Starting phenix.real_space_refine (version: dev) on Wed Feb 22 17:48:10 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8crt_26958/02_2023/8crt_26958_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8crt_26958/02_2023/8crt_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_2023/8crt_26958.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8crt_26958/02_2023/8crt_26958.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8crt_26958/02_2023/8crt_26958_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8crt_26958/02_2023/8crt_26958_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 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 "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-4877/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 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 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: 11.77, per 1000 atoms: 0.66 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: 8.03 Conformation dependent library (CDL) restraints added in 3.2 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: 1.95 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: 5.82 Time building geometry restraints manager: 8.47 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 - 20.48: 10217 20.48 - 40.96: 355 40.96 - 61.44: 67 61.44 - 81.92: 9 81.92 - 102.40: 9 Dihedral angle restraints: 10657 sinusoidal: 4066 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 50.00 -52.40 102.40 1 2.00e+01 2.50e-03 2.92e+01 dihedral pdb=" C2 NAG F 2 " pdb=" C3 NAG F 2 " pdb=" C4 NAG F 2 " pdb=" C5 NAG F 2 " ideal model delta sinusoidal sigma weight residual 50.00 -51.95 101.95 1 2.00e+01 2.50e-03 2.90e+01 dihedral pdb=" C1 NAG F 2 " pdb=" C2 NAG F 2 " pdb=" C3 NAG F 2 " pdb=" C4 NAG F 2 " ideal model delta sinusoidal sigma weight residual -50.00 40.91 -90.91 1 2.00e+01 2.50e-03 2.44e+01 ... (remaining 10654 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1962 0.034 - 0.068: 742 0.068 - 0.102: 190 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 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. 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: 4.620 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: 0.010 Extract box with map and model: 20.880 Check model and map are aligned: 0.300 Process input model: 51.910 Find NCS groups from input model: 1.080 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Set scattering table: 0.190 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 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= 0.207 Angle : 0.577 8.279 24960 Z= 0.352 Chirality : 0.041 0.170 2982 Planarity : 0.005 0.060 3032 Dihedral : 11.637 102.396 6427 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.45 % Favored : 98.50 % Rotamer Outliers : 2.36 % 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 *********************** 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 : 2.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 6 residues processed: 368 average time/residue: 1.0568 time to fit residues: 447.9028 Evaluate side-chains 297 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 291 time to evaluate : 2.035 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 5 residues processed: 1 average time/residue: 0.1692 time to fit residues: 3.2371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7361 moved from start: 0.1401 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= 0.365 Angle : 0.587 8.216 24960 Z= 0.305 Chirality : 0.043 0.157 2982 Planarity : 0.005 0.079 3032 Dihedral : 6.394 102.755 2483 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.59 % Favored : 98.37 % Rotamer Outliers : 3.51 % 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: 1.75 (0.17), residues: 2276 helix: 1.68 (0.13), residues: 1597 sheet: None (None), residues: 0 loop : 0.04 (0.23), residues: 679 *********************** 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 354 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 288 time to evaluate : 2.027 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 66 outliers final: 25 residues processed: 315 average time/residue: 1.0302 time to fit residues: 376.6753 Evaluate side-chains 297 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 272 time to evaluate : 1.880 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 15 residues processed: 10 average time/residue: 0.6422 time to fit residues: 10.5815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 115 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 172 optimal weight: 3.9990 chunk 140 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 chunk 207 optimal weight: 20.0000 chunk 224 optimal weight: 5.9990 chunk 184 optimal weight: 10.0000 chunk 205 optimal weight: 7.9990 chunk 70 optimal weight: 0.9980 chunk 166 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 ** 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 18364 Z= 0.176 Angle : 0.508 7.095 24960 Z= 0.261 Chirality : 0.040 0.252 2982 Planarity : 0.004 0.049 3032 Dihedral : 6.252 102.821 2483 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer Outliers : 3.14 % 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: 2.06 (0.17), residues: 2276 helix: 1.94 (0.13), residues: 1597 sheet: None (None), residues: 0 loop : 0.06 (0.23), residues: 679 *********************** 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 343 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 284 time to evaluate : 2.133 Fit side-chains revert: symmetry clash outliers start: 59 outliers final: 27 residues processed: 311 average time/residue: 1.0208 time to fit residues: 369.0484 Evaluate side-chains 292 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 265 time to evaluate : 2.045 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 19 residues processed: 9 average time/residue: 0.5852 time to fit residues: 9.2017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 204 optimal weight: 5.9990 chunk 155 optimal weight: 40.0000 chunk 107 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 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: 0.9990 chunk 59 optimal weight: 0.8980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 102 GLN ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.1702 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= 0.194 Angle : 0.505 8.236 24960 Z= 0.259 Chirality : 0.040 0.134 2982 Planarity : 0.004 0.048 3032 Dihedral : 6.200 102.808 2483 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer Outliers : 3.09 % 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: 2.20 (0.17), residues: 2276 helix: 2.02 (0.13), residues: 1598 sheet: None (None), residues: 0 loop : 0.21 (0.23), residues: 678 *********************** 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 334 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 276 time to evaluate : 2.162 Fit side-chains revert: symmetry clash outliers start: 58 outliers final: 33 residues processed: 304 average time/residue: 1.0274 time to fit residues: 361.8612 Evaluate side-chains 298 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 265 time to evaluate : 2.029 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 22 residues processed: 12 average time/residue: 0.2953 time to fit residues: 8.0461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 chunk 3 optimal weight: 7.9990 chunk 164 optimal weight: 0.9990 chunk 90 optimal weight: 5.9990 chunk 188 optimal weight: 0.0770 chunk 152 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 112 optimal weight: 0.9980 chunk 197 optimal weight: 2.9990 chunk 55 optimal weight: 0.0020 overall best weight: 0.5548 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 102 GLN ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 18364 Z= 0.137 Angle : 0.480 9.130 24960 Z= 0.245 Chirality : 0.038 0.136 2982 Planarity : 0.004 0.048 3032 Dihedral : 6.084 102.819 2483 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer Outliers : 2.98 % 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: 2.43 (0.18), residues: 2276 helix: 2.19 (0.13), residues: 1593 sheet: None (None), residues: 0 loop : 0.30 (0.24), residues: 683 *********************** 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 336 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 280 time to evaluate : 1.838 Fit side-chains revert: symmetry clash outliers start: 56 outliers final: 30 residues processed: 315 average time/residue: 1.0573 time to fit residues: 386.7257 Evaluate side-chains 303 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 273 time to evaluate : 2.030 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 22 residues processed: 9 average time/residue: 0.3348 time to fit residues: 7.1992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 74 optimal weight: 1.9990 chunk 198 optimal weight: 6.9990 chunk 43 optimal weight: 4.9990 chunk 129 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 220 optimal weight: 0.0020 chunk 183 optimal weight: 10.0000 chunk 102 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 72 optimal weight: 6.9990 chunk 115 optimal weight: 7.9990 overall best weight: 2.9996 ------------------------------------------------------------------------------- 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 ** 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: 0.7365 moved from start: 0.2042 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= 0.328 Angle : 0.576 9.865 24960 Z= 0.296 Chirality : 0.042 0.146 2982 Planarity : 0.005 0.049 3032 Dihedral : 6.286 102.808 2483 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer Outliers : 3.25 % 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: 1.98 (0.17), residues: 2276 helix: 1.85 (0.13), residues: 1593 sheet: None (None), residues: 0 loop : 0.12 (0.24), residues: 683 *********************** 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 337 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 276 time to evaluate : 2.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 61 outliers final: 35 residues processed: 313 average time/residue: 1.0088 time to fit residues: 366.4449 Evaluate side-chains 309 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 274 time to evaluate : 2.057 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 24 residues processed: 12 average time/residue: 0.3084 time to fit residues: 8.5548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 212 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 125 optimal weight: 5.9990 chunk 161 optimal weight: 10.0000 chunk 124 optimal weight: 10.0000 chunk 185 optimal weight: 5.9990 chunk 123 optimal weight: 9.9990 chunk 219 optimal weight: 6.9990 chunk 137 optimal weight: 30.0000 chunk 133 optimal weight: 6.9990 chunk 101 optimal weight: 1.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 331 HIS Q 58 HIS Q 102 GLN Q 395 ASN C 447 GLN ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.079 18364 Z= 0.517 Angle : 0.691 9.823 24960 Z= 0.354 Chirality : 0.047 0.192 2982 Planarity : 0.005 0.051 3032 Dihedral : 6.623 102.952 2483 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer Outliers : 3.46 % 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: 1.20 (0.17), residues: 2276 helix: 1.30 (0.13), residues: 1575 sheet: None (None), residues: 0 loop : -0.23 (0.22), residues: 701 *********************** 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 354 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 289 time to evaluate : 2.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 65 outliers final: 38 residues processed: 324 average time/residue: 0.9964 time to fit residues: 374.9299 Evaluate side-chains 308 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 270 time to evaluate : 1.814 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 23 residues processed: 15 average time/residue: 0.4788 time to fit residues: 12.3897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 135 optimal weight: 3.9990 chunk 87 optimal weight: 0.1980 chunk 131 optimal weight: 7.9990 chunk 66 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 chunk 149 optimal weight: 0.0060 chunk 108 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 172 optimal weight: 0.8980 overall best weight: 0.5596 ------------------------------------------------------------------------------- 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 ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 18364 Z= 0.156 Angle : 0.535 12.273 24960 Z= 0.270 Chirality : 0.039 0.177 2982 Planarity : 0.004 0.050 3032 Dihedral : 6.264 102.821 2483 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer Outliers : 2.09 % 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: 1.89 (0.17), residues: 2276 helix: 1.80 (0.13), residues: 1592 sheet: None (None), residues: 0 loop : 0.04 (0.24), residues: 684 *********************** 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 315 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 276 time to evaluate : 1.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 24 residues processed: 298 average time/residue: 1.0678 time to fit residues: 367.9588 Evaluate side-chains 292 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 268 time to evaluate : 2.003 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 17 residues processed: 8 average time/residue: 0.4842 time to fit residues: 7.9138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 199 optimal weight: 5.9990 chunk 210 optimal weight: 5.9990 chunk 192 optimal weight: 9.9990 chunk 204 optimal weight: 0.5980 chunk 123 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 160 optimal weight: 8.9990 chunk 62 optimal weight: 3.9990 chunk 185 optimal weight: 2.9990 chunk 193 optimal weight: 5.9990 chunk 134 optimal weight: 9.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- 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 ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.2496 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= 0.365 Angle : 0.612 9.550 24960 Z= 0.312 Chirality : 0.044 0.275 2982 Planarity : 0.005 0.051 3032 Dihedral : 6.366 102.835 2483 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer Outliers : 2.36 % 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: 1.64 (0.17), residues: 2276 helix: 1.65 (0.13), residues: 1577 sheet: None (None), residues: 0 loop : -0.10 (0.23), residues: 699 *********************** 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 315 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 271 time to evaluate : 1.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 25 residues processed: 297 average time/residue: 1.0693 time to fit residues: 366.8035 Evaluate side-chains 291 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 266 time to evaluate : 2.147 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 19 residues processed: 7 average time/residue: 0.2532 time to fit residues: 5.7673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 6.9990 chunk 132 optimal weight: 3.9990 chunk 102 optimal weight: 0.6980 chunk 150 optimal weight: 5.9990 chunk 227 optimal weight: 0.0770 chunk 209 optimal weight: 0.0970 chunk 180 optimal weight: 20.0000 chunk 18 optimal weight: 1.9990 chunk 139 optimal weight: 4.9990 chunk 110 optimal weight: 0.8980 chunk 143 optimal weight: 9.9990 overall best weight: 0.7538 ------------------------------------------------------------------------------- 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 ** 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: 0.7306 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.073 18364 Z= 0.171 Angle : 0.539 10.202 24960 Z= 0.270 Chirality : 0.039 0.183 2982 Planarity : 0.004 0.050 3032 Dihedral : 6.186 102.800 2483 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer Outliers : 1.47 % 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: 1.89 (0.13), residues: 1586 sheet: None (None), residues: 0 loop : 0.04 (0.23), residues: 690 ********************** 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 310 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 283 time to evaluate : 2.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 19 residues processed: 304 average time/residue: 1.0841 time to fit residues: 382.9609 Evaluate side-chains 293 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 274 time to evaluate : 2.160 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 17 residues processed: 3 average time/residue: 0.2921 time to fit residues: 4.3874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 166 optimal weight: 9.9990 chunk 26 optimal weight: 0.0170 chunk 50 optimal weight: 0.9980 chunk 181 optimal weight: 5.9990 chunk 75 optimal weight: 0.6980 chunk 186 optimal weight: 6.9990 chunk 22 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 159 optimal weight: 9.9990 overall best weight: 1.0820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 102 GLN Q 114 ASN C 447 GLN ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 630 GLN E 804 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.224865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.134330 restraints weight = 32807.128| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 1.89 r_work: 0.3276 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4330 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4330 r_free = 0.4330 target_work(ls_wunit_k1) = 0.225 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4330 r_free = 0.4330 target_work(ls_wunit_k1) = 0.225 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4330 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 18364 Z= 0.184 Angle : 0.545 10.295 24960 Z= 0.274 Chirality : 0.040 0.168 2982 Planarity : 0.004 0.048 3032 Dihedral : 6.114 102.827 2483 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer Outliers : 1.47 % 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: 2.02 (0.17), residues: 2276 helix: 1.95 (0.13), residues: 1589 sheet: None (None), residues: 0 loop : -0.02 (0.23), residues: 687 =============================================================================== Job complete usr+sys time: 7471.99 seconds wall clock time: 132 minutes 54.07 seconds (7974.07 seconds total)