Starting phenix.real_space_refine on Thu Jun 27 20:32:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bp6_44762/06_2024/9bp6_44762_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bp6_44762/06_2024/9bp6_44762.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bp6_44762/06_2024/9bp6_44762.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bp6_44762/06_2024/9bp6_44762.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bp6_44762/06_2024/9bp6_44762_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bp6_44762/06_2024/9bp6_44762_updated.pdb" } resolution = 3.1 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= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 4 5.21 5 S 93 5.16 5 C 8562 2.51 5 N 2320 2.21 5 O 2640 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 120": "OD1" <-> "OD2" Residue "A ASP 199": "OD1" <-> "OD2" Residue "A GLU 279": "OE1" <-> "OE2" Residue "A TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 322": "OD1" <-> "OD2" Residue "B GLU 69": "OE1" <-> "OE2" Residue "B PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 111": "OE1" <-> "OE2" Residue "B TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 328": "OE1" <-> "OE2" Residue "B ARG 359": "NH1" <-> "NH2" Residue "I TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 77": "OE1" <-> "OE2" Residue "I PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 168": "OE1" <-> "OE2" Residue "I ASP 199": "OD1" <-> "OD2" Residue "I GLU 207": "OE1" <-> "OE2" Residue "I GLU 279": "OE1" <-> "OE2" Residue "I TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 297": "OE1" <-> "OE2" Residue "I GLU 417": "OE1" <-> "OE2" Residue "I TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 111": "OE1" <-> "OE2" Residue "Q GLU 157": "OE1" <-> "OE2" Residue "Q GLU 194": "OE1" <-> "OE2" Residue "Q ASP 209": "OD1" <-> "OD2" Residue "Q ASP 327": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 13631 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3405 Classifications: {'peptide': 437} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 416} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 3348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3348 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 408} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "I" Number of atoms: 3389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3389 Classifications: {'peptide': 437} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 416} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "Q" Number of atoms: 3357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3357 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 408} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 10.14, per 1000 atoms: 0.74 Number of scatterers: 13631 At special positions: 0 Unit cell: (74.2, 75.26, 196.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 93 16.00 P 12 15.00 Mg 4 11.99 O 2640 8.00 N 2320 7.00 C 8562 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.00 Conformation dependent library (CDL) restraints added in 2.8 seconds 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3196 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 80 helices and 10 sheets defined 48.6% alpha, 14.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.49 Creating SS restraints... Processing helix chain 'A' and resid 10 through 28 removed outlier: 3.778A pdb=" N ALA A 19 " --> pdb=" O GLN A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 46 No H-bonds generated for 'chain 'A' and resid 44 through 46' Processing helix chain 'A' and resid 48 through 51 removed outlier: 3.564A pdb=" N THR A 51 " --> pdb=" O SER A 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 48 through 51' Processing helix chain 'A' and resid 72 through 80 Processing helix chain 'A' and resid 82 through 84 No H-bonds generated for 'chain 'A' and resid 82 through 84' Processing helix chain 'A' and resid 103 through 107 Processing helix chain 'A' and resid 111 through 128 removed outlier: 4.473A pdb=" N ASP A 116 " --> pdb=" O LYS A 112 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N LEU A 117 " --> pdb=" O GLU A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 160 removed outlier: 4.450A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 196 removed outlier: 4.304A pdb=" N HIS A 192 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N THR A 193 " --> pdb=" O LEU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 215 Processing helix chain 'A' and resid 224 through 243 removed outlier: 4.546A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N LEU A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 259 Processing helix chain 'A' and resid 278 through 283 removed outlier: 3.785A pdb=" N TYR A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N HIS A 283 " --> pdb=" O GLU A 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 278 through 283' Processing helix chain 'A' and resid 288 through 296 removed outlier: 3.848A pdb=" N PHE A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 300 No H-bonds generated for 'chain 'A' and resid 298 through 300' Processing helix chain 'A' and resid 325 through 337 Processing helix chain 'A' and resid 382 through 400 removed outlier: 3.869A pdb=" N ALA A 400 " --> pdb=" O LEU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 411 removed outlier: 3.559A pdb=" N GLU A 411 " --> pdb=" O TRP A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 435 Processing helix chain 'B' and resid 10 through 27 Processing helix chain 'B' and resid 41 through 45 Processing helix chain 'B' and resid 47 through 49 No H-bonds generated for 'chain 'B' and resid 47 through 49' Processing helix chain 'B' and resid 55 through 57 No H-bonds generated for 'chain 'B' and resid 55 through 57' Processing helix chain 'B' and resid 71 through 77 Processing helix chain 'B' and resid 87 through 89 No H-bonds generated for 'chain 'B' and resid 87 through 89' Processing helix chain 'B' and resid 101 through 105 Processing helix chain 'B' and resid 107 through 126 removed outlier: 4.190A pdb=" N GLU B 111 " --> pdb=" O THR B 107 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU B 112 " --> pdb=" O GLU B 108 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ASP B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N SER B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 158 Processing helix chain 'B' and resid 181 through 194 removed outlier: 4.235A pdb=" N HIS B 190 " --> pdb=" O THR B 186 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N GLN B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 213 Processing helix chain 'B' and resid 222 through 236 removed outlier: 3.640A pdb=" N THR B 232 " --> pdb=" O LEU B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 241 No H-bonds generated for 'chain 'B' and resid 238 through 241' Processing helix chain 'B' and resid 250 through 257 Processing helix chain 'B' and resid 278 through 281 Processing helix chain 'B' and resid 286 through 294 Processing helix chain 'B' and resid 296 through 298 No H-bonds generated for 'chain 'B' and resid 296 through 298' Processing helix chain 'B' and resid 305 through 307 No H-bonds generated for 'chain 'B' and resid 305 through 307' Processing helix chain 'B' and resid 323 through 336 Processing helix chain 'B' and resid 372 through 389 removed outlier: 3.560A pdb=" N GLN B 375 " --> pdb=" O THR B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 399 removed outlier: 4.217A pdb=" N HIS B 396 " --> pdb=" O ALA B 393 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N TRP B 397 " --> pdb=" O PHE B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 427 Processing helix chain 'I' and resid 10 through 28 Processing helix chain 'I' and resid 44 through 52 removed outlier: 3.893A pdb=" N SER I 48 " --> pdb=" O GLY I 45 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N PHE I 49 " --> pdb=" O ASP I 46 " (cutoff:3.500A) Processing helix chain 'I' and resid 73 through 79 Processing helix chain 'I' and resid 89 through 91 No H-bonds generated for 'chain 'I' and resid 89 through 91' Processing helix chain 'I' and resid 103 through 107 Processing helix chain 'I' and resid 111 through 128 removed outlier: 4.295A pdb=" N ASP I 116 " --> pdb=" O LYS I 112 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N LEU I 117 " --> pdb=" O GLU I 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 144 through 160 Processing helix chain 'I' and resid 183 through 197 removed outlier: 4.301A pdb=" N HIS I 192 " --> pdb=" O ILE I 188 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N THR I 193 " --> pdb=" O LEU I 189 " (cutoff:3.500A) Processing helix chain 'I' and resid 206 through 217 Processing helix chain 'I' and resid 224 through 243 removed outlier: 4.551A pdb=" N SER I 241 " --> pdb=" O SER I 237 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N LEU I 242 " --> pdb=" O ILE I 238 " (cutoff:3.500A) Processing helix chain 'I' and resid 252 through 259 Processing helix chain 'I' and resid 278 through 281 No H-bonds generated for 'chain 'I' and resid 278 through 281' Processing helix chain 'I' and resid 288 through 296 Processing helix chain 'I' and resid 325 through 337 Processing helix chain 'I' and resid 383 through 401 removed outlier: 4.102A pdb=" N LEU I 397 " --> pdb=" O LYS I 394 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ALA I 400 " --> pdb=" O LEU I 397 " (cutoff:3.500A) Processing helix chain 'I' and resid 405 through 411 removed outlier: 3.688A pdb=" N GLU I 411 " --> pdb=" O TRP I 407 " (cutoff:3.500A) Processing helix chain 'I' and resid 415 through 435 removed outlier: 3.798A pdb=" N VAL I 435 " --> pdb=" O TYR I 432 " (cutoff:3.500A) Processing helix chain 'Q' and resid 10 through 28 Processing helix chain 'Q' and resid 41 through 45 Processing helix chain 'Q' and resid 47 through 49 No H-bonds generated for 'chain 'Q' and resid 47 through 49' Processing helix chain 'Q' and resid 70 through 77 Processing helix chain 'Q' and resid 82 through 84 No H-bonds generated for 'chain 'Q' and resid 82 through 84' Processing helix chain 'Q' and resid 87 through 89 No H-bonds generated for 'chain 'Q' and resid 87 through 89' Processing helix chain 'Q' and resid 101 through 105 Processing helix chain 'Q' and resid 109 through 125 removed outlier: 4.209A pdb=" N ASP Q 114 " --> pdb=" O ALA Q 110 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N SER Q 115 " --> pdb=" O GLU Q 111 " (cutoff:3.500A) Processing helix chain 'Q' and resid 143 through 158 Processing helix chain 'Q' and resid 181 through 194 removed outlier: 3.886A pdb=" N HIS Q 190 " --> pdb=" O THR Q 186 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N GLN Q 191 " --> pdb=" O LEU Q 187 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU Q 194 " --> pdb=" O HIS Q 190 " (cutoff:3.500A) Processing helix chain 'Q' and resid 204 through 213 Processing helix chain 'Q' and resid 222 through 236 Processing helix chain 'Q' and resid 238 through 241 No H-bonds generated for 'chain 'Q' and resid 238 through 241' Processing helix chain 'Q' and resid 250 through 257 Processing helix chain 'Q' and resid 276 through 281 removed outlier: 4.097A pdb=" N GLN Q 280 " --> pdb=" O ARG Q 276 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N TYR Q 281 " --> pdb=" O GLY Q 277 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 276 through 281' Processing helix chain 'Q' and resid 286 through 294 Processing helix chain 'Q' and resid 296 through 298 No H-bonds generated for 'chain 'Q' and resid 296 through 298' Processing helix chain 'Q' and resid 323 through 336 Processing helix chain 'Q' and resid 338 through 340 No H-bonds generated for 'chain 'Q' and resid 338 through 340' Processing helix chain 'Q' and resid 372 through 390 removed outlier: 3.589A pdb=" N GLN Q 375 " --> pdb=" O THR Q 372 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ARG Q 390 " --> pdb=" O ALA Q 387 " (cutoff:3.500A) Processing helix chain 'Q' and resid 395 through 401 Processing helix chain 'Q' and resid 405 through 427 Processing sheet with id= A, first strand: chain 'A' and resid 92 through 94 removed outlier: 8.011A pdb=" N ILE A 93 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N PHE A 67 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N SER A 140 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N HIS A 139 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N CYS A 200 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N SER A 170 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N PHE A 202 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N TYR A 172 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL A 204 " --> pdb=" O TYR A 172 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 53 through 55 Processing sheet with id= C, first strand: chain 'A' and resid 269 through 273 Processing sheet with id= D, first strand: chain 'B' and resid 90 through 92 removed outlier: 8.289A pdb=" N VAL B 91 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LEU B 65 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N ILE B 64 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N HIS B 6 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N VAL B 66 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N GLN B 8 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N VAL B 5 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N PHE B 133 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N ILE B 7 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LEU B 135 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N ALA B 9 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N HIS B 137 " --> pdb=" O ALA B 9 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ILE B 163 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N LEU B 135 " --> pdb=" O ILE B 163 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ASN B 165 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N HIS B 137 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N PHE B 167 " --> pdb=" O HIS B 137 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N GLU B 198 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N SER B 168 " --> pdb=" O GLU B 198 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N TYR B 200 " --> pdb=" O SER B 168 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N VAL B 170 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ILE B 202 " --> pdb=" O VAL B 170 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N ASP B 203 " --> pdb=" O PRO B 268 " (cutoff:3.500A) removed outlier: 12.110A pdb=" N PHE B 270 " --> pdb=" O ASP B 203 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N PHE B 265 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N SER B 371 " --> pdb=" O PHE B 265 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 51 through 53 Processing sheet with id= F, first strand: chain 'I' and resid 92 through 94 removed outlier: 8.127A pdb=" N ILE I 93 " --> pdb=" O ALA I 65 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N PHE I 67 " --> pdb=" O ILE I 93 " (cutoff:3.500A) removed outlier: 8.630A pdb=" N VAL I 66 " --> pdb=" O CYS I 4 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N SER I 6 " --> pdb=" O VAL I 66 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N VAL I 68 " --> pdb=" O SER I 6 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N HIS I 8 " --> pdb=" O VAL I 68 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N ILE I 5 " --> pdb=" O GLN I 133 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N PHE I 135 " --> pdb=" O ILE I 5 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ILE I 7 " --> pdb=" O PHE I 135 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N VAL I 137 " --> pdb=" O ILE I 7 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N VAL I 9 " --> pdb=" O VAL I 137 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N HIS I 139 " --> pdb=" O VAL I 9 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N LEU I 167 " --> pdb=" O VAL I 137 " (cutoff:3.500A) removed outlier: 8.295A pdb=" N HIS I 139 " --> pdb=" O LEU I 167 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N PHE I 169 " --> pdb=" O HIS I 139 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N CYS I 200 " --> pdb=" O GLU I 168 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N SER I 170 " --> pdb=" O CYS I 200 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N PHE I 202 " --> pdb=" O SER I 170 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N TYR I 172 " --> pdb=" O PHE I 202 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N VAL I 204 " --> pdb=" O TYR I 172 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'I' and resid 53 through 55 Processing sheet with id= H, first strand: chain 'I' and resid 269 through 273 removed outlier: 3.590A pdb=" N ALA I 314 " --> pdb=" O ASN I 380 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'Q' and resid 90 through 92 removed outlier: 8.423A pdb=" N VAL Q 91 " --> pdb=" O ALA Q 63 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU Q 65 " --> pdb=" O VAL Q 91 " (cutoff:3.500A) removed outlier: 8.431A pdb=" N ILE Q 64 " --> pdb=" O ILE Q 4 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N HIS Q 6 " --> pdb=" O ILE Q 64 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N VAL Q 66 " --> pdb=" O HIS Q 6 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N GLN Q 8 " --> pdb=" O VAL Q 66 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N VAL Q 5 " --> pdb=" O GLN Q 131 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N PHE Q 133 " --> pdb=" O VAL Q 5 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N ILE Q 7 " --> pdb=" O PHE Q 133 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU Q 135 " --> pdb=" O ILE Q 7 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N ALA Q 9 " --> pdb=" O LEU Q 135 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N HIS Q 137 " --> pdb=" O ALA Q 9 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ILE Q 163 " --> pdb=" O PHE Q 133 " (cutoff:3.500A) removed outlier: 8.650A pdb=" N LEU Q 135 " --> pdb=" O ILE Q 163 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ASN Q 165 " --> pdb=" O LEU Q 135 " (cutoff:3.500A) removed outlier: 8.311A pdb=" N HIS Q 137 " --> pdb=" O ASN Q 165 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N PHE Q 167 " --> pdb=" O HIS Q 137 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N GLU Q 198 " --> pdb=" O THR Q 166 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N SER Q 168 " --> pdb=" O GLU Q 198 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N TYR Q 200 " --> pdb=" O SER Q 168 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N VAL Q 170 " --> pdb=" O TYR Q 200 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ILE Q 202 " --> pdb=" O VAL Q 170 " (cutoff:3.500A) removed outlier: 8.477A pdb=" N ASP Q 203 " --> pdb=" O PRO Q 268 " (cutoff:3.500A) removed outlier: 11.876A pdb=" N PHE Q 270 " --> pdb=" O ASP Q 203 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N PHE Q 265 " --> pdb=" O SER Q 371 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N SER Q 371 " --> pdb=" O PHE Q 265 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'Q' and resid 51 through 53 600 hydrogen bonds defined for protein. 1545 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: 4.53 Time building geometry restraints manager: 6.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4494 1.34 - 1.47: 3358 1.47 - 1.59: 5921 1.59 - 1.72: 16 1.72 - 1.85: 150 Bond restraints: 13939 Sorted by residual: bond pdb=" N MET B 257 " pdb=" CA MET B 257 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.32e-02 5.74e+03 8.73e+00 bond pdb=" N ILE A 219 " pdb=" CA ILE A 219 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.19e-02 7.06e+03 8.11e+00 bond pdb=" N GLU A 220 " pdb=" CA GLU A 220 " ideal model delta sigma weight residual 1.459 1.493 -0.033 1.19e-02 7.06e+03 7.89e+00 bond pdb=" N LEU I 132 " pdb=" CA LEU I 132 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.23e-02 6.61e+03 7.75e+00 bond pdb=" N CYS A 129 " pdb=" CA CYS A 129 " ideal model delta sigma weight residual 1.455 1.491 -0.036 1.30e-02 5.92e+03 7.53e+00 ... (remaining 13934 not shown) Histogram of bond angle deviations from ideal: 98.27 - 105.44: 329 105.44 - 112.61: 6890 112.61 - 119.78: 5044 119.78 - 126.95: 6499 126.95 - 134.12: 186 Bond angle restraints: 18948 Sorted by residual: angle pdb=" CB MET I 425 " pdb=" CG MET I 425 " pdb=" SD MET I 425 " ideal model delta sigma weight residual 112.70 126.59 -13.89 3.00e+00 1.11e-01 2.14e+01 angle pdb=" N GLY I 134 " pdb=" CA GLY I 134 " pdb=" C GLY I 134 " ideal model delta sigma weight residual 111.27 118.44 -7.17 1.67e+00 3.59e-01 1.84e+01 angle pdb=" CB MET A 154 " pdb=" CG MET A 154 " pdb=" SD MET A 154 " ideal model delta sigma weight residual 112.70 124.23 -11.53 3.00e+00 1.11e-01 1.48e+01 angle pdb=" CB ARG Q 359 " pdb=" CG ARG Q 359 " pdb=" CD ARG Q 359 " ideal model delta sigma weight residual 111.30 119.77 -8.47 2.30e+00 1.89e-01 1.36e+01 angle pdb=" N LYS A 326 " pdb=" CA LYS A 326 " pdb=" CB LYS A 326 " ideal model delta sigma weight residual 110.01 104.95 5.06 1.45e+00 4.76e-01 1.22e+01 ... (remaining 18943 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.74: 8098 35.74 - 71.48: 180 71.48 - 107.22: 18 107.22 - 142.96: 4 142.96 - 178.69: 2 Dihedral angle restraints: 8302 sinusoidal: 3312 harmonic: 4990 Sorted by residual: dihedral pdb=" C5' GTP A 501 " pdb=" O5' GTP A 501 " pdb=" PA GTP A 501 " pdb=" O3A GTP A 501 " ideal model delta sinusoidal sigma weight residual 69.27 -109.43 178.69 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' GTP I 501 " pdb=" O5' GTP I 501 " pdb=" PA GTP I 501 " pdb=" O3A GTP I 501 " ideal model delta sinusoidal sigma weight residual 69.27 -125.51 -165.22 1 2.00e+01 2.50e-03 4.72e+01 dihedral pdb=" C8 GTP A 501 " pdb=" C1' GTP A 501 " pdb=" N9 GTP A 501 " pdb=" O4' GTP A 501 " ideal model delta sinusoidal sigma weight residual 104.59 -34.91 139.50 1 2.00e+01 2.50e-03 4.23e+01 ... (remaining 8299 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1763 0.066 - 0.133: 265 0.133 - 0.199: 46 0.199 - 0.265: 1 0.265 - 0.332: 3 Chirality restraints: 2078 Sorted by residual: chirality pdb=" CB THR I 191 " pdb=" CA THR I 191 " pdb=" OG1 THR I 191 " pdb=" CG2 THR I 191 " both_signs ideal model delta sigma weight residual False 2.55 2.22 0.33 2.00e-01 2.50e+01 2.75e+00 chirality pdb=" CB THR A 191 " pdb=" CA THR A 191 " pdb=" OG1 THR A 191 " pdb=" CG2 THR A 191 " both_signs ideal model delta sigma weight residual False 2.55 2.26 0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" CA ILE A 219 " pdb=" N ILE A 219 " pdb=" C ILE A 219 " pdb=" CB ILE A 219 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.27 2.00e-01 2.50e+01 1.78e+00 ... (remaining 2075 not shown) Planarity restraints: 2467 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 218 " 0.017 2.00e-02 2.50e+03 3.50e-02 1.23e+01 pdb=" C ASP A 218 " -0.061 2.00e-02 2.50e+03 pdb=" O ASP A 218 " 0.023 2.00e-02 2.50e+03 pdb=" N ILE A 219 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG I 214 " -0.256 9.50e-02 1.11e+02 1.15e-01 9.65e+00 pdb=" NE ARG I 214 " 0.023 2.00e-02 2.50e+03 pdb=" CZ ARG I 214 " -0.018 2.00e-02 2.50e+03 pdb=" NH1 ARG I 214 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG I 214 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS I 88 " -0.049 5.00e-02 4.00e+02 7.36e-02 8.68e+00 pdb=" N PRO I 89 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO I 89 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO I 89 " -0.041 5.00e-02 4.00e+02 ... (remaining 2464 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 67 2.55 - 3.14: 10736 3.14 - 3.73: 21392 3.73 - 4.31: 30052 4.31 - 4.90: 51349 Nonbonded interactions: 113596 Sorted by model distance: nonbonded pdb=" O3G G2P Q 501 " pdb="MG MG Q 502 " model vdw 1.963 2.170 nonbonded pdb=" O1G GTP I 501 " pdb="MG MG I 502 " model vdw 1.963 2.170 nonbonded pdb=" O2B G2P Q 501 " pdb="MG MG Q 502 " model vdw 1.964 2.170 nonbonded pdb=" O1G GTP A 501 " pdb="MG MG A 502 " model vdw 1.971 2.170 nonbonded pdb=" OE2 GLU Q 69 " pdb="MG MG Q 502 " model vdw 1.979 2.170 ... (remaining 113591 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' and (resid 1 through 120 or (resid 121 and (name N or name CA or name \ C or name O or name CB )) or resid 122 through 162 or (resid 163 and (name N or \ name CA or name C or name O or name CB )) or resid 164 through 220 or (resid 22 \ 1 and (name N or name CA or name C or name O or name CB )) or resid 222 through \ 441 or resid 501 through 502)) selection = chain 'I' } ncs_group { reference = chain 'B' selection = (chain 'Q' and ((resid 1 and (name N or name CA or name C or name O or name CB ) \ ) or resid 2 through 281 or (resid 282 through 283 and (name N or name CA or nam \ e C or name O or name CB )) or resid 284 through 429 or resid 501 through 502)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 13.500 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: 0.010 Extract box with map and model: 39.550 Check model and map are aligned: 0.100 Set scattering table: 0.150 Process input model: 44.550 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 101.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 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 : 0.005 0.056 13939 Z= 0.350 Angle : 0.882 13.893 18948 Z= 0.464 Chirality : 0.051 0.332 2078 Planarity : 0.006 0.115 2467 Dihedral : 16.030 178.695 5106 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.14 % Allowed : 12.78 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.29 (0.19), residues: 1720 helix: 1.18 (0.18), residues: 792 sheet: 0.51 (0.33), residues: 232 loop : -1.06 (0.22), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 21 HIS 0.008 0.001 HIS B 307 PHE 0.028 0.002 PHE B 20 TYR 0.020 0.002 TYR A 210 ARG 0.021 0.001 ARG I 214 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 308 time to evaluate : 1.695 Fit side-chains REVERT: A 77 GLU cc_start: 0.7998 (tm-30) cc_final: 0.7796 (mt-10) REVERT: A 120 ASP cc_start: 0.6782 (m-30) cc_final: 0.6245 (m-30) REVERT: A 290 GLU cc_start: 0.7645 (mp0) cc_final: 0.7362 (mp0) REVERT: A 313 MET cc_start: 0.8068 (mtm) cc_final: 0.7798 (ttm) REVERT: B 69 GLU cc_start: 0.7769 (pt0) cc_final: 0.6271 (pm20) REVERT: B 163 ILE cc_start: 0.8458 (mt) cc_final: 0.8162 (tp) REVERT: B 164 MET cc_start: 0.7680 (ttm) cc_final: 0.7426 (mtp) REVERT: B 262 ARG cc_start: 0.7878 (mtm180) cc_final: 0.7626 (mtm-85) REVERT: B 281 TYR cc_start: 0.6253 (m-80) cc_final: 0.5573 (m-80) REVERT: B 307 HIS cc_start: 0.7700 (m-70) cc_final: 0.7368 (m90) REVERT: B 320 ARG cc_start: 0.8175 (mtp85) cc_final: 0.7941 (mtp85) REVERT: B 407 GLU cc_start: 0.7541 (mp0) cc_final: 0.7163 (tt0) REVERT: I 75 ILE cc_start: 0.7320 (mm) cc_final: 0.6923 (mm) REVERT: I 280 LYS cc_start: 0.7681 (mttt) cc_final: 0.6083 (mmtt) REVERT: I 287 SER cc_start: 0.7048 (t) cc_final: 0.6767 (p) REVERT: I 414 GLU cc_start: 0.7526 (mt-10) cc_final: 0.7303 (mt-10) REVERT: Q 22 GLU cc_start: 0.7893 (tt0) cc_final: 0.7479 (mt-10) REVERT: Q 83 GLN cc_start: 0.7638 (tp40) cc_final: 0.7225 (tt0) REVERT: Q 108 GLU cc_start: 0.6695 (mm-30) cc_final: 0.6419 (mm-30) REVERT: Q 125 GLU cc_start: 0.7197 (OUTLIER) cc_final: 0.6532 (mp0) REVERT: Q 176 SER cc_start: 0.8404 (p) cc_final: 0.8029 (t) REVERT: Q 274 THR cc_start: 0.8795 (p) cc_final: 0.8528 (p) REVERT: Q 275 SER cc_start: 0.6504 (t) cc_final: 0.6060 (t) REVERT: Q 284 LEU cc_start: 0.6915 (tp) cc_final: 0.6570 (pt) REVERT: Q 288 GLU cc_start: 0.7478 (mp0) cc_final: 0.7054 (mp0) REVERT: Q 425 TYR cc_start: 0.7297 (m-80) cc_final: 0.6985 (m-80) outliers start: 2 outliers final: 0 residues processed: 309 average time/residue: 0.2942 time to fit residues: 126.6829 Evaluate side-chains 167 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 166 time to evaluate : 1.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 125 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 0.7980 chunk 128 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 133 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 154 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 HIS A 101 ASN A 133 GLN A 226 ASN A 329 ASN A 372 GLN B 99 ASN B 307 HIS B 414 ASN I 50 ASN I 88 HIS I 128 GLN I 300 ASN Q 6 HIS Q 8 GLN Q 99 ASN Q 190 HIS Q 247 ASN Q 279 GLN Q 348 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 13939 Z= 0.364 Angle : 0.646 10.635 18948 Z= 0.343 Chirality : 0.048 0.233 2078 Planarity : 0.006 0.057 2467 Dihedral : 11.259 169.868 1972 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.75 % Allowed : 13.40 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.20 (0.20), residues: 1720 helix: 0.92 (0.18), residues: 782 sheet: 0.41 (0.32), residues: 256 loop : -0.82 (0.23), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 21 HIS 0.009 0.002 HIS Q 190 PHE 0.023 0.002 PHE B 20 TYR 0.016 0.002 TYR Q 425 ARG 0.005 0.001 ARG A 390 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 163 time to evaluate : 1.535 Fit side-chains revert: symmetry clash REVERT: A 120 ASP cc_start: 0.6991 (m-30) cc_final: 0.6329 (m-30) REVERT: A 200 CYS cc_start: 0.7910 (m) cc_final: 0.7683 (t) REVERT: A 214 ARG cc_start: 0.7626 (ttp80) cc_final: 0.7262 (ttp80) REVERT: A 290 GLU cc_start: 0.7923 (mp0) cc_final: 0.7579 (mp0) REVERT: A 432 TYR cc_start: 0.7659 (OUTLIER) cc_final: 0.6183 (t80) REVERT: B 164 MET cc_start: 0.7908 (ttm) cc_final: 0.7613 (mtp) REVERT: B 307 HIS cc_start: 0.7851 (m170) cc_final: 0.7346 (m90) REVERT: B 406 MET cc_start: 0.7145 (mpp) cc_final: 0.6837 (mpp) REVERT: B 407 GLU cc_start: 0.7956 (mp0) cc_final: 0.7717 (tt0) REVERT: I 128 GLN cc_start: 0.6417 (tt0) cc_final: 0.5991 (mp10) REVERT: I 150 THR cc_start: 0.7839 (m) cc_final: 0.7588 (t) REVERT: I 213 CYS cc_start: 0.6890 (t) cc_final: 0.6622 (m) REVERT: I 227 LEU cc_start: 0.7674 (OUTLIER) cc_final: 0.7295 (mt) REVERT: I 377 MET cc_start: 0.7843 (ttp) cc_final: 0.7541 (ttp) REVERT: I 414 GLU cc_start: 0.7476 (mt-10) cc_final: 0.7095 (mt-10) REVERT: Q 22 GLU cc_start: 0.7624 (tt0) cc_final: 0.7278 (mt-10) REVERT: Q 108 GLU cc_start: 0.6576 (mm-30) cc_final: 0.6258 (mm-30) REVERT: Q 163 ILE cc_start: 0.8107 (mt) cc_final: 0.7479 (pt) REVERT: Q 164 MET cc_start: 0.8193 (OUTLIER) cc_final: 0.7790 (ttt) REVERT: Q 176 SER cc_start: 0.8546 (p) cc_final: 0.8199 (t) REVERT: Q 203 ASP cc_start: 0.6652 (t0) cc_final: 0.6172 (t0) REVERT: Q 267 MET cc_start: 0.8214 (ttm) cc_final: 0.7823 (ttm) REVERT: Q 275 SER cc_start: 0.6961 (t) cc_final: 0.6515 (t) REVERT: Q 279 GLN cc_start: 0.6507 (OUTLIER) cc_final: 0.6295 (mm-40) REVERT: Q 288 GLU cc_start: 0.7223 (mp0) cc_final: 0.7016 (mp0) REVERT: Q 336 LYS cc_start: 0.8116 (mmtm) cc_final: 0.7881 (mmtt) REVERT: Q 403 MET cc_start: 0.8539 (mtp) cc_final: 0.8192 (mtp) REVERT: Q 415 MET cc_start: 0.7060 (ttp) cc_final: 0.6859 (ttp) outliers start: 40 outliers final: 21 residues processed: 194 average time/residue: 0.3017 time to fit residues: 84.9342 Evaluate side-chains 168 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 143 time to evaluate : 1.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 217 LEU Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 239 THR Chi-restraints excluded: chain I residue 253 THR Chi-restraints excluded: chain Q residue 31 ASP Chi-restraints excluded: chain Q residue 41 ASP Chi-restraints excluded: chain Q residue 66 VAL Chi-restraints excluded: chain Q residue 88 ASP Chi-restraints excluded: chain Q residue 138 SER Chi-restraints excluded: chain Q residue 143 THR Chi-restraints excluded: chain Q residue 164 MET Chi-restraints excluded: chain Q residue 190 HIS Chi-restraints excluded: chain Q residue 279 GLN Chi-restraints excluded: chain Q residue 304 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 85 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 128 optimal weight: 0.9990 chunk 105 optimal weight: 0.5980 chunk 42 optimal weight: 0.7980 chunk 154 optimal weight: 0.8980 chunk 167 optimal weight: 1.9990 chunk 137 optimal weight: 0.6980 chunk 153 optimal weight: 0.6980 chunk 52 optimal weight: 0.5980 chunk 124 optimal weight: 0.0370 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 ASN B 8 GLN B 37 HIS B 245 GLN B 247 ASN I 101 ASN ** I 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 190 HIS Q 279 GLN Q 347 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 13939 Z= 0.231 Angle : 0.525 7.767 18948 Z= 0.278 Chirality : 0.044 0.211 2078 Planarity : 0.005 0.053 2467 Dihedral : 10.916 169.096 1969 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.89 % Allowed : 12.78 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.24 (0.20), residues: 1720 helix: 0.98 (0.18), residues: 776 sheet: 0.35 (0.31), residues: 260 loop : -0.79 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 21 HIS 0.011 0.001 HIS Q 190 PHE 0.036 0.001 PHE B 20 TYR 0.010 0.001 TYR Q 425 ARG 0.005 0.000 ARG I 214 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 153 time to evaluate : 1.478 Fit side-chains revert: symmetry clash REVERT: A 120 ASP cc_start: 0.6990 (m-30) cc_final: 0.6325 (m-30) REVERT: A 200 CYS cc_start: 0.7935 (m) cc_final: 0.7716 (t) REVERT: A 214 ARG cc_start: 0.7633 (ttp80) cc_final: 0.7235 (ttp80) REVERT: A 290 GLU cc_start: 0.8037 (mp0) cc_final: 0.7675 (mp0) REVERT: A 432 TYR cc_start: 0.7543 (OUTLIER) cc_final: 0.6066 (t80) REVERT: B 164 MET cc_start: 0.7908 (ttm) cc_final: 0.7531 (mtp) REVERT: B 307 HIS cc_start: 0.7748 (m170) cc_final: 0.7236 (m90) REVERT: B 406 MET cc_start: 0.7200 (mpp) cc_final: 0.6889 (mpp) REVERT: B 407 GLU cc_start: 0.7982 (mp0) cc_final: 0.7715 (tt0) REVERT: I 1 MET cc_start: 0.6906 (tpp) cc_final: 0.6703 (tpp) REVERT: I 128 GLN cc_start: 0.6527 (tt0) cc_final: 0.6120 (mp10) REVERT: I 150 THR cc_start: 0.7889 (m) cc_final: 0.7642 (t) REVERT: I 213 CYS cc_start: 0.6927 (t) cc_final: 0.6582 (m) REVERT: I 214 ARG cc_start: 0.6983 (ttm-80) cc_final: 0.6443 (ttp80) REVERT: I 309 HIS cc_start: 0.7317 (m-70) cc_final: 0.6875 (m-70) REVERT: I 377 MET cc_start: 0.7802 (ttp) cc_final: 0.7356 (ttp) REVERT: I 414 GLU cc_start: 0.7583 (mt-10) cc_final: 0.7259 (mt-10) REVERT: Q 125 GLU cc_start: 0.7132 (OUTLIER) cc_final: 0.6403 (mp0) REVERT: Q 163 ILE cc_start: 0.8174 (mt) cc_final: 0.7596 (pt) REVERT: Q 164 MET cc_start: 0.8207 (OUTLIER) cc_final: 0.7810 (ttt) REVERT: Q 176 SER cc_start: 0.8604 (p) cc_final: 0.8244 (t) REVERT: Q 267 MET cc_start: 0.8212 (ttm) cc_final: 0.7912 (ttm) REVERT: Q 288 GLU cc_start: 0.7356 (mp0) cc_final: 0.7079 (mp0) REVERT: Q 320 ARG cc_start: 0.8315 (tpp80) cc_final: 0.7708 (mmt180) REVERT: Q 336 LYS cc_start: 0.8075 (mmtm) cc_final: 0.7772 (mmtt) outliers start: 42 outliers final: 18 residues processed: 187 average time/residue: 0.2878 time to fit residues: 76.6400 Evaluate side-chains 164 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 143 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 417 GLU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain I residue 239 THR Chi-restraints excluded: chain I residue 378 LEU Chi-restraints excluded: chain Q residue 31 ASP Chi-restraints excluded: chain Q residue 55 THR Chi-restraints excluded: chain Q residue 88 ASP Chi-restraints excluded: chain Q residue 125 GLU Chi-restraints excluded: chain Q residue 138 SER Chi-restraints excluded: chain Q residue 164 MET Chi-restraints excluded: chain Q residue 190 HIS Chi-restraints excluded: chain Q residue 199 THR Chi-restraints excluded: chain Q residue 274 THR Chi-restraints excluded: chain Q residue 304 ASP Chi-restraints excluded: chain Q residue 365 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 152 optimal weight: 0.6980 chunk 116 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 103 optimal weight: 0.5980 chunk 155 optimal weight: 0.4980 chunk 164 optimal weight: 0.1980 chunk 81 optimal weight: 0.9990 chunk 147 optimal weight: 0.3980 chunk 44 optimal weight: 0.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 HIS B 8 GLN I 31 GLN ** I 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 190 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.3683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13939 Z= 0.216 Angle : 0.501 7.017 18948 Z= 0.265 Chirality : 0.043 0.223 2078 Planarity : 0.004 0.053 2467 Dihedral : 10.764 168.304 1969 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.75 % Allowed : 13.20 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.25 (0.20), residues: 1720 helix: 0.99 (0.19), residues: 776 sheet: 0.35 (0.31), residues: 260 loop : -0.79 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 21 HIS 0.013 0.001 HIS Q 190 PHE 0.031 0.001 PHE B 20 TYR 0.010 0.001 TYR Q 425 ARG 0.005 0.000 ARG A 308 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 157 time to evaluate : 1.557 Fit side-chains revert: symmetry clash REVERT: A 120 ASP cc_start: 0.6993 (m-30) cc_final: 0.6334 (m-30) REVERT: A 214 ARG cc_start: 0.7732 (ttp80) cc_final: 0.7391 (ttp80) REVERT: A 290 GLU cc_start: 0.8045 (mp0) cc_final: 0.7645 (mp0) REVERT: A 432 TYR cc_start: 0.7484 (OUTLIER) cc_final: 0.6093 (t80) REVERT: B 164 MET cc_start: 0.7967 (ttm) cc_final: 0.7505 (mtp) REVERT: B 299 MET cc_start: 0.7861 (mmp) cc_final: 0.7582 (mmt) REVERT: B 307 HIS cc_start: 0.7736 (m170) cc_final: 0.7247 (m90) REVERT: B 406 MET cc_start: 0.7229 (mpp) cc_final: 0.6922 (mpp) REVERT: B 407 GLU cc_start: 0.7996 (mp0) cc_final: 0.7783 (tt0) REVERT: I 128 GLN cc_start: 0.6481 (tt0) cc_final: 0.6080 (mp10) REVERT: I 150 THR cc_start: 0.7890 (m) cc_final: 0.7646 (t) REVERT: I 205 ASP cc_start: 0.7572 (t0) cc_final: 0.6902 (t0) REVERT: I 213 CYS cc_start: 0.6969 (t) cc_final: 0.6595 (m) REVERT: I 214 ARG cc_start: 0.7112 (ttm-80) cc_final: 0.6549 (ttp80) REVERT: I 309 HIS cc_start: 0.7392 (m-70) cc_final: 0.6981 (m-70) REVERT: I 377 MET cc_start: 0.7786 (ttp) cc_final: 0.7501 (ttp) REVERT: I 414 GLU cc_start: 0.7614 (mt-10) cc_final: 0.7287 (mt-10) REVERT: Q 125 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.6572 (mp0) REVERT: Q 163 ILE cc_start: 0.8141 (mt) cc_final: 0.7631 (pt) REVERT: Q 164 MET cc_start: 0.8089 (OUTLIER) cc_final: 0.7799 (ttm) REVERT: Q 176 SER cc_start: 0.8566 (p) cc_final: 0.8199 (t) REVERT: Q 203 ASP cc_start: 0.6699 (t0) cc_final: 0.6160 (t0) REVERT: Q 288 GLU cc_start: 0.7366 (mp0) cc_final: 0.7049 (mp0) REVERT: Q 297 LYS cc_start: 0.8511 (mmtt) cc_final: 0.7907 (mmtt) REVERT: Q 306 ARG cc_start: 0.7885 (mtt180) cc_final: 0.7558 (mtt180) REVERT: Q 320 ARG cc_start: 0.8328 (tpp80) cc_final: 0.7757 (mmt180) REVERT: Q 336 LYS cc_start: 0.8026 (mmtm) cc_final: 0.7735 (mmtt) outliers start: 40 outliers final: 28 residues processed: 187 average time/residue: 0.3113 time to fit residues: 81.0141 Evaluate side-chains 178 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 147 time to evaluate : 1.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain A residue 417 GLU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain I residue 31 GLN Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain I residue 234 ILE Chi-restraints excluded: chain I residue 239 THR Chi-restraints excluded: chain I residue 291 ILE Chi-restraints excluded: chain I residue 363 VAL Chi-restraints excluded: chain I residue 378 LEU Chi-restraints excluded: chain Q residue 31 ASP Chi-restraints excluded: chain Q residue 55 THR Chi-restraints excluded: chain Q residue 66 VAL Chi-restraints excluded: chain Q residue 88 ASP Chi-restraints excluded: chain Q residue 125 GLU Chi-restraints excluded: chain Q residue 138 SER Chi-restraints excluded: chain Q residue 164 MET Chi-restraints excluded: chain Q residue 199 THR Chi-restraints excluded: chain Q residue 274 THR Chi-restraints excluded: chain Q residue 365 VAL Chi-restraints excluded: chain Q residue 386 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 0.9990 chunk 93 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 140 optimal weight: 0.7980 chunk 113 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 147 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 309 HIS B 8 GLN ** I 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.4079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 13939 Z= 0.323 Angle : 0.561 7.484 18948 Z= 0.297 Chirality : 0.045 0.261 2078 Planarity : 0.005 0.051 2467 Dihedral : 11.011 167.479 1969 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.57 % Allowed : 14.02 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 (0.20), residues: 1720 helix: 0.78 (0.19), residues: 774 sheet: 0.12 (0.30), residues: 272 loop : -0.81 (0.23), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 21 HIS 0.005 0.001 HIS A 192 PHE 0.028 0.002 PHE B 20 TYR 0.013 0.001 TYR Q 425 ARG 0.005 0.000 ARG A 308 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 146 time to evaluate : 1.595 Fit side-chains REVERT: A 120 ASP cc_start: 0.7072 (m-30) cc_final: 0.6409 (m-30) REVERT: A 214 ARG cc_start: 0.7813 (ttp80) cc_final: 0.7547 (ttp80) REVERT: A 290 GLU cc_start: 0.8175 (mp0) cc_final: 0.7718 (mp0) REVERT: A 358 GLN cc_start: 0.8382 (tp40) cc_final: 0.8010 (mm-40) REVERT: A 432 TYR cc_start: 0.7556 (OUTLIER) cc_final: 0.6118 (t80) REVERT: B 164 MET cc_start: 0.8021 (ttm) cc_final: 0.7498 (mtp) REVERT: B 299 MET cc_start: 0.7848 (mmp) cc_final: 0.7647 (mmt) REVERT: B 307 HIS cc_start: 0.7608 (m170) cc_final: 0.7163 (m90) REVERT: B 394 PHE cc_start: 0.5194 (OUTLIER) cc_final: 0.4808 (t80) REVERT: B 406 MET cc_start: 0.7419 (mpp) cc_final: 0.5853 (mpp) REVERT: B 407 GLU cc_start: 0.7994 (mp0) cc_final: 0.7595 (mt-10) REVERT: I 114 ILE cc_start: 0.7856 (mm) cc_final: 0.7413 (tt) REVERT: I 128 GLN cc_start: 0.6513 (tt0) cc_final: 0.6141 (mp10) REVERT: I 150 THR cc_start: 0.7951 (m) cc_final: 0.7676 (t) REVERT: I 205 ASP cc_start: 0.7778 (t0) cc_final: 0.7066 (t0) REVERT: I 213 CYS cc_start: 0.7105 (t) cc_final: 0.6670 (m) REVERT: I 214 ARG cc_start: 0.7297 (ttm-80) cc_final: 0.6690 (ttp80) REVERT: I 309 HIS cc_start: 0.7636 (m-70) cc_final: 0.7203 (m-70) REVERT: I 414 GLU cc_start: 0.7653 (mt-10) cc_final: 0.7319 (mt-10) REVERT: Q 125 GLU cc_start: 0.7274 (OUTLIER) cc_final: 0.6588 (mp0) REVERT: Q 164 MET cc_start: 0.8182 (OUTLIER) cc_final: 0.7862 (ttm) REVERT: Q 176 SER cc_start: 0.8621 (p) cc_final: 0.8253 (t) REVERT: Q 288 GLU cc_start: 0.7366 (mp0) cc_final: 0.7120 (mp0) REVERT: Q 297 LYS cc_start: 0.8513 (mmtt) cc_final: 0.8017 (mmtm) REVERT: Q 300 MET cc_start: 0.7767 (mmt) cc_final: 0.6664 (mtt) REVERT: Q 306 ARG cc_start: 0.8021 (mtt180) cc_final: 0.7677 (mtt180) REVERT: Q 336 LYS cc_start: 0.8037 (mmtm) cc_final: 0.7709 (mmtt) outliers start: 52 outliers final: 41 residues processed: 185 average time/residue: 0.2870 time to fit residues: 74.4310 Evaluate side-chains 186 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 141 time to evaluate : 1.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain A residue 417 GLU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain I residue 3 GLU Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain I residue 234 ILE Chi-restraints excluded: chain I residue 239 THR Chi-restraints excluded: chain I residue 253 THR Chi-restraints excluded: chain I residue 285 GLN Chi-restraints excluded: chain I residue 291 ILE Chi-restraints excluded: chain I residue 328 VAL Chi-restraints excluded: chain I residue 378 LEU Chi-restraints excluded: chain Q residue 31 ASP Chi-restraints excluded: chain Q residue 41 ASP Chi-restraints excluded: chain Q residue 55 THR Chi-restraints excluded: chain Q residue 66 VAL Chi-restraints excluded: chain Q residue 88 ASP Chi-restraints excluded: chain Q residue 125 GLU Chi-restraints excluded: chain Q residue 138 SER Chi-restraints excluded: chain Q residue 164 MET Chi-restraints excluded: chain Q residue 199 THR Chi-restraints excluded: chain Q residue 275 SER Chi-restraints excluded: chain Q residue 365 VAL Chi-restraints excluded: chain Q residue 386 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 55 optimal weight: 2.9990 chunk 147 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 96 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 164 optimal weight: 0.6980 chunk 136 optimal weight: 0.8980 chunk 76 optimal weight: 0.0370 chunk 13 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 86 optimal weight: 0.9990 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 309 HIS B 8 GLN ** I 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.4193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13939 Z= 0.268 Angle : 0.532 8.623 18948 Z= 0.279 Chirality : 0.044 0.235 2078 Planarity : 0.004 0.051 2467 Dihedral : 10.904 166.508 1969 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.92 % Allowed : 14.43 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 (0.20), residues: 1720 helix: 0.80 (0.19), residues: 774 sheet: 0.05 (0.30), residues: 272 loop : -0.80 (0.23), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 21 HIS 0.005 0.001 HIS Q 396 PHE 0.026 0.001 PHE B 20 TYR 0.011 0.001 TYR Q 425 ARG 0.006 0.000 ARG A 308 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 149 time to evaluate : 1.449 Fit side-chains REVERT: A 120 ASP cc_start: 0.7060 (m-30) cc_final: 0.6416 (m-30) REVERT: A 163 LYS cc_start: 0.8869 (tmtt) cc_final: 0.8283 (mmtm) REVERT: A 290 GLU cc_start: 0.8197 (mp0) cc_final: 0.7718 (mp0) REVERT: A 358 GLN cc_start: 0.8351 (tp40) cc_final: 0.7953 (mm-40) REVERT: A 432 TYR cc_start: 0.7526 (OUTLIER) cc_final: 0.6148 (t80) REVERT: B 111 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.8067 (mp0) REVERT: B 307 HIS cc_start: 0.7584 (m170) cc_final: 0.7172 (m90) REVERT: B 394 PHE cc_start: 0.4995 (OUTLIER) cc_final: 0.4634 (t80) REVERT: B 403 MET cc_start: 0.8575 (mtp) cc_final: 0.8358 (ttt) REVERT: B 406 MET cc_start: 0.7195 (mpp) cc_final: 0.6306 (mpp) REVERT: B 414 ASN cc_start: 0.8441 (m110) cc_final: 0.8205 (m110) REVERT: I 1 MET cc_start: 0.6587 (tpp) cc_final: 0.5950 (tpt) REVERT: I 18 ASN cc_start: 0.6756 (m110) cc_final: 0.6449 (m-40) REVERT: I 114 ILE cc_start: 0.7807 (mm) cc_final: 0.7356 (tt) REVERT: I 128 GLN cc_start: 0.6488 (tt0) cc_final: 0.6131 (mp10) REVERT: I 150 THR cc_start: 0.7925 (m) cc_final: 0.7650 (t) REVERT: I 205 ASP cc_start: 0.7715 (t0) cc_final: 0.7076 (t0) REVERT: I 213 CYS cc_start: 0.7105 (t) cc_final: 0.6652 (m) REVERT: I 214 ARG cc_start: 0.7220 (ttm-80) cc_final: 0.6626 (ttp80) REVERT: I 309 HIS cc_start: 0.7646 (m-70) cc_final: 0.7244 (m-70) REVERT: I 341 ILE cc_start: 0.6504 (OUTLIER) cc_final: 0.6162 (mp) REVERT: I 414 GLU cc_start: 0.7757 (mt-10) cc_final: 0.7418 (mt-10) REVERT: Q 125 GLU cc_start: 0.7261 (OUTLIER) cc_final: 0.6537 (mp0) REVERT: Q 164 MET cc_start: 0.8126 (OUTLIER) cc_final: 0.7809 (ttm) REVERT: Q 176 SER cc_start: 0.8473 (p) cc_final: 0.8081 (t) REVERT: Q 288 GLU cc_start: 0.7341 (mp0) cc_final: 0.7106 (mp0) REVERT: Q 297 LYS cc_start: 0.8420 (mmtt) cc_final: 0.7826 (mmtm) REVERT: Q 300 MET cc_start: 0.7837 (OUTLIER) cc_final: 0.6877 (mtt) REVERT: Q 306 ARG cc_start: 0.8069 (mtt180) cc_final: 0.7732 (mtt180) REVERT: Q 320 ARG cc_start: 0.8097 (tpp80) cc_final: 0.7707 (mtp85) REVERT: Q 336 LYS cc_start: 0.7995 (mmtm) cc_final: 0.7770 (mmtt) outliers start: 57 outliers final: 40 residues processed: 194 average time/residue: 0.2964 time to fit residues: 80.5194 Evaluate side-chains 192 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 145 time to evaluate : 1.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain A residue 417 GLU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain I residue 3 GLU Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain I residue 234 ILE Chi-restraints excluded: chain I residue 239 THR Chi-restraints excluded: chain I residue 253 THR Chi-restraints excluded: chain I residue 285 GLN Chi-restraints excluded: chain I residue 291 ILE Chi-restraints excluded: chain I residue 328 VAL Chi-restraints excluded: chain I residue 341 ILE Chi-restraints excluded: chain I residue 378 LEU Chi-restraints excluded: chain Q residue 31 ASP Chi-restraints excluded: chain Q residue 55 THR Chi-restraints excluded: chain Q residue 66 VAL Chi-restraints excluded: chain Q residue 88 ASP Chi-restraints excluded: chain Q residue 125 GLU Chi-restraints excluded: chain Q residue 138 SER Chi-restraints excluded: chain Q residue 164 MET Chi-restraints excluded: chain Q residue 199 THR Chi-restraints excluded: chain Q residue 275 SER Chi-restraints excluded: chain Q residue 300 MET Chi-restraints excluded: chain Q residue 312 THR Chi-restraints excluded: chain Q residue 365 VAL Chi-restraints excluded: chain Q residue 386 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 158 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 93 optimal weight: 0.6980 chunk 120 optimal weight: 0.5980 chunk 138 optimal weight: 0.9990 chunk 91 optimal weight: 0.8980 chunk 163 optimal weight: 0.9980 chunk 102 optimal weight: 0.9980 chunk 99 optimal weight: 0.9990 chunk 75 optimal weight: 0.0070 chunk 101 optimal weight: 0.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 309 HIS ** I 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.4307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13939 Z= 0.255 Angle : 0.523 6.878 18948 Z= 0.275 Chirality : 0.044 0.240 2078 Planarity : 0.004 0.051 2467 Dihedral : 10.861 166.275 1969 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 4.12 % Allowed : 13.75 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.06 (0.20), residues: 1720 helix: 0.83 (0.19), residues: 774 sheet: 0.01 (0.30), residues: 272 loop : -0.78 (0.23), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 21 HIS 0.005 0.001 HIS Q 396 PHE 0.025 0.001 PHE B 20 TYR 0.011 0.001 TYR Q 425 ARG 0.006 0.000 ARG A 308 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 151 time to evaluate : 1.598 Fit side-chains REVERT: A 120 ASP cc_start: 0.7060 (m-30) cc_final: 0.6414 (m-30) REVERT: A 163 LYS cc_start: 0.8872 (tmtt) cc_final: 0.8275 (mmtm) REVERT: A 290 GLU cc_start: 0.8196 (mp0) cc_final: 0.7703 (mp0) REVERT: A 358 GLN cc_start: 0.8362 (tp40) cc_final: 0.7923 (mm-40) REVERT: A 432 TYR cc_start: 0.7427 (OUTLIER) cc_final: 0.6047 (t80) REVERT: B 111 GLU cc_start: 0.8688 (OUTLIER) cc_final: 0.8057 (mp0) REVERT: B 203 ASP cc_start: 0.6830 (t0) cc_final: 0.6353 (t0) REVERT: B 307 HIS cc_start: 0.7548 (m170) cc_final: 0.7134 (m90) REVERT: B 394 PHE cc_start: 0.4958 (OUTLIER) cc_final: 0.4612 (t80) REVERT: B 414 ASN cc_start: 0.8440 (m110) cc_final: 0.8180 (m110) REVERT: I 1 MET cc_start: 0.6495 (tpp) cc_final: 0.5801 (tpt) REVERT: I 18 ASN cc_start: 0.6726 (m110) cc_final: 0.6414 (m-40) REVERT: I 114 ILE cc_start: 0.7809 (mm) cc_final: 0.7342 (tt) REVERT: I 128 GLN cc_start: 0.6442 (tt0) cc_final: 0.6091 (mp10) REVERT: I 150 THR cc_start: 0.7919 (m) cc_final: 0.7650 (t) REVERT: I 213 CYS cc_start: 0.7109 (t) cc_final: 0.6647 (m) REVERT: I 214 ARG cc_start: 0.7306 (ttm-80) cc_final: 0.6691 (ttp80) REVERT: I 309 HIS cc_start: 0.7654 (m-70) cc_final: 0.7270 (m-70) REVERT: I 341 ILE cc_start: 0.6480 (OUTLIER) cc_final: 0.6141 (mp) REVERT: I 414 GLU cc_start: 0.7802 (mt-10) cc_final: 0.7453 (mt-10) REVERT: Q 125 GLU cc_start: 0.7273 (OUTLIER) cc_final: 0.6559 (mp0) REVERT: Q 164 MET cc_start: 0.8219 (OUTLIER) cc_final: 0.7780 (ttm) REVERT: Q 176 SER cc_start: 0.8451 (p) cc_final: 0.8068 (t) REVERT: Q 211 CYS cc_start: 0.8309 (m) cc_final: 0.7943 (m) REVERT: Q 288 GLU cc_start: 0.7341 (mp0) cc_final: 0.7109 (mp0) REVERT: Q 297 LYS cc_start: 0.8416 (mmtt) cc_final: 0.7803 (mmtm) REVERT: Q 300 MET cc_start: 0.7815 (OUTLIER) cc_final: 0.6891 (mtt) REVERT: Q 306 ARG cc_start: 0.8105 (mtt180) cc_final: 0.7777 (mtt180) REVERT: Q 307 HIS cc_start: 0.7136 (m-70) cc_final: 0.6913 (m170) REVERT: Q 320 ARG cc_start: 0.8081 (tpp80) cc_final: 0.7708 (mtp85) REVERT: Q 336 LYS cc_start: 0.7987 (mmtm) cc_final: 0.7759 (mmtt) outliers start: 60 outliers final: 45 residues processed: 197 average time/residue: 0.2889 time to fit residues: 80.6183 Evaluate side-chains 201 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 149 time to evaluate : 1.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 417 GLU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain I residue 3 GLU Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain I residue 234 ILE Chi-restraints excluded: chain I residue 239 THR Chi-restraints excluded: chain I residue 253 THR Chi-restraints excluded: chain I residue 285 GLN Chi-restraints excluded: chain I residue 291 ILE Chi-restraints excluded: chain I residue 304 LYS Chi-restraints excluded: chain I residue 328 VAL Chi-restraints excluded: chain I residue 341 ILE Chi-restraints excluded: chain I residue 378 LEU Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 31 ASP Chi-restraints excluded: chain Q residue 41 ASP Chi-restraints excluded: chain Q residue 55 THR Chi-restraints excluded: chain Q residue 66 VAL Chi-restraints excluded: chain Q residue 88 ASP Chi-restraints excluded: chain Q residue 125 GLU Chi-restraints excluded: chain Q residue 138 SER Chi-restraints excluded: chain Q residue 164 MET Chi-restraints excluded: chain Q residue 199 THR Chi-restraints excluded: chain Q residue 219 THR Chi-restraints excluded: chain Q residue 275 SER Chi-restraints excluded: chain Q residue 300 MET Chi-restraints excluded: chain Q residue 312 THR Chi-restraints excluded: chain Q residue 365 VAL Chi-restraints excluded: chain Q residue 386 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 1.9990 chunk 97 optimal weight: 0.5980 chunk 49 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 104 optimal weight: 0.8980 chunk 111 optimal weight: 0.8980 chunk 81 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 128 optimal weight: 0.9980 chunk 149 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN A 309 HIS B 8 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.4452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 13939 Z= 0.321 Angle : 0.565 7.203 18948 Z= 0.296 Chirality : 0.045 0.274 2078 Planarity : 0.005 0.050 2467 Dihedral : 11.023 167.011 1969 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 4.40 % Allowed : 13.40 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.10 (0.20), residues: 1720 helix: 0.71 (0.19), residues: 772 sheet: -0.08 (0.31), residues: 272 loop : -0.87 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 21 HIS 0.006 0.001 HIS Q 396 PHE 0.024 0.002 PHE B 20 TYR 0.013 0.001 TYR Q 425 ARG 0.007 0.000 ARG A 308 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 153 time to evaluate : 1.280 Fit side-chains revert: symmetry clash REVERT: A 120 ASP cc_start: 0.7069 (m-30) cc_final: 0.6420 (m-30) REVERT: A 163 LYS cc_start: 0.8861 (tmtt) cc_final: 0.8261 (mmtm) REVERT: A 290 GLU cc_start: 0.8209 (mp0) cc_final: 0.7688 (mp0) REVERT: A 425 MET cc_start: 0.7967 (tpt) cc_final: 0.7696 (tpt) REVERT: A 432 TYR cc_start: 0.7447 (OUTLIER) cc_final: 0.6126 (t80) REVERT: B 108 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7709 (mm-30) REVERT: B 111 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.7968 (mp0) REVERT: B 203 ASP cc_start: 0.6958 (t0) cc_final: 0.6502 (t0) REVERT: B 307 HIS cc_start: 0.7529 (m170) cc_final: 0.7137 (m90) REVERT: B 394 PHE cc_start: 0.5056 (OUTLIER) cc_final: 0.4702 (t80) REVERT: B 414 ASN cc_start: 0.8467 (m110) cc_final: 0.8261 (m-40) REVERT: I 1 MET cc_start: 0.6582 (tpp) cc_final: 0.5876 (tpt) REVERT: I 18 ASN cc_start: 0.6771 (m110) cc_final: 0.6469 (m-40) REVERT: I 114 ILE cc_start: 0.7887 (mm) cc_final: 0.7425 (tt) REVERT: I 128 GLN cc_start: 0.6611 (tt0) cc_final: 0.6339 (mp10) REVERT: I 150 THR cc_start: 0.7946 (m) cc_final: 0.7674 (t) REVERT: I 205 ASP cc_start: 0.7743 (t0) cc_final: 0.7295 (t0) REVERT: I 213 CYS cc_start: 0.7162 (t) cc_final: 0.6673 (m) REVERT: I 214 ARG cc_start: 0.7291 (ttm-80) cc_final: 0.6674 (ttp80) REVERT: I 227 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7450 (mt) REVERT: I 309 HIS cc_start: 0.7664 (m-70) cc_final: 0.7279 (m-70) REVERT: I 341 ILE cc_start: 0.6470 (OUTLIER) cc_final: 0.6131 (mp) REVERT: I 414 GLU cc_start: 0.7837 (mt-10) cc_final: 0.7476 (mt-10) REVERT: Q 125 GLU cc_start: 0.7255 (OUTLIER) cc_final: 0.6565 (mp0) REVERT: Q 164 MET cc_start: 0.8189 (OUTLIER) cc_final: 0.7917 (ttm) REVERT: Q 176 SER cc_start: 0.8459 (p) cc_final: 0.8068 (t) REVERT: Q 288 GLU cc_start: 0.7336 (mp0) cc_final: 0.7105 (mp0) REVERT: Q 297 LYS cc_start: 0.8465 (mmtt) cc_final: 0.7887 (mmtm) REVERT: Q 300 MET cc_start: 0.7987 (OUTLIER) cc_final: 0.7059 (mtt) REVERT: Q 306 ARG cc_start: 0.8092 (mtt180) cc_final: 0.7723 (mtt180) REVERT: Q 307 HIS cc_start: 0.7124 (m-70) cc_final: 0.6885 (m170) REVERT: Q 336 LYS cc_start: 0.7986 (mmtm) cc_final: 0.7747 (mmtt) outliers start: 64 outliers final: 48 residues processed: 203 average time/residue: 0.2724 time to fit residues: 78.7307 Evaluate side-chains 206 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 150 time to evaluate : 1.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 356 ASN Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 417 GLU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 410 GLU Chi-restraints excluded: chain I residue 3 GLU Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 234 ILE Chi-restraints excluded: chain I residue 239 THR Chi-restraints excluded: chain I residue 253 THR Chi-restraints excluded: chain I residue 285 GLN Chi-restraints excluded: chain I residue 291 ILE Chi-restraints excluded: chain I residue 304 LYS Chi-restraints excluded: chain I residue 328 VAL Chi-restraints excluded: chain I residue 341 ILE Chi-restraints excluded: chain I residue 378 LEU Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 31 ASP Chi-restraints excluded: chain Q residue 41 ASP Chi-restraints excluded: chain Q residue 55 THR Chi-restraints excluded: chain Q residue 66 VAL Chi-restraints excluded: chain Q residue 88 ASP Chi-restraints excluded: chain Q residue 125 GLU Chi-restraints excluded: chain Q residue 138 SER Chi-restraints excluded: chain Q residue 164 MET Chi-restraints excluded: chain Q residue 190 HIS Chi-restraints excluded: chain Q residue 219 THR Chi-restraints excluded: chain Q residue 275 SER Chi-restraints excluded: chain Q residue 300 MET Chi-restraints excluded: chain Q residue 365 VAL Chi-restraints excluded: chain Q residue 386 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 156 optimal weight: 0.8980 chunk 143 optimal weight: 0.3980 chunk 152 optimal weight: 0.5980 chunk 91 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 137 optimal weight: 0.5980 chunk 144 optimal weight: 0.9990 chunk 100 optimal weight: 0.5980 chunk 161 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 HIS B 6 HIS B 8 GLN ** I 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.4474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13939 Z= 0.246 Angle : 0.521 7.115 18948 Z= 0.274 Chirality : 0.044 0.258 2078 Planarity : 0.004 0.051 2467 Dihedral : 10.882 167.308 1969 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.99 % Allowed : 14.09 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.03 (0.20), residues: 1720 helix: 0.80 (0.19), residues: 772 sheet: -0.09 (0.31), residues: 272 loop : -0.87 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 21 HIS 0.005 0.001 HIS Q 396 PHE 0.023 0.001 PHE B 20 TYR 0.010 0.001 TYR Q 425 ARG 0.006 0.000 ARG A 308 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 151 time to evaluate : 1.670 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 ASP cc_start: 0.7064 (m-30) cc_final: 0.6415 (m-30) REVERT: A 163 LYS cc_start: 0.8850 (tmtt) cc_final: 0.8259 (mmtm) REVERT: A 290 GLU cc_start: 0.8215 (mp0) cc_final: 0.7696 (mp0) REVERT: A 425 MET cc_start: 0.8047 (tpt) cc_final: 0.7738 (tpt) REVERT: A 432 TYR cc_start: 0.7421 (OUTLIER) cc_final: 0.6051 (t80) REVERT: B 108 GLU cc_start: 0.8119 (mm-30) cc_final: 0.7689 (mm-30) REVERT: B 111 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.7974 (mp0) REVERT: B 203 ASP cc_start: 0.6952 (t0) cc_final: 0.6518 (t0) REVERT: B 394 PHE cc_start: 0.4962 (OUTLIER) cc_final: 0.4612 (t80) REVERT: I 18 ASN cc_start: 0.6698 (m110) cc_final: 0.6380 (m-40) REVERT: I 114 ILE cc_start: 0.7814 (mm) cc_final: 0.7363 (tt) REVERT: I 128 GLN cc_start: 0.6533 (tt0) cc_final: 0.6307 (mp10) REVERT: I 150 THR cc_start: 0.7936 (m) cc_final: 0.7659 (t) REVERT: I 205 ASP cc_start: 0.7681 (t0) cc_final: 0.7229 (t0) REVERT: I 213 CYS cc_start: 0.7119 (t) cc_final: 0.6630 (m) REVERT: I 214 ARG cc_start: 0.7328 (ttm-80) cc_final: 0.6742 (ttp80) REVERT: I 227 LEU cc_start: 0.7704 (OUTLIER) cc_final: 0.7288 (mt) REVERT: I 309 HIS cc_start: 0.7654 (m-70) cc_final: 0.7283 (m-70) REVERT: I 341 ILE cc_start: 0.6472 (OUTLIER) cc_final: 0.6141 (mp) REVERT: I 414 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7476 (mt-10) REVERT: Q 125 GLU cc_start: 0.7268 (OUTLIER) cc_final: 0.6555 (mp0) REVERT: Q 164 MET cc_start: 0.8235 (OUTLIER) cc_final: 0.7964 (ttm) REVERT: Q 176 SER cc_start: 0.8442 (p) cc_final: 0.8065 (t) REVERT: Q 288 GLU cc_start: 0.7325 (mp0) cc_final: 0.7108 (mp0) REVERT: Q 297 LYS cc_start: 0.8409 (mmtt) cc_final: 0.7820 (mmtm) REVERT: Q 300 MET cc_start: 0.7961 (OUTLIER) cc_final: 0.7058 (mtt) REVERT: Q 306 ARG cc_start: 0.8131 (mtt180) cc_final: 0.7787 (mtt180) REVERT: Q 336 LYS cc_start: 0.7987 (mmtm) cc_final: 0.7745 (mmtt) outliers start: 58 outliers final: 46 residues processed: 195 average time/residue: 0.2829 time to fit residues: 78.4116 Evaluate side-chains 200 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 146 time to evaluate : 1.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain A residue 417 GLU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 410 GLU Chi-restraints excluded: chain I residue 3 GLU Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain I residue 204 VAL Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 234 ILE Chi-restraints excluded: chain I residue 239 THR Chi-restraints excluded: chain I residue 253 THR Chi-restraints excluded: chain I residue 285 GLN Chi-restraints excluded: chain I residue 291 ILE Chi-restraints excluded: chain I residue 304 LYS Chi-restraints excluded: chain I residue 328 VAL Chi-restraints excluded: chain I residue 341 ILE Chi-restraints excluded: chain I residue 378 LEU Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 31 ASP Chi-restraints excluded: chain Q residue 41 ASP Chi-restraints excluded: chain Q residue 55 THR Chi-restraints excluded: chain Q residue 66 VAL Chi-restraints excluded: chain Q residue 88 ASP Chi-restraints excluded: chain Q residue 125 GLU Chi-restraints excluded: chain Q residue 138 SER Chi-restraints excluded: chain Q residue 164 MET Chi-restraints excluded: chain Q residue 219 THR Chi-restraints excluded: chain Q residue 275 SER Chi-restraints excluded: chain Q residue 300 MET Chi-restraints excluded: chain Q residue 312 THR Chi-restraints excluded: chain Q residue 365 VAL Chi-restraints excluded: chain Q residue 386 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 0.2980 chunk 76 optimal weight: 0.2980 chunk 112 optimal weight: 1.9990 chunk 169 optimal weight: 0.9990 chunk 155 optimal weight: 1.9990 chunk 134 optimal weight: 0.1980 chunk 14 optimal weight: 0.9980 chunk 104 optimal weight: 0.8980 chunk 82 optimal weight: 0.1980 chunk 107 optimal weight: 0.6980 chunk 143 optimal weight: 0.5980 overall best weight: 0.3180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 HIS ** I 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.4462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13939 Z= 0.171 Angle : 0.489 8.954 18948 Z= 0.254 Chirality : 0.042 0.206 2078 Planarity : 0.004 0.054 2467 Dihedral : 10.502 165.008 1969 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.82 % Allowed : 15.74 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.15 (0.20), residues: 1720 helix: 0.99 (0.19), residues: 766 sheet: 0.02 (0.30), residues: 272 loop : -0.82 (0.22), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP I 21 HIS 0.004 0.001 HIS Q 396 PHE 0.023 0.001 PHE B 20 TYR 0.008 0.001 TYR I 24 ARG 0.007 0.000 ARG A 215 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 157 time to evaluate : 1.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 ASP cc_start: 0.7038 (m-30) cc_final: 0.6382 (m-30) REVERT: A 163 LYS cc_start: 0.8878 (tmtt) cc_final: 0.8181 (mmtm) REVERT: A 425 MET cc_start: 0.8115 (tpt) cc_final: 0.7860 (tpt) REVERT: A 432 TYR cc_start: 0.7361 (OUTLIER) cc_final: 0.6099 (t80) REVERT: B 203 ASP cc_start: 0.6820 (t0) cc_final: 0.6379 (t0) REVERT: B 394 PHE cc_start: 0.4819 (OUTLIER) cc_final: 0.4490 (t80) REVERT: I 114 ILE cc_start: 0.7734 (mm) cc_final: 0.7309 (tt) REVERT: I 128 GLN cc_start: 0.6210 (tt0) cc_final: 0.5953 (mp10) REVERT: I 150 THR cc_start: 0.7899 (m) cc_final: 0.7666 (t) REVERT: I 205 ASP cc_start: 0.7640 (t0) cc_final: 0.7049 (t0) REVERT: I 213 CYS cc_start: 0.7017 (t) cc_final: 0.6618 (m) REVERT: I 214 ARG cc_start: 0.7308 (ttm-80) cc_final: 0.6844 (ttp80) REVERT: I 227 LEU cc_start: 0.7684 (OUTLIER) cc_final: 0.7322 (mt) REVERT: I 254 GLU cc_start: 0.3556 (mm-30) cc_final: 0.3208 (mm-30) REVERT: I 309 HIS cc_start: 0.7618 (m-70) cc_final: 0.7285 (m-70) REVERT: I 414 GLU cc_start: 0.7792 (mt-10) cc_final: 0.7454 (mt-10) REVERT: Q 125 GLU cc_start: 0.7260 (OUTLIER) cc_final: 0.6520 (mp0) REVERT: Q 163 ILE cc_start: 0.8199 (mt) cc_final: 0.7770 (pt) REVERT: Q 176 SER cc_start: 0.8433 (p) cc_final: 0.8043 (t) REVERT: Q 211 CYS cc_start: 0.8297 (m) cc_final: 0.7964 (m) REVERT: Q 297 LYS cc_start: 0.8420 (mmtt) cc_final: 0.7815 (mmtm) REVERT: Q 300 MET cc_start: 0.7735 (mmt) cc_final: 0.6976 (mtt) REVERT: Q 306 ARG cc_start: 0.7978 (mtt180) cc_final: 0.7714 (mtt180) REVERT: Q 336 LYS cc_start: 0.7971 (mmtm) cc_final: 0.7767 (mmtt) outliers start: 41 outliers final: 32 residues processed: 193 average time/residue: 0.3050 time to fit residues: 82.8182 Evaluate side-chains 184 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 148 time to evaluate : 1.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain A residue 417 GLU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 410 GLU Chi-restraints excluded: chain I residue 3 GLU Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 234 ILE Chi-restraints excluded: chain I residue 239 THR Chi-restraints excluded: chain I residue 285 GLN Chi-restraints excluded: chain I residue 291 ILE Chi-restraints excluded: chain I residue 304 LYS Chi-restraints excluded: chain I residue 328 VAL Chi-restraints excluded: chain Q residue 31 ASP Chi-restraints excluded: chain Q residue 66 VAL Chi-restraints excluded: chain Q residue 88 ASP Chi-restraints excluded: chain Q residue 125 GLU Chi-restraints excluded: chain Q residue 138 SER Chi-restraints excluded: chain Q residue 365 VAL Chi-restraints excluded: chain Q residue 386 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 41 optimal weight: 0.8980 chunk 124 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 24 optimal weight: 0.0870 chunk 118 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 HIS A 309 HIS B 6 HIS ** I 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.096172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.080199 restraints weight = 20285.568| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 2.16 r_work: 0.3013 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.4531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13939 Z= 0.276 Angle : 0.540 8.363 18948 Z= 0.282 Chirality : 0.044 0.210 2078 Planarity : 0.005 0.051 2467 Dihedral : 10.689 164.430 1969 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.89 % Allowed : 15.53 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 (0.20), residues: 1720 helix: 0.89 (0.19), residues: 760 sheet: -0.05 (0.31), residues: 272 loop : -0.91 (0.22), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 21 HIS 0.006 0.001 HIS Q 307 PHE 0.023 0.001 PHE B 20 TYR 0.011 0.001 TYR Q 425 ARG 0.008 0.000 ARG A 308 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3373.18 seconds wall clock time: 61 minutes 5.19 seconds (3665.19 seconds total)