Starting phenix.real_space_refine on Sun Mar 17 23:17:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6znm_11317/03_2024/6znm_11317_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6znm_11317/03_2024/6znm_11317.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6znm_11317/03_2024/6znm_11317.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6znm_11317/03_2024/6znm_11317.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6znm_11317/03_2024/6znm_11317_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6znm_11317/03_2024/6znm_11317_updated.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 3 6.06 5 P 9 5.49 5 S 97 5.16 5 C 12189 2.51 5 N 3377 2.21 5 O 3578 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G GLU 87": "OE1" <-> "OE2" Residue "G ARG 121": "NH1" <-> "NH2" Residue "G ARG 199": "NH1" <-> "NH2" Residue "G GLU 237": "OE1" <-> "OE2" Residue "G GLU 270": "OE1" <-> "OE2" Residue "G ARG 291": "NH1" <-> "NH2" Residue "G ARG 329": "NH1" <-> "NH2" Residue "G ARG 369": "NH1" <-> "NH2" Residue "H TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 177": "NH1" <-> "NH2" Residue "H ARG 183": "NH1" <-> "NH2" Residue "H GLU 226": "OE1" <-> "OE2" Residue "H GLU 316": "OE1" <-> "OE2" Residue "I GLU 237": "OE1" <-> "OE2" Residue "I ARG 373": "NH1" <-> "NH2" Residue "J GLU 22": "OE1" <-> "OE2" Residue "J ARG 85": "NH1" <-> "NH2" Residue "J GLU 114": "OE1" <-> "OE2" Residue "J GLU 204": "OE1" <-> "OE2" Residue "J GLU 253": "OE1" <-> "OE2" Residue "J ARG 263": "NH1" <-> "NH2" Residue "J GLU 276": "OE1" <-> "OE2" Residue "M ARG 74": "NH1" <-> "NH2" Residue "M GLU 84": "OE1" <-> "OE2" Residue "U GLU 22": "OE1" <-> "OE2" Residue "U GLU 44": "OE1" <-> "OE2" Residue "U GLU 52": "OE1" <-> "OE2" Residue "U GLU 58": "OE1" <-> "OE2" Residue "U GLU 91": "OE1" <-> "OE2" Residue "U GLU 135": "OE1" <-> "OE2" Residue "U GLU 139": "OE1" <-> "OE2" Residue "U ARG 151": "NH1" <-> "NH2" Residue "V ARG 24": "NH1" <-> "NH2" Residue "V ARG 49": "NH1" <-> "NH2" Residue "Y ARG 31": "NH1" <-> "NH2" Residue "Y ARG 37": "NH1" <-> "NH2" Residue "Y GLU 45": "OE1" <-> "OE2" Residue "Y GLU 56": "OE1" <-> "OE2" Residue "Y ARG 86": "NH1" <-> "NH2" Residue "Y ARG 119": "NH1" <-> "NH2" Residue "Y GLU 149": "OE1" <-> "OE2" Residue "Y GLU 161": "OE1" <-> "OE2" Residue "Y ARG 164": "NH1" <-> "NH2" Residue "Y ARG 255": "NH1" <-> "NH2" Residue "Y ARG 272": "NH1" <-> "NH2" Residue "Y ARG 280": "NH1" <-> "NH2" Residue "Y ARG 285": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 19253 Number of models: 1 Model: "" Number of chains: 15 Chain: "G" Number of atoms: 2956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2956 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Chain: "H" Number of atoms: 2885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2885 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Chain: "I" Number of atoms: 2941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2941 Classifications: {'peptide': 370} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "J" Number of atoms: 2932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 2932 Classifications: {'peptide': 379} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 24, 'TRANS': 354} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "M" Number of atoms: 583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 583 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 69} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "U" Number of atoms: 1224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1224 Classifications: {'peptide': 167} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 12, 'TRANS': 154} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 3, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "V" Number of atoms: 1260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1260 Classifications: {'peptide': 179} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 10, 'TRANS': 168} Unresolved non-hydrogen bonds: 125 Unresolved non-hydrogen angles: 152 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 85 Chain: "X" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 693 Classifications: {'peptide': 139} Incomplete info: {'truncation_to_alanine': 135} Link IDs: {'TRANS': 138} Unresolved non-hydrogen bonds: 385 Unresolved non-hydrogen angles: 516 Unresolved non-hydrogen dihedrals: 263 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 10, 'UNK:plan-1': 64, 'ASP:plan': 5, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 3, 'GLU:plan': 11, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 223 Chain: "Y" Number of atoms: 2956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 2956 Classifications: {'peptide': 410} Incomplete info: {'truncation_to_alanine': 96} Link IDs: {'PTRANS': 30, 'TRANS': 379} Chain breaks: 2 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 335 Unresolved non-hydrogen angles: 425 Unresolved non-hydrogen dihedrals: 266 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 14, 'PHE:plan': 3, 'GLU:plan': 21, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 219 Chain: "x" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 708 Classifications: {'peptide': 142} Incomplete info: {'truncation_to_alanine': 138} Link IDs: {'TRANS': 141} Unresolved non-hydrogen bonds: 391 Unresolved non-hydrogen angles: 525 Unresolved non-hydrogen dihedrals: 266 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 10, 'UNK:plan-1': 67, 'ASP:plan': 5, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 3, 'GLU:plan': 11, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 226 Chain: "G" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 15737 SG CYS Y 33 72.733 59.691 78.362 1.00306.96 S ATOM 17294 SG CYS Y 287 72.128 56.100 78.822 1.00267.58 S ATOM 15872 SG CYS Y 51 92.579 27.815 81.460 1.00244.54 S ATOM 16016 SG CYS Y 70 90.642 24.158 82.493 1.00231.81 S ATOM 16057 SG CYS Y 76 104.743 27.852 86.501 1.00252.50 S ATOM 16212 SG CYS Y 114 109.394 27.453 86.629 1.00262.38 S Time building chain proxies: 10.31, per 1000 atoms: 0.54 Number of scatterers: 19253 At special positions: 0 Unit cell: (160.8, 99.16, 222.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 3 29.99 S 97 16.00 P 9 15.00 O 3578 8.00 N 3377 7.00 C 12189 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.02 Conformation dependent library (CDL) restraints added in 3.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN Y 501 " pdb="ZN ZN Y 501 " - pdb=" SG CYS Y 287 " pdb="ZN ZN Y 501 " - pdb=" SG CYS Y 33 " pdb=" ZN Y 502 " pdb="ZN ZN Y 502 " - pdb=" SG CYS Y 51 " pdb="ZN ZN Y 502 " - pdb=" SG CYS Y 70 " pdb=" ZN Y 503 " pdb="ZN ZN Y 503 " - pdb=" SG CYS Y 114 " pdb="ZN ZN Y 503 " - pdb=" SG CYS Y 76 " 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4882 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 77 helices and 26 sheets defined 39.3% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.74 Creating SS restraints... Processing helix chain 'G' and resid 60 through 64 Processing helix chain 'G' and resid 83 through 94 removed outlier: 3.579A pdb=" N TYR G 94 " --> pdb=" O TRP G 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 118 through 130 Processing helix chain 'G' and resid 142 through 150 removed outlier: 3.687A pdb=" N TYR G 148 " --> pdb=" O VAL G 144 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR G 150 " --> pdb=" O SER G 146 " (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 201 Processing helix chain 'G' and resid 208 through 220 removed outlier: 3.845A pdb=" N GLU G 212 " --> pdb=" O SER G 208 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ILE G 213 " --> pdb=" O SER G 209 " (cutoff:3.500A) Processing helix chain 'G' and resid 228 through 233 removed outlier: 3.611A pdb=" N THR G 233 " --> pdb=" O GLN G 229 " (cutoff:3.500A) Processing helix chain 'G' and resid 252 through 262 removed outlier: 3.665A pdb=" N ARG G 255 " --> pdb=" O GLY G 252 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG G 257 " --> pdb=" O SER G 254 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ALA G 258 " --> pdb=" O ARG G 255 " (cutoff:3.500A) Proline residue: G 259 - end of helix Processing helix chain 'G' and resid 275 through 285 removed outlier: 3.573A pdb=" N VAL G 280 " --> pdb=" O HIS G 276 " (cutoff:3.500A) Processing helix chain 'G' and resid 288 through 296 removed outlier: 4.311A pdb=" N ARG G 292 " --> pdb=" O ASP G 289 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N PHE G 295 " --> pdb=" O ARG G 292 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER G 296 " --> pdb=" O THR G 293 " (cutoff:3.500A) Processing helix chain 'G' and resid 303 through 305 No H-bonds generated for 'chain 'G' and resid 303 through 305' Processing helix chain 'G' and resid 310 through 321 removed outlier: 3.529A pdb=" N LYS G 319 " --> pdb=" O LEU G 315 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS G 320 " --> pdb=" O SER G 316 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU G 321 " --> pdb=" O GLU G 317 " (cutoff:3.500A) Processing helix chain 'G' and resid 339 through 349 Processing helix chain 'G' and resid 351 through 356 Processing helix chain 'G' and resid 360 through 366 Processing helix chain 'G' and resid 368 through 374 Processing helix chain 'H' and resid 56 through 60 Processing helix chain 'H' and resid 79 through 90 Processing helix chain 'H' and resid 113 through 125 Processing helix chain 'H' and resid 137 through 145 removed outlier: 3.704A pdb=" N LEU H 142 " --> pdb=" O ALA H 138 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N TYR H 143 " --> pdb=" O VAL H 139 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA H 144 " --> pdb=" O LEU H 140 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N SER H 145 " --> pdb=" O SER H 141 " (cutoff:3.500A) Processing helix chain 'H' and resid 182 through 196 removed outlier: 3.606A pdb=" N LYS H 191 " --> pdb=" O ASP H 187 " (cutoff:3.500A) Processing helix chain 'H' and resid 203 through 216 Processing helix chain 'H' and resid 223 through 232 Processing helix chain 'H' and resid 251 through 262 removed outlier: 3.537A pdb=" N ARG H 256 " --> pdb=" O GLU H 253 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N CYS H 257 " --> pdb=" O ARG H 254 " (cutoff:3.500A) Proline residue: H 258 - end of helix Processing helix chain 'H' and resid 274 through 284 removed outlier: 3.629A pdb=" N THR H 278 " --> pdb=" O ILE H 274 " (cutoff:3.500A) Processing helix chain 'H' and resid 289 through 295 Processing helix chain 'H' and resid 302 through 304 No H-bonds generated for 'chain 'H' and resid 302 through 304' Processing helix chain 'H' and resid 309 through 320 Processing helix chain 'H' and resid 338 through 348 removed outlier: 3.542A pdb=" N GLY H 342 " --> pdb=" O SER H 338 " (cutoff:3.500A) Processing helix chain 'H' and resid 350 through 354 removed outlier: 3.501A pdb=" N GLN H 354 " --> pdb=" O THR H 351 " (cutoff:3.500A) Processing helix chain 'H' and resid 359 through 365 Processing helix chain 'H' and resid 367 through 372 Processing helix chain 'I' and resid 60 through 64 Processing helix chain 'I' and resid 83 through 93 Processing helix chain 'I' and resid 118 through 130 Processing helix chain 'I' and resid 142 through 150 removed outlier: 3.692A pdb=" N LEU I 147 " --> pdb=" O ALA I 143 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TYR I 148 " --> pdb=" O VAL I 144 " (cutoff:3.500A) Processing helix chain 'I' and resid 187 through 201 Processing helix chain 'I' and resid 208 through 220 removed outlier: 3.792A pdb=" N GLU I 212 " --> pdb=" O SER I 208 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ILE I 213 " --> pdb=" O SER I 209 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL I 214 " --> pdb=" O GLU I 210 " (cutoff:3.500A) Processing helix chain 'I' and resid 228 through 233 Processing helix chain 'I' and resid 252 through 263 removed outlier: 3.804A pdb=" N ARG I 257 " --> pdb=" O SER I 254 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ALA I 258 " --> pdb=" O ARG I 255 " (cutoff:3.500A) Proline residue: I 259 - end of helix Processing helix chain 'I' and resid 275 through 285 removed outlier: 3.593A pdb=" N LEU I 279 " --> pdb=" O ILE I 275 " (cutoff:3.500A) Processing helix chain 'I' and resid 288 through 296 removed outlier: 4.605A pdb=" N ARG I 292 " --> pdb=" O MET I 288 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N THR I 293 " --> pdb=" O ASP I 289 " (cutoff:3.500A) Processing helix chain 'I' and resid 310 through 321 removed outlier: 3.506A pdb=" N SER I 316 " --> pdb=" O ASP I 312 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS I 320 " --> pdb=" O SER I 316 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU I 321 " --> pdb=" O GLU I 317 " (cutoff:3.500A) Processing helix chain 'I' and resid 339 through 349 removed outlier: 3.505A pdb=" N GLY I 344 " --> pdb=" O THR I 340 " (cutoff:3.500A) Processing helix chain 'I' and resid 353 through 356 No H-bonds generated for 'chain 'I' and resid 353 through 356' Processing helix chain 'I' and resid 360 through 366 Processing helix chain 'I' and resid 369 through 375 Processing helix chain 'J' and resid 61 through 77 Processing helix chain 'J' and resid 99 through 111 Processing helix chain 'J' and resid 123 through 131 removed outlier: 3.584A pdb=" N LEU J 129 " --> pdb=" O LEU J 125 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR J 130 " --> pdb=" O MET J 126 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LEU J 131 " --> pdb=" O ALA J 127 " (cutoff:3.500A) Processing helix chain 'J' and resid 158 through 160 No H-bonds generated for 'chain 'J' and resid 158 through 160' Processing helix chain 'J' and resid 168 through 181 Processing helix chain 'J' and resid 204 through 213 Processing helix chain 'J' and resid 220 through 231 removed outlier: 3.564A pdb=" N LYS J 225 " --> pdb=" O THR J 221 " (cutoff:3.500A) Processing helix chain 'J' and resid 260 through 271 removed outlier: 3.925A pdb=" N ASP J 264 " --> pdb=" O GLY J 260 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N VAL J 267 " --> pdb=" O ARG J 263 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N GLU J 268 " --> pdb=" O ASP J 264 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ILE J 269 " --> pdb=" O SER J 265 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N LEU J 270 " --> pdb=" O VAL J 266 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N PHE J 271 " --> pdb=" O VAL J 267 " (cutoff:3.500A) Processing helix chain 'J' and resid 280 through 290 removed outlier: 4.236A pdb=" N ILE J 284 " --> pdb=" O VAL J 280 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LEU J 285 " --> pdb=" O ALA J 281 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN J 290 " --> pdb=" O ASP J 286 " (cutoff:3.500A) Processing helix chain 'J' and resid 296 through 301 Processing helix chain 'J' and resid 308 through 311 Processing helix chain 'J' and resid 315 through 328 removed outlier: 3.849A pdb=" N GLU J 328 " --> pdb=" O ARG J 324 " (cutoff:3.500A) Processing helix chain 'J' and resid 330 through 333 No H-bonds generated for 'chain 'J' and resid 330 through 333' Processing helix chain 'J' and resid 350 through 352 No H-bonds generated for 'chain 'J' and resid 350 through 352' Processing helix chain 'J' and resid 354 through 362 removed outlier: 3.635A pdb=" N GLY J 358 " --> pdb=" O ALA J 354 " (cutoff:3.500A) Processing helix chain 'J' and resid 365 through 371 removed outlier: 4.041A pdb=" N SER J 370 " --> pdb=" O ASP J 366 " (cutoff:3.500A) Processing helix chain 'J' and resid 375 through 381 Processing helix chain 'M' and resid 4 through 8 removed outlier: 3.584A pdb=" N ASP M 8 " --> pdb=" O PRO M 4 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 4 through 8' Processing helix chain 'M' and resid 52 through 59 removed outlier: 3.504A pdb=" N ASP M 57 " --> pdb=" O ASN M 53 " (cutoff:3.500A) Processing helix chain 'U' and resid 66 through 69 No H-bonds generated for 'chain 'U' and resid 66 through 69' Processing helix chain 'U' and resid 162 through 170 removed outlier: 3.928A pdb=" N MET U 168 " --> pdb=" O LEU U 164 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N LYS U 169 " --> pdb=" O ASP U 165 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE U 170 " --> pdb=" O PHE U 166 " (cutoff:3.500A) Processing helix chain 'V' and resid 162 through 175 removed outlier: 4.140A pdb=" N ILE V 166 " --> pdb=" O GLN V 162 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ASP V 167 " --> pdb=" O GLU V 163 " (cutoff:3.500A) Processing helix chain 'X' and resid 252 through 387 Processing helix chain 'Y' and resid 60 through 66 removed outlier: 3.500A pdb=" N LEU Y 65 " --> pdb=" O ALA Y 61 " (cutoff:3.500A) Processing helix chain 'Y' and resid 118 through 121 No H-bonds generated for 'chain 'Y' and resid 118 through 121' Processing helix chain 'Y' and resid 142 through 171 removed outlier: 3.516A pdb=" N GLU Y 158 " --> pdb=" O LEU Y 154 " (cutoff:3.500A) Processing helix chain 'Y' and resid 252 through 256 Processing helix chain 'Y' and resid 309 through 311 No H-bonds generated for 'chain 'Y' and resid 309 through 311' Processing helix chain 'Y' and resid 447 through 451 Processing helix chain 'x' and resid 252 through 389 removed outlier: 4.021A pdb=" N ALA x 256 " --> pdb=" O GLU x 252 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLU x 257 " --> pdb=" O SER x 253 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'G' and resid 137 through 141 removed outlier: 7.130A pdb=" N VAL G 108 " --> pdb=" O PHE G 138 " (cutoff:3.500A) removed outlier: 8.342A pdb=" N SER G 140 " --> pdb=" O VAL G 108 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LEU G 110 " --> pdb=" O SER G 140 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N VAL G 12 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N THR G 111 " --> pdb=" O VAL G 12 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N ILE G 14 " --> pdb=" O THR G 111 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'G' and resid 39 through 42 Processing sheet with id= C, first strand: chain 'G' and resid 330 through 332 removed outlier: 6.319A pdb=" N ILE G 298 " --> pdb=" O SER G 331 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N VAL G 156 " --> pdb=" O VAL G 299 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N SER G 301 " --> pdb=" O VAL G 156 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU G 158 " --> pdb=" O SER G 301 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'G' and resid 240 through 242 Processing sheet with id= E, first strand: chain 'H' and resid 29 through 32 removed outlier: 3.678A pdb=" N PHE H 31 " --> pdb=" O CYS H 17 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N VAL H 10 " --> pdb=" O PRO H 102 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N LEU H 104 " --> pdb=" O VAL H 10 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ASN H 12 " --> pdb=" O LEU H 104 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N THR H 106 " --> pdb=" O ASN H 12 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TYR H 133 " --> pdb=" O VAL H 103 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'H' and resid 52 through 54 removed outlier: 3.576A pdb=" N VAL H 35 " --> pdb=" O LYS H 68 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARG H 37 " --> pdb=" O THR H 66 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'H' and resid 297 through 300 removed outlier: 6.744A pdb=" N ILE H 151 " --> pdb=" O VAL H 298 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N SER H 300 " --> pdb=" O ILE H 151 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N MET H 153 " --> pdb=" O SER H 300 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL H 152 " --> pdb=" O VAL H 163 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'H' and resid 239 through 241 Processing sheet with id= I, first strand: chain 'I' and resid 137 through 141 removed outlier: 7.238A pdb=" N VAL I 108 " --> pdb=" O PHE I 138 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N SER I 140 " --> pdb=" O VAL I 108 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N LEU I 110 " --> pdb=" O SER I 140 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N VAL I 12 " --> pdb=" O LEU I 109 " (cutoff:3.500A) removed outlier: 8.555A pdb=" N THR I 111 " --> pdb=" O VAL I 12 " (cutoff:3.500A) removed outlier: 8.422A pdb=" N ILE I 14 " --> pdb=" O THR I 111 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE I 21 " --> pdb=" O PHE I 35 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TYR I 33 " --> pdb=" O ALA I 23 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'I' and resid 39 through 42 Processing sheet with id= K, first strand: chain 'I' and resid 298 through 301 removed outlier: 6.230A pdb=" N VAL I 156 " --> pdb=" O VAL I 299 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N SER I 301 " --> pdb=" O VAL I 156 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU I 158 " --> pdb=" O SER I 301 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'I' and resid 240 through 242 Processing sheet with id= M, first strand: chain 'J' and resid 118 through 122 removed outlier: 7.429A pdb=" N VAL J 89 " --> pdb=" O LEU J 119 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N ALA J 121 " --> pdb=" O VAL J 89 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL J 91 " --> pdb=" O ALA J 121 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N VAL J 16 " --> pdb=" O VAL J 90 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N ILE J 92 " --> pdb=" O VAL J 16 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ILE J 18 " --> pdb=" O ILE J 92 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'J' and resid 303 through 306 removed outlier: 6.509A pdb=" N MET J 137 " --> pdb=" O VAL J 304 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N ILE J 306 " --> pdb=" O MET J 137 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N LEU J 139 " --> pdb=" O ILE J 306 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VAL J 138 " --> pdb=" O LEU J 149 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'J' and resid 246 through 250 Processing sheet with id= P, first strand: chain 'U' and resid 23 through 25 removed outlier: 6.677A pdb=" N ILE U 41 " --> pdb=" O ARG U 24 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'U' and resid 88 through 90 removed outlier: 7.005A pdb=" N ASN U 105 " --> pdb=" O VAL U 89 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'U' and resid 141 through 143 Processing sheet with id= S, first strand: chain 'V' and resid 8 through 10 Processing sheet with id= T, first strand: chain 'V' and resid 15 through 17 Processing sheet with id= U, first strand: chain 'V' and resid 144 through 147 removed outlier: 3.623A pdb=" N GLY V 155 " --> pdb=" O VAL V 145 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N SER V 147 " --> pdb=" O PHE V 153 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N PHE V 153 " --> pdb=" O SER V 147 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'Y' and resid 84 through 86 Processing sheet with id= W, first strand: chain 'Y' and resid 330 through 333 Processing sheet with id= X, first strand: chain 'Y' and resid 423 through 431 Processing sheet with id= Y, first strand: chain 'Y' and resid 43 through 50 removed outlier: 3.702A pdb=" N SER Y 281 " --> pdb=" O GLU Y 45 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP Y 47 " --> pdb=" O LYS Y 279 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N LYS Y 279 " --> pdb=" O ASP Y 47 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N HIS Y 49 " --> pdb=" O LEU Y 277 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU Y 277 " --> pdb=" O HIS Y 49 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'Y' and resid 69 through 74 removed outlier: 4.298A pdb=" N LYS Y 274 " --> pdb=" O CYS Y 70 " (cutoff:3.500A) 721 hydrogen bonds defined for protein. 2019 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: 5.40 Time building geometry restraints manager: 7.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3664 1.33 - 1.45: 4489 1.45 - 1.57: 11320 1.57 - 1.70: 14 1.70 - 1.82: 145 Bond restraints: 19632 Sorted by residual: bond pdb=" C4 ADP G 800 " pdb=" C5 ADP G 800 " ideal model delta sigma weight residual 1.490 1.382 0.108 2.00e-02 2.50e+03 2.91e+01 bond pdb=" C4 ADP J 800 " pdb=" C5 ADP J 800 " ideal model delta sigma weight residual 1.490 1.383 0.107 2.00e-02 2.50e+03 2.87e+01 bond pdb=" C4 ADP I 800 " pdb=" C5 ADP I 800 " ideal model delta sigma weight residual 1.490 1.383 0.107 2.00e-02 2.50e+03 2.86e+01 bond pdb=" N ILE Y 321 " pdb=" CA ILE Y 321 " ideal model delta sigma weight residual 1.456 1.496 -0.040 8.70e-03 1.32e+04 2.09e+01 bond pdb=" N LEU V 177 " pdb=" CA LEU V 177 " ideal model delta sigma weight residual 1.453 1.490 -0.037 8.30e-03 1.45e+04 1.97e+01 ... (remaining 19627 not shown) Histogram of bond angle deviations from ideal: 97.49 - 104.94: 511 104.94 - 112.39: 9502 112.39 - 119.84: 8911 119.84 - 127.29: 7667 127.29 - 134.74: 121 Bond angle restraints: 26712 Sorted by residual: angle pdb=" N PRO Y 438 " pdb=" CA PRO Y 438 " pdb=" CB PRO Y 438 " ideal model delta sigma weight residual 103.30 110.08 -6.78 8.00e-01 1.56e+00 7.19e+01 angle pdb=" PB ATP H 401 " pdb=" O3B ATP H 401 " pdb=" PG ATP H 401 " ideal model delta sigma weight residual 139.87 132.15 7.72 1.00e+00 1.00e+00 5.96e+01 angle pdb=" PA ATP H 401 " pdb=" O3A ATP H 401 " pdb=" PB ATP H 401 " ideal model delta sigma weight residual 136.83 129.78 7.05 1.00e+00 1.00e+00 4.97e+01 angle pdb=" N PRO Y 447 " pdb=" CA PRO Y 447 " pdb=" CB PRO Y 447 " ideal model delta sigma weight residual 103.25 110.12 -6.87 1.05e+00 9.07e-01 4.28e+01 angle pdb=" N PRO Y 441 " pdb=" CA PRO Y 441 " pdb=" CB PRO Y 441 " ideal model delta sigma weight residual 103.25 110.06 -6.81 1.05e+00 9.07e-01 4.20e+01 ... (remaining 26707 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.85: 11590 30.85 - 61.69: 275 61.69 - 92.54: 11 92.54 - 123.38: 4 123.38 - 154.23: 3 Dihedral angle restraints: 11883 sinusoidal: 4332 harmonic: 7551 Sorted by residual: dihedral pdb=" C5' ADP G 800 " pdb=" O5' ADP G 800 " pdb=" PA ADP G 800 " pdb=" O2A ADP G 800 " ideal model delta sinusoidal sigma weight residual -60.00 94.23 -154.23 1 2.00e+01 2.50e-03 4.56e+01 dihedral pdb=" C5' ADP I 800 " pdb=" O5' ADP I 800 " pdb=" PA ADP I 800 " pdb=" O2A ADP I 800 " ideal model delta sinusoidal sigma weight residual -60.00 87.27 -147.27 1 2.00e+01 2.50e-03 4.42e+01 dihedral pdb=" O2A ADP I 800 " pdb=" O3A ADP I 800 " pdb=" PA ADP I 800 " pdb=" PB ADP I 800 " ideal model delta sinusoidal sigma weight residual -60.00 70.65 -130.65 1 2.00e+01 2.50e-03 3.96e+01 ... (remaining 11880 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1146 0.047 - 0.093: 948 0.093 - 0.140: 668 0.140 - 0.187: 266 0.187 - 0.234: 58 Chirality restraints: 3086 Sorted by residual: chirality pdb=" CA VAL H 9 " pdb=" N VAL H 9 " pdb=" C VAL H 9 " pdb=" CB VAL H 9 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CB VAL G 318 " pdb=" CA VAL G 318 " pdb=" CG1 VAL G 318 " pdb=" CG2 VAL G 318 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA VAL J 17 " pdb=" N VAL J 17 " pdb=" C VAL J 17 " pdb=" CB VAL J 17 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 3083 not shown) Planarity restraints: 3456 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP G 357 " 0.036 2.00e-02 2.50e+03 2.87e-02 2.05e+01 pdb=" CG TRP G 357 " -0.080 2.00e-02 2.50e+03 pdb=" CD1 TRP G 357 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP G 357 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP G 357 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP G 357 " 0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP G 357 " 0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 357 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 357 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP G 357 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP G 357 " 0.012 2.00e-02 2.50e+03 2.48e-02 6.15e+00 pdb=" C TRP G 357 " -0.043 2.00e-02 2.50e+03 pdb=" O TRP G 357 " 0.016 2.00e-02 2.50e+03 pdb=" N VAL G 358 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA UNK X 348 " 0.012 2.00e-02 2.50e+03 2.47e-02 6.08e+00 pdb=" C UNK X 348 " -0.043 2.00e-02 2.50e+03 pdb=" O UNK X 348 " 0.016 2.00e-02 2.50e+03 pdb=" N UNK X 349 " 0.014 2.00e-02 2.50e+03 ... (remaining 3453 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.41: 9 2.41 - 3.03: 9635 3.03 - 3.66: 29364 3.66 - 4.28: 41379 4.28 - 4.90: 69456 Nonbonded interactions: 149843 Sorted by model distance: nonbonded pdb=" NH2 ARG Y 37 " pdb="ZN ZN Y 501 " model vdw 1.790 2.310 nonbonded pdb=" O LEU G 267 " pdb=" NE2 HIS H 173 " model vdw 2.214 2.520 nonbonded pdb=" N ALA G 49 " pdb=" OH TYR I 148 " model vdw 2.235 2.520 nonbonded pdb=" O THR G 111 " pdb=" OG1 THR G 111 " model vdw 2.265 2.440 nonbonded pdb=" O GLY G 67 " pdb=" OD2 ASP I 287 " model vdw 2.308 3.040 ... (remaining 149838 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 'G' and (resid 7 through 361 or (resid 362 and (name N or name CA or name \ C or name O or name CB )) or resid 363 or (resid 364 through 366 and (name N or \ name CA or name C or name O or name CB )) or resid 367 through 376 or resid 800 \ )) selection = chain 'I' } ncs_group { reference = chain 'X' selection = (chain 'x' and resid 251 through 389) } 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: 1.040 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: 4.990 Check model and map are aligned: 0.270 Set scattering table: 0.180 Process input model: 54.000 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 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 : 0.013 0.118 19632 Z= 0.899 Angle : 1.750 12.947 26712 Z= 1.285 Chirality : 0.087 0.234 3086 Planarity : 0.003 0.029 3456 Dihedral : 13.499 154.227 7001 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.24 % Favored : 92.64 % Rotamer: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.56 (0.15), residues: 2444 helix: -0.58 (0.16), residues: 813 sheet: -2.29 (0.28), residues: 283 loop : -2.35 (0.14), residues: 1348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.080 0.003 TRP G 357 HIS 0.017 0.002 HIS G 372 PHE 0.016 0.002 PHE M 71 TYR 0.019 0.002 TYR I 38 ARG 0.017 0.001 ARG G 329 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 2158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 511 time to evaluate : 2.202 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: G 10 GLN cc_start: 0.9333 (mm-40) cc_final: 0.9108 (tp40) REVERT: G 34 CYS cc_start: 0.9100 (p) cc_final: 0.8733 (p) REVERT: G 37 ASN cc_start: 0.9001 (t0) cc_final: 0.8739 (t0) REVERT: G 86 MET cc_start: 0.9670 (tpp) cc_final: 0.9461 (tpp) REVERT: G 95 SER cc_start: 0.9429 (t) cc_final: 0.9200 (p) REVERT: G 98 GLN cc_start: 0.9059 (mm-40) cc_final: 0.8640 (mp10) REVERT: G 100 GLN cc_start: 0.9300 (tt0) cc_final: 0.8947 (mt0) REVERT: G 146 SER cc_start: 0.9766 (t) cc_final: 0.9493 (p) REVERT: G 160 SER cc_start: 0.9096 (m) cc_final: 0.8780 (p) REVERT: G 181 MET cc_start: 0.8232 (mmm) cc_final: 0.7686 (tpp) REVERT: G 184 ASP cc_start: 0.8367 (m-30) cc_final: 0.7518 (m-30) REVERT: G 227 ASN cc_start: 0.8802 (m-40) cc_final: 0.7887 (t0) REVERT: G 240 GLN cc_start: 0.9027 (pt0) cc_final: 0.8792 (pt0) REVERT: G 271 GLU cc_start: 0.9160 (mm-30) cc_final: 0.8706 (pt0) REVERT: G 280 VAL cc_start: 0.9571 (m) cc_final: 0.9364 (p) REVERT: G 284 GLN cc_start: 0.9256 (mt0) cc_final: 0.8790 (pt0) REVERT: G 286 SER cc_start: 0.8740 (m) cc_final: 0.8344 (p) REVERT: G 306 LEU cc_start: 0.9327 (mt) cc_final: 0.8970 (mt) REVERT: G 338 TYR cc_start: 0.9111 (m-80) cc_final: 0.8714 (m-80) REVERT: G 352 THR cc_start: 0.9137 (t) cc_final: 0.8440 (m) REVERT: G 356 MET cc_start: 0.9104 (mtp) cc_final: 0.8832 (mtp) REVERT: H 44 MET cc_start: 0.8858 (ptm) cc_final: 0.8422 (ppp) REVERT: H 47 MET cc_start: 0.8606 (mmm) cc_final: 0.8302 (mmp) REVERT: H 78 ASN cc_start: 0.8886 (t0) cc_final: 0.8532 (t0) REVERT: H 82 MET cc_start: 0.9436 (tpt) cc_final: 0.8830 (tpp) REVERT: H 103 VAL cc_start: 0.9350 (t) cc_final: 0.8900 (p) REVERT: H 132 MET cc_start: 0.8557 (tpt) cc_final: 0.8091 (tpt) REVERT: H 153 MET cc_start: 0.8401 (tmm) cc_final: 0.7799 (tpt) REVERT: H 165 ILE cc_start: 0.9139 (mt) cc_final: 0.8904 (mp) REVERT: H 184 ASP cc_start: 0.9066 (m-30) cc_final: 0.8836 (m-30) REVERT: H 195 GLU cc_start: 0.9143 (mt-10) cc_final: 0.8729 (mt-10) REVERT: H 227 MET cc_start: 0.9203 (mtp) cc_final: 0.8962 (mmm) REVERT: H 272 CYS cc_start: 0.8260 (p) cc_final: 0.7619 (p) REVERT: H 283 MET cc_start: 0.9032 (mmm) cc_final: 0.8813 (mmm) REVERT: H 291 LYS cc_start: 0.9263 (tttt) cc_final: 0.8939 (mptt) REVERT: H 325 MET cc_start: 0.8766 (mmm) cc_final: 0.8463 (mmt) REVERT: H 355 MET cc_start: 0.9106 (mtp) cc_final: 0.8793 (mpp) REVERT: I 100 GLN cc_start: 0.9110 (tt0) cc_final: 0.8879 (tt0) REVERT: I 105 GLU cc_start: 0.8714 (mm-30) cc_final: 0.8212 (tm-30) REVERT: I 106 HIS cc_start: 0.9051 (m-70) cc_final: 0.8453 (m90) REVERT: I 112 GLU cc_start: 0.9386 (mm-30) cc_final: 0.8533 (tt0) REVERT: I 116 ASN cc_start: 0.7665 (m-40) cc_final: 0.6137 (m-40) REVERT: I 159 ASP cc_start: 0.9139 (t0) cc_final: 0.8563 (t70) REVERT: I 181 MET cc_start: 0.8290 (tpp) cc_final: 0.7764 (mmt) REVERT: I 189 ASP cc_start: 0.9262 (m-30) cc_final: 0.8692 (m-30) REVERT: I 268 ILE cc_start: 0.9471 (tp) cc_final: 0.9252 (tp) REVERT: I 334 GLN cc_start: 0.8796 (tt0) cc_final: 0.8405 (tp40) REVERT: I 356 MET cc_start: 0.8768 (mtt) cc_final: 0.8386 (mtt) REVERT: I 357 TRP cc_start: 0.9082 (p-90) cc_final: 0.8856 (p-90) REVERT: J 27 CYS cc_start: 0.9003 (m) cc_final: 0.8674 (m) REVERT: J 91 VAL cc_start: 0.8766 (t) cc_final: 0.8549 (t) REVERT: J 137 MET cc_start: 0.7304 (tpp) cc_final: 0.6925 (tpt) REVERT: J 141 CYS cc_start: 0.8872 (m) cc_final: 0.8621 (p) REVERT: J 145 GLU cc_start: 0.8620 (pt0) cc_final: 0.8171 (mm-30) REVERT: J 178 GLN cc_start: 0.9227 (mm-40) cc_final: 0.8987 (mm-40) REVERT: J 179 LEU cc_start: 0.9321 (mt) cc_final: 0.9089 (pp) REVERT: J 227 GLN cc_start: 0.9324 (mt0) cc_final: 0.9033 (mt0) REVERT: J 231 PHE cc_start: 0.8545 (m-10) cc_final: 0.8188 (m-10) REVERT: J 289 MET cc_start: 0.8858 (ttp) cc_final: 0.8623 (ttm) REVERT: J 301 GLU cc_start: 0.8695 (mt-10) cc_final: 0.8264 (pt0) REVERT: J 311 MET cc_start: 0.9425 (tpp) cc_final: 0.8796 (mtm) REVERT: J 322 GLU cc_start: 0.9527 (tp30) cc_final: 0.8803 (tp30) REVERT: J 326 LEU cc_start: 0.9110 (mt) cc_final: 0.8603 (mt) REVERT: J 352 CYS cc_start: 0.9009 (m) cc_final: 0.7895 (p) REVERT: J 387 TRP cc_start: 0.8428 (p-90) cc_final: 0.7917 (p-90) REVERT: M 38 GLU cc_start: 0.9053 (mm-30) cc_final: 0.8774 (pm20) REVERT: M 39 GLU cc_start: 0.7926 (tp30) cc_final: 0.7434 (tp30) REVERT: M 62 LYS cc_start: 0.8136 (mmtp) cc_final: 0.6573 (tttt) REVERT: M 64 VAL cc_start: 0.7808 (m) cc_final: 0.7345 (m) REVERT: M 77 LYS cc_start: 0.8783 (mmmt) cc_final: 0.8252 (mmtm) REVERT: U 24 ARG cc_start: 0.8955 (mtp-110) cc_final: 0.7824 (ttp80) REVERT: U 36 HIS cc_start: 0.9327 (m-70) cc_final: 0.8873 (m90) REVERT: U 57 GLU cc_start: 0.8769 (mt-10) cc_final: 0.8523 (pt0) REVERT: U 84 ILE cc_start: 0.9353 (mt) cc_final: 0.7770 (mt) REVERT: U 90 PHE cc_start: 0.8409 (m-80) cc_final: 0.7229 (m-80) REVERT: U 95 TYR cc_start: 0.7907 (t80) cc_final: 0.7322 (t80) REVERT: U 112 TYR cc_start: 0.9201 (t80) cc_final: 0.8387 (t80) REVERT: U 125 ILE cc_start: 0.8723 (mm) cc_final: 0.8464 (tp) REVERT: U 139 GLU cc_start: 0.8873 (tp30) cc_final: 0.8224 (tp30) REVERT: U 150 ARG cc_start: 0.8591 (mtm180) cc_final: 0.8016 (mtt90) REVERT: U 153 GLN cc_start: 0.9520 (tt0) cc_final: 0.9268 (mm-40) REVERT: U 168 MET cc_start: 0.9039 (mmt) cc_final: 0.8797 (mmp) REVERT: V 8 TYR cc_start: 0.8615 (m-80) cc_final: 0.8333 (m-80) REVERT: V 25 GLN cc_start: 0.9148 (tp-100) cc_final: 0.8637 (tm-30) REVERT: V 92 PHE cc_start: 0.8010 (t80) cc_final: 0.7785 (t80) REVERT: V 100 ASN cc_start: 0.9070 (m-40) cc_final: 0.8420 (t0) REVERT: V 114 CYS cc_start: 0.7336 (p) cc_final: 0.6729 (p) REVERT: V 120 CYS cc_start: 0.8888 (t) cc_final: 0.8643 (m) REVERT: V 125 CYS cc_start: 0.8865 (m) cc_final: 0.7736 (p) REVERT: V 161 THR cc_start: 0.9191 (m) cc_final: 0.8942 (p) REVERT: Y 27 LEU cc_start: 0.9473 (mt) cc_final: 0.9164 (tt) REVERT: Y 36 LEU cc_start: 0.9163 (pt) cc_final: 0.8746 (pp) REVERT: Y 45 GLU cc_start: 0.7366 (mm-30) cc_final: 0.6652 (mp0) REVERT: Y 56 GLU cc_start: 0.9223 (mm-30) cc_final: 0.8922 (mp0) REVERT: Y 58 MET cc_start: 0.8553 (mtp) cc_final: 0.8075 (ttm) REVERT: Y 62 GLU cc_start: 0.8826 (tt0) cc_final: 0.8527 (tp30) REVERT: Y 80 MET cc_start: 0.8765 (mpp) cc_final: 0.8410 (mtm) REVERT: Y 158 GLU cc_start: 0.8890 (tm-30) cc_final: 0.8651 (tm-30) REVERT: Y 221 ILE cc_start: 0.7843 (mt) cc_final: 0.7443 (tt) REVERT: Y 224 GLU cc_start: 0.9373 (pt0) cc_final: 0.9020 (pm20) REVERT: Y 242 ARG cc_start: 0.9297 (ttt180) cc_final: 0.9016 (ptm-80) REVERT: Y 257 LEU cc_start: 0.9229 (mt) cc_final: 0.8731 (mm) REVERT: Y 289 HIS cc_start: 0.7478 (t70) cc_final: 0.6900 (t-90) outliers start: 0 outliers final: 0 residues processed: 511 average time/residue: 0.3262 time to fit residues: 245.7443 Evaluate side-chains 293 residues out of total 2158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 293 time to evaluate : 2.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 193 optimal weight: 7.9990 chunk 173 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 117 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 179 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 chunk 133 optimal weight: 0.0270 chunk 207 optimal weight: 1.9990 overall best weight: 0.9440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 120 ASN G 297 ASN ** H 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 152 GLN ** Y 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19632 Z= 0.198 Angle : 0.618 9.919 26712 Z= 0.309 Chirality : 0.043 0.157 3086 Planarity : 0.004 0.040 3456 Dihedral : 8.950 165.146 2860 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.31 % Favored : 96.60 % Rotamer: Outliers : 0.05 % Allowed : 3.18 % Favored : 96.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.16), residues: 2444 helix: 1.12 (0.17), residues: 837 sheet: -1.58 (0.25), residues: 368 loop : -1.78 (0.15), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP G 357 HIS 0.005 0.001 HIS G 65 PHE 0.030 0.002 PHE G 353 TYR 0.018 0.001 TYR Y 12 ARG 0.004 0.001 ARG J 107 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 327 time to evaluate : 2.340 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: G 10 GLN cc_start: 0.9514 (mm-40) cc_final: 0.8895 (tp40) REVERT: G 44 HIS cc_start: 0.8476 (m-70) cc_final: 0.8064 (m-70) REVERT: G 86 MET cc_start: 0.9576 (tpp) cc_final: 0.9170 (tpp) REVERT: G 141 MET cc_start: 0.7301 (mmm) cc_final: 0.5215 (mmt) REVERT: G 146 SER cc_start: 0.9733 (t) cc_final: 0.9400 (p) REVERT: G 181 MET cc_start: 0.7591 (mmm) cc_final: 0.7126 (tpp) REVERT: G 184 ASP cc_start: 0.8128 (m-30) cc_final: 0.7745 (m-30) REVERT: G 271 GLU cc_start: 0.9304 (mm-30) cc_final: 0.8830 (pt0) REVERT: G 284 GLN cc_start: 0.9307 (mt0) cc_final: 0.8968 (pt0) REVERT: G 352 THR cc_start: 0.9422 (t) cc_final: 0.9142 (t) REVERT: G 371 ILE cc_start: 0.9489 (mm) cc_final: 0.9270 (mm) REVERT: H 44 MET cc_start: 0.9028 (ptm) cc_final: 0.8548 (ppp) REVERT: H 47 MET cc_start: 0.8478 (mmm) cc_final: 0.8123 (mmp) REVERT: H 72 GLU cc_start: 0.8394 (mt-10) cc_final: 0.8023 (mp0) REVERT: H 78 ASN cc_start: 0.8865 (t0) cc_final: 0.8589 (t0) REVERT: H 82 MET cc_start: 0.9454 (tpt) cc_final: 0.8707 (tpp) REVERT: H 103 VAL cc_start: 0.9386 (t) cc_final: 0.9072 (p) REVERT: H 153 MET cc_start: 0.9018 (tmm) cc_final: 0.8241 (tmm) REVERT: H 184 ASP cc_start: 0.9206 (m-30) cc_final: 0.8985 (m-30) REVERT: H 195 GLU cc_start: 0.9295 (mt-10) cc_final: 0.8944 (tt0) REVERT: H 215 LYS cc_start: 0.9096 (mmtm) cc_final: 0.8855 (mppt) REVERT: H 261 LEU cc_start: 0.9133 (mt) cc_final: 0.8726 (mt) REVERT: H 272 CYS cc_start: 0.8256 (p) cc_final: 0.7472 (p) REVERT: H 291 LYS cc_start: 0.9197 (tttt) cc_final: 0.8831 (mptt) REVERT: H 325 MET cc_start: 0.8998 (mmm) cc_final: 0.8558 (mmt) REVERT: H 355 MET cc_start: 0.9078 (mtp) cc_final: 0.8840 (mpp) REVERT: I 100 GLN cc_start: 0.9340 (tt0) cc_final: 0.9052 (tp40) REVERT: I 112 GLU cc_start: 0.9361 (mm-30) cc_final: 0.8602 (tt0) REVERT: I 116 ASN cc_start: 0.7022 (m-40) cc_final: 0.5570 (m-40) REVERT: I 139 ILE cc_start: 0.9366 (mt) cc_final: 0.8833 (tp) REVERT: I 141 MET cc_start: 0.7139 (mmm) cc_final: 0.6561 (mmm) REVERT: I 189 ASP cc_start: 0.9308 (m-30) cc_final: 0.8777 (m-30) REVERT: I 334 GLN cc_start: 0.8867 (tt0) cc_final: 0.8395 (tp-100) REVERT: I 356 MET cc_start: 0.8855 (mtt) cc_final: 0.8421 (mpp) REVERT: J 19 ASP cc_start: 0.8095 (t0) cc_final: 0.7724 (t0) REVERT: J 137 MET cc_start: 0.7373 (tpp) cc_final: 0.6816 (tpt) REVERT: J 145 GLU cc_start: 0.8698 (pt0) cc_final: 0.8173 (mm-30) REVERT: J 178 GLN cc_start: 0.9319 (mm-40) cc_final: 0.9019 (mm-40) REVERT: J 179 LEU cc_start: 0.9446 (mt) cc_final: 0.9150 (pp) REVERT: J 301 GLU cc_start: 0.8706 (mt-10) cc_final: 0.8437 (mm-30) REVERT: J 311 MET cc_start: 0.9472 (tpp) cc_final: 0.8769 (mtt) REVERT: J 322 GLU cc_start: 0.9468 (tp30) cc_final: 0.8931 (tp30) REVERT: J 326 LEU cc_start: 0.9205 (mt) cc_final: 0.8855 (mt) REVERT: J 352 CYS cc_start: 0.8897 (m) cc_final: 0.7996 (p) REVERT: J 387 TRP cc_start: 0.8427 (p-90) cc_final: 0.7962 (p-90) REVERT: M 21 GLU cc_start: 0.9543 (pt0) cc_final: 0.8986 (mp0) REVERT: M 38 GLU cc_start: 0.9180 (mm-30) cc_final: 0.8862 (pm20) REVERT: M 39 GLU cc_start: 0.8317 (tp30) cc_final: 0.7586 (tp30) REVERT: M 46 GLU cc_start: 0.8556 (tm-30) cc_final: 0.8133 (tm-30) REVERT: M 58 LYS cc_start: 0.9583 (ttpt) cc_final: 0.9305 (tttt) REVERT: M 62 LYS cc_start: 0.8588 (mmtp) cc_final: 0.7297 (tttt) REVERT: M 69 LEU cc_start: 0.7489 (tt) cc_final: 0.7034 (tp) REVERT: U 36 HIS cc_start: 0.9368 (m-70) cc_final: 0.8689 (m90) REVERT: U 38 LYS cc_start: 0.9016 (mmtt) cc_final: 0.8812 (mmmt) REVERT: U 90 PHE cc_start: 0.8427 (m-80) cc_final: 0.8083 (m-80) REVERT: U 95 TYR cc_start: 0.7928 (t80) cc_final: 0.7414 (t80) REVERT: U 101 MET cc_start: 0.9518 (mtm) cc_final: 0.9124 (mtt) REVERT: U 112 TYR cc_start: 0.9187 (t80) cc_final: 0.8598 (t80) REVERT: V 8 TYR cc_start: 0.8709 (m-80) cc_final: 0.8368 (m-80) REVERT: V 25 GLN cc_start: 0.9232 (tp-100) cc_final: 0.8628 (tm-30) REVERT: V 40 THR cc_start: 0.8756 (m) cc_final: 0.8498 (p) REVERT: V 90 HIS cc_start: 0.8912 (m-70) cc_final: 0.8418 (m170) REVERT: V 100 ASN cc_start: 0.9029 (m-40) cc_final: 0.8522 (t0) REVERT: V 114 CYS cc_start: 0.8533 (p) cc_final: 0.8183 (p) REVERT: V 120 CYS cc_start: 0.8973 (t) cc_final: 0.8569 (m) REVERT: V 161 THR cc_start: 0.9204 (m) cc_final: 0.8805 (p) REVERT: V 165 MET cc_start: 0.9602 (mmm) cc_final: 0.8952 (mtp) REVERT: V 176 PHE cc_start: 0.9188 (t80) cc_final: 0.8826 (t80) REVERT: Y 27 LEU cc_start: 0.9340 (mt) cc_final: 0.9071 (mt) REVERT: Y 58 MET cc_start: 0.8749 (mtp) cc_final: 0.8212 (ttm) REVERT: Y 163 ASP cc_start: 0.9442 (m-30) cc_final: 0.9221 (m-30) REVERT: Y 221 ILE cc_start: 0.8025 (mt) cc_final: 0.7671 (tt) REVERT: Y 252 LEU cc_start: 0.9148 (tt) cc_final: 0.8874 (tt) REVERT: Y 289 HIS cc_start: 0.7446 (t70) cc_final: 0.6978 (t-90) REVERT: Y 301 ILE cc_start: 0.8218 (pt) cc_final: 0.7924 (pt) outliers start: 1 outliers final: 0 residues processed: 328 average time/residue: 0.2899 time to fit residues: 146.3459 Evaluate side-chains 225 residues out of total 2158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 225 time to evaluate : 2.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 115 optimal weight: 0.5980 chunk 64 optimal weight: 4.9990 chunk 173 optimal weight: 6.9990 chunk 141 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 chunk 208 optimal weight: 5.9990 chunk 225 optimal weight: 10.0000 chunk 185 optimal weight: 0.9990 chunk 206 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 167 optimal weight: 10.0000 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 371 HIS I 178 HIS U 87 ASN ** U 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 254 GLN Y 268 GLN Y 273 HIS ** Y 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.3391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 19632 Z= 0.315 Angle : 0.620 9.994 26712 Z= 0.308 Chirality : 0.042 0.153 3086 Planarity : 0.004 0.048 3456 Dihedral : 8.750 179.076 2860 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.26 % Favored : 95.66 % Rotamer: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.16), residues: 2444 helix: 1.56 (0.18), residues: 829 sheet: -1.30 (0.26), residues: 356 loop : -1.35 (0.16), residues: 1259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.003 TRP G 357 HIS 0.006 0.001 HIS G 276 PHE 0.021 0.002 PHE I 128 TYR 0.014 0.002 TYR Y 326 ARG 0.011 0.001 ARG V 70 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 265 time to evaluate : 2.185 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: G 75 MET cc_start: 0.8671 (ttp) cc_final: 0.7286 (tmm) REVERT: G 86 MET cc_start: 0.9596 (tpp) cc_final: 0.9215 (tpp) REVERT: G 141 MET cc_start: 0.8131 (mmp) cc_final: 0.7878 (mmm) REVERT: G 142 GLN cc_start: 0.8871 (mt0) cc_final: 0.8015 (mp10) REVERT: G 181 MET cc_start: 0.7557 (mmm) cc_final: 0.7231 (tpp) REVERT: G 184 ASP cc_start: 0.7874 (m-30) cc_final: 0.7350 (m-30) REVERT: G 240 GLN cc_start: 0.8200 (pp30) cc_final: 0.7718 (tm-30) REVERT: G 270 GLU cc_start: 0.8522 (tp30) cc_final: 0.8248 (tp30) REVERT: G 271 GLU cc_start: 0.9412 (mm-30) cc_final: 0.8952 (pt0) REVERT: G 338 TYR cc_start: 0.9272 (m-80) cc_final: 0.8985 (m-80) REVERT: H 44 MET cc_start: 0.8876 (ptm) cc_final: 0.8422 (ppp) REVERT: H 47 MET cc_start: 0.8626 (mmm) cc_final: 0.8406 (mmp) REVERT: H 72 GLU cc_start: 0.8560 (mt-10) cc_final: 0.8092 (mp0) REVERT: H 78 ASN cc_start: 0.8587 (t0) cc_final: 0.8250 (t0) REVERT: H 82 MET cc_start: 0.9513 (tpt) cc_final: 0.8930 (tpp) REVERT: H 117 GLU cc_start: 0.9357 (tp30) cc_final: 0.9120 (tp30) REVERT: H 153 MET cc_start: 0.9041 (tmm) cc_final: 0.7971 (tmm) REVERT: H 184 ASP cc_start: 0.9219 (m-30) cc_final: 0.8996 (m-30) REVERT: H 195 GLU cc_start: 0.9312 (mt-10) cc_final: 0.8922 (tt0) REVERT: H 217 CYS cc_start: 0.9604 (m) cc_final: 0.9380 (m) REVERT: H 227 MET cc_start: 0.9099 (mmm) cc_final: 0.8694 (mmm) REVERT: H 272 CYS cc_start: 0.8274 (p) cc_final: 0.7867 (p) REVERT: H 291 LYS cc_start: 0.9224 (tttt) cc_final: 0.8873 (mptt) REVERT: H 325 MET cc_start: 0.9023 (mmm) cc_final: 0.8385 (mmt) REVERT: I 100 GLN cc_start: 0.9287 (tt0) cc_final: 0.9049 (tm-30) REVERT: I 112 GLU cc_start: 0.9305 (mm-30) cc_final: 0.8441 (tt0) REVERT: I 116 ASN cc_start: 0.7388 (m-40) cc_final: 0.5834 (m-40) REVERT: I 141 MET cc_start: 0.7521 (mmp) cc_final: 0.7296 (mmm) REVERT: I 159 ASP cc_start: 0.8909 (t0) cc_final: 0.8384 (t70) REVERT: I 189 ASP cc_start: 0.9309 (m-30) cc_final: 0.8731 (m-30) REVERT: I 356 MET cc_start: 0.8817 (mtt) cc_final: 0.8431 (mpp) REVERT: J 137 MET cc_start: 0.7508 (tpp) cc_final: 0.6954 (tpt) REVERT: J 145 GLU cc_start: 0.8793 (pt0) cc_final: 0.8193 (mm-30) REVERT: J 178 GLN cc_start: 0.9283 (mm-40) cc_final: 0.8953 (mm-40) REVERT: J 215 CYS cc_start: 0.9304 (m) cc_final: 0.9094 (m) REVERT: J 289 MET cc_start: 0.8815 (ttm) cc_final: 0.8483 (ttm) REVERT: J 301 GLU cc_start: 0.8790 (mt-10) cc_final: 0.8540 (mm-30) REVERT: J 311 MET cc_start: 0.9462 (tpp) cc_final: 0.8929 (mmm) REVERT: J 322 GLU cc_start: 0.9497 (tp30) cc_final: 0.8853 (tp30) REVERT: J 326 LEU cc_start: 0.9245 (mt) cc_final: 0.8810 (mt) REVERT: J 352 CYS cc_start: 0.8888 (m) cc_final: 0.8227 (p) REVERT: J 387 TRP cc_start: 0.8728 (p-90) cc_final: 0.8370 (p-90) REVERT: M 21 GLU cc_start: 0.9442 (pt0) cc_final: 0.8897 (pm20) REVERT: M 38 GLU cc_start: 0.9288 (mm-30) cc_final: 0.8837 (pm20) REVERT: M 39 GLU cc_start: 0.8558 (tp30) cc_final: 0.7628 (tp30) REVERT: M 46 GLU cc_start: 0.8465 (tm-30) cc_final: 0.7953 (tm-30) REVERT: M 58 LYS cc_start: 0.9569 (ttpt) cc_final: 0.9268 (tttt) REVERT: M 62 LYS cc_start: 0.8682 (mmtp) cc_final: 0.7300 (tttt) REVERT: M 66 THR cc_start: 0.9244 (t) cc_final: 0.8936 (m) REVERT: M 77 LYS cc_start: 0.8816 (mmpt) cc_final: 0.8507 (mmtm) REVERT: U 38 LYS cc_start: 0.8998 (mmtt) cc_final: 0.8795 (mmmt) REVERT: U 57 GLU cc_start: 0.9329 (mt-10) cc_final: 0.8782 (pt0) REVERT: U 95 TYR cc_start: 0.7886 (t80) cc_final: 0.7366 (t80) REVERT: U 101 MET cc_start: 0.9524 (mtm) cc_final: 0.8830 (mtm) REVERT: U 112 TYR cc_start: 0.9154 (t80) cc_final: 0.8529 (t80) REVERT: U 131 LEU cc_start: 0.8742 (pp) cc_final: 0.8517 (pp) REVERT: U 150 ARG cc_start: 0.8400 (mtm180) cc_final: 0.7965 (mtt90) REVERT: U 168 MET cc_start: 0.9009 (mmp) cc_final: 0.8655 (mmm) REVERT: V 8 TYR cc_start: 0.8764 (m-80) cc_final: 0.8321 (m-80) REVERT: V 25 GLN cc_start: 0.9416 (tp-100) cc_final: 0.8733 (tm-30) REVERT: V 100 ASN cc_start: 0.8786 (m-40) cc_final: 0.8429 (t0) REVERT: V 103 GLN cc_start: 0.9187 (tp-100) cc_final: 0.8940 (tp-100) REVERT: V 114 CYS cc_start: 0.8631 (p) cc_final: 0.8342 (p) REVERT: V 120 CYS cc_start: 0.9075 (t) cc_final: 0.8658 (m) REVERT: V 125 CYS cc_start: 0.8792 (m) cc_final: 0.8560 (m) REVERT: V 154 SER cc_start: 0.9627 (t) cc_final: 0.9367 (p) REVERT: V 176 PHE cc_start: 0.9218 (t80) cc_final: 0.8854 (t80) REVERT: Y 27 LEU cc_start: 0.9377 (mt) cc_final: 0.9135 (mt) REVERT: Y 58 MET cc_start: 0.8944 (mtp) cc_final: 0.8316 (ttm) REVERT: Y 80 MET cc_start: 0.9067 (mtp) cc_final: 0.8766 (mtm) REVERT: Y 163 ASP cc_start: 0.9466 (m-30) cc_final: 0.9204 (m-30) REVERT: Y 221 ILE cc_start: 0.8189 (mt) cc_final: 0.7907 (tt) REVERT: Y 289 HIS cc_start: 0.7617 (t70) cc_final: 0.7216 (t-90) REVERT: Y 301 ILE cc_start: 0.8357 (pt) cc_final: 0.8021 (pt) outliers start: 0 outliers final: 0 residues processed: 265 average time/residue: 0.2966 time to fit residues: 122.3893 Evaluate side-chains 212 residues out of total 2158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 212 time to evaluate : 2.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 205 optimal weight: 7.9990 chunk 156 optimal weight: 20.0000 chunk 108 optimal weight: 0.0050 chunk 23 optimal weight: 5.9990 chunk 99 optimal weight: 5.9990 chunk 139 optimal weight: 0.0970 chunk 209 optimal weight: 6.9990 chunk 221 optimal weight: 30.0000 chunk 109 optimal weight: 0.8980 chunk 198 optimal weight: 5.9990 chunk 59 optimal weight: 8.9990 overall best weight: 2.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 276 HIS G 284 GLN ** G 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 101 HIS ** H 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 344 HIS ** U 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 273 HIS ** Y 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.3972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 19632 Z= 0.289 Angle : 0.592 10.023 26712 Z= 0.292 Chirality : 0.042 0.139 3086 Planarity : 0.004 0.045 3456 Dihedral : 8.265 168.259 2860 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.38 % Favored : 95.54 % Rotamer: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.17), residues: 2444 helix: 1.76 (0.18), residues: 821 sheet: -1.06 (0.27), residues: 358 loop : -1.07 (0.16), residues: 1265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP G 357 HIS 0.006 0.001 HIS Y 273 PHE 0.016 0.002 PHE Y 261 TYR 0.015 0.001 TYR U 144 ARG 0.008 0.000 ARG V 70 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 255 time to evaluate : 2.164 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: G 75 MET cc_start: 0.8658 (ttp) cc_final: 0.7095 (tmm) REVERT: G 86 MET cc_start: 0.9598 (tpp) cc_final: 0.9203 (tpp) REVERT: G 111 THR cc_start: 0.8279 (t) cc_final: 0.7901 (t) REVERT: G 142 GLN cc_start: 0.8755 (mt0) cc_final: 0.7924 (mp10) REVERT: G 176 MET cc_start: 0.7535 (mmp) cc_final: 0.7050 (mmm) REVERT: G 181 MET cc_start: 0.7649 (mmm) cc_final: 0.7386 (tpp) REVERT: G 271 GLU cc_start: 0.9382 (mm-30) cc_final: 0.9030 (pt0) REVERT: G 284 GLN cc_start: 0.9473 (mt0) cc_final: 0.9219 (mt0) REVERT: H 44 MET cc_start: 0.8706 (ptm) cc_final: 0.8240 (ppp) REVERT: H 47 MET cc_start: 0.8727 (mmm) cc_final: 0.8404 (mmp) REVERT: H 72 GLU cc_start: 0.8556 (mt-10) cc_final: 0.8056 (mp0) REVERT: H 78 ASN cc_start: 0.8322 (t0) cc_final: 0.7990 (t0) REVERT: H 82 MET cc_start: 0.9563 (tpt) cc_final: 0.8990 (tpp) REVERT: H 153 MET cc_start: 0.9326 (tmm) cc_final: 0.8546 (tmm) REVERT: H 184 ASP cc_start: 0.9190 (m-30) cc_final: 0.8984 (m-30) REVERT: H 195 GLU cc_start: 0.9321 (mt-10) cc_final: 0.8945 (tt0) REVERT: H 217 CYS cc_start: 0.9560 (m) cc_final: 0.9252 (m) REVERT: H 227 MET cc_start: 0.9080 (mmm) cc_final: 0.8640 (mmm) REVERT: H 272 CYS cc_start: 0.8145 (p) cc_final: 0.7727 (p) REVERT: H 291 LYS cc_start: 0.9251 (tttt) cc_final: 0.8901 (mptt) REVERT: H 325 MET cc_start: 0.8957 (mmm) cc_final: 0.8388 (mmt) REVERT: H 355 MET cc_start: 0.9366 (mmp) cc_final: 0.8659 (mtp) REVERT: I 13 VAL cc_start: 0.9279 (t) cc_final: 0.8948 (m) REVERT: I 75 MET cc_start: 0.8907 (ttp) cc_final: 0.7777 (ptm) REVERT: I 100 GLN cc_start: 0.9342 (tt0) cc_final: 0.9054 (tm-30) REVERT: I 112 GLU cc_start: 0.9334 (mm-30) cc_final: 0.8518 (tt0) REVERT: I 116 ASN cc_start: 0.7764 (m-40) cc_final: 0.6236 (m-40) REVERT: I 159 ASP cc_start: 0.8868 (t0) cc_final: 0.8334 (t70) REVERT: I 189 ASP cc_start: 0.9305 (m-30) cc_final: 0.8700 (m-30) REVERT: I 271 GLU cc_start: 0.8986 (tp30) cc_final: 0.8194 (tt0) REVERT: I 356 MET cc_start: 0.8752 (mtt) cc_final: 0.8388 (mtt) REVERT: J 37 CYS cc_start: 0.7993 (t) cc_final: 0.6217 (t) REVERT: J 56 GLN cc_start: 0.8642 (mt0) cc_final: 0.8409 (mt0) REVERT: J 137 MET cc_start: 0.7562 (tpp) cc_final: 0.7002 (tpp) REVERT: J 178 GLN cc_start: 0.9234 (mm-40) cc_final: 0.8883 (mm-40) REVERT: J 289 MET cc_start: 0.8778 (ttm) cc_final: 0.8465 (ttm) REVERT: J 301 GLU cc_start: 0.8920 (mt-10) cc_final: 0.8595 (mm-30) REVERT: J 311 MET cc_start: 0.9461 (tpp) cc_final: 0.8948 (mmm) REVERT: J 322 GLU cc_start: 0.9502 (tp30) cc_final: 0.8944 (tp30) REVERT: J 326 LEU cc_start: 0.9304 (mt) cc_final: 0.9030 (mt) REVERT: J 352 CYS cc_start: 0.8888 (m) cc_final: 0.8465 (p) REVERT: J 387 TRP cc_start: 0.8844 (p-90) cc_final: 0.8561 (p-90) REVERT: M 21 GLU cc_start: 0.9329 (pt0) cc_final: 0.8906 (pm20) REVERT: M 38 GLU cc_start: 0.9273 (mm-30) cc_final: 0.8948 (pm20) REVERT: M 46 GLU cc_start: 0.8496 (tm-30) cc_final: 0.7953 (tm-30) REVERT: M 51 ASN cc_start: 0.9728 (t0) cc_final: 0.9234 (t0) REVERT: M 58 LYS cc_start: 0.9587 (ttpt) cc_final: 0.9271 (tttt) REVERT: M 62 LYS cc_start: 0.8837 (mmtp) cc_final: 0.7468 (tttt) REVERT: M 67 LYS cc_start: 0.9535 (tppp) cc_final: 0.9315 (tppp) REVERT: M 77 LYS cc_start: 0.8899 (mmpt) cc_final: 0.8625 (mmtm) REVERT: U 38 LYS cc_start: 0.8970 (mmtt) cc_final: 0.8731 (mmmt) REVERT: U 82 MET cc_start: 0.9240 (tpt) cc_final: 0.8952 (mmm) REVERT: U 95 TYR cc_start: 0.7932 (t80) cc_final: 0.7425 (t80) REVERT: U 99 MET cc_start: 0.7800 (mmm) cc_final: 0.7596 (mmm) REVERT: U 112 TYR cc_start: 0.9100 (t80) cc_final: 0.8505 (t80) REVERT: U 131 LEU cc_start: 0.8679 (pp) cc_final: 0.8429 (pp) REVERT: U 168 MET cc_start: 0.8927 (mmp) cc_final: 0.8697 (mmm) REVERT: V 8 TYR cc_start: 0.8729 (m-80) cc_final: 0.8036 (m-80) REVERT: V 25 GLN cc_start: 0.9449 (tp-100) cc_final: 0.8758 (tm-30) REVERT: V 34 ILE cc_start: 0.8609 (pt) cc_final: 0.8370 (pt) REVERT: V 100 ASN cc_start: 0.8920 (m-40) cc_final: 0.8347 (t0) REVERT: V 103 GLN cc_start: 0.9201 (tp-100) cc_final: 0.8894 (tp-100) REVERT: V 114 CYS cc_start: 0.8744 (p) cc_final: 0.8390 (p) REVERT: V 120 CYS cc_start: 0.9134 (t) cc_final: 0.8642 (m) REVERT: V 125 CYS cc_start: 0.8692 (m) cc_final: 0.8462 (m) REVERT: V 154 SER cc_start: 0.9598 (t) cc_final: 0.9343 (p) REVERT: V 157 LEU cc_start: 0.8728 (mt) cc_final: 0.8177 (mt) REVERT: V 165 MET cc_start: 0.9635 (mmm) cc_final: 0.9031 (mtp) REVERT: V 176 PHE cc_start: 0.9236 (t80) cc_final: 0.8872 (t80) REVERT: Y 27 LEU cc_start: 0.9369 (mt) cc_final: 0.9149 (mt) REVERT: Y 80 MET cc_start: 0.9006 (mtp) cc_final: 0.8744 (mtm) REVERT: Y 163 ASP cc_start: 0.9471 (m-30) cc_final: 0.9186 (m-30) REVERT: Y 289 HIS cc_start: 0.7732 (t70) cc_final: 0.7459 (t-90) REVERT: Y 301 ILE cc_start: 0.8370 (pt) cc_final: 0.8034 (pt) outliers start: 0 outliers final: 0 residues processed: 255 average time/residue: 0.2949 time to fit residues: 116.4272 Evaluate side-chains 203 residues out of total 2158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 203 time to evaluate : 2.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 184 optimal weight: 7.9990 chunk 125 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 164 optimal weight: 7.9990 chunk 91 optimal weight: 4.9990 chunk 188 optimal weight: 0.0570 chunk 153 optimal weight: 0.7980 chunk 0 optimal weight: 10.9990 chunk 113 optimal weight: 0.7980 chunk 198 optimal weight: 7.9990 chunk 55 optimal weight: 6.9990 overall best weight: 1.1302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 56 GLN ** U 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.4137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19632 Z= 0.178 Angle : 0.543 9.841 26712 Z= 0.264 Chirality : 0.041 0.215 3086 Planarity : 0.004 0.044 3456 Dihedral : 7.870 162.393 2860 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.93 % Favored : 95.99 % Rotamer: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.17), residues: 2444 helix: 1.82 (0.18), residues: 823 sheet: -0.94 (0.27), residues: 365 loop : -0.91 (0.17), residues: 1256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP G 357 HIS 0.008 0.001 HIS V 109 PHE 0.041 0.001 PHE G 193 TYR 0.013 0.001 TYR V 13 ARG 0.002 0.000 ARG V 70 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 256 time to evaluate : 2.307 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: G 75 MET cc_start: 0.8687 (ttp) cc_final: 0.7191 (tmm) REVERT: G 86 MET cc_start: 0.9616 (tpp) cc_final: 0.9246 (tpp) REVERT: G 140 SER cc_start: 0.9247 (t) cc_final: 0.8758 (t) REVERT: G 141 MET cc_start: 0.8394 (mmm) cc_final: 0.7919 (mmm) REVERT: G 142 GLN cc_start: 0.8433 (mt0) cc_final: 0.7977 (mp10) REVERT: G 176 MET cc_start: 0.7217 (mmp) cc_final: 0.6687 (mmm) REVERT: G 181 MET cc_start: 0.7594 (mmm) cc_final: 0.7316 (tpp) REVERT: G 184 ASP cc_start: 0.7810 (p0) cc_final: 0.7294 (p0) REVERT: G 189 ASP cc_start: 0.9367 (m-30) cc_final: 0.8833 (m-30) REVERT: G 240 GLN cc_start: 0.8334 (tt0) cc_final: 0.8111 (tt0) REVERT: G 271 GLU cc_start: 0.9376 (mm-30) cc_final: 0.9046 (pt0) REVERT: G 284 GLN cc_start: 0.9504 (mt0) cc_final: 0.9223 (mt0) REVERT: H 44 MET cc_start: 0.8773 (ptm) cc_final: 0.8440 (ppp) REVERT: H 47 MET cc_start: 0.8740 (mmm) cc_final: 0.8459 (mmp) REVERT: H 72 GLU cc_start: 0.8545 (mt-10) cc_final: 0.8035 (mp0) REVERT: H 78 ASN cc_start: 0.8361 (t0) cc_final: 0.7924 (t0) REVERT: H 82 MET cc_start: 0.9492 (tpt) cc_final: 0.8897 (tpp) REVERT: H 153 MET cc_start: 0.9372 (tmm) cc_final: 0.8466 (tmm) REVERT: H 195 GLU cc_start: 0.9301 (mt-10) cc_final: 0.8927 (tt0) REVERT: H 217 CYS cc_start: 0.9600 (m) cc_final: 0.9226 (m) REVERT: H 272 CYS cc_start: 0.8164 (p) cc_final: 0.7709 (p) REVERT: H 291 LYS cc_start: 0.9233 (tttt) cc_final: 0.8902 (mptt) REVERT: H 325 MET cc_start: 0.8917 (mmm) cc_final: 0.8361 (mmt) REVERT: H 355 MET cc_start: 0.9356 (mmp) cc_final: 0.8629 (mtp) REVERT: I 13 VAL cc_start: 0.9332 (t) cc_final: 0.9004 (m) REVERT: I 100 GLN cc_start: 0.9387 (tt0) cc_final: 0.9126 (tm-30) REVERT: I 112 GLU cc_start: 0.9313 (mm-30) cc_final: 0.8524 (tt0) REVERT: I 116 ASN cc_start: 0.7763 (m-40) cc_final: 0.6290 (m-40) REVERT: I 146 SER cc_start: 0.9455 (t) cc_final: 0.9226 (m) REVERT: I 159 ASP cc_start: 0.8878 (t0) cc_final: 0.8410 (t70) REVERT: I 176 MET cc_start: 0.8234 (mpp) cc_final: 0.7206 (mpp) REVERT: I 189 ASP cc_start: 0.9066 (m-30) cc_final: 0.8434 (m-30) REVERT: I 268 ILE cc_start: 0.9508 (tp) cc_final: 0.8877 (tp) REVERT: I 270 GLU cc_start: 0.7690 (mm-30) cc_final: 0.7468 (mm-30) REVERT: I 271 GLU cc_start: 0.8972 (tp30) cc_final: 0.8148 (tt0) REVERT: I 356 MET cc_start: 0.8732 (mtt) cc_final: 0.8367 (mtt) REVERT: J 37 CYS cc_start: 0.7102 (t) cc_final: 0.6467 (t) REVERT: J 56 GLN cc_start: 0.8560 (mt0) cc_final: 0.8348 (mt0) REVERT: J 137 MET cc_start: 0.7512 (tpp) cc_final: 0.6928 (tpp) REVERT: J 178 GLN cc_start: 0.9230 (mm-40) cc_final: 0.8869 (mm-40) REVERT: J 289 MET cc_start: 0.8832 (ttm) cc_final: 0.8470 (ttm) REVERT: J 301 GLU cc_start: 0.8972 (mt-10) cc_final: 0.8744 (tp30) REVERT: J 311 MET cc_start: 0.9412 (tpp) cc_final: 0.8947 (mmm) REVERT: J 322 GLU cc_start: 0.9509 (tp30) cc_final: 0.8954 (tp30) REVERT: J 326 LEU cc_start: 0.9305 (mt) cc_final: 0.8993 (mt) REVERT: J 352 CYS cc_start: 0.8877 (m) cc_final: 0.8480 (p) REVERT: J 387 TRP cc_start: 0.8735 (p-90) cc_final: 0.8326 (p-90) REVERT: M 21 GLU cc_start: 0.9272 (pt0) cc_final: 0.8884 (pm20) REVERT: M 38 GLU cc_start: 0.9288 (mm-30) cc_final: 0.8890 (pm20) REVERT: M 46 GLU cc_start: 0.8507 (tm-30) cc_final: 0.7949 (tm-30) REVERT: M 58 LYS cc_start: 0.9611 (ttpt) cc_final: 0.9178 (pttt) REVERT: M 62 LYS cc_start: 0.8792 (mmtp) cc_final: 0.7428 (tttt) REVERT: M 67 LYS cc_start: 0.9519 (tppp) cc_final: 0.9305 (tppp) REVERT: M 77 LYS cc_start: 0.8967 (mmpt) cc_final: 0.8680 (mmtm) REVERT: U 10 LYS cc_start: 0.9572 (tptp) cc_final: 0.9302 (mmtm) REVERT: U 82 MET cc_start: 0.9146 (tpt) cc_final: 0.8820 (mmm) REVERT: U 95 TYR cc_start: 0.7917 (t80) cc_final: 0.7414 (t80) REVERT: U 99 MET cc_start: 0.7809 (mmm) cc_final: 0.7457 (mmm) REVERT: U 112 TYR cc_start: 0.9126 (t80) cc_final: 0.8561 (t80) REVERT: U 131 LEU cc_start: 0.8666 (pp) cc_final: 0.8458 (pp) REVERT: U 144 TYR cc_start: 0.8593 (p90) cc_final: 0.8383 (p90) REVERT: U 148 CYS cc_start: 0.8843 (m) cc_final: 0.8544 (m) REVERT: U 150 ARG cc_start: 0.8362 (mtm180) cc_final: 0.7763 (mtt90) REVERT: U 167 LEU cc_start: 0.9774 (mm) cc_final: 0.9434 (pp) REVERT: U 168 MET cc_start: 0.8876 (mmp) cc_final: 0.8568 (mmm) REVERT: V 8 TYR cc_start: 0.8699 (m-80) cc_final: 0.8060 (m-80) REVERT: V 25 GLN cc_start: 0.9454 (tp-100) cc_final: 0.8758 (tm-30) REVERT: V 34 ILE cc_start: 0.8618 (pt) cc_final: 0.8377 (pt) REVERT: V 52 LEU cc_start: 0.8411 (tp) cc_final: 0.8165 (tp) REVERT: V 100 ASN cc_start: 0.8823 (m-40) cc_final: 0.8306 (t0) REVERT: V 103 GLN cc_start: 0.9198 (tp-100) cc_final: 0.8900 (tp-100) REVERT: V 114 CYS cc_start: 0.8690 (p) cc_final: 0.8408 (p) REVERT: V 120 CYS cc_start: 0.9202 (t) cc_final: 0.8687 (m) REVERT: V 125 CYS cc_start: 0.8657 (m) cc_final: 0.8369 (m) REVERT: V 154 SER cc_start: 0.9568 (t) cc_final: 0.9310 (p) REVERT: V 157 LEU cc_start: 0.8759 (mt) cc_final: 0.8207 (mt) REVERT: V 176 PHE cc_start: 0.9258 (t80) cc_final: 0.8852 (t80) REVERT: Y 27 LEU cc_start: 0.9394 (mt) cc_final: 0.9182 (mt) REVERT: Y 163 ASP cc_start: 0.9461 (m-30) cc_final: 0.9167 (m-30) REVERT: Y 273 HIS cc_start: 0.9246 (m-70) cc_final: 0.8887 (m-70) REVERT: Y 289 HIS cc_start: 0.7734 (t70) cc_final: 0.7474 (t-90) REVERT: Y 301 ILE cc_start: 0.8295 (pt) cc_final: 0.7901 (pt) outliers start: 0 outliers final: 0 residues processed: 256 average time/residue: 0.3005 time to fit residues: 118.2654 Evaluate side-chains 208 residues out of total 2158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 208 time to evaluate : 2.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 74 optimal weight: 10.0000 chunk 199 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 129 optimal weight: 7.9990 chunk 54 optimal weight: 6.9990 chunk 221 optimal weight: 30.0000 chunk 183 optimal weight: 1.9990 chunk 102 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 116 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 44 HIS G 166 HIS ** G 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 262 GLN Y 273 HIS ** Y 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.4646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 19632 Z= 0.388 Angle : 0.655 9.738 26712 Z= 0.321 Chirality : 0.042 0.194 3086 Planarity : 0.004 0.041 3456 Dihedral : 7.968 152.102 2860 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.83 % Favored : 95.09 % Rotamer: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.17), residues: 2444 helix: 1.61 (0.18), residues: 821 sheet: -0.97 (0.28), residues: 333 loop : -0.82 (0.17), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.003 TRP G 357 HIS 0.007 0.001 HIS Y 273 PHE 0.015 0.002 PHE Y 261 TYR 0.013 0.002 TYR G 197 ARG 0.003 0.000 ARG H 290 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 224 time to evaluate : 2.188 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: G 48 MET cc_start: 0.8100 (ttp) cc_final: 0.7714 (tmm) REVERT: G 75 MET cc_start: 0.8779 (ttp) cc_final: 0.7353 (tmm) REVERT: G 86 MET cc_start: 0.9598 (tpp) cc_final: 0.9201 (tpp) REVERT: G 111 THR cc_start: 0.8777 (t) cc_final: 0.8312 (t) REVERT: G 142 GLN cc_start: 0.8677 (mt0) cc_final: 0.8191 (mp10) REVERT: G 176 MET cc_start: 0.6991 (mmp) cc_final: 0.6326 (mmm) REVERT: G 181 MET cc_start: 0.7726 (mmm) cc_final: 0.7522 (tpp) REVERT: G 184 ASP cc_start: 0.7718 (p0) cc_final: 0.7327 (p0) REVERT: G 284 GLN cc_start: 0.9511 (mt0) cc_final: 0.9204 (mt0) REVERT: H 44 MET cc_start: 0.8566 (ptm) cc_final: 0.8102 (ppp) REVERT: H 47 MET cc_start: 0.8852 (mmm) cc_final: 0.8533 (mmp) REVERT: H 72 GLU cc_start: 0.8676 (mt-10) cc_final: 0.8124 (mp0) REVERT: H 82 MET cc_start: 0.9550 (tpt) cc_final: 0.9106 (tpt) REVERT: H 153 MET cc_start: 0.9366 (tmm) cc_final: 0.8630 (tmm) REVERT: H 195 GLU cc_start: 0.9301 (mt-10) cc_final: 0.8900 (tt0) REVERT: H 217 CYS cc_start: 0.9585 (m) cc_final: 0.9297 (m) REVERT: H 227 MET cc_start: 0.9065 (mmm) cc_final: 0.8678 (mmm) REVERT: H 272 CYS cc_start: 0.8099 (p) cc_final: 0.7643 (p) REVERT: H 291 LYS cc_start: 0.9242 (tttt) cc_final: 0.8898 (mptt) REVERT: H 325 MET cc_start: 0.9033 (mmm) cc_final: 0.8344 (mmt) REVERT: H 355 MET cc_start: 0.9219 (mmp) cc_final: 0.8799 (mmm) REVERT: I 13 VAL cc_start: 0.9274 (t) cc_final: 0.8967 (m) REVERT: I 100 GLN cc_start: 0.9348 (tt0) cc_final: 0.8909 (tp40) REVERT: I 159 ASP cc_start: 0.8660 (t0) cc_final: 0.8211 (t70) REVERT: I 189 ASP cc_start: 0.9108 (m-30) cc_final: 0.8503 (m-30) REVERT: I 268 ILE cc_start: 0.9490 (tp) cc_final: 0.9045 (tp) REVERT: I 271 GLU cc_start: 0.9014 (tp30) cc_final: 0.8171 (tt0) REVERT: I 356 MET cc_start: 0.8792 (mtt) cc_final: 0.8468 (mtt) REVERT: J 37 CYS cc_start: 0.7347 (t) cc_final: 0.6806 (t) REVERT: J 44 LYS cc_start: 0.9496 (mttt) cc_final: 0.9236 (tppt) REVERT: J 48 MET cc_start: 0.9117 (mpp) cc_final: 0.8747 (mpp) REVERT: J 137 MET cc_start: 0.7481 (tpp) cc_final: 0.6959 (tpp) REVERT: J 178 GLN cc_start: 0.9231 (mm-40) cc_final: 0.8959 (mm-40) REVERT: J 289 MET cc_start: 0.8782 (ttm) cc_final: 0.8422 (ttm) REVERT: J 301 GLU cc_start: 0.9006 (mt-10) cc_final: 0.8554 (tp30) REVERT: J 311 MET cc_start: 0.9478 (tpp) cc_final: 0.9022 (mmm) REVERT: J 322 GLU cc_start: 0.9509 (tp30) cc_final: 0.9026 (tp30) REVERT: J 326 LEU cc_start: 0.9335 (mt) cc_final: 0.9110 (mt) REVERT: M 21 GLU cc_start: 0.9213 (pt0) cc_final: 0.8932 (pm20) REVERT: M 38 GLU cc_start: 0.9327 (mm-30) cc_final: 0.8998 (pm20) REVERT: M 46 GLU cc_start: 0.8385 (tm-30) cc_final: 0.7784 (tm-30) REVERT: M 51 ASN cc_start: 0.9528 (t0) cc_final: 0.9303 (t0) REVERT: M 58 LYS cc_start: 0.9585 (ttpt) cc_final: 0.9162 (pttt) REVERT: M 62 LYS cc_start: 0.8865 (mmtp) cc_final: 0.7679 (tttt) REVERT: M 77 LYS cc_start: 0.9027 (mmpt) cc_final: 0.8713 (mmtm) REVERT: U 95 TYR cc_start: 0.7957 (t80) cc_final: 0.7453 (t80) REVERT: U 112 TYR cc_start: 0.9064 (t80) cc_final: 0.8447 (t80) REVERT: U 131 LEU cc_start: 0.8794 (pp) cc_final: 0.8427 (pp) REVERT: U 148 CYS cc_start: 0.8898 (m) cc_final: 0.8614 (m) REVERT: U 150 ARG cc_start: 0.8292 (mtm180) cc_final: 0.7685 (mtt90) REVERT: U 167 LEU cc_start: 0.9801 (mm) cc_final: 0.9575 (mm) REVERT: U 168 MET cc_start: 0.9003 (mmp) cc_final: 0.8633 (mmp) REVERT: U 169 LYS cc_start: 0.9685 (mmtm) cc_final: 0.9432 (mmtm) REVERT: V 6 LEU cc_start: 0.9145 (mt) cc_final: 0.8472 (tp) REVERT: V 8 TYR cc_start: 0.8677 (m-80) cc_final: 0.7926 (m-80) REVERT: V 25 GLN cc_start: 0.9484 (tp-100) cc_final: 0.8750 (tm-30) REVERT: V 34 ILE cc_start: 0.8660 (pt) cc_final: 0.8429 (pt) REVERT: V 100 ASN cc_start: 0.8756 (m-40) cc_final: 0.8541 (m-40) REVERT: V 103 GLN cc_start: 0.9211 (tp-100) cc_final: 0.8856 (tp-100) REVERT: V 120 CYS cc_start: 0.9218 (t) cc_final: 0.8691 (m) REVERT: V 125 CYS cc_start: 0.8656 (m) cc_final: 0.8449 (m) REVERT: V 126 CYS cc_start: 0.8955 (p) cc_final: 0.8640 (p) REVERT: V 154 SER cc_start: 0.9523 (t) cc_final: 0.9274 (p) REVERT: V 157 LEU cc_start: 0.8712 (mt) cc_final: 0.8134 (mt) REVERT: V 176 PHE cc_start: 0.9274 (t80) cc_final: 0.8887 (t80) REVERT: Y 27 LEU cc_start: 0.9268 (mt) cc_final: 0.9041 (mt) REVERT: Y 123 MET cc_start: 0.8452 (mtp) cc_final: 0.8197 (mtp) REVERT: Y 163 ASP cc_start: 0.9477 (m-30) cc_final: 0.9186 (m-30) REVERT: Y 273 HIS cc_start: 0.9221 (m90) cc_final: 0.8828 (m-70) REVERT: Y 301 ILE cc_start: 0.8453 (pt) cc_final: 0.8125 (pt) outliers start: 0 outliers final: 0 residues processed: 224 average time/residue: 0.3007 time to fit residues: 104.4944 Evaluate side-chains 182 residues out of total 2158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 182 time to evaluate : 2.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 213 optimal weight: 0.3980 chunk 24 optimal weight: 6.9990 chunk 126 optimal weight: 4.9990 chunk 161 optimal weight: 30.0000 chunk 125 optimal weight: 0.8980 chunk 186 optimal weight: 10.0000 chunk 123 optimal weight: 2.9990 chunk 220 optimal weight: 30.0000 chunk 138 optimal weight: 0.8980 chunk 134 optimal weight: 3.9990 chunk 101 optimal weight: 0.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 37 ASN G 240 GLN ** G 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.4699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19632 Z= 0.189 Angle : 0.562 9.788 26712 Z= 0.272 Chirality : 0.042 0.210 3086 Planarity : 0.004 0.039 3456 Dihedral : 7.606 143.184 2860 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.97 % Favored : 95.95 % Rotamer: Outliers : 0.05 % Allowed : 0.65 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.17), residues: 2444 helix: 1.78 (0.19), residues: 819 sheet: -1.16 (0.27), residues: 372 loop : -0.68 (0.17), residues: 1253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP G 357 HIS 0.005 0.001 HIS J 79 PHE 0.019 0.001 PHE G 193 TYR 0.017 0.001 TYR G 197 ARG 0.005 0.000 ARG V 70 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 242 time to evaluate : 2.092 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: G 48 MET cc_start: 0.8445 (ttp) cc_final: 0.7805 (tmm) REVERT: G 75 MET cc_start: 0.8639 (ttp) cc_final: 0.7252 (tmm) REVERT: G 111 THR cc_start: 0.8734 (t) cc_final: 0.7819 (t) REVERT: G 140 SER cc_start: 0.9446 (t) cc_final: 0.8809 (p) REVERT: G 141 MET cc_start: 0.8126 (mmm) cc_final: 0.7728 (mmm) REVERT: G 142 GLN cc_start: 0.8585 (mt0) cc_final: 0.8222 (mp10) REVERT: G 176 MET cc_start: 0.6885 (mmp) cc_final: 0.6336 (mmm) REVERT: G 181 MET cc_start: 0.7626 (mmm) cc_final: 0.7396 (tpp) REVERT: G 184 ASP cc_start: 0.7787 (p0) cc_final: 0.7149 (p0) REVERT: G 189 ASP cc_start: 0.9412 (m-30) cc_final: 0.8904 (m-30) REVERT: G 206 HIS cc_start: 0.9287 (p-80) cc_final: 0.9063 (p-80) REVERT: G 284 GLN cc_start: 0.9533 (mt0) cc_final: 0.9215 (mt0) REVERT: H 44 MET cc_start: 0.8607 (ptm) cc_final: 0.8165 (ppp) REVERT: H 47 MET cc_start: 0.8688 (mmm) cc_final: 0.8327 (mmp) REVERT: H 72 GLU cc_start: 0.8647 (mt-10) cc_final: 0.8101 (mp0) REVERT: H 78 ASN cc_start: 0.8374 (t0) cc_final: 0.8023 (t0) REVERT: H 82 MET cc_start: 0.9534 (tpt) cc_final: 0.9191 (tpt) REVERT: H 153 MET cc_start: 0.9006 (tmm) cc_final: 0.8430 (tmm) REVERT: H 195 GLU cc_start: 0.9274 (mt-10) cc_final: 0.8815 (tt0) REVERT: H 217 CYS cc_start: 0.9610 (m) cc_final: 0.9249 (m) REVERT: H 227 MET cc_start: 0.8998 (mmm) cc_final: 0.8562 (mmm) REVERT: H 291 LYS cc_start: 0.9223 (tttt) cc_final: 0.8896 (mptt) REVERT: H 325 MET cc_start: 0.8939 (mmm) cc_final: 0.8400 (mmt) REVERT: H 355 MET cc_start: 0.9243 (mmp) cc_final: 0.8432 (mtp) REVERT: I 13 VAL cc_start: 0.9284 (t) cc_final: 0.8973 (m) REVERT: I 116 ASN cc_start: 0.8606 (t0) cc_final: 0.8319 (t0) REVERT: I 146 SER cc_start: 0.9429 (t) cc_final: 0.9224 (m) REVERT: I 159 ASP cc_start: 0.8872 (t0) cc_final: 0.8439 (t70) REVERT: I 189 ASP cc_start: 0.9102 (m-30) cc_final: 0.8462 (m-30) REVERT: I 240 GLN cc_start: 0.8442 (mm-40) cc_final: 0.8099 (tp-100) REVERT: I 270 GLU cc_start: 0.8118 (mm-30) cc_final: 0.7402 (mm-30) REVERT: I 271 GLU cc_start: 0.9033 (tp30) cc_final: 0.8141 (tt0) REVERT: I 356 MET cc_start: 0.8798 (mtt) cc_final: 0.8446 (mtt) REVERT: J 37 CYS cc_start: 0.7367 (t) cc_final: 0.6803 (t) REVERT: J 56 GLN cc_start: 0.8595 (mt0) cc_final: 0.8372 (mt0) REVERT: J 137 MET cc_start: 0.7496 (tpp) cc_final: 0.6921 (tpp) REVERT: J 178 GLN cc_start: 0.9261 (mm-40) cc_final: 0.8881 (mm-40) REVERT: J 215 CYS cc_start: 0.9245 (m) cc_final: 0.9038 (m) REVERT: J 289 MET cc_start: 0.8781 (ttm) cc_final: 0.8436 (ttm) REVERT: J 301 GLU cc_start: 0.9036 (mt-10) cc_final: 0.8661 (tp30) REVERT: J 311 MET cc_start: 0.9453 (tpp) cc_final: 0.8946 (mmm) REVERT: J 322 GLU cc_start: 0.9505 (tp30) cc_final: 0.8972 (tp30) REVERT: J 326 LEU cc_start: 0.9367 (mt) cc_final: 0.9028 (mt) REVERT: J 387 TRP cc_start: 0.8786 (p-90) cc_final: 0.8439 (p-90) REVERT: M 3 ASP cc_start: 0.9065 (m-30) cc_final: 0.8797 (t0) REVERT: M 21 GLU cc_start: 0.9233 (pt0) cc_final: 0.8913 (pm20) REVERT: M 38 GLU cc_start: 0.9304 (mm-30) cc_final: 0.8904 (pm20) REVERT: M 46 GLU cc_start: 0.8469 (tm-30) cc_final: 0.7903 (tm-30) REVERT: M 51 ASN cc_start: 0.9534 (t0) cc_final: 0.9306 (t0) REVERT: M 58 LYS cc_start: 0.9590 (ttpt) cc_final: 0.9147 (pttt) REVERT: M 62 LYS cc_start: 0.8845 (mmtp) cc_final: 0.7682 (tttt) REVERT: M 77 LYS cc_start: 0.9070 (mmpt) cc_final: 0.8754 (mmtm) REVERT: U 10 LYS cc_start: 0.9573 (tptp) cc_final: 0.9293 (mmtm) REVERT: U 82 MET cc_start: 0.9474 (tmm) cc_final: 0.9124 (tmm) REVERT: U 95 TYR cc_start: 0.8063 (t80) cc_final: 0.7631 (t80) REVERT: U 112 TYR cc_start: 0.9090 (t80) cc_final: 0.8424 (t80) REVERT: U 131 LEU cc_start: 0.8791 (pp) cc_final: 0.8490 (pp) REVERT: U 168 MET cc_start: 0.8993 (mmp) cc_final: 0.8593 (mmm) REVERT: U 169 LYS cc_start: 0.9677 (mmtm) cc_final: 0.9427 (mmtm) REVERT: V 8 TYR cc_start: 0.8671 (m-80) cc_final: 0.7954 (m-80) REVERT: V 25 GLN cc_start: 0.9487 (tp-100) cc_final: 0.8739 (tm-30) REVERT: V 34 ILE cc_start: 0.8589 (pt) cc_final: 0.8362 (pt) REVERT: V 52 LEU cc_start: 0.8469 (tp) cc_final: 0.8215 (tp) REVERT: V 103 GLN cc_start: 0.9219 (tp-100) cc_final: 0.8817 (tp-100) REVERT: V 120 CYS cc_start: 0.9216 (t) cc_final: 0.8694 (m) REVERT: V 125 CYS cc_start: 0.8625 (m) cc_final: 0.8418 (m) REVERT: V 126 CYS cc_start: 0.8976 (p) cc_final: 0.8600 (p) REVERT: V 127 LYS cc_start: 0.8582 (tttp) cc_final: 0.8141 (ttpp) REVERT: V 154 SER cc_start: 0.9509 (t) cc_final: 0.9263 (p) REVERT: V 157 LEU cc_start: 0.8752 (mt) cc_final: 0.8209 (mt) REVERT: V 176 PHE cc_start: 0.9272 (t80) cc_final: 0.8849 (t80) REVERT: Y 27 LEU cc_start: 0.9306 (mt) cc_final: 0.9090 (mt) REVERT: Y 163 ASP cc_start: 0.9458 (m-30) cc_final: 0.9150 (m-30) REVERT: Y 273 HIS cc_start: 0.9190 (m90) cc_final: 0.8727 (m-70) REVERT: Y 289 HIS cc_start: 0.7560 (t70) cc_final: 0.7146 (t70) REVERT: Y 301 ILE cc_start: 0.8443 (pt) cc_final: 0.8138 (pt) REVERT: Y 319 MET cc_start: 0.7920 (pmm) cc_final: 0.7627 (pmm) outliers start: 1 outliers final: 0 residues processed: 243 average time/residue: 0.2894 time to fit residues: 108.7368 Evaluate side-chains 204 residues out of total 2158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 204 time to evaluate : 2.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 136 optimal weight: 1.9990 chunk 88 optimal weight: 9.9990 chunk 131 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 42 optimal weight: 0.0980 chunk 140 optimal weight: 3.9990 chunk 150 optimal weight: 7.9990 chunk 109 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 173 optimal weight: 0.9980 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 263 GLN ** H 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 49 HIS ** Y 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.4935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 19632 Z= 0.260 Angle : 0.590 10.261 26712 Z= 0.285 Chirality : 0.042 0.156 3086 Planarity : 0.004 0.054 3456 Dihedral : 7.508 137.424 2860 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.87 % Favored : 95.05 % 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 : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.17), residues: 2444 helix: 1.68 (0.18), residues: 821 sheet: -0.96 (0.28), residues: 337 loop : -0.67 (0.17), residues: 1286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.003 TRP G 357 HIS 0.005 0.001 HIS V 109 PHE 0.009 0.001 PHE Y 261 TYR 0.013 0.001 TYR J 76 ARG 0.009 0.000 ARG V 70 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 230 time to evaluate : 2.117 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: G 48 MET cc_start: 0.8458 (ttp) cc_final: 0.7813 (tmm) REVERT: G 75 MET cc_start: 0.8559 (ttp) cc_final: 0.7233 (tmm) REVERT: G 140 SER cc_start: 0.9419 (t) cc_final: 0.8864 (p) REVERT: G 141 MET cc_start: 0.8053 (mmm) cc_final: 0.7821 (mmm) REVERT: G 142 GLN cc_start: 0.8598 (mt0) cc_final: 0.8121 (mp10) REVERT: G 176 MET cc_start: 0.6930 (mmp) cc_final: 0.6379 (mmm) REVERT: G 181 MET cc_start: 0.7603 (mmm) cc_final: 0.7381 (tpp) REVERT: G 184 ASP cc_start: 0.7858 (p0) cc_final: 0.7227 (p0) REVERT: G 189 ASP cc_start: 0.9396 (m-30) cc_final: 0.8898 (m-30) REVERT: G 206 HIS cc_start: 0.9322 (p-80) cc_final: 0.9090 (p-80) REVERT: G 240 GLN cc_start: 0.8668 (pp30) cc_final: 0.8213 (tm-30) REVERT: G 284 GLN cc_start: 0.9531 (mt0) cc_final: 0.9207 (mt0) REVERT: H 44 MET cc_start: 0.8598 (ptm) cc_final: 0.8139 (ppp) REVERT: H 47 MET cc_start: 0.8721 (mmm) cc_final: 0.8455 (mmp) REVERT: H 78 ASN cc_start: 0.8369 (t0) cc_final: 0.7985 (t0) REVERT: H 82 MET cc_start: 0.9527 (tpt) cc_final: 0.9199 (tpt) REVERT: H 153 MET cc_start: 0.9255 (tmm) cc_final: 0.8519 (tmm) REVERT: H 195 GLU cc_start: 0.9293 (mt-10) cc_final: 0.8887 (tt0) REVERT: H 217 CYS cc_start: 0.9642 (m) cc_final: 0.9283 (m) REVERT: H 227 MET cc_start: 0.9028 (mmm) cc_final: 0.8575 (mmm) REVERT: H 272 CYS cc_start: 0.7707 (p) cc_final: 0.7338 (p) REVERT: H 291 LYS cc_start: 0.9226 (tttt) cc_final: 0.8903 (mptt) REVERT: H 325 MET cc_start: 0.8992 (mmm) cc_final: 0.8373 (mmt) REVERT: H 355 MET cc_start: 0.9198 (mmp) cc_final: 0.8777 (mmm) REVERT: I 13 VAL cc_start: 0.9294 (t) cc_final: 0.8964 (m) REVERT: I 100 GLN cc_start: 0.9337 (tt0) cc_final: 0.8943 (tm-30) REVERT: I 116 ASN cc_start: 0.8588 (t0) cc_final: 0.8191 (t0) REVERT: I 159 ASP cc_start: 0.8885 (t0) cc_final: 0.8427 (t70) REVERT: I 189 ASP cc_start: 0.9120 (m-30) cc_final: 0.8501 (m-30) REVERT: I 270 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7563 (mm-30) REVERT: I 271 GLU cc_start: 0.9019 (tp30) cc_final: 0.8164 (tt0) REVERT: I 356 MET cc_start: 0.8794 (mtt) cc_final: 0.8374 (mtt) REVERT: J 37 CYS cc_start: 0.7410 (t) cc_final: 0.6818 (t) REVERT: J 137 MET cc_start: 0.7477 (tpp) cc_final: 0.6919 (tpp) REVERT: J 178 GLN cc_start: 0.9226 (mm-40) cc_final: 0.8934 (mm-40) REVERT: J 289 MET cc_start: 0.8785 (ttm) cc_final: 0.8450 (ttm) REVERT: J 301 GLU cc_start: 0.9066 (mt-10) cc_final: 0.8656 (tp30) REVERT: J 311 MET cc_start: 0.9475 (tpp) cc_final: 0.8913 (mmm) REVERT: J 322 GLU cc_start: 0.9490 (tp30) cc_final: 0.8969 (tp30) REVERT: J 326 LEU cc_start: 0.9369 (mt) cc_final: 0.9063 (mt) REVERT: J 387 TRP cc_start: 0.8857 (p-90) cc_final: 0.8525 (p-90) REVERT: M 38 GLU cc_start: 0.9334 (mm-30) cc_final: 0.8983 (pm20) REVERT: M 46 GLU cc_start: 0.8452 (tm-30) cc_final: 0.7986 (tm-30) REVERT: M 51 ASN cc_start: 0.9518 (t0) cc_final: 0.9254 (t0) REVERT: M 58 LYS cc_start: 0.9581 (ttpt) cc_final: 0.9242 (ptmt) REVERT: M 62 LYS cc_start: 0.8825 (mmtp) cc_final: 0.7714 (tttt) REVERT: M 77 LYS cc_start: 0.9120 (mmpt) cc_final: 0.8807 (mmtm) REVERT: U 38 LYS cc_start: 0.9048 (mmtm) cc_final: 0.8831 (mmmt) REVERT: U 91 GLU cc_start: 0.8797 (mm-30) cc_final: 0.8384 (mm-30) REVERT: U 95 TYR cc_start: 0.8076 (t80) cc_final: 0.7678 (t80) REVERT: U 112 TYR cc_start: 0.9086 (t80) cc_final: 0.8428 (t80) REVERT: U 131 LEU cc_start: 0.8797 (pp) cc_final: 0.8489 (pp) REVERT: U 148 CYS cc_start: 0.8894 (m) cc_final: 0.8621 (m) REVERT: U 150 ARG cc_start: 0.8205 (mtm180) cc_final: 0.7545 (mtt90) REVERT: U 167 LEU cc_start: 0.9812 (mm) cc_final: 0.9610 (mm) REVERT: U 168 MET cc_start: 0.9032 (mmp) cc_final: 0.8623 (mmm) REVERT: U 169 LYS cc_start: 0.9703 (mmtm) cc_final: 0.9454 (mmtm) REVERT: V 6 LEU cc_start: 0.9179 (mt) cc_final: 0.8449 (tp) REVERT: V 8 TYR cc_start: 0.8677 (m-80) cc_final: 0.7931 (m-80) REVERT: V 25 GLN cc_start: 0.9467 (tp-100) cc_final: 0.8739 (tm-30) REVERT: V 34 ILE cc_start: 0.8602 (pt) cc_final: 0.8374 (pt) REVERT: V 52 LEU cc_start: 0.8433 (tp) cc_final: 0.8176 (tp) REVERT: V 103 GLN cc_start: 0.9256 (tp-100) cc_final: 0.8819 (tp-100) REVERT: V 120 CYS cc_start: 0.9240 (t) cc_final: 0.8691 (m) REVERT: V 125 CYS cc_start: 0.8615 (m) cc_final: 0.8415 (m) REVERT: V 126 CYS cc_start: 0.8933 (p) cc_final: 0.8579 (p) REVERT: V 127 LYS cc_start: 0.8565 (tttp) cc_final: 0.8128 (ttpp) REVERT: V 154 SER cc_start: 0.9492 (t) cc_final: 0.9280 (p) REVERT: V 157 LEU cc_start: 0.8769 (mt) cc_final: 0.8210 (mt) REVERT: V 165 MET cc_start: 0.9553 (mmm) cc_final: 0.9171 (mtp) REVERT: V 176 PHE cc_start: 0.9294 (t80) cc_final: 0.8891 (t80) REVERT: Y 27 LEU cc_start: 0.9256 (mt) cc_final: 0.9049 (mt) REVERT: Y 163 ASP cc_start: 0.9459 (m-30) cc_final: 0.9169 (m-30) REVERT: Y 301 ILE cc_start: 0.8520 (pt) cc_final: 0.8209 (pt) REVERT: Y 319 MET cc_start: 0.7955 (pmm) cc_final: 0.7672 (pmm) outliers start: 0 outliers final: 0 residues processed: 230 average time/residue: 0.2954 time to fit residues: 106.0653 Evaluate side-chains 190 residues out of total 2158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 2.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 200 optimal weight: 0.9990 chunk 211 optimal weight: 2.9990 chunk 192 optimal weight: 3.9990 chunk 205 optimal weight: 6.9990 chunk 123 optimal weight: 7.9990 chunk 89 optimal weight: 5.9990 chunk 161 optimal weight: 30.0000 chunk 63 optimal weight: 2.9990 chunk 185 optimal weight: 0.7980 chunk 194 optimal weight: 2.9990 chunk 204 optimal weight: 5.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 16 ASN ** G 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 73 HIS ** H 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 262 GLN ** Y 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.5084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 19632 Z= 0.252 Angle : 0.581 11.333 26712 Z= 0.282 Chirality : 0.042 0.178 3086 Planarity : 0.004 0.039 3456 Dihedral : 7.336 133.939 2860 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.34 % Favored : 95.58 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.17), residues: 2444 helix: 1.76 (0.18), residues: 819 sheet: -1.18 (0.27), residues: 367 loop : -0.62 (0.17), residues: 1258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.002 TRP G 357 HIS 0.005 0.001 HIS J 79 PHE 0.036 0.001 PHE G 193 TYR 0.015 0.001 TYR G 197 ARG 0.006 0.000 ARG V 70 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 228 time to evaluate : 2.307 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: G 48 MET cc_start: 0.8458 (ttp) cc_final: 0.7823 (tmm) REVERT: G 75 MET cc_start: 0.8590 (ttp) cc_final: 0.7318 (tmm) REVERT: G 140 SER cc_start: 0.9415 (t) cc_final: 0.8860 (p) REVERT: G 142 GLN cc_start: 0.8565 (mt0) cc_final: 0.8211 (mp10) REVERT: G 176 MET cc_start: 0.6824 (mmp) cc_final: 0.6288 (mmm) REVERT: G 181 MET cc_start: 0.7590 (mmm) cc_final: 0.7363 (tpp) REVERT: G 184 ASP cc_start: 0.7825 (p0) cc_final: 0.7200 (p0) REVERT: G 189 ASP cc_start: 0.9423 (m-30) cc_final: 0.8973 (m-30) REVERT: G 240 GLN cc_start: 0.8651 (pp30) cc_final: 0.8194 (tm-30) REVERT: G 284 GLN cc_start: 0.9548 (mt0) cc_final: 0.9223 (mt0) REVERT: H 44 MET cc_start: 0.8559 (ptm) cc_final: 0.8174 (ppp) REVERT: H 78 ASN cc_start: 0.8374 (t0) cc_final: 0.7979 (t0) REVERT: H 82 MET cc_start: 0.9535 (tpt) cc_final: 0.9214 (tpt) REVERT: H 153 MET cc_start: 0.9264 (tmm) cc_final: 0.8682 (tmm) REVERT: H 195 GLU cc_start: 0.9282 (mt-10) cc_final: 0.8850 (tt0) REVERT: H 217 CYS cc_start: 0.9654 (m) cc_final: 0.9255 (m) REVERT: H 227 MET cc_start: 0.9030 (mmm) cc_final: 0.8565 (mmm) REVERT: H 291 LYS cc_start: 0.9233 (tttt) cc_final: 0.8904 (mptt) REVERT: H 325 MET cc_start: 0.8976 (mmm) cc_final: 0.8301 (mmt) REVERT: H 355 MET cc_start: 0.9174 (mmp) cc_final: 0.8753 (mmm) REVERT: I 13 VAL cc_start: 0.9323 (t) cc_final: 0.9003 (m) REVERT: I 100 GLN cc_start: 0.9305 (tt0) cc_final: 0.8936 (tm-30) REVERT: I 116 ASN cc_start: 0.8653 (t0) cc_final: 0.8329 (t0) REVERT: I 159 ASP cc_start: 0.8892 (t0) cc_final: 0.8407 (t70) REVERT: I 189 ASP cc_start: 0.9113 (m-30) cc_final: 0.8481 (m-30) REVERT: I 270 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7746 (mm-30) REVERT: I 271 GLU cc_start: 0.9034 (tp30) cc_final: 0.8185 (tt0) REVERT: I 356 MET cc_start: 0.8786 (mtt) cc_final: 0.8354 (mtt) REVERT: J 37 CYS cc_start: 0.7364 (t) cc_final: 0.6783 (t) REVERT: J 44 LYS cc_start: 0.9495 (mttt) cc_final: 0.9170 (tppt) REVERT: J 48 MET cc_start: 0.9176 (mpp) cc_final: 0.8912 (mpp) REVERT: J 137 MET cc_start: 0.7465 (tpp) cc_final: 0.6900 (tpt) REVERT: J 178 GLN cc_start: 0.9243 (mm-40) cc_final: 0.8922 (mm-40) REVERT: J 215 CYS cc_start: 0.9260 (m) cc_final: 0.9058 (m) REVERT: J 289 MET cc_start: 0.8788 (ttm) cc_final: 0.8458 (ttm) REVERT: J 301 GLU cc_start: 0.9070 (mt-10) cc_final: 0.8657 (tp30) REVERT: J 311 MET cc_start: 0.9440 (tpp) cc_final: 0.8923 (mmm) REVERT: J 322 GLU cc_start: 0.9486 (tp30) cc_final: 0.8958 (tp30) REVERT: J 326 LEU cc_start: 0.9366 (mt) cc_final: 0.9036 (mt) REVERT: J 387 TRP cc_start: 0.8843 (p-90) cc_final: 0.8509 (p-90) REVERT: M 38 GLU cc_start: 0.9338 (mm-30) cc_final: 0.8980 (pm20) REVERT: M 46 GLU cc_start: 0.8463 (tm-30) cc_final: 0.7993 (tm-30) REVERT: M 51 ASN cc_start: 0.9517 (t0) cc_final: 0.9237 (t0) REVERT: M 58 LYS cc_start: 0.9615 (ttpt) cc_final: 0.9258 (ptmt) REVERT: M 62 LYS cc_start: 0.8859 (mmtp) cc_final: 0.7740 (tttt) REVERT: M 77 LYS cc_start: 0.9128 (mmpt) cc_final: 0.8832 (mmtm) REVERT: U 38 LYS cc_start: 0.9049 (mmtm) cc_final: 0.8818 (mmmt) REVERT: U 95 TYR cc_start: 0.8072 (t80) cc_final: 0.7670 (t80) REVERT: U 99 MET cc_start: 0.7409 (mmm) cc_final: 0.7195 (mmp) REVERT: U 112 TYR cc_start: 0.9074 (t80) cc_final: 0.8432 (t80) REVERT: U 131 LEU cc_start: 0.8813 (pp) cc_final: 0.8541 (pp) REVERT: U 167 LEU cc_start: 0.9782 (mm) cc_final: 0.9523 (pp) REVERT: U 168 MET cc_start: 0.9030 (mmp) cc_final: 0.8723 (mmm) REVERT: U 169 LYS cc_start: 0.9729 (mmtm) cc_final: 0.9507 (mmtm) REVERT: V 6 LEU cc_start: 0.9165 (mt) cc_final: 0.7857 (tp) REVERT: V 8 TYR cc_start: 0.8681 (m-80) cc_final: 0.8078 (m-10) REVERT: V 25 GLN cc_start: 0.9472 (tp-100) cc_final: 0.8741 (tm-30) REVERT: V 34 ILE cc_start: 0.8568 (pt) cc_final: 0.8327 (pt) REVERT: V 70 ARG cc_start: 0.8278 (tmm-80) cc_final: 0.7973 (tmm-80) REVERT: V 103 GLN cc_start: 0.9247 (tp-100) cc_final: 0.8890 (tp-100) REVERT: V 120 CYS cc_start: 0.9251 (t) cc_final: 0.8713 (m) REVERT: V 125 CYS cc_start: 0.8643 (m) cc_final: 0.8424 (m) REVERT: V 126 CYS cc_start: 0.8958 (p) cc_final: 0.8555 (p) REVERT: V 127 LYS cc_start: 0.8628 (tttp) cc_final: 0.8328 (ttpp) REVERT: V 154 SER cc_start: 0.9436 (t) cc_final: 0.9160 (p) REVERT: V 165 MET cc_start: 0.9588 (mmm) cc_final: 0.9133 (mtp) REVERT: V 176 PHE cc_start: 0.9309 (t80) cc_final: 0.8856 (t80) REVERT: Y 27 LEU cc_start: 0.9243 (mt) cc_final: 0.9036 (mt) REVERT: Y 123 MET cc_start: 0.8468 (mtp) cc_final: 0.8235 (mtp) REVERT: Y 163 ASP cc_start: 0.9454 (m-30) cc_final: 0.9163 (m-30) REVERT: Y 319 MET cc_start: 0.7913 (pmm) cc_final: 0.7601 (pmm) outliers start: 0 outliers final: 0 residues processed: 228 average time/residue: 0.3062 time to fit residues: 107.2604 Evaluate side-chains 190 residues out of total 2158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 2.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 135 optimal weight: 2.9990 chunk 217 optimal weight: 40.0000 chunk 132 optimal weight: 0.9980 chunk 103 optimal weight: 5.9990 chunk 151 optimal weight: 2.9990 chunk 228 optimal weight: 8.9990 chunk 209 optimal weight: 0.0370 chunk 181 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 140 optimal weight: 3.9990 chunk 111 optimal weight: 7.9990 overall best weight: 1.1662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.5132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19632 Z= 0.180 Angle : 0.558 11.151 26712 Z= 0.269 Chirality : 0.042 0.158 3086 Planarity : 0.004 0.038 3456 Dihedral : 7.060 130.718 2860 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.38 % Favored : 95.54 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.17), residues: 2444 helix: 1.83 (0.19), residues: 818 sheet: -1.11 (0.28), residues: 362 loop : -0.58 (0.17), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP G 357 HIS 0.009 0.001 HIS V 109 PHE 0.009 0.001 PHE Y 261 TYR 0.024 0.001 TYR J 76 ARG 0.006 0.000 ARG V 70 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 230 time to evaluate : 2.405 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: G 48 MET cc_start: 0.8454 (ttp) cc_final: 0.7742 (tmm) REVERT: G 75 MET cc_start: 0.8550 (ttp) cc_final: 0.7348 (tmm) REVERT: G 140 SER cc_start: 0.9278 (t) cc_final: 0.8843 (p) REVERT: G 142 GLN cc_start: 0.8538 (mt0) cc_final: 0.8248 (mp10) REVERT: G 176 MET cc_start: 0.6878 (mmp) cc_final: 0.6531 (mmm) REVERT: G 181 MET cc_start: 0.7455 (mmm) cc_final: 0.7214 (tpp) REVERT: G 184 ASP cc_start: 0.7908 (p0) cc_final: 0.7312 (p0) REVERT: G 189 ASP cc_start: 0.9437 (m-30) cc_final: 0.8972 (m-30) REVERT: G 206 HIS cc_start: 0.9327 (p-80) cc_final: 0.9075 (p-80) REVERT: G 240 GLN cc_start: 0.8516 (pp30) cc_final: 0.8136 (tm-30) REVERT: G 284 GLN cc_start: 0.9545 (mt0) cc_final: 0.9213 (mt0) REVERT: H 44 MET cc_start: 0.8564 (ptm) cc_final: 0.8301 (ppp) REVERT: H 78 ASN cc_start: 0.8340 (t0) cc_final: 0.7929 (t0) REVERT: H 82 MET cc_start: 0.9406 (tpt) cc_final: 0.9201 (tpt) REVERT: H 153 MET cc_start: 0.9247 (tmm) cc_final: 0.8690 (tmm) REVERT: H 195 GLU cc_start: 0.9262 (mt-10) cc_final: 0.8797 (tt0) REVERT: H 217 CYS cc_start: 0.9668 (m) cc_final: 0.9235 (m) REVERT: H 291 LYS cc_start: 0.9225 (tttt) cc_final: 0.8907 (mptt) REVERT: H 325 MET cc_start: 0.8982 (mmm) cc_final: 0.8309 (mmt) REVERT: H 355 MET cc_start: 0.9182 (mmp) cc_final: 0.8411 (mtp) REVERT: I 13 VAL cc_start: 0.9335 (t) cc_final: 0.9004 (m) REVERT: I 86 MET cc_start: 0.9247 (tpp) cc_final: 0.8932 (tpp) REVERT: I 100 GLN cc_start: 0.9303 (tt0) cc_final: 0.8848 (tp40) REVERT: I 116 ASN cc_start: 0.8745 (t0) cc_final: 0.8439 (t0) REVERT: I 159 ASP cc_start: 0.8908 (t0) cc_final: 0.8398 (t70) REVERT: I 189 ASP cc_start: 0.9118 (m-30) cc_final: 0.8477 (m-30) REVERT: I 229 GLN cc_start: 0.9311 (mp10) cc_final: 0.9109 (mp10) REVERT: I 270 GLU cc_start: 0.8146 (mm-30) cc_final: 0.7716 (mm-30) REVERT: I 271 GLU cc_start: 0.9034 (tp30) cc_final: 0.8170 (tt0) REVERT: I 356 MET cc_start: 0.8755 (mtt) cc_final: 0.8251 (mtt) REVERT: I 373 ARG cc_start: 0.8711 (ptp-170) cc_final: 0.8484 (ptp-170) REVERT: J 37 CYS cc_start: 0.7317 (t) cc_final: 0.6749 (t) REVERT: J 44 LYS cc_start: 0.9495 (mttt) cc_final: 0.9200 (tppt) REVERT: J 137 MET cc_start: 0.7441 (tpp) cc_final: 0.6877 (tpp) REVERT: J 178 GLN cc_start: 0.9246 (mm-40) cc_final: 0.8923 (mm-40) REVERT: J 215 CYS cc_start: 0.9270 (m) cc_final: 0.9022 (m) REVERT: J 289 MET cc_start: 0.8815 (ttm) cc_final: 0.8496 (ttm) REVERT: J 301 GLU cc_start: 0.9060 (mt-10) cc_final: 0.8653 (tp30) REVERT: J 311 MET cc_start: 0.9434 (tpp) cc_final: 0.8950 (mmm) REVERT: J 322 GLU cc_start: 0.9497 (tp30) cc_final: 0.8982 (tp30) REVERT: J 326 LEU cc_start: 0.9369 (mt) cc_final: 0.9015 (mt) REVERT: J 387 TRP cc_start: 0.8762 (p-90) cc_final: 0.8342 (p-90) REVERT: M 38 GLU cc_start: 0.9339 (mm-30) cc_final: 0.8927 (pm20) REVERT: M 39 GLU cc_start: 0.8699 (tp30) cc_final: 0.6992 (tp30) REVERT: M 46 GLU cc_start: 0.8381 (tm-30) cc_final: 0.7936 (tm-30) REVERT: M 51 ASN cc_start: 0.9517 (t0) cc_final: 0.9243 (t0) REVERT: M 58 LYS cc_start: 0.9601 (ttpt) cc_final: 0.9262 (ptmt) REVERT: M 62 LYS cc_start: 0.8970 (mmtp) cc_final: 0.7976 (tttt) REVERT: M 77 LYS cc_start: 0.9135 (mmpt) cc_final: 0.8822 (mmtm) REVERT: U 38 LYS cc_start: 0.9049 (mmtm) cc_final: 0.8813 (mmmt) REVERT: U 95 TYR cc_start: 0.8069 (t80) cc_final: 0.7709 (t80) REVERT: U 99 MET cc_start: 0.7300 (mmm) cc_final: 0.7072 (mmp) REVERT: U 112 TYR cc_start: 0.9094 (t80) cc_final: 0.8429 (t80) REVERT: U 148 CYS cc_start: 0.8809 (m) cc_final: 0.8537 (m) REVERT: U 150 ARG cc_start: 0.8129 (mtm180) cc_final: 0.7426 (mtt90) REVERT: U 164 LEU cc_start: 0.9585 (mm) cc_final: 0.9341 (mm) REVERT: U 167 LEU cc_start: 0.9784 (mm) cc_final: 0.9443 (pp) REVERT: U 168 MET cc_start: 0.9000 (mmp) cc_final: 0.8442 (mmm) REVERT: U 169 LYS cc_start: 0.9730 (mmtm) cc_final: 0.9523 (mmtm) REVERT: V 6 LEU cc_start: 0.9158 (mt) cc_final: 0.7904 (tp) REVERT: V 8 TYR cc_start: 0.8643 (m-80) cc_final: 0.8102 (m-10) REVERT: V 25 GLN cc_start: 0.9460 (tp-100) cc_final: 0.8738 (tm-30) REVERT: V 34 ILE cc_start: 0.8554 (pt) cc_final: 0.8319 (pt) REVERT: V 70 ARG cc_start: 0.8325 (tmm-80) cc_final: 0.8033 (tmm-80) REVERT: V 103 GLN cc_start: 0.9233 (tp-100) cc_final: 0.8816 (tp-100) REVERT: V 120 CYS cc_start: 0.9262 (t) cc_final: 0.8713 (m) REVERT: V 125 CYS cc_start: 0.8648 (m) cc_final: 0.7673 (p) REVERT: V 126 CYS cc_start: 0.8895 (p) cc_final: 0.8600 (p) REVERT: V 154 SER cc_start: 0.9424 (t) cc_final: 0.9179 (p) REVERT: V 157 LEU cc_start: 0.8613 (mt) cc_final: 0.8023 (mt) REVERT: V 165 MET cc_start: 0.9601 (mmm) cc_final: 0.9176 (mtp) REVERT: V 176 PHE cc_start: 0.9306 (t80) cc_final: 0.8839 (t80) REVERT: Y 27 LEU cc_start: 0.9263 (mt) cc_final: 0.9050 (mt) REVERT: Y 123 MET cc_start: 0.8508 (mtp) cc_final: 0.8255 (mtp) REVERT: Y 163 ASP cc_start: 0.9430 (m-30) cc_final: 0.9130 (m-30) REVERT: Y 289 HIS cc_start: 0.7486 (t70) cc_final: 0.7075 (t70) REVERT: Y 319 MET cc_start: 0.8002 (pmm) cc_final: 0.7657 (pmm) outliers start: 0 outliers final: 0 residues processed: 230 average time/residue: 0.3040 time to fit residues: 109.0435 Evaluate side-chains 194 residues out of total 2158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 2.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 144 optimal weight: 4.9990 chunk 193 optimal weight: 0.8980 chunk 55 optimal weight: 5.9990 chunk 167 optimal weight: 5.9990 chunk 26 optimal weight: 0.1980 chunk 50 optimal weight: 4.9990 chunk 181 optimal weight: 0.0060 chunk 76 optimal weight: 0.0970 chunk 186 optimal weight: 10.0000 chunk 23 optimal weight: 0.0000 chunk 33 optimal weight: 0.9990 overall best weight: 0.2398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.063587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.043642 restraints weight = 89330.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.045182 restraints weight = 46804.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.046300 restraints weight = 29746.326| |-----------------------------------------------------------------------------| r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.5168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 19632 Z= 0.145 Angle : 0.558 10.344 26712 Z= 0.264 Chirality : 0.041 0.140 3086 Planarity : 0.004 0.038 3456 Dihedral : 6.650 124.181 2860 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.76 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.17), residues: 2444 helix: 1.83 (0.19), residues: 815 sheet: -0.96 (0.27), residues: 378 loop : -0.61 (0.17), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP G 357 HIS 0.010 0.001 HIS V 109 PHE 0.010 0.001 PHE I 128 TYR 0.014 0.001 TYR V 13 ARG 0.006 0.000 ARG J 78 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3599.75 seconds wall clock time: 66 minutes 8.24 seconds (3968.24 seconds total)