Starting phenix.real_space_refine on Fri Nov 17 15:43:43 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6njp_9391/11_2023/6njp_9391_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6njp_9391/11_2023/6njp_9391.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6njp_9391/11_2023/6njp_9391.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6njp_9391/11_2023/6njp_9391.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6njp_9391/11_2023/6njp_9391_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6njp_9391/11_2023/6njp_9391_updated.pdb" } resolution = 3.29 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Al 4 5.89 5 P 8 5.49 5 Mg 4 5.21 5 S 80 5.16 5 C 12408 2.51 5 N 3389 2.21 5 O 3702 1.98 5 F 12 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 66": "NH1" <-> "NH2" Residue "A PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 113": "NH1" <-> "NH2" Residue "A ARG 147": "NH1" <-> "NH2" Residue "A ARG 172": "NH1" <-> "NH2" Residue "A ARG 209": "NH1" <-> "NH2" Residue "A ARG 366": "NH1" <-> "NH2" Residue "A ARG 378": "NH1" <-> "NH2" Residue "A ARG 398": "NH1" <-> "NH2" Residue "B TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 113": "NH1" <-> "NH2" Residue "B ARG 147": "NH1" <-> "NH2" Residue "B PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 207": "NH1" <-> "NH2" Residue "B ARG 366": "NH1" <-> "NH2" Residue "B ARG 378": "NH1" <-> "NH2" Residue "C GLU 35": "OE1" <-> "OE2" Residue "C ARG 49": "NH1" <-> "NH2" Residue "C ARG 54": "NH1" <-> "NH2" Residue "C TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 66": "NH1" <-> "NH2" Residue "C ARG 147": "NH1" <-> "NH2" Residue "C PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 288": "NH1" <-> "NH2" Residue "C ARG 305": "NH1" <-> "NH2" Residue "C ARG 366": "NH1" <-> "NH2" Residue "C ARG 378": "NH1" <-> "NH2" Residue "D ARG 120": "NH1" <-> "NH2" Residue "D ARG 147": "NH1" <-> "NH2" Residue "D ARG 159": "NH1" <-> "NH2" Residue "D PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 207": "NH1" <-> "NH2" Residue "D ARG 235": "NH1" <-> "NH2" Residue "D ARG 288": "NH1" <-> "NH2" Residue "D ARG 378": "NH1" <-> "NH2" Residue "D ARG 398": "NH1" <-> "NH2" Residue "E GLU 35": "OE1" <-> "OE2" Residue "E TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 113": "NH1" <-> "NH2" Residue "E ARG 120": "NH1" <-> "NH2" Residue "E ARG 135": "NH1" <-> "NH2" Residue "E ARG 147": "NH1" <-> "NH2" Residue "E ARG 209": "NH1" <-> "NH2" Residue "E ARG 255": "NH1" <-> "NH2" Residue "E ARG 270": "NH1" <-> "NH2" Residue "E ARG 288": "NH1" <-> "NH2" Residue "E ARG 305": "NH1" <-> "NH2" Residue "E ARG 336": "NH1" <-> "NH2" Residue "E ARG 378": "NH1" <-> "NH2" Residue "F ARG 54": "NH1" <-> "NH2" Residue "F TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 105": "NH1" <-> "NH2" Residue "F ARG 147": "NH1" <-> "NH2" Residue "F ARG 172": "NH1" <-> "NH2" Residue "F ARG 207": "NH1" <-> "NH2" Residue "F ARG 209": "NH1" <-> "NH2" Residue "F ARG 255": "NH1" <-> "NH2" Residue "F ARG 347": "NH1" <-> "NH2" Residue "F ARG 378": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 19607 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3164 Classifications: {'peptide': 412} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 390} Chain: "B" Number of atoms: 3160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3160 Classifications: {'peptide': 412} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 390} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 3164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3164 Classifications: {'peptide': 412} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 390} Chain: "D" Number of atoms: 3169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3169 Classifications: {'peptide': 413} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 391} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 3164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3164 Classifications: {'peptide': 412} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 390} Chain: "F" Number of atoms: 3106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3106 Classifications: {'peptide': 405} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 383} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 531 Classifications: {'peptide': 64} Link IDs: {'TRANS': 63} Chain breaks: 1 Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "E" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Residues with excluded nonbonded symmetry interactions: 24 residue: pdb=" N GLU A 140 " occ=0.50 ... (7 atoms not shown) pdb=" OE2 GLU A 140 " occ=0.50 residue: pdb=" N PRO A 141 " occ=0.75 ... (5 atoms not shown) pdb=" CD PRO A 141 " occ=0.75 residue: pdb=" N PRO A 142 " occ=0.50 ... (5 atoms not shown) pdb=" CD PRO A 142 " occ=0.50 residue: pdb=" N GLN A 148 " occ=0.75 ... (7 atoms not shown) pdb=" NE2 GLN A 148 " occ=0.75 residue: pdb=" N GLU B 140 " occ=0.50 ... (7 atoms not shown) pdb=" OE2 GLU B 140 " occ=0.50 residue: pdb=" N PRO B 141 " occ=0.75 ... (5 atoms not shown) pdb=" CD PRO B 141 " occ=0.75 residue: pdb=" N PRO B 142 " occ=0.50 ... (5 atoms not shown) pdb=" CD PRO B 142 " occ=0.50 residue: pdb=" N GLN B 148 " occ=0.75 ... (7 atoms not shown) pdb=" NE2 GLN B 148 " occ=0.75 residue: pdb=" N GLU C 140 " occ=0.50 ... (7 atoms not shown) pdb=" OE2 GLU C 140 " occ=0.50 residue: pdb=" N PRO C 141 " occ=0.75 ... (5 atoms not shown) pdb=" CD PRO C 141 " occ=0.75 residue: pdb=" N PRO C 142 " occ=0.50 ... (5 atoms not shown) pdb=" CD PRO C 142 " occ=0.50 residue: pdb=" N GLN C 148 " occ=0.75 ... (7 atoms not shown) pdb=" NE2 GLN C 148 " occ=0.75 ... (remaining 12 not shown) Time building chain proxies: 9.87, per 1000 atoms: 0.50 Number of scatterers: 19607 At special positions: 0 Unit cell: (123.42, 118.32, 121.38, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 80 16.00 P 8 15.00 Al 4 13.00 Mg 4 11.99 F 12 9.00 O 3702 8.00 N 3389 7.00 C 12408 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.54 Conformation dependent library (CDL) restraints added in 3.9 seconds 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4640 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 91 helices and 19 sheets defined 35.3% alpha, 14.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.11 Creating SS restraints... Processing helix chain 'A' and resid 159 through 163 Processing helix chain 'A' and resid 183 through 193 Processing helix chain 'A' and resid 208 through 215 Processing helix chain 'A' and resid 220 through 223 No H-bonds generated for 'chain 'A' and resid 220 through 223' Processing helix chain 'A' and resid 237 through 256 removed outlier: 4.754A pdb=" N ALA A 244 " --> pdb=" O ARG A 240 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N PHE A 245 " --> pdb=" O MET A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 282 Processing helix chain 'A' and resid 293 through 303 Proline residue: A 300 - end of helix Processing helix chain 'A' and resid 330 through 338 Processing helix chain 'A' and resid 348 through 351 No H-bonds generated for 'chain 'A' and resid 348 through 351' Processing helix chain 'A' and resid 374 through 397 removed outlier: 3.544A pdb=" N ALA A 381 " --> pdb=" O LEU A 377 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU A 382 " --> pdb=" O ARG A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 424 removed outlier: 3.519A pdb=" N LYS A 412 " --> pdb=" O PRO A 408 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA A 413 " --> pdb=" O GLU A 409 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N LYS A 418 " --> pdb=" O ILE A 414 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N LEU A 419 " --> pdb=" O LYS A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 445 Processing helix chain 'B' and resid 108 through 110 No H-bonds generated for 'chain 'B' and resid 108 through 110' Processing helix chain 'B' and resid 159 through 163 Processing helix chain 'B' and resid 183 through 193 Processing helix chain 'B' and resid 208 through 216 removed outlier: 3.607A pdb=" N VAL B 211 " --> pdb=" O GLY B 208 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASN B 212 " --> pdb=" O ARG B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 225 removed outlier: 4.377A pdb=" N LYS B 225 " --> pdb=" O SER B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 256 removed outlier: 5.398A pdb=" N ALA B 244 " --> pdb=" O ARG B 240 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N PHE B 245 " --> pdb=" O MET B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 281 Processing helix chain 'B' and resid 293 through 304 Proline residue: B 300 - end of helix Processing helix chain 'B' and resid 330 through 336 Processing helix chain 'B' and resid 347 through 350 No H-bonds generated for 'chain 'B' and resid 347 through 350' Processing helix chain 'B' and resid 368 through 371 No H-bonds generated for 'chain 'B' and resid 368 through 371' Processing helix chain 'B' and resid 374 through 391 Processing helix chain 'B' and resid 394 through 398 Processing helix chain 'B' and resid 408 through 423 removed outlier: 5.332A pdb=" N LYS B 418 " --> pdb=" O ILE B 414 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N LEU B 419 " --> pdb=" O LYS B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 445 Processing helix chain 'C' and resid 108 through 110 No H-bonds generated for 'chain 'C' and resid 108 through 110' Processing helix chain 'C' and resid 144 through 146 No H-bonds generated for 'chain 'C' and resid 144 through 146' Processing helix chain 'C' and resid 159 through 161 No H-bonds generated for 'chain 'C' and resid 159 through 161' Processing helix chain 'C' and resid 183 through 191 Processing helix chain 'C' and resid 208 through 217 removed outlier: 3.510A pdb=" N VAL C 211 " --> pdb=" O GLY C 208 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASN C 212 " --> pdb=" O ARG C 209 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N PHE C 214 " --> pdb=" O VAL C 211 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU C 217 " --> pdb=" O PHE C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 225 removed outlier: 4.629A pdb=" N LYS C 225 " --> pdb=" O SER C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 241 Processing helix chain 'C' and resid 244 through 256 Processing helix chain 'C' and resid 268 through 281 Processing helix chain 'C' and resid 293 through 296 No H-bonds generated for 'chain 'C' and resid 293 through 296' Processing helix chain 'C' and resid 300 through 305 removed outlier: 5.173A pdb=" N ARG C 305 " --> pdb=" O LYS C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 338 Processing helix chain 'C' and resid 348 through 351 No H-bonds generated for 'chain 'C' and resid 348 through 351' Processing helix chain 'C' and resid 368 through 371 No H-bonds generated for 'chain 'C' and resid 368 through 371' Processing helix chain 'C' and resid 374 through 399 removed outlier: 4.969A pdb=" N LEU C 395 " --> pdb=" O LYS C 391 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N LEU C 396 " --> pdb=" O ASN C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 415 removed outlier: 3.510A pdb=" N LYS C 412 " --> pdb=" O PRO C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 424 Processing helix chain 'C' and resid 434 through 445 Processing helix chain 'D' and resid 108 through 110 No H-bonds generated for 'chain 'D' and resid 108 through 110' Processing helix chain 'D' and resid 159 through 163 Processing helix chain 'D' and resid 183 through 193 Processing helix chain 'D' and resid 208 through 216 removed outlier: 3.668A pdb=" N VAL D 211 " --> pdb=" O GLY D 208 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ASN D 212 " --> pdb=" O ARG D 209 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N PHE D 214 " --> pdb=" O VAL D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 225 removed outlier: 4.493A pdb=" N LYS D 225 " --> pdb=" O SER D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 256 removed outlier: 5.436A pdb=" N ALA D 244 " --> pdb=" O ARG D 240 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N PHE D 245 " --> pdb=" O MET D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 281 Processing helix chain 'D' and resid 293 through 305 Proline residue: D 300 - end of helix removed outlier: 4.622A pdb=" N ARG D 305 " --> pdb=" O LYS D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 338 Processing helix chain 'D' and resid 347 through 349 No H-bonds generated for 'chain 'D' and resid 347 through 349' Processing helix chain 'D' and resid 374 through 396 removed outlier: 4.897A pdb=" N LEU D 395 " --> pdb=" O LYS D 391 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N LEU D 396 " --> pdb=" O ASN D 392 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 415 removed outlier: 3.745A pdb=" N LYS D 412 " --> pdb=" O PRO D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 424 removed outlier: 3.934A pdb=" N ASN D 422 " --> pdb=" O LYS D 418 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N PHE D 423 " --> pdb=" O LEU D 419 " (cutoff:3.500A) Processing helix chain 'D' and resid 434 through 445 Processing helix chain 'E' and resid 160 through 163 No H-bonds generated for 'chain 'E' and resid 160 through 163' Processing helix chain 'E' and resid 183 through 192 Processing helix chain 'E' and resid 208 through 215 removed outlier: 3.658A pdb=" N VAL E 211 " --> pdb=" O GLY E 208 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASN E 212 " --> pdb=" O ARG E 209 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE E 214 " --> pdb=" O VAL E 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 223 No H-bonds generated for 'chain 'E' and resid 220 through 223' Processing helix chain 'E' and resid 237 through 257 removed outlier: 5.264A pdb=" N ALA E 244 " --> pdb=" O ARG E 240 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N PHE E 245 " --> pdb=" O MET E 241 " (cutoff:3.500A) Processing helix chain 'E' and resid 268 through 280 Processing helix chain 'E' and resid 293 through 302 Proline residue: E 300 - end of helix Processing helix chain 'E' and resid 333 through 337 Processing helix chain 'E' and resid 347 through 350 No H-bonds generated for 'chain 'E' and resid 347 through 350' Processing helix chain 'E' and resid 374 through 393 removed outlier: 4.123A pdb=" N ASN E 392 " --> pdb=" O ALA E 388 " (cutoff:3.500A) Processing helix chain 'E' and resid 395 through 398 No H-bonds generated for 'chain 'E' and resid 395 through 398' Processing helix chain 'E' and resid 408 through 415 removed outlier: 3.559A pdb=" N LYS E 415 " --> pdb=" O ASP E 411 " (cutoff:3.500A) Processing helix chain 'E' and resid 417 through 423 Processing helix chain 'E' and resid 434 through 445 Processing helix chain 'F' and resid 108 through 110 No H-bonds generated for 'chain 'F' and resid 108 through 110' Processing helix chain 'F' and resid 144 through 146 No H-bonds generated for 'chain 'F' and resid 144 through 146' Processing helix chain 'F' and resid 159 through 164 Processing helix chain 'F' and resid 183 through 191 Processing helix chain 'F' and resid 209 through 217 removed outlier: 4.075A pdb=" N ALA F 216 " --> pdb=" O GLU F 213 " (cutoff:3.500A) Processing helix chain 'F' and resid 220 through 223 No H-bonds generated for 'chain 'F' and resid 220 through 223' Processing helix chain 'F' and resid 237 through 255 removed outlier: 4.890A pdb=" N ALA F 244 " --> pdb=" O ARG F 240 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N PHE F 245 " --> pdb=" O MET F 241 " (cutoff:3.500A) Processing helix chain 'F' and resid 268 through 282 Processing helix chain 'F' and resid 293 through 304 Proline residue: F 300 - end of helix Processing helix chain 'F' and resid 332 through 336 Processing helix chain 'F' and resid 347 through 350 No H-bonds generated for 'chain 'F' and resid 347 through 350' Processing helix chain 'F' and resid 360 through 362 No H-bonds generated for 'chain 'F' and resid 360 through 362' Processing helix chain 'F' and resid 374 through 388 Processing helix chain 'F' and resid 391 through 398 removed outlier: 4.132A pdb=" N LEU F 395 " --> pdb=" O LYS F 391 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N LEU F 396 " --> pdb=" O ASN F 392 " (cutoff:3.500A) Processing helix chain 'F' and resid 411 through 423 removed outlier: 3.765A pdb=" N LYS F 415 " --> pdb=" O ASP F 411 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N LYS F 418 " --> pdb=" O ILE F 414 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N LEU F 419 " --> pdb=" O LYS F 415 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ILE F 420 " --> pdb=" O ASN F 416 " (cutoff:3.500A) Processing helix chain 'F' and resid 434 through 444 removed outlier: 3.668A pdb=" N ILE F 438 " --> pdb=" O TYR F 434 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N GLU F 439 " --> pdb=" O GLU F 435 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 26 removed outlier: 3.913A pdb=" N LEU G 6 " --> pdb=" O LEU G 2 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N SER G 7 " --> pdb=" O ASP G 3 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N SER G 19 " --> pdb=" O ARG G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 113 removed outlier: 3.741A pdb=" N ASP G 96 " --> pdb=" O ARG G 92 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N SER G 97 " --> pdb=" O SER G 93 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLN G 98 " --> pdb=" O LEU G 94 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG G 100 " --> pdb=" O ASP G 96 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 37 through 41 removed outlier: 3.875A pdb=" N LYS A 37 " --> pdb=" O ARG A 49 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LYS A 47 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA A 72 " --> pdb=" O PHE A 79 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N LEU A 81 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N VAL A 70 " --> pdb=" O LEU A 81 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ARG A 66 " --> pdb=" O ILE A 61 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 103 through 106 Processing sheet with id= C, first strand: chain 'A' and resid 317 through 321 removed outlier: 6.451A pdb=" N ILE A 173 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N VAL A 320 " --> pdb=" O ILE A 173 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ILE A 175 " --> pdb=" O VAL A 320 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 226 through 230 removed outlier: 6.628A pdb=" N ILE A 199 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N VAL A 229 " --> pdb=" O ILE A 199 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LEU A 201 " --> pdb=" O VAL A 229 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ILE A 198 " --> pdb=" O ASN A 260 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N SER A 313 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N LEU A 263 " --> pdb=" O SER A 313 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N THR A 315 " --> pdb=" O LEU A 263 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N MET A 265 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 37 through 41 removed outlier: 3.636A pdb=" N LYS B 37 " --> pdb=" O ARG B 49 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LYS B 47 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N ILE B 41 " --> pdb=" O ILE B 45 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N ILE B 45 " --> pdb=" O ILE B 41 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N LEU B 81 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N VAL B 70 " --> pdb=" O LEU B 81 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ARG B 66 " --> pdb=" O ILE B 61 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 103 through 106 Processing sheet with id= G, first strand: chain 'B' and resid 342 through 344 removed outlier: 8.012A pdb=" N ILE B 343 " --> pdb=" O ARG B 172 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N GLY B 174 " --> pdb=" O ILE B 343 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N ILE B 173 " --> pdb=" O ILE B 314 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ALA B 316 " --> pdb=" O ILE B 173 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N ILE B 175 " --> pdb=" O ALA B 316 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N TYR B 318 " --> pdb=" O ILE B 175 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N ALA B 177 " --> pdb=" O TYR B 318 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N VAL B 320 " --> pdb=" O ALA B 177 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N VAL B 261 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N ILE B 317 " --> pdb=" O VAL B 261 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LEU B 263 " --> pdb=" O ILE B 317 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N THR B 319 " --> pdb=" O LEU B 263 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N MET B 265 " --> pdb=" O THR B 319 " (cutoff:3.500A) removed outlier: 8.625A pdb=" N LEU B 321 " --> pdb=" O MET B 265 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ILE B 198 " --> pdb=" O LEU B 262 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N MET B 264 " --> pdb=" O ILE B 198 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N VAL B 200 " --> pdb=" O MET B 264 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N ASP B 266 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N ALA B 202 " --> pdb=" O ASP B 266 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 37 through 41 removed outlier: 3.792A pdb=" N LYS C 37 " --> pdb=" O ARG C 49 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LYS C 47 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N ILE C 41 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N ILE C 45 " --> pdb=" O ILE C 41 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA C 72 " --> pdb=" O PHE C 79 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N LEU C 81 " --> pdb=" O VAL C 70 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N VAL C 70 " --> pdb=" O LEU C 81 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ARG C 66 " --> pdb=" O ILE C 61 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 103 through 106 Processing sheet with id= J, first strand: chain 'C' and resid 113 through 115 removed outlier: 3.919A pdb=" N ARG C 113 " --> pdb=" O CYS C 226 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU C 228 " --> pdb=" O ARG C 113 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ILE C 199 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N VAL C 229 " --> pdb=" O ILE C 199 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LEU C 201 " --> pdb=" O VAL C 229 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N SER C 313 " --> pdb=" O VAL C 261 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N LEU C 263 " --> pdb=" O SER C 313 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N THR C 315 " --> pdb=" O LEU C 263 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N MET C 265 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ILE C 317 " --> pdb=" O MET C 265 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 93 through 95 removed outlier: 3.832A pdb=" N GLN D 93 " --> pdb=" O ILE D 38 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY D 36 " --> pdb=" O LEU D 95 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N LYS D 47 " --> pdb=" O ILE D 39 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA D 72 " --> pdb=" O PHE D 79 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LEU D 81 " --> pdb=" O VAL D 70 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N VAL D 70 " --> pdb=" O LEU D 81 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY D 99 " --> pdb=" O PHE D 58 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N LYS D 60 " --> pdb=" O TYR D 97 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N TYR D 97 " --> pdb=" O LYS D 60 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 103 through 106 Processing sheet with id= M, first strand: chain 'D' and resid 113 through 115 removed outlier: 3.852A pdb=" N ARG D 113 " --> pdb=" O CYS D 226 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ILE D 199 " --> pdb=" O VAL D 227 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N VAL D 229 " --> pdb=" O ILE D 199 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LEU D 201 " --> pdb=" O VAL D 229 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N THR D 231 " --> pdb=" O LEU D 201 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N LEU D 203 " --> pdb=" O THR D 231 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE D 204 " --> pdb=" O ASP D 266 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N SER D 313 " --> pdb=" O VAL D 261 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N LEU D 263 " --> pdb=" O SER D 313 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N THR D 315 " --> pdb=" O LEU D 263 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N MET D 265 " --> pdb=" O THR D 315 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE D 317 " --> pdb=" O MET D 265 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 37 through 41 removed outlier: 3.905A pdb=" N LYS E 37 " --> pdb=" O ARG E 49 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N LYS E 47 " --> pdb=" O ILE E 39 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N LEU E 81 " --> pdb=" O VAL E 70 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N VAL E 70 " --> pdb=" O LEU E 81 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N LYS E 60 " --> pdb=" O TYR E 97 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N TYR E 97 " --> pdb=" O LYS E 60 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 103 through 106 Processing sheet with id= P, first strand: chain 'E' and resid 113 through 115 removed outlier: 3.739A pdb=" N ARG E 113 " --> pdb=" O CYS E 226 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ILE E 199 " --> pdb=" O VAL E 227 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N VAL E 229 " --> pdb=" O ILE E 199 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LEU E 201 " --> pdb=" O VAL E 229 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N THR E 231 " --> pdb=" O LEU E 201 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N LEU E 203 " --> pdb=" O THR E 231 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LEU E 262 " --> pdb=" O VAL E 200 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N ALA E 202 " --> pdb=" O LEU E 262 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N MET E 264 " --> pdb=" O ALA E 202 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ILE E 204 " --> pdb=" O MET E 264 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N ASP E 266 " --> pdb=" O ILE E 204 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N GLU E 206 " --> pdb=" O ASP E 266 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'F' and resid 37 through 41 removed outlier: 3.517A pdb=" N LYS F 37 " --> pdb=" O ARG F 49 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LYS F 47 " --> pdb=" O ILE F 39 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LEU F 81 " --> pdb=" O VAL F 70 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N VAL F 70 " --> pdb=" O LEU F 81 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'F' and resid 103 through 106 removed outlier: 3.658A pdb=" N PHE F 133 " --> pdb=" O VAL F 106 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 342 through 344 removed outlier: 6.906A pdb=" N GLY F 174 " --> pdb=" O ILE F 343 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL F 261 " --> pdb=" O THR F 315 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N ILE F 317 " --> pdb=" O VAL F 261 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LEU F 263 " --> pdb=" O ILE F 317 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N THR F 319 " --> pdb=" O LEU F 263 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N MET F 265 " --> pdb=" O THR F 319 " (cutoff:3.500A) removed outlier: 8.706A pdb=" N LEU F 321 " --> pdb=" O MET F 265 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ILE F 198 " --> pdb=" O LEU F 262 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N MET F 264 " --> pdb=" O ILE F 198 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL F 200 " --> pdb=" O MET F 264 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N ASP F 266 " --> pdb=" O VAL F 200 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ALA F 202 " --> pdb=" O ASP F 266 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU F 201 " --> pdb=" O VAL F 227 " (cutoff:3.500A) 628 hydrogen bonds defined for protein. 1782 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.60 Time building geometry restraints manager: 8.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4177 1.33 - 1.45: 3979 1.45 - 1.57: 11595 1.57 - 1.69: 20 1.69 - 1.81: 134 Bond restraints: 19905 Sorted by residual: bond pdb=" F1 AF3 C 602 " pdb="AL AF3 C 602 " ideal model delta sigma weight residual 1.637 1.734 -0.097 2.00e-02 2.50e+03 2.33e+01 bond pdb=" F1 AF3 E 602 " pdb="AL AF3 E 602 " ideal model delta sigma weight residual 1.637 1.733 -0.096 2.00e-02 2.50e+03 2.32e+01 bond pdb=" F1 AF3 B 602 " pdb="AL AF3 B 602 " ideal model delta sigma weight residual 1.637 1.733 -0.096 2.00e-02 2.50e+03 2.31e+01 bond pdb=" F1 AF3 D 602 " pdb="AL AF3 D 602 " ideal model delta sigma weight residual 1.637 1.733 -0.096 2.00e-02 2.50e+03 2.31e+01 bond pdb=" C ALA A 139 " pdb=" N GLU A 140 " ideal model delta sigma weight residual 1.329 1.272 0.057 1.35e-02 5.49e+03 1.77e+01 ... (remaining 19900 not shown) Histogram of bond angle deviations from ideal: 96.98 - 104.82: 413 104.82 - 112.65: 10259 112.65 - 120.49: 9168 120.49 - 128.33: 6999 128.33 - 136.16: 99 Bond angle restraints: 26938 Sorted by residual: angle pdb=" C ASP E 74 " pdb=" N GLU E 75 " pdb=" CA GLU E 75 " ideal model delta sigma weight residual 121.54 133.04 -11.50 1.91e+00 2.74e-01 3.63e+01 angle pdb=" C SER B 313 " pdb=" N ILE B 314 " pdb=" CA ILE B 314 " ideal model delta sigma weight residual 123.19 117.56 5.63 1.24e+00 6.50e-01 2.06e+01 angle pdb=" N VAL A 327 " pdb=" CA VAL A 327 " pdb=" C VAL A 327 " ideal model delta sigma weight residual 113.16 106.42 6.74 1.49e+00 4.50e-01 2.05e+01 angle pdb=" C TYR F 97 " pdb=" N GLN F 98 " pdb=" CA GLN F 98 " ideal model delta sigma weight residual 122.61 129.48 -6.87 1.56e+00 4.11e-01 1.94e+01 angle pdb=" C ASP C 74 " pdb=" N GLU C 75 " pdb=" CA GLU C 75 " ideal model delta sigma weight residual 121.54 129.77 -8.23 1.91e+00 2.74e-01 1.86e+01 ... (remaining 26933 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.15: 11964 30.15 - 60.30: 192 60.30 - 90.45: 16 90.45 - 120.60: 0 120.60 - 150.75: 4 Dihedral angle restraints: 12176 sinusoidal: 4949 harmonic: 7227 Sorted by residual: dihedral pdb=" C5' ADP E 600 " pdb=" O5' ADP E 600 " pdb=" PA ADP E 600 " pdb=" O2A ADP E 600 " ideal model delta sinusoidal sigma weight residual -60.00 90.75 -150.75 1 2.00e+01 2.50e-03 4.49e+01 dihedral pdb=" C5' ADP D 600 " pdb=" O5' ADP D 600 " pdb=" PA ADP D 600 " pdb=" O2A ADP D 600 " ideal model delta sinusoidal sigma weight residual -60.00 89.03 -149.03 1 2.00e+01 2.50e-03 4.46e+01 dihedral pdb=" C5' ADP C 600 " pdb=" O5' ADP C 600 " pdb=" PA ADP C 600 " pdb=" O2A ADP C 600 " ideal model delta sinusoidal sigma weight residual -60.00 87.67 -147.67 1 2.00e+01 2.50e-03 4.43e+01 ... (remaining 12173 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 2736 0.097 - 0.193: 349 0.193 - 0.290: 29 0.290 - 0.386: 3 0.386 - 0.483: 2 Chirality restraints: 3119 Sorted by residual: chirality pdb=" CB ILE F 314 " pdb=" CA ILE F 314 " pdb=" CG1 ILE F 314 " pdb=" CG2 ILE F 314 " both_signs ideal model delta sigma weight residual False 2.64 2.16 0.48 2.00e-01 2.50e+01 5.83e+00 chirality pdb=" CB ILE F 204 " pdb=" CA ILE F 204 " pdb=" CG1 ILE F 204 " pdb=" CG2 ILE F 204 " both_signs ideal model delta sigma weight residual False 2.64 2.22 0.42 2.00e-01 2.50e+01 4.46e+00 chirality pdb=" CB ILE A 317 " pdb=" CA ILE A 317 " pdb=" CG1 ILE A 317 " pdb=" CG2 ILE A 317 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.32e+00 ... (remaining 3116 not shown) Planarity restraints: 3473 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 131 " 0.046 5.00e-02 4.00e+02 6.90e-02 7.61e+00 pdb=" N PRO C 132 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO C 132 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 132 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 329 " -0.044 5.00e-02 4.00e+02 6.56e-02 6.88e+00 pdb=" N PRO D 330 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO D 330 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 330 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE F 83 " -0.013 2.00e-02 2.50e+03 2.53e-02 6.39e+00 pdb=" C PHE F 83 " 0.044 2.00e-02 2.50e+03 pdb=" O PHE F 83 " -0.016 2.00e-02 2.50e+03 pdb=" N GLU F 84 " -0.015 2.00e-02 2.50e+03 ... (remaining 3470 not shown) Histogram of nonbonded interaction distances: 1.28 - 2.00: 5 2.00 - 2.73: 1299 2.73 - 3.45: 26808 3.45 - 4.18: 46138 4.18 - 4.90: 84483 Nonbonded interactions: 158733 Sorted by model distance: nonbonded pdb=" O ILE B 161 " pdb=" O LEU B 165 " model vdw 1.276 3.040 nonbonded pdb=" OG SER B 184 " pdb="MG MG B 601 " model vdw 1.814 2.170 nonbonded pdb=" OG SER C 184 " pdb="MG MG C 601 " model vdw 1.842 2.170 nonbonded pdb=" OG SER D 184 " pdb="MG MG D 601 " model vdw 1.954 2.170 nonbonded pdb=" OG SER E 184 " pdb="MG MG E 601 " model vdw 1.983 2.170 ... (remaining 158728 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 35 and (name N or name CA or name C or name O or name CB \ )) or resid 36 through 322 or resid 330 through 446)) selection = (chain 'B' and (resid 35 through 322 or resid 330 through 446)) selection = (chain 'C' and ((resid 35 and (name N or name CA or name C or name O or name CB \ )) or resid 36 through 322 or resid 330 through 446)) selection = (chain 'D' and ((resid 35 and (name N or name CA or name C or name O or name CB \ )) or resid 36 through 322 or resid 330 through 446)) selection = (chain 'E' and ((resid 35 and (name N or name CA or name C or name O or name CB \ )) or resid 36 through 322 or resid 330 through 446)) selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.30 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.560 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: 2.800 Check model and map are aligned: 0.290 Set scattering table: 0.170 Process input model: 52.820 Find NCS groups from input model: 1.740 Set up NCS constraints: 0.110 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.097 19905 Z= 0.565 Angle : 1.171 14.194 26938 Z= 0.622 Chirality : 0.066 0.483 3119 Planarity : 0.008 0.069 3473 Dihedral : 11.572 150.745 7536 Min Nonbonded Distance : 1.276 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 0.67 % Allowed : 5.67 % Favored : 93.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.04 (0.13), residues: 2512 helix: -3.08 (0.12), residues: 937 sheet: -1.90 (0.23), residues: 431 loop : -2.53 (0.15), residues: 1144 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 353 time to evaluate : 2.207 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 4 residues processed: 365 average time/residue: 0.3776 time to fit residues: 198.1793 Evaluate side-chains 220 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 216 time to evaluate : 2.116 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1720 time to fit residues: 4.2221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 211 optimal weight: 0.9980 chunk 190 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 chunk 64 optimal weight: 0.6980 chunk 128 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 196 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 146 optimal weight: 3.9990 chunk 227 optimal weight: 4.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 416 ASN ** A 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 ASN ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 421 GLN C 98 GLN D 416 ASN D 421 GLN E 376 HIS ** F 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 26 GLN G 106 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19905 Z= 0.193 Angle : 0.645 10.150 26938 Z= 0.316 Chirality : 0.045 0.171 3119 Planarity : 0.005 0.055 3473 Dihedral : 7.358 123.149 2800 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 2.76 % Allowed : 9.20 % Favored : 88.04 % 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: -2.67 (0.15), residues: 2512 helix: -1.32 (0.16), residues: 924 sheet: -1.65 (0.24), residues: 434 loop : -2.11 (0.16), residues: 1154 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 241 time to evaluate : 2.335 Fit side-chains revert: symmetry clash outliers start: 58 outliers final: 24 residues processed: 284 average time/residue: 0.3575 time to fit residues: 150.4933 Evaluate side-chains 235 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 211 time to evaluate : 2.243 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.1756 time to fit residues: 11.0683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 126 optimal weight: 9.9990 chunk 70 optimal weight: 2.9990 chunk 189 optimal weight: 4.9990 chunk 155 optimal weight: 4.9990 chunk 62 optimal weight: 0.5980 chunk 228 optimal weight: 10.0000 chunk 246 optimal weight: 20.0000 chunk 203 optimal weight: 4.9990 chunk 226 optimal weight: 9.9990 chunk 77 optimal weight: 2.9990 chunk 183 optimal weight: 0.9980 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 212 ASN F 257 GLN F 426 GLN G 26 GLN G 106 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 19905 Z= 0.290 Angle : 0.676 9.029 26938 Z= 0.327 Chirality : 0.047 0.183 3119 Planarity : 0.005 0.047 3473 Dihedral : 7.029 119.917 2800 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 2.67 % Allowed : 11.92 % Favored : 85.41 % 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: -2.13 (0.16), residues: 2512 helix: -0.83 (0.17), residues: 961 sheet: -1.26 (0.25), residues: 418 loop : -1.91 (0.16), residues: 1133 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 226 time to evaluate : 2.203 Fit side-chains outliers start: 56 outliers final: 24 residues processed: 275 average time/residue: 0.3518 time to fit residues: 144.8725 Evaluate side-chains 229 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 205 time to evaluate : 2.293 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.1760 time to fit residues: 11.0101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 225 optimal weight: 5.9990 chunk 171 optimal weight: 4.9990 chunk 118 optimal weight: 9.9990 chunk 25 optimal weight: 5.9990 chunk 108 optimal weight: 0.0070 chunk 153 optimal weight: 5.9990 chunk 229 optimal weight: 9.9990 chunk 242 optimal weight: 9.9990 chunk 119 optimal weight: 2.9990 chunk 217 optimal weight: 7.9990 chunk 65 optimal weight: 4.9990 overall best weight: 3.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 GLN ** E 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 426 GLN G 24 ASN G 106 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 19905 Z= 0.401 Angle : 0.735 10.568 26938 Z= 0.355 Chirality : 0.049 0.196 3119 Planarity : 0.005 0.048 3473 Dihedral : 7.142 121.061 2800 Min Nonbonded Distance : 1.751 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 2.57 % Allowed : 14.49 % Favored : 82.94 % 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: -2.05 (0.16), residues: 2512 helix: -0.77 (0.16), residues: 976 sheet: -1.13 (0.25), residues: 427 loop : -1.92 (0.17), residues: 1109 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 221 time to evaluate : 2.198 Fit side-chains outliers start: 54 outliers final: 21 residues processed: 264 average time/residue: 0.3631 time to fit residues: 142.0841 Evaluate side-chains 227 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 206 time to evaluate : 2.237 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.1981 time to fit residues: 10.6100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 202 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 180 optimal weight: 0.8980 chunk 100 optimal weight: 6.9990 chunk 207 optimal weight: 3.9990 chunk 167 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 123 optimal weight: 10.0000 chunk 217 optimal weight: 8.9990 chunk 61 optimal weight: 0.9980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 109 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19905 Z= 0.221 Angle : 0.629 9.420 26938 Z= 0.301 Chirality : 0.045 0.214 3119 Planarity : 0.004 0.046 3473 Dihedral : 6.607 119.009 2800 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 1.81 % Allowed : 15.59 % Favored : 82.60 % 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: -1.64 (0.16), residues: 2512 helix: -0.38 (0.17), residues: 968 sheet: -1.04 (0.26), residues: 411 loop : -1.68 (0.17), residues: 1133 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 232 time to evaluate : 2.382 Fit side-chains outliers start: 38 outliers final: 16 residues processed: 259 average time/residue: 0.3674 time to fit residues: 141.2659 Evaluate side-chains 228 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 212 time to evaluate : 2.425 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1865 time to fit residues: 8.8373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 81 optimal weight: 7.9990 chunk 218 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 142 optimal weight: 0.9990 chunk 59 optimal weight: 10.0000 chunk 242 optimal weight: 9.9990 chunk 201 optimal weight: 9.9990 chunk 112 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 80 optimal weight: 9.9990 chunk 127 optimal weight: 4.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 421 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 19905 Z= 0.343 Angle : 0.698 10.099 26938 Z= 0.335 Chirality : 0.048 0.187 3119 Planarity : 0.005 0.047 3473 Dihedral : 6.779 120.783 2800 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 1.76 % Allowed : 17.25 % Favored : 80.98 % 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: -1.70 (0.16), residues: 2512 helix: -0.43 (0.17), residues: 968 sheet: -0.99 (0.26), residues: 414 loop : -1.74 (0.17), residues: 1130 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 218 time to evaluate : 2.492 Fit side-chains revert: symmetry clash outliers start: 37 outliers final: 18 residues processed: 247 average time/residue: 0.3660 time to fit residues: 134.2797 Evaluate side-chains 226 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 208 time to evaluate : 2.332 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1857 time to fit residues: 9.4841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 234 optimal weight: 9.9990 chunk 27 optimal weight: 8.9990 chunk 138 optimal weight: 0.9980 chunk 177 optimal weight: 0.5980 chunk 137 optimal weight: 0.8980 chunk 204 optimal weight: 2.9990 chunk 135 optimal weight: 0.5980 chunk 241 optimal weight: 30.0000 chunk 151 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 111 optimal weight: 5.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 152 GLN F 353 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19905 Z= 0.181 Angle : 0.606 9.779 26938 Z= 0.290 Chirality : 0.045 0.171 3119 Planarity : 0.004 0.050 3473 Dihedral : 6.232 118.328 2800 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.10 % Allowed : 17.59 % Favored : 81.32 % 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: -1.39 (0.16), residues: 2512 helix: -0.10 (0.17), residues: 971 sheet: -0.88 (0.26), residues: 413 loop : -1.62 (0.17), residues: 1128 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 222 time to evaluate : 2.210 Fit side-chains outliers start: 23 outliers final: 9 residues processed: 243 average time/residue: 0.3794 time to fit residues: 136.0154 Evaluate side-chains 217 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 208 time to evaluate : 2.048 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1848 time to fit residues: 6.0804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 149 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 144 optimal weight: 4.9990 chunk 72 optimal weight: 6.9990 chunk 47 optimal weight: 6.9990 chunk 46 optimal weight: 0.8980 chunk 153 optimal weight: 0.6980 chunk 164 optimal weight: 0.6980 chunk 119 optimal weight: 9.9990 chunk 22 optimal weight: 7.9990 chunk 190 optimal weight: 2.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 421 GLN E 152 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19905 Z= 0.229 Angle : 0.634 10.256 26938 Z= 0.301 Chirality : 0.046 0.244 3119 Planarity : 0.004 0.060 3473 Dihedral : 6.150 117.867 2800 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 0.71 % Allowed : 18.02 % Favored : 81.27 % 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: -1.31 (0.17), residues: 2512 helix: -0.05 (0.17), residues: 968 sheet: -0.79 (0.26), residues: 420 loop : -1.57 (0.17), residues: 1124 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 216 time to evaluate : 2.347 Fit side-chains outliers start: 15 outliers final: 7 residues processed: 227 average time/residue: 0.3805 time to fit residues: 127.8929 Evaluate side-chains 210 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 203 time to evaluate : 2.218 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2398 time to fit residues: 5.8433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 220 optimal weight: 0.8980 chunk 231 optimal weight: 3.9990 chunk 211 optimal weight: 9.9990 chunk 225 optimal weight: 1.9990 chunk 135 optimal weight: 0.8980 chunk 98 optimal weight: 6.9990 chunk 177 optimal weight: 4.9990 chunk 69 optimal weight: 0.7980 chunk 203 optimal weight: 0.6980 chunk 213 optimal weight: 8.9990 chunk 224 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 152 GLN F 212 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19905 Z= 0.169 Angle : 0.610 11.249 26938 Z= 0.285 Chirality : 0.044 0.212 3119 Planarity : 0.004 0.052 3473 Dihedral : 5.737 114.618 2800 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 0.38 % Allowed : 18.54 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.17), residues: 2512 helix: 0.21 (0.18), residues: 962 sheet: -0.69 (0.26), residues: 417 loop : -1.45 (0.17), residues: 1133 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 217 time to evaluate : 2.163 Fit side-chains outliers start: 8 outliers final: 2 residues processed: 223 average time/residue: 0.3889 time to fit residues: 127.3578 Evaluate side-chains 205 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 203 time to evaluate : 2.236 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1745 time to fit residues: 3.6820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 148 optimal weight: 2.9990 chunk 238 optimal weight: 5.9990 chunk 145 optimal weight: 6.9990 chunk 113 optimal weight: 6.9990 chunk 165 optimal weight: 7.9990 chunk 250 optimal weight: 2.9990 chunk 230 optimal weight: 0.0370 chunk 199 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 chunk 153 optimal weight: 5.9990 chunk 122 optimal weight: 5.9990 overall best weight: 3.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 19905 Z= 0.321 Angle : 0.689 10.725 26938 Z= 0.328 Chirality : 0.048 0.215 3119 Planarity : 0.005 0.064 3473 Dihedral : 6.075 117.906 2800 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 0.57 % Allowed : 18.49 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.16), residues: 2512 helix: -0.06 (0.17), residues: 973 sheet: -0.71 (0.26), residues: 415 loop : -1.58 (0.17), residues: 1124 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 207 time to evaluate : 2.502 Fit side-chains outliers start: 12 outliers final: 6 residues processed: 215 average time/residue: 0.3793 time to fit residues: 121.8417 Evaluate side-chains 212 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 206 time to evaluate : 2.456 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2074 time to fit residues: 5.5853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 158 optimal weight: 6.9990 chunk 212 optimal weight: 10.0000 chunk 61 optimal weight: 0.8980 chunk 183 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 55 optimal weight: 0.7980 chunk 199 optimal weight: 6.9990 chunk 83 optimal weight: 0.0370 chunk 204 optimal weight: 7.9990 chunk 25 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 257 GLN ** A 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.134482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.110077 restraints weight = 26181.106| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 1.42 r_work: 0.3078 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3042 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3042 r_free = 0.3042 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3023 r_free = 0.3023 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3023 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 19905 Z= 0.151 Angle : 0.600 11.133 26938 Z= 0.282 Chirality : 0.044 0.211 3119 Planarity : 0.004 0.054 3473 Dihedral : 5.522 112.728 2800 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.29 % Allowed : 18.73 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.17), residues: 2512 helix: 0.30 (0.18), residues: 960 sheet: -0.56 (0.26), residues: 416 loop : -1.39 (0.18), residues: 1136 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4055.35 seconds wall clock time: 74 minutes 29.20 seconds (4469.20 seconds total)