Starting phenix.real_space_refine on Sun Feb 18 02:04:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6f0x_4166/02_2024/6f0x_4166_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6f0x_4166/02_2024/6f0x_4166.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6f0x_4166/02_2024/6f0x_4166.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6f0x_4166/02_2024/6f0x_4166.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6f0x_4166/02_2024/6f0x_4166_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6f0x_4166/02_2024/6f0x_4166_neut_updated.pdb" } resolution = 4.6 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= 0.003 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 15 5.49 5 S 69 5.16 5 C 13043 2.51 5 N 3511 2.21 5 O 3812 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 261": "NH1" <-> "NH2" Residue "P PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 144": "NH1" <-> "NH2" Residue "P ARG 192": "NH1" <-> "NH2" Residue "P ARG 219": "NH1" <-> "NH2" Residue "Z ARG 35": "NH1" <-> "NH2" Residue "Z ARG 99": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 20450 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2410 Classifications: {'peptide': 308} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 9, 'TRANS': 298} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "B" Number of atoms: 3097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3097 Classifications: {'peptide': 398} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 11, 'TRANS': 386} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 5, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "C" Number of atoms: 3077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3077 Classifications: {'peptide': 398} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 11, 'TRANS': 386} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 109 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 6, 'HIS:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 49 Chain: "D" Number of atoms: 3118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3118 Classifications: {'peptide': 398} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 11, 'TRANS': 386} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 3, 'HIS:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 29 Chain: "E" Number of atoms: 3071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3071 Classifications: {'peptide': 398} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 11, 'TRANS': 386} Chain breaks: 2 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 117 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 6, 'HIS:plan': 1, 'ASN:plan1': 3, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 54 Chain: "F" Number of atoms: 2241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2241 Classifications: {'peptide': 282} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 274} Chain breaks: 4 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "P" Number of atoms: 1563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1563 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 14, 'TRANS': 179} Chain breaks: 3 Chain: "Q" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 70 Classifications: {'peptide': 9} Link IDs: {'PTRANS': 1, 'TRANS': 7} Chain: "Z" Number of atoms: 1648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1648 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 197} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.74, per 1000 atoms: 0.53 Number of scatterers: 20450 At special positions: 0 Unit cell: (145.86, 144.43, 147.29, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 69 16.00 P 15 15.00 O 3812 8.00 N 3511 7.00 C 13043 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS Z 79 " - pdb=" SG CYS Z 106 " distance=2.03 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 Atom "HETATM20319 O3B AGS A 901 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=13, symmetry=0 Number of additional bonds: simple=13, symmetry=0 Coordination: Other bonds: Time building additional restraints: 9.62 Conformation dependent library (CDL) restraints added in 3.9 seconds 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4978 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 93 helices and 15 sheets defined 42.9% alpha, 8.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.92 Creating SS restraints... Processing helix chain 'A' and resid 130 through 132 No H-bonds generated for 'chain 'A' and resid 130 through 132' Processing helix chain 'A' and resid 145 through 161 removed outlier: 4.313A pdb=" N SER A 160 " --> pdb=" O THR A 156 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ASP A 161 " --> pdb=" O LEU A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 200 Processing helix chain 'A' and resid 214 through 217 No H-bonds generated for 'chain 'A' and resid 214 through 217' Processing helix chain 'A' and resid 222 through 240 Processing helix chain 'A' and resid 254 through 257 No H-bonds generated for 'chain 'A' and resid 254 through 257' Processing helix chain 'A' and resid 274 through 289 Processing helix chain 'A' and resid 324 through 340 Processing helix chain 'A' and resid 353 through 358 Processing helix chain 'A' and resid 368 through 380 Processing helix chain 'A' and resid 385 through 397 Proline residue: A 392 - end of helix Processing helix chain 'A' and resid 409 through 427 Processing helix chain 'B' and resid 35 through 49 Processing helix chain 'B' and resid 64 through 69 Processing helix chain 'B' and resid 130 through 132 No H-bonds generated for 'chain 'B' and resid 130 through 132' Processing helix chain 'B' and resid 135 through 138 No H-bonds generated for 'chain 'B' and resid 135 through 138' Processing helix chain 'B' and resid 145 through 162 removed outlier: 3.748A pdb=" N VAL B 153 " --> pdb=" O LEU B 149 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU B 157 " --> pdb=" O VAL B 153 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N LEU B 158 " --> pdb=" O MET B 154 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N PHE B 159 " --> pdb=" O THR B 155 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER B 160 " --> pdb=" O THR B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 200 Processing helix chain 'B' and resid 214 through 217 Processing helix chain 'B' and resid 224 through 241 removed outlier: 3.748A pdb=" N LYS B 231 " --> pdb=" O LYS B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 261 removed outlier: 3.701A pdb=" N THR B 258 " --> pdb=" O GLU B 255 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N ALA B 259 " --> pdb=" O SER B 256 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N ALA B 260 " --> pdb=" O LEU B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 287 removed outlier: 4.587A pdb=" N ALA B 279 " --> pdb=" O ARG B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 304 No H-bonds generated for 'chain 'B' and resid 302 through 304' Processing helix chain 'B' and resid 308 through 311 No H-bonds generated for 'chain 'B' and resid 308 through 311' Processing helix chain 'B' and resid 324 through 340 Processing helix chain 'B' and resid 353 through 358 Processing helix chain 'B' and resid 368 through 378 Processing helix chain 'B' and resid 385 through 398 Proline residue: B 392 - end of helix Processing helix chain 'B' and resid 407 through 428 Processing helix chain 'C' and resid 35 through 49 Processing helix chain 'C' and resid 64 through 69 Processing helix chain 'C' and resid 130 through 132 No H-bonds generated for 'chain 'C' and resid 130 through 132' Processing helix chain 'C' and resid 135 through 137 No H-bonds generated for 'chain 'C' and resid 135 through 137' Processing helix chain 'C' and resid 145 through 162 removed outlier: 4.056A pdb=" N VAL C 153 " --> pdb=" O LEU C 149 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N MET C 154 " --> pdb=" O LEU C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 202 removed outlier: 3.557A pdb=" N SER C 201 " --> pdb=" O THR C 197 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N SER C 202 " --> pdb=" O ILE C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 217 No H-bonds generated for 'chain 'C' and resid 214 through 217' Processing helix chain 'C' and resid 224 through 241 removed outlier: 3.895A pdb=" N LYS C 231 " --> pdb=" O LYS C 227 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU C 239 " --> pdb=" O LYS C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 267 No H-bonds generated for 'chain 'C' and resid 265 through 267' Processing helix chain 'C' and resid 270 through 289 removed outlier: 4.495A pdb=" N ARG C 275 " --> pdb=" O SER C 271 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ARG C 289 " --> pdb=" O ASP C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 304 No H-bonds generated for 'chain 'C' and resid 302 through 304' Processing helix chain 'C' and resid 307 through 312 Processing helix chain 'C' and resid 324 through 340 Processing helix chain 'C' and resid 353 through 358 Processing helix chain 'C' and resid 365 through 380 removed outlier: 3.920A pdb=" N LEU C 369 " --> pdb=" O ASN C 365 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N SER C 370 " --> pdb=" O VAL C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 398 Proline residue: C 392 - end of helix Processing helix chain 'C' and resid 410 through 427 Processing helix chain 'D' and resid 35 through 49 Processing helix chain 'D' and resid 64 through 69 Processing helix chain 'D' and resid 145 through 160 removed outlier: 3.869A pdb=" N VAL D 153 " --> pdb=" O LEU D 149 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N MET D 154 " --> pdb=" O LEU D 150 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU D 157 " --> pdb=" O VAL D 153 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU D 158 " --> pdb=" O MET D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 199 Processing helix chain 'D' and resid 214 through 216 No H-bonds generated for 'chain 'D' and resid 214 through 216' Processing helix chain 'D' and resid 224 through 241 Processing helix chain 'D' and resid 254 through 258 Processing helix chain 'D' and resid 268 through 289 removed outlier: 4.489A pdb=" N ALA D 279 " --> pdb=" O ARG D 275 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N ARG D 289 " --> pdb=" O ASP D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 340 Processing helix chain 'D' and resid 353 through 358 Processing helix chain 'D' and resid 368 through 380 Processing helix chain 'D' and resid 385 through 399 Proline residue: D 392 - end of helix Processing helix chain 'D' and resid 410 through 428 Processing helix chain 'E' and resid 35 through 49 Processing helix chain 'E' and resid 64 through 69 Processing helix chain 'E' and resid 130 through 132 No H-bonds generated for 'chain 'E' and resid 130 through 132' Processing helix chain 'E' and resid 135 through 138 No H-bonds generated for 'chain 'E' and resid 135 through 138' Processing helix chain 'E' and resid 145 through 162 removed outlier: 3.668A pdb=" N VAL E 153 " --> pdb=" O LEU E 149 " (cutoff:3.500A) Processing helix chain 'E' and resid 185 through 198 Processing helix chain 'E' and resid 226 through 240 Processing helix chain 'E' and resid 254 through 256 No H-bonds generated for 'chain 'E' and resid 254 through 256' Processing helix chain 'E' and resid 271 through 286 Processing helix chain 'E' and resid 324 through 340 Processing helix chain 'E' and resid 353 through 358 Processing helix chain 'E' and resid 367 through 380 Processing helix chain 'E' and resid 385 through 388 No H-bonds generated for 'chain 'E' and resid 385 through 388' Processing helix chain 'E' and resid 391 through 399 Processing helix chain 'E' and resid 410 through 427 Processing helix chain 'F' and resid 130 through 132 No H-bonds generated for 'chain 'F' and resid 130 through 132' Processing helix chain 'F' and resid 145 through 162 removed outlier: 3.709A pdb=" N ASP F 151 " --> pdb=" O SER F 147 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N TYR F 152 " --> pdb=" O HIS F 148 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N VAL F 153 " --> pdb=" O LEU F 149 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU F 158 " --> pdb=" O MET F 154 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LYS F 162 " --> pdb=" O LEU F 158 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 199 Processing helix chain 'F' and resid 228 through 241 Processing helix chain 'F' and resid 255 through 258 Processing helix chain 'F' and resid 274 through 287 Processing helix chain 'F' and resid 324 through 338 Processing helix chain 'F' and resid 353 through 358 Processing helix chain 'F' and resid 367 through 378 Processing helix chain 'F' and resid 385 through 398 Proline residue: F 392 - end of helix Processing helix chain 'F' and resid 407 through 423 Processing helix chain 'P' and resid 67 through 83 Processing helix chain 'P' and resid 123 through 144 Processing helix chain 'P' and resid 183 through 196 Processing helix chain 'P' and resid 255 through 258 No H-bonds generated for 'chain 'P' and resid 255 through 258' Processing helix chain 'Z' and resid 13 through 34 Processing helix chain 'Z' and resid 59 through 77 Processing helix chain 'Z' and resid 108 through 111 Processing helix chain 'Z' and resid 121 through 140 removed outlier: 3.686A pdb=" N VAL Z 139 " --> pdb=" O ILE Z 135 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N THR Z 140 " --> pdb=" O THR Z 136 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 123 through 126 removed outlier: 3.504A pdb=" N GLN A 208 " --> pdb=" O LEU A 246 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU A 250 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N GLN A 317 " --> pdb=" O HIS A 178 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 72 through 75 removed outlier: 4.090A pdb=" N SER B 72 " --> pdb=" O HIS B 26 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER B 74 " --> pdb=" O GLU B 24 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU B 24 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN B 27 " --> pdb=" O PHE B 100 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 123 through 126 removed outlier: 3.732A pdb=" N PHE B 248 " --> pdb=" O GLN B 208 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ASP B 252 " --> pdb=" O ILE B 212 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR B 298 " --> pdb=" O ILE B 251 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLN B 253 " --> pdb=" O THR B 298 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ILE B 315 " --> pdb=" O LEU B 176 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N HIS B 178 " --> pdb=" O ILE B 315 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N GLN B 317 " --> pdb=" O HIS B 178 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 20 through 22 removed outlier: 5.965A pdb=" N THR C 94 " --> pdb=" O VAL C 21 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'C' and resid 25 through 27 Processing sheet with id= F, first strand: chain 'C' and resid 122 through 126 removed outlier: 3.579A pdb=" N ASN C 123 " --> pdb=" O GLU C 211 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 20 through 22 removed outlier: 6.107A pdb=" N THR D 94 " --> pdb=" O VAL D 21 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'D' and resid 99 through 101 removed outlier: 6.462A pdb=" N VAL D 25 " --> pdb=" O PHE D 100 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER D 74 " --> pdb=" O GLU D 24 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N HIS D 26 " --> pdb=" O SER D 72 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N SER D 72 " --> pdb=" O HIS D 26 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 122 through 126 removed outlier: 4.430A pdb=" N ILE D 212 " --> pdb=" O LEU D 250 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ILE D 315 " --> pdb=" O LEU D 176 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N HIS D 178 " --> pdb=" O ILE D 315 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N GLN D 317 " --> pdb=" O HIS D 178 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 123 through 126 Processing sheet with id= K, first strand: chain 'F' and resid 123 through 126 Processing sheet with id= L, first strand: chain 'F' and resid 249 through 251 Processing sheet with id= M, first strand: chain 'P' and resid 261 through 264 removed outlier: 3.778A pdb=" N ALA P 215 " --> pdb=" O PHE P 263 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N ARG P 149 " --> pdb=" O GLN P 216 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS P 240 " --> pdb=" O PHE P 164 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N GLU P 166 " --> pdb=" O LYS P 240 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N THR P 242 " --> pdb=" O GLU P 166 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ASP P 168 " --> pdb=" O THR P 242 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'Z' and resid 44 through 48 Processing sheet with id= O, first strand: chain 'Z' and resid 178 through 182 removed outlier: 7.624A pdb=" N LEU Z 97 " --> pdb=" O LYS Z 200 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE Z 88 " --> pdb=" O LEU Z 97 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ARG Z 99 " --> pdb=" O VAL Z 86 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N VAL Z 86 " --> pdb=" O ARG Z 99 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N GLN Z 101 " --> pdb=" O LEU Z 84 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU Z 84 " --> pdb=" O GLN Z 101 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ASP Z 103 " --> pdb=" O GLN Z 82 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N GLN Z 82 " --> pdb=" O ASP Z 103 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N TYR Z 156 " --> pdb=" O GLN Z 82 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N LEU Z 84 " --> pdb=" O LEU Z 154 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N LEU Z 154 " --> pdb=" O LEU Z 84 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N VAL Z 86 " --> pdb=" O ASP Z 152 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ASP Z 152 " --> pdb=" O VAL Z 86 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ILE Z 88 " --> pdb=" O SER Z 150 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N SER Z 150 " --> pdb=" O ILE Z 88 " (cutoff:3.500A) 825 hydrogen bonds defined for protein. 2361 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.14 Time building geometry restraints manager: 10.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 6830 1.36 - 1.51: 6079 1.51 - 1.65: 7801 1.65 - 1.80: 49 1.80 - 1.94: 50 Bond restraints: 20809 Sorted by residual: bond pdb=" CA ASP C 137 " pdb=" C ASP C 137 " ideal model delta sigma weight residual 1.523 1.454 0.069 1.80e-02 3.09e+03 1.47e+01 bond pdb=" O2B AGS A 901 " pdb=" PB AGS A 901 " ideal model delta sigma weight residual 1.531 1.474 0.057 1.60e-02 3.91e+03 1.28e+01 bond pdb=" O2B AGS D 901 " pdb=" PB AGS D 901 " ideal model delta sigma weight residual 1.531 1.475 0.056 1.60e-02 3.91e+03 1.24e+01 bond pdb=" O2A AGS E 901 " pdb=" PA AGS E 901 " ideal model delta sigma weight residual 1.531 1.475 0.056 1.60e-02 3.91e+03 1.21e+01 bond pdb=" O2A AGS A 901 " pdb=" PA AGS A 901 " ideal model delta sigma weight residual 1.531 1.478 0.053 1.60e-02 3.91e+03 1.10e+01 ... (remaining 20804 not shown) Histogram of bond angle deviations from ideal: 98.39 - 105.54: 337 105.54 - 112.69: 11868 112.69 - 119.85: 6476 119.85 - 127.00: 9337 127.00 - 134.15: 226 Bond angle restraints: 28244 Sorted by residual: angle pdb=" CA ALA C 130 " pdb=" C ALA C 130 " pdb=" O ALA C 130 " ideal model delta sigma weight residual 120.51 113.28 7.23 1.43e+00 4.89e-01 2.55e+01 angle pdb=" N GLU D 269 " pdb=" CA GLU D 269 " pdb=" C GLU D 269 " ideal model delta sigma weight residual 113.45 106.48 6.97 1.39e+00 5.18e-01 2.51e+01 angle pdb=" N GLY D 409 " pdb=" CA GLY D 409 " pdb=" C GLY D 409 " ideal model delta sigma weight residual 113.18 102.19 10.99 2.37e+00 1.78e-01 2.15e+01 angle pdb=" N ASN E 172 " pdb=" CA ASN E 172 " pdb=" C ASN E 172 " ideal model delta sigma weight residual 110.44 115.59 -5.15 1.20e+00 6.94e-01 1.85e+01 angle pdb=" N VAL A 310 " pdb=" CA VAL A 310 " pdb=" C VAL A 310 " ideal model delta sigma weight residual 113.00 107.62 5.38 1.30e+00 5.92e-01 1.71e+01 ... (remaining 28239 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.53: 12408 27.53 - 55.06: 184 55.06 - 82.59: 19 82.59 - 110.11: 1 110.11 - 137.64: 2 Dihedral angle restraints: 12614 sinusoidal: 5006 harmonic: 7608 Sorted by residual: dihedral pdb=" CA LEU D 127 " pdb=" C LEU D 127 " pdb=" N PRO D 128 " pdb=" CA PRO D 128 " ideal model delta harmonic sigma weight residual -180.00 -123.13 -56.87 0 5.00e+00 4.00e-02 1.29e+02 dihedral pdb=" CA LEU C 127 " pdb=" C LEU C 127 " pdb=" N PRO C 128 " pdb=" CA PRO C 128 " ideal model delta harmonic sigma weight residual -180.00 -124.97 -55.03 0 5.00e+00 4.00e-02 1.21e+02 dihedral pdb=" CA LEU F 127 " pdb=" C LEU F 127 " pdb=" N PRO F 128 " pdb=" CA PRO F 128 " ideal model delta harmonic sigma weight residual -180.00 -125.94 -54.06 0 5.00e+00 4.00e-02 1.17e+02 ... (remaining 12611 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.122: 3289 0.122 - 0.244: 75 0.244 - 0.366: 1 0.366 - 0.488: 0 0.488 - 0.610: 4 Chirality restraints: 3369 Sorted by residual: chirality pdb=" PB AGS B 901 " pdb=" O2B AGS B 901 " pdb=" O3A AGS B 901 " pdb=" O3B AGS B 901 " both_signs ideal model delta sigma weight residual True 3.18 2.57 0.61 2.00e-01 2.50e+01 9.30e+00 chirality pdb=" PB AGS D 901 " pdb=" O2B AGS D 901 " pdb=" O3A AGS D 901 " pdb=" O3B AGS D 901 " both_signs ideal model delta sigma weight residual True 3.18 2.58 0.60 2.00e-01 2.50e+01 9.00e+00 chirality pdb=" PB AGS E 901 " pdb=" O2B AGS E 901 " pdb=" O3A AGS E 901 " pdb=" O3B AGS E 901 " both_signs ideal model delta sigma weight residual True 3.18 2.60 0.58 2.00e-01 2.50e+01 8.39e+00 ... (remaining 3366 not shown) Planarity restraints: 3526 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 127 " 0.069 5.00e-02 4.00e+02 1.05e-01 1.77e+01 pdb=" N PRO D 128 " -0.182 5.00e-02 4.00e+02 pdb=" CA PRO D 128 " 0.057 5.00e-02 4.00e+02 pdb=" CD PRO D 128 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 127 " 0.063 5.00e-02 4.00e+02 9.59e-02 1.47e+01 pdb=" N PRO C 128 " -0.166 5.00e-02 4.00e+02 pdb=" CA PRO C 128 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO C 128 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU F 127 " 0.055 5.00e-02 4.00e+02 8.35e-02 1.11e+01 pdb=" N PRO F 128 " -0.144 5.00e-02 4.00e+02 pdb=" CA PRO F 128 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO F 128 " 0.045 5.00e-02 4.00e+02 ... (remaining 3523 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.49: 289 2.49 - 3.09: 17991 3.09 - 3.69: 32075 3.69 - 4.30: 47241 4.30 - 4.90: 71187 Nonbonded interactions: 168783 Sorted by model distance: nonbonded pdb=" NH1 ARG E 173 " pdb=" O LYS E 288 " model vdw 1.884 2.520 nonbonded pdb=" OE2 GLU B 24 " pdb=" NZ LYS B 195 " model vdw 1.902 2.520 nonbonded pdb=" OE2 GLU F 255 " pdb=" OG SER F 299 " model vdw 1.932 2.440 nonbonded pdb=" OD1 ASN D 103 " pdb=" NZ LYS P 229 " model vdw 1.955 2.520 nonbonded pdb=" OD2 ASP D 244 " pdb=" NH1 ARG P 233 " model vdw 1.983 2.520 ... (remaining 168778 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 122 through 216 or resid 227 through 261 or resid 272 thro \ ugh 345 or resid 347 through 424)) selection = (chain 'F' and (resid 122 through 260 or (resid 261 and (name N or name CA or na \ me C or name O or name CB )) or resid 272 through 305 or (resid 306 through 308 \ and (name N or name CA or name C or name O or name CB )) or resid 309 through 42 \ 4)) } ncs_group { reference = (chain 'B' and (resid 19 through 118 or (resid 119 through 122 and (name N or na \ me CA or name C or name O or name CB )) or resid 123 through 127 or (resid 128 t \ hrough 130 and (name N or name CA or name C or name O or name CB )) or resid 131 \ through 214 or (resid 215 and (name N or name CA or name C or name O or name CB \ )) or resid 216 through 261 or (resid 262 through 266 and (name N or name CA or \ name C or name O or name CB )) or (resid 267 through 273 and (name N or name CA \ or name C or name O or name CB )) or resid 274 through 313 or (resid 314 and (n \ ame N or name CA or name C or name O or name CB )) or resid 315 through 424 or ( \ resid 425 through 429 and (name N or name CA or name C or name O or name CB )) o \ r resid 901)) selection = (chain 'C' and (resid 19 through 127 or (resid 128 through 130 and (name N or na \ me CA or name C or name O or name CB )) or resid 131 through 261 or (resid 262 t \ hrough 266 and (name N or name CA or name C or name O or name CB )) or resid 267 \ through 424 or (resid 425 through 429 and (name N or name CA or name C or name \ O or name CB )) or resid 901)) selection = (chain 'D' and (resid 19 through 106 or (resid 107 through 122 and (name N or na \ me CA or name C or name O or name CB )) or resid 123 through 127 or (resid 128 t \ hrough 130 and (name N or name CA or name C or name O or name CB )) or resid 131 \ through 261 or (resid 262 through 266 and (name N or name CA or name C or name \ O or name CB )) or resid 267 through 313 or (resid 314 and (name N or name CA or \ name C or name O or name CB )) or resid 315 through 424 or (resid 425 through 4 \ 29 and (name N or name CA or name C or name O or name CB )) or resid 901)) selection = (chain 'E' and (resid 19 through 119 or (resid 120 through 122 and (name N or na \ me CA or name C or name O or name CB )) or resid 123 through 313 or (resid 314 a \ nd (name N or name CA or name C or name O or name CB )) or resid 315 through 429 \ or resid 901)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 2.100 Check model and map are aligned: 0.340 Set scattering table: 0.210 Process input model: 57.890 Find NCS groups from input model: 1.340 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 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 : 0.007 0.069 20809 Z= 0.447 Angle : 0.969 12.290 28244 Z= 0.517 Chirality : 0.054 0.610 3369 Planarity : 0.005 0.105 3526 Dihedral : 10.339 137.642 7633 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 34.29 Ramachandran Plot: Outliers : 0.51 % Allowed : 17.55 % Favored : 81.94 % Rotamer: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.17 % Twisted General : 0.20 % 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: -5.29 (0.13), residues: 2541 helix: -3.23 (0.10), residues: 1123 sheet: -3.01 (0.24), residues: 339 loop : -3.89 (0.16), residues: 1079 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP A 221 HIS 0.011 0.002 HIS B 178 PHE 0.030 0.003 PHE C 248 TYR 0.025 0.003 TYR C 141 ARG 0.020 0.001 ARG D 265 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 896 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 896 time to evaluate : 2.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 TRP cc_start: 0.7815 (m-90) cc_final: 0.7561 (m100) REVERT: A 137 ASP cc_start: 0.8938 (m-30) cc_final: 0.8434 (p0) REVERT: A 150 LEU cc_start: 0.9401 (tp) cc_final: 0.9079 (tp) REVERT: A 168 LEU cc_start: 0.9497 (mt) cc_final: 0.9282 (pt) REVERT: A 173 ARG cc_start: 0.6999 (mtt90) cc_final: 0.6383 (mpt-90) REVERT: A 200 LEU cc_start: 0.9230 (mt) cc_final: 0.8483 (tp) REVERT: A 233 PHE cc_start: 0.7608 (m-80) cc_final: 0.7221 (m-80) REVERT: A 250 LEU cc_start: 0.9672 (tp) cc_final: 0.9415 (tp) REVERT: A 327 ILE cc_start: 0.9475 (mt) cc_final: 0.8178 (mt) REVERT: A 335 LEU cc_start: 0.9518 (mt) cc_final: 0.9289 (mt) REVERT: A 354 ARG cc_start: 0.8617 (ttt180) cc_final: 0.8356 (tmm-80) REVERT: A 358 MET cc_start: 0.8330 (mtm) cc_final: 0.8121 (tmm) REVERT: A 375 ASP cc_start: 0.9390 (m-30) cc_final: 0.8584 (t0) REVERT: A 377 SER cc_start: 0.7557 (m) cc_final: 0.7335 (t) REVERT: A 393 PHE cc_start: 0.9098 (t80) cc_final: 0.8645 (t80) REVERT: A 398 LEU cc_start: 0.9198 (mt) cc_final: 0.8968 (mt) REVERT: A 399 TYR cc_start: 0.8290 (m-80) cc_final: 0.7985 (m-80) REVERT: A 424 GLU cc_start: 0.8801 (mt-10) cc_final: 0.8494 (mt-10) REVERT: B 68 ARG cc_start: 0.9061 (tpt90) cc_final: 0.8755 (tpt90) REVERT: B 105 ASP cc_start: 0.8605 (t0) cc_final: 0.8173 (p0) REVERT: B 135 LEU cc_start: 0.8932 (tp) cc_final: 0.8672 (tp) REVERT: B 146 LYS cc_start: 0.9073 (mtmt) cc_final: 0.8869 (mttp) REVERT: B 188 LEU cc_start: 0.9673 (tp) cc_final: 0.9418 (tp) REVERT: B 189 CYS cc_start: 0.9319 (m) cc_final: 0.9115 (m) REVERT: B 209 LEU cc_start: 0.9296 (tp) cc_final: 0.8732 (tp) REVERT: B 224 GLU cc_start: 0.8110 (tp30) cc_final: 0.7403 (tt0) REVERT: B 231 LYS cc_start: 0.8374 (mttt) cc_final: 0.7865 (tmtt) REVERT: B 244 ASP cc_start: 0.8036 (m-30) cc_final: 0.7642 (m-30) REVERT: B 281 LEU cc_start: 0.9495 (mt) cc_final: 0.8992 (mp) REVERT: B 296 LEU cc_start: 0.9047 (mt) cc_final: 0.8596 (mt) REVERT: B 327 ILE cc_start: 0.9673 (mt) cc_final: 0.9387 (mt) REVERT: B 329 LYS cc_start: 0.9156 (mttt) cc_final: 0.8776 (mtmm) REVERT: B 335 LEU cc_start: 0.9802 (mt) cc_final: 0.9547 (mt) REVERT: B 336 GLU cc_start: 0.9088 (mm-30) cc_final: 0.8758 (mm-30) REVERT: B 339 MET cc_start: 0.8246 (mtt) cc_final: 0.7964 (mmt) REVERT: B 399 TYR cc_start: 0.8851 (m-80) cc_final: 0.8613 (m-80) REVERT: B 408 GLU cc_start: 0.9028 (mp0) cc_final: 0.8740 (tm-30) REVERT: B 419 ASP cc_start: 0.9408 (m-30) cc_final: 0.8994 (m-30) REVERT: C 56 TYR cc_start: 0.6419 (t80) cc_final: 0.6095 (m-80) REVERT: C 58 TRP cc_start: 0.8736 (m-90) cc_final: 0.6818 (m-90) REVERT: C 98 HIS cc_start: 0.6773 (m-70) cc_final: 0.6524 (m-70) REVERT: C 102 LEU cc_start: 0.8945 (mt) cc_final: 0.8715 (mt) REVERT: C 135 LEU cc_start: 0.9488 (tp) cc_final: 0.9069 (tt) REVERT: C 192 LEU cc_start: 0.9702 (tp) cc_final: 0.9398 (tt) REVERT: C 196 LEU cc_start: 0.9592 (mt) cc_final: 0.9356 (mt) REVERT: C 209 LEU cc_start: 0.9208 (tp) cc_final: 0.8983 (tp) REVERT: C 211 GLU cc_start: 0.7446 (tp30) cc_final: 0.6991 (tp30) REVERT: C 224 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7406 (mm-30) REVERT: C 331 TYR cc_start: 0.9107 (m-10) cc_final: 0.8678 (m-10) REVERT: C 383 LEU cc_start: 0.8633 (mt) cc_final: 0.8432 (mt) REVERT: D 27 GLN cc_start: 0.9448 (tt0) cc_final: 0.9235 (tt0) REVERT: D 108 SER cc_start: 0.9228 (m) cc_final: 0.8964 (t) REVERT: D 135 LEU cc_start: 0.8275 (tp) cc_final: 0.8058 (mp) REVERT: D 136 TRP cc_start: 0.8749 (t-100) cc_final: 0.8518 (t60) REVERT: D 141 TYR cc_start: 0.8609 (m-80) cc_final: 0.8319 (m-80) REVERT: D 158 LEU cc_start: 0.9101 (tp) cc_final: 0.8537 (tt) REVERT: D 159 PHE cc_start: 0.7510 (m-80) cc_final: 0.6744 (m-80) REVERT: D 165 ASN cc_start: 0.8355 (t0) cc_final: 0.7671 (t0) REVERT: D 171 TRP cc_start: 0.8255 (p-90) cc_final: 0.7151 (p-90) REVERT: D 188 LEU cc_start: 0.9341 (tp) cc_final: 0.8905 (tp) REVERT: D 189 CYS cc_start: 0.9221 (m) cc_final: 0.9013 (m) REVERT: D 190 LYS cc_start: 0.9306 (mttt) cc_final: 0.9020 (mtmt) REVERT: D 192 LEU cc_start: 0.9624 (tp) cc_final: 0.9252 (tp) REVERT: D 196 LEU cc_start: 0.9787 (mt) cc_final: 0.9506 (mt) REVERT: D 208 GLN cc_start: 0.8337 (mm-40) cc_final: 0.7849 (mm-40) REVERT: D 209 LEU cc_start: 0.9165 (tp) cc_final: 0.8798 (tp) REVERT: D 211 GLU cc_start: 0.9092 (tt0) cc_final: 0.8651 (tt0) REVERT: D 224 GLU cc_start: 0.9026 (mm-30) cc_final: 0.8434 (tp30) REVERT: D 234 GLN cc_start: 0.9006 (tp40) cc_final: 0.8578 (tm-30) REVERT: D 248 PHE cc_start: 0.9539 (m-80) cc_final: 0.9214 (m-80) REVERT: D 281 LEU cc_start: 0.9309 (mt) cc_final: 0.9098 (mt) REVERT: D 283 GLN cc_start: 0.9498 (mm-40) cc_final: 0.8897 (mm-40) REVERT: D 286 GLN cc_start: 0.8274 (mt0) cc_final: 0.8012 (mt0) REVERT: D 329 LYS cc_start: 0.8935 (mttt) cc_final: 0.8599 (mmtt) REVERT: D 368 LYS cc_start: 0.9451 (tttt) cc_final: 0.9038 (ptmm) REVERT: D 391 LEU cc_start: 0.9553 (mt) cc_final: 0.9241 (mt) REVERT: D 396 HIS cc_start: 0.7845 (t-90) cc_final: 0.7542 (t-90) REVERT: D 423 GLU cc_start: 0.9255 (mt-10) cc_final: 0.8703 (mm-30) REVERT: D 424 GLU cc_start: 0.8650 (mt-10) cc_final: 0.8107 (mt-10) REVERT: E 24 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7437 (pp20) REVERT: E 27 GLN cc_start: 0.7751 (tt0) cc_final: 0.7035 (tt0) REVERT: E 58 TRP cc_start: 0.7376 (m-90) cc_final: 0.6396 (m-90) REVERT: E 62 ASP cc_start: 0.8195 (m-30) cc_final: 0.7696 (t0) REVERT: E 72 SER cc_start: 0.8136 (p) cc_final: 0.7491 (p) REVERT: E 125 TRP cc_start: 0.6709 (m-90) cc_final: 0.6315 (m-10) REVERT: E 148 HIS cc_start: 0.8484 (m170) cc_final: 0.8260 (m90) REVERT: E 154 MET cc_start: 0.8924 (tpt) cc_final: 0.8556 (ttm) REVERT: E 155 THR cc_start: 0.9589 (m) cc_final: 0.9254 (p) REVERT: E 167 ASN cc_start: 0.9572 (m-40) cc_final: 0.9320 (m110) REVERT: E 192 LEU cc_start: 0.9854 (tp) cc_final: 0.9639 (tp) REVERT: E 195 LYS cc_start: 0.9180 (tppt) cc_final: 0.8933 (tppt) REVERT: E 209 LEU cc_start: 0.8918 (tp) cc_final: 0.8362 (tp) REVERT: E 211 GLU cc_start: 0.7848 (tt0) cc_final: 0.7370 (tm-30) REVERT: E 212 ILE cc_start: 0.7496 (tt) cc_final: 0.7222 (tt) REVERT: E 254 VAL cc_start: 0.9572 (t) cc_final: 0.9360 (m) REVERT: E 316 LYS cc_start: 0.8365 (mttt) cc_final: 0.8102 (mttt) REVERT: E 328 PHE cc_start: 0.9183 (t80) cc_final: 0.8680 (t80) REVERT: E 339 MET cc_start: 0.7604 (mtt) cc_final: 0.7380 (mtm) REVERT: E 388 LEU cc_start: 0.9258 (mt) cc_final: 0.8940 (mt) REVERT: F 136 TRP cc_start: 0.7969 (t-100) cc_final: 0.7454 (t-100) REVERT: F 194 GLN cc_start: 0.8927 (tp40) cc_final: 0.8693 (tp40) REVERT: F 195 LYS cc_start: 0.8879 (tppt) cc_final: 0.8562 (tppt) REVERT: F 196 LEU cc_start: 0.9015 (mt) cc_final: 0.8807 (mt) REVERT: F 289 ARG cc_start: 0.7542 (mtt180) cc_final: 0.7214 (tpt170) REVERT: F 328 PHE cc_start: 0.8429 (t80) cc_final: 0.8086 (t80) REVERT: F 332 LEU cc_start: 0.9320 (mt) cc_final: 0.9062 (mt) REVERT: F 339 MET cc_start: 0.8506 (mtt) cc_final: 0.7331 (ttt) REVERT: F 396 HIS cc_start: 0.8760 (t-90) cc_final: 0.8459 (t70) REVERT: P 60 PHE cc_start: 0.8509 (m-10) cc_final: 0.8094 (m-10) REVERT: P 67 GLU cc_start: 0.8548 (mt-10) cc_final: 0.7965 (mm-30) REVERT: P 71 GLN cc_start: 0.9388 (mt0) cc_final: 0.8900 (mp10) REVERT: P 78 LYS cc_start: 0.9169 (mttt) cc_final: 0.8589 (mttt) REVERT: P 79 HIS cc_start: 0.8714 (t70) cc_final: 0.8264 (t70) REVERT: P 80 ILE cc_start: 0.9733 (mt) cc_final: 0.9527 (mm) REVERT: P 83 GLN cc_start: 0.9355 (mm-40) cc_final: 0.9111 (mm-40) REVERT: P 87 LEU cc_start: 0.9473 (mt) cc_final: 0.9187 (mt) REVERT: P 93 GLN cc_start: 0.8663 (mt0) cc_final: 0.7336 (mt0) REVERT: P 151 LEU cc_start: 0.9228 (mt) cc_final: 0.9004 (mt) REVERT: P 162 LYS cc_start: 0.8971 (mmmt) cc_final: 0.8752 (mmmm) REVERT: P 167 LEU cc_start: 0.8704 (tp) cc_final: 0.8221 (tp) REVERT: P 171 LEU cc_start: 0.8588 (mt) cc_final: 0.8192 (tt) REVERT: P 186 CYS cc_start: 0.9187 (m) cc_final: 0.8556 (m) REVERT: P 204 GLN cc_start: 0.8717 (tp40) cc_final: 0.8368 (pm20) REVERT: P 212 VAL cc_start: 0.9491 (t) cc_final: 0.9106 (m) REVERT: P 218 HIS cc_start: 0.8526 (t-90) cc_final: 0.8191 (t-90) REVERT: P 223 GLU cc_start: 0.8206 (tp30) cc_final: 0.7596 (tp30) REVERT: P 243 VAL cc_start: 0.9299 (t) cc_final: 0.8710 (t) REVERT: P 259 ASP cc_start: 0.8592 (m-30) cc_final: 0.8355 (m-30) REVERT: P 260 TYR cc_start: 0.8580 (m-10) cc_final: 0.7937 (m-10) REVERT: P 264 GLN cc_start: 0.9398 (tt0) cc_final: 0.9079 (tm-30) REVERT: P 272 PHE cc_start: 0.8310 (p90) cc_final: 0.7871 (p90) REVERT: Z 5 LEU cc_start: 0.9156 (pp) cc_final: 0.8394 (pp) REVERT: Z 7 ARG cc_start: 0.7707 (ttp-110) cc_final: 0.7425 (ttp-170) REVERT: Z 26 PHE cc_start: 0.8738 (m-80) cc_final: 0.8500 (m-80) REVERT: Z 33 TYR cc_start: 0.9086 (t80) cc_final: 0.8464 (t80) REVERT: Z 84 LEU cc_start: 0.6774 (tp) cc_final: 0.6533 (tp) REVERT: Z 90 ASN cc_start: 0.8508 (t0) cc_final: 0.8013 (t0) REVERT: Z 92 GLU cc_start: 0.8143 (tp30) cc_final: 0.7617 (pm20) REVERT: Z 113 ASP cc_start: 0.7488 (m-30) cc_final: 0.7194 (m-30) REVERT: Z 125 GLN cc_start: 0.8998 (tt0) cc_final: 0.8396 (tm-30) REVERT: Z 127 GLU cc_start: 0.8769 (mt-10) cc_final: 0.8419 (tt0) REVERT: Z 141 PHE cc_start: 0.8375 (p90) cc_final: 0.7686 (p90) REVERT: Z 192 LYS cc_start: 0.8764 (tttm) cc_final: 0.8456 (tttt) REVERT: Z 194 ASN cc_start: 0.8891 (m-40) cc_final: 0.8641 (m110) outliers start: 0 outliers final: 0 residues processed: 896 average time/residue: 0.3678 time to fit residues: 480.5114 Evaluate side-chains 598 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 598 time to evaluate : 2.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 213 optimal weight: 5.9990 chunk 191 optimal weight: 8.9990 chunk 106 optimal weight: 20.0000 chunk 65 optimal weight: 3.9990 chunk 129 optimal weight: 0.9980 chunk 102 optimal weight: 10.0000 chunk 198 optimal weight: 30.0000 chunk 76 optimal weight: 7.9990 chunk 120 optimal weight: 4.9990 chunk 147 optimal weight: 9.9990 chunk 229 optimal weight: 3.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 HIS A 317 GLN B 69 ASN B 103 ASN C 101 GLN C 283 GLN C 374 ASN C 396 HIS D 47 ASN ** D 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 133 HIS E 49 HIS ** E 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 GLN ** E 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 253 GLN E 286 GLN ** E 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 253 GLN ** P 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 66 ASN ** Z 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 125 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 20809 Z= 0.298 Angle : 0.784 10.913 28244 Z= 0.402 Chirality : 0.048 0.225 3369 Planarity : 0.006 0.095 3526 Dihedral : 10.329 135.755 2854 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 25.38 Ramachandran Plot: Outliers : 0.28 % Allowed : 12.08 % Favored : 87.64 % Rotamer: Outliers : 0.18 % Allowed : 2.80 % Favored : 97.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.17 % Twisted General : 0.12 % 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: -3.63 (0.15), residues: 2541 helix: -1.76 (0.13), residues: 1104 sheet: -2.34 (0.24), residues: 357 loop : -3.05 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP P 257 HIS 0.008 0.002 HIS B 49 PHE 0.035 0.002 PHE E 393 TYR 0.030 0.002 TYR A 331 ARG 0.013 0.001 ARG Z 7 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 751 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 747 time to evaluate : 2.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 ASP cc_start: 0.8952 (m-30) cc_final: 0.8415 (p0) REVERT: A 168 LEU cc_start: 0.9492 (mt) cc_final: 0.9214 (pt) REVERT: A 173 ARG cc_start: 0.7113 (mtt90) cc_final: 0.6275 (mpt-90) REVERT: A 211 GLU cc_start: 0.9250 (mt-10) cc_final: 0.8942 (mt-10) REVERT: A 275 ARG cc_start: 0.7918 (ptm160) cc_final: 0.7476 (ptm-80) REVERT: A 286 GLN cc_start: 0.9209 (tt0) cc_final: 0.8983 (tt0) REVERT: A 296 LEU cc_start: 0.9733 (mt) cc_final: 0.9467 (mt) REVERT: A 331 TYR cc_start: 0.8269 (m-80) cc_final: 0.7686 (m-80) REVERT: A 354 ARG cc_start: 0.8834 (ttt180) cc_final: 0.8565 (ttp80) REVERT: A 377 SER cc_start: 0.7145 (m) cc_final: 0.6162 (t) REVERT: A 390 LYS cc_start: 0.8935 (tptp) cc_final: 0.8691 (tptp) REVERT: A 393 PHE cc_start: 0.9004 (t80) cc_final: 0.8673 (t80) REVERT: A 399 TYR cc_start: 0.8183 (m-80) cc_final: 0.7912 (m-80) REVERT: A 424 GLU cc_start: 0.8740 (mt-10) cc_final: 0.8430 (mt-10) REVERT: B 68 ARG cc_start: 0.9166 (tpt90) cc_final: 0.8846 (tpt90) REVERT: B 123 ASN cc_start: 0.8801 (m-40) cc_final: 0.7998 (m-40) REVERT: B 127 LEU cc_start: 0.9128 (tp) cc_final: 0.8857 (tp) REVERT: B 141 TYR cc_start: 0.7102 (m-80) cc_final: 0.6564 (m-80) REVERT: B 154 MET cc_start: 0.9335 (mmm) cc_final: 0.8949 (mmm) REVERT: B 187 SER cc_start: 0.9199 (m) cc_final: 0.8971 (p) REVERT: B 188 LEU cc_start: 0.9687 (tp) cc_final: 0.9341 (tp) REVERT: B 189 CYS cc_start: 0.9281 (m) cc_final: 0.8853 (m) REVERT: B 204 TYR cc_start: 0.8456 (m-80) cc_final: 0.8114 (m-80) REVERT: B 211 GLU cc_start: 0.9127 (tt0) cc_final: 0.8548 (tt0) REVERT: B 218 PHE cc_start: 0.9089 (m-80) cc_final: 0.8406 (m-80) REVERT: B 224 GLU cc_start: 0.8127 (tp30) cc_final: 0.7591 (tt0) REVERT: B 231 LYS cc_start: 0.8264 (mttt) cc_final: 0.7735 (tmtt) REVERT: B 248 PHE cc_start: 0.9464 (m-80) cc_final: 0.9229 (m-80) REVERT: B 291 SER cc_start: 0.9069 (m) cc_final: 0.8802 (p) REVERT: B 296 LEU cc_start: 0.9269 (mt) cc_final: 0.8931 (mt) REVERT: B 327 ILE cc_start: 0.9590 (mt) cc_final: 0.9375 (mt) REVERT: B 328 PHE cc_start: 0.9132 (t80) cc_final: 0.8701 (t80) REVERT: B 329 LYS cc_start: 0.9163 (mttt) cc_final: 0.8731 (mtmm) REVERT: B 335 LEU cc_start: 0.9828 (mt) cc_final: 0.9559 (mt) REVERT: B 336 GLU cc_start: 0.8978 (mm-30) cc_final: 0.8654 (mm-30) REVERT: B 339 MET cc_start: 0.8126 (mtt) cc_final: 0.7877 (mmt) REVERT: B 399 TYR cc_start: 0.9124 (m-80) cc_final: 0.8501 (m-80) REVERT: C 56 TYR cc_start: 0.6447 (t80) cc_final: 0.6191 (m-80) REVERT: C 98 HIS cc_start: 0.7000 (m-70) cc_final: 0.6793 (m-70) REVERT: C 102 LEU cc_start: 0.8874 (mt) cc_final: 0.8630 (mt) REVERT: C 135 LEU cc_start: 0.9351 (tp) cc_final: 0.8778 (mm) REVERT: C 163 ASN cc_start: 0.8502 (t0) cc_final: 0.8295 (t0) REVERT: C 175 VAL cc_start: 0.9504 (t) cc_final: 0.9274 (t) REVERT: C 189 CYS cc_start: 0.9234 (m) cc_final: 0.9012 (m) REVERT: C 192 LEU cc_start: 0.9651 (tp) cc_final: 0.9386 (tt) REVERT: C 341 CYS cc_start: 0.8367 (m) cc_final: 0.8158 (t) REVERT: C 347 ARG cc_start: 0.8949 (ptp-110) cc_final: 0.8650 (ptp-110) REVERT: C 368 LYS cc_start: 0.9366 (pttm) cc_final: 0.9075 (pttp) REVERT: C 388 LEU cc_start: 0.9333 (mm) cc_final: 0.9057 (mm) REVERT: C 391 LEU cc_start: 0.9752 (mt) cc_final: 0.9235 (mt) REVERT: D 48 ARG cc_start: 0.8573 (ttm170) cc_final: 0.7906 (mtt-85) REVERT: D 123 ASN cc_start: 0.9037 (m-40) cc_final: 0.8396 (m-40) REVERT: D 133 HIS cc_start: 0.8143 (t-90) cc_final: 0.7838 (t70) REVERT: D 136 TRP cc_start: 0.8685 (t-100) cc_final: 0.8481 (t60) REVERT: D 141 TYR cc_start: 0.8792 (m-80) cc_final: 0.8573 (m-80) REVERT: D 158 LEU cc_start: 0.9059 (tp) cc_final: 0.8637 (tt) REVERT: D 168 LEU cc_start: 0.9494 (mt) cc_final: 0.9173 (tt) REVERT: D 169 ILE cc_start: 0.9516 (mp) cc_final: 0.9275 (mm) REVERT: D 171 TRP cc_start: 0.8197 (p-90) cc_final: 0.7079 (p-90) REVERT: D 192 LEU cc_start: 0.9631 (tp) cc_final: 0.9178 (tp) REVERT: D 196 LEU cc_start: 0.9723 (mt) cc_final: 0.9472 (mt) REVERT: D 209 LEU cc_start: 0.9237 (tp) cc_final: 0.8911 (tp) REVERT: D 211 GLU cc_start: 0.8905 (tt0) cc_final: 0.8665 (tt0) REVERT: D 234 GLN cc_start: 0.8960 (tp40) cc_final: 0.8557 (tm-30) REVERT: D 244 ASP cc_start: 0.8196 (t0) cc_final: 0.7896 (t0) REVERT: D 248 PHE cc_start: 0.9458 (m-80) cc_final: 0.9142 (m-80) REVERT: D 281 LEU cc_start: 0.9184 (mt) cc_final: 0.8947 (mt) REVERT: D 316 LYS cc_start: 0.9224 (mttt) cc_final: 0.8787 (mtpt) REVERT: D 329 LYS cc_start: 0.8925 (mttt) cc_final: 0.8596 (mmtt) REVERT: D 351 LEU cc_start: 0.8275 (mt) cc_final: 0.8063 (mt) REVERT: D 355 GLU cc_start: 0.9142 (mt-10) cc_final: 0.8770 (mt-10) REVERT: D 368 LYS cc_start: 0.9450 (tttt) cc_final: 0.8910 (ptmm) REVERT: D 391 LEU cc_start: 0.9589 (mt) cc_final: 0.9341 (mt) REVERT: D 423 GLU cc_start: 0.9240 (mt-10) cc_final: 0.8764 (pp20) REVERT: E 27 GLN cc_start: 0.7710 (tt0) cc_final: 0.6856 (tt0) REVERT: E 58 TRP cc_start: 0.7248 (m-90) cc_final: 0.6215 (m-90) REVERT: E 62 ASP cc_start: 0.8018 (m-30) cc_final: 0.7692 (t0) REVERT: E 154 MET cc_start: 0.8964 (tpt) cc_final: 0.8594 (ttm) REVERT: E 155 THR cc_start: 0.9553 (m) cc_final: 0.9297 (p) REVERT: E 167 ASN cc_start: 0.9514 (m-40) cc_final: 0.8736 (p0) REVERT: E 172 ASN cc_start: 0.9510 (m-40) cc_final: 0.9277 (m110) REVERT: E 316 LYS cc_start: 0.8205 (mttt) cc_final: 0.7955 (mttt) REVERT: E 328 PHE cc_start: 0.9157 (t80) cc_final: 0.8626 (t80) REVERT: E 383 LEU cc_start: 0.7783 (mt) cc_final: 0.7428 (mt) REVERT: E 388 LEU cc_start: 0.9276 (mt) cc_final: 0.9026 (mt) REVERT: F 136 TRP cc_start: 0.7822 (t-100) cc_final: 0.7158 (t-100) REVERT: F 194 GLN cc_start: 0.8799 (tp40) cc_final: 0.8490 (tp40) REVERT: F 195 LYS cc_start: 0.8834 (tppt) cc_final: 0.8529 (tppt) REVERT: F 196 LEU cc_start: 0.9047 (mt) cc_final: 0.8802 (mt) REVERT: F 289 ARG cc_start: 0.7492 (mtt180) cc_final: 0.7044 (tpt170) REVERT: F 328 PHE cc_start: 0.8431 (t80) cc_final: 0.8043 (t80) REVERT: F 332 LEU cc_start: 0.9360 (mt) cc_final: 0.9066 (mt) REVERT: F 339 MET cc_start: 0.8615 (mtt) cc_final: 0.8280 (mpp) REVERT: F 396 HIS cc_start: 0.8756 (t-90) cc_final: 0.8409 (t70) REVERT: P 60 PHE cc_start: 0.8507 (m-10) cc_final: 0.8158 (m-10) REVERT: P 67 GLU cc_start: 0.8526 (mt-10) cc_final: 0.7801 (mm-30) REVERT: P 71 GLN cc_start: 0.9389 (mt0) cc_final: 0.9085 (mp10) REVERT: P 78 LYS cc_start: 0.8905 (mttt) cc_final: 0.8588 (mttp) REVERT: P 93 GLN cc_start: 0.8349 (mt0) cc_final: 0.7886 (mt0) REVERT: P 151 LEU cc_start: 0.9278 (mt) cc_final: 0.9010 (mt) REVERT: P 186 CYS cc_start: 0.9194 (m) cc_final: 0.8580 (m) REVERT: P 212 VAL cc_start: 0.9474 (t) cc_final: 0.9140 (m) REVERT: P 218 HIS cc_start: 0.8661 (t-90) cc_final: 0.8215 (t-90) REVERT: P 257 TRP cc_start: 0.8718 (m100) cc_final: 0.8451 (m100) REVERT: P 260 TYR cc_start: 0.8476 (m-10) cc_final: 0.7609 (m-10) REVERT: P 264 GLN cc_start: 0.9447 (tt0) cc_final: 0.9036 (tm-30) REVERT: P 272 PHE cc_start: 0.8470 (p90) cc_final: 0.7933 (p90) REVERT: P 274 GLU cc_start: 0.6080 (mp0) cc_final: 0.4929 (mp0) REVERT: Q 130 ILE cc_start: 0.8689 (mt) cc_final: 0.8485 (mt) REVERT: Z 4 GLN cc_start: 0.7602 (mt0) cc_final: 0.7312 (mt0) REVERT: Z 24 PHE cc_start: 0.8278 (m-80) cc_final: 0.7687 (m-80) REVERT: Z 26 PHE cc_start: 0.8822 (m-80) cc_final: 0.8443 (m-80) REVERT: Z 33 TYR cc_start: 0.9086 (t80) cc_final: 0.8692 (t80) REVERT: Z 47 GLN cc_start: 0.7366 (tp40) cc_final: 0.7061 (tp40) REVERT: Z 49 TYR cc_start: 0.6453 (m-80) cc_final: 0.6073 (m-80) REVERT: Z 53 LEU cc_start: 0.8821 (mt) cc_final: 0.8553 (mt) REVERT: Z 75 TRP cc_start: 0.8921 (m-10) cc_final: 0.8716 (m-10) REVERT: Z 90 ASN cc_start: 0.8374 (t0) cc_final: 0.8065 (t0) REVERT: Z 92 GLU cc_start: 0.8151 (tp30) cc_final: 0.7607 (pm20) REVERT: Z 113 ASP cc_start: 0.7575 (m-30) cc_final: 0.7354 (m-30) REVERT: Z 125 GLN cc_start: 0.8848 (tt0) cc_final: 0.8627 (tp40) REVERT: Z 127 GLU cc_start: 0.8946 (mt-10) cc_final: 0.8589 (tt0) REVERT: Z 191 HIS cc_start: 0.8056 (m90) cc_final: 0.7593 (m90) outliers start: 4 outliers final: 0 residues processed: 749 average time/residue: 0.3288 time to fit residues: 373.3285 Evaluate side-chains 574 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 574 time to evaluate : 2.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 127 optimal weight: 7.9990 chunk 71 optimal weight: 8.9990 chunk 191 optimal weight: 6.9990 chunk 156 optimal weight: 9.9990 chunk 63 optimal weight: 0.5980 chunk 230 optimal weight: 30.0000 chunk 248 optimal weight: 9.9990 chunk 204 optimal weight: 6.9990 chunk 228 optimal weight: 6.9990 chunk 78 optimal weight: 4.9990 chunk 184 optimal weight: 10.0000 overall best weight: 5.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 HIS ** A 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 ASN C 47 ASN C 69 ASN C 178 HIS ** C 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 396 HIS ** D 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 317 GLN ** E 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 GLN ** E 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 148 HIS F 167 ASN ** F 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 253 GLN ** P 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 194 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 20809 Z= 0.343 Angle : 0.802 14.196 28244 Z= 0.408 Chirality : 0.049 0.230 3369 Planarity : 0.005 0.099 3526 Dihedral : 10.145 135.423 2854 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 27.26 Ramachandran Plot: Outliers : 0.28 % Allowed : 12.67 % Favored : 87.05 % Rotamer: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.17 % Twisted General : 0.16 % 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: -3.13 (0.15), residues: 2541 helix: -1.28 (0.14), residues: 1118 sheet: -2.14 (0.25), residues: 351 loop : -2.87 (0.18), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 136 HIS 0.011 0.002 HIS B 178 PHE 0.046 0.002 PHE P 72 TYR 0.030 0.002 TYR F 204 ARG 0.012 0.001 ARG A 289 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 663 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 663 time to evaluate : 3.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 ASP cc_start: 0.8927 (m-30) cc_final: 0.8631 (p0) REVERT: A 141 TYR cc_start: 0.7806 (m-10) cc_final: 0.7589 (m-10) REVERT: A 151 ASP cc_start: 0.8559 (m-30) cc_final: 0.8145 (m-30) REVERT: A 173 ARG cc_start: 0.7241 (mtt90) cc_final: 0.6632 (mpt-90) REVERT: A 211 GLU cc_start: 0.9110 (mt-10) cc_final: 0.8666 (mt-10) REVERT: A 286 GLN cc_start: 0.9132 (tt0) cc_final: 0.8684 (pt0) REVERT: A 296 LEU cc_start: 0.9724 (mt) cc_final: 0.9245 (mt) REVERT: A 327 ILE cc_start: 0.9562 (mt) cc_final: 0.8575 (mt) REVERT: A 331 TYR cc_start: 0.8448 (m-80) cc_final: 0.7896 (m-80) REVERT: A 390 LYS cc_start: 0.8954 (tptp) cc_final: 0.8733 (tptp) REVERT: A 393 PHE cc_start: 0.8930 (t80) cc_final: 0.8376 (t80) REVERT: A 399 TYR cc_start: 0.8175 (m-80) cc_final: 0.7809 (m-10) REVERT: A 424 GLU cc_start: 0.8738 (mt-10) cc_final: 0.8306 (mt-10) REVERT: B 68 ARG cc_start: 0.9129 (tpt90) cc_final: 0.8824 (tpt90) REVERT: B 123 ASN cc_start: 0.8776 (m-40) cc_final: 0.8180 (m-40) REVERT: B 127 LEU cc_start: 0.9125 (tp) cc_final: 0.8794 (tp) REVERT: B 141 TYR cc_start: 0.6803 (m-80) cc_final: 0.6599 (m-80) REVERT: B 154 MET cc_start: 0.9369 (mmm) cc_final: 0.8924 (mmm) REVERT: B 188 LEU cc_start: 0.9719 (tp) cc_final: 0.9470 (tp) REVERT: B 189 CYS cc_start: 0.9261 (m) cc_final: 0.8943 (m) REVERT: B 211 GLU cc_start: 0.9002 (tt0) cc_final: 0.8552 (tt0) REVERT: B 217 LEU cc_start: 0.9498 (mm) cc_final: 0.9165 (mm) REVERT: B 224 GLU cc_start: 0.8090 (tp30) cc_final: 0.7882 (tt0) REVERT: B 231 LYS cc_start: 0.8288 (mttt) cc_final: 0.7890 (tmtt) REVERT: B 296 LEU cc_start: 0.9252 (mt) cc_final: 0.8756 (mt) REVERT: B 328 PHE cc_start: 0.9123 (t80) cc_final: 0.8697 (t80) REVERT: B 329 LYS cc_start: 0.9168 (mttt) cc_final: 0.8732 (mtmm) REVERT: B 335 LEU cc_start: 0.9829 (mt) cc_final: 0.9546 (mt) REVERT: B 336 GLU cc_start: 0.8981 (mm-30) cc_final: 0.8709 (mm-30) REVERT: B 339 MET cc_start: 0.8195 (mtt) cc_final: 0.7868 (mmt) REVERT: B 398 LEU cc_start: 0.9508 (mt) cc_final: 0.9236 (tt) REVERT: C 141 TYR cc_start: 0.8286 (t80) cc_final: 0.7963 (t80) REVERT: C 148 HIS cc_start: 0.9290 (m90) cc_final: 0.9059 (m90) REVERT: C 163 ASN cc_start: 0.8568 (t0) cc_final: 0.8293 (t0) REVERT: C 189 CYS cc_start: 0.9057 (m) cc_final: 0.8825 (m) REVERT: C 192 LEU cc_start: 0.9682 (tp) cc_final: 0.9391 (tt) REVERT: C 224 GLU cc_start: 0.8162 (tp30) cc_final: 0.7792 (tp30) REVERT: C 228 LEU cc_start: 0.9539 (pp) cc_final: 0.8902 (pp) REVERT: C 253 GLN cc_start: 0.8927 (mt0) cc_final: 0.8457 (mp10) REVERT: C 368 LYS cc_start: 0.9337 (pttm) cc_final: 0.8937 (pttp) REVERT: C 391 LEU cc_start: 0.9740 (mt) cc_final: 0.9067 (mt) REVERT: C 407 ILE cc_start: 0.9138 (pt) cc_final: 0.8059 (pt) REVERT: D 27 GLN cc_start: 0.9427 (tt0) cc_final: 0.9188 (tt0) REVERT: D 48 ARG cc_start: 0.8575 (ttm170) cc_final: 0.7958 (mtt-85) REVERT: D 133 HIS cc_start: 0.7925 (t-90) cc_final: 0.7718 (t70) REVERT: D 136 TRP cc_start: 0.8752 (t-100) cc_final: 0.8518 (t60) REVERT: D 141 TYR cc_start: 0.8816 (m-80) cc_final: 0.8107 (m-80) REVERT: D 158 LEU cc_start: 0.9131 (tp) cc_final: 0.8660 (tt) REVERT: D 168 LEU cc_start: 0.9516 (mt) cc_final: 0.9254 (tt) REVERT: D 169 ILE cc_start: 0.9473 (mp) cc_final: 0.9267 (mm) REVERT: D 171 TRP cc_start: 0.8309 (p-90) cc_final: 0.6871 (p-90) REVERT: D 188 LEU cc_start: 0.9396 (tp) cc_final: 0.8777 (tp) REVERT: D 190 LYS cc_start: 0.9244 (ttmt) cc_final: 0.8963 (mmmt) REVERT: D 192 LEU cc_start: 0.9561 (tp) cc_final: 0.9224 (tp) REVERT: D 209 LEU cc_start: 0.8622 (tp) cc_final: 0.8139 (tp) REVERT: D 211 GLU cc_start: 0.8958 (tt0) cc_final: 0.8699 (tt0) REVERT: D 218 PHE cc_start: 0.7540 (t80) cc_final: 0.7321 (t80) REVERT: D 234 GLN cc_start: 0.8948 (tp40) cc_final: 0.8595 (tm-30) REVERT: D 244 ASP cc_start: 0.8311 (t0) cc_final: 0.8006 (t0) REVERT: D 248 PHE cc_start: 0.9530 (m-80) cc_final: 0.9105 (m-80) REVERT: D 255 GLU cc_start: 0.8999 (pt0) cc_final: 0.8071 (pm20) REVERT: D 278 ASN cc_start: 0.9072 (p0) cc_final: 0.8656 (p0) REVERT: D 281 LEU cc_start: 0.9271 (mt) cc_final: 0.9018 (mt) REVERT: D 303 GLU cc_start: 0.8389 (tp30) cc_final: 0.7897 (tp30) REVERT: D 329 LYS cc_start: 0.8972 (mttt) cc_final: 0.8620 (mmtt) REVERT: D 351 LEU cc_start: 0.8280 (mt) cc_final: 0.8002 (mt) REVERT: D 355 GLU cc_start: 0.9115 (mt-10) cc_final: 0.8784 (mt-10) REVERT: D 390 LYS cc_start: 0.9173 (mttt) cc_final: 0.8778 (mmtp) REVERT: D 391 LEU cc_start: 0.9580 (mt) cc_final: 0.9340 (mt) REVERT: D 420 LYS cc_start: 0.9264 (tttt) cc_final: 0.8764 (tttt) REVERT: D 423 GLU cc_start: 0.9236 (mt-10) cc_final: 0.8999 (pp20) REVERT: E 26 HIS cc_start: 0.6409 (t-90) cc_final: 0.5907 (t-90) REVERT: E 27 GLN cc_start: 0.7948 (tt0) cc_final: 0.7157 (tt0) REVERT: E 58 TRP cc_start: 0.7287 (m-90) cc_final: 0.6194 (m-90) REVERT: E 62 ASP cc_start: 0.8006 (m-30) cc_final: 0.7652 (t0) REVERT: E 72 SER cc_start: 0.8449 (p) cc_final: 0.7743 (m) REVERT: E 148 HIS cc_start: 0.8670 (m90) cc_final: 0.8383 (m90) REVERT: E 154 MET cc_start: 0.9050 (tpt) cc_final: 0.8647 (ttm) REVERT: E 189 CYS cc_start: 0.9325 (t) cc_final: 0.9108 (t) REVERT: E 211 GLU cc_start: 0.7930 (tm-30) cc_final: 0.7607 (tm-30) REVERT: E 316 LYS cc_start: 0.8379 (mttt) cc_final: 0.7940 (mttt) REVERT: E 328 PHE cc_start: 0.9195 (t80) cc_final: 0.8650 (t80) REVERT: E 375 ASP cc_start: 0.8835 (m-30) cc_final: 0.8340 (p0) REVERT: E 383 LEU cc_start: 0.7793 (mt) cc_final: 0.7389 (mt) REVERT: E 388 LEU cc_start: 0.9348 (mt) cc_final: 0.9081 (mt) REVERT: F 136 TRP cc_start: 0.7757 (t-100) cc_final: 0.7245 (t-100) REVERT: F 194 GLN cc_start: 0.8753 (tp40) cc_final: 0.8456 (tp40) REVERT: F 195 LYS cc_start: 0.8799 (tppt) cc_final: 0.8533 (tppt) REVERT: F 196 LEU cc_start: 0.8939 (mt) cc_final: 0.8621 (mt) REVERT: F 289 ARG cc_start: 0.7537 (mtt180) cc_final: 0.7008 (tpt170) REVERT: F 328 PHE cc_start: 0.8408 (t80) cc_final: 0.8027 (t80) REVERT: F 332 LEU cc_start: 0.9110 (mt) cc_final: 0.8885 (mt) REVERT: F 338 LEU cc_start: 0.9162 (mt) cc_final: 0.8960 (mt) REVERT: F 339 MET cc_start: 0.8744 (mtt) cc_final: 0.8404 (mpp) REVERT: F 375 ASP cc_start: 0.8125 (m-30) cc_final: 0.7921 (m-30) REVERT: F 396 HIS cc_start: 0.8810 (t-90) cc_final: 0.8405 (t70) REVERT: F 401 GLN cc_start: 0.8486 (mt0) cc_final: 0.7997 (mm110) REVERT: P 60 PHE cc_start: 0.8420 (m-10) cc_final: 0.8107 (m-10) REVERT: P 67 GLU cc_start: 0.8365 (mt-10) cc_final: 0.7420 (mm-30) REVERT: P 71 GLN cc_start: 0.9384 (mt0) cc_final: 0.9175 (mp10) REVERT: P 81 MET cc_start: 0.9322 (mmm) cc_final: 0.8828 (tpp) REVERT: P 85 GLN cc_start: 0.8926 (mp10) cc_final: 0.8725 (mp10) REVERT: P 139 GLU cc_start: 0.9018 (mt-10) cc_final: 0.8484 (tm-30) REVERT: P 151 LEU cc_start: 0.9283 (mt) cc_final: 0.9055 (mt) REVERT: P 154 LEU cc_start: 0.9123 (mp) cc_final: 0.8907 (mp) REVERT: P 202 GLU cc_start: 0.9215 (pm20) cc_final: 0.8840 (pm20) REVERT: P 212 VAL cc_start: 0.9498 (t) cc_final: 0.9186 (m) REVERT: P 218 HIS cc_start: 0.8719 (t-90) cc_final: 0.8279 (t70) REVERT: P 257 TRP cc_start: 0.8532 (m100) cc_final: 0.8002 (m100) REVERT: P 260 TYR cc_start: 0.8340 (m-10) cc_final: 0.7911 (m-10) REVERT: P 264 GLN cc_start: 0.9428 (tt0) cc_final: 0.9049 (tm-30) REVERT: P 272 PHE cc_start: 0.8332 (p90) cc_final: 0.7980 (p90) REVERT: P 274 GLU cc_start: 0.6004 (mp0) cc_final: 0.4837 (mp0) REVERT: Q 130 ILE cc_start: 0.8677 (mt) cc_final: 0.8094 (mt) REVERT: Z 4 GLN cc_start: 0.7463 (mt0) cc_final: 0.7170 (mt0) REVERT: Z 24 PHE cc_start: 0.8310 (m-80) cc_final: 0.7795 (m-80) REVERT: Z 33 TYR cc_start: 0.9085 (t80) cc_final: 0.8663 (t80) REVERT: Z 49 TYR cc_start: 0.6416 (m-80) cc_final: 0.6113 (m-80) REVERT: Z 113 ASP cc_start: 0.7594 (m-30) cc_final: 0.7311 (m-30) REVERT: Z 127 GLU cc_start: 0.8985 (mt-10) cc_final: 0.8607 (tt0) REVERT: Z 173 GLN cc_start: 0.7924 (tp-100) cc_final: 0.7453 (mp10) REVERT: Z 192 LYS cc_start: 0.8719 (tttm) cc_final: 0.8325 (tptm) REVERT: Z 194 ASN cc_start: 0.8957 (m-40) cc_final: 0.8372 (p0) outliers start: 0 outliers final: 0 residues processed: 663 average time/residue: 0.3213 time to fit residues: 325.9137 Evaluate side-chains 533 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 533 time to evaluate : 2.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 227 optimal weight: 6.9990 chunk 173 optimal weight: 8.9990 chunk 119 optimal weight: 6.9990 chunk 25 optimal weight: 10.0000 chunk 109 optimal weight: 10.0000 chunk 154 optimal weight: 20.0000 chunk 230 optimal weight: 20.0000 chunk 244 optimal weight: 40.0000 chunk 120 optimal weight: 6.9990 chunk 218 optimal weight: 0.0770 chunk 65 optimal weight: 4.9990 overall best weight: 5.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 HIS A 178 HIS ** A 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 GLN C 178 HIS ** C 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 ASN C 396 HIS ** D 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 253 GLN ** P 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 47 GLN ** Z 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.3587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 20809 Z= 0.327 Angle : 0.777 12.794 28244 Z= 0.396 Chirality : 0.048 0.218 3369 Planarity : 0.005 0.100 3526 Dihedral : 10.026 136.161 2854 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 26.94 Ramachandran Plot: Outliers : 0.24 % Allowed : 12.20 % Favored : 87.56 % Rotamer: Outliers : 0.05 % Allowed : 3.30 % Favored : 96.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.17 % Twisted General : 0.20 % 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: -2.83 (0.16), residues: 2541 helix: -1.04 (0.14), residues: 1122 sheet: -1.96 (0.26), residues: 343 loop : -2.71 (0.19), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 221 HIS 0.009 0.002 HIS B 178 PHE 0.026 0.002 PHE D 132 TYR 0.033 0.002 TYR F 204 ARG 0.006 0.001 ARG Z 14 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 632 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 631 time to evaluate : 2.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 ASP cc_start: 0.9017 (m-30) cc_final: 0.8497 (p0) REVERT: A 141 TYR cc_start: 0.8064 (m-80) cc_final: 0.7853 (m-10) REVERT: A 173 ARG cc_start: 0.7608 (mtt90) cc_final: 0.7161 (mpt-90) REVERT: A 296 LEU cc_start: 0.9727 (mt) cc_final: 0.9247 (mt) REVERT: A 331 TYR cc_start: 0.8706 (m-10) cc_final: 0.8080 (m-80) REVERT: A 393 PHE cc_start: 0.8890 (t80) cc_final: 0.8471 (t80) REVERT: B 27 GLN cc_start: 0.7749 (tt0) cc_final: 0.7542 (tt0) REVERT: B 68 ARG cc_start: 0.9119 (tpt90) cc_final: 0.8816 (tpt90) REVERT: B 105 ASP cc_start: 0.8506 (t0) cc_final: 0.8217 (p0) REVERT: B 123 ASN cc_start: 0.8811 (m-40) cc_final: 0.8268 (m-40) REVERT: B 127 LEU cc_start: 0.9204 (tp) cc_final: 0.8859 (tp) REVERT: B 141 TYR cc_start: 0.6903 (m-80) cc_final: 0.6634 (m-80) REVERT: B 188 LEU cc_start: 0.9709 (tp) cc_final: 0.9454 (tp) REVERT: B 189 CYS cc_start: 0.9275 (m) cc_final: 0.9015 (m) REVERT: B 211 GLU cc_start: 0.9002 (tt0) cc_final: 0.8508 (tt0) REVERT: B 224 GLU cc_start: 0.8201 (tp30) cc_final: 0.7805 (tt0) REVERT: B 231 LYS cc_start: 0.8279 (mttt) cc_final: 0.7938 (tmtt) REVERT: B 296 LEU cc_start: 0.9248 (mt) cc_final: 0.8630 (mt) REVERT: B 327 ILE cc_start: 0.9593 (mt) cc_final: 0.9376 (mt) REVERT: B 328 PHE cc_start: 0.9120 (t80) cc_final: 0.8311 (t80) REVERT: B 329 LYS cc_start: 0.9161 (mttt) cc_final: 0.8624 (mtmm) REVERT: B 335 LEU cc_start: 0.9828 (mt) cc_final: 0.9538 (mt) REVERT: B 339 MET cc_start: 0.8219 (mtt) cc_final: 0.7876 (mmt) REVERT: B 398 LEU cc_start: 0.9535 (mt) cc_final: 0.9270 (tt) REVERT: C 23 VAL cc_start: 0.8998 (t) cc_final: 0.8733 (t) REVERT: C 148 HIS cc_start: 0.9298 (m90) cc_final: 0.9076 (m90) REVERT: C 163 ASN cc_start: 0.8599 (t0) cc_final: 0.8318 (t0) REVERT: C 192 LEU cc_start: 0.9681 (tp) cc_final: 0.9358 (tt) REVERT: C 196 LEU cc_start: 0.9625 (mt) cc_final: 0.9322 (mt) REVERT: C 224 GLU cc_start: 0.8255 (tp30) cc_final: 0.7997 (tm-30) REVERT: C 228 LEU cc_start: 0.9581 (pp) cc_final: 0.8690 (pp) REVERT: C 253 GLN cc_start: 0.9015 (mt0) cc_final: 0.8430 (mp10) REVERT: C 368 LYS cc_start: 0.9243 (pttm) cc_final: 0.8936 (pttp) REVERT: C 391 LEU cc_start: 0.9698 (mt) cc_final: 0.9027 (mt) REVERT: D 27 GLN cc_start: 0.9398 (tt0) cc_final: 0.9153 (tt0) REVERT: D 48 ARG cc_start: 0.8424 (ttm170) cc_final: 0.7867 (mtt-85) REVERT: D 141 TYR cc_start: 0.8842 (m-80) cc_final: 0.8141 (m-80) REVERT: D 158 LEU cc_start: 0.9140 (tp) cc_final: 0.8683 (tt) REVERT: D 171 TRP cc_start: 0.7702 (p-90) cc_final: 0.7237 (p-90) REVERT: D 188 LEU cc_start: 0.9402 (tp) cc_final: 0.8799 (tp) REVERT: D 192 LEU cc_start: 0.9595 (tp) cc_final: 0.9173 (tp) REVERT: D 196 LEU cc_start: 0.9742 (mt) cc_final: 0.9477 (mt) REVERT: D 211 GLU cc_start: 0.8807 (tt0) cc_final: 0.8273 (tt0) REVERT: D 234 GLN cc_start: 0.8929 (tp40) cc_final: 0.8593 (tm-30) REVERT: D 244 ASP cc_start: 0.8290 (t0) cc_final: 0.8001 (t0) REVERT: D 248 PHE cc_start: 0.9497 (m-80) cc_final: 0.9071 (m-80) REVERT: D 278 ASN cc_start: 0.9075 (p0) cc_final: 0.8708 (p0) REVERT: D 298 THR cc_start: 0.9656 (m) cc_final: 0.9359 (p) REVERT: D 303 GLU cc_start: 0.8391 (tp30) cc_final: 0.8100 (tp30) REVERT: D 316 LYS cc_start: 0.8731 (mtpt) cc_final: 0.8456 (mtpt) REVERT: D 317 GLN cc_start: 0.8996 (tp-100) cc_final: 0.8768 (tp-100) REVERT: D 329 LYS cc_start: 0.8902 (mttt) cc_final: 0.8493 (mmpt) REVERT: D 351 LEU cc_start: 0.8300 (mt) cc_final: 0.8038 (tp) REVERT: D 355 GLU cc_start: 0.9134 (mt-10) cc_final: 0.8877 (mt-10) REVERT: D 390 LYS cc_start: 0.9170 (mttt) cc_final: 0.8770 (mmtp) REVERT: D 391 LEU cc_start: 0.9566 (mt) cc_final: 0.9319 (mt) REVERT: D 420 LYS cc_start: 0.9313 (tttt) cc_final: 0.8658 (tttt) REVERT: D 423 GLU cc_start: 0.9169 (mt-10) cc_final: 0.8957 (pp20) REVERT: E 24 GLU cc_start: 0.7135 (pp20) cc_final: 0.6889 (pp20) REVERT: E 26 HIS cc_start: 0.6298 (t-90) cc_final: 0.5744 (t70) REVERT: E 27 GLN cc_start: 0.8146 (tt0) cc_final: 0.7592 (tt0) REVERT: E 58 TRP cc_start: 0.7306 (m-90) cc_final: 0.6191 (m-90) REVERT: E 62 ASP cc_start: 0.7773 (m-30) cc_final: 0.7559 (t0) REVERT: E 148 HIS cc_start: 0.8673 (m90) cc_final: 0.8372 (m90) REVERT: E 154 MET cc_start: 0.9057 (tpt) cc_final: 0.8655 (ttm) REVERT: E 211 GLU cc_start: 0.7682 (tm-30) cc_final: 0.7477 (tm-30) REVERT: E 304 LYS cc_start: 0.9112 (pptt) cc_final: 0.8900 (pptt) REVERT: E 328 PHE cc_start: 0.9172 (t80) cc_final: 0.8614 (t80) REVERT: E 335 LEU cc_start: 0.9087 (mt) cc_final: 0.8885 (mt) REVERT: E 383 LEU cc_start: 0.7857 (mt) cc_final: 0.7441 (mt) REVERT: E 388 LEU cc_start: 0.9341 (mt) cc_final: 0.9066 (mt) REVERT: F 136 TRP cc_start: 0.7726 (t-100) cc_final: 0.7349 (t-100) REVERT: F 195 LYS cc_start: 0.8798 (tppt) cc_final: 0.8456 (tppt) REVERT: F 196 LEU cc_start: 0.8905 (mt) cc_final: 0.8557 (mt) REVERT: F 289 ARG cc_start: 0.7503 (mtt180) cc_final: 0.6902 (tpt170) REVERT: F 328 PHE cc_start: 0.8417 (t80) cc_final: 0.8021 (t80) REVERT: F 338 LEU cc_start: 0.9130 (mt) cc_final: 0.8927 (mt) REVERT: F 339 MET cc_start: 0.8780 (mtt) cc_final: 0.8401 (mpp) REVERT: F 358 MET cc_start: 0.7323 (ptt) cc_final: 0.7062 (ppp) REVERT: F 396 HIS cc_start: 0.8781 (t-90) cc_final: 0.8469 (t70) REVERT: P 67 GLU cc_start: 0.8402 (mt-10) cc_final: 0.7537 (mm-30) REVERT: P 74 CYS cc_start: 0.9643 (m) cc_final: 0.9430 (m) REVERT: P 78 LYS cc_start: 0.9218 (mtmm) cc_final: 0.8996 (mttp) REVERT: P 80 ILE cc_start: 0.9796 (mp) cc_final: 0.9477 (tp) REVERT: P 85 GLN cc_start: 0.8946 (mp10) cc_final: 0.8586 (mp10) REVERT: P 139 GLU cc_start: 0.9112 (mt-10) cc_final: 0.8686 (tm-30) REVERT: P 151 LEU cc_start: 0.9238 (mt) cc_final: 0.8919 (mt) REVERT: P 212 VAL cc_start: 0.9477 (t) cc_final: 0.9185 (m) REVERT: P 218 HIS cc_start: 0.8727 (t-90) cc_final: 0.8366 (t-90) REVERT: P 264 GLN cc_start: 0.9321 (tt0) cc_final: 0.8977 (tm-30) REVERT: P 272 PHE cc_start: 0.8575 (p90) cc_final: 0.8111 (p90) REVERT: P 274 GLU cc_start: 0.5784 (mp0) cc_final: 0.5147 (mp0) REVERT: Q 130 ILE cc_start: 0.8810 (mt) cc_final: 0.8398 (mt) REVERT: Z 4 GLN cc_start: 0.7666 (mt0) cc_final: 0.7356 (mt0) REVERT: Z 20 VAL cc_start: 0.9770 (p) cc_final: 0.9549 (p) REVERT: Z 24 PHE cc_start: 0.8322 (m-80) cc_final: 0.7497 (m-80) REVERT: Z 26 PHE cc_start: 0.8755 (m-80) cc_final: 0.8495 (m-80) REVERT: Z 47 GLN cc_start: 0.7496 (tp-100) cc_final: 0.7147 (tp40) REVERT: Z 113 ASP cc_start: 0.7649 (m-30) cc_final: 0.7413 (m-30) REVERT: Z 127 GLU cc_start: 0.9007 (mt-10) cc_final: 0.8632 (tt0) REVERT: Z 192 LYS cc_start: 0.8650 (tttm) cc_final: 0.8286 (tptm) REVERT: Z 194 ASN cc_start: 0.8856 (m-40) cc_final: 0.8333 (p0) outliers start: 1 outliers final: 1 residues processed: 631 average time/residue: 0.3067 time to fit residues: 298.7136 Evaluate side-chains 520 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 519 time to evaluate : 2.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 203 optimal weight: 4.9990 chunk 138 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 chunk 182 optimal weight: 10.0000 chunk 100 optimal weight: 6.9990 chunk 208 optimal weight: 0.0980 chunk 169 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 124 optimal weight: 0.9980 chunk 219 optimal weight: 10.0000 chunk 61 optimal weight: 0.9980 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 HIS ** A 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 317 GLN A 396 HIS C 178 HIS ** C 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 ASN D 49 HIS D 69 ASN ** D 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 133 HIS ** D 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 253 GLN ** P 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 93 GLN ** Z 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 173 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.4067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 20809 Z= 0.216 Angle : 0.697 11.082 28244 Z= 0.356 Chirality : 0.047 0.260 3369 Planarity : 0.005 0.104 3526 Dihedral : 9.760 132.561 2854 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 21.62 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.96 % Favored : 89.77 % Rotamer: Outliers : 0.09 % Allowed : 1.94 % Favored : 97.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.17 % Twisted General : 0.12 % 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: -2.22 (0.16), residues: 2541 helix: -0.55 (0.15), residues: 1127 sheet: -1.62 (0.26), residues: 355 loop : -2.39 (0.19), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP D 136 HIS 0.006 0.001 HIS A 215 PHE 0.035 0.002 PHE E 309 TYR 0.033 0.002 TYR F 204 ARG 0.007 0.001 ARG Z 14 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 654 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 652 time to evaluate : 2.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 ASP cc_start: 0.8897 (m-30) cc_final: 0.8377 (p0) REVERT: A 173 ARG cc_start: 0.7653 (mtt90) cc_final: 0.7146 (mpt-90) REVERT: A 213 ASN cc_start: 0.8908 (t0) cc_final: 0.8325 (t0) REVERT: A 250 LEU cc_start: 0.9458 (tp) cc_final: 0.9255 (tp) REVERT: A 287 ILE cc_start: 0.8502 (pt) cc_final: 0.8163 (pt) REVERT: A 290 HIS cc_start: 0.8363 (m90) cc_final: 0.7858 (m90) REVERT: A 296 LEU cc_start: 0.9666 (mt) cc_final: 0.9104 (mt) REVERT: A 331 TYR cc_start: 0.8705 (m-10) cc_final: 0.8198 (m-80) REVERT: A 393 PHE cc_start: 0.8866 (t80) cc_final: 0.8453 (t80) REVERT: A 398 LEU cc_start: 0.9072 (mt) cc_final: 0.8839 (tp) REVERT: B 68 ARG cc_start: 0.9112 (tpt90) cc_final: 0.8831 (tpt90) REVERT: B 123 ASN cc_start: 0.8781 (m-40) cc_final: 0.8274 (m-40) REVERT: B 127 LEU cc_start: 0.9111 (tp) cc_final: 0.8707 (tp) REVERT: B 141 TYR cc_start: 0.7157 (m-80) cc_final: 0.6818 (m-80) REVERT: B 154 MET cc_start: 0.9469 (mmm) cc_final: 0.9215 (mmm) REVERT: B 188 LEU cc_start: 0.9669 (tp) cc_final: 0.9414 (tp) REVERT: B 189 CYS cc_start: 0.9290 (m) cc_final: 0.9081 (m) REVERT: B 211 GLU cc_start: 0.9002 (tt0) cc_final: 0.8605 (tt0) REVERT: B 219 SER cc_start: 0.7735 (p) cc_final: 0.6262 (t) REVERT: B 231 LYS cc_start: 0.8224 (mttt) cc_final: 0.7872 (tmtt) REVERT: B 296 LEU cc_start: 0.9198 (mt) cc_final: 0.8855 (mt) REVERT: B 327 ILE cc_start: 0.9538 (mt) cc_final: 0.9318 (mt) REVERT: B 328 PHE cc_start: 0.9130 (t80) cc_final: 0.8379 (t80) REVERT: B 329 LYS cc_start: 0.9091 (mttt) cc_final: 0.8561 (mtmm) REVERT: B 335 LEU cc_start: 0.9845 (mt) cc_final: 0.9575 (mt) REVERT: B 339 MET cc_start: 0.8166 (mtt) cc_final: 0.7846 (mmt) REVERT: B 424 GLU cc_start: 0.8265 (mt-10) cc_final: 0.7919 (mt-10) REVERT: C 23 VAL cc_start: 0.9081 (t) cc_final: 0.8811 (t) REVERT: C 98 HIS cc_start: 0.6486 (m-70) cc_final: 0.6049 (m90) REVERT: C 141 TYR cc_start: 0.8024 (t80) cc_final: 0.7689 (t80) REVERT: C 148 HIS cc_start: 0.9228 (m90) cc_final: 0.9003 (m90) REVERT: C 163 ASN cc_start: 0.8568 (t0) cc_final: 0.8267 (t0) REVERT: C 189 CYS cc_start: 0.9097 (m) cc_final: 0.8814 (m) REVERT: C 224 GLU cc_start: 0.8147 (tp30) cc_final: 0.7696 (tp30) REVERT: C 228 LEU cc_start: 0.9526 (pp) cc_final: 0.8836 (pp) REVERT: C 248 PHE cc_start: 0.9125 (m-10) cc_final: 0.8302 (m-10) REVERT: C 339 MET cc_start: 0.6978 (ttp) cc_final: 0.6404 (tmm) REVERT: C 347 ARG cc_start: 0.8911 (ptp-110) cc_final: 0.8498 (mtp85) REVERT: C 368 LYS cc_start: 0.9199 (pttm) cc_final: 0.8915 (pttp) REVERT: C 391 LEU cc_start: 0.9669 (mt) cc_final: 0.8955 (mt) REVERT: D 48 ARG cc_start: 0.8242 (ttm170) cc_final: 0.7699 (mtt180) REVERT: D 141 TYR cc_start: 0.8867 (m-80) cc_final: 0.8286 (m-80) REVERT: D 158 LEU cc_start: 0.9048 (tp) cc_final: 0.8503 (tt) REVERT: D 159 PHE cc_start: 0.7290 (m-80) cc_final: 0.6424 (m-80) REVERT: D 171 TRP cc_start: 0.7651 (p-90) cc_final: 0.7228 (p-90) REVERT: D 188 LEU cc_start: 0.9399 (tp) cc_final: 0.8792 (tp) REVERT: D 190 LYS cc_start: 0.9296 (tttt) cc_final: 0.8729 (mmmt) REVERT: D 192 LEU cc_start: 0.9525 (tp) cc_final: 0.9210 (tp) REVERT: D 196 LEU cc_start: 0.9705 (mt) cc_final: 0.9471 (mt) REVERT: D 209 LEU cc_start: 0.8368 (tp) cc_final: 0.7783 (tp) REVERT: D 211 GLU cc_start: 0.8750 (tt0) cc_final: 0.8413 (tt0) REVERT: D 241 ASP cc_start: 0.8887 (m-30) cc_final: 0.8684 (m-30) REVERT: D 244 ASP cc_start: 0.8294 (t0) cc_final: 0.8075 (t0) REVERT: D 248 PHE cc_start: 0.9356 (m-80) cc_final: 0.9090 (m-10) REVERT: D 255 GLU cc_start: 0.8917 (pt0) cc_final: 0.8049 (pm20) REVERT: D 281 LEU cc_start: 0.9183 (mt) cc_final: 0.8899 (mt) REVERT: D 298 THR cc_start: 0.9591 (m) cc_final: 0.9198 (p) REVERT: D 317 GLN cc_start: 0.9075 (tp-100) cc_final: 0.8875 (tp-100) REVERT: D 329 LYS cc_start: 0.8895 (mttt) cc_final: 0.8568 (mmtt) REVERT: D 351 LEU cc_start: 0.8252 (mt) cc_final: 0.7992 (tp) REVERT: D 355 GLU cc_start: 0.9128 (mt-10) cc_final: 0.8864 (mt-10) REVERT: D 390 LYS cc_start: 0.9138 (mttt) cc_final: 0.8612 (mmtp) REVERT: D 391 LEU cc_start: 0.9567 (mt) cc_final: 0.9343 (mt) REVERT: D 420 LYS cc_start: 0.9298 (tttt) cc_final: 0.8456 (ttmt) REVERT: D 423 GLU cc_start: 0.9214 (mt-10) cc_final: 0.9000 (pp20) REVERT: E 24 GLU cc_start: 0.7097 (pp20) cc_final: 0.6848 (pp20) REVERT: E 26 HIS cc_start: 0.6104 (t-90) cc_final: 0.5174 (t-90) REVERT: E 27 GLN cc_start: 0.8009 (tt0) cc_final: 0.7597 (tt0) REVERT: E 28 ARG cc_start: 0.7177 (mmt180) cc_final: 0.6889 (mmt180) REVERT: E 40 LEU cc_start: 0.8311 (mt) cc_final: 0.8109 (mp) REVERT: E 58 TRP cc_start: 0.7365 (m-90) cc_final: 0.6201 (m-90) REVERT: E 72 SER cc_start: 0.8339 (p) cc_final: 0.7917 (p) REVERT: E 148 HIS cc_start: 0.8483 (m90) cc_final: 0.8132 (m90) REVERT: E 154 MET cc_start: 0.8961 (tpt) cc_final: 0.8574 (ttm) REVERT: E 172 ASN cc_start: 0.9504 (m-40) cc_final: 0.9194 (m110) REVERT: E 189 CYS cc_start: 0.9311 (t) cc_final: 0.9018 (t) REVERT: E 209 LEU cc_start: 0.8770 (mm) cc_final: 0.7984 (tp) REVERT: E 250 LEU cc_start: 0.9191 (tp) cc_final: 0.8934 (tp) REVERT: E 253 GLN cc_start: 0.9169 (mt0) cc_final: 0.8938 (mt0) REVERT: E 328 PHE cc_start: 0.9162 (t80) cc_final: 0.8616 (t80) REVERT: E 388 LEU cc_start: 0.9318 (mt) cc_final: 0.8958 (mt) REVERT: F 136 TRP cc_start: 0.7740 (t-100) cc_final: 0.7372 (t-100) REVERT: F 195 LYS cc_start: 0.8805 (tppt) cc_final: 0.8412 (tppt) REVERT: F 196 LEU cc_start: 0.8860 (mt) cc_final: 0.8473 (mt) REVERT: F 328 PHE cc_start: 0.8444 (t80) cc_final: 0.8122 (t80) REVERT: F 338 LEU cc_start: 0.9036 (mt) cc_final: 0.8805 (mt) REVERT: F 339 MET cc_start: 0.8712 (mtt) cc_final: 0.8372 (mpp) REVERT: F 396 HIS cc_start: 0.8973 (t-90) cc_final: 0.8530 (t70) REVERT: P 67 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7614 (tp30) REVERT: P 78 LYS cc_start: 0.9012 (mtmm) cc_final: 0.8733 (mttp) REVERT: P 91 TYR cc_start: 0.9063 (t80) cc_final: 0.8835 (t80) REVERT: P 128 LEU cc_start: 0.9370 (mm) cc_final: 0.9040 (mt) REVERT: P 139 GLU cc_start: 0.9024 (mt-10) cc_final: 0.8812 (mt-10) REVERT: P 151 LEU cc_start: 0.9066 (mt) cc_final: 0.8787 (mt) REVERT: P 186 CYS cc_start: 0.9422 (m) cc_final: 0.9035 (p) REVERT: P 218 HIS cc_start: 0.8700 (t-90) cc_final: 0.8451 (t-90) REVERT: P 223 GLU cc_start: 0.8442 (tp30) cc_final: 0.8240 (tm-30) REVERT: P 264 GLN cc_start: 0.9324 (tt0) cc_final: 0.8930 (tm-30) REVERT: P 272 PHE cc_start: 0.8435 (p90) cc_final: 0.8015 (p90) REVERT: Q 130 ILE cc_start: 0.8732 (mt) cc_final: 0.8526 (mt) REVERT: Z 4 GLN cc_start: 0.7440 (mt0) cc_final: 0.7114 (mt0) REVERT: Z 24 PHE cc_start: 0.8367 (m-80) cc_final: 0.7640 (m-80) REVERT: Z 26 PHE cc_start: 0.8814 (m-80) cc_final: 0.8386 (m-80) REVERT: Z 49 TYR cc_start: 0.6742 (m-80) cc_final: 0.5986 (m-80) REVERT: Z 53 LEU cc_start: 0.8739 (mt) cc_final: 0.8058 (mt) REVERT: Z 75 TRP cc_start: 0.8938 (m-10) cc_final: 0.8716 (m-10) REVERT: Z 90 ASN cc_start: 0.8481 (t0) cc_final: 0.7722 (t0) REVERT: Z 92 GLU cc_start: 0.7670 (tp30) cc_final: 0.7372 (pm20) REVERT: Z 113 ASP cc_start: 0.7494 (m-30) cc_final: 0.7238 (m-30) REVERT: Z 173 GLN cc_start: 0.8194 (OUTLIER) cc_final: 0.7595 (mt0) outliers start: 2 outliers final: 0 residues processed: 654 average time/residue: 0.3157 time to fit residues: 316.7295 Evaluate side-chains 513 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 512 time to evaluate : 2.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 82 optimal weight: 8.9990 chunk 220 optimal weight: 0.2980 chunk 48 optimal weight: 0.8980 chunk 143 optimal weight: 9.9990 chunk 60 optimal weight: 1.9990 chunk 244 optimal weight: 9.9990 chunk 203 optimal weight: 4.9990 chunk 113 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 80 optimal weight: 2.9990 chunk 128 optimal weight: 4.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 HIS ** A 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 GLN B 167 ASN C 178 HIS C 283 GLN C 374 ASN C 396 HIS ** D 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 133 HIS ** D 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 125 GLN Z 29 ASN ** Z 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 173 GLN Z 194 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.4422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20809 Z= 0.223 Angle : 0.697 10.477 28244 Z= 0.357 Chirality : 0.047 0.270 3369 Planarity : 0.005 0.104 3526 Dihedral : 9.537 134.943 2854 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 22.10 Ramachandran Plot: Outliers : 0.31 % Allowed : 9.41 % Favored : 90.28 % Rotamer: Outliers : 0.14 % Allowed : 1.76 % Favored : 98.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.17 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.16), residues: 2541 helix: -0.34 (0.15), residues: 1119 sheet: -1.56 (0.26), residues: 359 loop : -2.27 (0.19), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 221 HIS 0.009 0.001 HIS C 396 PHE 0.034 0.002 PHE C 248 TYR 0.024 0.002 TYR F 204 ARG 0.018 0.001 ARG A 378 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 625 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 622 time to evaluate : 2.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 ASP cc_start: 0.8914 (m-30) cc_final: 0.8394 (p0) REVERT: A 173 ARG cc_start: 0.7430 (mtt90) cc_final: 0.6964 (mpt-90) REVERT: A 213 ASN cc_start: 0.8806 (t0) cc_final: 0.8320 (t0) REVERT: A 275 ARG cc_start: 0.7821 (ptm160) cc_final: 0.7091 (mpt180) REVERT: A 287 ILE cc_start: 0.8493 (pt) cc_final: 0.8143 (pt) REVERT: A 290 HIS cc_start: 0.8375 (m90) cc_final: 0.7873 (m90) REVERT: A 296 LEU cc_start: 0.9657 (mt) cc_final: 0.9054 (mt) REVERT: A 391 LEU cc_start: 0.9066 (mt) cc_final: 0.8643 (mt) REVERT: A 399 TYR cc_start: 0.8283 (m-80) cc_final: 0.7900 (m-80) REVERT: B 68 ARG cc_start: 0.9095 (tpt90) cc_final: 0.8809 (tpt90) REVERT: B 123 ASN cc_start: 0.8750 (m-40) cc_final: 0.7686 (m-40) REVERT: B 127 LEU cc_start: 0.9111 (tp) cc_final: 0.8723 (tp) REVERT: B 141 TYR cc_start: 0.7093 (m-80) cc_final: 0.6872 (m-80) REVERT: B 154 MET cc_start: 0.9456 (mmm) cc_final: 0.9184 (mmm) REVERT: B 211 GLU cc_start: 0.8985 (tt0) cc_final: 0.8566 (tt0) REVERT: B 231 LYS cc_start: 0.8222 (mttt) cc_final: 0.7861 (tmtt) REVERT: B 296 LEU cc_start: 0.9220 (mt) cc_final: 0.8634 (mt) REVERT: B 327 ILE cc_start: 0.9546 (mt) cc_final: 0.9269 (mt) REVERT: B 328 PHE cc_start: 0.9140 (t80) cc_final: 0.8273 (t80) REVERT: B 329 LYS cc_start: 0.9078 (mttt) cc_final: 0.8564 (mtmm) REVERT: B 335 LEU cc_start: 0.9837 (mt) cc_final: 0.9557 (mt) REVERT: B 339 MET cc_start: 0.8162 (mtt) cc_final: 0.7845 (mmt) REVERT: B 399 TYR cc_start: 0.8935 (m-80) cc_final: 0.8271 (m-80) REVERT: C 141 TYR cc_start: 0.7990 (t80) cc_final: 0.7638 (t80) REVERT: C 163 ASN cc_start: 0.8547 (t0) cc_final: 0.8292 (t0) REVERT: C 185 LYS cc_start: 0.9477 (ttmt) cc_final: 0.9081 (ttmt) REVERT: C 224 GLU cc_start: 0.8143 (tp30) cc_final: 0.7691 (tp30) REVERT: C 228 LEU cc_start: 0.9513 (pp) cc_final: 0.8731 (pp) REVERT: C 283 GLN cc_start: 0.9107 (mm110) cc_final: 0.8428 (mm110) REVERT: C 347 ARG cc_start: 0.8902 (ptp-110) cc_final: 0.8484 (mtt90) REVERT: C 368 LYS cc_start: 0.9237 (pttm) cc_final: 0.8923 (pttp) REVERT: C 391 LEU cc_start: 0.9661 (mt) cc_final: 0.8928 (mt) REVERT: D 27 GLN cc_start: 0.9328 (tt0) cc_final: 0.9091 (tt0) REVERT: D 48 ARG cc_start: 0.8291 (ttm170) cc_final: 0.7621 (mtt-85) REVERT: D 141 TYR cc_start: 0.8880 (m-80) cc_final: 0.8487 (m-80) REVERT: D 158 LEU cc_start: 0.8999 (tp) cc_final: 0.8423 (tt) REVERT: D 159 PHE cc_start: 0.7216 (m-80) cc_final: 0.6515 (m-80) REVERT: D 171 TRP cc_start: 0.7846 (p-90) cc_final: 0.7170 (p-90) REVERT: D 192 LEU cc_start: 0.9562 (tp) cc_final: 0.9270 (tp) REVERT: D 196 LEU cc_start: 0.9716 (mt) cc_final: 0.9505 (mt) REVERT: D 209 LEU cc_start: 0.8430 (tp) cc_final: 0.8005 (tp) REVERT: D 211 GLU cc_start: 0.8684 (tt0) cc_final: 0.8362 (tt0) REVERT: D 240 ILE cc_start: 0.9471 (mm) cc_final: 0.9256 (mm) REVERT: D 241 ASP cc_start: 0.8782 (m-30) cc_final: 0.8516 (m-30) REVERT: D 244 ASP cc_start: 0.8367 (t0) cc_final: 0.8124 (t0) REVERT: D 248 PHE cc_start: 0.9365 (m-80) cc_final: 0.9134 (m-10) REVERT: D 255 GLU cc_start: 0.8857 (pt0) cc_final: 0.8042 (pm20) REVERT: D 298 THR cc_start: 0.9580 (m) cc_final: 0.9174 (p) REVERT: D 299 SER cc_start: 0.9271 (p) cc_final: 0.8788 (p) REVERT: D 316 LYS cc_start: 0.8243 (mtpt) cc_final: 0.7620 (mtpt) REVERT: D 329 LYS cc_start: 0.9009 (mttt) cc_final: 0.8761 (mmtt) REVERT: D 358 MET cc_start: 0.8631 (mtm) cc_final: 0.8344 (mtm) REVERT: D 390 LYS cc_start: 0.9141 (mttt) cc_final: 0.8643 (mmtp) REVERT: D 391 LEU cc_start: 0.9562 (mt) cc_final: 0.9334 (mt) REVERT: D 420 LYS cc_start: 0.9292 (tttt) cc_final: 0.8417 (ttmt) REVERT: D 423 GLU cc_start: 0.9203 (mt-10) cc_final: 0.8984 (pp20) REVERT: E 26 HIS cc_start: 0.5912 (t-90) cc_final: 0.5165 (t-90) REVERT: E 27 GLN cc_start: 0.7963 (tt0) cc_final: 0.7516 (tt0) REVERT: E 58 TRP cc_start: 0.7415 (m-90) cc_final: 0.6237 (m-90) REVERT: E 72 SER cc_start: 0.8274 (p) cc_final: 0.7723 (p) REVERT: E 154 MET cc_start: 0.8833 (tpt) cc_final: 0.8387 (ttm) REVERT: E 173 ARG cc_start: 0.8908 (mmt180) cc_final: 0.7932 (mpt-90) REVERT: E 189 CYS cc_start: 0.9327 (t) cc_final: 0.9111 (t) REVERT: E 209 LEU cc_start: 0.8778 (mm) cc_final: 0.7986 (tp) REVERT: E 227 LYS cc_start: 0.9087 (tptp) cc_final: 0.8768 (tptp) REVERT: E 247 VAL cc_start: 0.8669 (p) cc_final: 0.8267 (m) REVERT: E 250 LEU cc_start: 0.9257 (tp) cc_final: 0.8995 (tp) REVERT: E 304 LYS cc_start: 0.9183 (pptt) cc_final: 0.8948 (pptt) REVERT: E 316 LYS cc_start: 0.8570 (mtmm) cc_final: 0.8334 (mtmm) REVERT: E 328 PHE cc_start: 0.9175 (t80) cc_final: 0.8648 (t80) REVERT: E 388 LEU cc_start: 0.9297 (mt) cc_final: 0.8947 (mt) REVERT: F 136 TRP cc_start: 0.7750 (t-100) cc_final: 0.7377 (t-100) REVERT: F 159 PHE cc_start: 0.8939 (m-80) cc_final: 0.8729 (m-80) REVERT: F 195 LYS cc_start: 0.8815 (tppt) cc_final: 0.8395 (tppt) REVERT: F 196 LEU cc_start: 0.8955 (mt) cc_final: 0.8577 (mt) REVERT: F 328 PHE cc_start: 0.8438 (t80) cc_final: 0.8114 (t80) REVERT: F 338 LEU cc_start: 0.9036 (mt) cc_final: 0.8806 (mt) REVERT: F 339 MET cc_start: 0.8740 (mtt) cc_final: 0.8348 (mpp) REVERT: F 396 HIS cc_start: 0.8944 (t-90) cc_final: 0.8639 (t70) REVERT: P 67 GLU cc_start: 0.8023 (mt-10) cc_final: 0.7617 (tp30) REVERT: P 81 MET cc_start: 0.9459 (mmm) cc_final: 0.8916 (mmm) REVERT: P 151 LEU cc_start: 0.9041 (mt) cc_final: 0.8783 (mt) REVERT: P 214 MET cc_start: 0.8064 (mtp) cc_final: 0.7694 (mtp) REVERT: P 218 HIS cc_start: 0.8688 (t-90) cc_final: 0.8418 (t70) REVERT: P 226 PHE cc_start: 0.9469 (m-10) cc_final: 0.8757 (m-10) REVERT: P 264 GLN cc_start: 0.9268 (tt0) cc_final: 0.8946 (tp40) REVERT: P 272 PHE cc_start: 0.8431 (p90) cc_final: 0.8012 (p90) REVERT: P 274 GLU cc_start: 0.5933 (mp0) cc_final: 0.5557 (mp0) REVERT: Z 4 GLN cc_start: 0.7546 (mt0) cc_final: 0.7233 (mt0) REVERT: Z 24 PHE cc_start: 0.8331 (m-80) cc_final: 0.7702 (m-80) REVERT: Z 29 ASN cc_start: 0.8271 (OUTLIER) cc_final: 0.7809 (t0) REVERT: Z 75 TRP cc_start: 0.9071 (m-10) cc_final: 0.8769 (m-10) REVERT: Z 113 ASP cc_start: 0.7541 (m-30) cc_final: 0.7279 (m-30) REVERT: Z 166 LYS cc_start: 0.7784 (mttt) cc_final: 0.7455 (pttm) REVERT: Z 194 ASN cc_start: 0.8966 (m-40) cc_final: 0.8602 (m110) REVERT: Z 195 SER cc_start: 0.8199 (m) cc_final: 0.7677 (t) REVERT: Z 196 MET cc_start: 0.7291 (tmm) cc_final: 0.6992 (tmm) outliers start: 3 outliers final: 1 residues processed: 625 average time/residue: 0.3130 time to fit residues: 300.7512 Evaluate side-chains 504 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 502 time to evaluate : 2.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 236 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 139 optimal weight: 7.9990 chunk 178 optimal weight: 20.0000 chunk 138 optimal weight: 3.9990 chunk 206 optimal weight: 6.9990 chunk 136 optimal weight: 2.9990 chunk 243 optimal weight: 10.0000 chunk 152 optimal weight: 1.9990 chunk 148 optimal weight: 8.9990 chunk 112 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 HIS A 194 GLN ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 GLN A 396 HIS C 178 HIS ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 283 GLN C 374 ASN D 47 ASN ** D 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 253 GLN E 286 GLN ** F 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.4601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 20809 Z= 0.234 Angle : 0.702 10.335 28244 Z= 0.359 Chirality : 0.047 0.270 3369 Planarity : 0.005 0.104 3526 Dihedral : 9.427 134.879 2854 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 22.62 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.76 % Favored : 89.96 % Rotamer: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.17 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.16), residues: 2541 helix: -0.30 (0.15), residues: 1120 sheet: -1.48 (0.26), residues: 359 loop : -2.22 (0.20), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 221 HIS 0.009 0.001 HIS A 215 PHE 0.030 0.002 PHE D 422 TYR 0.032 0.002 TYR F 204 ARG 0.013 0.001 ARG C 261 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 615 time to evaluate : 2.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 ASP cc_start: 0.8957 (m-30) cc_final: 0.8403 (p0) REVERT: A 173 ARG cc_start: 0.7369 (mtt90) cc_final: 0.6923 (mpt-90) REVERT: A 213 ASN cc_start: 0.8790 (t0) cc_final: 0.8284 (t0) REVERT: A 250 LEU cc_start: 0.9315 (tp) cc_final: 0.9061 (tp) REVERT: A 275 ARG cc_start: 0.7631 (ptm160) cc_final: 0.6904 (mpt180) REVERT: A 287 ILE cc_start: 0.8509 (pt) cc_final: 0.8185 (pt) REVERT: A 290 HIS cc_start: 0.8337 (m90) cc_final: 0.7857 (m90) REVERT: A 296 LEU cc_start: 0.9671 (mt) cc_final: 0.9057 (mt) REVERT: A 391 LEU cc_start: 0.9102 (mt) cc_final: 0.8744 (mt) REVERT: A 393 PHE cc_start: 0.8650 (t80) cc_final: 0.8340 (t80) REVERT: A 398 LEU cc_start: 0.8932 (mt) cc_final: 0.8718 (tp) REVERT: B 68 ARG cc_start: 0.8962 (tpt90) cc_final: 0.8654 (tpt90) REVERT: B 123 ASN cc_start: 0.8790 (m-40) cc_final: 0.8346 (m-40) REVERT: B 127 LEU cc_start: 0.9088 (tp) cc_final: 0.8700 (tp) REVERT: B 141 TYR cc_start: 0.7114 (m-80) cc_final: 0.6765 (m-80) REVERT: B 154 MET cc_start: 0.9446 (mmm) cc_final: 0.9199 (mmm) REVERT: B 187 SER cc_start: 0.9538 (m) cc_final: 0.9150 (p) REVERT: B 188 LEU cc_start: 0.9755 (tp) cc_final: 0.9476 (tp) REVERT: B 189 CYS cc_start: 0.9243 (m) cc_final: 0.9037 (m) REVERT: B 190 LYS cc_start: 0.9288 (mtmt) cc_final: 0.8845 (ttmm) REVERT: B 209 LEU cc_start: 0.9613 (tp) cc_final: 0.9291 (tp) REVERT: B 231 LYS cc_start: 0.8229 (mttt) cc_final: 0.7864 (tmtt) REVERT: B 296 LEU cc_start: 0.9217 (mt) cc_final: 0.8686 (mt) REVERT: B 327 ILE cc_start: 0.9563 (mt) cc_final: 0.9291 (mt) REVERT: B 328 PHE cc_start: 0.9164 (t80) cc_final: 0.8301 (t80) REVERT: B 329 LYS cc_start: 0.9081 (mttt) cc_final: 0.8542 (mtmm) REVERT: B 335 LEU cc_start: 0.9836 (mt) cc_final: 0.9552 (mt) REVERT: B 339 MET cc_start: 0.8180 (mtt) cc_final: 0.7866 (mmt) REVERT: B 399 TYR cc_start: 0.8922 (m-80) cc_final: 0.8498 (m-80) REVERT: C 141 TYR cc_start: 0.8198 (t80) cc_final: 0.7935 (t80) REVERT: C 163 ASN cc_start: 0.8587 (t0) cc_final: 0.8320 (t0) REVERT: C 224 GLU cc_start: 0.8172 (tp30) cc_final: 0.7817 (tp30) REVERT: C 228 LEU cc_start: 0.9510 (pp) cc_final: 0.8774 (pp) REVERT: C 283 GLN cc_start: 0.9267 (mm-40) cc_final: 0.8694 (mm110) REVERT: C 347 ARG cc_start: 0.8903 (ptp-110) cc_final: 0.8494 (mtt90) REVERT: C 368 LYS cc_start: 0.9219 (pttm) cc_final: 0.8887 (pttp) REVERT: C 391 LEU cc_start: 0.9589 (mt) cc_final: 0.8857 (mt) REVERT: D 27 GLN cc_start: 0.9345 (tt0) cc_final: 0.9087 (tt0) REVERT: D 48 ARG cc_start: 0.8292 (ttm170) cc_final: 0.7594 (mtt-85) REVERT: D 158 LEU cc_start: 0.9005 (tp) cc_final: 0.8667 (tp) REVERT: D 159 PHE cc_start: 0.7296 (m-80) cc_final: 0.6690 (m-80) REVERT: D 171 TRP cc_start: 0.7822 (p-90) cc_final: 0.6864 (p-90) REVERT: D 189 CYS cc_start: 0.9044 (m) cc_final: 0.8815 (m) REVERT: D 192 LEU cc_start: 0.9630 (tp) cc_final: 0.9358 (tp) REVERT: D 196 LEU cc_start: 0.9719 (mt) cc_final: 0.9496 (mt) REVERT: D 209 LEU cc_start: 0.8264 (tp) cc_final: 0.7751 (tp) REVERT: D 211 GLU cc_start: 0.8672 (tt0) cc_final: 0.8438 (tt0) REVERT: D 244 ASP cc_start: 0.8423 (t0) cc_final: 0.8209 (t0) REVERT: D 248 PHE cc_start: 0.9352 (m-80) cc_final: 0.9080 (m-10) REVERT: D 255 GLU cc_start: 0.8875 (pt0) cc_final: 0.8053 (pm20) REVERT: D 278 ASN cc_start: 0.8883 (p0) cc_final: 0.8676 (p0) REVERT: D 298 THR cc_start: 0.9547 (m) cc_final: 0.9145 (p) REVERT: D 299 SER cc_start: 0.9260 (p) cc_final: 0.8817 (p) REVERT: D 329 LYS cc_start: 0.9012 (mttt) cc_final: 0.8702 (mmpt) REVERT: D 355 GLU cc_start: 0.9153 (mt-10) cc_final: 0.8924 (mt-10) REVERT: D 358 MET cc_start: 0.8605 (mtm) cc_final: 0.8334 (mtm) REVERT: D 390 LYS cc_start: 0.9169 (mttt) cc_final: 0.8673 (mmtp) REVERT: D 391 LEU cc_start: 0.9549 (mt) cc_final: 0.9337 (mt) REVERT: D 420 LYS cc_start: 0.9304 (tttt) cc_final: 0.8385 (ttmt) REVERT: D 423 GLU cc_start: 0.9239 (mt-10) cc_final: 0.9026 (pp20) REVERT: D 424 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7893 (mt-10) REVERT: E 26 HIS cc_start: 0.5882 (t-90) cc_final: 0.5015 (t-90) REVERT: E 27 GLN cc_start: 0.7923 (tt0) cc_final: 0.7383 (tt0) REVERT: E 72 SER cc_start: 0.8487 (p) cc_final: 0.7902 (p) REVERT: E 141 TYR cc_start: 0.7885 (m-10) cc_final: 0.7583 (m-10) REVERT: E 148 HIS cc_start: 0.8532 (m90) cc_final: 0.8145 (m90) REVERT: E 154 MET cc_start: 0.8716 (tpt) cc_final: 0.8345 (ttm) REVERT: E 189 CYS cc_start: 0.9480 (t) cc_final: 0.8806 (t) REVERT: E 192 LEU cc_start: 0.9800 (tp) cc_final: 0.9547 (tp) REVERT: E 211 GLU cc_start: 0.7465 (tm-30) cc_final: 0.7223 (tm-30) REVERT: E 212 ILE cc_start: 0.8106 (pt) cc_final: 0.7444 (tp) REVERT: E 227 LYS cc_start: 0.9088 (tptp) cc_final: 0.8782 (tptp) REVERT: E 247 VAL cc_start: 0.8730 (p) cc_final: 0.8320 (m) REVERT: E 250 LEU cc_start: 0.9241 (tp) cc_final: 0.8922 (tp) REVERT: E 316 LYS cc_start: 0.8504 (mtmm) cc_final: 0.8181 (mtmm) REVERT: E 328 PHE cc_start: 0.9171 (t80) cc_final: 0.8642 (t80) REVERT: E 375 ASP cc_start: 0.8813 (m-30) cc_final: 0.8107 (t70) REVERT: E 388 LEU cc_start: 0.9300 (mt) cc_final: 0.8960 (mt) REVERT: F 136 TRP cc_start: 0.7864 (t-100) cc_final: 0.7469 (t-100) REVERT: F 195 LYS cc_start: 0.8816 (tppt) cc_final: 0.8474 (tppt) REVERT: F 200 LEU cc_start: 0.8836 (mm) cc_final: 0.8292 (pp) REVERT: F 289 ARG cc_start: 0.7636 (mtt180) cc_final: 0.6705 (tpt170) REVERT: F 328 PHE cc_start: 0.8434 (t80) cc_final: 0.8203 (t80) REVERT: F 338 LEU cc_start: 0.9027 (mt) cc_final: 0.8809 (mt) REVERT: F 339 MET cc_start: 0.8719 (mtt) cc_final: 0.8366 (mpp) REVERT: F 396 HIS cc_start: 0.9024 (t-90) cc_final: 0.8629 (t70) REVERT: P 67 GLU cc_start: 0.8039 (mt-10) cc_final: 0.7808 (pp20) REVERT: P 81 MET cc_start: 0.9455 (mmm) cc_final: 0.8950 (mmm) REVERT: P 125 GLN cc_start: 0.7169 (mm110) cc_final: 0.6299 (pm20) REVERT: P 139 GLU cc_start: 0.8819 (mt-10) cc_final: 0.8291 (tm-30) REVERT: P 150 VAL cc_start: 0.9343 (t) cc_final: 0.9115 (t) REVERT: P 214 MET cc_start: 0.8063 (mtp) cc_final: 0.7721 (mtp) REVERT: P 264 GLN cc_start: 0.9222 (tt0) cc_final: 0.8985 (tp40) REVERT: P 272 PHE cc_start: 0.8377 (p90) cc_final: 0.8013 (p90) REVERT: P 274 GLU cc_start: 0.6189 (mp0) cc_final: 0.5717 (mp0) REVERT: Z 24 PHE cc_start: 0.8353 (m-80) cc_final: 0.7595 (m-80) REVERT: Z 75 TRP cc_start: 0.9092 (m-10) cc_final: 0.8748 (m-10) REVERT: Z 90 ASN cc_start: 0.8535 (t0) cc_final: 0.7701 (t0) REVERT: Z 92 GLU cc_start: 0.7727 (tp30) cc_final: 0.7443 (pm20) REVERT: Z 113 ASP cc_start: 0.7277 (m-30) cc_final: 0.6976 (m-30) REVERT: Z 194 ASN cc_start: 0.8839 (m-40) cc_final: 0.8567 (m110) outliers start: 0 outliers final: 0 residues processed: 615 average time/residue: 0.2979 time to fit residues: 284.9489 Evaluate side-chains 496 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 496 time to evaluate : 2.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 150 optimal weight: 20.0000 chunk 97 optimal weight: 10.0000 chunk 145 optimal weight: 0.1980 chunk 73 optimal weight: 7.9990 chunk 47 optimal weight: 10.0000 chunk 155 optimal weight: 30.0000 chunk 166 optimal weight: 3.9990 chunk 120 optimal weight: 6.9990 chunk 22 optimal weight: 0.1980 chunk 191 optimal weight: 1.9990 chunk 221 optimal weight: 8.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 317 GLN A 396 HIS B 167 ASN C 178 HIS ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 ASN C 396 HIS ** D 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.4772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 20809 Z= 0.234 Angle : 0.697 10.146 28244 Z= 0.356 Chirality : 0.047 0.351 3369 Planarity : 0.005 0.104 3526 Dihedral : 9.341 134.711 2854 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 22.37 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.33 % Favored : 90.44 % Rotamer: Outliers : 0.05 % Allowed : 0.99 % Favored : 98.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.17 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.17), residues: 2541 helix: -0.21 (0.15), residues: 1121 sheet: -1.38 (0.26), residues: 357 loop : -2.07 (0.20), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP E 136 HIS 0.010 0.001 HIS A 215 PHE 0.034 0.002 PHE A 159 TYR 0.031 0.002 TYR D 141 ARG 0.011 0.001 ARG Z 133 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 608 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 607 time to evaluate : 2.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 ASP cc_start: 0.8959 (m-30) cc_final: 0.8387 (p0) REVERT: A 173 ARG cc_start: 0.7409 (mtt90) cc_final: 0.6957 (mpt-90) REVERT: A 213 ASN cc_start: 0.8710 (t0) cc_final: 0.8182 (t0) REVERT: A 250 LEU cc_start: 0.9363 (tp) cc_final: 0.9138 (tp) REVERT: A 275 ARG cc_start: 0.7637 (ptm160) cc_final: 0.6944 (mpt180) REVERT: A 287 ILE cc_start: 0.8486 (pt) cc_final: 0.8151 (pt) REVERT: A 290 HIS cc_start: 0.8327 (m90) cc_final: 0.7854 (m90) REVERT: A 296 LEU cc_start: 0.9662 (mt) cc_final: 0.9053 (mt) REVERT: A 311 ASP cc_start: 0.8266 (t0) cc_final: 0.8056 (t0) REVERT: A 391 LEU cc_start: 0.8994 (mt) cc_final: 0.8627 (mt) REVERT: A 393 PHE cc_start: 0.8695 (t80) cc_final: 0.8471 (t80) REVERT: A 398 LEU cc_start: 0.8953 (mt) cc_final: 0.8725 (tp) REVERT: A 410 PHE cc_start: 0.9021 (t80) cc_final: 0.8715 (t80) REVERT: B 68 ARG cc_start: 0.8915 (tpt90) cc_final: 0.8623 (tpt90) REVERT: B 127 LEU cc_start: 0.9060 (tp) cc_final: 0.8647 (tp) REVERT: B 141 TYR cc_start: 0.7214 (m-80) cc_final: 0.6956 (m-80) REVERT: B 154 MET cc_start: 0.9447 (mmm) cc_final: 0.9147 (mmm) REVERT: B 187 SER cc_start: 0.9595 (m) cc_final: 0.9235 (p) REVERT: B 190 LYS cc_start: 0.9358 (mtmt) cc_final: 0.9086 (mtpt) REVERT: B 211 GLU cc_start: 0.8832 (tt0) cc_final: 0.8094 (tp30) REVERT: B 231 LYS cc_start: 0.8228 (mttt) cc_final: 0.7870 (tmtt) REVERT: B 250 LEU cc_start: 0.9277 (tp) cc_final: 0.8113 (tp) REVERT: B 296 LEU cc_start: 0.9138 (mt) cc_final: 0.8476 (mt) REVERT: B 327 ILE cc_start: 0.9551 (mt) cc_final: 0.9237 (mt) REVERT: B 328 PHE cc_start: 0.9166 (t80) cc_final: 0.8689 (t80) REVERT: B 329 LYS cc_start: 0.9085 (mttt) cc_final: 0.8829 (mmmm) REVERT: B 335 LEU cc_start: 0.9830 (mt) cc_final: 0.9535 (mt) REVERT: B 339 MET cc_start: 0.8194 (mtt) cc_final: 0.7877 (mmt) REVERT: B 388 LEU cc_start: 0.9725 (mm) cc_final: 0.9509 (mm) REVERT: C 141 TYR cc_start: 0.8175 (t80) cc_final: 0.7929 (t80) REVERT: C 163 ASN cc_start: 0.8544 (t0) cc_final: 0.8338 (t0) REVERT: C 224 GLU cc_start: 0.8157 (tp30) cc_final: 0.7651 (tp30) REVERT: C 228 LEU cc_start: 0.9500 (pp) cc_final: 0.8763 (pp) REVERT: C 368 LYS cc_start: 0.9225 (pttm) cc_final: 0.8900 (pttp) REVERT: D 27 GLN cc_start: 0.9358 (tt0) cc_final: 0.9060 (tt0) REVERT: D 48 ARG cc_start: 0.8378 (ttm170) cc_final: 0.7784 (mtt180) REVERT: D 158 LEU cc_start: 0.8994 (tp) cc_final: 0.8759 (tp) REVERT: D 171 TRP cc_start: 0.7660 (p-90) cc_final: 0.6453 (p-90) REVERT: D 192 LEU cc_start: 0.9636 (tp) cc_final: 0.9343 (tp) REVERT: D 196 LEU cc_start: 0.9713 (mt) cc_final: 0.9509 (mt) REVERT: D 211 GLU cc_start: 0.8583 (tt0) cc_final: 0.8285 (tt0) REVERT: D 244 ASP cc_start: 0.8463 (t0) cc_final: 0.8226 (t0) REVERT: D 248 PHE cc_start: 0.9356 (m-80) cc_final: 0.9058 (m-10) REVERT: D 255 GLU cc_start: 0.8862 (pt0) cc_final: 0.8032 (pm20) REVERT: D 298 THR cc_start: 0.9542 (m) cc_final: 0.9298 (p) REVERT: D 299 SER cc_start: 0.9228 (p) cc_final: 0.8803 (p) REVERT: D 316 LYS cc_start: 0.8240 (mtpt) cc_final: 0.7577 (mtpt) REVERT: D 329 LYS cc_start: 0.8976 (mttt) cc_final: 0.8662 (mmpt) REVERT: D 355 GLU cc_start: 0.9180 (mt-10) cc_final: 0.8955 (mt-10) REVERT: D 358 MET cc_start: 0.8604 (mtm) cc_final: 0.8330 (mtm) REVERT: D 390 LYS cc_start: 0.9210 (mttt) cc_final: 0.8712 (mmtp) REVERT: D 391 LEU cc_start: 0.9551 (mt) cc_final: 0.9341 (mt) REVERT: D 420 LYS cc_start: 0.9287 (tttt) cc_final: 0.8348 (ttmt) REVERT: D 423 GLU cc_start: 0.9232 (mt-10) cc_final: 0.9026 (pp20) REVERT: D 424 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7924 (mt-10) REVERT: E 26 HIS cc_start: 0.5813 (t-90) cc_final: 0.4897 (t-90) REVERT: E 62 ASP cc_start: 0.7654 (m-30) cc_final: 0.7452 (t0) REVERT: E 72 SER cc_start: 0.8306 (p) cc_final: 0.7457 (p) REVERT: E 141 TYR cc_start: 0.8150 (m-10) cc_final: 0.7773 (m-10) REVERT: E 148 HIS cc_start: 0.8508 (m90) cc_final: 0.8186 (m90) REVERT: E 154 MET cc_start: 0.8713 (tpt) cc_final: 0.8343 (ttm) REVERT: E 176 LEU cc_start: 0.9729 (tp) cc_final: 0.9439 (tp) REVERT: E 177 LEU cc_start: 0.9470 (mp) cc_final: 0.9031 (tp) REVERT: E 189 CYS cc_start: 0.9244 (t) cc_final: 0.8708 (t) REVERT: E 209 LEU cc_start: 0.8754 (mm) cc_final: 0.7950 (tp) REVERT: E 212 ILE cc_start: 0.8120 (pt) cc_final: 0.7521 (tp) REVERT: E 227 LYS cc_start: 0.9037 (tptp) cc_final: 0.8707 (tptp) REVERT: E 247 VAL cc_start: 0.8803 (p) cc_final: 0.8365 (m) REVERT: E 250 LEU cc_start: 0.9227 (tp) cc_final: 0.8973 (tp) REVERT: E 282 THR cc_start: 0.9375 (p) cc_final: 0.9118 (p) REVERT: E 316 LYS cc_start: 0.8531 (mtmm) cc_final: 0.8182 (mtmm) REVERT: E 328 PHE cc_start: 0.9159 (t80) cc_final: 0.8624 (t80) REVERT: E 375 ASP cc_start: 0.8804 (m-30) cc_final: 0.8090 (t70) REVERT: E 388 LEU cc_start: 0.9323 (mt) cc_final: 0.8989 (mt) REVERT: F 200 LEU cc_start: 0.8860 (mm) cc_final: 0.8288 (pp) REVERT: F 328 PHE cc_start: 0.8457 (t80) cc_final: 0.8223 (t80) REVERT: F 338 LEU cc_start: 0.8999 (mt) cc_final: 0.8789 (mt) REVERT: F 339 MET cc_start: 0.8711 (mtt) cc_final: 0.8351 (mpp) REVERT: F 396 HIS cc_start: 0.8935 (t-90) cc_final: 0.8662 (t70) REVERT: P 67 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7810 (pp20) REVERT: P 78 LYS cc_start: 0.8969 (mtmm) cc_final: 0.8755 (mttp) REVERT: P 81 MET cc_start: 0.9427 (mmm) cc_final: 0.8883 (mmm) REVERT: P 125 GLN cc_start: 0.7160 (mm110) cc_final: 0.6286 (pm20) REVERT: P 139 GLU cc_start: 0.8794 (mt-10) cc_final: 0.8358 (tm-30) REVERT: P 150 VAL cc_start: 0.9377 (t) cc_final: 0.9123 (t) REVERT: P 151 LEU cc_start: 0.8985 (mt) cc_final: 0.8772 (mt) REVERT: P 186 CYS cc_start: 0.9430 (m) cc_final: 0.9014 (p) REVERT: P 214 MET cc_start: 0.8028 (mtp) cc_final: 0.7621 (mtp) REVERT: P 264 GLN cc_start: 0.9191 (tt0) cc_final: 0.8894 (tp40) REVERT: P 274 GLU cc_start: 0.6012 (mp0) cc_final: 0.5707 (mp0) REVERT: Z 4 GLN cc_start: 0.7378 (mt0) cc_final: 0.7096 (mt0) REVERT: Z 24 PHE cc_start: 0.8070 (m-80) cc_final: 0.7542 (m-80) REVERT: Z 26 PHE cc_start: 0.9149 (m-80) cc_final: 0.8741 (m-80) REVERT: Z 75 TRP cc_start: 0.9109 (m-10) cc_final: 0.8748 (m-10) REVERT: Z 90 ASN cc_start: 0.8570 (t0) cc_final: 0.7764 (t0) REVERT: Z 113 ASP cc_start: 0.7275 (m-30) cc_final: 0.6972 (m-30) REVERT: Z 194 ASN cc_start: 0.8801 (m-40) cc_final: 0.8562 (m110) outliers start: 1 outliers final: 1 residues processed: 608 average time/residue: 0.3207 time to fit residues: 305.6904 Evaluate side-chains 499 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 498 time to evaluate : 2.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 233 optimal weight: 6.9990 chunk 213 optimal weight: 9.9990 chunk 227 optimal weight: 10.0000 chunk 136 optimal weight: 10.0000 chunk 98 optimal weight: 6.9990 chunk 178 optimal weight: 0.9980 chunk 69 optimal weight: 20.0000 chunk 205 optimal weight: 4.9990 chunk 214 optimal weight: 5.9990 chunk 226 optimal weight: 0.0770 chunk 149 optimal weight: 8.9990 overall best weight: 3.8144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 GLN A 396 HIS B 167 ASN ** B 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 178 HIS ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 ASN C 396 HIS ** D 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 167 ASN ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 374 ASN E 412 GLN ** F 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.4904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 20809 Z= 0.280 Angle : 0.736 11.148 28244 Z= 0.378 Chirality : 0.047 0.271 3369 Planarity : 0.005 0.104 3526 Dihedral : 9.550 136.050 2854 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 23.57 Ramachandran Plot: Outliers : 0.28 % Allowed : 10.67 % Favored : 89.06 % Rotamer: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.17 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.17), residues: 2541 helix: -0.23 (0.15), residues: 1111 sheet: -1.36 (0.26), residues: 358 loop : -2.08 (0.20), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP E 136 HIS 0.011 0.002 HIS A 215 PHE 0.029 0.002 PHE Z 26 TYR 0.029 0.002 TYR A 152 ARG 0.015 0.001 ARG B 386 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 591 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 591 time to evaluate : 2.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 ASP cc_start: 0.8909 (m-30) cc_final: 0.8364 (p0) REVERT: A 150 LEU cc_start: 0.9054 (tp) cc_final: 0.8749 (tp) REVERT: A 154 MET cc_start: 0.9104 (ttm) cc_final: 0.8700 (ptm) REVERT: A 173 ARG cc_start: 0.7439 (mtt90) cc_final: 0.6978 (mpt-90) REVERT: A 213 ASN cc_start: 0.8716 (t0) cc_final: 0.8261 (t0) REVERT: A 247 VAL cc_start: 0.9386 (t) cc_final: 0.8890 (t) REVERT: A 275 ARG cc_start: 0.7766 (ptm160) cc_final: 0.7136 (mpt180) REVERT: A 287 ILE cc_start: 0.8487 (pt) cc_final: 0.8202 (pt) REVERT: A 290 HIS cc_start: 0.8446 (m90) cc_final: 0.7691 (m90) REVERT: A 292 ASN cc_start: 0.8225 (p0) cc_final: 0.5241 (t0) REVERT: A 296 LEU cc_start: 0.9672 (mt) cc_final: 0.9216 (mt) REVERT: A 311 ASP cc_start: 0.8255 (t0) cc_final: 0.8048 (t0) REVERT: A 331 TYR cc_start: 0.8763 (m-10) cc_final: 0.8265 (m-80) REVERT: A 391 LEU cc_start: 0.9004 (mt) cc_final: 0.8661 (mt) REVERT: A 393 PHE cc_start: 0.8759 (t80) cc_final: 0.8534 (t80) REVERT: A 398 LEU cc_start: 0.8914 (mt) cc_final: 0.8356 (tp) REVERT: A 410 PHE cc_start: 0.9072 (t80) cc_final: 0.8801 (t80) REVERT: B 68 ARG cc_start: 0.8944 (tpt90) cc_final: 0.8649 (tpt90) REVERT: B 123 ASN cc_start: 0.8218 (m-40) cc_final: 0.7342 (m-40) REVERT: B 127 LEU cc_start: 0.9029 (tp) cc_final: 0.8615 (tp) REVERT: B 141 TYR cc_start: 0.7160 (m-80) cc_final: 0.6849 (m-80) REVERT: B 154 MET cc_start: 0.9425 (mmm) cc_final: 0.9171 (mmm) REVERT: B 187 SER cc_start: 0.9538 (m) cc_final: 0.9311 (p) REVERT: B 188 LEU cc_start: 0.9806 (tp) cc_final: 0.9485 (tp) REVERT: B 190 LYS cc_start: 0.9382 (mtmt) cc_final: 0.9104 (mtpt) REVERT: B 211 GLU cc_start: 0.8802 (tt0) cc_final: 0.8513 (tt0) REVERT: B 231 LYS cc_start: 0.8231 (mttt) cc_final: 0.7880 (tmtt) REVERT: B 296 LEU cc_start: 0.9133 (mt) cc_final: 0.8434 (mt) REVERT: B 327 ILE cc_start: 0.9677 (mt) cc_final: 0.9447 (mt) REVERT: B 328 PHE cc_start: 0.9178 (t80) cc_final: 0.8535 (t80) REVERT: B 329 LYS cc_start: 0.9097 (mttt) cc_final: 0.8833 (mmmm) REVERT: B 335 LEU cc_start: 0.9833 (mt) cc_final: 0.9509 (mt) REVERT: B 339 MET cc_start: 0.8232 (mtt) cc_final: 0.7904 (mmt) REVERT: C 141 TYR cc_start: 0.8171 (t80) cc_final: 0.7952 (t80) REVERT: C 163 ASN cc_start: 0.8628 (t0) cc_final: 0.8365 (t0) REVERT: C 224 GLU cc_start: 0.8200 (tp30) cc_final: 0.7753 (tp30) REVERT: C 228 LEU cc_start: 0.9493 (pp) cc_final: 0.8685 (pp) REVERT: C 253 GLN cc_start: 0.9054 (mt0) cc_final: 0.8830 (mt0) REVERT: C 283 GLN cc_start: 0.9268 (mm-40) cc_final: 0.8689 (mm110) REVERT: C 347 ARG cc_start: 0.8904 (ptp-110) cc_final: 0.8686 (mtp85) REVERT: C 368 LYS cc_start: 0.9253 (pttm) cc_final: 0.8951 (pttp) REVERT: D 27 GLN cc_start: 0.9394 (tt0) cc_final: 0.9051 (tt0) REVERT: D 48 ARG cc_start: 0.8451 (ttm170) cc_final: 0.7768 (mtt180) REVERT: D 124 HIS cc_start: 0.8745 (t-90) cc_final: 0.8295 (t-90) REVERT: D 158 LEU cc_start: 0.8997 (tp) cc_final: 0.8646 (tp) REVERT: D 159 PHE cc_start: 0.7503 (m-80) cc_final: 0.6756 (m-80) REVERT: D 171 TRP cc_start: 0.7724 (p-90) cc_final: 0.6347 (p-90) REVERT: D 192 LEU cc_start: 0.9629 (tp) cc_final: 0.9367 (tp) REVERT: D 211 GLU cc_start: 0.8498 (tt0) cc_final: 0.8097 (tt0) REVERT: D 240 ILE cc_start: 0.9448 (mm) cc_final: 0.9198 (mm) REVERT: D 248 PHE cc_start: 0.9384 (m-80) cc_final: 0.9105 (m-10) REVERT: D 255 GLU cc_start: 0.8853 (pt0) cc_final: 0.8036 (pm20) REVERT: D 296 LEU cc_start: 0.9289 (mt) cc_final: 0.8989 (mt) REVERT: D 298 THR cc_start: 0.9598 (m) cc_final: 0.9317 (p) REVERT: D 299 SER cc_start: 0.9225 (p) cc_final: 0.8835 (p) REVERT: D 329 LYS cc_start: 0.8960 (mttt) cc_final: 0.8677 (mmpt) REVERT: D 355 GLU cc_start: 0.9174 (mt-10) cc_final: 0.8941 (mt-10) REVERT: D 358 MET cc_start: 0.8644 (mtm) cc_final: 0.8369 (mtm) REVERT: D 390 LYS cc_start: 0.9229 (mttt) cc_final: 0.8714 (mmtp) REVERT: D 391 LEU cc_start: 0.9545 (mt) cc_final: 0.9339 (mt) REVERT: D 420 LYS cc_start: 0.9295 (tttt) cc_final: 0.8294 (ttmt) REVERT: D 424 GLU cc_start: 0.8265 (mt-10) cc_final: 0.7940 (mt-10) REVERT: E 62 ASP cc_start: 0.7777 (m-30) cc_final: 0.7532 (t0) REVERT: E 148 HIS cc_start: 0.8626 (m90) cc_final: 0.8224 (m90) REVERT: E 154 MET cc_start: 0.8710 (tpt) cc_final: 0.8342 (ttm) REVERT: E 168 LEU cc_start: 0.9444 (mp) cc_final: 0.8279 (tt) REVERT: E 189 CYS cc_start: 0.9324 (t) cc_final: 0.8984 (t) REVERT: E 247 VAL cc_start: 0.8797 (p) cc_final: 0.8308 (m) REVERT: E 316 LYS cc_start: 0.8574 (mtmm) cc_final: 0.8257 (mtmm) REVERT: E 358 MET cc_start: 0.6731 (ptp) cc_final: 0.6342 (pmm) REVERT: E 375 ASP cc_start: 0.8804 (m-30) cc_final: 0.8118 (t70) REVERT: E 388 LEU cc_start: 0.9308 (mt) cc_final: 0.8954 (mt) REVERT: F 136 TRP cc_start: 0.7875 (t-100) cc_final: 0.7494 (t-100) REVERT: F 159 PHE cc_start: 0.8856 (m-80) cc_final: 0.8653 (m-80) REVERT: F 192 LEU cc_start: 0.9649 (tp) cc_final: 0.9443 (tp) REVERT: F 195 LYS cc_start: 0.8858 (tppt) cc_final: 0.8461 (tppt) REVERT: F 200 LEU cc_start: 0.8879 (mm) cc_final: 0.8328 (pp) REVERT: F 338 LEU cc_start: 0.9029 (mt) cc_final: 0.8801 (mt) REVERT: F 339 MET cc_start: 0.8732 (mtt) cc_final: 0.8339 (mpp) REVERT: F 396 HIS cc_start: 0.9045 (t-90) cc_final: 0.8636 (t70) REVERT: P 55 MET cc_start: 0.8228 (tpt) cc_final: 0.6783 (mpp) REVERT: P 67 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7834 (pp20) REVERT: P 81 MET cc_start: 0.9430 (mmm) cc_final: 0.8918 (mmm) REVERT: P 85 GLN cc_start: 0.8965 (mp-120) cc_final: 0.8669 (mp10) REVERT: P 87 LEU cc_start: 0.9324 (mm) cc_final: 0.9094 (mm) REVERT: P 125 GLN cc_start: 0.6966 (mm110) cc_final: 0.6017 (pm20) REVERT: P 139 GLU cc_start: 0.8913 (mt-10) cc_final: 0.8402 (tm-30) REVERT: P 150 VAL cc_start: 0.9371 (t) cc_final: 0.9111 (t) REVERT: P 151 LEU cc_start: 0.9023 (mt) cc_final: 0.8809 (mt) REVERT: P 186 CYS cc_start: 0.9438 (m) cc_final: 0.9148 (m) REVERT: P 214 MET cc_start: 0.8041 (mtp) cc_final: 0.7813 (mtp) REVERT: P 274 GLU cc_start: 0.6682 (mp0) cc_final: 0.5793 (mp0) REVERT: Z 4 GLN cc_start: 0.7442 (mt0) cc_final: 0.7137 (mt0) REVERT: Z 24 PHE cc_start: 0.8104 (m-80) cc_final: 0.7523 (m-80) REVERT: Z 75 TRP cc_start: 0.9126 (m-10) cc_final: 0.8779 (m-10) REVERT: Z 113 ASP cc_start: 0.7330 (m-30) cc_final: 0.6978 (m-30) outliers start: 0 outliers final: 0 residues processed: 591 average time/residue: 0.2997 time to fit residues: 276.8040 Evaluate side-chains 473 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 473 time to evaluate : 2.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 240 optimal weight: 7.9990 chunk 146 optimal weight: 4.9990 chunk 113 optimal weight: 0.9980 chunk 167 optimal weight: 6.9990 chunk 252 optimal weight: 3.9990 chunk 231 optimal weight: 0.4980 chunk 200 optimal weight: 7.9990 chunk 20 optimal weight: 6.9990 chunk 155 optimal weight: 0.7980 chunk 123 optimal weight: 5.9990 chunk 159 optimal weight: 2.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 396 HIS B 167 ASN C 208 GLN C 374 ASN C 396 HIS ** D 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 69 ASN E 167 ASN ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.5164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 20809 Z= 0.215 Angle : 0.716 10.007 28244 Z= 0.364 Chirality : 0.048 0.277 3369 Planarity : 0.005 0.110 3526 Dihedral : 9.304 134.621 2854 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 21.54 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.62 % Favored : 91.11 % Rotamer: Outliers : 0.09 % Allowed : 0.41 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.17 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.17), residues: 2541 helix: -0.12 (0.15), residues: 1122 sheet: -1.23 (0.27), residues: 354 loop : -1.97 (0.20), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 221 HIS 0.011 0.001 HIS A 215 PHE 0.025 0.002 PHE D 422 TYR 0.030 0.002 TYR D 141 ARG 0.019 0.001 ARG B 386 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 612 time to evaluate : 2.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 ASP cc_start: 0.8856 (m-30) cc_final: 0.8331 (p0) REVERT: A 173 ARG cc_start: 0.7453 (mtt90) cc_final: 0.7000 (mpt-90) REVERT: A 213 ASN cc_start: 0.8610 (t0) cc_final: 0.8168 (t0) REVERT: A 275 ARG cc_start: 0.7799 (ptm160) cc_final: 0.6979 (mpt180) REVERT: A 287 ILE cc_start: 0.8483 (pt) cc_final: 0.8174 (pt) REVERT: A 290 HIS cc_start: 0.8638 (m90) cc_final: 0.8145 (m90) REVERT: A 296 LEU cc_start: 0.9655 (mt) cc_final: 0.9180 (mt) REVERT: A 311 ASP cc_start: 0.8267 (t0) cc_final: 0.8042 (t0) REVERT: A 331 TYR cc_start: 0.8820 (m-10) cc_final: 0.8284 (m-80) REVERT: A 377 SER cc_start: 0.8039 (t) cc_final: 0.7541 (p) REVERT: A 399 TYR cc_start: 0.8106 (m-80) cc_final: 0.7407 (m-80) REVERT: A 410 PHE cc_start: 0.8881 (t80) cc_final: 0.8582 (t80) REVERT: B 68 ARG cc_start: 0.8916 (tpt90) cc_final: 0.8615 (tpt90) REVERT: B 123 ASN cc_start: 0.8197 (m-40) cc_final: 0.7285 (m-40) REVERT: B 127 LEU cc_start: 0.8975 (tp) cc_final: 0.8536 (tp) REVERT: B 135 LEU cc_start: 0.8999 (tt) cc_final: 0.8460 (mm) REVERT: B 141 TYR cc_start: 0.7228 (m-80) cc_final: 0.7021 (m-80) REVERT: B 168 LEU cc_start: 0.9410 (mt) cc_final: 0.9035 (mt) REVERT: B 187 SER cc_start: 0.9530 (m) cc_final: 0.9318 (p) REVERT: B 190 LYS cc_start: 0.9369 (mtmt) cc_final: 0.9097 (mtpt) REVERT: B 211 GLU cc_start: 0.8747 (tt0) cc_final: 0.8479 (tt0) REVERT: B 231 LYS cc_start: 0.8263 (mttt) cc_final: 0.7868 (tmtt) REVERT: B 296 LEU cc_start: 0.9217 (mt) cc_final: 0.8577 (mt) REVERT: B 327 ILE cc_start: 0.9535 (mt) cc_final: 0.9260 (mt) REVERT: B 328 PHE cc_start: 0.9158 (t80) cc_final: 0.8815 (t80) REVERT: B 329 LYS cc_start: 0.9055 (mttt) cc_final: 0.8832 (mmmm) REVERT: B 335 LEU cc_start: 0.9819 (mt) cc_final: 0.9572 (mt) REVERT: B 339 MET cc_start: 0.8205 (mtt) cc_final: 0.7888 (mmt) REVERT: B 362 ILE cc_start: 0.8786 (tp) cc_final: 0.8518 (pt) REVERT: B 388 LEU cc_start: 0.9722 (mm) cc_final: 0.9447 (mm) REVERT: B 410 PHE cc_start: 0.9292 (t80) cc_final: 0.9043 (t80) REVERT: B 419 ASP cc_start: 0.9102 (m-30) cc_final: 0.8651 (m-30) REVERT: C 141 TYR cc_start: 0.8183 (t80) cc_final: 0.7933 (t80) REVERT: C 167 ASN cc_start: 0.8615 (m-40) cc_final: 0.8374 (m-40) REVERT: C 224 GLU cc_start: 0.8133 (tp30) cc_final: 0.7696 (tp30) REVERT: C 228 LEU cc_start: 0.9478 (pp) cc_final: 0.8675 (pp) REVERT: C 248 PHE cc_start: 0.9059 (m-80) cc_final: 0.8689 (m-80) REVERT: C 253 GLN cc_start: 0.9011 (mt0) cc_final: 0.8766 (mt0) REVERT: C 339 MET cc_start: 0.7168 (ttp) cc_final: 0.6705 (tmm) REVERT: C 347 ARG cc_start: 0.8918 (ptp-110) cc_final: 0.8502 (mtp85) REVERT: C 368 LYS cc_start: 0.9193 (pttm) cc_final: 0.8882 (pttp) REVERT: D 27 GLN cc_start: 0.9344 (tt0) cc_final: 0.9019 (tt0) REVERT: D 48 ARG cc_start: 0.8417 (ttm170) cc_final: 0.7723 (mtt180) REVERT: D 133 HIS cc_start: 0.7760 (t70) cc_final: 0.7473 (t70) REVERT: D 154 MET cc_start: 0.9340 (tpp) cc_final: 0.8846 (mtt) REVERT: D 158 LEU cc_start: 0.8997 (tp) cc_final: 0.8460 (tt) REVERT: D 168 LEU cc_start: 0.9696 (mt) cc_final: 0.9233 (tt) REVERT: D 171 TRP cc_start: 0.7655 (p-90) cc_final: 0.6313 (p-90) REVERT: D 192 LEU cc_start: 0.9648 (tp) cc_final: 0.9234 (tp) REVERT: D 211 GLU cc_start: 0.8322 (tt0) cc_final: 0.8016 (tt0) REVERT: D 248 PHE cc_start: 0.9358 (m-80) cc_final: 0.9053 (m-10) REVERT: D 296 LEU cc_start: 0.9237 (mt) cc_final: 0.8956 (mt) REVERT: D 298 THR cc_start: 0.9589 (m) cc_final: 0.9253 (p) REVERT: D 329 LYS cc_start: 0.8970 (mttt) cc_final: 0.8703 (mmpt) REVERT: D 355 GLU cc_start: 0.9211 (mt-10) cc_final: 0.8938 (mt-10) REVERT: D 358 MET cc_start: 0.8627 (mtm) cc_final: 0.8344 (mtm) REVERT: D 369 LEU cc_start: 0.9362 (pp) cc_final: 0.9040 (tt) REVERT: D 390 LYS cc_start: 0.9279 (mttt) cc_final: 0.8830 (mmtp) REVERT: D 391 LEU cc_start: 0.9566 (mt) cc_final: 0.9362 (mt) REVERT: D 420 LYS cc_start: 0.8973 (tttt) cc_final: 0.8483 (ttmt) REVERT: D 424 GLU cc_start: 0.8639 (mt-10) cc_final: 0.7970 (mt-10) REVERT: E 133 HIS cc_start: 0.8440 (t70) cc_final: 0.8066 (t70) REVERT: E 148 HIS cc_start: 0.8641 (m90) cc_final: 0.8434 (m90) REVERT: E 154 MET cc_start: 0.8702 (tpt) cc_final: 0.8324 (ttm) REVERT: E 189 CYS cc_start: 0.9441 (t) cc_final: 0.9002 (t) REVERT: E 209 LEU cc_start: 0.8749 (mm) cc_final: 0.7931 (tp) REVERT: E 247 VAL cc_start: 0.8842 (p) cc_final: 0.8399 (m) REVERT: E 316 LYS cc_start: 0.8499 (mtmm) cc_final: 0.8195 (mtmm) REVERT: E 328 PHE cc_start: 0.9169 (t80) cc_final: 0.8646 (t80) REVERT: E 375 ASP cc_start: 0.8790 (m-30) cc_final: 0.8100 (t70) REVERT: E 388 LEU cc_start: 0.9326 (mt) cc_final: 0.8991 (mt) REVERT: F 136 TRP cc_start: 0.7899 (t-100) cc_final: 0.7556 (t-100) REVERT: F 195 LYS cc_start: 0.8852 (tppt) cc_final: 0.8499 (tppt) REVERT: F 200 LEU cc_start: 0.8847 (mm) cc_final: 0.8279 (pp) REVERT: F 328 PHE cc_start: 0.8469 (t80) cc_final: 0.8260 (t80) REVERT: F 338 LEU cc_start: 0.9023 (mt) cc_final: 0.8774 (mt) REVERT: F 339 MET cc_start: 0.8738 (mtt) cc_final: 0.8293 (mpp) REVERT: F 396 HIS cc_start: 0.8971 (t-90) cc_final: 0.8640 (t70) REVERT: P 55 MET cc_start: 0.8187 (tpt) cc_final: 0.6667 (mpp) REVERT: P 67 GLU cc_start: 0.8006 (mt-10) cc_final: 0.7787 (pp20) REVERT: P 81 MET cc_start: 0.9386 (mmm) cc_final: 0.8886 (mmm) REVERT: P 125 GLN cc_start: 0.6978 (mm110) cc_final: 0.5944 (pm20) REVERT: P 134 VAL cc_start: 0.9387 (t) cc_final: 0.9082 (t) REVERT: P 139 GLU cc_start: 0.8819 (mt-10) cc_final: 0.8289 (tm-30) REVERT: P 150 VAL cc_start: 0.9358 (t) cc_final: 0.9094 (t) REVERT: P 151 LEU cc_start: 0.9008 (mt) cc_final: 0.8790 (mt) REVERT: P 186 CYS cc_start: 0.9414 (m) cc_final: 0.8965 (p) REVERT: P 214 MET cc_start: 0.7911 (mtp) cc_final: 0.7567 (mtp) REVERT: P 225 TRP cc_start: 0.9369 (t-100) cc_final: 0.8706 (t-100) REVERT: P 264 GLN cc_start: 0.9125 (tt0) cc_final: 0.8882 (tp40) REVERT: P 272 PHE cc_start: 0.8534 (p90) cc_final: 0.8247 (p90) REVERT: P 274 GLU cc_start: 0.6805 (mp0) cc_final: 0.5946 (mp0) REVERT: Z 24 PHE cc_start: 0.8148 (m-80) cc_final: 0.7558 (m-80) REVERT: Z 75 TRP cc_start: 0.9129 (m-10) cc_final: 0.8703 (m-10) REVERT: Z 113 ASP cc_start: 0.7343 (m-30) cc_final: 0.7059 (m-30) REVERT: Z 128 ILE cc_start: 0.8956 (mm) cc_final: 0.8755 (mm) REVERT: Z 196 MET cc_start: 0.7231 (tmm) cc_final: 0.6933 (tmm) outliers start: 2 outliers final: 1 residues processed: 614 average time/residue: 0.3354 time to fit residues: 323.1241 Evaluate side-chains 498 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 497 time to evaluate : 2.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 213 optimal weight: 10.0000 chunk 61 optimal weight: 0.0570 chunk 185 optimal weight: 20.0000 chunk 29 optimal weight: 10.0000 chunk 55 optimal weight: 0.0470 chunk 201 optimal weight: 20.0000 chunk 84 optimal weight: 3.9990 chunk 206 optimal weight: 0.5980 chunk 25 optimal weight: 10.0000 chunk 37 optimal weight: 10.0000 chunk 176 optimal weight: 0.0040 overall best weight: 0.9410 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 396 HIS B 167 ASN C 178 HIS C 374 ASN C 396 HIS ** D 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 348 GLN ** E 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.117315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.091320 restraints weight = 60830.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.094348 restraints weight = 38057.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.096469 restraints weight = 26848.623| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.5458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20809 Z= 0.194 Angle : 0.708 9.978 28244 Z= 0.359 Chirality : 0.048 0.279 3369 Planarity : 0.005 0.105 3526 Dihedral : 9.166 134.666 2854 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 20.59 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.50 % Favored : 91.26 % Rotamer: Outliers : 0.05 % Allowed : 0.32 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.17 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.17), residues: 2541 helix: 0.02 (0.15), residues: 1127 sheet: -1.09 (0.27), residues: 353 loop : -1.91 (0.20), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP D 136 HIS 0.010 0.001 HIS A 215 PHE 0.023 0.002 PHE A 159 TYR 0.035 0.002 TYR B 399 ARG 0.010 0.001 ARG Q 132 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5661.68 seconds wall clock time: 102 minutes 52.61 seconds (6172.61 seconds total)