Starting phenix.real_space_refine on Wed Apr 10 13:22:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6njp_9391/04_2024/6njp_9391_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6njp_9391/04_2024/6njp_9391.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6njp_9391/04_2024/6njp_9391.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6njp_9391/04_2024/6njp_9391.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6njp_9391/04_2024/6njp_9391_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6njp_9391/04_2024/6njp_9391_updated.pdb" } resolution = 3.29 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= 0.001 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: 8 Type Number sf(0) Gaussians Al 4 5.89 5 P 8 5.49 5 Mg 4 5.21 5 S 80 5.16 5 C 12408 2.51 5 N 3389 2.21 5 O 3702 1.98 5 F 12 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 66": "NH1" <-> "NH2" Residue "A PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 113": "NH1" <-> "NH2" Residue "A ARG 147": "NH1" <-> "NH2" Residue "A ARG 172": "NH1" <-> "NH2" Residue "A ARG 209": "NH1" <-> "NH2" Residue "A ARG 366": "NH1" <-> "NH2" Residue "A ARG 378": "NH1" <-> "NH2" Residue "A ARG 398": "NH1" <-> "NH2" Residue "B TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 113": "NH1" <-> "NH2" Residue "B ARG 147": "NH1" <-> "NH2" Residue "B PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 207": "NH1" <-> "NH2" Residue "B ARG 366": "NH1" <-> "NH2" Residue "B ARG 378": "NH1" <-> "NH2" Residue "C GLU 35": "OE1" <-> "OE2" Residue "C ARG 49": "NH1" <-> "NH2" Residue "C ARG 54": "NH1" <-> "NH2" Residue "C TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 66": "NH1" <-> "NH2" Residue "C ARG 147": "NH1" <-> "NH2" Residue "C PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 288": "NH1" <-> "NH2" Residue "C ARG 305": "NH1" <-> "NH2" Residue "C ARG 366": "NH1" <-> "NH2" Residue "C ARG 378": "NH1" <-> "NH2" Residue "D ARG 120": "NH1" <-> "NH2" Residue "D ARG 147": "NH1" <-> "NH2" Residue "D ARG 159": "NH1" <-> "NH2" Residue "D PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 207": "NH1" <-> "NH2" Residue "D ARG 235": "NH1" <-> "NH2" Residue "D ARG 288": "NH1" <-> "NH2" Residue "D ARG 378": "NH1" <-> "NH2" Residue "D ARG 398": "NH1" <-> "NH2" Residue "E GLU 35": "OE1" <-> "OE2" Residue "E TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 113": "NH1" <-> "NH2" Residue "E ARG 120": "NH1" <-> "NH2" Residue "E ARG 135": "NH1" <-> "NH2" Residue "E ARG 147": "NH1" <-> "NH2" Residue "E ARG 209": "NH1" <-> "NH2" Residue "E ARG 255": "NH1" <-> "NH2" Residue "E ARG 270": "NH1" <-> "NH2" Residue "E ARG 288": "NH1" <-> "NH2" Residue "E ARG 305": "NH1" <-> "NH2" Residue "E ARG 336": "NH1" <-> "NH2" Residue "E ARG 378": "NH1" <-> "NH2" Residue "F ARG 54": "NH1" <-> "NH2" Residue "F TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 105": "NH1" <-> "NH2" Residue "F ARG 147": "NH1" <-> "NH2" Residue "F ARG 172": "NH1" <-> "NH2" Residue "F ARG 207": "NH1" <-> "NH2" Residue "F ARG 209": "NH1" <-> "NH2" Residue "F ARG 255": "NH1" <-> "NH2" Residue "F ARG 347": "NH1" <-> "NH2" Residue "F ARG 378": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 19607 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3164 Classifications: {'peptide': 412} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 390} Chain: "B" Number of atoms: 3160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3160 Classifications: {'peptide': 412} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 390} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 3164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3164 Classifications: {'peptide': 412} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 390} Chain: "D" Number of atoms: 3169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3169 Classifications: {'peptide': 413} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 391} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 3164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3164 Classifications: {'peptide': 412} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 390} Chain: "F" Number of atoms: 3106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3106 Classifications: {'peptide': 405} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 383} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 531 Classifications: {'peptide': 64} Link IDs: {'TRANS': 63} Chain breaks: 1 Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "E" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Residues with excluded nonbonded symmetry interactions: 24 residue: pdb=" N GLU A 140 " occ=0.50 ... (7 atoms not shown) pdb=" OE2 GLU A 140 " occ=0.50 residue: pdb=" N PRO A 141 " occ=0.75 ... (5 atoms not shown) pdb=" CD PRO A 141 " occ=0.75 residue: pdb=" N PRO A 142 " occ=0.50 ... (5 atoms not shown) pdb=" CD PRO A 142 " occ=0.50 residue: pdb=" N GLN A 148 " occ=0.75 ... (7 atoms not shown) pdb=" NE2 GLN A 148 " occ=0.75 residue: pdb=" N GLU B 140 " occ=0.50 ... (7 atoms not shown) pdb=" OE2 GLU B 140 " occ=0.50 residue: pdb=" N PRO B 141 " occ=0.75 ... (5 atoms not shown) pdb=" CD PRO B 141 " occ=0.75 residue: pdb=" N PRO B 142 " occ=0.50 ... (5 atoms not shown) pdb=" CD PRO B 142 " occ=0.50 residue: pdb=" N GLN B 148 " occ=0.75 ... (7 atoms not shown) pdb=" NE2 GLN B 148 " occ=0.75 residue: pdb=" N GLU C 140 " occ=0.50 ... (7 atoms not shown) pdb=" OE2 GLU C 140 " occ=0.50 residue: pdb=" N PRO C 141 " occ=0.75 ... (5 atoms not shown) pdb=" CD PRO C 141 " occ=0.75 residue: pdb=" N PRO C 142 " occ=0.50 ... (5 atoms not shown) pdb=" CD PRO C 142 " occ=0.50 residue: pdb=" N GLN C 148 " occ=0.75 ... (7 atoms not shown) pdb=" NE2 GLN C 148 " occ=0.75 ... (remaining 12 not shown) Time building chain proxies: 10.34, per 1000 atoms: 0.53 Number of scatterers: 19607 At special positions: 0 Unit cell: (123.42, 118.32, 121.38, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 80 16.00 P 8 15.00 Al 4 13.00 Mg 4 11.99 F 12 9.00 O 3702 8.00 N 3389 7.00 C 12408 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.45 Conformation dependent library (CDL) restraints added in 3.9 seconds 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4640 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 91 helices and 19 sheets defined 35.3% alpha, 14.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.97 Creating SS restraints... Processing helix chain 'A' and resid 159 through 163 Processing helix chain 'A' and resid 183 through 193 Processing helix chain 'A' and resid 208 through 215 Processing helix chain 'A' and resid 220 through 223 No H-bonds generated for 'chain 'A' and resid 220 through 223' Processing helix chain 'A' and resid 237 through 256 removed outlier: 4.754A pdb=" N ALA A 244 " --> pdb=" O ARG A 240 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N PHE A 245 " --> pdb=" O MET A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 282 Processing helix chain 'A' and resid 293 through 303 Proline residue: A 300 - end of helix Processing helix chain 'A' and resid 330 through 338 Processing helix chain 'A' and resid 348 through 351 No H-bonds generated for 'chain 'A' and resid 348 through 351' Processing helix chain 'A' and resid 374 through 397 removed outlier: 3.544A pdb=" N ALA A 381 " --> pdb=" O LEU A 377 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU A 382 " --> pdb=" O ARG A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 424 removed outlier: 3.519A pdb=" N LYS A 412 " --> pdb=" O PRO A 408 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA A 413 " --> pdb=" O GLU A 409 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N LYS A 418 " --> pdb=" O ILE A 414 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N LEU A 419 " --> pdb=" O LYS A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 445 Processing helix chain 'B' and resid 108 through 110 No H-bonds generated for 'chain 'B' and resid 108 through 110' Processing helix chain 'B' and resid 159 through 163 Processing helix chain 'B' and resid 183 through 193 Processing helix chain 'B' and resid 208 through 216 removed outlier: 3.607A pdb=" N VAL B 211 " --> pdb=" O GLY B 208 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASN B 212 " --> pdb=" O ARG B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 225 removed outlier: 4.377A pdb=" N LYS B 225 " --> pdb=" O SER B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 256 removed outlier: 5.398A pdb=" N ALA B 244 " --> pdb=" O ARG B 240 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N PHE B 245 " --> pdb=" O MET B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 281 Processing helix chain 'B' and resid 293 through 304 Proline residue: B 300 - end of helix Processing helix chain 'B' and resid 330 through 336 Processing helix chain 'B' and resid 347 through 350 No H-bonds generated for 'chain 'B' and resid 347 through 350' Processing helix chain 'B' and resid 368 through 371 No H-bonds generated for 'chain 'B' and resid 368 through 371' Processing helix chain 'B' and resid 374 through 391 Processing helix chain 'B' and resid 394 through 398 Processing helix chain 'B' and resid 408 through 423 removed outlier: 5.332A pdb=" N LYS B 418 " --> pdb=" O ILE B 414 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N LEU B 419 " --> pdb=" O LYS B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 445 Processing helix chain 'C' and resid 108 through 110 No H-bonds generated for 'chain 'C' and resid 108 through 110' Processing helix chain 'C' and resid 144 through 146 No H-bonds generated for 'chain 'C' and resid 144 through 146' Processing helix chain 'C' and resid 159 through 161 No H-bonds generated for 'chain 'C' and resid 159 through 161' Processing helix chain 'C' and resid 183 through 191 Processing helix chain 'C' and resid 208 through 217 removed outlier: 3.510A pdb=" N VAL C 211 " --> pdb=" O GLY C 208 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASN C 212 " --> pdb=" O ARG C 209 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N PHE C 214 " --> pdb=" O VAL C 211 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU C 217 " --> pdb=" O PHE C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 225 removed outlier: 4.629A pdb=" N LYS C 225 " --> pdb=" O SER C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 241 Processing helix chain 'C' and resid 244 through 256 Processing helix chain 'C' and resid 268 through 281 Processing helix chain 'C' and resid 293 through 296 No H-bonds generated for 'chain 'C' and resid 293 through 296' Processing helix chain 'C' and resid 300 through 305 removed outlier: 5.173A pdb=" N ARG C 305 " --> pdb=" O LYS C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 338 Processing helix chain 'C' and resid 348 through 351 No H-bonds generated for 'chain 'C' and resid 348 through 351' Processing helix chain 'C' and resid 368 through 371 No H-bonds generated for 'chain 'C' and resid 368 through 371' Processing helix chain 'C' and resid 374 through 399 removed outlier: 4.969A pdb=" N LEU C 395 " --> pdb=" O LYS C 391 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N LEU C 396 " --> pdb=" O ASN C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 415 removed outlier: 3.510A pdb=" N LYS C 412 " --> pdb=" O PRO C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 424 Processing helix chain 'C' and resid 434 through 445 Processing helix chain 'D' and resid 108 through 110 No H-bonds generated for 'chain 'D' and resid 108 through 110' Processing helix chain 'D' and resid 159 through 163 Processing helix chain 'D' and resid 183 through 193 Processing helix chain 'D' and resid 208 through 216 removed outlier: 3.668A pdb=" N VAL D 211 " --> pdb=" O GLY D 208 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ASN D 212 " --> pdb=" O ARG D 209 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N PHE D 214 " --> pdb=" O VAL D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 225 removed outlier: 4.493A pdb=" N LYS D 225 " --> pdb=" O SER D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 256 removed outlier: 5.436A pdb=" N ALA D 244 " --> pdb=" O ARG D 240 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N PHE D 245 " --> pdb=" O MET D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 281 Processing helix chain 'D' and resid 293 through 305 Proline residue: D 300 - end of helix removed outlier: 4.622A pdb=" N ARG D 305 " --> pdb=" O LYS D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 338 Processing helix chain 'D' and resid 347 through 349 No H-bonds generated for 'chain 'D' and resid 347 through 349' Processing helix chain 'D' and resid 374 through 396 removed outlier: 4.897A pdb=" N LEU D 395 " --> pdb=" O LYS D 391 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N LEU D 396 " --> pdb=" O ASN D 392 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 415 removed outlier: 3.745A pdb=" N LYS D 412 " --> pdb=" O PRO D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 424 removed outlier: 3.934A pdb=" N ASN D 422 " --> pdb=" O LYS D 418 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N PHE D 423 " --> pdb=" O LEU D 419 " (cutoff:3.500A) Processing helix chain 'D' and resid 434 through 445 Processing helix chain 'E' and resid 160 through 163 No H-bonds generated for 'chain 'E' and resid 160 through 163' Processing helix chain 'E' and resid 183 through 192 Processing helix chain 'E' and resid 208 through 215 removed outlier: 3.658A pdb=" N VAL E 211 " --> pdb=" O GLY E 208 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASN E 212 " --> pdb=" O ARG E 209 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE E 214 " --> pdb=" O VAL E 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 223 No H-bonds generated for 'chain 'E' and resid 220 through 223' Processing helix chain 'E' and resid 237 through 257 removed outlier: 5.264A pdb=" N ALA E 244 " --> pdb=" O ARG E 240 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N PHE E 245 " --> pdb=" O MET E 241 " (cutoff:3.500A) Processing helix chain 'E' and resid 268 through 280 Processing helix chain 'E' and resid 293 through 302 Proline residue: E 300 - end of helix Processing helix chain 'E' and resid 333 through 337 Processing helix chain 'E' and resid 347 through 350 No H-bonds generated for 'chain 'E' and resid 347 through 350' Processing helix chain 'E' and resid 374 through 393 removed outlier: 4.123A pdb=" N ASN E 392 " --> pdb=" O ALA E 388 " (cutoff:3.500A) Processing helix chain 'E' and resid 395 through 398 No H-bonds generated for 'chain 'E' and resid 395 through 398' Processing helix chain 'E' and resid 408 through 415 removed outlier: 3.559A pdb=" N LYS E 415 " --> pdb=" O ASP E 411 " (cutoff:3.500A) Processing helix chain 'E' and resid 417 through 423 Processing helix chain 'E' and resid 434 through 445 Processing helix chain 'F' and resid 108 through 110 No H-bonds generated for 'chain 'F' and resid 108 through 110' Processing helix chain 'F' and resid 144 through 146 No H-bonds generated for 'chain 'F' and resid 144 through 146' Processing helix chain 'F' and resid 159 through 164 Processing helix chain 'F' and resid 183 through 191 Processing helix chain 'F' and resid 209 through 217 removed outlier: 4.075A pdb=" N ALA F 216 " --> pdb=" O GLU F 213 " (cutoff:3.500A) Processing helix chain 'F' and resid 220 through 223 No H-bonds generated for 'chain 'F' and resid 220 through 223' Processing helix chain 'F' and resid 237 through 255 removed outlier: 4.890A pdb=" N ALA F 244 " --> pdb=" O ARG F 240 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N PHE F 245 " --> pdb=" O MET F 241 " (cutoff:3.500A) Processing helix chain 'F' and resid 268 through 282 Processing helix chain 'F' and resid 293 through 304 Proline residue: F 300 - end of helix Processing helix chain 'F' and resid 332 through 336 Processing helix chain 'F' and resid 347 through 350 No H-bonds generated for 'chain 'F' and resid 347 through 350' Processing helix chain 'F' and resid 360 through 362 No H-bonds generated for 'chain 'F' and resid 360 through 362' Processing helix chain 'F' and resid 374 through 388 Processing helix chain 'F' and resid 391 through 398 removed outlier: 4.132A pdb=" N LEU F 395 " --> pdb=" O LYS F 391 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N LEU F 396 " --> pdb=" O ASN F 392 " (cutoff:3.500A) Processing helix chain 'F' and resid 411 through 423 removed outlier: 3.765A pdb=" N LYS F 415 " --> pdb=" O ASP F 411 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N LYS F 418 " --> pdb=" O ILE F 414 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N LEU F 419 " --> pdb=" O LYS F 415 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ILE F 420 " --> pdb=" O ASN F 416 " (cutoff:3.500A) Processing helix chain 'F' and resid 434 through 444 removed outlier: 3.668A pdb=" N ILE F 438 " --> pdb=" O TYR F 434 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N GLU F 439 " --> pdb=" O GLU F 435 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 26 removed outlier: 3.913A pdb=" N LEU G 6 " --> pdb=" O LEU G 2 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N SER G 7 " --> pdb=" O ASP G 3 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N SER G 19 " --> pdb=" O ARG G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 113 removed outlier: 3.741A pdb=" N ASP G 96 " --> pdb=" O ARG G 92 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N SER G 97 " --> pdb=" O SER G 93 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLN G 98 " --> pdb=" O LEU G 94 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG G 100 " --> pdb=" O ASP G 96 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 37 through 41 removed outlier: 3.875A pdb=" N LYS A 37 " --> pdb=" O ARG A 49 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LYS A 47 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA A 72 " --> pdb=" O PHE A 79 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N LEU A 81 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N VAL A 70 " --> pdb=" O LEU A 81 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ARG A 66 " --> pdb=" O ILE A 61 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 103 through 106 Processing sheet with id= C, first strand: chain 'A' and resid 317 through 321 removed outlier: 6.451A pdb=" N ILE A 173 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N VAL A 320 " --> pdb=" O ILE A 173 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ILE A 175 " --> pdb=" O VAL A 320 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 226 through 230 removed outlier: 6.628A pdb=" N ILE A 199 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N VAL A 229 " --> pdb=" O ILE A 199 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LEU A 201 " --> pdb=" O VAL A 229 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ILE A 198 " --> pdb=" O ASN A 260 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N SER A 313 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N LEU A 263 " --> pdb=" O SER A 313 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N THR A 315 " --> pdb=" O LEU A 263 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N MET A 265 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 37 through 41 removed outlier: 3.636A pdb=" N LYS B 37 " --> pdb=" O ARG B 49 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LYS B 47 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N ILE B 41 " --> pdb=" O ILE B 45 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N ILE B 45 " --> pdb=" O ILE B 41 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N LEU B 81 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N VAL B 70 " --> pdb=" O LEU B 81 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ARG B 66 " --> pdb=" O ILE B 61 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 103 through 106 Processing sheet with id= G, first strand: chain 'B' and resid 342 through 344 removed outlier: 8.012A pdb=" N ILE B 343 " --> pdb=" O ARG B 172 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N GLY B 174 " --> pdb=" O ILE B 343 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N ILE B 173 " --> pdb=" O ILE B 314 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ALA B 316 " --> pdb=" O ILE B 173 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N ILE B 175 " --> pdb=" O ALA B 316 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N TYR B 318 " --> pdb=" O ILE B 175 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N ALA B 177 " --> pdb=" O TYR B 318 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N VAL B 320 " --> pdb=" O ALA B 177 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N VAL B 261 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N ILE B 317 " --> pdb=" O VAL B 261 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LEU B 263 " --> pdb=" O ILE B 317 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N THR B 319 " --> pdb=" O LEU B 263 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N MET B 265 " --> pdb=" O THR B 319 " (cutoff:3.500A) removed outlier: 8.625A pdb=" N LEU B 321 " --> pdb=" O MET B 265 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ILE B 198 " --> pdb=" O LEU B 262 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N MET B 264 " --> pdb=" O ILE B 198 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N VAL B 200 " --> pdb=" O MET B 264 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N ASP B 266 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N ALA B 202 " --> pdb=" O ASP B 266 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 37 through 41 removed outlier: 3.792A pdb=" N LYS C 37 " --> pdb=" O ARG C 49 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LYS C 47 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N ILE C 41 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N ILE C 45 " --> pdb=" O ILE C 41 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA C 72 " --> pdb=" O PHE C 79 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N LEU C 81 " --> pdb=" O VAL C 70 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N VAL C 70 " --> pdb=" O LEU C 81 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ARG C 66 " --> pdb=" O ILE C 61 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 103 through 106 Processing sheet with id= J, first strand: chain 'C' and resid 113 through 115 removed outlier: 3.919A pdb=" N ARG C 113 " --> pdb=" O CYS C 226 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU C 228 " --> pdb=" O ARG C 113 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ILE C 199 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N VAL C 229 " --> pdb=" O ILE C 199 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LEU C 201 " --> pdb=" O VAL C 229 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N SER C 313 " --> pdb=" O VAL C 261 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N LEU C 263 " --> pdb=" O SER C 313 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N THR C 315 " --> pdb=" O LEU C 263 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N MET C 265 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ILE C 317 " --> pdb=" O MET C 265 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 93 through 95 removed outlier: 3.832A pdb=" N GLN D 93 " --> pdb=" O ILE D 38 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY D 36 " --> pdb=" O LEU D 95 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N LYS D 47 " --> pdb=" O ILE D 39 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA D 72 " --> pdb=" O PHE D 79 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LEU D 81 " --> pdb=" O VAL D 70 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N VAL D 70 " --> pdb=" O LEU D 81 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY D 99 " --> pdb=" O PHE D 58 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N LYS D 60 " --> pdb=" O TYR D 97 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N TYR D 97 " --> pdb=" O LYS D 60 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 103 through 106 Processing sheet with id= M, first strand: chain 'D' and resid 113 through 115 removed outlier: 3.852A pdb=" N ARG D 113 " --> pdb=" O CYS D 226 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ILE D 199 " --> pdb=" O VAL D 227 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N VAL D 229 " --> pdb=" O ILE D 199 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LEU D 201 " --> pdb=" O VAL D 229 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N THR D 231 " --> pdb=" O LEU D 201 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N LEU D 203 " --> pdb=" O THR D 231 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE D 204 " --> pdb=" O ASP D 266 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N SER D 313 " --> pdb=" O VAL D 261 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N LEU D 263 " --> pdb=" O SER D 313 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N THR D 315 " --> pdb=" O LEU D 263 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N MET D 265 " --> pdb=" O THR D 315 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE D 317 " --> pdb=" O MET D 265 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 37 through 41 removed outlier: 3.905A pdb=" N LYS E 37 " --> pdb=" O ARG E 49 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N LYS E 47 " --> pdb=" O ILE E 39 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N LEU E 81 " --> pdb=" O VAL E 70 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N VAL E 70 " --> pdb=" O LEU E 81 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N LYS E 60 " --> pdb=" O TYR E 97 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N TYR E 97 " --> pdb=" O LYS E 60 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 103 through 106 Processing sheet with id= P, first strand: chain 'E' and resid 113 through 115 removed outlier: 3.739A pdb=" N ARG E 113 " --> pdb=" O CYS E 226 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ILE E 199 " --> pdb=" O VAL E 227 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N VAL E 229 " --> pdb=" O ILE E 199 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LEU E 201 " --> pdb=" O VAL E 229 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N THR E 231 " --> pdb=" O LEU E 201 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N LEU E 203 " --> pdb=" O THR E 231 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LEU E 262 " --> pdb=" O VAL E 200 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N ALA E 202 " --> pdb=" O LEU E 262 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N MET E 264 " --> pdb=" O ALA E 202 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ILE E 204 " --> pdb=" O MET E 264 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N ASP E 266 " --> pdb=" O ILE E 204 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N GLU E 206 " --> pdb=" O ASP E 266 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'F' and resid 37 through 41 removed outlier: 3.517A pdb=" N LYS F 37 " --> pdb=" O ARG F 49 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LYS F 47 " --> pdb=" O ILE F 39 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LEU F 81 " --> pdb=" O VAL F 70 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N VAL F 70 " --> pdb=" O LEU F 81 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'F' and resid 103 through 106 removed outlier: 3.658A pdb=" N PHE F 133 " --> pdb=" O VAL F 106 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 342 through 344 removed outlier: 6.906A pdb=" N GLY F 174 " --> pdb=" O ILE F 343 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL F 261 " --> pdb=" O THR F 315 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N ILE F 317 " --> pdb=" O VAL F 261 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LEU F 263 " --> pdb=" O ILE F 317 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N THR F 319 " --> pdb=" O LEU F 263 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N MET F 265 " --> pdb=" O THR F 319 " (cutoff:3.500A) removed outlier: 8.706A pdb=" N LEU F 321 " --> pdb=" O MET F 265 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ILE F 198 " --> pdb=" O LEU F 262 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N MET F 264 " --> pdb=" O ILE F 198 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL F 200 " --> pdb=" O MET F 264 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N ASP F 266 " --> pdb=" O VAL F 200 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ALA F 202 " --> pdb=" O ASP F 266 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU F 201 " --> pdb=" O VAL F 227 " (cutoff:3.500A) 628 hydrogen bonds defined for protein. 1782 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.43 Time building geometry restraints manager: 8.06 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: 4177 1.33 - 1.45: 3979 1.45 - 1.57: 11595 1.57 - 1.69: 20 1.69 - 1.81: 134 Bond restraints: 19905 Sorted by residual: bond pdb=" F1 AF3 C 602 " pdb="AL AF3 C 602 " ideal model delta sigma weight residual 1.637 1.734 -0.097 2.00e-02 2.50e+03 2.33e+01 bond pdb=" F1 AF3 E 602 " pdb="AL AF3 E 602 " ideal model delta sigma weight residual 1.637 1.733 -0.096 2.00e-02 2.50e+03 2.32e+01 bond pdb=" F1 AF3 B 602 " pdb="AL AF3 B 602 " ideal model delta sigma weight residual 1.637 1.733 -0.096 2.00e-02 2.50e+03 2.31e+01 bond pdb=" F1 AF3 D 602 " pdb="AL AF3 D 602 " ideal model delta sigma weight residual 1.637 1.733 -0.096 2.00e-02 2.50e+03 2.31e+01 bond pdb=" C ALA A 139 " pdb=" N GLU A 140 " ideal model delta sigma weight residual 1.329 1.272 0.057 1.35e-02 5.49e+03 1.77e+01 ... (remaining 19900 not shown) Histogram of bond angle deviations from ideal: 96.98 - 104.82: 413 104.82 - 112.65: 10259 112.65 - 120.49: 9168 120.49 - 128.33: 6999 128.33 - 136.16: 99 Bond angle restraints: 26938 Sorted by residual: angle pdb=" C ASP E 74 " pdb=" N GLU E 75 " pdb=" CA GLU E 75 " ideal model delta sigma weight residual 121.54 133.04 -11.50 1.91e+00 2.74e-01 3.63e+01 angle pdb=" C SER B 313 " pdb=" N ILE B 314 " pdb=" CA ILE B 314 " ideal model delta sigma weight residual 123.19 117.56 5.63 1.24e+00 6.50e-01 2.06e+01 angle pdb=" N VAL A 327 " pdb=" CA VAL A 327 " pdb=" C VAL A 327 " ideal model delta sigma weight residual 113.16 106.42 6.74 1.49e+00 4.50e-01 2.05e+01 angle pdb=" C TYR F 97 " pdb=" N GLN F 98 " pdb=" CA GLN F 98 " ideal model delta sigma weight residual 122.61 129.48 -6.87 1.56e+00 4.11e-01 1.94e+01 angle pdb=" C ASP C 74 " pdb=" N GLU C 75 " pdb=" CA GLU C 75 " ideal model delta sigma weight residual 121.54 129.77 -8.23 1.91e+00 2.74e-01 1.86e+01 ... (remaining 26933 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.15: 11964 30.15 - 60.30: 192 60.30 - 90.45: 16 90.45 - 120.60: 0 120.60 - 150.75: 4 Dihedral angle restraints: 12176 sinusoidal: 4949 harmonic: 7227 Sorted by residual: dihedral pdb=" C5' ADP E 600 " pdb=" O5' ADP E 600 " pdb=" PA ADP E 600 " pdb=" O2A ADP E 600 " ideal model delta sinusoidal sigma weight residual -60.00 90.75 -150.75 1 2.00e+01 2.50e-03 4.49e+01 dihedral pdb=" C5' ADP D 600 " pdb=" O5' ADP D 600 " pdb=" PA ADP D 600 " pdb=" O2A ADP D 600 " ideal model delta sinusoidal sigma weight residual -60.00 89.03 -149.03 1 2.00e+01 2.50e-03 4.46e+01 dihedral pdb=" C5' ADP C 600 " pdb=" O5' ADP C 600 " pdb=" PA ADP C 600 " pdb=" O2A ADP C 600 " ideal model delta sinusoidal sigma weight residual -60.00 87.67 -147.67 1 2.00e+01 2.50e-03 4.43e+01 ... (remaining 12173 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 2736 0.097 - 0.193: 349 0.193 - 0.290: 29 0.290 - 0.386: 3 0.386 - 0.483: 2 Chirality restraints: 3119 Sorted by residual: chirality pdb=" CB ILE F 314 " pdb=" CA ILE F 314 " pdb=" CG1 ILE F 314 " pdb=" CG2 ILE F 314 " both_signs ideal model delta sigma weight residual False 2.64 2.16 0.48 2.00e-01 2.50e+01 5.83e+00 chirality pdb=" CB ILE F 204 " pdb=" CA ILE F 204 " pdb=" CG1 ILE F 204 " pdb=" CG2 ILE F 204 " both_signs ideal model delta sigma weight residual False 2.64 2.22 0.42 2.00e-01 2.50e+01 4.46e+00 chirality pdb=" CB ILE A 317 " pdb=" CA ILE A 317 " pdb=" CG1 ILE A 317 " pdb=" CG2 ILE A 317 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.32e+00 ... (remaining 3116 not shown) Planarity restraints: 3473 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 131 " 0.046 5.00e-02 4.00e+02 6.90e-02 7.61e+00 pdb=" N PRO C 132 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO C 132 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 132 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 329 " -0.044 5.00e-02 4.00e+02 6.56e-02 6.88e+00 pdb=" N PRO D 330 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO D 330 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 330 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE F 83 " -0.013 2.00e-02 2.50e+03 2.53e-02 6.39e+00 pdb=" C PHE F 83 " 0.044 2.00e-02 2.50e+03 pdb=" O PHE F 83 " -0.016 2.00e-02 2.50e+03 pdb=" N GLU F 84 " -0.015 2.00e-02 2.50e+03 ... (remaining 3470 not shown) Histogram of nonbonded interaction distances: 1.28 - 2.00: 5 2.00 - 2.73: 1299 2.73 - 3.45: 26808 3.45 - 4.18: 46138 4.18 - 4.90: 84483 Nonbonded interactions: 158733 Sorted by model distance: nonbonded pdb=" O ILE B 161 " pdb=" O LEU B 165 " model vdw 1.276 3.040 nonbonded pdb=" OG SER B 184 " pdb="MG MG B 601 " model vdw 1.814 2.170 nonbonded pdb=" OG SER C 184 " pdb="MG MG C 601 " model vdw 1.842 2.170 nonbonded pdb=" OG SER D 184 " pdb="MG MG D 601 " model vdw 1.954 2.170 nonbonded pdb=" OG SER E 184 " pdb="MG MG E 601 " model vdw 1.983 2.170 ... (remaining 158728 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 35 and (name N or name CA or name C or name O or name CB \ )) or resid 36 through 322 or resid 330 through 446)) selection = (chain 'B' and (resid 35 through 322 or resid 330 through 446)) selection = (chain 'C' and ((resid 35 and (name N or name CA or name C or name O or name CB \ )) or resid 36 through 322 or resid 330 through 446)) selection = (chain 'D' and ((resid 35 and (name N or name CA or name C or name O or name CB \ )) or resid 36 through 322 or resid 330 through 446)) selection = (chain 'E' and ((resid 35 and (name N or name CA or name C or name O or name CB \ )) or resid 36 through 322 or resid 330 through 446)) selection = chain 'F' } 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=0.30 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 2.870 Check model and map are aligned: 0.260 Set scattering table: 0.160 Process input model: 52.900 Find NCS groups from input model: 1.600 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 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 : 0.009 0.097 19905 Z= 0.565 Angle : 1.171 14.194 26938 Z= 0.622 Chirality : 0.066 0.483 3119 Planarity : 0.008 0.069 3473 Dihedral : 11.572 150.745 7536 Min Nonbonded Distance : 1.276 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 0.67 % Allowed : 5.67 % Favored : 93.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.80 % 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: -4.04 (0.13), residues: 2512 helix: -3.08 (0.12), residues: 937 sheet: -1.90 (0.23), residues: 431 loop : -2.53 (0.15), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 94 HIS 0.010 0.002 HIS D 342 PHE 0.039 0.004 PHE D 83 TYR 0.021 0.003 TYR A 90 ARG 0.013 0.001 ARG E 305 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 353 time to evaluate : 2.193 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 TYR cc_start: 0.6704 (m-80) cc_final: 0.6289 (m-80) REVERT: A 97 TYR cc_start: 0.7059 (t80) cc_final: 0.6726 (t80) REVERT: A 241 MET cc_start: 0.8515 (ttp) cc_final: 0.8238 (ttt) REVERT: A 311 LYS cc_start: 0.8945 (tttp) cc_final: 0.8554 (ttpt) REVERT: A 378 ARG cc_start: 0.7334 (ppp-140) cc_final: 0.7122 (ttm-80) REVERT: A 392 ASN cc_start: 0.7652 (t0) cc_final: 0.7429 (t0) REVERT: B 66 ARG cc_start: 0.8080 (mtm180) cc_final: 0.7815 (mtm180) REVERT: B 80 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8493 (pp) REVERT: B 401 GLU cc_start: 0.7230 (tm-30) cc_final: 0.6984 (tm-30) REVERT: B 407 ASP cc_start: 0.6656 (t70) cc_final: 0.6229 (t70) REVERT: C 35 GLU cc_start: 0.6867 (OUTLIER) cc_final: 0.5850 (mp0) REVERT: C 54 ARG cc_start: 0.7953 (mmt90) cc_final: 0.7682 (mmm-85) REVERT: C 74 ASP cc_start: 0.7667 (t70) cc_final: 0.7458 (t0) REVERT: C 116 ASP cc_start: 0.7687 (t0) cc_final: 0.7469 (t0) REVERT: C 151 ASP cc_start: 0.8015 (p0) cc_final: 0.7784 (p0) REVERT: C 260 ASN cc_start: 0.8156 (m-40) cc_final: 0.7288 (t0) REVERT: C 378 ARG cc_start: 0.7842 (ttp80) cc_final: 0.7623 (mtm110) REVERT: D 66 ARG cc_start: 0.6885 (mtm180) cc_final: 0.6525 (mtm180) REVERT: D 85 HIS cc_start: 0.8222 (p90) cc_final: 0.7428 (m-70) REVERT: D 348 GLU cc_start: 0.8122 (pp20) cc_final: 0.7812 (pm20) REVERT: E 47 LYS cc_start: 0.8340 (ttmt) cc_final: 0.8122 (ttmt) REVERT: E 415 LYS cc_start: 0.8672 (ttpm) cc_final: 0.8419 (ttmm) REVERT: F 54 ARG cc_start: 0.7021 (mtp-110) cc_final: 0.6790 (mtt180) REVERT: F 77 GLU cc_start: 0.6243 (mp0) cc_final: 0.5924 (mp0) REVERT: F 368 MET cc_start: 0.6861 (mtm) cc_final: 0.6624 (mtp) REVERT: F 422 ASN cc_start: 0.7717 (p0) cc_final: 0.7444 (p0) outliers start: 14 outliers final: 4 residues processed: 365 average time/residue: 0.3900 time to fit residues: 204.2719 Evaluate side-chains 234 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 228 time to evaluate : 2.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain F residue 227 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 211 optimal weight: 3.9990 chunk 190 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 chunk 64 optimal weight: 0.6980 chunk 128 optimal weight: 0.1980 chunk 101 optimal weight: 2.9990 chunk 196 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 146 optimal weight: 3.9990 chunk 227 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 416 ASN ** A 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 ASN ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 421 GLN C 98 GLN D 416 ASN D 421 GLN E 376 HIS ** F 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 26 GLN G 106 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19905 Z= 0.182 Angle : 0.640 10.413 26938 Z= 0.312 Chirality : 0.045 0.169 3119 Planarity : 0.005 0.055 3473 Dihedral : 7.582 123.289 2811 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.72 % Allowed : 9.29 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.15), residues: 2512 helix: -1.37 (0.16), residues: 932 sheet: -1.66 (0.24), residues: 434 loop : -2.10 (0.16), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 94 HIS 0.005 0.001 HIS F 354 PHE 0.018 0.001 PHE D 58 TYR 0.018 0.002 TYR A 390 ARG 0.005 0.000 ARG E 378 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 250 time to evaluate : 2.375 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 155 ILE cc_start: 0.8053 (mp) cc_final: 0.7677 (mm) REVERT: A 215 LEU cc_start: 0.7543 (pp) cc_final: 0.7224 (mt) REVERT: A 241 MET cc_start: 0.8380 (ttp) cc_final: 0.8101 (ttt) REVERT: A 311 LYS cc_start: 0.8891 (tttp) cc_final: 0.8384 (ttpp) REVERT: A 378 ARG cc_start: 0.7414 (OUTLIER) cc_final: 0.7209 (ttm-80) REVERT: A 392 ASN cc_start: 0.7759 (t0) cc_final: 0.7498 (t0) REVERT: A 416 ASN cc_start: 0.7991 (m-40) cc_final: 0.7733 (m110) REVERT: B 80 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8475 (pp) REVERT: B 162 ASP cc_start: 0.8413 (OUTLIER) cc_final: 0.8175 (t0) REVERT: B 348 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7536 (pm20) REVERT: B 407 ASP cc_start: 0.6567 (t70) cc_final: 0.6117 (t70) REVERT: C 35 GLU cc_start: 0.7220 (OUTLIER) cc_final: 0.6432 (mp0) REVERT: C 54 ARG cc_start: 0.7807 (mmt90) cc_final: 0.7484 (mmm-85) REVERT: C 116 ASP cc_start: 0.7642 (t0) cc_final: 0.7391 (t0) REVERT: C 151 ASP cc_start: 0.7971 (p0) cc_final: 0.7696 (p0) REVERT: C 443 LYS cc_start: 0.8009 (mttt) cc_final: 0.7803 (mttt) REVERT: D 126 ILE cc_start: 0.6168 (OUTLIER) cc_final: 0.5924 (pp) REVERT: D 346 THR cc_start: 0.8926 (m) cc_final: 0.8515 (p) REVERT: D 348 GLU cc_start: 0.7992 (pp20) cc_final: 0.7632 (pm20) REVERT: D 396 LEU cc_start: 0.7431 (OUTLIER) cc_final: 0.7200 (pp) REVERT: E 329 ASP cc_start: 0.7652 (t70) cc_final: 0.7090 (m-30) REVERT: E 411 ASP cc_start: 0.7694 (t0) cc_final: 0.7054 (m-30) REVERT: F 54 ARG cc_start: 0.7160 (mtp-110) cc_final: 0.6849 (ttt180) REVERT: F 386 LEU cc_start: 0.6080 (OUTLIER) cc_final: 0.5849 (mp) REVERT: F 390 TYR cc_start: 0.6827 (t80) cc_final: 0.6616 (t80) REVERT: F 411 ASP cc_start: 0.5133 (p0) cc_final: 0.4380 (t0) REVERT: F 418 LYS cc_start: 0.6853 (tppt) cc_final: 0.6429 (tppt) REVERT: F 422 ASN cc_start: 0.7130 (p0) cc_final: 0.6857 (p0) outliers start: 57 outliers final: 21 residues processed: 294 average time/residue: 0.3547 time to fit residues: 155.0316 Evaluate side-chains 245 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 216 time to evaluate : 2.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 CYS Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 378 ARG Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 348 GLU Chi-restraints excluded: chain B residue 353 ASN Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 433 SER Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 191 CYS Chi-restraints excluded: chain E residue 261 VAL Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 314 ILE Chi-restraints excluded: chain F residue 333 ASP Chi-restraints excluded: chain F residue 346 THR Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain G residue 2 LEU Chi-restraints excluded: chain G residue 6 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 126 optimal weight: 8.9990 chunk 70 optimal weight: 6.9990 chunk 189 optimal weight: 0.9990 chunk 155 optimal weight: 6.9990 chunk 62 optimal weight: 0.5980 chunk 228 optimal weight: 9.9990 chunk 246 optimal weight: 5.9990 chunk 203 optimal weight: 7.9990 chunk 226 optimal weight: 9.9990 chunk 77 optimal weight: 10.0000 chunk 183 optimal weight: 7.9990 overall best weight: 4.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 257 GLN F 426 GLN G 106 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 19905 Z= 0.451 Angle : 0.767 10.985 26938 Z= 0.374 Chirality : 0.051 0.185 3119 Planarity : 0.006 0.053 3473 Dihedral : 7.717 121.052 2810 Min Nonbonded Distance : 1.746 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 4.39 % Allowed : 11.49 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.16), residues: 2512 helix: -1.01 (0.16), residues: 946 sheet: -1.28 (0.25), residues: 433 loop : -1.99 (0.16), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 94 HIS 0.008 0.002 HIS D 342 PHE 0.021 0.002 PHE E 79 TYR 0.018 0.002 TYR C 402 ARG 0.007 0.001 ARG E 305 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 235 time to evaluate : 2.423 Fit side-chains REVERT: A 80 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.7940 (tp) REVERT: A 90 TYR cc_start: 0.6492 (m-80) cc_final: 0.6218 (m-80) REVERT: A 97 TYR cc_start: 0.7388 (t80) cc_final: 0.7156 (t80) REVERT: A 102 PHE cc_start: 0.8179 (t80) cc_final: 0.7592 (t80) REVERT: A 215 LEU cc_start: 0.7780 (pp) cc_final: 0.7459 (mt) REVERT: A 241 MET cc_start: 0.8529 (ttp) cc_final: 0.8257 (ttt) REVERT: A 317 ILE cc_start: 0.8790 (OUTLIER) cc_final: 0.8364 (mt) REVERT: B 348 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7573 (pm20) REVERT: B 394 GLU cc_start: 0.7805 (pt0) cc_final: 0.7552 (pt0) REVERT: B 407 ASP cc_start: 0.6515 (t70) cc_final: 0.5973 (t70) REVERT: C 54 ARG cc_start: 0.7984 (mmt90) cc_final: 0.7724 (mmm-85) REVERT: C 116 ASP cc_start: 0.7763 (t0) cc_final: 0.7464 (t0) REVERT: C 151 ASP cc_start: 0.8141 (p0) cc_final: 0.7927 (p0) REVERT: C 378 ARG cc_start: 0.7830 (mtm110) cc_final: 0.7405 (ttp80) REVERT: D 67 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.8000 (pp) REVERT: D 348 GLU cc_start: 0.8010 (pp20) cc_final: 0.7692 (pm20) REVERT: D 396 LEU cc_start: 0.7680 (OUTLIER) cc_final: 0.7373 (pp) REVERT: E 404 MET cc_start: 0.7915 (tpp) cc_final: 0.7564 (tpt) REVERT: E 411 ASP cc_start: 0.7662 (t0) cc_final: 0.7231 (m-30) REVERT: F 54 ARG cc_start: 0.7184 (mtp-110) cc_final: 0.6812 (ttm170) REVERT: F 234 ASP cc_start: 0.7997 (OUTLIER) cc_final: 0.7676 (m-30) REVERT: F 375 GLU cc_start: 0.7837 (pt0) cc_final: 0.7632 (pt0) REVERT: F 377 LEU cc_start: 0.6233 (OUTLIER) cc_final: 0.6031 (pp) REVERT: F 386 LEU cc_start: 0.5963 (OUTLIER) cc_final: 0.5753 (mp) REVERT: F 390 TYR cc_start: 0.6849 (t80) cc_final: 0.6547 (t80) REVERT: F 418 LYS cc_start: 0.7027 (tppt) cc_final: 0.6523 (tppt) REVERT: F 422 ASN cc_start: 0.7224 (p0) cc_final: 0.6946 (p0) outliers start: 92 outliers final: 52 residues processed: 314 average time/residue: 0.3462 time to fit residues: 163.6469 Evaluate side-chains 272 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 212 time to evaluate : 2.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 418 LYS Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 348 GLU Chi-restraints excluded: chain B residue 353 ASN Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 431 ILE Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 85 HIS Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 234 ASP Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain E residue 77 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 191 CYS Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain E residue 261 VAL Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 393 VAL Chi-restraints excluded: chain E residue 428 THR Chi-restraints excluded: chain F residue 58 PHE Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain F residue 228 LEU Chi-restraints excluded: chain F residue 234 ASP Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 314 ILE Chi-restraints excluded: chain F residue 333 ASP Chi-restraints excluded: chain F residue 346 THR Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 426 GLN Chi-restraints excluded: chain F residue 444 VAL Chi-restraints excluded: chain G residue 6 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 225 optimal weight: 1.9990 chunk 171 optimal weight: 3.9990 chunk 118 optimal weight: 7.9990 chunk 25 optimal weight: 0.0030 chunk 108 optimal weight: 0.9980 chunk 153 optimal weight: 0.9990 chunk 229 optimal weight: 10.0000 chunk 242 optimal weight: 10.0000 chunk 119 optimal weight: 2.9990 chunk 217 optimal weight: 7.9990 chunk 65 optimal weight: 0.7980 overall best weight: 0.9594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 GLN ** E 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 212 ASN G 24 ASN G 26 GLN G 106 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 19905 Z= 0.161 Angle : 0.594 10.412 26938 Z= 0.286 Chirality : 0.044 0.160 3119 Planarity : 0.004 0.044 3473 Dihedral : 6.746 116.783 2807 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.24 % Allowed : 13.68 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.80 % 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: -1.65 (0.16), residues: 2512 helix: -0.27 (0.17), residues: 925 sheet: -1.09 (0.26), residues: 416 loop : -1.73 (0.17), residues: 1171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 94 HIS 0.004 0.001 HIS F 354 PHE 0.015 0.001 PHE D 58 TYR 0.017 0.001 TYR C 390 ARG 0.006 0.000 ARG F 105 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 235 time to evaluate : 2.429 Fit side-chains REVERT: A 90 TYR cc_start: 0.6751 (m-80) cc_final: 0.6270 (m-80) REVERT: A 215 LEU cc_start: 0.7435 (pp) cc_final: 0.7087 (mt) REVERT: A 241 MET cc_start: 0.8449 (ttp) cc_final: 0.8185 (ttt) REVERT: A 317 ILE cc_start: 0.8720 (OUTLIER) cc_final: 0.8342 (mt) REVERT: B 407 ASP cc_start: 0.6613 (t70) cc_final: 0.6115 (t70) REVERT: C 47 LYS cc_start: 0.8060 (ptmt) cc_final: 0.7810 (ptpt) REVERT: C 54 ARG cc_start: 0.7841 (mmt90) cc_final: 0.7475 (mmm-85) REVERT: C 116 ASP cc_start: 0.7660 (t0) cc_final: 0.7358 (t0) REVERT: C 151 ASP cc_start: 0.7946 (p0) cc_final: 0.7677 (p0) REVERT: C 431 ILE cc_start: 0.8089 (OUTLIER) cc_final: 0.7359 (mm) REVERT: D 346 THR cc_start: 0.8900 (OUTLIER) cc_final: 0.8654 (p) REVERT: D 348 GLU cc_start: 0.8000 (pp20) cc_final: 0.7669 (pm20) REVERT: D 396 LEU cc_start: 0.7616 (OUTLIER) cc_final: 0.7370 (pp) REVERT: E 404 MET cc_start: 0.7665 (tpp) cc_final: 0.7400 (tpt) REVERT: E 411 ASP cc_start: 0.7606 (t0) cc_final: 0.7318 (m-30) REVERT: F 143 ASP cc_start: 0.5620 (OUTLIER) cc_final: 0.5366 (p0) REVERT: F 234 ASP cc_start: 0.7828 (OUTLIER) cc_final: 0.7546 (m-30) REVERT: F 375 GLU cc_start: 0.7805 (pt0) cc_final: 0.7605 (pt0) REVERT: F 382 GLU cc_start: 0.7471 (OUTLIER) cc_final: 0.7021 (pt0) REVERT: F 385 LYS cc_start: 0.8136 (ptpp) cc_final: 0.7611 (mmtt) REVERT: F 390 TYR cc_start: 0.6816 (t80) cc_final: 0.6580 (t80) REVERT: F 418 LYS cc_start: 0.7203 (tppt) cc_final: 0.6965 (tppt) REVERT: F 422 ASN cc_start: 0.7260 (p0) cc_final: 0.6929 (p0) outliers start: 68 outliers final: 37 residues processed: 290 average time/residue: 0.3626 time to fit residues: 155.6249 Evaluate side-chains 256 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 212 time to evaluate : 2.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 431 ILE Chi-restraints excluded: chain C residue 433 SER Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain E residue 69 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 191 CYS Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain F residue 143 ASP Chi-restraints excluded: chain F residue 234 ASP Chi-restraints excluded: chain F residue 314 ILE Chi-restraints excluded: chain F residue 333 ASP Chi-restraints excluded: chain F residue 370 ASN Chi-restraints excluded: chain F residue 382 GLU Chi-restraints excluded: chain F residue 393 VAL Chi-restraints excluded: chain F residue 444 VAL Chi-restraints excluded: chain G residue 2 LEU Chi-restraints excluded: chain G residue 6 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 202 optimal weight: 7.9990 chunk 137 optimal weight: 6.9990 chunk 3 optimal weight: 7.9990 chunk 180 optimal weight: 7.9990 chunk 100 optimal weight: 10.0000 chunk 207 optimal weight: 9.9990 chunk 167 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 123 optimal weight: 0.0980 chunk 217 optimal weight: 10.0000 chunk 61 optimal weight: 0.8980 overall best weight: 4.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 421 GLN G 26 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 19905 Z= 0.433 Angle : 0.741 10.659 26938 Z= 0.358 Chirality : 0.050 0.177 3119 Planarity : 0.005 0.049 3473 Dihedral : 7.153 120.870 2805 Min Nonbonded Distance : 1.750 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 3.81 % Allowed : 15.01 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.80 % 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: -1.81 (0.16), residues: 2512 helix: -0.52 (0.17), residues: 955 sheet: -1.08 (0.27), residues: 402 loop : -1.78 (0.17), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 94 HIS 0.009 0.001 HIS F 354 PHE 0.019 0.002 PHE C 58 TYR 0.016 0.002 TYR C 402 ARG 0.006 0.001 ARG F 105 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 215 time to evaluate : 2.365 Fit side-chains revert: symmetry clash REVERT: A 97 TYR cc_start: 0.7493 (t80) cc_final: 0.7279 (t80) REVERT: A 102 PHE cc_start: 0.8050 (t80) cc_final: 0.7714 (t80) REVERT: A 215 LEU cc_start: 0.7590 (pp) cc_final: 0.7233 (mt) REVERT: A 241 MET cc_start: 0.8537 (ttp) cc_final: 0.8287 (ttt) REVERT: A 317 ILE cc_start: 0.8793 (OUTLIER) cc_final: 0.8348 (mt) REVERT: B 280 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8832 (mp) REVERT: B 348 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7482 (pm20) REVERT: B 401 GLU cc_start: 0.7130 (tm-30) cc_final: 0.6661 (tm-30) REVERT: B 407 ASP cc_start: 0.6628 (t70) cc_final: 0.6051 (t70) REVERT: C 54 ARG cc_start: 0.7978 (mmt90) cc_final: 0.7677 (mmm-85) REVERT: C 116 ASP cc_start: 0.7807 (t0) cc_final: 0.7513 (t0) REVERT: C 378 ARG cc_start: 0.7943 (mtp-110) cc_final: 0.7452 (ttp80) REVERT: C 431 ILE cc_start: 0.8325 (OUTLIER) cc_final: 0.7589 (mm) REVERT: D 346 THR cc_start: 0.8909 (OUTLIER) cc_final: 0.8609 (p) REVERT: D 348 GLU cc_start: 0.7900 (pp20) cc_final: 0.7672 (pm20) REVERT: D 378 ARG cc_start: 0.7564 (ttm110) cc_final: 0.7147 (tpp-160) REVERT: D 396 LEU cc_start: 0.7802 (OUTLIER) cc_final: 0.7501 (pp) REVERT: F 143 ASP cc_start: 0.5633 (OUTLIER) cc_final: 0.5385 (p0) REVERT: F 234 ASP cc_start: 0.7953 (OUTLIER) cc_final: 0.7630 (m-30) REVERT: F 385 LYS cc_start: 0.8050 (ptpp) cc_final: 0.7663 (mmtt) REVERT: F 390 TYR cc_start: 0.6894 (t80) cc_final: 0.6578 (t80) outliers start: 80 outliers final: 50 residues processed: 284 average time/residue: 0.3517 time to fit residues: 149.3543 Evaluate side-chains 266 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 208 time to evaluate : 2.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 348 GLU Chi-restraints excluded: chain B residue 353 ASN Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 431 ILE Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain D residue 85 HIS Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 234 ASP Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain E residue 69 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 191 CYS Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain E residue 261 VAL Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 393 VAL Chi-restraints excluded: chain E residue 428 THR Chi-restraints excluded: chain F residue 143 ASP Chi-restraints excluded: chain F residue 228 LEU Chi-restraints excluded: chain F residue 234 ASP Chi-restraints excluded: chain F residue 333 ASP Chi-restraints excluded: chain F residue 346 THR Chi-restraints excluded: chain F residue 370 ASN Chi-restraints excluded: chain F residue 393 VAL Chi-restraints excluded: chain F residue 444 VAL Chi-restraints excluded: chain G residue 6 LEU Chi-restraints excluded: chain G residue 26 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 81 optimal weight: 6.9990 chunk 218 optimal weight: 0.9990 chunk 47 optimal weight: 6.9990 chunk 142 optimal weight: 1.9990 chunk 59 optimal weight: 8.9990 chunk 242 optimal weight: 4.9990 chunk 201 optimal weight: 3.9990 chunk 112 optimal weight: 6.9990 chunk 20 optimal weight: 7.9990 chunk 80 optimal weight: 0.8980 chunk 127 optimal weight: 0.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 152 GLN G 26 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19905 Z= 0.220 Angle : 0.629 8.871 26938 Z= 0.302 Chirality : 0.045 0.185 3119 Planarity : 0.004 0.045 3473 Dihedral : 6.676 118.595 2805 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 3.57 % Allowed : 16.40 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.80 % 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: -1.54 (0.16), residues: 2512 helix: -0.22 (0.17), residues: 951 sheet: -0.99 (0.26), residues: 413 loop : -1.68 (0.17), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 94 HIS 0.007 0.001 HIS F 354 PHE 0.015 0.001 PHE D 58 TYR 0.017 0.002 TYR C 390 ARG 0.006 0.000 ARG F 105 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 220 time to evaluate : 2.394 Fit side-chains REVERT: A 102 PHE cc_start: 0.8016 (t80) cc_final: 0.7728 (t80) REVERT: A 215 LEU cc_start: 0.7390 (pp) cc_final: 0.7018 (mt) REVERT: A 241 MET cc_start: 0.8474 (ttp) cc_final: 0.8230 (ttt) REVERT: A 317 ILE cc_start: 0.8721 (OUTLIER) cc_final: 0.8321 (mt) REVERT: B 401 GLU cc_start: 0.7258 (tm-30) cc_final: 0.6703 (tm-30) REVERT: B 407 ASP cc_start: 0.6608 (t70) cc_final: 0.6103 (t70) REVERT: C 47 LYS cc_start: 0.8052 (ptmt) cc_final: 0.7839 (mtmt) REVERT: C 54 ARG cc_start: 0.7890 (mmt90) cc_final: 0.7592 (mmm-85) REVERT: C 105 ARG cc_start: 0.8662 (ttm-80) cc_final: 0.8451 (mtp85) REVERT: C 116 ASP cc_start: 0.7733 (t0) cc_final: 0.7424 (t0) REVERT: C 264 MET cc_start: 0.8901 (mtm) cc_final: 0.8628 (mtp) REVERT: C 378 ARG cc_start: 0.7865 (mtp-110) cc_final: 0.7409 (ttp80) REVERT: C 431 ILE cc_start: 0.8219 (OUTLIER) cc_final: 0.7539 (mm) REVERT: D 346 THR cc_start: 0.8889 (OUTLIER) cc_final: 0.8651 (p) REVERT: D 348 GLU cc_start: 0.7969 (pp20) cc_final: 0.7679 (pm20) REVERT: D 378 ARG cc_start: 0.7477 (ttm110) cc_final: 0.7059 (tpp-160) REVERT: D 396 LEU cc_start: 0.7736 (OUTLIER) cc_final: 0.7459 (pp) REVERT: F 54 ARG cc_start: 0.6791 (ttt180) cc_final: 0.6496 (ttt180) REVERT: F 143 ASP cc_start: 0.5618 (OUTLIER) cc_final: 0.5379 (p0) REVERT: F 234 ASP cc_start: 0.7871 (OUTLIER) cc_final: 0.7584 (m-30) REVERT: F 299 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8688 (tp) REVERT: F 360 ILE cc_start: 0.8672 (mt) cc_final: 0.8436 (mm) REVERT: F 385 LYS cc_start: 0.8069 (ptpp) cc_final: 0.7668 (mmtt) REVERT: F 390 TYR cc_start: 0.6782 (t80) cc_final: 0.6376 (t80) REVERT: F 422 ASN cc_start: 0.6948 (p0) cc_final: 0.6679 (p0) outliers start: 75 outliers final: 47 residues processed: 279 average time/residue: 0.3549 time to fit residues: 147.6634 Evaluate side-chains 262 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 208 time to evaluate : 2.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 431 ILE Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain D residue 85 HIS Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain E residue 69 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 191 CYS Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain E residue 261 VAL Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 404 MET Chi-restraints excluded: chain F residue 143 ASP Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 228 LEU Chi-restraints excluded: chain F residue 234 ASP Chi-restraints excluded: chain F residue 299 LEU Chi-restraints excluded: chain F residue 314 ILE Chi-restraints excluded: chain F residue 333 ASP Chi-restraints excluded: chain F residue 346 THR Chi-restraints excluded: chain F residue 362 LEU Chi-restraints excluded: chain F residue 370 ASN Chi-restraints excluded: chain F residue 393 VAL Chi-restraints excluded: chain F residue 444 VAL Chi-restraints excluded: chain G residue 2 LEU Chi-restraints excluded: chain G residue 6 LEU Chi-restraints excluded: chain G residue 26 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 234 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 chunk 138 optimal weight: 2.9990 chunk 177 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 204 optimal weight: 2.9990 chunk 135 optimal weight: 6.9990 chunk 241 optimal weight: 0.0970 chunk 151 optimal weight: 0.7980 chunk 147 optimal weight: 3.9990 chunk 111 optimal weight: 0.0870 overall best weight: 1.3960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 353 ASN G 26 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19905 Z= 0.191 Angle : 0.606 9.512 26938 Z= 0.290 Chirality : 0.045 0.163 3119 Planarity : 0.004 0.049 3473 Dihedral : 6.334 118.192 2803 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 3.43 % Allowed : 16.63 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.80 % 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: -1.29 (0.17), residues: 2512 helix: 0.05 (0.18), residues: 937 sheet: -0.90 (0.26), residues: 416 loop : -1.56 (0.17), residues: 1159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 94 HIS 0.006 0.001 HIS F 354 PHE 0.014 0.001 PHE D 58 TYR 0.016 0.001 TYR D 390 ARG 0.007 0.000 ARG F 105 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 217 time to evaluate : 2.379 Fit side-chains REVERT: A 102 PHE cc_start: 0.7875 (t80) cc_final: 0.7603 (t80) REVERT: A 215 LEU cc_start: 0.7277 (pp) cc_final: 0.6996 (mt) REVERT: A 241 MET cc_start: 0.8467 (ttp) cc_final: 0.8221 (ttt) REVERT: A 317 ILE cc_start: 0.8744 (OUTLIER) cc_final: 0.8335 (mt) REVERT: B 401 GLU cc_start: 0.7265 (tm-30) cc_final: 0.6642 (tm-30) REVERT: B 407 ASP cc_start: 0.6621 (t70) cc_final: 0.6117 (t70) REVERT: B 414 ILE cc_start: 0.7572 (OUTLIER) cc_final: 0.7365 (mp) REVERT: C 54 ARG cc_start: 0.7860 (mmt90) cc_final: 0.7593 (mmm-85) REVERT: C 116 ASP cc_start: 0.7696 (t0) cc_final: 0.7395 (t0) REVERT: C 264 MET cc_start: 0.8923 (mtm) cc_final: 0.8675 (mtp) REVERT: C 378 ARG cc_start: 0.7802 (mtp-110) cc_final: 0.7372 (ttp80) REVERT: C 431 ILE cc_start: 0.8228 (OUTLIER) cc_final: 0.7610 (mm) REVERT: C 435 GLU cc_start: 0.7397 (pm20) cc_final: 0.6880 (pm20) REVERT: D 348 GLU cc_start: 0.7977 (pp20) cc_final: 0.7685 (pm20) REVERT: D 378 ARG cc_start: 0.7469 (ttm110) cc_final: 0.7040 (tpp-160) REVERT: D 396 LEU cc_start: 0.7728 (OUTLIER) cc_final: 0.7487 (pp) REVERT: F 54 ARG cc_start: 0.6924 (ttt180) cc_final: 0.6712 (ttt180) REVERT: F 143 ASP cc_start: 0.5625 (OUTLIER) cc_final: 0.5371 (p0) REVERT: F 234 ASP cc_start: 0.7826 (OUTLIER) cc_final: 0.7537 (m-30) REVERT: F 385 LYS cc_start: 0.8071 (ptpp) cc_final: 0.7583 (mmtt) REVERT: F 390 TYR cc_start: 0.6663 (t80) cc_final: 0.6304 (t80) outliers start: 72 outliers final: 48 residues processed: 277 average time/residue: 0.3510 time to fit residues: 146.1473 Evaluate side-chains 254 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 200 time to evaluate : 2.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 431 ILE Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain D residue 85 HIS Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain E residue 69 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 191 CYS Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain E residue 261 VAL Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 404 MET Chi-restraints excluded: chain F residue 143 ASP Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 228 LEU Chi-restraints excluded: chain F residue 234 ASP Chi-restraints excluded: chain F residue 302 LEU Chi-restraints excluded: chain F residue 314 ILE Chi-restraints excluded: chain F residue 333 ASP Chi-restraints excluded: chain F residue 346 THR Chi-restraints excluded: chain F residue 393 VAL Chi-restraints excluded: chain F residue 444 VAL Chi-restraints excluded: chain G residue 2 LEU Chi-restraints excluded: chain G residue 26 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 149 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 144 optimal weight: 5.9990 chunk 72 optimal weight: 0.0040 chunk 47 optimal weight: 6.9990 chunk 46 optimal weight: 9.9990 chunk 153 optimal weight: 5.9990 chunk 164 optimal weight: 8.9990 chunk 119 optimal weight: 20.0000 chunk 22 optimal weight: 5.9990 chunk 190 optimal weight: 0.9990 overall best weight: 3.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 421 GLN E 152 GLN E 257 GLN G 26 GLN G 109 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 19905 Z= 0.358 Angle : 0.693 10.670 26938 Z= 0.334 Chirality : 0.048 0.171 3119 Planarity : 0.005 0.052 3473 Dihedral : 6.684 119.457 2803 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 3.96 % Allowed : 16.21 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.80 % 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: -1.47 (0.16), residues: 2512 helix: -0.17 (0.17), residues: 943 sheet: -0.93 (0.26), residues: 413 loop : -1.62 (0.17), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 94 HIS 0.006 0.001 HIS D 342 PHE 0.021 0.002 PHE G 117 TYR 0.015 0.002 TYR D 390 ARG 0.007 0.001 ARG C 113 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 203 time to evaluate : 2.494 Fit side-chains REVERT: A 215 LEU cc_start: 0.7491 (pp) cc_final: 0.7107 (mt) REVERT: A 241 MET cc_start: 0.8494 (ttp) cc_final: 0.8237 (ttt) REVERT: A 317 ILE cc_start: 0.8802 (OUTLIER) cc_final: 0.8407 (mt) REVERT: B 280 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8830 (mp) REVERT: B 401 GLU cc_start: 0.7235 (tm-30) cc_final: 0.6700 (tm-30) REVERT: B 407 ASP cc_start: 0.6624 (t70) cc_final: 0.6089 (t70) REVERT: B 417 ARG cc_start: 0.7300 (ttt90) cc_final: 0.7063 (ttt90) REVERT: C 54 ARG cc_start: 0.7938 (mmt90) cc_final: 0.7652 (mmm-85) REVERT: C 116 ASP cc_start: 0.7832 (t0) cc_final: 0.7509 (t0) REVERT: C 264 MET cc_start: 0.8908 (mtm) cc_final: 0.8673 (mtp) REVERT: C 378 ARG cc_start: 0.7851 (mtp-110) cc_final: 0.7383 (ttp80) REVERT: C 431 ILE cc_start: 0.8267 (OUTLIER) cc_final: 0.7618 (mm) REVERT: D 348 GLU cc_start: 0.7841 (pp20) cc_final: 0.7622 (pm20) REVERT: D 378 ARG cc_start: 0.7541 (ttm110) cc_final: 0.7117 (tpp-160) REVERT: D 396 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7556 (pp) REVERT: E 86 VAL cc_start: 0.7215 (OUTLIER) cc_final: 0.6996 (m) REVERT: F 143 ASP cc_start: 0.5685 (OUTLIER) cc_final: 0.5442 (p0) REVERT: F 234 ASP cc_start: 0.7934 (OUTLIER) cc_final: 0.7624 (m-30) REVERT: F 299 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8689 (tp) REVERT: F 377 LEU cc_start: 0.6379 (OUTLIER) cc_final: 0.6172 (pp) REVERT: F 385 LYS cc_start: 0.8114 (ptpp) cc_final: 0.7640 (mmtt) REVERT: F 390 TYR cc_start: 0.6678 (t80) cc_final: 0.6279 (t80) outliers start: 83 outliers final: 58 residues processed: 274 average time/residue: 0.3679 time to fit residues: 150.5886 Evaluate side-chains 270 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 203 time to evaluate : 2.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 418 LYS Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 353 ASN Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 431 ILE Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain D residue 85 HIS Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 234 ASP Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 265 MET Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain E residue 69 GLU Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 191 CYS Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain E residue 261 VAL Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 404 MET Chi-restraints excluded: chain E residue 409 GLU Chi-restraints excluded: chain E residue 428 THR Chi-restraints excluded: chain F residue 143 ASP Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 228 LEU Chi-restraints excluded: chain F residue 234 ASP Chi-restraints excluded: chain F residue 299 LEU Chi-restraints excluded: chain F residue 302 LEU Chi-restraints excluded: chain F residue 314 ILE Chi-restraints excluded: chain F residue 333 ASP Chi-restraints excluded: chain F residue 346 THR Chi-restraints excluded: chain F residue 362 LEU Chi-restraints excluded: chain F residue 370 ASN Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 393 VAL Chi-restraints excluded: chain F residue 444 VAL Chi-restraints excluded: chain G residue 26 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 220 optimal weight: 0.8980 chunk 231 optimal weight: 0.0000 chunk 211 optimal weight: 5.9990 chunk 225 optimal weight: 1.9990 chunk 135 optimal weight: 0.4980 chunk 98 optimal weight: 0.4980 chunk 177 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 203 optimal weight: 0.9990 chunk 213 optimal weight: 0.0980 chunk 224 optimal weight: 7.9990 overall best weight: 0.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 257 GLN ** A 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 257 GLN G 26 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 19905 Z= 0.132 Angle : 0.576 10.654 26938 Z= 0.273 Chirality : 0.043 0.145 3119 Planarity : 0.004 0.052 3473 Dihedral : 5.744 115.322 2803 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.14 % Allowed : 18.30 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.80 % 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: -0.98 (0.17), residues: 2512 helix: 0.39 (0.18), residues: 935 sheet: -0.78 (0.26), residues: 416 loop : -1.45 (0.17), residues: 1161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 94 HIS 0.005 0.001 HIS D 376 PHE 0.024 0.001 PHE G 117 TYR 0.017 0.001 TYR D 390 ARG 0.006 0.000 ARG F 105 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 221 time to evaluate : 2.318 Fit side-chains revert: symmetry clash REVERT: A 162 ASP cc_start: 0.7888 (t70) cc_final: 0.7634 (m-30) REVERT: A 241 MET cc_start: 0.8392 (ttp) cc_final: 0.8135 (ttt) REVERT: A 317 ILE cc_start: 0.8729 (OUTLIER) cc_final: 0.8349 (mt) REVERT: B 241 MET cc_start: 0.8458 (ttp) cc_final: 0.7953 (ttp) REVERT: B 401 GLU cc_start: 0.7294 (tm-30) cc_final: 0.6758 (tm-30) REVERT: B 407 ASP cc_start: 0.6460 (t70) cc_final: 0.6037 (t70) REVERT: B 414 ILE cc_start: 0.7385 (OUTLIER) cc_final: 0.7172 (mp) REVERT: C 54 ARG cc_start: 0.7840 (mmt90) cc_final: 0.7563 (mmm-85) REVERT: C 116 ASP cc_start: 0.7660 (t0) cc_final: 0.7348 (t0) REVERT: C 378 ARG cc_start: 0.7766 (mtp-110) cc_final: 0.7313 (ttp80) REVERT: C 382 GLU cc_start: 0.7364 (tt0) cc_final: 0.7125 (tt0) REVERT: C 435 GLU cc_start: 0.7234 (pm20) cc_final: 0.6718 (pm20) REVERT: D 138 TYR cc_start: 0.8436 (m-10) cc_final: 0.8192 (m-80) REVERT: D 378 ARG cc_start: 0.7419 (ttm110) cc_final: 0.6997 (tpp-160) REVERT: E 86 VAL cc_start: 0.6788 (OUTLIER) cc_final: 0.6529 (m) REVERT: F 54 ARG cc_start: 0.6758 (ttt180) cc_final: 0.6525 (ttt180) REVERT: F 143 ASP cc_start: 0.5649 (OUTLIER) cc_final: 0.5401 (p0) REVERT: F 234 ASP cc_start: 0.7780 (OUTLIER) cc_final: 0.7477 (m-30) REVERT: F 377 LEU cc_start: 0.6208 (OUTLIER) cc_final: 0.6001 (pp) REVERT: F 385 LYS cc_start: 0.8081 (ptpp) cc_final: 0.7577 (mmtt) REVERT: F 390 TYR cc_start: 0.6573 (t80) cc_final: 0.6182 (t80) outliers start: 45 outliers final: 33 residues processed: 259 average time/residue: 0.3829 time to fit residues: 148.5227 Evaluate side-chains 237 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 198 time to evaluate : 2.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 418 LYS Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain D residue 85 HIS Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain E residue 69 GLU Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 191 CYS Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain E residue 261 VAL Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 394 GLU Chi-restraints excluded: chain F residue 143 ASP Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 234 ASP Chi-restraints excluded: chain F residue 302 LEU Chi-restraints excluded: chain F residue 314 ILE Chi-restraints excluded: chain F residue 333 ASP Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 444 VAL Chi-restraints excluded: chain G residue 26 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 148 optimal weight: 0.9990 chunk 238 optimal weight: 20.0000 chunk 145 optimal weight: 6.9990 chunk 113 optimal weight: 5.9990 chunk 165 optimal weight: 6.9990 chunk 250 optimal weight: 6.9990 chunk 230 optimal weight: 3.9990 chunk 199 optimal weight: 6.9990 chunk 20 optimal weight: 0.9990 chunk 153 optimal weight: 0.8980 chunk 122 optimal weight: 7.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 257 GLN ** A 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 19905 Z= 0.286 Angle : 0.648 9.999 26938 Z= 0.311 Chirality : 0.046 0.161 3119 Planarity : 0.004 0.054 3473 Dihedral : 6.059 115.941 2803 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 2.57 % Allowed : 18.30 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.80 % 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: 2512 helix: 0.33 (0.18), residues: 919 sheet: -0.73 (0.26), residues: 413 loop : -1.44 (0.17), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 94 HIS 0.006 0.001 HIS D 342 PHE 0.029 0.002 PHE G 117 TYR 0.016 0.002 TYR C 97 ARG 0.006 0.000 ARG F 105 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 211 time to evaluate : 2.344 Fit side-chains REVERT: A 241 MET cc_start: 0.8485 (ttp) cc_final: 0.8234 (ttt) REVERT: A 317 ILE cc_start: 0.8798 (OUTLIER) cc_final: 0.8399 (mt) REVERT: B 280 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8811 (mp) REVERT: B 401 GLU cc_start: 0.7238 (tm-30) cc_final: 0.6765 (tm-30) REVERT: B 407 ASP cc_start: 0.6618 (t70) cc_final: 0.6142 (t70) REVERT: B 414 ILE cc_start: 0.7500 (OUTLIER) cc_final: 0.7276 (mp) REVERT: C 54 ARG cc_start: 0.7899 (mmt90) cc_final: 0.7624 (mmm-85) REVERT: C 116 ASP cc_start: 0.7793 (t0) cc_final: 0.7479 (t0) REVERT: C 378 ARG cc_start: 0.7855 (mtp-110) cc_final: 0.7372 (ttp80) REVERT: C 435 GLU cc_start: 0.7454 (pm20) cc_final: 0.6886 (pm20) REVERT: D 138 TYR cc_start: 0.8474 (m-10) cc_final: 0.8264 (m-80) REVERT: D 348 GLU cc_start: 0.7648 (pp20) cc_final: 0.7434 (pm20) REVERT: D 378 ARG cc_start: 0.7524 (ttm110) cc_final: 0.7088 (tpp-160) REVERT: E 86 VAL cc_start: 0.7036 (OUTLIER) cc_final: 0.6801 (m) REVERT: F 143 ASP cc_start: 0.5675 (OUTLIER) cc_final: 0.5421 (p0) REVERT: F 234 ASP cc_start: 0.7818 (OUTLIER) cc_final: 0.7531 (m-30) REVERT: F 377 LEU cc_start: 0.6276 (OUTLIER) cc_final: 0.6065 (pp) REVERT: F 385 LYS cc_start: 0.8043 (ptpp) cc_final: 0.7562 (mmtt) REVERT: F 390 TYR cc_start: 0.6577 (t80) cc_final: 0.6148 (t80) outliers start: 54 outliers final: 38 residues processed: 257 average time/residue: 0.3597 time to fit residues: 137.2644 Evaluate side-chains 246 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 201 time to evaluate : 2.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 418 LYS Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain D residue 85 HIS Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain E residue 69 GLU Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 191 CYS Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain E residue 261 VAL Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 394 GLU Chi-restraints excluded: chain F residue 143 ASP Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 234 ASP Chi-restraints excluded: chain F residue 302 LEU Chi-restraints excluded: chain F residue 314 ILE Chi-restraints excluded: chain F residue 333 ASP Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 444 VAL Chi-restraints excluded: chain G residue 26 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 158 optimal weight: 4.9990 chunk 212 optimal weight: 8.9990 chunk 61 optimal weight: 5.9990 chunk 183 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 199 optimal weight: 7.9990 chunk 83 optimal weight: 0.5980 chunk 204 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 212 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.131874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.109060 restraints weight = 26323.095| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 1.44 r_work: 0.3025 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2923 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2923 r_free = 0.2923 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2903 r_free = 0.2903 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2903 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19905 Z= 0.193 Angle : 0.602 9.727 26938 Z= 0.287 Chirality : 0.045 0.155 3119 Planarity : 0.004 0.054 3473 Dihedral : 5.725 113.619 2803 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.43 % Allowed : 18.35 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.80 % 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: -0.91 (0.17), residues: 2512 helix: 0.41 (0.18), residues: 933 sheet: -0.66 (0.26), residues: 417 loop : -1.39 (0.17), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 94 HIS 0.003 0.001 HIS F 354 PHE 0.029 0.001 PHE G 117 TYR 0.016 0.001 TYR C 97 ARG 0.007 0.000 ARG F 105 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4267.04 seconds wall clock time: 78 minutes 45.27 seconds (4725.27 seconds total)