Starting phenix.real_space_refine on Sat Feb 17 07:34:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8crt_26958/02_2024/8crt_26958_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8crt_26958/02_2024/8crt_26958.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8crt_26958/02_2024/8crt_26958.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8crt_26958/02_2024/8crt_26958.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8crt_26958/02_2024/8crt_26958_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8crt_26958/02_2024/8crt_26958_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.100 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: 4 Type Number sf(0) Gaussians S 106 5.16 5 C 11913 2.51 5 N 2872 2.21 5 O 3034 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "K PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 719": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 824": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 878": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 544": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 824": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 17925 Number of models: 1 Model: "" Number of chains: 12 Chain: "K" Number of atoms: 2943 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 380, 2919 Classifications: {'peptide': 380} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'TRANS': 365} Chain breaks: 5 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 380, 2919 Classifications: {'peptide': 380} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'TRANS': 365} Chain breaks: 5 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 2962 Chain: "L" Number of atoms: 2938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 2938 Classifications: {'peptide': 388} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 376} 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: "Q" Number of atoms: 2954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 2954 Classifications: {'peptide': 390} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 378} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "P" Number of atoms: 248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 248 Classifications: {'peptide': 33} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 31} Chain: "B" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 302 Classifications: {'peptide': 40} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 38} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 302 Classifications: {'peptide': 40} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 38} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 4063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 4063 Classifications: {'peptide': 517} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 488} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 4063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 4063 Classifications: {'peptide': 517} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 488} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N ATYR K 34 " occ=0.55 ... (22 atoms not shown) pdb=" OH BTYR K 34 " occ=0.45 residue: pdb=" N ATYR K 242 " occ=0.55 ... (22 atoms not shown) pdb=" OH BTYR K 242 " occ=0.45 Time building chain proxies: 11.28, per 1000 atoms: 0.63 Number of scatterers: 17925 At special positions: 0 Unit cell: (163.095, 115.37, 126.99, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 106 16.00 O 3034 8.00 N 2872 7.00 C 11913 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A 1 " - " ASN C 642 " " NAG F 1 " - " ASN E 642 " Time building additional restraints: 7.77 Conformation dependent library (CDL) restraints added in 4.3 seconds 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4230 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 97 helices and 2 sheets defined 69.2% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.84 Creating SS restraints... Processing helix chain 'K' and resid 12 through 31 Processing helix chain 'K' and resid 44 through 65 removed outlier: 3.781A pdb=" N VAL K 50 " --> pdb=" O ALA K 46 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLY K 51 " --> pdb=" O SER K 47 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU K 62 " --> pdb=" O ALA K 58 " (cutoff:3.500A) Processing helix chain 'K' and resid 73 through 98 removed outlier: 3.869A pdb=" N GLN K 89 " --> pdb=" O ALA K 85 " (cutoff:3.500A) Processing helix chain 'K' and resid 110 through 129 removed outlier: 3.520A pdb=" N VAL K 123 " --> pdb=" O SER K 119 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLY K 128 " --> pdb=" O LEU K 124 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N ALA K 129 " --> pdb=" O ILE K 125 " (cutoff:3.500A) Processing helix chain 'K' and resid 136 through 161 Processing helix chain 'K' and resid 166 through 186 removed outlier: 3.758A pdb=" N ARG K 170 " --> pdb=" O MET K 167 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N HIS K 171 " --> pdb=" O ASN K 168 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N TYR K 173 " --> pdb=" O ARG K 170 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE K 175 " --> pdb=" O PHE K 172 " (cutoff:3.500A) Processing helix chain 'K' and resid 203 through 222 Proline residue: K 221 - end of helix Processing helix chain 'K' and resid 231 through 255 Processing helix chain 'K' and resid 267 through 280 removed outlier: 5.189A pdb=" N LEU K 275 " --> pdb=" O HIS K 271 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N ALA K 276 " --> pdb=" O SER K 272 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N GLY K 277 " --> pdb=" O ALA K 273 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N GLY K 278 " --> pdb=" O VAL K 274 " (cutoff:3.500A) Processing helix chain 'K' and resid 285 through 287 No H-bonds generated for 'chain 'K' and resid 285 through 287' Processing helix chain 'K' and resid 291 through 314 Proline residue: K 313 - end of helix Processing helix chain 'K' and resid 327 through 349 removed outlier: 3.736A pdb=" N VAL K 348 " --> pdb=" O ILE K 344 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU K 349 " --> pdb=" O VAL K 345 " (cutoff:3.500A) Processing helix chain 'K' and resid 361 through 388 Processing helix chain 'K' and resid 391 through 393 No H-bonds generated for 'chain 'K' and resid 391 through 393' Processing helix chain 'K' and resid 398 through 400 No H-bonds generated for 'chain 'K' and resid 398 through 400' Processing helix chain 'K' and resid 404 through 406 No H-bonds generated for 'chain 'K' and resid 404 through 406' Processing helix chain 'L' and resid 4 through 23 Processing helix chain 'L' and resid 51 through 68 removed outlier: 4.176A pdb=" N PHE L 65 " --> pdb=" O ILE L 61 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N GLY L 66 " --> pdb=" O PHE L 62 " (cutoff:3.500A) Processing helix chain 'L' and resid 76 through 103 removed outlier: 3.840A pdb=" N GLN L 92 " --> pdb=" O ALA L 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 112 through 129 Processing helix chain 'L' and resid 138 through 161 removed outlier: 3.624A pdb=" N VAL L 150 " --> pdb=" O ILE L 146 " (cutoff:3.500A) Processing helix chain 'L' and resid 175 through 188 Processing helix chain 'L' and resid 205 through 227 removed outlier: 3.720A pdb=" N ILE L 213 " --> pdb=" O LEU L 209 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLY L 214 " --> pdb=" O PHE L 210 " (cutoff:3.500A) Proline residue: L 223 - end of helix Processing helix chain 'L' and resid 234 through 261 removed outlier: 3.772A pdb=" N LEU L 252 " --> pdb=" O ALA L 248 " (cutoff:3.500A) Processing helix chain 'L' and resid 263 through 265 No H-bonds generated for 'chain 'L' and resid 263 through 265' Processing helix chain 'L' and resid 269 through 282 removed outlier: 4.322A pdb=" N THR L 276 " --> pdb=" O ILE L 272 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N LEU L 277 " --> pdb=" O GLN L 273 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ALA L 278 " --> pdb=" O ASN L 274 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N GLY L 279 " --> pdb=" O ALA L 275 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N GLY L 280 " --> pdb=" O THR L 276 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL L 281 " --> pdb=" O LEU L 277 " (cutoff:3.500A) Processing helix chain 'L' and resid 292 through 320 removed outlier: 4.629A pdb=" N THR L 315 " --> pdb=" O TYR L 311 " (cutoff:3.500A) Proline residue: L 316 - end of helix Processing helix chain 'L' and resid 330 through 350 removed outlier: 5.240A pdb=" N LEU L 336 " --> pdb=" O ASN L 332 " (cutoff:3.500A) Proline residue: L 337 - end of helix Processing helix chain 'L' and resid 358 through 383 Processing helix chain 'L' and resid 399 through 401 No H-bonds generated for 'chain 'L' and resid 399 through 401' Processing helix chain 'Q' and resid 4 through 23 Processing helix chain 'Q' and resid 47 through 68 Proline residue: Q 52 - end of helix removed outlier: 4.241A pdb=" N PHE Q 65 " --> pdb=" O ILE Q 61 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N GLY Q 66 " --> pdb=" O PHE Q 62 " (cutoff:3.500A) Processing helix chain 'Q' and resid 76 through 103 removed outlier: 3.789A pdb=" N GLN Q 92 " --> pdb=" O ALA Q 88 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR Q 95 " --> pdb=" O LEU Q 91 " (cutoff:3.500A) Processing helix chain 'Q' and resid 112 through 129 removed outlier: 3.589A pdb=" N ALA Q 118 " --> pdb=" O ASN Q 114 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASP Q 119 " --> pdb=" O MET Q 115 " (cutoff:3.500A) Processing helix chain 'Q' and resid 138 through 161 removed outlier: 3.665A pdb=" N VAL Q 150 " --> pdb=" O ILE Q 146 " (cutoff:3.500A) Processing helix chain 'Q' and resid 175 through 188 Processing helix chain 'Q' and resid 192 through 194 No H-bonds generated for 'chain 'Q' and resid 192 through 194' Processing helix chain 'Q' and resid 205 through 227 Proline residue: Q 223 - end of helix Processing helix chain 'Q' and resid 234 through 261 removed outlier: 3.660A pdb=" N LEU Q 252 " --> pdb=" O ALA Q 248 " (cutoff:3.500A) Processing helix chain 'Q' and resid 263 through 265 No H-bonds generated for 'chain 'Q' and resid 263 through 265' Processing helix chain 'Q' and resid 269 through 282 removed outlier: 4.264A pdb=" N THR Q 276 " --> pdb=" O ILE Q 272 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N LEU Q 277 " --> pdb=" O GLN Q 273 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ALA Q 278 " --> pdb=" O ASN Q 274 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N GLY Q 279 " --> pdb=" O ALA Q 275 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N GLY Q 280 " --> pdb=" O THR Q 276 " (cutoff:3.500A) Processing helix chain 'Q' and resid 293 through 320 removed outlier: 4.744A pdb=" N THR Q 315 " --> pdb=" O TYR Q 311 " (cutoff:3.500A) Proline residue: Q 316 - end of helix Processing helix chain 'Q' and resid 330 through 350 removed outlier: 5.305A pdb=" N LEU Q 336 " --> pdb=" O ASN Q 332 " (cutoff:3.500A) Proline residue: Q 337 - end of helix Processing helix chain 'Q' and resid 358 through 383 Processing helix chain 'Q' and resid 399 through 401 No H-bonds generated for 'chain 'Q' and resid 399 through 401' Processing helix chain 'P' and resid 60 through 90 Processing helix chain 'B' and resid 89 through 113 Processing helix chain 'D' and resid 89 through 113 Processing helix chain 'C' and resid 380 through 400 removed outlier: 3.518A pdb=" N ARG C 389 " --> pdb=" O ASP C 385 " (cutoff:3.500A) Proline residue: C 391 - end of helix removed outlier: 5.409A pdb=" N LEU C 394 " --> pdb=" O TYR C 390 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N SER C 395 " --> pdb=" O PRO C 391 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE C 397 " --> pdb=" O TYR C 393 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N ALA C 400 " --> pdb=" O ASP C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 430 removed outlier: 3.707A pdb=" N PHE C 414 " --> pdb=" O ILE C 410 " (cutoff:3.500A) Proline residue: C 419 - end of helix Processing helix chain 'C' and resid 437 through 454 Processing helix chain 'C' and resid 466 through 482 Processing helix chain 'C' and resid 486 through 506 removed outlier: 3.797A pdb=" N LEU C 499 " --> pdb=" O PHE C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 515 removed outlier: 3.543A pdb=" N LEU C 512 " --> pdb=" O GLY C 509 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL C 513 " --> pdb=" O SER C 510 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG C 514 " --> pdb=" O PHE C 511 " (cutoff:3.500A) Processing helix chain 'C' and resid 518 through 546 removed outlier: 3.558A pdb=" N LEU C 540 " --> pdb=" O THR C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 570 through 592 Processing helix chain 'C' and resid 599 through 607 Processing helix chain 'C' and resid 609 through 622 Processing helix chain 'C' and resid 661 through 689 removed outlier: 3.753A pdb=" N PHE C 665 " --> pdb=" O ILE C 661 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N ALA C 668 " --> pdb=" O MET C 664 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N LEU C 669 " --> pdb=" O PHE C 665 " (cutoff:3.500A) Proline residue: C 670 - end of helix Processing helix chain 'C' and resid 692 through 694 No H-bonds generated for 'chain 'C' and resid 692 through 694' Processing helix chain 'C' and resid 702 through 718 Processing helix chain 'C' and resid 728 through 737 Processing helix chain 'C' and resid 761 through 773 Processing helix chain 'C' and resid 777 through 782 removed outlier: 4.248A pdb=" N ARG C 782 " --> pdb=" O PRO C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 785 through 798 Processing helix chain 'C' and resid 804 through 813 removed outlier: 4.230A pdb=" N PHE C 813 " --> pdb=" O ILE C 809 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 818 No H-bonds generated for 'chain 'C' and resid 816 through 818' Processing helix chain 'C' and resid 823 through 826 No H-bonds generated for 'chain 'C' and resid 823 through 826' Processing helix chain 'C' and resid 830 through 851 Processing helix chain 'C' and resid 856 through 871 Proline residue: C 860 - end of helix Proline residue: C 868 - end of helix Processing helix chain 'C' and resid 873 through 877 removed outlier: 3.935A pdb=" N ILE C 877 " --> pdb=" O LEU C 873 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 873 through 877' Processing helix chain 'C' and resid 880 through 886 Processing helix chain 'E' and resid 380 through 392 Proline residue: E 391 - end of helix Processing helix chain 'E' and resid 395 through 400 removed outlier: 5.262A pdb=" N ALA E 400 " --> pdb=" O ASP E 396 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 430 removed outlier: 3.688A pdb=" N PHE E 414 " --> pdb=" O ILE E 410 " (cutoff:3.500A) Proline residue: E 419 - end of helix Processing helix chain 'E' and resid 437 through 454 Processing helix chain 'E' and resid 466 through 482 Processing helix chain 'E' and resid 486 through 506 removed outlier: 3.524A pdb=" N LEU E 499 " --> pdb=" O PHE E 495 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU E 503 " --> pdb=" O LEU E 499 " (cutoff:3.500A) Processing helix chain 'E' and resid 509 through 515 removed outlier: 3.654A pdb=" N LEU E 512 " --> pdb=" O GLY E 509 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL E 513 " --> pdb=" O SER E 510 " (cutoff:3.500A) Processing helix chain 'E' and resid 518 through 546 removed outlier: 3.597A pdb=" N LEU E 540 " --> pdb=" O THR E 536 " (cutoff:3.500A) Processing helix chain 'E' and resid 570 through 592 Processing helix chain 'E' and resid 599 through 607 Processing helix chain 'E' and resid 609 through 622 Processing helix chain 'E' and resid 661 through 689 removed outlier: 3.722A pdb=" N PHE E 665 " --> pdb=" O ILE E 661 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N ALA E 668 " --> pdb=" O MET E 664 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N LEU E 669 " --> pdb=" O PHE E 665 " (cutoff:3.500A) Proline residue: E 670 - end of helix Processing helix chain 'E' and resid 692 through 694 No H-bonds generated for 'chain 'E' and resid 692 through 694' Processing helix chain 'E' and resid 702 through 718 removed outlier: 3.671A pdb=" N LEU E 718 " --> pdb=" O GLY E 714 " (cutoff:3.500A) Processing helix chain 'E' and resid 728 through 737 Processing helix chain 'E' and resid 761 through 773 Processing helix chain 'E' and resid 777 through 782 removed outlier: 3.868A pdb=" N ARG E 782 " --> pdb=" O PRO E 778 " (cutoff:3.500A) Processing helix chain 'E' and resid 785 through 798 Processing helix chain 'E' and resid 804 through 813 removed outlier: 4.086A pdb=" N PHE E 813 " --> pdb=" O ILE E 809 " (cutoff:3.500A) Processing helix chain 'E' and resid 816 through 818 No H-bonds generated for 'chain 'E' and resid 816 through 818' Processing helix chain 'E' and resid 823 through 826 No H-bonds generated for 'chain 'E' and resid 823 through 826' Processing helix chain 'E' and resid 830 through 851 Processing helix chain 'E' and resid 856 through 871 Proline residue: E 860 - end of helix Proline residue: E 868 - end of helix removed outlier: 3.505A pdb=" N ARG E 871 " --> pdb=" O PRO E 868 " (cutoff:3.500A) Processing helix chain 'E' and resid 874 through 876 No H-bonds generated for 'chain 'E' and resid 874 through 876' Processing helix chain 'E' and resid 880 through 886 Processing sheet with id= A, first strand: chain 'C' and resid 739 through 742 removed outlier: 5.394A pdb=" N GLY C 742 " --> pdb=" O ILE C 753 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N ILE C 753 " --> pdb=" O GLY C 742 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'E' and resid 739 through 741 1099 hydrogen bonds defined for protein. 3208 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.17 Time building geometry restraints manager: 8.26 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: 3120 1.33 - 1.45: 4630 1.45 - 1.57: 10424 1.57 - 1.69: 0 1.69 - 1.82: 190 Bond restraints: 18364 Sorted by residual: bond pdb=" N VAL K 223 " pdb=" CA VAL K 223 " ideal model delta sigma weight residual 1.460 1.499 -0.039 1.21e-02 6.83e+03 1.03e+01 bond pdb=" N VAL Q 57 " pdb=" CA VAL Q 57 " ideal model delta sigma weight residual 1.460 1.496 -0.036 1.21e-02 6.83e+03 9.10e+00 bond pdb=" N ARG K 229 " pdb=" CA ARG K 229 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.25e-02 6.40e+03 7.87e+00 bond pdb=" N TRP K 220 " pdb=" CA TRP K 220 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.04e-02 9.25e+03 7.63e+00 bond pdb=" N VAL Q 59 " pdb=" CA VAL Q 59 " ideal model delta sigma weight residual 1.460 1.493 -0.033 1.21e-02 6.83e+03 7.43e+00 ... (remaining 18359 not shown) Histogram of bond angle deviations from ideal: 98.56 - 105.69: 455 105.69 - 112.83: 10001 112.83 - 119.96: 6277 119.96 - 127.10: 8015 127.10 - 134.23: 212 Bond angle restraints: 24960 Sorted by residual: angle pdb=" C BTYR K 34 " pdb=" N ASP K 35 " pdb=" CA ASP K 35 " ideal model delta sigma weight residual 121.70 129.98 -8.28 1.80e+00 3.09e-01 2.12e+01 angle pdb=" N ILE Q 116 " pdb=" CA ILE Q 116 " pdb=" C ILE Q 116 " ideal model delta sigma weight residual 111.58 107.15 4.43 1.06e+00 8.90e-01 1.75e+01 angle pdb=" C PRO K 226 " pdb=" CA PRO K 226 " pdb=" CB PRO K 226 " ideal model delta sigma weight residual 113.06 106.68 6.38 1.59e+00 3.96e-01 1.61e+01 angle pdb=" N ASP Q 119 " pdb=" CA ASP Q 119 " pdb=" C ASP Q 119 " ideal model delta sigma weight residual 113.23 108.62 4.61 1.24e+00 6.50e-01 1.38e+01 angle pdb=" N ASN K 224 " pdb=" CA ASN K 224 " pdb=" C ASN K 224 " ideal model delta sigma weight residual 112.93 108.77 4.16 1.12e+00 7.97e-01 1.38e+01 ... (remaining 24955 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.24: 10375 21.24 - 42.47: 349 42.47 - 63.71: 73 63.71 - 84.94: 11 84.94 - 106.18: 21 Dihedral angle restraints: 10829 sinusoidal: 4238 harmonic: 6591 Sorted by residual: dihedral pdb=" C2 NAG A 2 " pdb=" C3 NAG A 2 " pdb=" C4 NAG A 2 " pdb=" C5 NAG A 2 " ideal model delta sinusoidal sigma weight residual 53.78 -52.40 106.18 1 3.00e+01 1.11e-03 1.36e+01 dihedral pdb=" C2 NAG A 2 " pdb=" C3 NAG A 2 " pdb=" C4 NAG A 2 " pdb=" O4 NAG A 2 " ideal model delta sinusoidal sigma weight residual 175.11 68.97 106.14 1 3.00e+01 1.11e-03 1.36e+01 dihedral pdb=" C2 NAG F 2 " pdb=" C3 NAG F 2 " pdb=" C4 NAG F 2 " pdb=" O4 NAG F 2 " ideal model delta sinusoidal sigma weight residual 175.11 69.31 105.80 1 3.00e+01 1.11e-03 1.36e+01 ... (remaining 10826 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1956 0.034 - 0.068: 744 0.068 - 0.102: 194 0.102 - 0.136: 79 0.136 - 0.170: 9 Chirality restraints: 2982 Sorted by residual: chirality pdb=" CA ILE Q 116 " pdb=" N ILE Q 116 " pdb=" C ILE Q 116 " pdb=" CB ILE Q 116 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.21e-01 chirality pdb=" CA MET K 238 " pdb=" N MET K 238 " pdb=" C MET K 238 " pdb=" CB MET K 238 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.46e-01 chirality pdb=" CA PHE Q 47 " pdb=" N PHE Q 47 " pdb=" C PHE Q 47 " pdb=" CB PHE Q 47 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.43e-01 ... (remaining 2979 not shown) Planarity restraints: 3034 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR K 241 " -0.027 2.00e-02 2.50e+03 5.45e-02 2.98e+01 pdb=" C THR K 241 " 0.094 2.00e-02 2.50e+03 pdb=" O THR K 241 " -0.035 2.00e-02 2.50e+03 pdb=" N ATYR K 242 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ATYR K 242 " -0.026 2.00e-02 2.50e+03 5.32e-02 2.83e+01 pdb=" C ATYR K 242 " 0.092 2.00e-02 2.50e+03 pdb=" O ATYR K 242 " -0.034 2.00e-02 2.50e+03 pdb=" N TYR K 243 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA BTYR K 242 " -0.026 2.00e-02 2.50e+03 5.27e-02 2.77e+01 pdb=" C BTYR K 242 " 0.091 2.00e-02 2.50e+03 pdb=" O BTYR K 242 " -0.034 2.00e-02 2.50e+03 pdb=" N TYR K 243 " -0.031 2.00e-02 2.50e+03 ... (remaining 3031 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1541 2.74 - 3.28: 18675 3.28 - 3.82: 32055 3.82 - 4.36: 37471 4.36 - 4.90: 65154 Nonbonded interactions: 154896 Sorted by model distance: nonbonded pdb=" OE1 GLU C 472 " pdb=" OH TYR C 486 " model vdw 2.205 2.440 nonbonded pdb=" O PHE K 28 " pdb=" OG1 THR K 32 " model vdw 2.212 2.440 nonbonded pdb=" OE1 GLU E 472 " pdb=" OH TYR E 486 " model vdw 2.213 2.440 nonbonded pdb=" OD2 ASP K 404 " pdb=" OH TYR L 205 " model vdw 2.255 2.440 nonbonded pdb=" OG SER L 171 " pdb=" O VAL L 281 " model vdw 2.276 2.440 ... (remaining 154891 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' selection = chain 'F' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'L' selection = (chain 'Q' and (resid 1 through 26 or resid 48 through 409)) } 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=0.45 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.420 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: 19.960 Check model and map are aligned: 0.360 Set scattering table: 0.190 Process input model: 53.470 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.120 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:12.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7014 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 : 0.003 0.039 18364 Z= 0.211 Angle : 0.582 8.279 24960 Z= 0.353 Chirality : 0.041 0.170 2982 Planarity : 0.005 0.060 3032 Dihedral : 12.634 106.176 6599 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.45 % Favored : 98.50 % Rotamer: Outliers : 2.36 % Allowed : 4.45 % Favored : 93.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % 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: 1.86 (0.17), residues: 2276 helix: 1.75 (0.13), residues: 1581 sheet: None (None), residues: 0 loop : 0.15 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 217 HIS 0.009 0.001 HIS Q 58 PHE 0.011 0.001 PHE L 129 TYR 0.017 0.001 TYR Q 244 ARG 0.004 0.000 ARG Q 2 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 335 time to evaluate : 1.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 225 SER cc_start: 0.8495 (p) cc_final: 0.8142 (m) REVERT: K 235 LYS cc_start: 0.8142 (OUTLIER) cc_final: 0.7635 (mtmt) REVERT: K 338 LEU cc_start: 0.7437 (OUTLIER) cc_final: 0.7014 (pp) REVERT: K 382 LEU cc_start: 0.8001 (mt) cc_final: 0.7785 (tp) REVERT: K 383 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7661 (mp) REVERT: L 196 LYS cc_start: 0.7708 (mttp) cc_final: 0.7302 (mtpp) REVERT: L 305 MET cc_start: 0.8933 (ttp) cc_final: 0.8708 (ttm) REVERT: L 312 LYS cc_start: 0.8336 (tptt) cc_final: 0.8057 (tptt) REVERT: L 321 LYS cc_start: 0.8323 (mmtp) cc_final: 0.8089 (mmtt) REVERT: L 323 ARG cc_start: 0.8249 (mpt-90) cc_final: 0.7780 (mtm-85) REVERT: L 358 MET cc_start: 0.6785 (ttp) cc_final: 0.5966 (ttp) REVERT: L 378 MET cc_start: 0.7444 (mtp) cc_final: 0.7169 (mtp) REVERT: Q 378 MET cc_start: 0.8114 (mtm) cc_final: 0.7478 (tmm) REVERT: Q 404 LYS cc_start: 0.8622 (OUTLIER) cc_final: 0.8092 (ttpt) REVERT: P 83 TYR cc_start: 0.5297 (OUTLIER) cc_final: 0.5096 (t80) REVERT: C 729 VAL cc_start: 0.7116 (OUTLIER) cc_final: 0.6914 (t) REVERT: E 624 ILE cc_start: 0.6676 (mt) cc_final: 0.6243 (tp) REVERT: E 785 LEU cc_start: 0.4034 (mt) cc_final: 0.3127 (mt) outliers start: 44 outliers final: 6 residues processed: 368 average time/residue: 1.0402 time to fit residues: 439.7746 Evaluate side-chains 305 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 293 time to evaluate : 2.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 235 LYS Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain K residue 338 LEU Chi-restraints excluded: chain K residue 383 LEU Chi-restraints excluded: chain L residue 356 THR Chi-restraints excluded: chain Q residue 404 LYS Chi-restraints excluded: chain P residue 83 TYR Chi-restraints excluded: chain P residue 87 ARG Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain E residue 826 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 20.0000 chunk 172 optimal weight: 9.9990 chunk 95 optimal weight: 4.9990 chunk 59 optimal weight: 0.7980 chunk 116 optimal weight: 8.9990 chunk 92 optimal weight: 5.9990 chunk 178 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 108 optimal weight: 6.9990 chunk 133 optimal weight: 20.0000 chunk 207 optimal weight: 6.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 49 GLN Q 98 GLN Q 102 GLN C 377 GLN ** C 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 521 GLN C 630 GLN C 651 HIS C 683 GLN C 819 HIS E 377 GLN E 457 GLN E 593 ASN E 651 HIS ** E 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 703 HIS ** E 819 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 834 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 18364 Z= 0.368 Angle : 0.596 8.236 24960 Z= 0.307 Chirality : 0.044 0.203 2982 Planarity : 0.005 0.066 3032 Dihedral : 8.554 73.731 2685 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.59 % Favored : 98.37 % Rotamer: Outliers : 3.61 % Allowed : 10.21 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % 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: 1.74 (0.17), residues: 2276 helix: 1.67 (0.13), residues: 1597 sheet: None (None), residues: 0 loop : 0.03 (0.23), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 831 HIS 0.010 0.001 HIS Q 58 PHE 0.022 0.002 PHE L 129 TYR 0.022 0.002 TYR K 178 ARG 0.005 0.001 ARG C 730 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 287 time to evaluate : 1.930 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 338 LEU cc_start: 0.7494 (tm) cc_final: 0.7071 (pp) REVERT: K 362 GLN cc_start: 0.5937 (OUTLIER) cc_final: 0.5495 (tp40) REVERT: K 382 LEU cc_start: 0.8152 (mt) cc_final: 0.7862 (tp) REVERT: K 383 LEU cc_start: 0.7942 (OUTLIER) cc_final: 0.7636 (mp) REVERT: L 196 LYS cc_start: 0.7836 (mttp) cc_final: 0.7338 (mtpp) REVERT: L 312 LYS cc_start: 0.8433 (tptt) cc_final: 0.8045 (tmtt) REVERT: L 321 LYS cc_start: 0.8334 (mmtp) cc_final: 0.8088 (mmtt) REVERT: L 323 ARG cc_start: 0.8285 (mpt-90) cc_final: 0.7779 (mtm-85) REVERT: L 378 MET cc_start: 0.7519 (mtp) cc_final: 0.7288 (mtt) REVERT: Q 101 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8488 (mp) REVERT: Q 369 ILE cc_start: 0.8793 (mt) cc_final: 0.8581 (mt) REVERT: Q 378 MET cc_start: 0.8207 (mtm) cc_final: 0.7492 (tmm) REVERT: Q 404 LYS cc_start: 0.8744 (OUTLIER) cc_final: 0.8044 (tmtt) REVERT: P 83 TYR cc_start: 0.5390 (OUTLIER) cc_final: 0.5144 (t80) REVERT: C 442 ILE cc_start: 0.6444 (mt) cc_final: 0.6185 (mt) REVERT: C 864 ILE cc_start: 0.4524 (OUTLIER) cc_final: 0.4295 (mm) REVERT: E 488 VAL cc_start: 0.5545 (t) cc_final: 0.5294 (t) REVERT: E 605 ILE cc_start: 0.6568 (OUTLIER) cc_final: 0.6215 (mp) REVERT: E 624 ILE cc_start: 0.6647 (mt) cc_final: 0.6280 (tp) outliers start: 68 outliers final: 23 residues processed: 318 average time/residue: 1.0359 time to fit residues: 380.7495 Evaluate side-chains 306 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 276 time to evaluate : 2.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 248 SER Chi-restraints excluded: chain K residue 293 LEU Chi-restraints excluded: chain K residue 305 SER Chi-restraints excluded: chain K residue 337 LEU Chi-restraints excluded: chain K residue 362 GLN Chi-restraints excluded: chain K residue 383 LEU Chi-restraints excluded: chain L residue 102 GLN Chi-restraints excluded: chain L residue 203 SER Chi-restraints excluded: chain L residue 229 ILE Chi-restraints excluded: chain L residue 356 THR Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain Q residue 162 ILE Chi-restraints excluded: chain Q residue 277 LEU Chi-restraints excluded: chain Q residue 367 SER Chi-restraints excluded: chain Q residue 404 LYS Chi-restraints excluded: chain P residue 83 TYR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 586 MET Chi-restraints excluded: chain C residue 684 ILE Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 864 ILE Chi-restraints excluded: chain C residue 881 VAL Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 418 SER Chi-restraints excluded: chain E residue 528 ILE Chi-restraints excluded: chain E residue 605 ILE Chi-restraints excluded: chain E residue 732 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 115 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 chunk 172 optimal weight: 0.8980 chunk 140 optimal weight: 0.9980 chunk 57 optimal weight: 0.6980 chunk 207 optimal weight: 20.0000 chunk 224 optimal weight: 6.9990 chunk 184 optimal weight: 9.9990 chunk 205 optimal weight: 20.0000 chunk 70 optimal weight: 5.9990 chunk 166 optimal weight: 0.9980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 171 HIS L 331 HIS Q 102 GLN Q 331 HIS C 447 GLN ** C 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 819 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18364 Z= 0.188 Angle : 0.522 7.758 24960 Z= 0.265 Chirality : 0.040 0.281 2982 Planarity : 0.005 0.049 3032 Dihedral : 6.988 55.241 2665 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 3.25 % Allowed : 12.41 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % 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: 2.03 (0.17), residues: 2276 helix: 1.91 (0.13), residues: 1597 sheet: None (None), residues: 0 loop : 0.07 (0.23), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 831 HIS 0.005 0.001 HIS K 329 PHE 0.023 0.001 PHE C 582 TYR 0.019 0.001 TYR K 178 ARG 0.004 0.000 ARG C 832 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 280 time to evaluate : 1.968 Fit side-chains revert: symmetry clash REVERT: K 20 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.8725 (tt) REVERT: K 338 LEU cc_start: 0.7461 (tm) cc_final: 0.7020 (pp) REVERT: K 362 GLN cc_start: 0.5923 (OUTLIER) cc_final: 0.5475 (tp40) REVERT: K 382 LEU cc_start: 0.8109 (mt) cc_final: 0.7741 (tp) REVERT: K 383 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7563 (mp) REVERT: L 196 LYS cc_start: 0.7857 (mttp) cc_final: 0.7277 (tptp) REVERT: L 199 GLU cc_start: 0.7613 (tm-30) cc_final: 0.7227 (tm-30) REVERT: L 312 LYS cc_start: 0.8369 (tptt) cc_final: 0.7975 (tmtt) REVERT: L 321 LYS cc_start: 0.8331 (mmtp) cc_final: 0.8094 (mmtt) REVERT: L 323 ARG cc_start: 0.8266 (mpt-90) cc_final: 0.7772 (mtm-85) REVERT: L 378 MET cc_start: 0.7475 (mtp) cc_final: 0.7246 (mtt) REVERT: Q 378 MET cc_start: 0.8168 (mtm) cc_final: 0.7464 (tmm) REVERT: Q 404 LYS cc_start: 0.8716 (OUTLIER) cc_final: 0.8034 (tmtt) REVERT: P 83 TYR cc_start: 0.5379 (OUTLIER) cc_final: 0.5160 (t80) REVERT: C 442 ILE cc_start: 0.6367 (mt) cc_final: 0.6096 (mt) REVERT: C 586 MET cc_start: 0.6129 (OUTLIER) cc_final: 0.5856 (mmt) outliers start: 61 outliers final: 26 residues processed: 307 average time/residue: 1.0299 time to fit residues: 364.5612 Evaluate side-chains 298 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 266 time to evaluate : 2.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 11 ARG Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 293 LEU Chi-restraints excluded: chain K residue 305 SER Chi-restraints excluded: chain K residue 362 GLN Chi-restraints excluded: chain K residue 383 LEU Chi-restraints excluded: chain L residue 102 GLN Chi-restraints excluded: chain L residue 203 SER Chi-restraints excluded: chain L residue 229 ILE Chi-restraints excluded: chain L residue 259 SER Chi-restraints excluded: chain L residue 356 THR Chi-restraints excluded: chain Q residue 277 LEU Chi-restraints excluded: chain Q residue 358 MET Chi-restraints excluded: chain Q residue 367 SER Chi-restraints excluded: chain Q residue 404 LYS Chi-restraints excluded: chain Q residue 408 THR Chi-restraints excluded: chain P residue 83 TYR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain C residue 504 VAL Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 586 MET Chi-restraints excluded: chain C residue 664 MET Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 881 VAL Chi-restraints excluded: chain E residue 418 SER Chi-restraints excluded: chain E residue 605 ILE Chi-restraints excluded: chain E residue 615 LEU Chi-restraints excluded: chain E residue 732 VAL Chi-restraints excluded: chain E residue 826 LYS Chi-restraints excluded: chain E residue 869 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 204 optimal weight: 1.9990 chunk 155 optimal weight: 10.0000 chunk 107 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 139 optimal weight: 5.9990 chunk 208 optimal weight: 20.0000 chunk 220 optimal weight: 7.9990 chunk 108 optimal weight: 2.9990 chunk 197 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 102 GLN C 447 GLN ** C 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 819 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18364 Z= 0.224 Angle : 0.523 8.164 24960 Z= 0.267 Chirality : 0.040 0.148 2982 Planarity : 0.004 0.048 3032 Dihedral : 6.129 57.758 2665 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 3.46 % Allowed : 13.40 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % 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: 2.16 (0.17), residues: 2276 helix: 1.98 (0.13), residues: 1588 sheet: None (None), residues: 0 loop : 0.21 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 831 HIS 0.006 0.001 HIS Q 58 PHE 0.016 0.001 PHE Q 257 TYR 0.018 0.002 TYR K 178 ARG 0.011 0.000 ARG P 87 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 273 time to evaluate : 1.994 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 338 LEU cc_start: 0.7464 (OUTLIER) cc_final: 0.7044 (pp) REVERT: K 362 GLN cc_start: 0.5932 (OUTLIER) cc_final: 0.5482 (tp40) REVERT: K 382 LEU cc_start: 0.8115 (mt) cc_final: 0.7719 (tp) REVERT: K 383 LEU cc_start: 0.7894 (OUTLIER) cc_final: 0.7600 (mp) REVERT: L 196 LYS cc_start: 0.7888 (mttp) cc_final: 0.7310 (tptp) REVERT: L 199 GLU cc_start: 0.7643 (tm-30) cc_final: 0.7247 (tm-30) REVERT: L 312 LYS cc_start: 0.8384 (tptt) cc_final: 0.7992 (tmtt) REVERT: L 321 LYS cc_start: 0.8323 (mmtp) cc_final: 0.8105 (mmtt) REVERT: L 323 ARG cc_start: 0.8281 (mpt-90) cc_final: 0.7768 (mtm-85) REVERT: L 378 MET cc_start: 0.7472 (mtp) cc_final: 0.7239 (mtt) REVERT: Q 378 MET cc_start: 0.8171 (mtm) cc_final: 0.7451 (tmm) REVERT: Q 404 LYS cc_start: 0.8695 (tmtm) cc_final: 0.8058 (tmtt) REVERT: P 83 TYR cc_start: 0.5392 (OUTLIER) cc_final: 0.5150 (t80) REVERT: C 442 ILE cc_start: 0.6382 (mt) cc_final: 0.6130 (mt) REVERT: E 605 ILE cc_start: 0.6824 (OUTLIER) cc_final: 0.6377 (mp) REVERT: E 679 PHE cc_start: 0.3319 (t80) cc_final: 0.3075 (t80) outliers start: 65 outliers final: 32 residues processed: 304 average time/residue: 1.0027 time to fit residues: 352.6449 Evaluate side-chains 305 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 268 time to evaluate : 1.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 11 ARG Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 293 LEU Chi-restraints excluded: chain K residue 305 SER Chi-restraints excluded: chain K residue 337 LEU Chi-restraints excluded: chain K residue 338 LEU Chi-restraints excluded: chain K residue 362 GLN Chi-restraints excluded: chain K residue 383 LEU Chi-restraints excluded: chain L residue 7 LEU Chi-restraints excluded: chain L residue 60 MET Chi-restraints excluded: chain L residue 102 GLN Chi-restraints excluded: chain L residue 203 SER Chi-restraints excluded: chain L residue 229 ILE Chi-restraints excluded: chain L residue 259 SER Chi-restraints excluded: chain L residue 356 THR Chi-restraints excluded: chain Q residue 277 LEU Chi-restraints excluded: chain Q residue 358 MET Chi-restraints excluded: chain Q residue 367 SER Chi-restraints excluded: chain Q residue 408 THR Chi-restraints excluded: chain P residue 83 TYR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 614 ILE Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 864 ILE Chi-restraints excluded: chain C residue 881 VAL Chi-restraints excluded: chain E residue 418 SER Chi-restraints excluded: chain E residue 528 ILE Chi-restraints excluded: chain E residue 605 ILE Chi-restraints excluded: chain E residue 615 LEU Chi-restraints excluded: chain E residue 732 VAL Chi-restraints excluded: chain E residue 780 LEU Chi-restraints excluded: chain E residue 841 ILE Chi-restraints excluded: chain E residue 869 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 183 optimal weight: 30.0000 chunk 125 optimal weight: 8.9990 chunk 3 optimal weight: 6.9990 chunk 164 optimal weight: 6.9990 chunk 90 optimal weight: 1.9990 chunk 188 optimal weight: 10.0000 chunk 152 optimal weight: 8.9990 chunk 0 optimal weight: 5.9990 chunk 112 optimal weight: 3.9990 chunk 197 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 102 GLN Q 331 HIS ** C 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 819 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 18364 Z= 0.310 Angle : 0.563 8.874 24960 Z= 0.289 Chirality : 0.042 0.145 2982 Planarity : 0.005 0.047 3032 Dihedral : 5.900 57.672 2661 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 4.24 % Allowed : 13.51 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % 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: 1.90 (0.17), residues: 2276 helix: 1.78 (0.13), residues: 1597 sheet: None (None), residues: 0 loop : 0.11 (0.24), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 831 HIS 0.007 0.001 HIS Q 58 PHE 0.024 0.002 PHE E 591 TYR 0.018 0.002 TYR K 178 ARG 0.006 0.000 ARG P 87 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 268 time to evaluate : 2.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 275 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.7933 (mm) REVERT: K 338 LEU cc_start: 0.7467 (OUTLIER) cc_final: 0.7052 (pp) REVERT: K 362 GLN cc_start: 0.5951 (OUTLIER) cc_final: 0.5487 (tp40) REVERT: K 382 LEU cc_start: 0.8168 (mt) cc_final: 0.7849 (tp) REVERT: K 383 LEU cc_start: 0.7896 (OUTLIER) cc_final: 0.7606 (mp) REVERT: L 196 LYS cc_start: 0.7919 (mttp) cc_final: 0.7402 (mtpp) REVERT: L 199 GLU cc_start: 0.7681 (tm-30) cc_final: 0.7251 (tm-30) REVERT: L 312 LYS cc_start: 0.8422 (tptt) cc_final: 0.8008 (tmtt) REVERT: L 321 LYS cc_start: 0.8344 (mmtp) cc_final: 0.8121 (mmtt) REVERT: L 323 ARG cc_start: 0.8293 (mpt-90) cc_final: 0.7768 (mtm-85) REVERT: L 378 MET cc_start: 0.7490 (mtp) cc_final: 0.7269 (mtt) REVERT: Q 101 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8443 (mp) REVERT: Q 378 MET cc_start: 0.8201 (mtm) cc_final: 0.7463 (tmm) REVERT: Q 404 LYS cc_start: 0.8712 (tmtm) cc_final: 0.8036 (tmtt) REVERT: P 83 TYR cc_start: 0.5434 (OUTLIER) cc_final: 0.5165 (t80) REVERT: C 442 ILE cc_start: 0.6435 (mt) cc_final: 0.6176 (mt) REVERT: C 473 GLU cc_start: 0.6500 (OUTLIER) cc_final: 0.6053 (tm-30) REVERT: C 586 MET cc_start: 0.6164 (mmm) cc_final: 0.5821 (mmt) REVERT: E 605 ILE cc_start: 0.6893 (OUTLIER) cc_final: 0.6542 (mp) REVERT: E 624 ILE cc_start: 0.6750 (mt) cc_final: 0.6269 (tp) REVERT: E 741 MET cc_start: 0.3580 (mmt) cc_final: 0.3210 (mmt) outliers start: 80 outliers final: 39 residues processed: 311 average time/residue: 1.0327 time to fit residues: 368.8839 Evaluate side-chains 306 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 259 time to evaluate : 1.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 11 ARG Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 248 SER Chi-restraints excluded: chain K residue 275 LEU Chi-restraints excluded: chain K residue 293 LEU Chi-restraints excluded: chain K residue 305 SER Chi-restraints excluded: chain K residue 337 LEU Chi-restraints excluded: chain K residue 338 LEU Chi-restraints excluded: chain K residue 362 GLN Chi-restraints excluded: chain K residue 383 LEU Chi-restraints excluded: chain L residue 60 MET Chi-restraints excluded: chain L residue 102 GLN Chi-restraints excluded: chain L residue 203 SER Chi-restraints excluded: chain L residue 259 SER Chi-restraints excluded: chain L residue 356 THR Chi-restraints excluded: chain Q residue 100 ILE Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain Q residue 156 GLU Chi-restraints excluded: chain Q residue 277 LEU Chi-restraints excluded: chain Q residue 358 MET Chi-restraints excluded: chain Q residue 367 SER Chi-restraints excluded: chain Q residue 408 THR Chi-restraints excluded: chain P residue 83 TYR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain C residue 473 GLU Chi-restraints excluded: chain C residue 504 VAL Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 602 ARG Chi-restraints excluded: chain C residue 614 ILE Chi-restraints excluded: chain C residue 664 MET Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 704 LEU Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 832 ARG Chi-restraints excluded: chain C residue 864 ILE Chi-restraints excluded: chain C residue 881 VAL Chi-restraints excluded: chain C residue 887 ASP Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 528 ILE Chi-restraints excluded: chain E residue 605 ILE Chi-restraints excluded: chain E residue 615 LEU Chi-restraints excluded: chain E residue 732 VAL Chi-restraints excluded: chain E residue 780 LEU Chi-restraints excluded: chain E residue 869 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 74 optimal weight: 2.9990 chunk 198 optimal weight: 5.9990 chunk 43 optimal weight: 0.8980 chunk 129 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 220 optimal weight: 0.6980 chunk 183 optimal weight: 10.0000 chunk 102 optimal weight: 0.3980 chunk 18 optimal weight: 2.9990 chunk 72 optimal weight: 7.9990 chunk 115 optimal weight: 3.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 58 HIS Q 102 GLN Q 331 HIS C 447 GLN ** C 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 819 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 840 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7090 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18364 Z= 0.178 Angle : 0.513 10.255 24960 Z= 0.263 Chirality : 0.039 0.190 2982 Planarity : 0.004 0.051 3032 Dihedral : 5.676 58.334 2661 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 3.19 % Allowed : 15.08 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % 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: 2.11 (0.17), residues: 2276 helix: 1.96 (0.13), residues: 1596 sheet: None (None), residues: 0 loop : 0.15 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 16 HIS 0.004 0.001 HIS K 329 PHE 0.020 0.001 PHE Q 294 TYR 0.016 0.001 TYR K 178 ARG 0.006 0.000 ARG E 646 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 271 time to evaluate : 1.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 275 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7870 (mm) REVERT: K 338 LEU cc_start: 0.7420 (OUTLIER) cc_final: 0.6999 (pp) REVERT: K 362 GLN cc_start: 0.5935 (OUTLIER) cc_final: 0.5479 (tp40) REVERT: K 382 LEU cc_start: 0.8111 (mt) cc_final: 0.7705 (tp) REVERT: K 383 LEU cc_start: 0.7913 (OUTLIER) cc_final: 0.7626 (mp) REVERT: L 196 LYS cc_start: 0.7931 (mttp) cc_final: 0.7346 (tptp) REVERT: L 199 GLU cc_start: 0.7664 (tm-30) cc_final: 0.7226 (tm-30) REVERT: L 312 LYS cc_start: 0.8370 (tptt) cc_final: 0.7963 (tmtt) REVERT: L 321 LYS cc_start: 0.8329 (mmtp) cc_final: 0.8113 (mmtt) REVERT: L 323 ARG cc_start: 0.8272 (mpt-90) cc_final: 0.7750 (mtm-85) REVERT: L 378 MET cc_start: 0.7467 (mtp) cc_final: 0.7238 (mtt) REVERT: Q 378 MET cc_start: 0.8169 (mtm) cc_final: 0.7445 (tmm) REVERT: Q 404 LYS cc_start: 0.8687 (tmtm) cc_final: 0.7974 (tmtt) REVERT: P 83 TYR cc_start: 0.5400 (OUTLIER) cc_final: 0.5140 (t80) REVERT: C 442 ILE cc_start: 0.6300 (mt) cc_final: 0.6041 (mt) REVERT: C 586 MET cc_start: 0.6063 (mmm) cc_final: 0.5772 (mmt) REVERT: E 624 ILE cc_start: 0.6680 (mt) cc_final: 0.6305 (tp) REVERT: E 741 MET cc_start: 0.3562 (mmt) cc_final: 0.3191 (mmt) REVERT: E 791 ILE cc_start: 0.3658 (OUTLIER) cc_final: 0.3442 (mm) outliers start: 60 outliers final: 32 residues processed: 304 average time/residue: 1.0163 time to fit residues: 356.5333 Evaluate side-chains 293 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 255 time to evaluate : 2.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 11 ARG Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 275 LEU Chi-restraints excluded: chain K residue 293 LEU Chi-restraints excluded: chain K residue 305 SER Chi-restraints excluded: chain K residue 338 LEU Chi-restraints excluded: chain K residue 362 GLN Chi-restraints excluded: chain K residue 383 LEU Chi-restraints excluded: chain L residue 102 GLN Chi-restraints excluded: chain L residue 203 SER Chi-restraints excluded: chain L residue 229 ILE Chi-restraints excluded: chain L residue 259 SER Chi-restraints excluded: chain L residue 356 THR Chi-restraints excluded: chain L residue 387 LEU Chi-restraints excluded: chain Q residue 156 GLU Chi-restraints excluded: chain Q residue 277 LEU Chi-restraints excluded: chain Q residue 367 SER Chi-restraints excluded: chain Q residue 408 THR Chi-restraints excluded: chain P residue 83 TYR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain C residue 504 VAL Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 602 ARG Chi-restraints excluded: chain C residue 704 LEU Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 864 ILE Chi-restraints excluded: chain C residue 881 VAL Chi-restraints excluded: chain C residue 887 ASP Chi-restraints excluded: chain E residue 418 SER Chi-restraints excluded: chain E residue 528 ILE Chi-restraints excluded: chain E residue 615 LEU Chi-restraints excluded: chain E residue 732 VAL Chi-restraints excluded: chain E residue 780 LEU Chi-restraints excluded: chain E residue 791 ILE Chi-restraints excluded: chain E residue 869 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 212 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 125 optimal weight: 10.0000 chunk 161 optimal weight: 9.9990 chunk 124 optimal weight: 8.9990 chunk 185 optimal weight: 0.3980 chunk 123 optimal weight: 5.9990 chunk 219 optimal weight: 10.0000 chunk 137 optimal weight: 20.0000 chunk 133 optimal weight: 1.9990 chunk 101 optimal weight: 6.9990 overall best weight: 3.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 331 HIS Q 102 GLN Q 331 HIS ** C 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 593 ASN ** E 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 819 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 18364 Z= 0.374 Angle : 0.615 10.806 24960 Z= 0.316 Chirality : 0.044 0.163 2982 Planarity : 0.005 0.054 3032 Dihedral : 5.750 55.803 2661 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.72 % Allowed : 15.03 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % 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: 1.69 (0.17), residues: 2276 helix: 1.64 (0.13), residues: 1581 sheet: None (None), residues: 0 loop : 0.03 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 831 HIS 0.006 0.001 HIS Q 154 PHE 0.024 0.002 PHE C 582 TYR 0.026 0.002 TYR K 178 ARG 0.004 0.000 ARG K 234 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 274 time to evaluate : 2.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 238 MET cc_start: 0.8243 (OUTLIER) cc_final: 0.7819 (mtt) REVERT: K 275 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.7967 (mm) REVERT: K 338 LEU cc_start: 0.7489 (OUTLIER) cc_final: 0.7056 (pp) REVERT: K 362 GLN cc_start: 0.5991 (OUTLIER) cc_final: 0.5523 (tp40) REVERT: K 382 LEU cc_start: 0.8210 (mt) cc_final: 0.7849 (tp) REVERT: K 383 LEU cc_start: 0.7911 (OUTLIER) cc_final: 0.7632 (mp) REVERT: L 196 LYS cc_start: 0.7984 (mttp) cc_final: 0.7405 (mtpp) REVERT: L 199 GLU cc_start: 0.7691 (tm-30) cc_final: 0.7252 (tm-30) REVERT: L 321 LYS cc_start: 0.8332 (mmtp) cc_final: 0.8112 (mmtt) REVERT: L 323 ARG cc_start: 0.8303 (mpt-90) cc_final: 0.7776 (mtm-85) REVERT: L 378 MET cc_start: 0.7509 (mtp) cc_final: 0.7285 (mtt) REVERT: Q 101 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8445 (mp) REVERT: Q 378 MET cc_start: 0.8203 (mtm) cc_final: 0.7465 (tmm) REVERT: Q 404 LYS cc_start: 0.8717 (tmtm) cc_final: 0.8042 (tmtt) REVERT: P 83 TYR cc_start: 0.5431 (OUTLIER) cc_final: 0.5151 (t80) REVERT: C 442 ILE cc_start: 0.6411 (mt) cc_final: 0.6169 (mt) REVERT: C 473 GLU cc_start: 0.6532 (OUTLIER) cc_final: 0.6312 (tm-30) REVERT: E 605 ILE cc_start: 0.6930 (OUTLIER) cc_final: 0.6502 (mp) REVERT: E 624 ILE cc_start: 0.6776 (mt) cc_final: 0.6247 (tp) REVERT: E 679 PHE cc_start: 0.3294 (t80) cc_final: 0.2976 (t80) REVERT: E 741 MET cc_start: 0.3634 (mmt) cc_final: 0.3195 (mmt) outliers start: 70 outliers final: 41 residues processed: 316 average time/residue: 1.0374 time to fit residues: 377.4279 Evaluate side-chains 314 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 264 time to evaluate : 1.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 11 ARG Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 60 LEU Chi-restraints excluded: chain K residue 238 MET Chi-restraints excluded: chain K residue 275 LEU Chi-restraints excluded: chain K residue 293 LEU Chi-restraints excluded: chain K residue 305 SER Chi-restraints excluded: chain K residue 337 LEU Chi-restraints excluded: chain K residue 338 LEU Chi-restraints excluded: chain K residue 362 GLN Chi-restraints excluded: chain K residue 383 LEU Chi-restraints excluded: chain L residue 102 GLN Chi-restraints excluded: chain L residue 203 SER Chi-restraints excluded: chain L residue 229 ILE Chi-restraints excluded: chain L residue 259 SER Chi-restraints excluded: chain L residue 356 THR Chi-restraints excluded: chain L residue 387 LEU Chi-restraints excluded: chain Q residue 100 ILE Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain Q residue 156 GLU Chi-restraints excluded: chain Q residue 277 LEU Chi-restraints excluded: chain Q residue 358 MET Chi-restraints excluded: chain Q residue 367 SER Chi-restraints excluded: chain P residue 83 TYR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain C residue 473 GLU Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain C residue 504 VAL Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 602 ARG Chi-restraints excluded: chain C residue 614 ILE Chi-restraints excluded: chain C residue 664 MET Chi-restraints excluded: chain C residue 684 ILE Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 704 LEU Chi-restraints excluded: chain C residue 765 LEU Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 864 ILE Chi-restraints excluded: chain C residue 881 VAL Chi-restraints excluded: chain C residue 887 ASP Chi-restraints excluded: chain E residue 418 SER Chi-restraints excluded: chain E residue 528 ILE Chi-restraints excluded: chain E residue 605 ILE Chi-restraints excluded: chain E residue 615 LEU Chi-restraints excluded: chain E residue 732 VAL Chi-restraints excluded: chain E residue 780 LEU Chi-restraints excluded: chain E residue 869 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 135 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 131 optimal weight: 8.9990 chunk 66 optimal weight: 0.7980 chunk 43 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 139 optimal weight: 6.9990 chunk 149 optimal weight: 9.9990 chunk 108 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 chunk 172 optimal weight: 7.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 331 HIS Q 102 GLN Q 331 HIS C 447 GLN ** C 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 18364 Z= 0.172 Angle : 0.530 11.258 24960 Z= 0.269 Chirality : 0.040 0.168 2982 Planarity : 0.004 0.050 3032 Dihedral : 5.463 53.850 2661 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 2.93 % Allowed : 16.54 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % 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: 1.98 (0.18), residues: 2276 helix: 1.88 (0.13), residues: 1596 sheet: None (None), residues: 0 loop : 0.04 (0.23), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP K 16 HIS 0.004 0.001 HIS K 329 PHE 0.021 0.001 PHE Q 294 TYR 0.019 0.001 TYR K 178 ARG 0.006 0.000 ARG E 646 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 257 time to evaluate : 2.416 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 238 MET cc_start: 0.8191 (OUTLIER) cc_final: 0.7761 (mtt) REVERT: K 275 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.7871 (mm) REVERT: K 338 LEU cc_start: 0.7398 (OUTLIER) cc_final: 0.6964 (pp) REVERT: K 362 GLN cc_start: 0.5957 (OUTLIER) cc_final: 0.5474 (tp40) REVERT: K 382 LEU cc_start: 0.8108 (mt) cc_final: 0.7724 (tp) REVERT: K 383 LEU cc_start: 0.7849 (OUTLIER) cc_final: 0.7600 (mp) REVERT: L 196 LYS cc_start: 0.8001 (mttp) cc_final: 0.7398 (tptp) REVERT: L 199 GLU cc_start: 0.7661 (tm-30) cc_final: 0.7213 (tm-30) REVERT: L 312 LYS cc_start: 0.8405 (tptt) cc_final: 0.7917 (tmtt) REVERT: L 321 LYS cc_start: 0.8324 (mmtp) cc_final: 0.8123 (mmtt) REVERT: L 323 ARG cc_start: 0.8279 (mpt-90) cc_final: 0.7756 (mtm-85) REVERT: L 378 MET cc_start: 0.7467 (mtp) cc_final: 0.7242 (mtt) REVERT: Q 378 MET cc_start: 0.8164 (mtm) cc_final: 0.7441 (tmm) REVERT: Q 404 LYS cc_start: 0.8696 (tmtm) cc_final: 0.7989 (tmtt) REVERT: P 83 TYR cc_start: 0.5381 (OUTLIER) cc_final: 0.5140 (t80) REVERT: C 393 TYR cc_start: 0.6069 (OUTLIER) cc_final: 0.5176 (m-10) REVERT: C 442 ILE cc_start: 0.6253 (mt) cc_final: 0.6011 (mt) REVERT: C 473 GLU cc_start: 0.6456 (OUTLIER) cc_final: 0.6145 (tm-30) REVERT: C 741 MET cc_start: 0.3828 (mmm) cc_final: 0.3297 (tmm) REVERT: E 605 ILE cc_start: 0.6785 (OUTLIER) cc_final: 0.6454 (mp) REVERT: E 741 MET cc_start: 0.3546 (mmt) cc_final: 0.3148 (mmt) REVERT: E 791 ILE cc_start: 0.3667 (OUTLIER) cc_final: 0.3466 (mm) outliers start: 55 outliers final: 30 residues processed: 287 average time/residue: 1.1771 time to fit residues: 386.8804 Evaluate side-chains 289 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 249 time to evaluate : 1.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 11 ARG Chi-restraints excluded: chain K residue 238 MET Chi-restraints excluded: chain K residue 275 LEU Chi-restraints excluded: chain K residue 293 LEU Chi-restraints excluded: chain K residue 305 SER Chi-restraints excluded: chain K residue 338 LEU Chi-restraints excluded: chain K residue 362 GLN Chi-restraints excluded: chain K residue 383 LEU Chi-restraints excluded: chain L residue 102 GLN Chi-restraints excluded: chain L residue 203 SER Chi-restraints excluded: chain L residue 229 ILE Chi-restraints excluded: chain L residue 259 SER Chi-restraints excluded: chain L residue 356 THR Chi-restraints excluded: chain L residue 387 LEU Chi-restraints excluded: chain Q residue 156 GLU Chi-restraints excluded: chain Q residue 277 LEU Chi-restraints excluded: chain Q residue 367 SER Chi-restraints excluded: chain P residue 83 TYR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain D residue 100 MET Chi-restraints excluded: chain C residue 393 TYR Chi-restraints excluded: chain C residue 473 GLU Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 602 ARG Chi-restraints excluded: chain C residue 704 LEU Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 864 ILE Chi-restraints excluded: chain C residue 881 VAL Chi-restraints excluded: chain C residue 887 ASP Chi-restraints excluded: chain E residue 418 SER Chi-restraints excluded: chain E residue 528 ILE Chi-restraints excluded: chain E residue 605 ILE Chi-restraints excluded: chain E residue 615 LEU Chi-restraints excluded: chain E residue 732 VAL Chi-restraints excluded: chain E residue 791 ILE Chi-restraints excluded: chain E residue 817 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 199 optimal weight: 8.9990 chunk 210 optimal weight: 20.0000 chunk 192 optimal weight: 9.9990 chunk 204 optimal weight: 3.9990 chunk 123 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 160 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 185 optimal weight: 1.9990 chunk 193 optimal weight: 7.9990 chunk 134 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 331 HIS Q 102 GLN Q 331 HIS Q 395 ASN ** C 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 840 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 18364 Z= 0.425 Angle : 0.647 9.665 24960 Z= 0.330 Chirality : 0.045 0.177 2982 Planarity : 0.005 0.053 3032 Dihedral : 5.658 55.744 2661 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.83 % Allowed : 17.02 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % 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: 1.46 (0.17), residues: 2276 helix: 1.52 (0.13), residues: 1576 sheet: None (None), residues: 0 loop : -0.21 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 831 HIS 0.007 0.001 HIS Q 154 PHE 0.022 0.002 PHE C 582 TYR 0.029 0.002 TYR K 178 ARG 0.004 0.000 ARG K 234 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 260 time to evaluate : 1.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 238 MET cc_start: 0.8249 (OUTLIER) cc_final: 0.7822 (mtt) REVERT: K 275 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.7992 (mm) REVERT: K 338 LEU cc_start: 0.7492 (OUTLIER) cc_final: 0.7059 (pp) REVERT: K 362 GLN cc_start: 0.6027 (OUTLIER) cc_final: 0.5527 (tp40) REVERT: K 382 LEU cc_start: 0.8227 (mt) cc_final: 0.7859 (tp) REVERT: K 383 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7602 (mp) REVERT: L 196 LYS cc_start: 0.8027 (mttp) cc_final: 0.7439 (mtpp) REVERT: L 199 GLU cc_start: 0.7689 (tm-30) cc_final: 0.7247 (tm-30) REVERT: L 321 LYS cc_start: 0.8325 (mmtp) cc_final: 0.8111 (mmtt) REVERT: L 323 ARG cc_start: 0.8300 (mpt-90) cc_final: 0.7789 (mtm-85) REVERT: L 378 MET cc_start: 0.7513 (mtp) cc_final: 0.7294 (mtt) REVERT: Q 101 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8467 (mp) REVERT: Q 378 MET cc_start: 0.8207 (mtm) cc_final: 0.7473 (tmm) REVERT: Q 404 LYS cc_start: 0.8739 (tmtm) cc_final: 0.8061 (tmtt) REVERT: P 83 TYR cc_start: 0.5433 (OUTLIER) cc_final: 0.5155 (t80) REVERT: C 435 MET cc_start: 0.5400 (OUTLIER) cc_final: 0.4814 (mtt) REVERT: C 442 ILE cc_start: 0.6422 (mt) cc_final: 0.6173 (mt) REVERT: C 473 GLU cc_start: 0.6584 (OUTLIER) cc_final: 0.6177 (tm-30) REVERT: E 605 ILE cc_start: 0.7016 (OUTLIER) cc_final: 0.6565 (mp) REVERT: E 624 ILE cc_start: 0.6900 (mt) cc_final: 0.6501 (tp) REVERT: E 679 PHE cc_start: 0.3362 (t80) cc_final: 0.2994 (t80) outliers start: 53 outliers final: 34 residues processed: 294 average time/residue: 1.0685 time to fit residues: 361.0456 Evaluate side-chains 307 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 263 time to evaluate : 1.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 11 ARG Chi-restraints excluded: chain K residue 60 LEU Chi-restraints excluded: chain K residue 238 MET Chi-restraints excluded: chain K residue 275 LEU Chi-restraints excluded: chain K residue 293 LEU Chi-restraints excluded: chain K residue 305 SER Chi-restraints excluded: chain K residue 338 LEU Chi-restraints excluded: chain K residue 362 GLN Chi-restraints excluded: chain K residue 383 LEU Chi-restraints excluded: chain L residue 102 GLN Chi-restraints excluded: chain L residue 149 ILE Chi-restraints excluded: chain L residue 203 SER Chi-restraints excluded: chain L residue 229 ILE Chi-restraints excluded: chain L residue 259 SER Chi-restraints excluded: chain L residue 356 THR Chi-restraints excluded: chain Q residue 100 ILE Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain Q residue 156 GLU Chi-restraints excluded: chain Q residue 277 LEU Chi-restraints excluded: chain Q residue 367 SER Chi-restraints excluded: chain P residue 83 TYR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain D residue 100 MET Chi-restraints excluded: chain C residue 435 MET Chi-restraints excluded: chain C residue 473 GLU Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 602 ARG Chi-restraints excluded: chain C residue 664 MET Chi-restraints excluded: chain C residue 704 LEU Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 864 ILE Chi-restraints excluded: chain C residue 881 VAL Chi-restraints excluded: chain C residue 887 ASP Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 418 SER Chi-restraints excluded: chain E residue 528 ILE Chi-restraints excluded: chain E residue 605 ILE Chi-restraints excluded: chain E residue 615 LEU Chi-restraints excluded: chain E residue 732 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 9.9990 chunk 132 optimal weight: 7.9990 chunk 102 optimal weight: 0.9990 chunk 150 optimal weight: 2.9990 chunk 227 optimal weight: 8.9990 chunk 209 optimal weight: 0.9990 chunk 180 optimal weight: 20.0000 chunk 18 optimal weight: 0.6980 chunk 139 optimal weight: 6.9990 chunk 110 optimal weight: 0.9990 chunk 143 optimal weight: 8.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 331 HIS Q 102 GLN Q 331 HIS ** C 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 18364 Z= 0.198 Angle : 0.561 12.566 24960 Z= 0.281 Chirality : 0.040 0.267 2982 Planarity : 0.004 0.051 3032 Dihedral : 5.441 53.921 2661 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.30 % Allowed : 17.49 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % 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 (0.18), residues: 2276 helix: 1.76 (0.13), residues: 1588 sheet: None (None), residues: 0 loop : -0.04 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP K 16 HIS 0.004 0.001 HIS K 329 PHE 0.022 0.001 PHE Q 294 TYR 0.022 0.001 TYR K 178 ARG 0.010 0.000 ARG E 646 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 262 time to evaluate : 1.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 238 MET cc_start: 0.8206 (OUTLIER) cc_final: 0.7769 (mtt) REVERT: K 275 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.7907 (mm) REVERT: K 338 LEU cc_start: 0.7408 (OUTLIER) cc_final: 0.6972 (pp) REVERT: K 362 GLN cc_start: 0.5983 (OUTLIER) cc_final: 0.5469 (tp40) REVERT: K 382 LEU cc_start: 0.8130 (mt) cc_final: 0.7816 (tp) REVERT: K 383 LEU cc_start: 0.7888 (OUTLIER) cc_final: 0.7608 (mp) REVERT: L 196 LYS cc_start: 0.8025 (mttp) cc_final: 0.7485 (mtpp) REVERT: L 199 GLU cc_start: 0.7657 (tm-30) cc_final: 0.7216 (tm-30) REVERT: L 312 LYS cc_start: 0.8443 (tptt) cc_final: 0.7964 (tmtt) REVERT: L 323 ARG cc_start: 0.8277 (mpt-90) cc_final: 0.7765 (mtm-85) REVERT: L 378 MET cc_start: 0.7477 (mtp) cc_final: 0.7256 (mtt) REVERT: Q 378 MET cc_start: 0.8173 (mtm) cc_final: 0.7445 (tmm) REVERT: Q 404 LYS cc_start: 0.8709 (tmtm) cc_final: 0.8008 (tmtt) REVERT: P 83 TYR cc_start: 0.5400 (OUTLIER) cc_final: 0.5127 (t80) REVERT: C 442 ILE cc_start: 0.6254 (mt) cc_final: 0.6004 (mt) REVERT: C 473 GLU cc_start: 0.6529 (OUTLIER) cc_final: 0.6216 (tm-30) REVERT: C 589 ARG cc_start: 0.6231 (ttt-90) cc_final: 0.5972 (ttt180) REVERT: C 741 MET cc_start: 0.3837 (mmm) cc_final: 0.3480 (mmt) REVERT: E 605 ILE cc_start: 0.6941 (OUTLIER) cc_final: 0.6445 (mp) REVERT: E 785 LEU cc_start: 0.4871 (mp) cc_final: 0.4655 (mt) outliers start: 43 outliers final: 30 residues processed: 289 average time/residue: 1.0898 time to fit residues: 361.3080 Evaluate side-chains 294 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 256 time to evaluate : 2.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 11 ARG Chi-restraints excluded: chain K residue 238 MET Chi-restraints excluded: chain K residue 275 LEU Chi-restraints excluded: chain K residue 293 LEU Chi-restraints excluded: chain K residue 305 SER Chi-restraints excluded: chain K residue 338 LEU Chi-restraints excluded: chain K residue 362 GLN Chi-restraints excluded: chain K residue 383 LEU Chi-restraints excluded: chain L residue 102 GLN Chi-restraints excluded: chain L residue 203 SER Chi-restraints excluded: chain L residue 259 SER Chi-restraints excluded: chain L residue 356 THR Chi-restraints excluded: chain Q residue 156 GLU Chi-restraints excluded: chain Q residue 277 LEU Chi-restraints excluded: chain Q residue 367 SER Chi-restraints excluded: chain P residue 83 TYR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain D residue 100 MET Chi-restraints excluded: chain C residue 473 GLU Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 544 PHE Chi-restraints excluded: chain C residue 586 MET Chi-restraints excluded: chain C residue 602 ARG Chi-restraints excluded: chain C residue 664 MET Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 704 LEU Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 864 ILE Chi-restraints excluded: chain C residue 881 VAL Chi-restraints excluded: chain C residue 887 ASP Chi-restraints excluded: chain E residue 528 ILE Chi-restraints excluded: chain E residue 605 ILE Chi-restraints excluded: chain E residue 615 LEU Chi-restraints excluded: chain E residue 732 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 8.9990 chunk 55 optimal weight: 2.9990 chunk 166 optimal weight: 10.0000 chunk 26 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 181 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 186 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 159 optimal weight: 20.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 331 HIS Q 102 GLN Q 114 ASN Q 331 HIS D 82 GLN ** C 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.222535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.132594 restraints weight = 32315.490| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.83 r_work: 0.3213 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3085 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3085 r_free = 0.3085 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3085 r_free = 0.3085 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3085 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 18364 Z= 0.385 Angle : 0.635 11.987 24960 Z= 0.322 Chirality : 0.044 0.190 2982 Planarity : 0.005 0.057 3032 Dihedral : 5.587 55.231 2661 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.62 % Allowed : 17.43 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % 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 (0.17), residues: 2276 helix: 1.54 (0.13), residues: 1573 sheet: None (None), residues: 0 loop : -0.21 (0.23), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 831 HIS 0.006 0.001 HIS Q 154 PHE 0.021 0.002 PHE Q 217 TYR 0.028 0.002 TYR K 178 ARG 0.006 0.000 ARG E 646 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7891.53 seconds wall clock time: 141 minutes 42.16 seconds (8502.16 seconds total)