_start: 0.8881 (ptp) cc_final: 0.8354 (tmm) outliers start: 0 outliers final: 0 residues processed: 1117 average time/residue: 0.3824 time to fit residues: 633.6079 Evaluate side-chains 1062 residues out of total 2539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1062 time to evaluate : 2.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 172 optimal weight: 7.9990 chunk 277 optimal weight: 30.0000 chunk 169 optimal weight: 4.9990 chunk 131 optimal weight: 2.9990 chunk 192 optimal weight: 10.0000 chunk 290 optimal weight: 1.9990 chunk 267 optimal weight: 1.9990 chunk 231 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 178 optimal weight: 1.9990 chunk 142 optimal weight: 8.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN A 167 ASN A 219 HIS A 220 ASN A 240 ASN ** A 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 GLN D 114 GLN ** D 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 422 GLN ** D 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 200 ASN F 8 HIS F 45 ASN F 48 HIS ** F 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 317 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.4162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 24510 Z= 0.295 Angle : 0.669 8.823 33263 Z= 0.345 Chirality : 0.045 0.343 3697 Planarity : 0.004 0.051 4105 Dihedral : 10.861 161.129 3510 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 19.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 0.04 % Allowed : 0.35 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.16), residues: 2917 helix: 0.98 (0.14), residues: 1427 sheet: -1.15 (0.27), residues: 379 loop : -1.29 (0.18), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP F 89 HIS 0.009 0.001 HIS G 274 PHE 0.024 0.002 PHE A 16 TYR 0.033 0.002 TYR B 165 ARG 0.010 0.001 ARG B 274 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1127 residues out of total 2539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1126 time to evaluate : 2.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 PHE cc_start: 0.8126 (m-80) cc_final: 0.7722 (m-10) REVERT: A 19 VAL cc_start: 0.8434 (m) cc_final: 0.8051 (p) REVERT: A 26 GLU cc_start: 0.7497 (pm20) cc_final: 0.7001 (pm20) REVERT: A 73 VAL cc_start: 0.8472 (t) cc_final: 0.8035 (p) REVERT: A 123 LYS cc_start: 0.8259 (mmmm) cc_final: 0.7946 (mmmm) REVERT: A 128 MET cc_start: 0.8153 (tpt) cc_final: 0.7760 (tpt) REVERT: A 146 PHE cc_start: 0.8329 (m-10) cc_final: 0.7892 (m-80) REVERT: A 148 SER cc_start: 0.7877 (t) cc_final: 0.7624 (t) REVERT: A 163 LEU cc_start: 0.8952 (tp) cc_final: 0.8736 (tt) REVERT: A 171 LYS cc_start: 0.8077 (mmtp) cc_final: 0.7790 (mmtp) REVERT: A 184 LYS cc_start: 0.8022 (mmtm) cc_final: 0.7776 (mmtm) REVERT: A 196 MET cc_start: 0.7460 (mmt) cc_final: 0.7121 (mmt) REVERT: A 213 ASP cc_start: 0.7829 (m-30) cc_final: 0.7328 (m-30) REVERT: A 224 ILE cc_start: 0.8246 (mt) cc_final: 0.8026 (mt) REVERT: A 235 LYS cc_start: 0.8076 (ttpt) cc_final: 0.7768 (ttpt) REVERT: A 241 MET cc_start: 0.8089 (mmm) cc_final: 0.7805 (mmm) REVERT: A 248 ASP cc_start: 0.7735 (m-30) cc_final: 0.7272 (m-30) REVERT: A 265 LYS cc_start: 0.8382 (ttpp) cc_final: 0.8043 (ttpp) REVERT: A 278 LYS cc_start: 0.8868 (tptm) cc_final: 0.8621 (mtpp) REVERT: A 316 CYS cc_start: 0.8171 (m) cc_final: 0.7861 (m) REVERT: A 411 LYS cc_start: 0.6997 (ttmm) cc_final: 0.6751 (ttmm) REVERT: A 423 LYS cc_start: 0.8466 (mmmm) cc_final: 0.8128 (mmmm) REVERT: A 426 GLN cc_start: 0.7777 (mt0) cc_final: 0.7384 (mt0) REVERT: B 3 GLU cc_start: 0.7542 (tt0) cc_final: 0.7307 (tt0) REVERT: B 4 ILE cc_start: 0.8981 (tp) cc_final: 0.8656 (tp) REVERT: B 13 GLN cc_start: 0.7937 (tp40) cc_final: 0.7254 (tp40) REVERT: B 23 MET cc_start: 0.8133 (tpp) cc_final: 0.7875 (mmt) REVERT: B 41 LYS cc_start: 0.8934 (ttmt) cc_final: 0.8653 (ttmt) REVERT: B 46 GLU cc_start: 0.7377 (tt0) cc_final: 0.7039 (tt0) REVERT: B 47 TYR cc_start: 0.8574 (m-80) cc_final: 0.6935 (m-80) REVERT: B 67 GLU cc_start: 0.7429 (tp30) cc_final: 0.7157 (tp30) REVERT: B 109 LYS cc_start: 0.8736 (tptp) cc_final: 0.8414 (tptp) REVERT: B 118 GLU cc_start: 0.7804 (tt0) cc_final: 0.7332 (tt0) REVERT: B 138 MET cc_start: 0.7875 (mmm) cc_final: 0.7412 (mmm) REVERT: B 145 SER cc_start: 0.8592 (p) cc_final: 0.7766 (p) REVERT: B 147 ASP cc_start: 0.7330 (m-30) cc_final: 0.7007 (m-30) REVERT: B 155 MET cc_start: 0.8081 (tpp) cc_final: 0.7672 (tpp) REVERT: B 194 VAL cc_start: 0.8705 (t) cc_final: 0.8399 (t) REVERT: B 235 LYS cc_start: 0.8562 (ttpt) cc_final: 0.8216 (ttpt) REVERT: B 245 SER cc_start: 0.8958 (t) cc_final: 0.8608 (p) REVERT: B 262 LYS cc_start: 0.8903 (mtmm) cc_final: 0.8604 (mtpp) REVERT: B 265 LYS cc_start: 0.8641 (ttpp) cc_final: 0.8303 (ttpp) REVERT: B 269 LYS cc_start: 0.8125 (mtmm) cc_final: 0.7225 (mtmm) REVERT: B 279 GLN cc_start: 0.8587 (tt0) cc_final: 0.8343 (tt0) REVERT: B 288 ASN cc_start: 0.8343 (m-40) cc_final: 0.8141 (m-40) REVERT: B 297 LEU cc_start: 0.8912 (mt) cc_final: 0.8614 (mp) REVERT: B 298 LYS cc_start: 0.8514 (ttmt) cc_final: 0.7792 (ttmt) REVERT: B 318 SER cc_start: 0.8122 (m) cc_final: 0.7525 (t) REVERT: B 345 GLU cc_start: 0.7983 (tt0) cc_final: 0.7691 (tt0) REVERT: B 384 MET cc_start: 0.8513 (mmm) cc_final: 0.8218 (mmt) REVERT: B 403 GLN cc_start: 0.7371 (tt0) cc_final: 0.6950 (pt0) REVERT: B 413 LYS cc_start: 0.8482 (tppt) cc_final: 0.8171 (tppt) REVERT: B 419 MET cc_start: 0.4823 (tpp) cc_final: 0.4236 (ttm) REVERT: B 427 LYS cc_start: 0.8113 (tttm) cc_final: 0.7893 (ttmm) REVERT: C 85 GLU cc_start: 0.8134 (mm-30) cc_final: 0.7774 (mm-30) REVERT: C 96 LYS cc_start: 0.8531 (mttt) cc_final: 0.8176 (mttt) REVERT: C 109 LYS cc_start: 0.9024 (tppt) cc_final: 0.8563 (mmmm) REVERT: C 140 GLN cc_start: 0.7887 (tm-30) cc_final: 0.7673 (tm-30) REVERT: C 166 MET cc_start: 0.7339 (tpt) cc_final: 0.6783 (tpt) REVERT: C 167 ASN cc_start: 0.8287 (p0) cc_final: 0.7780 (p0) REVERT: C 184 LYS cc_start: 0.8672 (mtmm) cc_final: 0.8426 (mtmm) REVERT: C 203 LYS cc_start: 0.8381 (mtmm) cc_final: 0.7919 (mtmm) REVERT: C 240 ASN cc_start: 0.7774 (t0) cc_final: 0.7113 (t0) REVERT: C 241 MET cc_start: 0.8119 (mmm) cc_final: 0.7689 (mmm) REVERT: C 263 MET cc_start: 0.7252 (mmm) cc_final: 0.6974 (mmm) REVERT: C 288 ASN cc_start: 0.8610 (m-40) cc_final: 0.8264 (m110) REVERT: C 292 SER cc_start: 0.8820 (m) cc_final: 0.8384 (t) REVERT: C 293 LEU cc_start: 0.9132 (tp) cc_final: 0.8757 (tp) REVERT: C 295 ASN cc_start: 0.8078 (t0) cc_final: 0.7749 (t0) REVERT: C 302 ASN cc_start: 0.7993 (t0) cc_final: 0.7697 (t0) REVERT: C 315 ILE cc_start: 0.8399 (pt) cc_final: 0.8193 (pt) REVERT: C 318 SER cc_start: 0.7977 (p) cc_final: 0.7420 (p) REVERT: C 331 THR cc_start: 0.8317 (m) cc_final: 0.8061 (t) REVERT: C 335 ILE cc_start: 0.8701 (mt) cc_final: 0.8372 (tp) REVERT: C 345 GLU cc_start: 0.7762 (tt0) cc_final: 0.7469 (tt0) REVERT: C 393 LEU cc_start: 0.8420 (mt) cc_final: 0.7989 (mt) REVERT: C 401 ILE cc_start: 0.8151 (mp) cc_final: 0.7771 (mt) REVERT: D 15 TYR cc_start: 0.8054 (t80) cc_final: 0.7366 (t80) REVERT: D 40 ILE cc_start: 0.9356 (mt) cc_final: 0.9068 (mm) REVERT: D 41 LYS cc_start: 0.8545 (ttpp) cc_final: 0.8110 (ttmm) REVERT: D 47 TYR cc_start: 0.8853 (m-80) cc_final: 0.8149 (m-80) REVERT: D 93 GLU cc_start: 0.7786 (mm-30) cc_final: 0.7365 (mm-30) REVERT: D 96 LYS cc_start: 0.8595 (ttpp) cc_final: 0.8024 (ttpp) REVERT: D 109 LYS cc_start: 0.8627 (ttmm) cc_final: 0.8168 (ttmm) REVERT: D 118 GLU cc_start: 0.7162 (tp30) cc_final: 0.6804 (tp30) REVERT: D 126 LYS cc_start: 0.8783 (tptt) cc_final: 0.8528 (tptt) REVERT: D 127 LYS cc_start: 0.7759 (ptpp) cc_final: 0.7540 (ptpp) REVERT: D 128 MET cc_start: 0.8705 (tpp) cc_final: 0.8467 (tpp) REVERT: D 139 ARG cc_start: 0.7850 (ptp-110) cc_final: 0.7538 (ptp-110) REVERT: D 143 SER cc_start: 0.8992 (m) cc_final: 0.8334 (t) REVERT: D 147 ASP cc_start: 0.7652 (p0) cc_final: 0.7257 (p0) REVERT: D 155 MET cc_start: 0.7353 (tpt) cc_final: 0.7016 (tpt) REVERT: D 159 GLU cc_start: 0.7438 (tp30) cc_final: 0.7188 (tp30) REVERT: D 189 THR cc_start: 0.8753 (p) cc_final: 0.8504 (p) REVERT: D 194 VAL cc_start: 0.8156 (m) cc_final: 0.7867 (m) REVERT: D 296 GLU cc_start: 0.7249 (pt0) cc_final: 0.6656 (pt0) REVERT: D 300 LYS cc_start: 0.7868 (mtmm) cc_final: 0.7155 (mtmm) REVERT: D 313 LEU cc_start: 0.8209 (pp) cc_final: 0.7953 (pp) REVERT: D 324 TYR cc_start: 0.7569 (m-80) cc_final: 0.7276 (m-80) REVERT: D 326 GLU cc_start: 0.7745 (mm-30) cc_final: 0.7360 (mm-30) REVERT: D 329 TYR cc_start: 0.6366 (t80) cc_final: 0.5709 (t80) REVERT: D 333 LYS cc_start: 0.8322 (ttmt) cc_final: 0.8083 (ttmt) REVERT: D 338 GLU cc_start: 0.7339 (mt-10) cc_final: 0.7084 (mt-10) REVERT: D 397 GLU cc_start: 0.7815 (mt-10) cc_final: 0.7568 (mt-10) REVERT: D 410 ASP cc_start: 0.7976 (t0) cc_final: 0.7197 (t0) REVERT: D 416 LYS cc_start: 0.8417 (mppt) cc_final: 0.8152 (mppt) REVERT: E 26 GLU cc_start: 0.7073 (mp0) cc_final: 0.6715 (mp0) REVERT: E 34 LYS cc_start: 0.8352 (tttp) cc_final: 0.7908 (tttp) REVERT: E 35 ASN cc_start: 0.8166 (m-40) cc_final: 0.7953 (m-40) REVERT: E 47 TYR cc_start: 0.6534 (t80) cc_final: 0.6316 (t80) REVERT: E 79 LYS cc_start: 0.8252 (mttt) cc_final: 0.7943 (tttt) REVERT: E 103 MET cc_start: 0.8114 (mmp) cc_final: 0.7678 (mmt) REVERT: E 139 ARG cc_start: 0.7400 (ttp80) cc_final: 0.7090 (ttp80) REVERT: E 155 MET cc_start: 0.8236 (tpp) cc_final: 0.7695 (tpp) REVERT: E 168 LYS cc_start: 0.7792 (mmpt) cc_final: 0.7549 (mmpt) REVERT: E 178 ILE cc_start: 0.8575 (mm) cc_final: 0.8090 (mm) REVERT: E 228 MET cc_start: 0.7683 (ptt) cc_final: 0.7472 (ptt) REVERT: E 241 MET cc_start: 0.7762 (mmm) cc_final: 0.7533 (mmm) REVERT: E 259 TYR cc_start: 0.9009 (t80) cc_final: 0.8590 (t80) REVERT: E 265 LYS cc_start: 0.8914 (mtmt) cc_final: 0.8538 (mtmt) REVERT: E 271 THR cc_start: 0.9117 (p) cc_final: 0.8708 (t) REVERT: E 296 GLU cc_start: 0.7694 (pt0) cc_final: 0.7437 (pt0) REVERT: E 301 LYS cc_start: 0.7947 (ptpp) cc_final: 0.7424 (ptpp) REVERT: E 326 GLU cc_start: 0.7637 (pt0) cc_final: 0.7390 (pt0) REVERT: E 333 LYS cc_start: 0.8098 (tttp) cc_final: 0.7801 (tttp) REVERT: E 416 LYS cc_start: 0.8098 (mttp) cc_final: 0.7845 (mttp) REVERT: F 7 SER cc_start: 0.9152 (m) cc_final: 0.8567 (p) REVERT: F 18 LYS cc_start: 0.8367 (tppt) cc_final: 0.8156 (tppt) REVERT: F 24 ASP cc_start: 0.8507 (t70) cc_final: 0.8303 (t70) REVERT: F 34 LYS cc_start: 0.9015 (ttmt) cc_final: 0.8377 (ttmm) REVERT: F 41 LYS cc_start: 0.8480 (tppp) cc_final: 0.8223 (tptm) REVERT: F 43 HIS cc_start: 0.8815 (t-90) cc_final: 0.8263 (t-90) REVERT: F 61 GLU cc_start: 0.7554 (mm-30) cc_final: 0.7204 (mm-30) REVERT: F 62 ASN cc_start: 0.7846 (t0) cc_final: 0.7439 (t0) REVERT: F 82 ASP cc_start: 0.7475 (t0) cc_final: 0.7203 (t0) REVERT: F 96 LYS cc_start: 0.8719 (ttpp) cc_final: 0.8207 (ttpp) REVERT: F 109 LYS cc_start: 0.8516 (tttm) cc_final: 0.8269 (tttm) REVERT: F 115 THR cc_start: 0.8842 (m) cc_final: 0.8318 (p) REVERT: F 119 LEU cc_start: 0.8592 (mt) cc_final: 0.8238 (mt) REVERT: F 123 LYS cc_start: 0.8550 (tppt) cc_final: 0.8225 (tppt) REVERT: F 137 ILE cc_start: 0.8715 (mt) cc_final: 0.8491 (mt) REVERT: F 155 MET cc_start: 0.6664 (tpp) cc_final: 0.6043 (tpp) REVERT: F 156 ASP cc_start: 0.7987 (t0) cc_final: 0.7757 (t0) REVERT: F 158 TYR cc_start: 0.7653 (p90) cc_final: 0.7297 (p90) REVERT: F 183 THR cc_start: 0.8181 (p) cc_final: 0.7844 (t) REVERT: F 226 MET cc_start: 0.7667 (mmm) cc_final: 0.7168 (mmp) REVERT: F 231 GLU cc_start: 0.8075 (mp0) cc_final: 0.7652 (mp0) REVERT: F 340 ARG cc_start: 0.8950 (ttt-90) cc_final: 0.8678 (ttt90) REVERT: F 418 LEU cc_start: 0.7774 (mp) cc_final: 0.7343 (pp) REVERT: F 419 MET cc_start: 0.4787 (tpt) cc_final: 0.4452 (tpt) REVERT: F 422 GLN cc_start: 0.7570 (mt0) cc_final: 0.7247 (mt0) REVERT: G 7 ILE cc_start: 0.9448 (pt) cc_final: 0.9065 (tp) REVERT: G 8 ASP cc_start: 0.8987 (m-30) cc_final: 0.8752 (m-30) REVERT: G 62 ASN cc_start: 0.7941 (t0) cc_final: 0.7635 (p0) REVERT: G 63 ILE cc_start: 0.9122 (mm) cc_final: 0.8872 (mp) REVERT: G 77 TYR cc_start: 0.9166 (t80) cc_final: 0.8783 (t80) REVERT: G 78 LEU cc_start: 0.9555 (mt) cc_final: 0.9346 (tp) REVERT: G 81 PHE cc_start: 0.8676 (m-80) cc_final: 0.8439 (m-80) REVERT: G 87 ARG cc_start: 0.8926 (tpp-160) cc_final: 0.8642 (tpp-160) REVERT: G 89 TYR cc_start: 0.8738 (t80) cc_final: 0.8327 (t80) REVERT: G 91 PHE cc_start: 0.9200 (t80) cc_final: 0.8972 (t80) REVERT: G 93 ILE cc_start: 0.9342 (tt) cc_final: 0.8980 (pt) REVERT: G 95 LYS cc_start: 0.9201 (mtpp) cc_final: 0.8797 (mtpp) REVERT: G 96 GLU cc_start: 0.8867 (mm-30) cc_final: 0.8567 (pp20) REVERT: G 97 LYS cc_start: 0.8867 (mttt) cc_final: 0.8351 (mtmt) REVERT: G 100 SER cc_start: 0.7990 (p) cc_final: 0.7283 (p) REVERT: G 147 LYS cc_start: 0.9255 (mmtm) cc_final: 0.8730 (mmmt) REVERT: G 158 GLU cc_start: 0.9308 (mt-10) cc_final: 0.9049 (mp0) REVERT: G 224 ARG cc_start: 0.8976 (ptp-110) cc_final: 0.8632 (ptp-170) REVERT: G 238 ASP cc_start: 0.9148 (m-30) cc_final: 0.8558 (m-30) REVERT: G 260 PHE cc_start: 0.8679 (m-80) cc_final: 0.8400 (m-80) REVERT: G 266 TRP cc_start: 0.8488 (m100) cc_final: 0.7942 (m100) REVERT: G 277 THR cc_start: 0.9390 (t) cc_final: 0.9158 (t) REVERT: G 281 MET cc_start: 0.9153 (mmp) cc_final: 0.8881 (mmm) REVERT: G 293 PHE cc_start: 0.7850 (m-80) cc_final: 0.7213 (m-10) REVERT: G 305 ASN cc_start: 0.9041 (t0) cc_final: 0.8763 (t0) REVERT: G 306 ASP cc_start: 0.8969 (t70) cc_final: 0.8736 (t70) REVERT: G 307 MET cc_start: 0.9305 (mmt) cc_final: 0.8790 (mmt) REVERT: G 309 ARG cc_start: 0.8599 (mtp180) cc_final: 0.8279 (mtm-85) REVERT: G 323 LYS cc_start: 0.9300 (pttm) cc_final: 0.9072 (pttm) REVERT: G 328 GLN cc_start: 0.8231 (tp40) cc_final: 0.7920 (tp40) REVERT: G 333 LYS cc_start: 0.9260 (mmtt) cc_final: 0.8907 (mmtt) REVERT: G 334 MET cc_start: 0.8911 (ptp) cc_final: 0.8338 (tmm) REVERT: G 335 ARG cc_start: 0.7833 (ttp-170) cc_final: 0.7515 (ttp-170) outliers start: 1 outliers final: 0 residues processed: 1126 average time/residue: 0.4217 time to fit residues: 713.3144 Evaluate side-chains 1078 residues out of total 2539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1078 time to evaluate : 2.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 184 optimal weight: 0.1980 chunk 246 optimal weight: 2.9990 chunk 70 optimal weight: 7.9990 chunk 213 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 232 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 238 optimal weight: 6.9990 chunk 29 optimal weight: 0.7980 chunk 42 optimal weight: 7.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 116 ASN A 193 ASN A 219 HIS A 220 ASN A 240 ASN A 295 ASN ** A 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 ASN ** C 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 GLN D 399 GLN D 422 GLN E 105 ASN F 8 HIS F 48 HIS F 87 HIS F 152 HIS ** F 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 288 ASN ** F 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.123074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.101959 restraints weight = 49721.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.105480 restraints weight = 26116.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.107863 restraints weight = 16057.854| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.4298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 24510 Z= 0.232 Angle : 0.650 14.357 33263 Z= 0.332 Chirality : 0.044 0.396 3697 Planarity : 0.004 0.058 4105 Dihedral : 10.780 161.531 3510 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 18.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.16), residues: 2917 helix: 0.98 (0.14), residues: 1423 sheet: -1.23 (0.27), residues: 381 loop : -1.25 (0.18), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.002 TRP G 294 HIS 0.015 0.001 HIS F 87 PHE 0.017 0.002 PHE E 16 TYR 0.032 0.002 TYR F 280 ARG 0.009 0.001 ARG C 236 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9651.74 seconds wall clock time: 171 minutes 36.81 seconds (10296.81 seconds total)