Starting phenix.real_space_refine on Sat Mar 16 09:23:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6plq_20372/03_2024/6plq_20372_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6plq_20372/03_2024/6plq_20372.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6plq_20372/03_2024/6plq_20372.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6plq_20372/03_2024/6plq_20372.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6plq_20372/03_2024/6plq_20372_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6plq_20372/03_2024/6plq_20372_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 100 5.16 5 C 9270 2.51 5 N 2290 2.21 5 O 2580 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 45": "NH1" <-> "NH2" Residue "A ARG 81": "NH1" <-> "NH2" Residue "A ARG 88": "NH1" <-> "NH2" Residue "A ARG 229": "NH1" <-> "NH2" Residue "A ARG 325": "NH1" <-> "NH2" Residue "B ARG 45": "NH1" <-> "NH2" Residue "B ARG 81": "NH1" <-> "NH2" Residue "B ARG 88": "NH1" <-> "NH2" Residue "B ARG 229": "NH1" <-> "NH2" Residue "B ARG 325": "NH1" <-> "NH2" Residue "C ARG 45": "NH1" <-> "NH2" Residue "C ARG 81": "NH1" <-> "NH2" Residue "C ARG 88": "NH1" <-> "NH2" Residue "C ARG 229": "NH1" <-> "NH2" Residue "C ARG 325": "NH1" <-> "NH2" Residue "D ARG 45": "NH1" <-> "NH2" Residue "D ARG 81": "NH1" <-> "NH2" Residue "D ARG 88": "NH1" <-> "NH2" Residue "D ARG 229": "NH1" <-> "NH2" Residue "D ARG 325": "NH1" <-> "NH2" Residue "E ARG 45": "NH1" <-> "NH2" Residue "E ARG 81": "NH1" <-> "NH2" Residue "E ARG 88": "NH1" <-> "NH2" Residue "E ARG 229": "NH1" <-> "NH2" Residue "E ARG 325": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14240 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2802 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2802 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 2802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2802 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 2802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2802 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 2802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2802 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'ABU': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'ABU': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'ABU': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'ABU': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'ABU': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.89, per 1000 atoms: 0.55 Number of scatterers: 14240 At special positions: 0 Unit cell: (105.786, 107.745, 135.824, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 100 16.00 O 2580 8.00 N 2290 7.00 C 9270 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 154 " - pdb=" SG CYS A 168 " distance=2.19 Simple disulfide: pdb=" SG CYS A 214 " - pdb=" SG CYS A 225 " distance=2.03 Simple disulfide: pdb=" SG CYS B 154 " - pdb=" SG CYS B 168 " distance=2.19 Simple disulfide: pdb=" SG CYS B 214 " - pdb=" SG CYS B 225 " distance=2.03 Simple disulfide: pdb=" SG CYS C 154 " - pdb=" SG CYS C 168 " distance=2.19 Simple disulfide: pdb=" SG CYS C 214 " - pdb=" SG CYS C 225 " distance=2.03 Simple disulfide: pdb=" SG CYS D 154 " - pdb=" SG CYS D 168 " distance=2.19 Simple disulfide: pdb=" SG CYS D 214 " - pdb=" SG CYS D 225 " distance=2.03 Simple disulfide: pdb=" SG CYS E 154 " - pdb=" SG CYS E 168 " distance=2.19 Simple disulfide: pdb=" SG CYS E 214 " - pdb=" SG CYS E 225 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " NAG-ASN " NAG F 1 " - " ASN A 54 " " NAG G 1 " - " ASN B 54 " " NAG H 1 " - " ASN C 54 " " NAG I 1 " - " ASN D 54 " " NAG J 1 " - " ASN E 54 " Time building additional restraints: 5.25 Conformation dependent library (CDL) restraints added in 2.5 seconds 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3320 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 55 helices and 20 sheets defined 35.5% alpha, 19.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.70 Creating SS restraints... Processing helix chain 'A' and resid 26 through 29 No H-bonds generated for 'chain 'A' and resid 26 through 29' Processing helix chain 'A' and resid 31 through 34 No H-bonds generated for 'chain 'A' and resid 31 through 34' Processing helix chain 'A' and resid 37 through 39 No H-bonds generated for 'chain 'A' and resid 37 through 39' Processing helix chain 'A' and resid 87 through 89 No H-bonds generated for 'chain 'A' and resid 87 through 89' Processing helix chain 'A' and resid 103 through 105 No H-bonds generated for 'chain 'A' and resid 103 through 105' Processing helix chain 'A' and resid 161 through 163 No H-bonds generated for 'chain 'A' and resid 161 through 163' Processing helix chain 'A' and resid 236 through 242 removed outlier: 4.070A pdb=" N ILE A 241 " --> pdb=" O GLY A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 259 removed outlier: 4.462A pdb=" N VAL A 251 " --> pdb=" O SER A 247 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N SER A 257 " --> pdb=" O LEU A 253 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N PHE A 258 " --> pdb=" O SER A 254 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N TRP A 259 " --> pdb=" O TRP A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 286 removed outlier: 3.552A pdb=" N GLY A 270 " --> pdb=" O PRO A 266 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR A 275 " --> pdb=" O LEU A 271 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL A 276 " --> pdb=" O GLY A 272 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N THR A 280 " --> pdb=" O VAL A 276 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR A 281 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN A 282 " --> pdb=" O THR A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 324 removed outlier: 3.501A pdb=" N VAL A 305 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU A 314 " --> pdb=" O VAL A 310 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE A 323 " --> pdb=" O ALA A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 426 removed outlier: 3.646A pdb=" N ILE A 396 " --> pdb=" O ARG A 392 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER A 397 " --> pdb=" O LYS A 393 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE A 402 " --> pdb=" O ARG A 398 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ASP A 403 " --> pdb=" O ALA A 399 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG A 407 " --> pdb=" O ASP A 403 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N VAL A 408 " --> pdb=" O THR A 404 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE A 410 " --> pdb=" O SER A 406 " (cutoff:3.500A) Proline residue: A 411 - end of helix removed outlier: 4.233A pdb=" N LEU A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE A 416 " --> pdb=" O LEU A 412 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TRP A 422 " --> pdb=" O ASN A 418 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR A 425 " --> pdb=" O TYR A 421 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N LYS A 426 " --> pdb=" O TRP A 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 29 No H-bonds generated for 'chain 'B' and resid 26 through 29' Processing helix chain 'B' and resid 31 through 34 No H-bonds generated for 'chain 'B' and resid 31 through 34' Processing helix chain 'B' and resid 37 through 39 No H-bonds generated for 'chain 'B' and resid 37 through 39' Processing helix chain 'B' and resid 87 through 89 No H-bonds generated for 'chain 'B' and resid 87 through 89' Processing helix chain 'B' and resid 103 through 105 No H-bonds generated for 'chain 'B' and resid 103 through 105' Processing helix chain 'B' and resid 161 through 163 No H-bonds generated for 'chain 'B' and resid 161 through 163' Processing helix chain 'B' and resid 236 through 242 removed outlier: 4.070A pdb=" N ILE B 241 " --> pdb=" O GLY B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 259 removed outlier: 4.462A pdb=" N VAL B 251 " --> pdb=" O SER B 247 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N SER B 257 " --> pdb=" O LEU B 253 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N PHE B 258 " --> pdb=" O SER B 254 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N TRP B 259 " --> pdb=" O TRP B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 286 removed outlier: 3.552A pdb=" N GLY B 270 " --> pdb=" O PRO B 266 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR B 275 " --> pdb=" O LEU B 271 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL B 276 " --> pdb=" O GLY B 272 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N THR B 280 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR B 281 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN B 282 " --> pdb=" O THR B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 324 removed outlier: 3.501A pdb=" N VAL B 305 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU B 314 " --> pdb=" O VAL B 310 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE B 323 " --> pdb=" O ALA B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 426 removed outlier: 3.646A pdb=" N ILE B 396 " --> pdb=" O ARG B 392 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER B 397 " --> pdb=" O LYS B 393 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE B 402 " --> pdb=" O ARG B 398 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ASP B 403 " --> pdb=" O ALA B 399 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ARG B 407 " --> pdb=" O ASP B 403 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N VAL B 408 " --> pdb=" O THR B 404 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE B 410 " --> pdb=" O SER B 406 " (cutoff:3.500A) Proline residue: B 411 - end of helix removed outlier: 4.234A pdb=" N LEU B 415 " --> pdb=" O PRO B 411 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE B 416 " --> pdb=" O LEU B 412 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TRP B 422 " --> pdb=" O ASN B 418 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR B 425 " --> pdb=" O TYR B 421 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N LYS B 426 " --> pdb=" O TRP B 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 29 No H-bonds generated for 'chain 'C' and resid 26 through 29' Processing helix chain 'C' and resid 31 through 34 No H-bonds generated for 'chain 'C' and resid 31 through 34' Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 87 through 89 No H-bonds generated for 'chain 'C' and resid 87 through 89' Processing helix chain 'C' and resid 103 through 105 No H-bonds generated for 'chain 'C' and resid 103 through 105' Processing helix chain 'C' and resid 161 through 163 No H-bonds generated for 'chain 'C' and resid 161 through 163' Processing helix chain 'C' and resid 236 through 242 removed outlier: 4.070A pdb=" N ILE C 241 " --> pdb=" O GLY C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 259 removed outlier: 4.461A pdb=" N VAL C 251 " --> pdb=" O SER C 247 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N SER C 257 " --> pdb=" O LEU C 253 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N PHE C 258 " --> pdb=" O SER C 254 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N TRP C 259 " --> pdb=" O TRP C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 286 removed outlier: 3.552A pdb=" N GLY C 270 " --> pdb=" O PRO C 266 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR C 275 " --> pdb=" O LEU C 271 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL C 276 " --> pdb=" O GLY C 272 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N THR C 280 " --> pdb=" O VAL C 276 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR C 281 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN C 282 " --> pdb=" O THR C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 324 removed outlier: 3.501A pdb=" N VAL C 305 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU C 314 " --> pdb=" O VAL C 310 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE C 323 " --> pdb=" O ALA C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 426 removed outlier: 3.647A pdb=" N ILE C 396 " --> pdb=" O ARG C 392 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER C 397 " --> pdb=" O LYS C 393 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE C 402 " --> pdb=" O ARG C 398 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ASP C 403 " --> pdb=" O ALA C 399 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG C 407 " --> pdb=" O ASP C 403 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N VAL C 408 " --> pdb=" O THR C 404 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE C 410 " --> pdb=" O SER C 406 " (cutoff:3.500A) Proline residue: C 411 - end of helix removed outlier: 4.234A pdb=" N LEU C 415 " --> pdb=" O PRO C 411 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE C 416 " --> pdb=" O LEU C 412 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TRP C 422 " --> pdb=" O ASN C 418 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR C 425 " --> pdb=" O TYR C 421 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N LYS C 426 " --> pdb=" O TRP C 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 29 No H-bonds generated for 'chain 'D' and resid 26 through 29' Processing helix chain 'D' and resid 31 through 34 No H-bonds generated for 'chain 'D' and resid 31 through 34' Processing helix chain 'D' and resid 37 through 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' Processing helix chain 'D' and resid 87 through 89 No H-bonds generated for 'chain 'D' and resid 87 through 89' Processing helix chain 'D' and resid 103 through 105 No H-bonds generated for 'chain 'D' and resid 103 through 105' Processing helix chain 'D' and resid 161 through 163 No H-bonds generated for 'chain 'D' and resid 161 through 163' Processing helix chain 'D' and resid 236 through 242 removed outlier: 4.071A pdb=" N ILE D 241 " --> pdb=" O GLY D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 259 removed outlier: 4.462A pdb=" N VAL D 251 " --> pdb=" O SER D 247 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N SER D 257 " --> pdb=" O LEU D 253 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N PHE D 258 " --> pdb=" O SER D 254 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N TRP D 259 " --> pdb=" O TRP D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 286 removed outlier: 3.552A pdb=" N GLY D 270 " --> pdb=" O PRO D 266 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR D 275 " --> pdb=" O LEU D 271 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL D 276 " --> pdb=" O GLY D 272 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N THR D 280 " --> pdb=" O VAL D 276 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N THR D 281 " --> pdb=" O LEU D 277 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN D 282 " --> pdb=" O THR D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 324 removed outlier: 3.501A pdb=" N VAL D 305 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU D 314 " --> pdb=" O VAL D 310 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE D 323 " --> pdb=" O ALA D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 392 through 426 removed outlier: 3.647A pdb=" N ILE D 396 " --> pdb=" O ARG D 392 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER D 397 " --> pdb=" O LYS D 393 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE D 402 " --> pdb=" O ARG D 398 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ASP D 403 " --> pdb=" O ALA D 399 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG D 407 " --> pdb=" O ASP D 403 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N VAL D 408 " --> pdb=" O THR D 404 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE D 410 " --> pdb=" O SER D 406 " (cutoff:3.500A) Proline residue: D 411 - end of helix removed outlier: 4.233A pdb=" N LEU D 415 " --> pdb=" O PRO D 411 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE D 416 " --> pdb=" O LEU D 412 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N TRP D 422 " --> pdb=" O ASN D 418 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR D 425 " --> pdb=" O TYR D 421 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N LYS D 426 " --> pdb=" O TRP D 422 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 29 No H-bonds generated for 'chain 'E' and resid 26 through 29' Processing helix chain 'E' and resid 31 through 34 No H-bonds generated for 'chain 'E' and resid 31 through 34' Processing helix chain 'E' and resid 37 through 39 No H-bonds generated for 'chain 'E' and resid 37 through 39' Processing helix chain 'E' and resid 87 through 89 No H-bonds generated for 'chain 'E' and resid 87 through 89' Processing helix chain 'E' and resid 103 through 105 No H-bonds generated for 'chain 'E' and resid 103 through 105' Processing helix chain 'E' and resid 161 through 163 No H-bonds generated for 'chain 'E' and resid 161 through 163' Processing helix chain 'E' and resid 236 through 242 removed outlier: 4.069A pdb=" N ILE E 241 " --> pdb=" O GLY E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 259 removed outlier: 4.462A pdb=" N VAL E 251 " --> pdb=" O SER E 247 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N SER E 257 " --> pdb=" O LEU E 253 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N PHE E 258 " --> pdb=" O SER E 254 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N TRP E 259 " --> pdb=" O TRP E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 265 through 286 removed outlier: 3.553A pdb=" N GLY E 270 " --> pdb=" O PRO E 266 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR E 275 " --> pdb=" O LEU E 271 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N VAL E 276 " --> pdb=" O GLY E 272 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N THR E 280 " --> pdb=" O VAL E 276 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR E 281 " --> pdb=" O LEU E 277 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN E 282 " --> pdb=" O THR E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 300 through 324 removed outlier: 3.501A pdb=" N VAL E 305 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU E 314 " --> pdb=" O VAL E 310 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE E 323 " --> pdb=" O ALA E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 392 through 426 removed outlier: 3.647A pdb=" N ILE E 396 " --> pdb=" O ARG E 392 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER E 397 " --> pdb=" O LYS E 393 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE E 402 " --> pdb=" O ARG E 398 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ASP E 403 " --> pdb=" O ALA E 399 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG E 407 " --> pdb=" O ASP E 403 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N VAL E 408 " --> pdb=" O THR E 404 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE E 410 " --> pdb=" O SER E 406 " (cutoff:3.500A) Proline residue: E 411 - end of helix removed outlier: 4.233A pdb=" N LEU E 415 " --> pdb=" O PRO E 411 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE E 416 " --> pdb=" O LEU E 412 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TRP E 422 " --> pdb=" O ASN E 418 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR E 425 " --> pdb=" O TYR E 421 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N LYS E 426 " --> pdb=" O TRP E 422 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 182 through 186 removed outlier: 6.142A pdb=" N VAL A 53 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N GLU A 185 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL A 55 " --> pdb=" O GLU A 185 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ASN A 54 " --> pdb=" O ASN A 85 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ASN A 85 " --> pdb=" O ASN A 54 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TRP A 84 " --> pdb=" O VAL A 142 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 192 through 194 removed outlier: 6.691A pdb=" N ILE A 59 " --> pdb=" O GLN A 193 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ASN A 77 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N PHE A 64 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ARG A 75 " --> pdb=" O PHE A 64 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 114 through 116 removed outlier: 3.795A pdb=" N MET A 170 " --> pdb=" O ALA A 228 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA A 228 " --> pdb=" O MET A 170 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU A 227 " --> pdb=" O ARG A 212 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG A 212 " --> pdb=" O GLU A 227 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 165 through 167 Processing sheet with id= E, first strand: chain 'B' and resid 182 through 186 removed outlier: 6.142A pdb=" N VAL B 53 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N GLU B 185 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL B 55 " --> pdb=" O GLU B 185 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ASN B 54 " --> pdb=" O ASN B 85 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ASN B 85 " --> pdb=" O ASN B 54 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TRP B 84 " --> pdb=" O VAL B 142 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 192 through 194 removed outlier: 6.691A pdb=" N ILE B 59 " --> pdb=" O GLN B 193 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ASN B 77 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N PHE B 64 " --> pdb=" O ARG B 75 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ARG B 75 " --> pdb=" O PHE B 64 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 114 through 116 removed outlier: 3.794A pdb=" N MET B 170 " --> pdb=" O ALA B 228 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA B 228 " --> pdb=" O MET B 170 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU B 227 " --> pdb=" O ARG B 212 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG B 212 " --> pdb=" O GLU B 227 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 165 through 167 Processing sheet with id= I, first strand: chain 'C' and resid 182 through 186 removed outlier: 6.142A pdb=" N VAL C 53 " --> pdb=" O ILE C 183 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N GLU C 185 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL C 55 " --> pdb=" O GLU C 185 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ASN C 54 " --> pdb=" O ASN C 85 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ASN C 85 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TRP C 84 " --> pdb=" O VAL C 142 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 192 through 194 removed outlier: 6.691A pdb=" N ILE C 59 " --> pdb=" O GLN C 193 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ASN C 77 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N PHE C 64 " --> pdb=" O ARG C 75 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N ARG C 75 " --> pdb=" O PHE C 64 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 114 through 116 removed outlier: 3.795A pdb=" N MET C 170 " --> pdb=" O ALA C 228 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA C 228 " --> pdb=" O MET C 170 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU C 227 " --> pdb=" O ARG C 212 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG C 212 " --> pdb=" O GLU C 227 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 165 through 167 Processing sheet with id= M, first strand: chain 'D' and resid 182 through 186 removed outlier: 6.142A pdb=" N VAL D 53 " --> pdb=" O ILE D 183 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N GLU D 185 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL D 55 " --> pdb=" O GLU D 185 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ASN D 54 " --> pdb=" O ASN D 85 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N ASN D 85 " --> pdb=" O ASN D 54 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TRP D 84 " --> pdb=" O VAL D 142 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 192 through 194 removed outlier: 6.691A pdb=" N ILE D 59 " --> pdb=" O GLN D 193 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ASN D 77 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N PHE D 64 " --> pdb=" O ARG D 75 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N ARG D 75 " --> pdb=" O PHE D 64 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 114 through 116 removed outlier: 3.794A pdb=" N MET D 170 " --> pdb=" O ALA D 228 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA D 228 " --> pdb=" O MET D 170 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU D 227 " --> pdb=" O ARG D 212 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG D 212 " --> pdb=" O GLU D 227 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 165 through 167 Processing sheet with id= Q, first strand: chain 'E' and resid 182 through 186 removed outlier: 6.142A pdb=" N VAL E 53 " --> pdb=" O ILE E 183 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N GLU E 185 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL E 55 " --> pdb=" O GLU E 185 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ASN E 54 " --> pdb=" O ASN E 85 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N ASN E 85 " --> pdb=" O ASN E 54 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TRP E 84 " --> pdb=" O VAL E 142 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 192 through 194 removed outlier: 6.691A pdb=" N ILE E 59 " --> pdb=" O GLN E 193 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ASN E 77 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N PHE E 64 " --> pdb=" O ARG E 75 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ARG E 75 " --> pdb=" O PHE E 64 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 114 through 116 removed outlier: 3.795A pdb=" N MET E 170 " --> pdb=" O ALA E 228 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA E 228 " --> pdb=" O MET E 170 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU E 227 " --> pdb=" O ARG E 212 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG E 212 " --> pdb=" O GLU E 227 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 165 through 167 410 hydrogen bonds defined for protein. 1230 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: 4.32 Time building geometry restraints manager: 5.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4385 1.34 - 1.46: 3523 1.46 - 1.58: 6507 1.58 - 1.70: 0 1.70 - 1.81: 170 Bond restraints: 14585 Sorted by residual: bond pdb=" C1 NAG H 1 " pdb=" O5 NAG H 1 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.76e+00 bond pdb=" C1 NAG J 1 " pdb=" O5 NAG J 1 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.75e+00 bond pdb=" C1 NAG I 1 " pdb=" O5 NAG I 1 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.75e+00 bond pdb=" C1 NAG G 1 " pdb=" O5 NAG G 1 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.74e+00 bond pdb=" C1 NAG F 1 " pdb=" O5 NAG F 1 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.71e+00 ... (remaining 14580 not shown) Histogram of bond angle deviations from ideal: 100.66 - 107.32: 550 107.32 - 113.99: 8264 113.99 - 120.66: 5763 120.66 - 127.33: 5037 127.33 - 133.99: 161 Bond angle restraints: 19775 Sorted by residual: angle pdb=" CB ABU C 504 " pdb=" CG ABU C 504 " pdb=" CD ABU C 504 " ideal model delta sigma weight residual 116.08 109.39 6.69 3.00e+00 1.11e-01 4.97e+00 angle pdb=" CB ABU B 504 " pdb=" CG ABU B 504 " pdb=" CD ABU B 504 " ideal model delta sigma weight residual 116.08 109.40 6.68 3.00e+00 1.11e-01 4.96e+00 angle pdb=" CB ABU A 504 " pdb=" CG ABU A 504 " pdb=" CD ABU A 504 " ideal model delta sigma weight residual 116.08 109.40 6.68 3.00e+00 1.11e-01 4.95e+00 angle pdb=" CB ABU D 504 " pdb=" CG ABU D 504 " pdb=" CD ABU D 504 " ideal model delta sigma weight residual 116.08 109.43 6.65 3.00e+00 1.11e-01 4.91e+00 angle pdb=" CB ABU E 504 " pdb=" CG ABU E 504 " pdb=" CD ABU E 504 " ideal model delta sigma weight residual 116.08 109.44 6.64 3.00e+00 1.11e-01 4.90e+00 ... (remaining 19770 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.75: 8725 21.75 - 43.50: 150 43.50 - 65.24: 5 65.24 - 86.99: 30 86.99 - 108.74: 20 Dihedral angle restraints: 8930 sinusoidal: 3815 harmonic: 5115 Sorted by residual: dihedral pdb=" CB CYS C 154 " pdb=" SG CYS C 154 " pdb=" SG CYS C 168 " pdb=" CB CYS C 168 " ideal model delta sinusoidal sigma weight residual 93.00 36.38 56.62 1 1.00e+01 1.00e-02 4.32e+01 dihedral pdb=" CB CYS D 154 " pdb=" SG CYS D 154 " pdb=" SG CYS D 168 " pdb=" CB CYS D 168 " ideal model delta sinusoidal sigma weight residual 93.00 36.39 56.61 1 1.00e+01 1.00e-02 4.32e+01 dihedral pdb=" CB CYS E 154 " pdb=" SG CYS E 154 " pdb=" SG CYS E 168 " pdb=" CB CYS E 168 " ideal model delta sinusoidal sigma weight residual 93.00 36.40 56.60 1 1.00e+01 1.00e-02 4.31e+01 ... (remaining 8927 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 2059 0.078 - 0.156: 196 0.156 - 0.235: 0 0.235 - 0.313: 5 0.313 - 0.391: 5 Chirality restraints: 2265 Sorted by residual: chirality pdb=" C1 BMA H 3 " pdb=" O4 NAG H 2 " pdb=" C2 BMA H 3 " pdb=" O5 BMA H 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-02 2.50e+03 3.82e+02 chirality pdb=" C1 BMA F 3 " pdb=" O4 NAG F 2 " pdb=" C2 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-02 2.50e+03 3.80e+02 chirality pdb=" C1 BMA G 3 " pdb=" O4 NAG G 2 " pdb=" C2 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-02 2.50e+03 3.80e+02 ... (remaining 2262 not shown) Planarity restraints: 2455 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP D 102 " 0.019 5.00e-02 4.00e+02 2.85e-02 1.30e+00 pdb=" N PRO D 103 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO D 103 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO D 103 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE D 410 " 0.019 5.00e-02 4.00e+02 2.85e-02 1.30e+00 pdb=" N PRO D 411 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO D 411 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO D 411 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 410 " 0.019 5.00e-02 4.00e+02 2.84e-02 1.29e+00 pdb=" N PRO C 411 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO C 411 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO C 411 " 0.016 5.00e-02 4.00e+02 ... (remaining 2452 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 4030 2.81 - 3.33: 12307 3.33 - 3.85: 21968 3.85 - 4.38: 27230 4.38 - 4.90: 45497 Nonbonded interactions: 111032 Sorted by model distance: nonbonded pdb=" OG1 THR C 178 " pdb=" OD1 ASN C 180 " model vdw 2.285 2.440 nonbonded pdb=" OG1 THR E 178 " pdb=" OD1 ASN E 180 " model vdw 2.286 2.440 nonbonded pdb=" OG1 THR A 178 " pdb=" OD1 ASN A 180 " model vdw 2.286 2.440 nonbonded pdb=" OG1 THR D 178 " pdb=" OD1 ASN D 180 " model vdw 2.286 2.440 nonbonded pdb=" OG1 THR B 178 " pdb=" OD1 ASN B 180 " model vdw 2.286 2.440 ... (remaining 111027 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.320 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: 7.370 Check model and map are aligned: 0.170 Set scattering table: 0.160 Process input model: 39.610 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.130 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3725 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 : 0.002 0.027 14585 Z= 0.133 Angle : 0.526 6.685 19775 Z= 0.258 Chirality : 0.046 0.391 2265 Planarity : 0.003 0.028 2450 Dihedral : 11.125 108.738 5580 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.40 (0.15), residues: 1710 helix: -4.20 (0.11), residues: 465 sheet: -2.53 (0.24), residues: 335 loop : -2.31 (0.17), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 422 HIS 0.001 0.000 HIS C 125 PHE 0.003 0.001 PHE B 258 TYR 0.004 0.000 TYR D 74 ARG 0.002 0.000 ARG E 234 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 409 time to evaluate : 1.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 409 average time/residue: 0.3138 time to fit residues: 175.2925 Evaluate side-chains 240 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 240 time to evaluate : 1.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 8.9990 chunk 128 optimal weight: 0.8980 chunk 71 optimal weight: 9.9990 chunk 44 optimal weight: 1.9990 chunk 86 optimal weight: 6.9990 chunk 68 optimal weight: 7.9990 chunk 133 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 81 optimal weight: 0.0040 chunk 99 optimal weight: 20.0000 chunk 154 optimal weight: 9.9990 overall best weight: 2.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN A 77 ASN A 82 GLN A 125 HIS ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 166 GLN ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 ASN B 82 GLN B 125 HIS B 131 ASN ** B 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 ASN ** C 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 GLN ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 HIS ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 ASN ** D 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 GLN D 125 HIS ** D 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 166 GLN ** D 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 ASN E 77 ASN E 82 GLN E 125 HIS E 131 ASN ** E 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4496 moved from start: 0.4339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14585 Z= 0.273 Angle : 0.757 8.387 19775 Z= 0.370 Chirality : 0.047 0.168 2265 Planarity : 0.005 0.030 2450 Dihedral : 9.800 65.305 2200 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 18.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.32 % Allowed : 13.74 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.31 (0.17), residues: 1710 helix: -2.41 (0.19), residues: 495 sheet: -2.20 (0.22), residues: 410 loop : -1.91 (0.18), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 186 HIS 0.013 0.003 HIS E 125 PHE 0.026 0.002 PHE B 79 TYR 0.021 0.002 TYR C 317 ARG 0.006 0.001 ARG A 81 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 267 time to evaluate : 1.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 PHE cc_start: 0.4428 (t80) cc_final: 0.4172 (t80) REVERT: A 106 LEU cc_start: 0.2751 (OUTLIER) cc_final: 0.2547 (mm) REVERT: A 119 GLU cc_start: 0.3031 (OUTLIER) cc_final: 0.2790 (tt0) REVERT: A 171 GLN cc_start: 0.7403 (pt0) cc_final: 0.7025 (pm20) REVERT: B 60 PHE cc_start: 0.4542 (t80) cc_final: 0.4236 (t80) REVERT: B 106 LEU cc_start: 0.3092 (OUTLIER) cc_final: 0.2814 (mm) REVERT: B 163 MET cc_start: 0.6401 (mmm) cc_final: 0.6064 (mmm) REVERT: B 171 GLN cc_start: 0.7438 (pt0) cc_final: 0.7039 (pm20) REVERT: C 60 PHE cc_start: 0.4581 (t80) cc_final: 0.4373 (t80) REVERT: C 106 LEU cc_start: 0.3134 (OUTLIER) cc_final: 0.2791 (mm) REVERT: C 171 GLN cc_start: 0.7381 (pt0) cc_final: 0.7010 (pm20) REVERT: D 106 LEU cc_start: 0.3010 (OUTLIER) cc_final: 0.2727 (mm) REVERT: D 171 GLN cc_start: 0.7396 (pt0) cc_final: 0.7071 (pm20) REVERT: E 106 LEU cc_start: 0.2962 (OUTLIER) cc_final: 0.2743 (mm) REVERT: E 171 GLN cc_start: 0.7325 (OUTLIER) cc_final: 0.6898 (pm20) outliers start: 36 outliers final: 16 residues processed: 291 average time/residue: 0.2598 time to fit residues: 109.7685 Evaluate side-chains 209 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 186 time to evaluate : 1.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain D residue 31 ASP Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 171 GLN Chi-restraints excluded: chain E residue 236 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 85 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 128 optimal weight: 0.1980 chunk 105 optimal weight: 10.0000 chunk 42 optimal weight: 0.3980 chunk 154 optimal weight: 9.9990 chunk 167 optimal weight: 1.9990 chunk 137 optimal weight: 6.9990 chunk 153 optimal weight: 0.5980 chunk 52 optimal weight: 7.9990 chunk 124 optimal weight: 10.0000 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 83 GLN C 141 ASN ** C 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 ASN E 171 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4659 moved from start: 0.5594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14585 Z= 0.199 Angle : 0.749 9.195 19775 Z= 0.357 Chirality : 0.046 0.193 2265 Planarity : 0.004 0.026 2450 Dihedral : 7.874 59.410 2200 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 16.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 4.00 % Allowed : 14.90 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (0.18), residues: 1710 helix: -1.35 (0.22), residues: 495 sheet: -1.42 (0.25), residues: 370 loop : -1.80 (0.18), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 84 HIS 0.004 0.001 HIS C 217 PHE 0.025 0.002 PHE A 414 TYR 0.023 0.002 TYR A 317 ARG 0.008 0.001 ARG D 268 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 218 time to evaluate : 1.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 GLN cc_start: 0.7401 (pt0) cc_final: 0.7065 (pm20) REVERT: B 171 GLN cc_start: 0.7427 (pt0) cc_final: 0.7087 (pm20) REVERT: C 141 ASN cc_start: 0.6374 (m-40) cc_final: 0.5914 (m-40) REVERT: C 160 ASN cc_start: 0.6270 (OUTLIER) cc_final: 0.5465 (p0) REVERT: C 171 GLN cc_start: 0.7447 (pt0) cc_final: 0.7017 (pm20) REVERT: D 133 LEU cc_start: 0.5761 (tp) cc_final: 0.5464 (tt) REVERT: D 171 GLN cc_start: 0.7338 (pt0) cc_final: 0.7085 (pm20) REVERT: E 60 PHE cc_start: 0.4380 (t80) cc_final: 0.3882 (t80) REVERT: E 171 GLN cc_start: 0.7482 (OUTLIER) cc_final: 0.6548 (pm20) REVERT: E 410 PHE cc_start: 0.6908 (m-10) cc_final: 0.6638 (m-80) outliers start: 62 outliers final: 36 residues processed: 260 average time/residue: 0.2237 time to fit residues: 88.9665 Evaluate side-chains 233 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 195 time to evaluate : 1.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 84 TRP Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 84 TRP Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 84 TRP Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain D residue 31 ASP Chi-restraints excluded: chain D residue 84 TRP Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 84 TRP Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain E residue 171 GLN Chi-restraints excluded: chain E residue 256 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 152 optimal weight: 0.9990 chunk 116 optimal weight: 0.9990 chunk 80 optimal weight: 0.9980 chunk 17 optimal weight: 7.9990 chunk 73 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 155 optimal weight: 10.0000 chunk 164 optimal weight: 9.9990 chunk 81 optimal weight: 7.9990 chunk 147 optimal weight: 9.9990 chunk 44 optimal weight: 7.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 171 GLN ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 GLN ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 171 GLN ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 171 GLN ** E 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4876 moved from start: 0.6437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14585 Z= 0.178 Angle : 0.719 9.622 19775 Z= 0.337 Chirality : 0.044 0.188 2265 Planarity : 0.004 0.050 2450 Dihedral : 6.232 59.451 2200 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 16.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 4.06 % Allowed : 16.65 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.92 (0.19), residues: 1710 helix: -0.68 (0.24), residues: 520 sheet: -1.06 (0.26), residues: 400 loop : -1.72 (0.19), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 302 HIS 0.005 0.001 HIS E 217 PHE 0.016 0.002 PHE C 161 TYR 0.029 0.002 TYR E 317 ARG 0.004 0.000 ARG B 135 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 206 time to evaluate : 1.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.4055 (OUTLIER) cc_final: 0.3847 (ptt) REVERT: A 156 MET cc_start: 0.6578 (mmt) cc_final: 0.6131 (mmm) REVERT: A 171 GLN cc_start: 0.7668 (pt0) cc_final: 0.7002 (pm20) REVERT: A 410 PHE cc_start: 0.7000 (m-10) cc_final: 0.6688 (m-80) REVERT: B 163 MET cc_start: 0.6790 (mmm) cc_final: 0.6570 (mmm) REVERT: B 171 GLN cc_start: 0.7632 (pt0) cc_final: 0.7042 (pm20) REVERT: B 410 PHE cc_start: 0.7040 (m-10) cc_final: 0.6722 (m-80) REVERT: C 28 GLU cc_start: 0.4546 (tt0) cc_final: 0.3871 (mm-30) REVERT: C 141 ASN cc_start: 0.6490 (m-40) cc_final: 0.6125 (m-40) REVERT: C 163 MET cc_start: 0.6882 (mmm) cc_final: 0.6655 (mmm) REVERT: C 171 GLN cc_start: 0.7583 (pt0) cc_final: 0.6928 (pm20) REVERT: C 410 PHE cc_start: 0.6885 (m-10) cc_final: 0.6562 (m-80) REVERT: D 156 MET cc_start: 0.6398 (mmt) cc_final: 0.5848 (mmm) REVERT: D 163 MET cc_start: 0.6884 (mmm) cc_final: 0.6552 (mmm) REVERT: D 171 GLN cc_start: 0.7607 (pt0) cc_final: 0.6968 (pm20) REVERT: D 410 PHE cc_start: 0.6974 (m-10) cc_final: 0.6650 (m-80) REVERT: E 171 GLN cc_start: 0.7617 (pt0) cc_final: 0.6451 (pm20) REVERT: E 410 PHE cc_start: 0.6961 (m-10) cc_final: 0.6641 (m-80) REVERT: E 418 ASN cc_start: 0.8620 (m-40) cc_final: 0.8202 (m110) outliers start: 63 outliers final: 46 residues processed: 256 average time/residue: 0.2076 time to fit residues: 82.8564 Evaluate side-chains 238 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 191 time to evaluate : 1.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 34 MET Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 84 TRP Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 58 ASN Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain D residue 31 ASP Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain E residue 256 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 2 optimal weight: 20.0000 chunk 122 optimal weight: 0.7980 chunk 67 optimal weight: 10.0000 chunk 140 optimal weight: 0.0980 chunk 113 optimal weight: 9.9990 chunk 0 optimal weight: 8.9990 chunk 83 optimal weight: 5.9990 chunk 147 optimal weight: 9.9990 chunk 41 optimal weight: 10.0000 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 ASN ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5730 moved from start: 0.9312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.115 14585 Z= 0.327 Angle : 0.879 12.083 19775 Z= 0.434 Chirality : 0.049 0.206 2265 Planarity : 0.005 0.048 2450 Dihedral : 5.750 50.838 2200 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 21.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 5.55 % Allowed : 17.10 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.20), residues: 1710 helix: -0.25 (0.24), residues: 515 sheet: -1.12 (0.26), residues: 405 loop : -1.59 (0.20), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 84 HIS 0.009 0.002 HIS C 217 PHE 0.026 0.003 PHE B 203 TYR 0.028 0.003 TYR E 218 ARG 0.010 0.001 ARG E 268 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 248 time to evaluate : 1.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 VAL cc_start: 0.7678 (t) cc_final: 0.7279 (t) REVERT: A 156 MET cc_start: 0.7737 (mmt) cc_final: 0.7434 (mmp) REVERT: A 418 ASN cc_start: 0.8928 (m-40) cc_final: 0.8542 (m110) REVERT: B 142 VAL cc_start: 0.7746 (t) cc_final: 0.7390 (t) REVERT: B 151 VAL cc_start: 0.6818 (OUTLIER) cc_final: 0.6603 (m) REVERT: B 171 GLN cc_start: 0.7816 (pt0) cc_final: 0.6716 (pm20) REVERT: B 418 ASN cc_start: 0.8925 (m-40) cc_final: 0.8506 (m110) REVERT: C 24 MET cc_start: 0.2744 (ttt) cc_final: 0.2446 (ttt) REVERT: C 142 VAL cc_start: 0.7768 (t) cc_final: 0.7391 (t) REVERT: C 171 GLN cc_start: 0.7907 (pt0) cc_final: 0.7140 (pm20) REVERT: C 418 ASN cc_start: 0.8915 (m-40) cc_final: 0.8536 (m110) REVERT: D 82 GLN cc_start: 0.8316 (tm-30) cc_final: 0.8111 (tm-30) REVERT: D 105 MET cc_start: 0.0517 (tmm) cc_final: 0.0284 (tmm) REVERT: D 163 MET cc_start: 0.7574 (mmm) cc_final: 0.7287 (mmm) REVERT: D 171 GLN cc_start: 0.7958 (pt0) cc_final: 0.6708 (pm20) REVERT: D 202 GLN cc_start: 0.7848 (pm20) cc_final: 0.7313 (mp-120) REVERT: D 418 ASN cc_start: 0.8945 (m-40) cc_final: 0.8538 (m110) REVERT: E 141 ASN cc_start: 0.6957 (OUTLIER) cc_final: 0.6683 (m-40) REVERT: E 142 VAL cc_start: 0.7698 (t) cc_final: 0.7288 (t) REVERT: E 171 GLN cc_start: 0.7787 (pt0) cc_final: 0.6989 (pm20) REVERT: E 202 GLN cc_start: 0.7976 (pm20) cc_final: 0.7613 (pm20) REVERT: E 418 ASN cc_start: 0.8978 (m-40) cc_final: 0.8553 (m110) outliers start: 86 outliers final: 55 residues processed: 324 average time/residue: 0.2144 time to fit residues: 109.3215 Evaluate side-chains 285 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 228 time to evaluate : 1.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 58 ASN Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 125 HIS Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain D residue 31 ASP Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 118 ASN Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain E residue 58 ASN Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 125 HIS Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 141 ASN Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 179 MET Chi-restraints excluded: chain E residue 243 MET Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 406 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 55 optimal weight: 0.9990 chunk 147 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 164 optimal weight: 9.9990 chunk 136 optimal weight: 0.4980 chunk 76 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 86 optimal weight: 8.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 62 ASN A 83 GLN ** B 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 83 GLN ** C 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 ASN D 83 GLN ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 ASN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 83 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5817 moved from start: 0.9890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14585 Z= 0.192 Angle : 0.821 15.564 19775 Z= 0.378 Chirality : 0.046 0.220 2265 Planarity : 0.004 0.062 2450 Dihedral : 5.640 54.732 2200 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.29 % Allowed : 21.61 % Favored : 75.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.26 (0.20), residues: 1710 helix: -0.00 (0.24), residues: 505 sheet: -0.68 (0.27), residues: 395 loop : -1.41 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 302 HIS 0.004 0.001 HIS A 217 PHE 0.013 0.001 PHE E 161 TYR 0.018 0.001 TYR B 74 ARG 0.016 0.000 ARG A 147 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 251 time to evaluate : 1.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.6196 (ptt) cc_final: 0.5909 (mtm) REVERT: A 156 MET cc_start: 0.7853 (mmt) cc_final: 0.7437 (mmm) REVERT: A 204 ILE cc_start: 0.8125 (mt) cc_final: 0.7814 (mt) REVERT: A 415 LEU cc_start: 0.8453 (pp) cc_final: 0.8102 (tt) REVERT: A 418 ASN cc_start: 0.8984 (m-40) cc_final: 0.8738 (m110) REVERT: B 171 GLN cc_start: 0.8225 (pt0) cc_final: 0.7104 (pm20) REVERT: B 415 LEU cc_start: 0.8439 (pp) cc_final: 0.8089 (tt) REVERT: B 418 ASN cc_start: 0.8981 (m-40) cc_final: 0.8594 (m110) REVERT: C 24 MET cc_start: 0.3091 (ttt) cc_final: 0.2776 (ttt) REVERT: C 171 GLN cc_start: 0.8219 (pt0) cc_final: 0.7109 (pm20) REVERT: C 415 LEU cc_start: 0.8409 (pp) cc_final: 0.8052 (tt) REVERT: C 418 ASN cc_start: 0.8959 (m-40) cc_final: 0.8637 (m110) REVERT: D 24 MET cc_start: 0.2302 (ttt) cc_final: 0.1923 (tmt) REVERT: D 130 ASP cc_start: 0.7407 (OUTLIER) cc_final: 0.7117 (p0) REVERT: D 171 GLN cc_start: 0.8228 (pt0) cc_final: 0.7162 (pm20) REVERT: D 415 LEU cc_start: 0.8463 (pp) cc_final: 0.8127 (tt) REVERT: D 418 ASN cc_start: 0.8975 (m-40) cc_final: 0.8739 (m110) REVERT: E 82 GLN cc_start: 0.8334 (tm-30) cc_final: 0.8099 (tm-30) REVERT: E 171 GLN cc_start: 0.8120 (pt0) cc_final: 0.6872 (pm20) REVERT: E 415 LEU cc_start: 0.8477 (pp) cc_final: 0.8121 (tt) REVERT: E 418 ASN cc_start: 0.9038 (m-40) cc_final: 0.8805 (m110) outliers start: 51 outliers final: 39 residues processed: 295 average time/residue: 0.2047 time to fit residues: 95.3262 Evaluate side-chains 271 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 231 time to evaluate : 1.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 58 ASN Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain D residue 31 ASP Chi-restraints excluded: chain D residue 34 MET Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 196 ASP Chi-restraints excluded: chain E residue 226 ILE Chi-restraints excluded: chain E residue 256 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 158 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 chunk 120 optimal weight: 0.4980 chunk 138 optimal weight: 0.0470 chunk 91 optimal weight: 6.9990 chunk 163 optimal weight: 0.7980 chunk 102 optimal weight: 10.0000 chunk 99 optimal weight: 9.9990 chunk 75 optimal weight: 0.0370 chunk 101 optimal weight: 0.9980 overall best weight: 0.4756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN A 62 ASN ** B 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 ASN ** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 ASN ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 ASN E 131 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5811 moved from start: 1.0141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14585 Z= 0.168 Angle : 0.774 12.174 19775 Z= 0.353 Chirality : 0.045 0.227 2265 Planarity : 0.004 0.051 2450 Dihedral : 5.390 52.855 2200 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.81 % Allowed : 22.32 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.08 (0.21), residues: 1710 helix: 0.00 (0.24), residues: 515 sheet: -0.42 (0.27), residues: 405 loop : -1.30 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 302 HIS 0.004 0.001 HIS A 217 PHE 0.015 0.001 PHE C 115 TYR 0.019 0.001 TYR A 317 ARG 0.008 0.000 ARG A 147 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 233 time to evaluate : 1.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.6159 (ptt) cc_final: 0.5820 (mtm) REVERT: A 156 MET cc_start: 0.7712 (mmt) cc_final: 0.7330 (mmm) REVERT: A 236 MET cc_start: 0.7603 (mmm) cc_final: 0.7399 (mmm) REVERT: A 415 LEU cc_start: 0.8463 (pp) cc_final: 0.8187 (tt) REVERT: B 171 GLN cc_start: 0.8371 (pt0) cc_final: 0.6948 (pm20) REVERT: B 415 LEU cc_start: 0.8496 (pp) cc_final: 0.8242 (tt) REVERT: B 418 ASN cc_start: 0.8999 (m-40) cc_final: 0.8781 (m110) REVERT: C 24 MET cc_start: 0.3092 (ttt) cc_final: 0.2762 (ttt) REVERT: C 171 GLN cc_start: 0.8017 (pt0) cc_final: 0.6890 (pm20) REVERT: C 262 MET cc_start: 0.1107 (tpt) cc_final: 0.0812 (mmm) REVERT: C 411 PRO cc_start: 0.8259 (Cg_exo) cc_final: 0.8015 (Cg_endo) REVERT: C 415 LEU cc_start: 0.8417 (pp) cc_final: 0.8103 (tt) REVERT: D 24 MET cc_start: 0.2128 (ttt) cc_final: 0.1879 (ttt) REVERT: D 130 ASP cc_start: 0.7404 (OUTLIER) cc_final: 0.7118 (p0) REVERT: D 171 GLN cc_start: 0.8400 (pt0) cc_final: 0.6881 (pm20) REVERT: D 415 LEU cc_start: 0.8467 (pp) cc_final: 0.8200 (tt) REVERT: E 82 GLN cc_start: 0.8381 (tm-30) cc_final: 0.8176 (tm-30) REVERT: E 171 GLN cc_start: 0.8157 (pt0) cc_final: 0.6706 (pm20) REVERT: E 202 GLN cc_start: 0.7951 (pm20) cc_final: 0.7302 (pm20) REVERT: E 415 LEU cc_start: 0.8490 (pp) cc_final: 0.8217 (tt) REVERT: E 418 ASN cc_start: 0.9033 (m-40) cc_final: 0.8804 (m110) outliers start: 59 outliers final: 48 residues processed: 287 average time/residue: 0.2035 time to fit residues: 91.7793 Evaluate side-chains 275 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 226 time to evaluate : 1.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 58 ASN Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 84 TRP Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 84 TRP Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 58 ASN Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 84 TRP Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain D residue 31 ASP Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 84 TRP Chi-restraints excluded: chain D residue 96 ASP Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 196 ASP Chi-restraints excluded: chain E residue 256 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 4.9990 chunk 97 optimal weight: 9.9990 chunk 49 optimal weight: 9.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 9.9990 chunk 104 optimal weight: 0.0040 chunk 111 optimal weight: 0.5980 chunk 81 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 128 optimal weight: 4.9990 chunk 149 optimal weight: 4.9990 overall best weight: 1.9198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 418 ASN D 58 ASN ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5978 moved from start: 1.0630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14585 Z= 0.195 Angle : 0.768 12.491 19775 Z= 0.353 Chirality : 0.045 0.222 2265 Planarity : 0.004 0.053 2450 Dihedral : 5.358 50.142 2200 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 16.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.81 % Allowed : 22.32 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.21), residues: 1710 helix: 0.10 (0.24), residues: 515 sheet: -0.22 (0.27), residues: 395 loop : -1.25 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 110 HIS 0.004 0.001 HIS D 217 PHE 0.014 0.001 PHE C 115 TYR 0.022 0.001 TYR A 317 ARG 0.017 0.001 ARG A 81 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 231 time to evaluate : 1.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.6443 (ptt) cc_final: 0.6155 (mtm) REVERT: A 156 MET cc_start: 0.7857 (mmt) cc_final: 0.7468 (mmm) REVERT: A 415 LEU cc_start: 0.8490 (pp) cc_final: 0.8241 (tt) REVERT: B 171 GLN cc_start: 0.8271 (pt0) cc_final: 0.6947 (pm20) REVERT: B 415 LEU cc_start: 0.8532 (pp) cc_final: 0.8305 (tt) REVERT: C 24 MET cc_start: 0.3362 (ttt) cc_final: 0.3018 (ttt) REVERT: C 171 GLN cc_start: 0.8440 (pt0) cc_final: 0.6892 (pm20) REVERT: C 262 MET cc_start: 0.1257 (tpt) cc_final: 0.0952 (mmm) REVERT: C 415 LEU cc_start: 0.8486 (pp) cc_final: 0.8213 (tt) REVERT: D 24 MET cc_start: 0.2243 (ttt) cc_final: 0.1923 (ttt) REVERT: D 130 ASP cc_start: 0.7569 (OUTLIER) cc_final: 0.7251 (p0) REVERT: D 171 GLN cc_start: 0.8254 (pt0) cc_final: 0.6831 (pm20) REVERT: D 415 LEU cc_start: 0.8572 (pp) cc_final: 0.8334 (tt) REVERT: E 82 GLN cc_start: 0.8413 (tm-30) cc_final: 0.8189 (tm-30) REVERT: E 202 GLN cc_start: 0.8016 (pm20) cc_final: 0.7329 (pm20) REVERT: E 236 MET cc_start: 0.7814 (mmm) cc_final: 0.7611 (mmp) REVERT: E 415 LEU cc_start: 0.8520 (pp) cc_final: 0.8256 (tt) REVERT: E 418 ASN cc_start: 0.9076 (m-40) cc_final: 0.8838 (m110) outliers start: 59 outliers final: 52 residues processed: 285 average time/residue: 0.2030 time to fit residues: 90.9348 Evaluate side-chains 284 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 231 time to evaluate : 1.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 58 ASN Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 84 TRP Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 168 CYS Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 58 ASN Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 84 TRP Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain D residue 31 ASP Chi-restraints excluded: chain D residue 34 MET Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 84 TRP Chi-restraints excluded: chain D residue 96 ASP Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 168 CYS Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 256 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 156 optimal weight: 8.9990 chunk 143 optimal weight: 6.9990 chunk 152 optimal weight: 0.2980 chunk 91 optimal weight: 6.9990 chunk 66 optimal weight: 0.8980 chunk 119 optimal weight: 2.9990 chunk 46 optimal weight: 8.9990 chunk 137 optimal weight: 10.0000 chunk 144 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 161 optimal weight: 10.0000 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 ASN ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6433 moved from start: 1.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.116 14585 Z= 0.289 Angle : 0.881 15.830 19775 Z= 0.428 Chirality : 0.049 0.475 2265 Planarity : 0.005 0.060 2450 Dihedral : 5.749 48.334 2200 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 18.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 4.00 % Allowed : 22.32 % Favored : 73.68 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.87 (0.21), residues: 1710 helix: 0.15 (0.25), residues: 480 sheet: -0.52 (0.26), residues: 405 loop : -0.97 (0.23), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 186 HIS 0.006 0.001 HIS A 217 PHE 0.037 0.002 PHE B 60 TYR 0.027 0.002 TYR A 317 ARG 0.012 0.001 ARG A 81 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 251 time to evaluate : 1.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.7228 (ptt) cc_final: 0.7000 (mtm) REVERT: A 179 MET cc_start: 0.7306 (mpp) cc_final: 0.6762 (mmm) REVERT: A 202 GLN cc_start: 0.8204 (pm20) cc_final: 0.7911 (pm20) REVERT: C 24 MET cc_start: 0.4446 (ttt) cc_final: 0.4209 (ttt) REVERT: C 202 GLN cc_start: 0.8366 (pm20) cc_final: 0.7721 (pm20) REVERT: D 24 MET cc_start: 0.2801 (ttt) cc_final: 0.2549 (ttt) REVERT: D 130 ASP cc_start: 0.7946 (OUTLIER) cc_final: 0.7688 (p0) REVERT: E 202 GLN cc_start: 0.8211 (pm20) cc_final: 0.7613 (pm20) outliers start: 62 outliers final: 53 residues processed: 303 average time/residue: 0.2241 time to fit residues: 103.3386 Evaluate side-chains 291 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 237 time to evaluate : 1.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 84 TRP Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 168 CYS Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 58 ASN Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain D residue 31 ASP Chi-restraints excluded: chain D residue 34 MET Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 96 ASP Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 226 ILE Chi-restraints excluded: chain E residue 243 MET Chi-restraints excluded: chain E residue 256 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 30.0000 chunk 76 optimal weight: 0.9980 chunk 112 optimal weight: 4.9990 chunk 169 optimal weight: 6.9990 chunk 155 optimal weight: 4.9990 chunk 134 optimal weight: 0.2980 chunk 14 optimal weight: 7.9990 chunk 104 optimal weight: 0.0010 chunk 82 optimal weight: 9.9990 chunk 107 optimal weight: 2.9990 chunk 143 optimal weight: 7.9990 overall best weight: 1.8590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6547 moved from start: 1.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 14585 Z= 0.226 Angle : 0.828 15.029 19775 Z= 0.383 Chirality : 0.046 0.260 2265 Planarity : 0.004 0.058 2450 Dihedral : 5.546 59.965 2200 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 16.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.84 % Allowed : 23.94 % Favored : 73.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.72 (0.21), residues: 1710 helix: 0.25 (0.25), residues: 480 sheet: -0.32 (0.26), residues: 405 loop : -0.92 (0.23), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 110 HIS 0.005 0.001 HIS C 125 PHE 0.045 0.002 PHE A 60 TYR 0.016 0.001 TYR A 317 ARG 0.009 0.000 ARG A 147 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 259 time to evaluate : 1.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 MET cc_start: 0.2847 (tpt) cc_final: 0.0959 (tpt) REVERT: A 179 MET cc_start: 0.7319 (mpp) cc_final: 0.6998 (mmm) REVERT: A 202 GLN cc_start: 0.8244 (pm20) cc_final: 0.7994 (pm20) REVERT: B 156 MET cc_start: 0.8387 (mmm) cc_final: 0.7985 (mmp) REVERT: B 179 MET cc_start: 0.7364 (mpp) cc_final: 0.6983 (mmm) REVERT: C 24 MET cc_start: 0.5253 (ttt) cc_final: 0.4367 (ttt) REVERT: C 163 MET cc_start: 0.7885 (mmm) cc_final: 0.7566 (mmm) REVERT: C 202 GLN cc_start: 0.8405 (pm20) cc_final: 0.7803 (pm20) REVERT: C 262 MET cc_start: 0.1419 (tpt) cc_final: 0.0402 (mtp) REVERT: D 130 ASP cc_start: 0.8062 (OUTLIER) cc_final: 0.7833 (p0) REVERT: D 179 MET cc_start: 0.7409 (mpp) cc_final: 0.6969 (mmm) REVERT: E 202 GLN cc_start: 0.8328 (pm20) cc_final: 0.7793 (pm20) REVERT: E 242 GLN cc_start: 0.7395 (tm-30) cc_final: 0.7191 (tm-30) outliers start: 44 outliers final: 42 residues processed: 298 average time/residue: 0.2365 time to fit residues: 105.8781 Evaluate side-chains 282 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 239 time to evaluate : 1.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 84 TRP Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 168 CYS Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 58 ASN Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain D residue 31 ASP Chi-restraints excluded: chain D residue 34 MET Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 96 ASP Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 226 ILE Chi-restraints excluded: chain E residue 256 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 41 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 135 optimal weight: 5.9990 chunk 56 optimal weight: 0.7980 chunk 138 optimal weight: 10.0000 chunk 17 optimal weight: 0.2980 chunk 24 optimal weight: 7.9990 chunk 118 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 ASN ** C 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 GLN ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.118767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.094861 restraints weight = 52201.960| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 7.26 r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 moved from start: 1.3489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 14585 Z= 0.196 Angle : 0.849 19.390 19775 Z= 0.385 Chirality : 0.045 0.226 2265 Planarity : 0.004 0.055 2450 Dihedral : 5.337 52.255 2200 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.90 % Allowed : 25.03 % Favored : 72.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.63 (0.21), residues: 1710 helix: 0.36 (0.25), residues: 480 sheet: -0.22 (0.26), residues: 405 loop : -0.92 (0.23), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 110 HIS 0.002 0.001 HIS A 125 PHE 0.030 0.001 PHE A 60 TYR 0.018 0.001 TYR B 74 ARG 0.007 0.000 ARG A 147 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3085.48 seconds wall clock time: 56 minutes 36.55 seconds (3396.55 seconds total)