Starting phenix.real_space_refine (version: 1.21rc1) on Sun Jul 9 12:02:17 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6njo_9390/07_2023/6njo_9390_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6njo_9390/07_2023/6njo_9390.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6njo_9390/07_2023/6njo_9390.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6njo_9390/07_2023/6njo_9390.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6njo_9390/07_2023/6njo_9390_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6njo_9390/07_2023/6njo_9390_updated.pdb" } resolution = 3.34 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= 0.001 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Al 4 5.89 5 P 8 5.49 5 Mg 4 5.21 5 S 78 5.16 5 C 12092 2.51 5 N 3282 2.21 5 O 3610 1.98 5 F 12 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 66": "NH1" <-> "NH2" Residue "A PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 113": "NH1" <-> "NH2" Residue "A ARG 147": "NH1" <-> "NH2" Residue "A ARG 172": "NH1" <-> "NH2" Residue "A ARG 209": "NH1" <-> "NH2" Residue "A ARG 366": "NH1" <-> "NH2" Residue "A ARG 378": "NH1" <-> "NH2" Residue "A ARG 398": "NH1" <-> "NH2" Residue "B TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 113": "NH1" <-> "NH2" Residue "B ARG 147": "NH1" <-> "NH2" Residue "B ARG 207": "NH1" <-> "NH2" Residue "B ARG 366": "NH1" <-> "NH2" Residue "B ARG 378": "NH1" <-> "NH2" Residue "C ARG 49": "NH1" <-> "NH2" Residue "C ARG 54": "NH1" <-> "NH2" Residue "C TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 66": "NH1" <-> "NH2" Residue "C ARG 147": "NH1" <-> "NH2" Residue "C ARG 288": "NH1" <-> "NH2" Residue "C ARG 305": "NH1" <-> "NH2" Residue "C ARG 366": "NH1" <-> "NH2" Residue "C ARG 378": "NH1" <-> "NH2" Residue "D TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 120": "NH1" <-> "NH2" Residue "D ARG 147": "NH1" <-> "NH2" Residue "D ARG 159": "NH1" <-> "NH2" Residue "D PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 207": "NH1" <-> "NH2" Residue "D ARG 235": "NH1" <-> "NH2" Residue "D ARG 288": "NH1" <-> "NH2" Residue "D ARG 378": "NH1" <-> "NH2" Residue "D ARG 398": "NH1" <-> "NH2" Residue "E TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 113": "NH1" <-> "NH2" Residue "E ARG 120": "NH1" <-> "NH2" Residue "E ARG 135": "NH1" <-> "NH2" Residue "E ARG 147": "NH1" <-> "NH2" Residue "E ARG 209": "NH1" <-> "NH2" Residue "E ARG 255": "NH1" <-> "NH2" Residue "E ARG 270": "NH1" <-> "NH2" Residue "E ARG 288": "NH1" <-> "NH2" Residue "E ARG 305": "NH1" <-> "NH2" Residue "E ARG 336": "NH1" <-> "NH2" Residue "E ARG 378": "NH1" <-> "NH2" Residue "F ARG 54": "NH1" <-> "NH2" Residue "F TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 105": "NH1" <-> "NH2" Residue "F ARG 147": "NH1" <-> "NH2" Residue "F ARG 172": "NH1" <-> "NH2" Residue "F ARG 207": "NH1" <-> "NH2" Residue "F ARG 209": "NH1" <-> "NH2" Residue "F ARG 255": "NH1" <-> "NH2" Residue "F ARG 347": "NH1" <-> "NH2" Residue "F ARG 378": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 19090 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3164 Classifications: {'peptide': 412} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 390} Chain: "B" Number of atoms: 3164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3164 Classifications: {'peptide': 412} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 390} Chain: "C" Number of atoms: 3164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3164 Classifications: {'peptide': 412} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 390} Chain: "D" Number of atoms: 3176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3176 Classifications: {'peptide': 413} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 391} Chain: "E" Number of atoms: 3164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3164 Classifications: {'peptide': 412} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 390} Chain: "F" Number of atoms: 3110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3110 Classifications: {'peptide': 405} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 383} Chain breaks: 1 Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "E" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Residues with excluded nonbonded symmetry interactions: 24 residue: pdb=" N GLU A 140 " occ=0.50 ... (7 atoms not shown) pdb=" OE2 GLU A 140 " occ=0.50 residue: pdb=" N PRO A 141 " occ=0.75 ... (5 atoms not shown) pdb=" CD PRO A 141 " occ=0.75 residue: pdb=" N PRO A 142 " occ=0.50 ... (5 atoms not shown) pdb=" CD PRO A 142 " occ=0.50 residue: pdb=" N GLN A 148 " occ=0.75 ... (7 atoms not shown) pdb=" NE2 GLN A 148 " occ=0.75 residue: pdb=" N GLU B 140 " occ=0.50 ... (7 atoms not shown) pdb=" OE2 GLU B 140 " occ=0.50 residue: pdb=" N PRO B 141 " occ=0.75 ... (5 atoms not shown) pdb=" CD PRO B 141 " occ=0.75 residue: pdb=" N PRO B 142 " occ=0.50 ... (5 atoms not shown) pdb=" CD PRO B 142 " occ=0.50 residue: pdb=" N GLN B 148 " occ=0.75 ... (7 atoms not shown) pdb=" NE2 GLN B 148 " occ=0.75 residue: pdb=" N GLU C 140 " occ=0.50 ... (7 atoms not shown) pdb=" OE2 GLU C 140 " occ=0.50 residue: pdb=" N PRO C 141 " occ=0.75 ... (5 atoms not shown) pdb=" CD PRO C 141 " occ=0.75 residue: pdb=" N PRO C 142 " occ=0.50 ... (5 atoms not shown) pdb=" CD PRO C 142 " occ=0.50 residue: pdb=" N GLN C 148 " occ=0.75 ... (7 atoms not shown) pdb=" NE2 GLN C 148 " occ=0.75 ... (remaining 12 not shown) Time building chain proxies: 9.33, per 1000 atoms: 0.49 Number of scatterers: 19090 At special positions: 0 Unit cell: (106.08, 118.32, 122.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 78 16.00 P 8 15.00 Al 4 13.00 Mg 4 11.99 F 12 9.00 O 3610 8.00 N 3282 7.00 C 12092 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.39 Conformation dependent library (CDL) restraints added in 2.9 seconds 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4512 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 88 helices and 18 sheets defined 33.5% alpha, 14.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.04 Creating SS restraints... Processing helix chain 'A' and resid 159 through 163 Processing helix chain 'A' and resid 183 through 193 Processing helix chain 'A' and resid 208 through 215 Processing helix chain 'A' and resid 220 through 223 No H-bonds generated for 'chain 'A' and resid 220 through 223' Processing helix chain 'A' and resid 237 through 256 removed outlier: 4.371A pdb=" N ALA A 244 " --> pdb=" O ARG A 240 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N PHE A 245 " --> pdb=" O MET A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 282 Processing helix chain 'A' and resid 293 through 303 Proline residue: A 300 - end of helix Processing helix chain 'A' and resid 330 through 338 Processing helix chain 'A' and resid 348 through 351 No H-bonds generated for 'chain 'A' and resid 348 through 351' Processing helix chain 'A' and resid 374 through 397 removed outlier: 3.862A pdb=" N CYS A 383 " --> pdb=" O ALA A 379 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS A 384 " --> pdb=" O ALA A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 415 Processing helix chain 'A' and resid 417 through 424 Processing helix chain 'A' and resid 434 through 444 Processing helix chain 'B' and resid 108 through 110 No H-bonds generated for 'chain 'B' and resid 108 through 110' Processing helix chain 'B' and resid 159 through 163 Processing helix chain 'B' and resid 183 through 193 Processing helix chain 'B' and resid 208 through 216 removed outlier: 3.551A pdb=" N VAL B 211 " --> pdb=" O GLY B 208 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASN B 212 " --> pdb=" O ARG B 209 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE B 214 " --> pdb=" O VAL B 211 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA B 216 " --> pdb=" O GLU B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 225 removed outlier: 5.035A pdb=" N LYS B 225 " --> pdb=" O SER B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 256 removed outlier: 5.175A pdb=" N ALA B 244 " --> pdb=" O ARG B 240 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N PHE B 245 " --> pdb=" O MET B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 281 Processing helix chain 'B' and resid 293 through 304 Proline residue: B 300 - end of helix Processing helix chain 'B' and resid 330 through 336 Processing helix chain 'B' and resid 347 through 350 No H-bonds generated for 'chain 'B' and resid 347 through 350' Processing helix chain 'B' and resid 368 through 371 No H-bonds generated for 'chain 'B' and resid 368 through 371' Processing helix chain 'B' and resid 374 through 391 Processing helix chain 'B' and resid 394 through 398 removed outlier: 3.742A pdb=" N ARG B 398 " --> pdb=" O LEU B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 422 removed outlier: 5.186A pdb=" N LYS B 418 " --> pdb=" O ILE B 414 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N LEU B 419 " --> pdb=" O LYS B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 445 Processing helix chain 'C' and resid 108 through 110 No H-bonds generated for 'chain 'C' and resid 108 through 110' Processing helix chain 'C' and resid 144 through 146 No H-bonds generated for 'chain 'C' and resid 144 through 146' Processing helix chain 'C' and resid 160 through 163 No H-bonds generated for 'chain 'C' and resid 160 through 163' Processing helix chain 'C' and resid 183 through 189 Processing helix chain 'C' and resid 208 through 213 removed outlier: 3.567A pdb=" N VAL C 211 " --> pdb=" O GLY C 208 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASN C 212 " --> pdb=" O ARG C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 225 removed outlier: 5.179A pdb=" N LYS C 225 " --> pdb=" O SER C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 241 Processing helix chain 'C' and resid 244 through 256 Processing helix chain 'C' and resid 268 through 281 Processing helix chain 'C' and resid 293 through 296 No H-bonds generated for 'chain 'C' and resid 293 through 296' Processing helix chain 'C' and resid 300 through 305 removed outlier: 5.546A pdb=" N ARG C 305 " --> pdb=" O LYS C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 336 Processing helix chain 'C' and resid 347 through 351 Processing helix chain 'C' and resid 368 through 371 No H-bonds generated for 'chain 'C' and resid 368 through 371' Processing helix chain 'C' and resid 374 through 399 removed outlier: 5.826A pdb=" N LEU C 395 " --> pdb=" O LYS C 391 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N LEU C 396 " --> pdb=" O ASN C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 424 removed outlier: 5.127A pdb=" N LYS C 418 " --> pdb=" O ILE C 414 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N LEU C 419 " --> pdb=" O LYS C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 434 through 445 Processing helix chain 'D' and resid 108 through 110 No H-bonds generated for 'chain 'D' and resid 108 through 110' Processing helix chain 'D' and resid 159 through 163 Processing helix chain 'D' and resid 183 through 193 Processing helix chain 'D' and resid 208 through 217 removed outlier: 3.520A pdb=" N VAL D 211 " --> pdb=" O GLY D 208 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASN D 212 " --> pdb=" O ARG D 209 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N PHE D 214 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU D 217 " --> pdb=" O PHE D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 225 removed outlier: 3.801A pdb=" N LYS D 225 " --> pdb=" O SER D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 256 removed outlier: 5.463A pdb=" N ALA D 244 " --> pdb=" O ARG D 240 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N PHE D 245 " --> pdb=" O MET D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 281 Processing helix chain 'D' and resid 293 through 298 Processing helix chain 'D' and resid 300 through 305 removed outlier: 5.233A pdb=" N ARG D 305 " --> pdb=" O LYS D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 338 Processing helix chain 'D' and resid 347 through 350 No H-bonds generated for 'chain 'D' and resid 347 through 350' Processing helix chain 'D' and resid 374 through 398 removed outlier: 4.768A pdb=" N LEU D 395 " --> pdb=" O LYS D 391 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N LEU D 396 " --> pdb=" O ASN D 392 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE D 397 " --> pdb=" O VAL D 393 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 415 Processing helix chain 'D' and resid 417 through 424 removed outlier: 3.861A pdb=" N ASN D 422 " --> pdb=" O LYS D 418 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N PHE D 423 " --> pdb=" O LEU D 419 " (cutoff:3.500A) Processing helix chain 'D' and resid 434 through 445 removed outlier: 3.505A pdb=" N ILE D 438 " --> pdb=" O TYR D 434 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 163 No H-bonds generated for 'chain 'E' and resid 160 through 163' Processing helix chain 'E' and resid 183 through 192 Processing helix chain 'E' and resid 208 through 215 removed outlier: 3.855A pdb=" N VAL E 211 " --> pdb=" O GLY E 208 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ASN E 212 " --> pdb=" O ARG E 209 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU E 215 " --> pdb=" O ASN E 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 223 No H-bonds generated for 'chain 'E' and resid 220 through 223' Processing helix chain 'E' and resid 237 through 256 removed outlier: 5.259A pdb=" N ALA E 244 " --> pdb=" O ARG E 240 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N PHE E 245 " --> pdb=" O MET E 241 " (cutoff:3.500A) Processing helix chain 'E' and resid 268 through 282 removed outlier: 3.687A pdb=" N ALA E 281 " --> pdb=" O ASP E 277 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N SER E 282 " --> pdb=" O VAL E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 293 through 302 Proline residue: E 300 - end of helix Processing helix chain 'E' and resid 333 through 337 Processing helix chain 'E' and resid 347 through 350 No H-bonds generated for 'chain 'E' and resid 347 through 350' Processing helix chain 'E' and resid 374 through 398 removed outlier: 3.955A pdb=" N ASN E 392 " --> pdb=" O ALA E 388 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU E 394 " --> pdb=" O TYR E 390 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LEU E 395 " --> pdb=" O LYS E 391 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N LEU E 396 " --> pdb=" O ASN E 392 " (cutoff:3.500A) Processing helix chain 'E' and resid 408 through 415 removed outlier: 3.848A pdb=" N LYS E 415 " --> pdb=" O ASP E 411 " (cutoff:3.500A) Processing helix chain 'E' and resid 417 through 424 Processing helix chain 'E' and resid 434 through 445 Processing helix chain 'F' and resid 108 through 110 No H-bonds generated for 'chain 'F' and resid 108 through 110' Processing helix chain 'F' and resid 144 through 146 No H-bonds generated for 'chain 'F' and resid 144 through 146' Processing helix chain 'F' and resid 159 through 164 Processing helix chain 'F' and resid 183 through 191 Processing helix chain 'F' and resid 210 through 215 Processing helix chain 'F' and resid 220 through 223 No H-bonds generated for 'chain 'F' and resid 220 through 223' Processing helix chain 'F' and resid 237 through 256 removed outlier: 5.292A pdb=" N ALA F 244 " --> pdb=" O ARG F 240 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N PHE F 245 " --> pdb=" O MET F 241 " (cutoff:3.500A) Processing helix chain 'F' and resid 268 through 282 Processing helix chain 'F' and resid 293 through 303 Proline residue: F 300 - end of helix Processing helix chain 'F' and resid 332 through 336 Processing helix chain 'F' and resid 374 through 387 Processing helix chain 'F' and resid 391 through 398 removed outlier: 4.186A pdb=" N LEU F 395 " --> pdb=" O LYS F 391 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N LEU F 396 " --> pdb=" O ASN F 392 " (cutoff:3.500A) Processing helix chain 'F' and resid 411 through 415 Processing helix chain 'F' and resid 418 through 423 Processing helix chain 'F' and resid 434 through 444 removed outlier: 3.554A pdb=" N ILE F 438 " --> pdb=" O TYR F 434 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU F 439 " --> pdb=" O GLU F 435 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 38 through 41 removed outlier: 6.791A pdb=" N LYS A 47 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N ILE A 41 " --> pdb=" O ILE A 45 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ILE A 45 " --> pdb=" O ILE A 41 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ALA A 72 " --> pdb=" O PHE A 79 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N LEU A 81 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N VAL A 70 " --> pdb=" O LEU A 81 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 103 through 106 Processing sheet with id= C, first strand: chain 'A' and resid 113 through 115 removed outlier: 4.096A pdb=" N ARG A 113 " --> pdb=" O CYS A 226 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ILE A 199 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N VAL A 229 " --> pdb=" O ILE A 199 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LEU A 201 " --> pdb=" O VAL A 229 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE A 198 " --> pdb=" O ASN A 260 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N SER A 313 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N LEU A 263 " --> pdb=" O SER A 313 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N THR A 315 " --> pdb=" O LEU A 263 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N MET A 265 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ILE A 317 " --> pdb=" O MET A 265 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 37 through 41 removed outlier: 3.770A pdb=" N LYS B 37 " --> pdb=" O ARG B 49 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LYS B 47 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N ILE B 41 " --> pdb=" O ILE B 45 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ILE B 45 " --> pdb=" O ILE B 41 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N LEU B 81 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N VAL B 70 " --> pdb=" O LEU B 81 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 103 through 106 Processing sheet with id= F, first strand: chain 'B' and resid 172 through 177 removed outlier: 8.039A pdb=" N ILE B 173 " --> pdb=" O ILE B 314 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ALA B 316 " --> pdb=" O ILE B 173 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N ILE B 175 " --> pdb=" O ALA B 316 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N TYR B 318 " --> pdb=" O ILE B 175 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N ALA B 177 " --> pdb=" O TYR B 318 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N VAL B 320 " --> pdb=" O ALA B 177 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ILE B 198 " --> pdb=" O LEU B 262 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N MET B 264 " --> pdb=" O ILE B 198 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N VAL B 200 " --> pdb=" O MET B 264 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N ASP B 266 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N ALA B 202 " --> pdb=" O ASP B 266 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 37 through 41 removed outlier: 3.754A pdb=" N LYS C 37 " --> pdb=" O ARG C 49 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N LYS C 47 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA C 72 " --> pdb=" O PHE C 79 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU C 81 " --> pdb=" O VAL C 70 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N VAL C 70 " --> pdb=" O LEU C 81 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ARG C 66 " --> pdb=" O ILE C 61 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N PHE C 58 " --> pdb=" O GLN C 98 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 103 through 106 Processing sheet with id= I, first strand: chain 'C' and resid 342 through 344 removed outlier: 8.532A pdb=" N ILE C 343 " --> pdb=" O ARG C 172 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N GLY C 174 " --> pdb=" O ILE C 343 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N ILE C 173 " --> pdb=" O ILE C 314 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ALA C 316 " --> pdb=" O ILE C 173 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N ILE C 175 " --> pdb=" O ALA C 316 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N TYR C 318 " --> pdb=" O ILE C 175 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N ALA C 177 " --> pdb=" O TYR C 318 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N VAL C 320 " --> pdb=" O ALA C 177 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ILE C 198 " --> pdb=" O LEU C 262 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N MET C 264 " --> pdb=" O ILE C 198 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL C 200 " --> pdb=" O MET C 264 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 93 through 95 removed outlier: 4.118A pdb=" N GLN D 93 " --> pdb=" O ILE D 38 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLY D 36 " --> pdb=" O LEU D 95 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LYS D 47 " --> pdb=" O ILE D 39 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N ILE D 41 " --> pdb=" O ILE D 45 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N ILE D 45 " --> pdb=" O ILE D 41 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N LEU D 81 " --> pdb=" O VAL D 70 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N VAL D 70 " --> pdb=" O LEU D 81 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N LYS D 60 " --> pdb=" O TYR D 97 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N TYR D 97 " --> pdb=" O LYS D 60 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 103 through 106 Processing sheet with id= L, first strand: chain 'D' and resid 113 through 115 removed outlier: 3.566A pdb=" N LEU D 228 " --> pdb=" O ARG D 113 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE D 198 " --> pdb=" O ASN D 260 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE D 204 " --> pdb=" O ASP D 266 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N SER D 313 " --> pdb=" O VAL D 261 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N LEU D 263 " --> pdb=" O SER D 313 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N THR D 315 " --> pdb=" O LEU D 263 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N MET D 265 " --> pdb=" O THR D 315 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ILE D 317 " --> pdb=" O MET D 265 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 36 through 38 removed outlier: 3.805A pdb=" N GLY E 36 " --> pdb=" O LEU E 95 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLN E 93 " --> pdb=" O ILE E 38 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N PHE E 79 " --> pdb=" O ILE E 71 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ARG E 49 " --> pdb=" O ILE E 38 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N ILE E 38 " --> pdb=" O ARG E 49 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 103 through 106 Processing sheet with id= O, first strand: chain 'E' and resid 342 through 344 removed outlier: 8.253A pdb=" N ILE E 343 " --> pdb=" O ARG E 172 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N GLY E 174 " --> pdb=" O ILE E 343 " (cutoff:3.500A) removed outlier: 8.382A pdb=" N ILE E 173 " --> pdb=" O ILE E 314 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ALA E 316 " --> pdb=" O ILE E 173 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N ILE E 175 " --> pdb=" O ALA E 316 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N TYR E 318 " --> pdb=" O ILE E 175 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N ALA E 177 " --> pdb=" O TYR E 318 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL E 320 " --> pdb=" O ALA E 177 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N VAL E 261 " --> pdb=" O THR E 315 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N ILE E 317 " --> pdb=" O VAL E 261 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU E 263 " --> pdb=" O ILE E 317 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N THR E 319 " --> pdb=" O LEU E 263 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N MET E 265 " --> pdb=" O THR E 319 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N LEU E 321 " --> pdb=" O MET E 265 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'F' and resid 37 through 41 removed outlier: 4.000A pdb=" N LYS F 37 " --> pdb=" O ARG F 49 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N LYS F 47 " --> pdb=" O ILE F 39 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N ILE F 41 " --> pdb=" O ILE F 45 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE F 45 " --> pdb=" O ILE F 41 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU F 81 " --> pdb=" O VAL F 70 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N VAL F 70 " --> pdb=" O LEU F 81 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'F' and resid 103 through 106 removed outlier: 3.760A pdb=" N PHE F 133 " --> pdb=" O VAL F 106 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'F' and resid 113 through 115 removed outlier: 4.112A pdb=" N ARG F 113 " --> pdb=" O CYS F 226 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU F 228 " --> pdb=" O ARG F 113 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE F 115 " --> pdb=" O LEU F 228 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ILE F 199 " --> pdb=" O VAL F 227 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N VAL F 229 " --> pdb=" O ILE F 199 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LEU F 201 " --> pdb=" O VAL F 229 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ILE F 173 " --> pdb=" O TYR F 318 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N VAL F 320 " --> pdb=" O ILE F 173 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ILE F 175 " --> pdb=" O VAL F 320 " (cutoff:3.500A) 592 hydrogen bonds defined for protein. 1713 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.01 Time building geometry restraints manager: 7.96 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: 5278 1.33 - 1.45: 3114 1.45 - 1.57: 10846 1.57 - 1.69: 20 1.69 - 1.82: 130 Bond restraints: 19388 Sorted by residual: bond pdb=" F3 AF3 C 602 " pdb="AL AF3 C 602 " ideal model delta sigma weight residual 1.637 1.733 -0.096 2.00e-02 2.50e+03 2.30e+01 bond pdb=" F3 AF3 B 602 " pdb="AL AF3 B 602 " ideal model delta sigma weight residual 1.637 1.732 -0.095 2.00e-02 2.50e+03 2.24e+01 bond pdb=" F3 AF3 D 602 " pdb="AL AF3 D 602 " ideal model delta sigma weight residual 1.637 1.731 -0.094 2.00e-02 2.50e+03 2.23e+01 bond pdb=" F3 AF3 E 602 " pdb="AL AF3 E 602 " ideal model delta sigma weight residual 1.637 1.730 -0.093 2.00e-02 2.50e+03 2.15e+01 bond pdb=" CB THR C 269 " pdb=" CG2 THR C 269 " ideal model delta sigma weight residual 1.521 1.439 0.082 3.30e-02 9.18e+02 6.18e+00 ... (remaining 19383 not shown) Histogram of bond angle deviations from ideal: 96.57 - 104.60: 391 104.60 - 112.63: 9957 112.63 - 120.66: 9503 120.66 - 128.69: 6317 128.69 - 136.72: 88 Bond angle restraints: 26256 Sorted by residual: angle pdb=" N ARG E 207 " pdb=" CA ARG E 207 " pdb=" C ARG E 207 " ideal model delta sigma weight residual 110.10 117.79 -7.69 1.49e+00 4.50e-01 2.67e+01 angle pdb=" C ASP E 74 " pdb=" N GLU E 75 " pdb=" CA GLU E 75 " ideal model delta sigma weight residual 121.54 131.19 -9.65 1.91e+00 2.74e-01 2.55e+01 angle pdb=" C ASP C 74 " pdb=" N GLU C 75 " pdb=" CA GLU C 75 " ideal model delta sigma weight residual 121.54 130.95 -9.41 1.91e+00 2.74e-01 2.43e+01 angle pdb=" C2' ADP C 600 " pdb=" C3' ADP C 600 " pdb=" C4' ADP C 600 " ideal model delta sigma weight residual 111.00 97.09 13.91 3.00e+00 1.11e-01 2.15e+01 angle pdb=" CA LEU E 339 " pdb=" CB LEU E 339 " pdb=" CG LEU E 339 " ideal model delta sigma weight residual 116.30 132.52 -16.22 3.50e+00 8.16e-02 2.15e+01 ... (remaining 26251 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.27: 11640 30.27 - 60.53: 173 60.53 - 90.80: 18 90.80 - 121.06: 2 121.06 - 151.33: 2 Dihedral angle restraints: 11835 sinusoidal: 4797 harmonic: 7038 Sorted by residual: dihedral pdb=" O1B ADP B 600 " pdb=" O3A ADP B 600 " pdb=" PB ADP B 600 " pdb=" PA ADP B 600 " ideal model delta sinusoidal sigma weight residual 300.00 148.67 151.33 1 2.00e+01 2.50e-03 4.51e+01 dihedral pdb=" C5' ADP B 600 " pdb=" O5' ADP B 600 " pdb=" PA ADP B 600 " pdb=" O2A ADP B 600 " ideal model delta sinusoidal sigma weight residual 300.00 175.76 124.25 1 2.00e+01 2.50e-03 3.75e+01 dihedral pdb=" CA TYR A 90 " pdb=" C TYR A 90 " pdb=" N CYS A 91 " pdb=" CA CYS A 91 " ideal model delta harmonic sigma weight residual 180.00 150.35 29.65 0 5.00e+00 4.00e-02 3.52e+01 ... (remaining 11832 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 2743 0.111 - 0.222: 277 0.222 - 0.332: 14 0.332 - 0.443: 4 0.443 - 0.554: 1 Chirality restraints: 3039 Sorted by residual: chirality pdb=" CB ILE F 199 " pdb=" CA ILE F 199 " pdb=" CG1 ILE F 199 " pdb=" CG2 ILE F 199 " both_signs ideal model delta sigma weight residual False 2.64 2.09 0.55 2.00e-01 2.50e+01 7.67e+00 chirality pdb=" CB ILE B 314 " pdb=" CA ILE B 314 " pdb=" CG1 ILE B 314 " pdb=" CG2 ILE B 314 " both_signs ideal model delta sigma weight residual False 2.64 2.21 0.44 2.00e-01 2.50e+01 4.83e+00 chirality pdb=" CB ILE F 314 " pdb=" CA ILE F 314 " pdb=" CG1 ILE F 314 " pdb=" CG2 ILE F 314 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.40 2.00e-01 2.50e+01 4.05e+00 ... (remaining 3036 not shown) Planarity restraints: 3388 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 131 " 0.048 5.00e-02 4.00e+02 7.23e-02 8.36e+00 pdb=" N PRO C 132 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO C 132 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO C 132 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 329 " -0.041 5.00e-02 4.00e+02 6.20e-02 6.15e+00 pdb=" N PRO D 330 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO D 330 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO D 330 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLN B 425 " 0.012 2.00e-02 2.50e+03 2.40e-02 5.74e+00 pdb=" CD GLN B 425 " -0.041 2.00e-02 2.50e+03 pdb=" OE1 GLN B 425 " 0.016 2.00e-02 2.50e+03 pdb=" NE2 GLN B 425 " 0.014 2.00e-02 2.50e+03 ... (remaining 3385 not shown) Histogram of nonbonded interaction distances: 1.36 - 2.07: 7 2.07 - 2.78: 3975 2.78 - 3.48: 24942 3.48 - 4.19: 44760 4.19 - 4.90: 80434 Nonbonded interactions: 154118 Sorted by model distance: nonbonded pdb=" O ILE B 161 " pdb=" O LEU B 165 " model vdw 1.361 3.040 nonbonded pdb=" OG SER B 184 " pdb="MG MG B 601 " model vdw 1.720 2.170 nonbonded pdb=" OG SER C 184 " pdb="MG MG C 601 " model vdw 1.921 2.170 nonbonded pdb=" NH1 ARG D 366 " pdb=" NH2 ARG E 207 " model vdw 1.929 3.200 nonbonded pdb=" OD1 ASP D 266 " pdb=" O HOH D1002 " model vdw 1.956 2.440 ... (remaining 154113 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 35 through 322 or resid 330 through 446)) selection = (chain 'B' and (resid 35 through 322 or resid 330 through 446)) selection = (chain 'C' and (resid 35 through 322 or resid 330 through 446)) selection = (chain 'D' and (resid 35 through 322 or resid 330 through 446)) selection = (chain 'E' and (resid 35 through 322 or resid 330 through 446)) selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.30 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.690 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: 3.610 Check model and map are aligned: 0.280 Set scattering table: 0.160 Process input model: 48.000 Find NCS groups from input model: 1.660 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 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 : 0.010 0.096 19388 Z= 0.643 Angle : 1.199 16.220 26256 Z= 0.609 Chirality : 0.069 0.554 3039 Planarity : 0.008 0.072 3388 Dihedral : 11.616 151.327 7323 Min Nonbonded Distance : 1.361 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer Outliers : 0.49 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 4.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.27 (0.13), residues: 2452 helix: -3.09 (0.12), residues: 919 sheet: -2.26 (0.22), residues: 440 loop : -2.72 (0.15), residues: 1093 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 315 time to evaluate : 2.215 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 3 residues processed: 325 average time/residue: 0.3882 time to fit residues: 178.7562 Evaluate side-chains 210 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 207 time to evaluate : 2.064 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1701 time to fit residues: 4.0533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 206 optimal weight: 5.9990 chunk 185 optimal weight: 0.9990 chunk 103 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 chunk 192 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 116 optimal weight: 0.9980 chunk 142 optimal weight: 3.9990 chunk 222 optimal weight: 7.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 260 ASN E 220 GLN E 353 ASN F 212 ASN F 257 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 19388 Z= 0.166 Angle : 0.632 8.482 26256 Z= 0.307 Chirality : 0.045 0.219 3039 Planarity : 0.005 0.063 3388 Dihedral : 7.445 126.940 2732 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer Outliers : 2.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.97 (0.15), residues: 2452 helix: -1.52 (0.16), residues: 934 sheet: -1.98 (0.22), residues: 455 loop : -2.26 (0.17), residues: 1063 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 243 time to evaluate : 2.391 Fit side-chains revert: symmetry clash outliers start: 43 outliers final: 18 residues processed: 277 average time/residue: 0.3599 time to fit residues: 145.6040 Evaluate side-chains 205 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 187 time to evaluate : 2.344 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1703 time to fit residues: 8.9855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 123 optimal weight: 0.6980 chunk 69 optimal weight: 7.9990 chunk 185 optimal weight: 8.9990 chunk 151 optimal weight: 6.9990 chunk 61 optimal weight: 0.8980 chunk 222 optimal weight: 10.0000 chunk 240 optimal weight: 10.0000 chunk 198 optimal weight: 10.0000 chunk 221 optimal weight: 9.9990 chunk 75 optimal weight: 7.9990 chunk 178 optimal weight: 1.9990 overall best weight: 3.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 85 HIS D 93 GLN E 376 HIS F 85 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.061 19388 Z= 0.384 Angle : 0.756 10.911 26256 Z= 0.363 Chirality : 0.049 0.235 3039 Planarity : 0.006 0.069 3388 Dihedral : 7.709 130.503 2732 Min Nonbonded Distance : 1.751 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer Outliers : 3.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.42 (0.16), residues: 2452 helix: -0.89 (0.17), residues: 901 sheet: -1.76 (0.23), residues: 449 loop : -2.08 (0.17), residues: 1102 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 202 time to evaluate : 2.215 Fit side-chains outliers start: 67 outliers final: 29 residues processed: 259 average time/residue: 0.3548 time to fit residues: 135.8029 Evaluate side-chains 210 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 181 time to evaluate : 2.248 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.1939 time to fit residues: 13.0599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 220 optimal weight: 9.9990 chunk 167 optimal weight: 10.0000 chunk 115 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 106 optimal weight: 0.9980 chunk 149 optimal weight: 3.9990 chunk 223 optimal weight: 4.9990 chunk 236 optimal weight: 9.9990 chunk 116 optimal weight: 8.9990 chunk 212 optimal weight: 6.9990 chunk 63 optimal weight: 5.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 HIS B 85 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.062 19388 Z= 0.424 Angle : 0.769 11.160 26256 Z= 0.368 Chirality : 0.050 0.428 3039 Planarity : 0.006 0.073 3388 Dihedral : 7.780 127.999 2732 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer Outliers : 2.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.16), residues: 2452 helix: -0.77 (0.17), residues: 920 sheet: -1.68 (0.24), residues: 450 loop : -1.93 (0.17), residues: 1082 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 193 time to evaluate : 2.345 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 20 residues processed: 235 average time/residue: 0.3814 time to fit residues: 131.2119 Evaluate side-chains 195 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 175 time to evaluate : 2.158 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.2068 time to fit residues: 10.6028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 197 optimal weight: 9.9990 chunk 134 optimal weight: 7.9990 chunk 3 optimal weight: 2.9990 chunk 176 optimal weight: 7.9990 chunk 97 optimal weight: 0.7980 chunk 202 optimal weight: 3.9990 chunk 163 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 120 optimal weight: 4.9990 chunk 212 optimal weight: 8.9990 chunk 59 optimal weight: 0.9980 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 85 HIS E 422 ASN F 392 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 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 : 0.005 0.048 19388 Z= 0.302 Angle : 0.687 10.770 26256 Z= 0.327 Chirality : 0.047 0.302 3039 Planarity : 0.005 0.055 3388 Dihedral : 7.378 115.082 2732 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer Outliers : 2.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.17), residues: 2452 helix: -0.36 (0.18), residues: 891 sheet: -1.58 (0.24), residues: 452 loop : -1.73 (0.18), residues: 1109 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 189 time to evaluate : 2.178 Fit side-chains outliers start: 45 outliers final: 15 residues processed: 222 average time/residue: 0.3672 time to fit residues: 119.8114 Evaluate side-chains 193 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 178 time to evaluate : 2.237 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1865 time to fit residues: 8.1233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 79 optimal weight: 2.9990 chunk 213 optimal weight: 0.2980 chunk 46 optimal weight: 10.0000 chunk 139 optimal weight: 10.0000 chunk 58 optimal weight: 6.9990 chunk 237 optimal weight: 10.0000 chunk 196 optimal weight: 0.9980 chunk 109 optimal weight: 0.1980 chunk 19 optimal weight: 10.0000 chunk 78 optimal weight: 3.9990 chunk 124 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 85 HIS C 93 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 19388 Z= 0.168 Angle : 0.600 9.247 26256 Z= 0.285 Chirality : 0.044 0.250 3039 Planarity : 0.004 0.049 3388 Dihedral : 6.666 101.490 2732 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer Outliers : 1.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.17), residues: 2452 helix: 0.07 (0.18), residues: 886 sheet: -1.41 (0.26), residues: 408 loop : -1.58 (0.17), residues: 1158 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 213 time to evaluate : 2.499 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 9 residues processed: 237 average time/residue: 0.3609 time to fit residues: 125.1203 Evaluate side-chains 187 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 178 time to evaluate : 2.061 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1677 time to fit residues: 5.7507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 228 optimal weight: 9.9990 chunk 26 optimal weight: 0.0770 chunk 135 optimal weight: 0.1980 chunk 173 optimal weight: 4.9990 chunk 134 optimal weight: 8.9990 chunk 199 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 chunk 236 optimal weight: 9.9990 chunk 147 optimal weight: 4.9990 chunk 143 optimal weight: 0.8980 chunk 109 optimal weight: 9.9990 overall best weight: 1.8342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 85 HIS C 93 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 19388 Z= 0.227 Angle : 0.642 9.885 26256 Z= 0.304 Chirality : 0.046 0.365 3039 Planarity : 0.004 0.047 3388 Dihedral : 6.577 93.007 2732 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer Outliers : 1.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.17), residues: 2452 helix: 0.15 (0.18), residues: 887 sheet: -1.33 (0.26), residues: 406 loop : -1.56 (0.18), residues: 1159 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 192 time to evaluate : 2.242 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 13 residues processed: 214 average time/residue: 0.3663 time to fit residues: 115.5782 Evaluate side-chains 196 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 183 time to evaluate : 2.234 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1826 time to fit residues: 7.7526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 146 optimal weight: 6.9990 chunk 94 optimal weight: 0.1980 chunk 141 optimal weight: 0.0980 chunk 71 optimal weight: 1.9990 chunk 46 optimal weight: 9.9990 chunk 45 optimal weight: 2.9990 chunk 150 optimal weight: 7.9990 chunk 160 optimal weight: 10.0000 chunk 116 optimal weight: 8.9990 chunk 22 optimal weight: 8.9990 chunk 185 optimal weight: 5.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 85 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 19388 Z= 0.260 Angle : 0.665 11.193 26256 Z= 0.313 Chirality : 0.046 0.404 3039 Planarity : 0.004 0.069 3388 Dihedral : 6.554 85.593 2732 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer Outliers : 0.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.17), residues: 2452 helix: 0.15 (0.18), residues: 896 sheet: -1.23 (0.25), residues: 436 loop : -1.60 (0.18), residues: 1120 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 192 time to evaluate : 2.358 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 7 residues processed: 203 average time/residue: 0.3739 time to fit residues: 111.2120 Evaluate side-chains 191 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 184 time to evaluate : 2.138 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1687 time to fit residues: 5.1285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 214 optimal weight: 20.0000 chunk 226 optimal weight: 5.9990 chunk 206 optimal weight: 7.9990 chunk 220 optimal weight: 0.9990 chunk 132 optimal weight: 9.9990 chunk 95 optimal weight: 0.5980 chunk 172 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 198 optimal weight: 9.9990 chunk 208 optimal weight: 8.9990 chunk 219 optimal weight: 5.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 85 HIS F 392 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.061 19388 Z= 0.370 Angle : 0.733 13.204 26256 Z= 0.348 Chirality : 0.049 0.500 3039 Planarity : 0.005 0.069 3388 Dihedral : 6.935 95.297 2732 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer Outliers : 0.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.17), residues: 2452 helix: -0.03 (0.18), residues: 893 sheet: -1.29 (0.25), residues: 442 loop : -1.65 (0.18), residues: 1117 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 186 time to evaluate : 2.480 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 5 residues processed: 201 average time/residue: 0.3827 time to fit residues: 113.0411 Evaluate side-chains 187 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 182 time to evaluate : 2.118 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1806 time to fit residues: 4.4995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 144 optimal weight: 4.9990 chunk 232 optimal weight: 7.9990 chunk 142 optimal weight: 3.9990 chunk 110 optimal weight: 0.7980 chunk 161 optimal weight: 0.9980 chunk 244 optimal weight: 0.9990 chunk 224 optimal weight: 3.9990 chunk 194 optimal weight: 0.9990 chunk 20 optimal weight: 6.9990 chunk 150 optimal weight: 0.0970 chunk 119 optimal weight: 6.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 85 HIS C 93 GLN C 220 GLN F 392 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.3077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 19388 Z= 0.153 Angle : 0.608 9.377 26256 Z= 0.286 Chirality : 0.045 0.380 3039 Planarity : 0.004 0.068 3388 Dihedral : 6.159 85.282 2732 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer Outliers : 0.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.17), residues: 2452 helix: 0.40 (0.19), residues: 878 sheet: -1.20 (0.26), residues: 405 loop : -1.44 (0.18), residues: 1169 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 195 time to evaluate : 2.325 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 198 average time/residue: 0.3964 time to fit residues: 114.5556 Evaluate side-chains 184 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 182 time to evaluate : 2.253 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1830 time to fit residues: 3.7621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 154 optimal weight: 5.9990 chunk 207 optimal weight: 8.9990 chunk 59 optimal weight: 0.0470 chunk 179 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 54 optimal weight: 8.9990 chunk 194 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 199 optimal weight: 3.9990 chunk 24 optimal weight: 10.0000 chunk 35 optimal weight: 9.9990 overall best weight: 3.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 85 HIS C 93 GLN E 416 ASN F 212 ASN F 392 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.143368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.119849 restraints weight = 34225.078| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.12 r_work: 0.2985 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2972 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2972 r_free = 0.2972 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2953 r_free = 0.2953 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2953 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.065 19388 Z= 0.393 Angle : 0.746 15.912 26256 Z= 0.354 Chirality : 0.050 0.547 3039 Planarity : 0.005 0.070 3388 Dihedral : 6.832 94.642 2732 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer Outliers : 0.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.17), residues: 2452 helix: 0.02 (0.18), residues: 892 sheet: -1.25 (0.25), residues: 438 loop : -1.58 (0.18), residues: 1122 =============================================================================== Job complete usr+sys time: 3477.05 seconds wall clock time: 64 minutes 8.11 seconds (3848.11 seconds total)