Starting phenix.real_space_refine on Mon Mar 18 00:53:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6znn_11318/03_2024/6znn_11318_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6znn_11318/03_2024/6znn_11318.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6znn_11318/03_2024/6znn_11318.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6znn_11318/03_2024/6znn_11318.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6znn_11318/03_2024/6znn_11318_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6znn_11318/03_2024/6znn_11318_neut_updated.pdb" } resolution = 4.5 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= 0.010 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 12313 2.51 5 N 3417 2.21 5 O 3618 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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 19457 Number of models: 1 Model: "" Number of chains: 17 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: "S" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 340 Classifications: {'peptide': 68} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'TRANS': 67} Unresolved non-hydrogen bonds: 136 Unresolved non-hydrogen angles: 204 Unresolved non-hydrogen dihedrals: 68 Planarities with less than four sites: {'UNK:plan-1': 68} Unresolved non-hydrogen planarities: 68 Chain: "T" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 340 Classifications: {'peptide': 68} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'TRANS': 67} Unresolved non-hydrogen bonds: 136 Unresolved non-hydrogen angles: 204 Unresolved non-hydrogen dihedrals: 68 Planarities with less than four sites: {'UNK:plan-1': 68} Unresolved non-hydrogen planarities: 68 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: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 465 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 93} Link IDs: {'TRANS': 92} Unresolved non-hydrogen bonds: 186 Unresolved non-hydrogen angles: 279 Unresolved non-hydrogen dihedrals: 93 Planarities with less than four sites: {'UNK:plan-1': 93} Unresolved non-hydrogen planarities: 93 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: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 460 Classifications: {'peptide': 92} Incomplete info: {'truncation_to_alanine': 92} Link IDs: {'TRANS': 91} Unresolved non-hydrogen bonds: 184 Unresolved non-hydrogen angles: 276 Unresolved non-hydrogen dihedrals: 92 Planarities with less than four sites: {'UNK:plan-1': 92} Unresolved non-hydrogen planarities: 92 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 16189 SG CYS Y 33 81.546 41.291 50.527 1.00176.12 S ATOM 17746 SG CYS Y 287 82.674 38.608 52.763 1.00182.93 S ATOM 16324 SG CYS Y 51 112.896 30.834 68.620 1.00172.70 S ATOM 16468 SG CYS Y 70 112.797 27.626 71.431 1.00168.75 S ATOM 16509 SG CYS Y 76 121.782 39.737 72.509 1.00177.86 S ATOM 16664 SG CYS Y 114 125.834 42.054 72.654 1.00177.90 S Time building chain proxies: 10.53, per 1000 atoms: 0.54 Number of scatterers: 19457 At special positions: 0 Unit cell: (171.52, 119.26, 176.88, 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 3618 8.00 N 3417 7.00 C 12313 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: 7.65 Conformation dependent library (CDL) restraints added in 3.4 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 " 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4970 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 79 helices and 26 sheets defined 43.4% alpha, 10.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.00 Creating SS restraints... Processing helix chain 'G' and resid 60 through 64 Processing helix chain 'G' and resid 83 through 94 removed outlier: 3.580A 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: 3.688A 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: 3.844A pdb=" N GLU G 212 " --> pdb=" O SER G 208 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ILE G 213 " --> pdb=" O SER G 209 " (cutoff:3.500A) Processing helix chain 'G' and resid 228 through 233 removed outlier: 3.610A pdb=" N THR G 233 " --> pdb=" O GLN G 229 " (cutoff:3.500A) Processing helix chain 'G' and resid 252 through 262 removed outlier: 3.666A pdb=" N ARG G 255 " --> pdb=" O GLY G 252 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG G 257 " --> pdb=" O SER G 254 " (cutoff:3.500A) removed outlier: 4.319A 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: 4.312A pdb=" N ARG G 292 " --> pdb=" O ASP G 289 " (cutoff:3.500A) removed outlier: 3.746A 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: 3.702A 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: 4.249A 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: 3.500A 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: 3.691A 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: 3.793A pdb=" N GLU I 212 " --> pdb=" O SER I 208 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE I 213 " --> pdb=" O SER I 209 " (cutoff:3.500A) removed outlier: 3.566A 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: 4.371A 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: 5.020A pdb=" N THR I 293 " --> pdb=" O ASP I 289 " (cutoff:3.500A) Processing helix chain 'I' and resid 310 through 321 removed outlier: 3.505A 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: 3.803A pdb=" N LEU I 321 " --> pdb=" O GLU I 317 " (cutoff:3.500A) Processing helix chain 'I' and resid 339 through 349 removed outlier: 3.504A 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: 4.745A 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: 5.183A pdb=" N LEU J 270 " --> pdb=" O VAL J 266 " (cutoff:3.500A) removed outlier: 4.118A 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: 3.850A 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: 3.634A pdb=" N GLY J 358 " --> pdb=" O ALA J 354 " (cutoff:3.500A) Processing helix chain 'J' and resid 365 through 371 removed outlier: 4.042A 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 'S' and resid 2 through 67 Processing helix chain 'T' and resid 2 through 67 removed outlier: 4.162A pdb=" N UNK T 27 " --> pdb=" O UNK T 23 " (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: 3.927A pdb=" N MET U 168 " --> pdb=" O LEU U 164 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N LYS U 169 " --> pdb=" O ASP U 165 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE U 170 " --> pdb=" O PHE U 166 " (cutoff:3.500A) Processing helix chain 'V' and resid 162 through 175 removed outlier: 4.141A 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 132 through 220 removed outlier: 3.929A pdb=" N UNK X 148 " --> pdb=" O UNK X 144 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N UNK X 154 " --> pdb=" O UNK X 150 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N UNK X 161 " --> pdb=" O UNK X 157 " (cutoff:3.500A) Processing helix chain 'Y' and resid 60 through 66 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: 3.517A 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 132 through 221 removed outlier: 4.129A pdb=" N UNK x 167 " --> pdb=" O UNK x 163 " (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: 6.912A 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: 8.023A 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: 6.318A 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: 3.677A 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: 6.319A pdb=" N LEU H 104 " --> pdb=" O VAL H 10 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ASN H 12 " --> pdb=" O LEU H 104 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N THR H 106 " --> pdb=" O ASN H 12 " (cutoff:3.500A) removed outlier: 3.717A 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: 3.655A 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: 6.745A 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: 6.220A pdb=" N MET H 153 " --> pdb=" O SER H 300 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE H 165 " --> pdb=" O GLY H 150 " (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: 7.237A 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: 6.966A 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: 8.423A 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: 3.845A 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: 6.231A pdb=" N VAL I 156 " --> pdb=" O VAL I 299 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N SER I 301 " --> pdb=" O VAL I 156 " (cutoff:3.500A) removed outlier: 6.298A 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: 6.677A pdb=" N VAL J 91 " --> pdb=" O ALA J 121 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N VAL J 16 " --> pdb=" O VAL J 90 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N ILE J 92 " --> pdb=" O VAL J 16 " (cutoff:3.500A) removed outlier: 6.511A 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: 6.508A 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: 6.715A 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) 747 hydrogen bonds defined for protein. 2097 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: 5.46 Time building geometry restraints manager: 8.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3716 1.33 - 1.45: 4525 1.45 - 1.58: 11434 1.58 - 1.70: 14 1.70 - 1.82: 145 Bond restraints: 19834 Sorted by residual: bond pdb=" C4 ADP G 800 " pdb=" C5 ADP G 800 " ideal model delta sigma weight residual 1.490 1.383 0.107 2.00e-02 2.50e+03 2.88e+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 2.85e+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 2.84e+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 2.08e+01 bond pdb=" N VAL V 140 " pdb=" CA VAL V 140 " ideal model delta sigma weight residual 1.456 1.496 -0.040 8.70e-03 1.32e+04 2.07e+01 ... (remaining 19829 not shown) Histogram of bond angle deviations from ideal: 97.58 - 105.02: 526 105.02 - 112.46: 9691 112.46 - 119.89: 9116 119.89 - 127.33: 7541 127.33 - 134.76: 120 Bond angle restraints: 26994 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 103.30 110.04 -6.74 8.00e-01 1.56e+00 7.09e+01 angle pdb=" PB ATP H 401 " pdb=" O3B ATP H 401 " pdb=" PG ATP H 401 " ideal model delta sigma weight residual 139.87 132.11 7.76 1.00e+00 1.00e+00 6.01e+01 angle pdb=" PA ATP H 401 " pdb=" O3A ATP H 401 " pdb=" PB ATP H 401 " ideal model delta sigma weight residual 136.83 129.79 7.04 1.00e+00 1.00e+00 4.96e+01 angle pdb=" N PRO Y 447 " pdb=" CA PRO Y 447 " pdb=" CB PRO Y 447 " ideal model delta sigma weight residual 103.25 110.16 -6.91 1.05e+00 9.07e-01 4.33e+01 angle pdb=" N PRO Y 441 " pdb=" CA PRO Y 441 " pdb=" CB PRO Y 441 " ideal model delta sigma weight residual 103.25 110.09 -6.84 1.05e+00 9.07e-01 4.24e+01 ... (remaining 26989 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.85: 11717 30.85 - 61.70: 275 61.70 - 92.55: 11 92.55 - 123.39: 4 123.39 - 154.24: 2 Dihedral angle restraints: 12009 sinusoidal: 4332 harmonic: 7677 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 94.25 -154.24 1 2.00e+01 2.50e-03 4.56e+01 dihedral pdb=" O1B ADP G 800 " pdb=" O3A ADP G 800 " pdb=" PB ADP G 800 " pdb=" PA ADP G 800 " ideal model delta sinusoidal sigma weight residual -60.00 71.57 -131.58 1 2.00e+01 2.50e-03 3.99e+01 dihedral pdb=" C5' ADP J 800 " pdb=" O5' ADP J 800 " pdb=" PA ADP J 800 " pdb=" O2A ADP J 800 " ideal model delta sinusoidal sigma weight residual -60.00 62.62 -122.62 1 2.00e+01 2.50e-03 3.69e+01 ... (remaining 12006 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1149 0.047 - 0.093: 984 0.093 - 0.140: 666 0.140 - 0.186: 266 0.186 - 0.233: 65 Chirality restraints: 3130 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 1.35e+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 1.25e+00 chirality pdb=" CA ILE G 185 " pdb=" N ILE G 185 " pdb=" C ILE G 185 " pdb=" CB ILE G 185 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 3127 not shown) Planarity restraints: 3494 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP G 357 " 0.035 2.00e-02 2.50e+03 2.81e-02 1.97e+01 pdb=" CG TRP G 357 " -0.078 2.00e-02 2.50e+03 pdb=" CD1 TRP G 357 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP G 357 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP G 357 " 0.008 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 " -0.002 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 THR G 375 " 0.009 2.00e-02 2.50e+03 1.92e-02 3.67e+00 pdb=" C THR G 375 " -0.033 2.00e-02 2.50e+03 pdb=" O THR G 375 " 0.012 2.00e-02 2.50e+03 pdb=" N PHE G 376 " 0.011 2.00e-02 2.50e+03 ... (remaining 3491 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.41: 9 2.41 - 3.03: 9652 3.03 - 3.66: 29700 3.66 - 4.28: 41560 4.28 - 4.90: 70399 Nonbonded interactions: 151320 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 2.215 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 151315 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 'S' selection = chain 'T' } ncs_group { reference = (chain 'X' and resid 132 through 223) selection = chain 'x' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.800 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: 4.810 Check model and map are aligned: 0.260 Set scattering table: 0.170 Process input model: 54.420 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.118 19834 Z= 0.902 Angle : 1.766 12.934 26994 Z= 1.285 Chirality : 0.087 0.233 3130 Planarity : 0.003 0.028 3494 Dihedral : 13.322 154.242 7039 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.70 % Favored : 92.17 % Rotamer: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % 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: -3.13 (0.14), residues: 2298 helix: -1.58 (0.16), residues: 669 sheet: -2.29 (0.28), residues: 283 loop : -2.37 (0.14), residues: 1346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.078 0.003 TRP G 357 HIS 0.017 0.002 HIS G 372 PHE 0.017 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) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 614 time to evaluate : 2.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 37 ASN cc_start: 0.8697 (t0) cc_final: 0.8094 (t0) REVERT: G 63 GLU cc_start: 0.9255 (tp30) cc_final: 0.8950 (tp30) REVERT: G 86 MET cc_start: 0.9532 (tpp) cc_final: 0.9265 (tpp) REVERT: G 157 VAL cc_start: 0.8674 (t) cc_final: 0.8227 (t) REVERT: G 210 GLU cc_start: 0.9409 (mt-10) cc_final: 0.9203 (mt-10) REVERT: G 278 VAL cc_start: 0.8546 (t) cc_final: 0.8254 (t) REVERT: G 279 LEU cc_start: 0.8581 (tp) cc_final: 0.8232 (tp) REVERT: G 342 ILE cc_start: 0.9480 (mt) cc_final: 0.9242 (tp) REVERT: G 346 ILE cc_start: 0.9408 (mt) cc_final: 0.9029 (tp) REVERT: G 347 LEU cc_start: 0.8742 (tp) cc_final: 0.8537 (tp) REVERT: H 8 LEU cc_start: 0.9521 (mt) cc_final: 0.9312 (mm) REVERT: H 78 ASN cc_start: 0.8597 (t0) cc_final: 0.7957 (t0) REVERT: H 82 MET cc_start: 0.9574 (tpt) cc_final: 0.9180 (tpp) REVERT: H 90 PHE cc_start: 0.9669 (m-80) cc_final: 0.9280 (m-80) REVERT: H 119 MET cc_start: 0.9715 (ttm) cc_final: 0.9406 (tmm) REVERT: H 120 THR cc_start: 0.9701 (p) cc_final: 0.8852 (t) REVERT: H 123 MET cc_start: 0.9620 (mmm) cc_final: 0.9368 (tpp) REVERT: H 129 THR cc_start: 0.9038 (p) cc_final: 0.7989 (t) REVERT: H 153 MET cc_start: 0.8774 (tmm) cc_final: 0.8423 (tmm) REVERT: H 184 ASP cc_start: 0.9071 (m-30) cc_final: 0.8828 (m-30) REVERT: H 192 ILE cc_start: 0.9676 (pt) cc_final: 0.9229 (pt) REVERT: H 272 CYS cc_start: 0.8714 (p) cc_final: 0.8032 (p) REVERT: H 296 ASN cc_start: 0.9443 (m-40) cc_final: 0.9136 (t0) REVERT: H 305 MET cc_start: 0.9114 (mtp) cc_final: 0.8745 (mmt) REVERT: I 21 ILE cc_start: 0.9176 (pt) cc_final: 0.8876 (mm) REVERT: I 37 ASN cc_start: 0.8891 (t0) cc_final: 0.8597 (t0) REVERT: I 75 MET cc_start: 0.7845 (ttm) cc_final: 0.7301 (tpp) REVERT: I 76 GLU cc_start: 0.8908 (mt-10) cc_final: 0.8569 (mp0) REVERT: I 85 ASP cc_start: 0.9290 (m-30) cc_final: 0.9032 (m-30) REVERT: I 86 MET cc_start: 0.9699 (tpt) cc_final: 0.9043 (tpt) REVERT: I 91 GLN cc_start: 0.9664 (tt0) cc_final: 0.9379 (tp-100) REVERT: I 115 LEU cc_start: 0.9289 (mt) cc_final: 0.8956 (tt) REVERT: I 142 GLN cc_start: 0.8699 (mt0) cc_final: 0.8295 (tt0) REVERT: I 157 VAL cc_start: 0.9733 (t) cc_final: 0.9494 (m) REVERT: I 160 SER cc_start: 0.9477 (m) cc_final: 0.9091 (p) REVERT: I 166 HIS cc_start: 0.8917 (p-80) cc_final: 0.8359 (p90) REVERT: I 172 GLU cc_start: 0.9074 (mm-30) cc_final: 0.8859 (mm-30) REVERT: I 189 ASP cc_start: 0.9200 (m-30) cc_final: 0.8385 (m-30) REVERT: I 288 MET cc_start: 0.9057 (mtp) cc_final: 0.8792 (tpp) REVERT: I 290 LEU cc_start: 0.9600 (mt) cc_final: 0.9339 (mt) REVERT: I 314 LEU cc_start: 0.9871 (tp) cc_final: 0.9665 (tp) REVERT: I 330 ILE cc_start: 0.9600 (mt) cc_final: 0.9362 (mp) REVERT: J 18 ILE cc_start: 0.9760 (pt) cc_final: 0.9248 (mm) REVERT: J 27 CYS cc_start: 0.8291 (m) cc_final: 0.7719 (m) REVERT: J 64 LEU cc_start: 0.9795 (tp) cc_final: 0.9548 (tp) REVERT: J 70 GLU cc_start: 0.9554 (mm-30) cc_final: 0.9026 (tp30) REVERT: J 114 GLU cc_start: 0.9459 (mt-10) cc_final: 0.8961 (mp0) REVERT: J 145 GLU cc_start: 0.9167 (pt0) cc_final: 0.8962 (mm-30) REVERT: J 178 GLN cc_start: 0.9742 (mm-40) cc_final: 0.9352 (mm-40) REVERT: J 326 LEU cc_start: 0.9682 (mt) cc_final: 0.9363 (mt) REVERT: J 327 VAL cc_start: 0.9683 (t) cc_final: 0.9374 (t) REVERT: J 341 PHE cc_start: 0.9062 (m-80) cc_final: 0.8637 (m-10) REVERT: J 368 LEU cc_start: 0.9716 (tp) cc_final: 0.9482 (mt) REVERT: M 50 VAL cc_start: 0.7766 (t) cc_final: 0.7561 (m) REVERT: M 64 VAL cc_start: 0.8065 (m) cc_final: 0.7248 (m) REVERT: M 69 LEU cc_start: 0.7791 (tt) cc_final: 0.6899 (tt) REVERT: V 103 GLN cc_start: 0.8979 (tp40) cc_final: 0.8657 (tm-30) REVERT: V 110 VAL cc_start: 0.9356 (t) cc_final: 0.9045 (t) REVERT: V 123 LYS cc_start: 0.9448 (mmtt) cc_final: 0.9216 (mmmm) REVERT: V 153 PHE cc_start: 0.9373 (t80) cc_final: 0.8549 (t80) REVERT: V 156 GLU cc_start: 0.7746 (mp0) cc_final: 0.7176 (mp0) REVERT: V 164 LEU cc_start: 0.9607 (tp) cc_final: 0.9377 (tt) REVERT: V 167 ASP cc_start: 0.9175 (t70) cc_final: 0.8906 (t0) REVERT: Y 36 LEU cc_start: 0.8600 (pt) cc_final: 0.8336 (tt) REVERT: Y 120 ASP cc_start: 0.8837 (m-30) cc_final: 0.8620 (m-30) REVERT: Y 230 ASP cc_start: 0.8892 (m-30) cc_final: 0.7349 (p0) REVERT: Y 252 LEU cc_start: 0.9588 (tt) cc_final: 0.9223 (tp) REVERT: Y 257 LEU cc_start: 0.9736 (mt) cc_final: 0.9329 (pp) REVERT: Y 261 PHE cc_start: 0.9139 (p90) cc_final: 0.8292 (p90) REVERT: Y 289 HIS cc_start: 0.6523 (t70) cc_final: 0.6279 (t-90) REVERT: Y 290 ASN cc_start: 0.8662 (t0) cc_final: 0.8176 (t0) REVERT: Y 297 ASN cc_start: 0.7917 (m110) cc_final: 0.7519 (m-40) outliers start: 0 outliers final: 0 residues processed: 614 average time/residue: 0.3139 time to fit residues: 286.6772 Evaluate side-chains 363 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 363 time to evaluate : 2.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 218 optimal weight: 3.9990 chunk 196 optimal weight: 7.9990 chunk 108 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 132 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 203 optimal weight: 30.0000 chunk 78 optimal weight: 6.9990 chunk 123 optimal weight: 6.9990 chunk 151 optimal weight: 5.9990 chunk 235 optimal weight: 7.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 297 ASN ** G 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 161 HIS I 16 ASN ** I 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 20 ASN ** V 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 162 GLN ** V 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 254 GLN Y 268 GLN ** Y 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 19834 Z= 0.249 Angle : 0.646 11.393 26994 Z= 0.326 Chirality : 0.042 0.212 3130 Planarity : 0.004 0.060 3494 Dihedral : 8.406 164.539 2898 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.26 % Favored : 95.65 % Rotamer: Outliers : 0.05 % Allowed : 2.86 % Favored : 97.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.16), residues: 2298 helix: 0.50 (0.19), residues: 700 sheet: -1.39 (0.26), residues: 331 loop : -1.78 (0.15), residues: 1267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP G 357 HIS 0.015 0.002 HIS V 109 PHE 0.025 0.002 PHE U 90 TYR 0.019 0.001 TYR U 144 ARG 0.011 0.001 ARG G 66 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 395 time to evaluate : 2.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 16 ASN cc_start: 0.9122 (p0) cc_final: 0.8367 (p0) REVERT: G 37 ASN cc_start: 0.9244 (t0) cc_final: 0.8870 (t0) REVERT: G 86 MET cc_start: 0.9623 (tpp) cc_final: 0.9353 (tpp) REVERT: G 97 ASP cc_start: 0.9438 (m-30) cc_final: 0.8824 (t0) REVERT: G 166 HIS cc_start: 0.7638 (p90) cc_final: 0.7071 (p-80) REVERT: G 215 LYS cc_start: 0.8815 (ptpt) cc_final: 0.8488 (ptpt) REVERT: G 227 ASN cc_start: 0.9034 (t0) cc_final: 0.8783 (t0) REVERT: G 268 ILE cc_start: 0.9463 (tp) cc_final: 0.8955 (tp) REVERT: G 290 LEU cc_start: 0.8131 (mp) cc_final: 0.7872 (mp) REVERT: G 314 LEU cc_start: 0.9331 (tp) cc_final: 0.9097 (tp) REVERT: G 346 ILE cc_start: 0.9527 (mt) cc_final: 0.9219 (tp) REVERT: H 8 LEU cc_start: 0.9576 (mt) cc_final: 0.9373 (mm) REVERT: H 16 MET cc_start: 0.9210 (mmm) cc_final: 0.8489 (mmm) REVERT: H 78 ASN cc_start: 0.8643 (t0) cc_final: 0.8142 (t0) REVERT: H 82 MET cc_start: 0.9693 (tpt) cc_final: 0.9328 (tpp) REVERT: H 83 GLU cc_start: 0.9548 (tt0) cc_final: 0.9217 (mt-10) REVERT: H 90 PHE cc_start: 0.9792 (m-80) cc_final: 0.9370 (m-10) REVERT: H 119 MET cc_start: 0.9644 (ttm) cc_final: 0.9392 (tmm) REVERT: H 120 THR cc_start: 0.9639 (p) cc_final: 0.9161 (t) REVERT: H 129 THR cc_start: 0.9238 (p) cc_final: 0.8586 (t) REVERT: H 132 MET cc_start: 0.9194 (tmm) cc_final: 0.8896 (ttp) REVERT: H 153 MET cc_start: 0.8434 (tmm) cc_final: 0.7841 (tmm) REVERT: H 154 ASP cc_start: 0.9608 (t0) cc_final: 0.9281 (t0) REVERT: H 190 MET cc_start: 0.9354 (mmm) cc_final: 0.9010 (mmm) REVERT: H 195 GLU cc_start: 0.9378 (mt-10) cc_final: 0.9119 (mt-10) REVERT: H 272 CYS cc_start: 0.8837 (p) cc_final: 0.8469 (p) REVERT: H 292 ASP cc_start: 0.9263 (m-30) cc_final: 0.9056 (m-30) REVERT: H 296 ASN cc_start: 0.9491 (m-40) cc_final: 0.9139 (t0) REVERT: H 313 MET cc_start: 0.9554 (mmp) cc_final: 0.9270 (mmm) REVERT: H 374 CYS cc_start: 0.7537 (p) cc_final: 0.7300 (p) REVERT: I 16 ASN cc_start: 0.9540 (m110) cc_final: 0.8878 (m-40) REVERT: I 86 MET cc_start: 0.9693 (tpt) cc_final: 0.9098 (tpt) REVERT: I 91 GLN cc_start: 0.9660 (tt0) cc_final: 0.9455 (tp-100) REVERT: I 157 VAL cc_start: 0.9720 (t) cc_final: 0.9507 (t) REVERT: I 160 SER cc_start: 0.9608 (m) cc_final: 0.9324 (p) REVERT: I 172 GLU cc_start: 0.9366 (mm-30) cc_final: 0.8995 (mm-30) REVERT: I 181 MET cc_start: 0.9281 (tpp) cc_final: 0.9008 (mmm) REVERT: I 189 ASP cc_start: 0.9292 (m-30) cc_final: 0.8716 (m-30) REVERT: I 300 LEU cc_start: 0.9714 (mt) cc_final: 0.9294 (mm) REVERT: J 18 ILE cc_start: 0.9777 (pt) cc_final: 0.9514 (tp) REVERT: J 64 LEU cc_start: 0.9831 (tp) cc_final: 0.9604 (tp) REVERT: J 70 GLU cc_start: 0.9659 (mm-30) cc_final: 0.9330 (mm-30) REVERT: J 114 GLU cc_start: 0.9559 (mt-10) cc_final: 0.9230 (mp0) REVERT: J 145 GLU cc_start: 0.9334 (pt0) cc_final: 0.8900 (mm-30) REVERT: J 178 GLN cc_start: 0.9715 (mm-40) cc_final: 0.9320 (mm-40) REVERT: J 204 GLU cc_start: 0.8518 (tp30) cc_final: 0.8220 (tp30) REVERT: J 311 MET cc_start: 0.9355 (mmt) cc_final: 0.8714 (mmt) REVERT: J 322 GLU cc_start: 0.9359 (tt0) cc_final: 0.8787 (mt-10) REVERT: J 387 TRP cc_start: 0.9065 (p-90) cc_final: 0.8771 (p-90) REVERT: U 38 LYS cc_start: 0.8565 (ttpp) cc_final: 0.8264 (tmmt) REVERT: U 52 GLU cc_start: 0.9178 (pm20) cc_final: 0.8705 (pm20) REVERT: U 90 PHE cc_start: 0.8637 (m-80) cc_final: 0.8315 (m-80) REVERT: U 125 ILE cc_start: 0.8596 (tp) cc_final: 0.8188 (tp) REVERT: U 139 GLU cc_start: 0.8189 (tp30) cc_final: 0.7636 (tp30) REVERT: U 144 TYR cc_start: 0.8556 (p90) cc_final: 0.8267 (p90) REVERT: V 123 LYS cc_start: 0.9464 (mmtt) cc_final: 0.9024 (mmtm) REVERT: V 138 THR cc_start: 0.9407 (t) cc_final: 0.8936 (m) REVERT: V 167 ASP cc_start: 0.9370 (t70) cc_final: 0.9145 (t0) REVERT: Y 163 ASP cc_start: 0.9155 (m-30) cc_final: 0.8913 (m-30) REVERT: Y 230 ASP cc_start: 0.8810 (m-30) cc_final: 0.8062 (p0) REVERT: Y 261 PHE cc_start: 0.9301 (p90) cc_final: 0.9059 (p90) REVERT: Y 276 LEU cc_start: 0.9556 (mt) cc_final: 0.9262 (mt) REVERT: Y 289 HIS cc_start: 0.6973 (t70) cc_final: 0.6608 (t70) REVERT: Y 290 ASN cc_start: 0.8787 (t0) cc_final: 0.8075 (t0) REVERT: Y 305 ILE cc_start: 0.8140 (tp) cc_final: 0.7790 (tp) REVERT: Y 334 LEU cc_start: 0.9049 (mm) cc_final: 0.8818 (tp) outliers start: 1 outliers final: 0 residues processed: 396 average time/residue: 0.2963 time to fit residues: 180.1755 Evaluate side-chains 285 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 285 time to evaluate : 2.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 130 optimal weight: 5.9990 chunk 72 optimal weight: 8.9990 chunk 195 optimal weight: 10.0000 chunk 160 optimal weight: 40.0000 chunk 64 optimal weight: 5.9990 chunk 235 optimal weight: 0.0970 chunk 254 optimal weight: 40.0000 chunk 209 optimal weight: 9.9990 chunk 233 optimal weight: 6.9990 chunk 80 optimal weight: 9.9990 chunk 189 optimal weight: 2.9990 overall best weight: 4.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 100 GLN ** H 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 371 HIS I 10 GLN ** I 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 56 GLN ** J 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 344 HIS J 379 ASN ** J 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 54 ASN ** U 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 60 HIS ** V 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.4476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 19834 Z= 0.378 Angle : 0.730 10.158 26994 Z= 0.364 Chirality : 0.042 0.152 3130 Planarity : 0.005 0.062 3494 Dihedral : 8.327 179.707 2898 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 16.90 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.18 % Favored : 94.73 % Rotamer: Outliers : 0.16 % Allowed : 4.48 % Favored : 95.36 % 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: -1.02 (0.17), residues: 2298 helix: 0.52 (0.19), residues: 711 sheet: -1.39 (0.25), residues: 346 loop : -1.15 (0.17), residues: 1241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP H 356 HIS 0.010 0.002 HIS G 77 PHE 0.029 0.002 PHE G 205 TYR 0.017 0.002 TYR G 33 ARG 0.009 0.001 ARG I 336 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 334 time to evaluate : 2.269 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: G 15 ASP cc_start: 0.8438 (t70) cc_final: 0.8065 (t0) REVERT: G 16 ASN cc_start: 0.9165 (p0) cc_final: 0.8641 (p0) REVERT: G 37 ASN cc_start: 0.9356 (t0) cc_final: 0.9003 (t0) REVERT: G 86 MET cc_start: 0.9650 (tpp) cc_final: 0.9361 (tpp) REVERT: G 215 LYS cc_start: 0.8830 (ptpt) cc_final: 0.8538 (ptpt) REVERT: G 290 LEU cc_start: 0.8238 (mp) cc_final: 0.8020 (mp) REVERT: G 346 ILE cc_start: 0.9616 (mt) cc_final: 0.9391 (tp) REVERT: H 16 MET cc_start: 0.9247 (mmm) cc_final: 0.8751 (mmm) REVERT: H 78 ASN cc_start: 0.8795 (t0) cc_final: 0.8549 (t0) REVERT: H 82 MET cc_start: 0.9696 (tpt) cc_final: 0.9243 (tpt) REVERT: H 83 GLU cc_start: 0.9595 (tt0) cc_final: 0.9205 (mt-10) REVERT: H 90 PHE cc_start: 0.9785 (m-80) cc_final: 0.9460 (m-10) REVERT: H 119 MET cc_start: 0.9759 (ttm) cc_final: 0.9401 (tmm) REVERT: H 120 THR cc_start: 0.9604 (p) cc_final: 0.9216 (p) REVERT: H 123 MET cc_start: 0.9696 (tpp) cc_final: 0.9397 (tpp) REVERT: H 129 THR cc_start: 0.9481 (p) cc_final: 0.9194 (t) REVERT: H 132 MET cc_start: 0.9322 (tmm) cc_final: 0.8952 (ttm) REVERT: H 154 ASP cc_start: 0.9523 (t0) cc_final: 0.9142 (t0) REVERT: H 184 ASP cc_start: 0.9319 (m-30) cc_final: 0.9059 (m-30) REVERT: H 190 MET cc_start: 0.9350 (mmm) cc_final: 0.9039 (mmm) REVERT: H 192 ILE cc_start: 0.9553 (pt) cc_final: 0.9018 (mm) REVERT: H 195 GLU cc_start: 0.9376 (mt-10) cc_final: 0.9100 (mt-10) REVERT: H 272 CYS cc_start: 0.8808 (p) cc_final: 0.8485 (p) REVERT: H 292 ASP cc_start: 0.9444 (m-30) cc_final: 0.8875 (p0) REVERT: H 305 MET cc_start: 0.9261 (mmt) cc_final: 0.8807 (mmm) REVERT: H 355 MET cc_start: 0.9730 (mmp) cc_final: 0.9438 (mmm) REVERT: H 374 CYS cc_start: 0.7678 (p) cc_final: 0.7436 (p) REVERT: I 37 ASN cc_start: 0.9101 (t0) cc_final: 0.8884 (t0) REVERT: I 86 MET cc_start: 0.9528 (tpt) cc_final: 0.9233 (tpt) REVERT: I 91 GLN cc_start: 0.9723 (tt0) cc_final: 0.9490 (tp-100) REVERT: I 160 SER cc_start: 0.9651 (m) cc_final: 0.9329 (p) REVERT: I 181 MET cc_start: 0.9335 (tpp) cc_final: 0.9082 (mmm) REVERT: I 189 ASP cc_start: 0.9499 (m-30) cc_final: 0.8939 (m-30) REVERT: I 270 GLU cc_start: 0.9157 (tp30) cc_final: 0.8738 (tm-30) REVERT: I 290 LEU cc_start: 0.9678 (mp) cc_final: 0.9425 (mt) REVERT: I 300 LEU cc_start: 0.9826 (mt) cc_final: 0.9575 (mm) REVERT: J 64 LEU cc_start: 0.9850 (tp) cc_final: 0.9640 (tp) REVERT: J 70 GLU cc_start: 0.9716 (mm-30) cc_final: 0.9363 (mp0) REVERT: J 145 GLU cc_start: 0.9466 (pt0) cc_final: 0.8887 (tt0) REVERT: J 178 GLN cc_start: 0.9658 (mm-40) cc_final: 0.9258 (mm-40) REVERT: J 204 GLU cc_start: 0.8642 (tp30) cc_final: 0.8386 (tp30) REVERT: J 311 MET cc_start: 0.9198 (mmt) cc_final: 0.8461 (mmt) REVERT: J 322 GLU cc_start: 0.9354 (tt0) cc_final: 0.8863 (mt-10) REVERT: J 387 TRP cc_start: 0.9376 (p-90) cc_final: 0.8983 (p-90) REVERT: U 38 LYS cc_start: 0.8838 (ttpp) cc_final: 0.8207 (tmmt) REVERT: U 52 GLU cc_start: 0.9130 (pm20) cc_final: 0.8827 (pm20) REVERT: U 110 LYS cc_start: 0.9467 (tttt) cc_final: 0.9247 (ttmt) REVERT: U 144 TYR cc_start: 0.8869 (p90) cc_final: 0.7441 (p90) REVERT: U 151 ARG cc_start: 0.8787 (ttm170) cc_final: 0.7750 (tpp80) REVERT: V 64 LYS cc_start: 0.9333 (mtmt) cc_final: 0.9120 (mtpt) REVERT: V 123 LYS cc_start: 0.9601 (mmtt) cc_final: 0.9096 (mmtm) REVERT: V 143 PHE cc_start: 0.9526 (m-10) cc_final: 0.9048 (m-80) REVERT: V 165 MET cc_start: 0.9228 (mmp) cc_final: 0.8936 (mmm) REVERT: Y 163 ASP cc_start: 0.9129 (m-30) cc_final: 0.8886 (m-30) REVERT: Y 230 ASP cc_start: 0.9092 (m-30) cc_final: 0.8282 (p0) REVERT: Y 260 ASP cc_start: 0.9120 (p0) cc_final: 0.8566 (p0) REVERT: Y 261 PHE cc_start: 0.9393 (p90) cc_final: 0.8840 (p90) outliers start: 3 outliers final: 3 residues processed: 337 average time/residue: 0.3138 time to fit residues: 164.8826 Evaluate side-chains 240 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 237 time to evaluate : 2.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 232 optimal weight: 2.9990 chunk 177 optimal weight: 9.9990 chunk 122 optimal weight: 6.9990 chunk 26 optimal weight: 4.9990 chunk 112 optimal weight: 8.9990 chunk 158 optimal weight: 20.0000 chunk 236 optimal weight: 20.0000 chunk 250 optimal weight: 20.0000 chunk 123 optimal weight: 0.8980 chunk 224 optimal weight: 10.0000 chunk 67 optimal weight: 9.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 101 HIS H 263 GLN ** I 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 275 ASN ** J 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 162 GLN ** V 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.5330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 19834 Z= 0.401 Angle : 0.732 12.891 26994 Z= 0.367 Chirality : 0.043 0.226 3130 Planarity : 0.005 0.067 3494 Dihedral : 8.156 173.363 2898 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 20.23 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.61 % Favored : 94.30 % Rotamer: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % 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: -0.94 (0.17), residues: 2298 helix: 0.35 (0.19), residues: 711 sheet: -1.48 (0.26), residues: 326 loop : -0.92 (0.17), residues: 1261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.003 TRP G 357 HIS 0.011 0.002 HIS G 77 PHE 0.025 0.002 PHE G 353 TYR 0.019 0.002 TYR V 107 ARG 0.021 0.001 ARG U 150 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 282 time to evaluate : 2.359 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: G 16 ASN cc_start: 0.9078 (p0) cc_final: 0.8415 (p0) REVERT: G 64 GLU cc_start: 0.9133 (mt-10) cc_final: 0.8874 (mt-10) REVERT: G 86 MET cc_start: 0.9487 (tpp) cc_final: 0.9264 (tpt) REVERT: G 215 LYS cc_start: 0.8825 (ptpt) cc_final: 0.8556 (ptpt) REVERT: H 16 MET cc_start: 0.9352 (mmm) cc_final: 0.8842 (mmm) REVERT: H 78 ASN cc_start: 0.8721 (t0) cc_final: 0.8418 (t0) REVERT: H 82 MET cc_start: 0.9738 (tpt) cc_final: 0.9292 (tpt) REVERT: H 83 GLU cc_start: 0.9564 (tt0) cc_final: 0.9294 (tm-30) REVERT: H 90 PHE cc_start: 0.9790 (m-80) cc_final: 0.9538 (m-10) REVERT: H 106 THR cc_start: 0.8898 (p) cc_final: 0.8554 (p) REVERT: H 119 MET cc_start: 0.9783 (ttm) cc_final: 0.9506 (tmm) REVERT: H 129 THR cc_start: 0.9562 (p) cc_final: 0.9277 (t) REVERT: H 132 MET cc_start: 0.9428 (tmm) cc_final: 0.8993 (ttm) REVERT: H 154 ASP cc_start: 0.9521 (t0) cc_final: 0.9271 (t0) REVERT: H 184 ASP cc_start: 0.9367 (m-30) cc_final: 0.9134 (m-30) REVERT: H 190 MET cc_start: 0.9417 (mmm) cc_final: 0.9048 (mmm) REVERT: H 192 ILE cc_start: 0.9521 (pt) cc_final: 0.9219 (mm) REVERT: H 217 CYS cc_start: 0.9426 (m) cc_final: 0.9191 (m) REVERT: H 267 LEU cc_start: 0.9583 (tt) cc_final: 0.9265 (tt) REVERT: H 269 MET cc_start: 0.9427 (mmm) cc_final: 0.8924 (mmm) REVERT: H 292 ASP cc_start: 0.9508 (m-30) cc_final: 0.9264 (p0) REVERT: H 305 MET cc_start: 0.9083 (mmt) cc_final: 0.8593 (mmm) REVERT: H 313 MET cc_start: 0.9659 (mmp) cc_final: 0.9451 (mmm) REVERT: H 355 MET cc_start: 0.9774 (mmp) cc_final: 0.9457 (mmm) REVERT: H 374 CYS cc_start: 0.7545 (p) cc_final: 0.7092 (t) REVERT: I 86 MET cc_start: 0.9693 (tpt) cc_final: 0.9377 (tpt) REVERT: I 91 GLN cc_start: 0.9737 (tt0) cc_final: 0.9467 (tp-100) REVERT: I 181 MET cc_start: 0.9369 (tpp) cc_final: 0.9161 (mmm) REVERT: I 189 ASP cc_start: 0.9464 (m-30) cc_final: 0.9065 (m-30) REVERT: I 270 GLU cc_start: 0.9342 (tp30) cc_final: 0.8849 (tm-30) REVERT: I 300 LEU cc_start: 0.9856 (mt) cc_final: 0.9567 (mm) REVERT: J 17 VAL cc_start: 0.9592 (t) cc_final: 0.9366 (m) REVERT: J 19 ASP cc_start: 0.9255 (t70) cc_final: 0.8871 (m-30) REVERT: J 64 LEU cc_start: 0.9857 (tp) cc_final: 0.9650 (tp) REVERT: J 70 GLU cc_start: 0.9737 (mm-30) cc_final: 0.9340 (tm-30) REVERT: J 114 GLU cc_start: 0.9631 (mt-10) cc_final: 0.9375 (mp0) REVERT: J 174 GLU cc_start: 0.9540 (tp30) cc_final: 0.8770 (tm-30) REVERT: J 178 GLN cc_start: 0.9670 (mm-40) cc_final: 0.9343 (mm-40) REVERT: J 204 GLU cc_start: 0.8554 (tp30) cc_final: 0.8338 (tp30) REVERT: J 311 MET cc_start: 0.9411 (mmt) cc_final: 0.8864 (mmt) REVERT: J 322 GLU cc_start: 0.9398 (tt0) cc_final: 0.9058 (mt-10) REVERT: J 387 TRP cc_start: 0.9560 (p-90) cc_final: 0.9198 (p-90) REVERT: U 52 GLU cc_start: 0.9253 (pm20) cc_final: 0.8929 (pm20) REVERT: U 151 ARG cc_start: 0.8604 (ttm170) cc_final: 0.7399 (tpp80) REVERT: V 64 LYS cc_start: 0.9308 (mtmt) cc_final: 0.9090 (mtpt) REVERT: V 122 LEU cc_start: 0.9627 (mp) cc_final: 0.9349 (mt) REVERT: V 123 LYS cc_start: 0.9630 (mmtt) cc_final: 0.9073 (mmtm) REVERT: V 143 PHE cc_start: 0.9551 (m-10) cc_final: 0.9134 (m-80) REVERT: Y 163 ASP cc_start: 0.9142 (m-30) cc_final: 0.8878 (m-30) REVERT: Y 230 ASP cc_start: 0.9239 (m-30) cc_final: 0.8195 (p0) REVERT: Y 260 ASP cc_start: 0.9141 (p0) cc_final: 0.8727 (p0) REVERT: Y 261 PHE cc_start: 0.9384 (p90) cc_final: 0.8869 (p90) REVERT: Y 290 ASN cc_start: 0.8931 (t0) cc_final: 0.8686 (t0) outliers start: 0 outliers final: 0 residues processed: 282 average time/residue: 0.3089 time to fit residues: 133.8759 Evaluate side-chains 206 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 206 time to evaluate : 2.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 208 optimal weight: 20.0000 chunk 142 optimal weight: 3.9990 chunk 3 optimal weight: 0.2980 chunk 186 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 213 optimal weight: 7.9990 chunk 173 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 127 optimal weight: 0.9990 chunk 224 optimal weight: 40.0000 chunk 63 optimal weight: 7.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 120 ASN ** G 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 193 GLN J 380 GLN U 97 GLN ** U 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 60 HIS ** V 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 268 GLN ** Y 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.5356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 19834 Z= 0.198 Angle : 0.589 10.338 26994 Z= 0.289 Chirality : 0.042 0.193 3130 Planarity : 0.004 0.044 3494 Dihedral : 7.644 167.052 2898 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.18 % Favored : 94.73 % Rotamer: Outliers : 0.16 % Allowed : 2.54 % Favored : 97.30 % 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: -0.49 (0.17), residues: 2298 helix: 0.72 (0.19), residues: 726 sheet: -1.13 (0.27), residues: 321 loop : -0.68 (0.17), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP G 357 HIS 0.010 0.001 HIS G 77 PHE 0.025 0.001 PHE I 193 TYR 0.016 0.001 TYR V 8 ARG 0.004 0.000 ARG U 151 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 281 time to evaluate : 2.421 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 15 ASP cc_start: 0.8518 (t0) cc_final: 0.8083 (t0) REVERT: G 16 ASN cc_start: 0.8707 (p0) cc_final: 0.8396 (p0) REVERT: G 75 MET cc_start: 0.7779 (tmm) cc_final: 0.7233 (tmm) REVERT: G 86 MET cc_start: 0.9591 (tpp) cc_final: 0.9155 (tpt) REVERT: G 215 LYS cc_start: 0.8830 (ptpt) cc_final: 0.8607 (ptpt) REVERT: H 16 MET cc_start: 0.9403 (mmm) cc_final: 0.8862 (mmm) REVERT: H 78 ASN cc_start: 0.8954 (t0) cc_final: 0.8700 (t0) REVERT: H 82 MET cc_start: 0.9687 (tpt) cc_final: 0.9162 (tpt) REVERT: H 90 PHE cc_start: 0.9793 (m-80) cc_final: 0.9530 (m-10) REVERT: H 119 MET cc_start: 0.9727 (ttm) cc_final: 0.9481 (tmm) REVERT: H 154 ASP cc_start: 0.9475 (t0) cc_final: 0.9100 (t0) REVERT: H 184 ASP cc_start: 0.9308 (m-30) cc_final: 0.9056 (m-30) REVERT: H 190 MET cc_start: 0.9389 (mmm) cc_final: 0.9020 (mmm) REVERT: H 217 CYS cc_start: 0.9425 (m) cc_final: 0.9128 (m) REVERT: H 292 ASP cc_start: 0.9478 (m-30) cc_final: 0.9240 (p0) REVERT: H 305 MET cc_start: 0.9101 (mmt) cc_final: 0.8677 (mmm) REVERT: H 311 ASP cc_start: 0.9653 (m-30) cc_final: 0.9142 (p0) REVERT: H 313 MET cc_start: 0.9688 (mmp) cc_final: 0.9373 (mmm) REVERT: H 355 MET cc_start: 0.9762 (mmp) cc_final: 0.9448 (mmm) REVERT: H 359 LYS cc_start: 0.9452 (mtpt) cc_final: 0.9188 (mttp) REVERT: H 374 CYS cc_start: 0.7622 (p) cc_final: 0.7125 (t) REVERT: I 66 ARG cc_start: 0.7908 (ptm-80) cc_final: 0.7443 (ptm-80) REVERT: I 86 MET cc_start: 0.9640 (tpt) cc_final: 0.9413 (tpt) REVERT: I 91 GLN cc_start: 0.9708 (tt0) cc_final: 0.9360 (tp-100) REVERT: I 181 MET cc_start: 0.9330 (tpp) cc_final: 0.9096 (mmm) REVERT: I 189 ASP cc_start: 0.9469 (m-30) cc_final: 0.9027 (m-30) REVERT: I 270 GLU cc_start: 0.9307 (tp30) cc_final: 0.8777 (tm-30) REVERT: I 300 LEU cc_start: 0.9851 (mt) cc_final: 0.9554 (mm) REVERT: I 351 ASP cc_start: 0.8755 (p0) cc_final: 0.8510 (t0) REVERT: J 19 ASP cc_start: 0.9192 (t70) cc_final: 0.8954 (t70) REVERT: J 64 LEU cc_start: 0.9820 (tp) cc_final: 0.9605 (tp) REVERT: J 70 GLU cc_start: 0.9707 (mm-30) cc_final: 0.9278 (mm-30) REVERT: J 114 GLU cc_start: 0.9618 (mt-10) cc_final: 0.9256 (mm-30) REVERT: J 178 GLN cc_start: 0.9639 (mm-40) cc_final: 0.9270 (mm110) REVERT: J 193 GLN cc_start: 0.8876 (OUTLIER) cc_final: 0.8673 (pp30) REVERT: J 204 GLU cc_start: 0.8547 (tp30) cc_final: 0.8315 (tp30) REVERT: J 208 GLU cc_start: 0.9126 (pp20) cc_final: 0.8782 (pp20) REVERT: J 311 MET cc_start: 0.9473 (mmt) cc_final: 0.8834 (mmm) REVERT: J 322 GLU cc_start: 0.9329 (tt0) cc_final: 0.8941 (mt-10) REVERT: J 387 TRP cc_start: 0.9431 (p-90) cc_final: 0.9113 (p-90) REVERT: U 38 LYS cc_start: 0.8720 (ttpp) cc_final: 0.8475 (tmmt) REVERT: U 52 GLU cc_start: 0.9178 (pm20) cc_final: 0.8864 (pm20) REVERT: U 92 VAL cc_start: 0.9406 (t) cc_final: 0.9160 (t) REVERT: U 99 MET cc_start: 0.8795 (tpt) cc_final: 0.7310 (tpp) REVERT: U 144 TYR cc_start: 0.8043 (p90) cc_final: 0.7501 (p90) REVERT: U 151 ARG cc_start: 0.8398 (ttm170) cc_final: 0.7353 (tpp80) REVERT: V 64 LYS cc_start: 0.9308 (mtmt) cc_final: 0.9064 (mtpt) REVERT: V 100 ASN cc_start: 0.8693 (t0) cc_final: 0.8479 (t0) REVERT: V 123 LYS cc_start: 0.9654 (mmtt) cc_final: 0.9085 (mmtm) REVERT: V 143 PHE cc_start: 0.9483 (m-10) cc_final: 0.9233 (m-80) REVERT: V 160 CYS cc_start: 0.8901 (t) cc_final: 0.7660 (p) REVERT: V 172 TYR cc_start: 0.9522 (t80) cc_final: 0.9290 (t80) REVERT: Y 163 ASP cc_start: 0.9098 (m-30) cc_final: 0.8856 (m-30) REVERT: Y 230 ASP cc_start: 0.8803 (m-30) cc_final: 0.8119 (p0) REVERT: Y 260 ASP cc_start: 0.9108 (p0) cc_final: 0.8649 (p0) REVERT: Y 261 PHE cc_start: 0.9360 (p90) cc_final: 0.8780 (p90) REVERT: Y 276 LEU cc_start: 0.9620 (mt) cc_final: 0.9384 (mt) outliers start: 3 outliers final: 0 residues processed: 284 average time/residue: 0.3065 time to fit residues: 135.0183 Evaluate side-chains 219 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 218 time to evaluate : 2.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 84 optimal weight: 6.9990 chunk 225 optimal weight: 9.9990 chunk 49 optimal weight: 3.9990 chunk 146 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 250 optimal weight: 20.0000 chunk 208 optimal weight: 20.0000 chunk 116 optimal weight: 1.9990 chunk 20 optimal weight: 7.9990 chunk 82 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 12 ASN ** H 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 280 ASN H 354 GLN ** I 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 351 ASN ** V 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 49 HIS ** Y 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.5784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 19834 Z= 0.290 Angle : 0.638 11.741 26994 Z= 0.313 Chirality : 0.041 0.213 3130 Planarity : 0.005 0.090 3494 Dihedral : 7.611 163.456 2898 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 18.30 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.53 % Favored : 94.39 % Rotamer: Outliers : 0.05 % Allowed : 1.89 % Favored : 98.06 % 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: -0.47 (0.17), residues: 2298 helix: 0.76 (0.20), residues: 716 sheet: -1.27 (0.26), residues: 338 loop : -0.60 (0.18), residues: 1244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.003 TRP G 357 HIS 0.017 0.002 HIS G 77 PHE 0.020 0.002 PHE U 90 TYR 0.016 0.001 TYR G 33 ARG 0.009 0.000 ARG U 150 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 264 time to evaluate : 2.413 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: G 16 ASN cc_start: 0.8939 (p0) cc_final: 0.8492 (p0) REVERT: G 75 MET cc_start: 0.7553 (tmm) cc_final: 0.6941 (tmm) REVERT: G 86 MET cc_start: 0.9473 (tpp) cc_final: 0.9172 (tpt) REVERT: G 215 LYS cc_start: 0.8909 (ptpt) cc_final: 0.8633 (ptpt) REVERT: H 16 MET cc_start: 0.9408 (mmm) cc_final: 0.8929 (mmm) REVERT: H 82 MET cc_start: 0.9697 (tpt) cc_final: 0.9231 (tpt) REVERT: H 106 THR cc_start: 0.8975 (p) cc_final: 0.8672 (p) REVERT: H 119 MET cc_start: 0.9744 (ttm) cc_final: 0.9536 (tmm) REVERT: H 154 ASP cc_start: 0.9603 (t0) cc_final: 0.9130 (t0) REVERT: H 190 MET cc_start: 0.9406 (mmm) cc_final: 0.8965 (mmm) REVERT: H 217 CYS cc_start: 0.9426 (m) cc_final: 0.9139 (m) REVERT: H 292 ASP cc_start: 0.9490 (m-30) cc_final: 0.9232 (p0) REVERT: H 305 MET cc_start: 0.9053 (mmt) cc_final: 0.8630 (mmm) REVERT: H 311 ASP cc_start: 0.9667 (m-30) cc_final: 0.9161 (p0) REVERT: H 313 MET cc_start: 0.9727 (mmp) cc_final: 0.9509 (mmm) REVERT: H 355 MET cc_start: 0.9794 (mmp) cc_final: 0.9504 (mmm) REVERT: H 374 CYS cc_start: 0.7718 (p) cc_final: 0.7175 (t) REVERT: I 66 ARG cc_start: 0.7858 (ptm-80) cc_final: 0.7421 (ptm-80) REVERT: I 86 MET cc_start: 0.9669 (tpt) cc_final: 0.9423 (tpt) REVERT: I 91 GLN cc_start: 0.9702 (tt0) cc_final: 0.9372 (tp-100) REVERT: I 110 LEU cc_start: 0.9491 (tp) cc_final: 0.9274 (tp) REVERT: I 181 MET cc_start: 0.9283 (tpp) cc_final: 0.9072 (mmm) REVERT: I 189 ASP cc_start: 0.9406 (m-30) cc_final: 0.9043 (m-30) REVERT: I 300 LEU cc_start: 0.9872 (mt) cc_final: 0.9666 (mm) REVERT: J 19 ASP cc_start: 0.9238 (t70) cc_final: 0.8940 (t70) REVERT: J 64 LEU cc_start: 0.9839 (tp) cc_final: 0.9613 (tp) REVERT: J 70 GLU cc_start: 0.9745 (mm-30) cc_final: 0.9269 (mm-30) REVERT: J 178 GLN cc_start: 0.9657 (mm-40) cc_final: 0.9298 (mm110) REVERT: J 204 GLU cc_start: 0.8553 (tp30) cc_final: 0.8341 (tp30) REVERT: J 311 MET cc_start: 0.9464 (mmt) cc_final: 0.8909 (mmt) REVERT: J 322 GLU cc_start: 0.9364 (tt0) cc_final: 0.8981 (mt-10) REVERT: J 387 TRP cc_start: 0.9491 (p-90) cc_final: 0.9124 (p-90) REVERT: U 38 LYS cc_start: 0.8833 (ttpp) cc_final: 0.8187 (tmmt) REVERT: U 52 GLU cc_start: 0.9232 (pm20) cc_final: 0.8866 (pm20) REVERT: U 82 MET cc_start: 0.8310 (mmp) cc_final: 0.7539 (mmp) REVERT: U 92 VAL cc_start: 0.9502 (t) cc_final: 0.9252 (t) REVERT: U 151 ARG cc_start: 0.8484 (ttm170) cc_final: 0.7467 (tpp80) REVERT: V 64 LYS cc_start: 0.9324 (mtmt) cc_final: 0.9066 (mtpt) REVERT: V 123 LYS cc_start: 0.9615 (mmtt) cc_final: 0.9094 (mmtm) REVERT: V 143 PHE cc_start: 0.9471 (m-10) cc_final: 0.9226 (m-80) REVERT: V 160 CYS cc_start: 0.8907 (t) cc_final: 0.7715 (p) REVERT: Y 163 ASP cc_start: 0.9090 (m-30) cc_final: 0.8832 (m-30) REVERT: Y 230 ASP cc_start: 0.8850 (m-30) cc_final: 0.8197 (p0) REVERT: Y 260 ASP cc_start: 0.9123 (p0) cc_final: 0.8651 (p0) REVERT: Y 261 PHE cc_start: 0.9385 (p90) cc_final: 0.8815 (p90) REVERT: Y 290 ASN cc_start: 0.8869 (t0) cc_final: 0.8667 (t0) outliers start: 1 outliers final: 0 residues processed: 265 average time/residue: 0.2967 time to fit residues: 121.0068 Evaluate side-chains 185 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 185 time to evaluate : 2.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 241 optimal weight: 20.0000 chunk 28 optimal weight: 3.9990 chunk 142 optimal weight: 0.7980 chunk 182 optimal weight: 8.9990 chunk 141 optimal weight: 4.9990 chunk 210 optimal weight: 7.9990 chunk 139 optimal weight: 4.9990 chunk 249 optimal weight: 5.9990 chunk 156 optimal weight: 30.0000 chunk 152 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 16 ASN ** I 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 49 HIS ** Y 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.5976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 19834 Z= 0.256 Angle : 0.621 11.197 26994 Z= 0.305 Chirality : 0.041 0.191 3130 Planarity : 0.004 0.058 3494 Dihedral : 7.411 152.990 2898 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 17.41 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.83 % Favored : 94.08 % Rotamer: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % 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: -0.38 (0.17), residues: 2298 helix: 0.72 (0.20), residues: 725 sheet: -1.14 (0.27), residues: 319 loop : -0.52 (0.18), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.003 TRP G 357 HIS 0.016 0.002 HIS G 77 PHE 0.019 0.002 PHE U 90 TYR 0.018 0.001 TYR G 197 ARG 0.006 0.000 ARG I 264 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 264 time to evaluate : 2.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 16 ASN cc_start: 0.8752 (p0) cc_final: 0.8354 (p0) REVERT: G 75 MET cc_start: 0.7674 (tmm) cc_final: 0.6950 (tmm) REVERT: G 86 MET cc_start: 0.9546 (tpp) cc_final: 0.9196 (tpt) REVERT: G 97 ASP cc_start: 0.9561 (m-30) cc_final: 0.9286 (t0) REVERT: G 215 LYS cc_start: 0.8904 (ptpt) cc_final: 0.8610 (ptpt) REVERT: H 16 MET cc_start: 0.9434 (mmm) cc_final: 0.8958 (mmm) REVERT: H 78 ASN cc_start: 0.9029 (t0) cc_final: 0.8822 (t0) REVERT: H 82 MET cc_start: 0.9671 (tpt) cc_final: 0.9180 (tpt) REVERT: H 106 THR cc_start: 0.9036 (p) cc_final: 0.8697 (p) REVERT: H 119 MET cc_start: 0.9752 (ttm) cc_final: 0.9457 (tmm) REVERT: H 154 ASP cc_start: 0.9536 (t0) cc_final: 0.9096 (t0) REVERT: H 184 ASP cc_start: 0.9339 (m-30) cc_final: 0.9127 (m-30) REVERT: H 187 ASP cc_start: 0.9732 (t0) cc_final: 0.9505 (m-30) REVERT: H 190 MET cc_start: 0.9377 (mmm) cc_final: 0.8968 (mmm) REVERT: H 217 CYS cc_start: 0.9390 (m) cc_final: 0.9159 (m) REVERT: H 269 MET cc_start: 0.9394 (mmm) cc_final: 0.8885 (mmm) REVERT: H 292 ASP cc_start: 0.9509 (m-30) cc_final: 0.9163 (p0) REVERT: H 305 MET cc_start: 0.9107 (mmt) cc_final: 0.8686 (mmm) REVERT: H 311 ASP cc_start: 0.9660 (m-30) cc_final: 0.9146 (p0) REVERT: H 355 MET cc_start: 0.9802 (mmp) cc_final: 0.9497 (mmm) REVERT: H 374 CYS cc_start: 0.7678 (p) cc_final: 0.7191 (t) REVERT: I 66 ARG cc_start: 0.7926 (ptm-80) cc_final: 0.7523 (ptm-80) REVERT: I 86 MET cc_start: 0.9664 (tpt) cc_final: 0.9357 (tpt) REVERT: I 91 GLN cc_start: 0.9683 (tt0) cc_final: 0.9349 (tp-100) REVERT: I 110 LEU cc_start: 0.9513 (tp) cc_final: 0.9302 (tp) REVERT: I 181 MET cc_start: 0.9300 (tpp) cc_final: 0.9098 (mmm) REVERT: I 189 ASP cc_start: 0.9396 (m-30) cc_final: 0.8995 (m-30) REVERT: I 300 LEU cc_start: 0.9867 (mt) cc_final: 0.9665 (mm) REVERT: J 19 ASP cc_start: 0.9203 (t70) cc_final: 0.8800 (t70) REVERT: J 64 LEU cc_start: 0.9826 (tp) cc_final: 0.9604 (tp) REVERT: J 70 GLU cc_start: 0.9717 (mm-30) cc_final: 0.9365 (tm-30) REVERT: J 178 GLN cc_start: 0.9653 (mm-40) cc_final: 0.9291 (mm110) REVERT: J 204 GLU cc_start: 0.8504 (tp30) cc_final: 0.8287 (tp30) REVERT: J 311 MET cc_start: 0.9578 (mmt) cc_final: 0.8923 (mmt) REVERT: J 322 GLU cc_start: 0.9355 (tt0) cc_final: 0.8994 (mt-10) REVERT: J 387 TRP cc_start: 0.9474 (p-90) cc_final: 0.9169 (p-90) REVERT: U 38 LYS cc_start: 0.8796 (ttpp) cc_final: 0.8584 (ttpp) REVERT: U 52 GLU cc_start: 0.9257 (pm20) cc_final: 0.8944 (pm20) REVERT: U 82 MET cc_start: 0.8596 (mmp) cc_final: 0.8352 (mmp) REVERT: U 144 TYR cc_start: 0.8430 (p90) cc_final: 0.7477 (p90) REVERT: U 151 ARG cc_start: 0.8492 (ttm170) cc_final: 0.8266 (ttm170) REVERT: V 64 LYS cc_start: 0.9252 (mtmt) cc_final: 0.9018 (mtpt) REVERT: V 100 ASN cc_start: 0.8707 (t0) cc_final: 0.8479 (t0) REVERT: V 123 LYS cc_start: 0.9580 (mmtt) cc_final: 0.9062 (mmtm) REVERT: V 143 PHE cc_start: 0.9483 (m-10) cc_final: 0.9237 (m-80) REVERT: Y 163 ASP cc_start: 0.9040 (m-30) cc_final: 0.8775 (m-30) REVERT: Y 230 ASP cc_start: 0.8982 (m-30) cc_final: 0.8175 (p0) REVERT: Y 260 ASP cc_start: 0.9156 (p0) cc_final: 0.8739 (p0) REVERT: Y 261 PHE cc_start: 0.9289 (p90) cc_final: 0.8691 (p90) outliers start: 0 outliers final: 0 residues processed: 264 average time/residue: 0.3030 time to fit residues: 124.4088 Evaluate side-chains 189 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 189 time to evaluate : 1.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 154 optimal weight: 10.0000 chunk 99 optimal weight: 6.9990 chunk 149 optimal weight: 9.9990 chunk 75 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 158 optimal weight: 20.0000 chunk 170 optimal weight: 4.9990 chunk 123 optimal weight: 10.0000 chunk 23 optimal weight: 6.9990 chunk 196 optimal weight: 0.1980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 12 ASN H 73 HIS ** H 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 16 ASN ** I 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 163 GLN ** V 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.6104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19834 Z= 0.218 Angle : 0.603 11.099 26994 Z= 0.293 Chirality : 0.041 0.183 3130 Planarity : 0.004 0.064 3494 Dihedral : 7.210 148.261 2898 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 16.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.83 % Favored : 94.08 % Rotamer: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % 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: -0.29 (0.18), residues: 2298 helix: 0.81 (0.20), residues: 713 sheet: -1.04 (0.27), residues: 323 loop : -0.48 (0.18), residues: 1262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.003 TRP G 357 HIS 0.013 0.001 HIS G 77 PHE 0.015 0.001 PHE U 90 TYR 0.019 0.001 TYR G 197 ARG 0.013 0.000 ARG U 150 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 262 time to evaluate : 2.311 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 16 ASN cc_start: 0.8877 (p0) cc_final: 0.8295 (p0) REVERT: G 75 MET cc_start: 0.7675 (tmm) cc_final: 0.6924 (tmm) REVERT: G 86 MET cc_start: 0.9576 (tpp) cc_final: 0.9294 (tpp) REVERT: G 97 ASP cc_start: 0.9556 (m-30) cc_final: 0.9288 (t0) REVERT: G 215 LYS cc_start: 0.8839 (ptpt) cc_final: 0.8544 (ptpt) REVERT: H 16 MET cc_start: 0.9416 (mmm) cc_final: 0.8940 (mmm) REVERT: H 44 MET cc_start: 0.9073 (ppp) cc_final: 0.8872 (ppp) REVERT: H 78 ASN cc_start: 0.9072 (t0) cc_final: 0.8872 (t0) REVERT: H 82 MET cc_start: 0.9698 (tpt) cc_final: 0.9238 (tpt) REVERT: H 106 THR cc_start: 0.8981 (p) cc_final: 0.8622 (p) REVERT: H 119 MET cc_start: 0.9760 (ttm) cc_final: 0.9459 (tmm) REVERT: H 154 ASP cc_start: 0.9534 (t0) cc_final: 0.9159 (t0) REVERT: H 184 ASP cc_start: 0.9316 (m-30) cc_final: 0.9100 (m-30) REVERT: H 187 ASP cc_start: 0.9728 (t0) cc_final: 0.9519 (m-30) REVERT: H 190 MET cc_start: 0.9389 (mmm) cc_final: 0.8998 (mmm) REVERT: H 217 CYS cc_start: 0.9395 (m) cc_final: 0.9097 (m) REVERT: H 267 LEU cc_start: 0.9543 (tt) cc_final: 0.9317 (tt) REVERT: H 269 MET cc_start: 0.9406 (mmm) cc_final: 0.9016 (mmm) REVERT: H 292 ASP cc_start: 0.9500 (m-30) cc_final: 0.9163 (p0) REVERT: H 305 MET cc_start: 0.9100 (mmt) cc_final: 0.8661 (mmm) REVERT: H 311 ASP cc_start: 0.9675 (m-30) cc_final: 0.9185 (p0) REVERT: H 313 MET cc_start: 0.9679 (mmp) cc_final: 0.9392 (mmm) REVERT: H 355 MET cc_start: 0.9797 (mmp) cc_final: 0.9491 (mmm) REVERT: H 374 CYS cc_start: 0.7603 (p) cc_final: 0.7152 (t) REVERT: I 66 ARG cc_start: 0.7908 (ptm-80) cc_final: 0.7484 (ptm-80) REVERT: I 91 GLN cc_start: 0.9664 (tt0) cc_final: 0.9290 (tp-100) REVERT: I 181 MET cc_start: 0.9304 (tpp) cc_final: 0.9097 (mmm) REVERT: I 189 ASP cc_start: 0.9281 (m-30) cc_final: 0.8900 (m-30) REVERT: J 19 ASP cc_start: 0.9178 (t70) cc_final: 0.8735 (t70) REVERT: J 64 LEU cc_start: 0.9807 (tp) cc_final: 0.9603 (tp) REVERT: J 70 GLU cc_start: 0.9718 (mm-30) cc_final: 0.9282 (mm-30) REVERT: J 204 GLU cc_start: 0.8534 (tp30) cc_final: 0.8280 (tp30) REVERT: J 311 MET cc_start: 0.9580 (mmt) cc_final: 0.8845 (mmt) REVERT: J 322 GLU cc_start: 0.9394 (tt0) cc_final: 0.8996 (mt-10) REVERT: J 387 TRP cc_start: 0.9416 (p-90) cc_final: 0.9155 (p-90) REVERT: U 36 HIS cc_start: 0.8446 (m90) cc_final: 0.8157 (m90) REVERT: U 38 LYS cc_start: 0.8859 (ttpp) cc_final: 0.8493 (tmmt) REVERT: U 52 GLU cc_start: 0.9245 (pm20) cc_final: 0.8932 (pm20) REVERT: U 92 VAL cc_start: 0.9460 (t) cc_final: 0.9237 (t) REVERT: U 99 MET cc_start: 0.8611 (tpp) cc_final: 0.7274 (tpt) REVERT: U 112 TYR cc_start: 0.8784 (t80) cc_final: 0.8281 (t80) REVERT: U 144 TYR cc_start: 0.7940 (p90) cc_final: 0.7425 (p90) REVERT: U 151 ARG cc_start: 0.8575 (ttm170) cc_final: 0.8294 (ttm170) REVERT: V 100 ASN cc_start: 0.8720 (t0) cc_final: 0.8433 (t0) REVERT: V 122 LEU cc_start: 0.9475 (mt) cc_final: 0.9225 (mt) REVERT: V 123 LYS cc_start: 0.9541 (mmtt) cc_final: 0.9054 (mmtm) REVERT: V 143 PHE cc_start: 0.9457 (m-10) cc_final: 0.9207 (m-80) REVERT: V 172 TYR cc_start: 0.9565 (t80) cc_final: 0.9281 (t80) REVERT: Y 163 ASP cc_start: 0.9043 (m-30) cc_final: 0.8771 (m-30) REVERT: Y 230 ASP cc_start: 0.8990 (m-30) cc_final: 0.8168 (p0) REVERT: Y 260 ASP cc_start: 0.9169 (p0) cc_final: 0.8747 (p0) REVERT: Y 261 PHE cc_start: 0.9285 (p90) cc_final: 0.8669 (p90) outliers start: 0 outliers final: 0 residues processed: 262 average time/residue: 0.2830 time to fit residues: 117.1697 Evaluate side-chains 191 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 191 time to evaluate : 2.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 227 optimal weight: 0.0000 chunk 239 optimal weight: 20.0000 chunk 218 optimal weight: 8.9990 chunk 232 optimal weight: 0.4980 chunk 140 optimal weight: 7.9990 chunk 101 optimal weight: 5.9990 chunk 182 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 210 optimal weight: 6.9990 chunk 220 optimal weight: 0.0050 chunk 231 optimal weight: 5.9990 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 16 ASN ** I 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 65 HIS ** I 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.6093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 19834 Z= 0.157 Angle : 0.594 11.166 26994 Z= 0.284 Chirality : 0.042 0.161 3130 Planarity : 0.004 0.057 3494 Dihedral : 6.891 144.614 2898 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.00 % Favored : 94.91 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % 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: -0.08 (0.18), residues: 2298 helix: 0.93 (0.20), residues: 703 sheet: -0.76 (0.27), residues: 316 loop : -0.35 (0.18), residues: 1279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.002 TRP G 357 HIS 0.010 0.001 HIS G 77 PHE 0.021 0.001 PHE G 193 TYR 0.029 0.001 TYR G 197 ARG 0.010 0.000 ARG U 150 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 277 time to evaluate : 2.207 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 16 ASN cc_start: 0.8839 (p0) cc_final: 0.8488 (p0) REVERT: G 75 MET cc_start: 0.7627 (tmm) cc_final: 0.6854 (tmm) REVERT: G 86 MET cc_start: 0.9578 (tpp) cc_final: 0.9319 (tpp) REVERT: G 97 ASP cc_start: 0.9543 (m-30) cc_final: 0.9268 (t0) REVERT: G 215 LYS cc_start: 0.8833 (ptpt) cc_final: 0.8554 (ptpt) REVERT: G 227 ASN cc_start: 0.9220 (t0) cc_final: 0.8940 (t0) REVERT: H 16 MET cc_start: 0.9442 (mmm) cc_final: 0.9026 (mmm) REVERT: H 44 MET cc_start: 0.9078 (ppp) cc_final: 0.8837 (ppp) REVERT: H 78 ASN cc_start: 0.9153 (t0) cc_final: 0.8946 (t0) REVERT: H 82 MET cc_start: 0.9656 (tpt) cc_final: 0.9324 (tpp) REVERT: H 90 PHE cc_start: 0.9783 (m-80) cc_final: 0.9522 (m-10) REVERT: H 106 THR cc_start: 0.8959 (p) cc_final: 0.8688 (p) REVERT: H 119 MET cc_start: 0.9742 (ttm) cc_final: 0.9507 (tmm) REVERT: H 154 ASP cc_start: 0.9420 (t0) cc_final: 0.9049 (t0) REVERT: H 184 ASP cc_start: 0.9294 (m-30) cc_final: 0.9062 (m-30) REVERT: H 187 ASP cc_start: 0.9709 (t0) cc_final: 0.9499 (m-30) REVERT: H 190 MET cc_start: 0.9369 (mmm) cc_final: 0.9061 (mmm) REVERT: H 217 CYS cc_start: 0.9382 (m) cc_final: 0.9069 (m) REVERT: H 269 MET cc_start: 0.9369 (mmm) cc_final: 0.9159 (mmm) REVERT: H 292 ASP cc_start: 0.9456 (m-30) cc_final: 0.9126 (p0) REVERT: H 305 MET cc_start: 0.9132 (mmt) cc_final: 0.8659 (mmm) REVERT: H 311 ASP cc_start: 0.9649 (m-30) cc_final: 0.9166 (p0) REVERT: H 313 MET cc_start: 0.9680 (mmp) cc_final: 0.9411 (mmm) REVERT: H 355 MET cc_start: 0.9768 (mmp) cc_final: 0.9480 (mmm) REVERT: H 374 CYS cc_start: 0.7561 (p) cc_final: 0.7162 (t) REVERT: I 66 ARG cc_start: 0.7964 (ptm-80) cc_final: 0.7536 (ptm-80) REVERT: I 86 MET cc_start: 0.9596 (tpt) cc_final: 0.9368 (tpt) REVERT: I 91 GLN cc_start: 0.9629 (tt0) cc_final: 0.9375 (tp-100) REVERT: I 110 LEU cc_start: 0.9438 (tp) cc_final: 0.8881 (tp) REVERT: I 181 MET cc_start: 0.9282 (tpp) cc_final: 0.9071 (mmm) REVERT: I 189 ASP cc_start: 0.9260 (m-30) cc_final: 0.8905 (m-30) REVERT: J 19 ASP cc_start: 0.9117 (t70) cc_final: 0.8654 (t70) REVERT: J 64 LEU cc_start: 0.9778 (tp) cc_final: 0.9548 (tp) REVERT: J 70 GLU cc_start: 0.9683 (mm-30) cc_final: 0.9288 (mm-30) REVERT: J 109 LEU cc_start: 0.9838 (mm) cc_final: 0.9412 (pp) REVERT: J 114 GLU cc_start: 0.9527 (mt-10) cc_final: 0.9298 (mm-30) REVERT: J 204 GLU cc_start: 0.8481 (tp30) cc_final: 0.8169 (tp30) REVERT: J 208 GLU cc_start: 0.9033 (pp20) cc_final: 0.8663 (pp20) REVERT: J 311 MET cc_start: 0.9573 (mmt) cc_final: 0.8832 (mmm) REVERT: J 322 GLU cc_start: 0.9377 (tt0) cc_final: 0.8967 (mt-10) REVERT: J 387 TRP cc_start: 0.9309 (p-90) cc_final: 0.9003 (p-90) REVERT: U 38 LYS cc_start: 0.8895 (ttpp) cc_final: 0.8528 (tmmt) REVERT: U 52 GLU cc_start: 0.9152 (pm20) cc_final: 0.8824 (pm20) REVERT: U 92 VAL cc_start: 0.9381 (t) cc_final: 0.8986 (p) REVERT: U 112 TYR cc_start: 0.8675 (t80) cc_final: 0.8207 (t80) REVERT: U 144 TYR cc_start: 0.7584 (p90) cc_final: 0.7250 (p90) REVERT: U 151 ARG cc_start: 0.8489 (ttm170) cc_final: 0.7590 (ttm170) REVERT: U 162 LEU cc_start: 0.9104 (pt) cc_final: 0.8818 (tp) REVERT: V 85 LEU cc_start: 0.9552 (pp) cc_final: 0.9083 (tt) REVERT: V 100 ASN cc_start: 0.8673 (t0) cc_final: 0.8368 (t0) REVERT: V 123 LYS cc_start: 0.9550 (mmtt) cc_final: 0.9266 (mmmt) REVERT: Y 163 ASP cc_start: 0.9041 (m-30) cc_final: 0.8777 (m-30) REVERT: Y 230 ASP cc_start: 0.8988 (m-30) cc_final: 0.8170 (p0) REVERT: Y 260 ASP cc_start: 0.9104 (p0) cc_final: 0.8781 (p0) REVERT: Y 276 LEU cc_start: 0.9657 (mt) cc_final: 0.9444 (mt) outliers start: 0 outliers final: 0 residues processed: 277 average time/residue: 0.2738 time to fit residues: 120.5832 Evaluate side-chains 204 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 204 time to evaluate : 2.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 152 optimal weight: 7.9990 chunk 245 optimal weight: 7.9990 chunk 150 optimal weight: 4.9990 chunk 116 optimal weight: 8.9990 chunk 171 optimal weight: 9.9990 chunk 258 optimal weight: 30.0000 chunk 237 optimal weight: 1.9990 chunk 205 optimal weight: 40.0000 chunk 21 optimal weight: 9.9990 chunk 158 optimal weight: 20.0000 chunk 125 optimal weight: 0.5980 overall best weight: 4.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 16 ASN ** I 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 65 HIS ** I 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 56 GLN ** J 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.6569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 19834 Z= 0.385 Angle : 0.715 12.437 26994 Z= 0.355 Chirality : 0.042 0.164 3130 Planarity : 0.005 0.076 3494 Dihedral : 7.120 135.770 2898 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 22.51 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.35 % Favored : 93.56 % Rotamer: Outliers : 0.05 % Allowed : 0.38 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.18), residues: 2298 helix: 0.50 (0.19), residues: 725 sheet: -1.13 (0.27), residues: 332 loop : -0.53 (0.18), residues: 1241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.003 TRP G 357 HIS 0.018 0.002 HIS G 77 PHE 0.028 0.002 PHE I 193 TYR 0.017 0.002 TYR U 144 ARG 0.010 0.001 ARG U 150 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 237 time to evaluate : 2.178 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 16 ASN cc_start: 0.8973 (p0) cc_final: 0.8511 (p0) REVERT: G 86 MET cc_start: 0.9643 (tpp) cc_final: 0.9441 (tpp) REVERT: G 97 ASP cc_start: 0.9563 (m-30) cc_final: 0.9356 (t0) REVERT: H 16 MET cc_start: 0.9396 (mmm) cc_final: 0.9005 (mmm) REVERT: H 44 MET cc_start: 0.9131 (ppp) cc_final: 0.8843 (ppp) REVERT: H 78 ASN cc_start: 0.9088 (t0) cc_final: 0.8874 (t0) REVERT: H 82 MET cc_start: 0.9709 (tpt) cc_final: 0.9331 (tpt) REVERT: H 106 THR cc_start: 0.9032 (p) cc_final: 0.8777 (p) REVERT: H 119 MET cc_start: 0.9787 (ttm) cc_final: 0.9485 (tmm) REVERT: H 154 ASP cc_start: 0.9493 (t0) cc_final: 0.9093 (t0) REVERT: H 187 ASP cc_start: 0.9737 (t0) cc_final: 0.9497 (m-30) REVERT: H 190 MET cc_start: 0.9409 (mmm) cc_final: 0.9021 (mmm) REVERT: H 217 CYS cc_start: 0.9417 (m) cc_final: 0.9170 (m) REVERT: H 267 LEU cc_start: 0.9573 (tt) cc_final: 0.9314 (tt) REVERT: H 269 MET cc_start: 0.9397 (mmm) cc_final: 0.9027 (mmm) REVERT: H 292 ASP cc_start: 0.9540 (m-30) cc_final: 0.9193 (p0) REVERT: H 305 MET cc_start: 0.9071 (mmt) cc_final: 0.8632 (mmm) REVERT: H 311 ASP cc_start: 0.9679 (m-30) cc_final: 0.9205 (p0) REVERT: H 313 MET cc_start: 0.9739 (mmp) cc_final: 0.9421 (mmm) REVERT: H 355 MET cc_start: 0.9799 (mmp) cc_final: 0.9504 (mmm) REVERT: I 66 ARG cc_start: 0.7976 (ptm-80) cc_final: 0.7573 (ptm-80) REVERT: I 86 MET cc_start: 0.9635 (tpt) cc_final: 0.9417 (tpt) REVERT: I 91 GLN cc_start: 0.9662 (tt0) cc_final: 0.9306 (tp-100) REVERT: I 110 LEU cc_start: 0.9427 (tp) cc_final: 0.9192 (tp) REVERT: I 189 ASP cc_start: 0.9264 (m-30) cc_final: 0.8912 (m-30) REVERT: J 19 ASP cc_start: 0.9185 (t70) cc_final: 0.8857 (t70) REVERT: J 64 LEU cc_start: 0.9841 (tp) cc_final: 0.9637 (tp) REVERT: J 70 GLU cc_start: 0.9722 (mm-30) cc_final: 0.9383 (tm-30) REVERT: J 92 ILE cc_start: 0.9424 (mt) cc_final: 0.9193 (mt) REVERT: J 114 GLU cc_start: 0.9566 (mt-10) cc_final: 0.9342 (mm-30) REVERT: J 174 GLU cc_start: 0.9492 (tp30) cc_final: 0.8819 (tm-30) REVERT: J 204 GLU cc_start: 0.8514 (tp30) cc_final: 0.8280 (tp30) REVERT: J 208 GLU cc_start: 0.9128 (pp20) cc_final: 0.8833 (pp20) REVERT: J 311 MET cc_start: 0.9563 (mmt) cc_final: 0.8919 (mmt) REVERT: J 319 LEU cc_start: 0.9839 (tp) cc_final: 0.9526 (mm) REVERT: J 322 GLU cc_start: 0.9415 (tt0) cc_final: 0.9030 (mt-10) REVERT: J 387 TRP cc_start: 0.9509 (p-90) cc_final: 0.9206 (p-90) REVERT: U 36 HIS cc_start: 0.8501 (m90) cc_final: 0.8290 (m90) REVERT: U 38 LYS cc_start: 0.8933 (ttpp) cc_final: 0.8690 (tmmt) REVERT: U 52 GLU cc_start: 0.9278 (pm20) cc_final: 0.8921 (pm20) REVERT: U 90 PHE cc_start: 0.8918 (m-80) cc_final: 0.8679 (m-80) REVERT: U 92 VAL cc_start: 0.9492 (t) cc_final: 0.9117 (t) REVERT: U 112 TYR cc_start: 0.8901 (t80) cc_final: 0.8403 (t80) REVERT: U 144 TYR cc_start: 0.8013 (p90) cc_final: 0.7743 (p90) REVERT: V 100 ASN cc_start: 0.8681 (t0) cc_final: 0.8435 (t0) REVERT: V 123 LYS cc_start: 0.9500 (mmtt) cc_final: 0.8888 (mmtm) REVERT: Y 113 PHE cc_start: 0.8817 (t80) cc_final: 0.8526 (t80) REVERT: Y 163 ASP cc_start: 0.8970 (m-30) cc_final: 0.8704 (m-30) REVERT: Y 230 ASP cc_start: 0.9024 (m-30) cc_final: 0.8099 (p0) REVERT: Y 260 ASP cc_start: 0.9187 (p0) cc_final: 0.8578 (p0) REVERT: Y 261 PHE cc_start: 0.9416 (p90) cc_final: 0.8915 (p90) outliers start: 1 outliers final: 0 residues processed: 238 average time/residue: 0.2813 time to fit residues: 106.1361 Evaluate side-chains 179 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 2.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 163 optimal weight: 10.0000 chunk 218 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 189 optimal weight: 7.9990 chunk 30 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 205 optimal weight: 40.0000 chunk 86 optimal weight: 6.9990 chunk 211 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 37 optimal weight: 8.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 306 GLN ** 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 = 0.2981 r_free = 0.2981 target = 0.044949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2530 r_free = 0.2530 target = 0.030241 restraints weight = 131606.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2574 r_free = 0.2574 target = 0.031519 restraints weight = 75676.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2604 r_free = 0.2604 target = 0.032428 restraints weight = 50796.798| |-----------------------------------------------------------------------------| r_work (final): 0.2566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.6553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19834 Z= 0.226 Angle : 0.610 10.481 26994 Z= 0.295 Chirality : 0.041 0.150 3130 Planarity : 0.004 0.046 3494 Dihedral : 6.823 122.379 2898 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 17.33 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.35 % Favored : 94.56 % 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: -0.22 (0.18), residues: 2298 helix: 0.74 (0.20), residues: 707 sheet: -0.99 (0.28), residues: 317 loop : -0.35 (0.18), residues: 1274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.003 TRP G 357 HIS 0.014 0.001 HIS G 77 PHE 0.017 0.001 PHE V 83 TYR 0.016 0.001 TYR I 94 ARG 0.004 0.000 ARG I 182 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3704.20 seconds wall clock time: 68 minutes 58.50 seconds (4138.50 seconds total)