Starting phenix.real_space_refine on Wed Mar 4 23:16:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6np0_0469/03_2026/6np0_0469_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6np0_0469/03_2026/6np0_0469.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6np0_0469/03_2026/6np0_0469_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6np0_0469/03_2026/6np0_0469_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6np0_0469/03_2026/6np0_0469.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6np0_0469/03_2026/6np0_0469.map" } resolution = 2.92 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.003 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: 5 Type Number sf(0) Gaussians S 50 5.16 5 Cl 1 4.86 5 C 11095 2.51 5 N 2720 2.21 5 O 3025 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16891 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 3260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3260 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 20, 'TRANS': 374} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 3260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3260 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 20, 'TRANS': 374} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 3260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3260 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 20, 'TRANS': 374} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 4 Chain: "D" Number of atoms: 3260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3260 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 20, 'TRANS': 374} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 4 Chain: "E" Number of atoms: 3260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3260 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 20, 'TRANS': 374} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 4 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" 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: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" 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: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 52 Unusual residues: {' CL': 1, 'CWB': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 51 Unusual residues: {'CWB': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 51 Unusual residues: {'CWB': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 74 Unusual residues: {'CWB': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 4.43, per 1000 atoms: 0.26 Number of scatterers: 16891 At special positions: 0 Unit cell: (104.272, 106.4, 173.432, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 50 16.00 O 3025 8.00 N 2720 7.00 C 11095 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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=5, 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 H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG G 1 " - " ASN A 148 " " NAG I 1 " - " ASN B 148 " " NAG K 1 " - " ASN C 148 " " NAG M 1 " - " ASN D 148 " " NAG O 1 " - " ASN E 148 " Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.75 Conformation dependent library (CDL) restraints added in 734.1 milliseconds 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3840 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 10 sheets defined 42.0% alpha, 22.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 13 through 20 Processing helix chain 'A' and resid 91 through 93 No H-bonds generated for 'chain 'A' and resid 91 through 93' Processing helix chain 'A' and resid 170 through 176 removed outlier: 3.647A pdb=" N SER A 176 " --> pdb=" O GLU A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 225 removed outlier: 3.674A pdb=" N ALA A 224 " --> pdb=" O LEU A 221 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL A 225 " --> pdb=" O PHE A 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 221 through 225' Processing helix chain 'A' and resid 227 through 242 removed outlier: 3.661A pdb=" N SER A 231 " --> pdb=" O LEU A 227 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N MET A 235 " --> pdb=" O SER A 231 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N VAL A 236 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL A 237 " --> pdb=" O PHE A 233 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASP A 238 " --> pdb=" O LEU A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 244 No H-bonds generated for 'chain 'A' and resid 243 through 244' Processing helix chain 'A' and resid 245 through 248 Processing helix chain 'A' and resid 249 through 271 removed outlier: 4.218A pdb=" N SER A 253 " --> pdb=" O GLY A 249 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE A 267 " --> pdb=" O SER A 263 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASP A 271 " --> pdb=" O ILE A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 308 removed outlier: 3.694A pdb=" N VAL A 285 " --> pdb=" O PRO A 281 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE A 296 " --> pdb=" O ALA A 292 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 332 removed outlier: 4.022A pdb=" N ILE A 332 " --> pdb=" O ARG A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 461 removed outlier: 3.706A pdb=" N SER A 408 " --> pdb=" O GLN A 404 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE A 409 " --> pdb=" O GLU A 405 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS A 415 " --> pdb=" O HIS A 411 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ARG A 416 " --> pdb=" O PHE A 412 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA A 423 " --> pdb=" O MET A 419 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL A 432 " --> pdb=" O ARG A 428 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE A 458 " --> pdb=" O THR A 454 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N TRP A 459 " --> pdb=" O LEU A 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 20 Processing helix chain 'B' and resid 91 through 93 No H-bonds generated for 'chain 'B' and resid 91 through 93' Processing helix chain 'B' and resid 170 through 176 removed outlier: 3.647A pdb=" N SER B 176 " --> pdb=" O GLU B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 225 removed outlier: 3.673A pdb=" N ALA B 224 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL B 225 " --> pdb=" O PHE B 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 221 through 225' Processing helix chain 'B' and resid 227 through 242 removed outlier: 3.660A pdb=" N SER B 231 " --> pdb=" O LEU B 227 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N MET B 235 " --> pdb=" O SER B 231 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N VAL B 236 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL B 237 " --> pdb=" O PHE B 233 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASP B 238 " --> pdb=" O LEU B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 244 No H-bonds generated for 'chain 'B' and resid 243 through 244' Processing helix chain 'B' and resid 245 through 248 Processing helix chain 'B' and resid 249 through 271 removed outlier: 4.218A pdb=" N SER B 253 " --> pdb=" O GLY B 249 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE B 267 " --> pdb=" O SER B 263 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASP B 271 " --> pdb=" O ILE B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 308 removed outlier: 3.694A pdb=" N VAL B 285 " --> pdb=" O PRO B 281 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE B 296 " --> pdb=" O ALA B 292 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR B 301 " --> pdb=" O SER B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 332 removed outlier: 4.021A pdb=" N ILE B 332 " --> pdb=" O ARG B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 461 removed outlier: 3.706A pdb=" N SER B 408 " --> pdb=" O GLN B 404 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE B 409 " --> pdb=" O GLU B 405 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS B 415 " --> pdb=" O HIS B 411 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ARG B 416 " --> pdb=" O PHE B 412 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA B 423 " --> pdb=" O MET B 419 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL B 432 " --> pdb=" O ARG B 428 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ILE B 458 " --> pdb=" O THR B 454 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N TRP B 459 " --> pdb=" O LEU B 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 20 Processing helix chain 'C' and resid 91 through 93 No H-bonds generated for 'chain 'C' and resid 91 through 93' Processing helix chain 'C' and resid 170 through 176 removed outlier: 3.647A pdb=" N SER C 176 " --> pdb=" O GLU C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 225 removed outlier: 3.674A pdb=" N ALA C 224 " --> pdb=" O LEU C 221 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL C 225 " --> pdb=" O PHE C 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 221 through 225' Processing helix chain 'C' and resid 227 through 242 removed outlier: 3.661A pdb=" N SER C 231 " --> pdb=" O LEU C 227 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N MET C 235 " --> pdb=" O SER C 231 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N VAL C 236 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL C 237 " --> pdb=" O PHE C 233 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASP C 238 " --> pdb=" O LEU C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 244 No H-bonds generated for 'chain 'C' and resid 243 through 244' Processing helix chain 'C' and resid 245 through 248 Processing helix chain 'C' and resid 249 through 271 removed outlier: 4.219A pdb=" N SER C 253 " --> pdb=" O GLY C 249 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE C 267 " --> pdb=" O SER C 263 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASP C 271 " --> pdb=" O ILE C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 308 removed outlier: 3.694A pdb=" N VAL C 285 " --> pdb=" O PRO C 281 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE C 296 " --> pdb=" O ALA C 292 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR C 301 " --> pdb=" O SER C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 332 removed outlier: 4.022A pdb=" N ILE C 332 " --> pdb=" O ARG C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 461 removed outlier: 3.706A pdb=" N SER C 408 " --> pdb=" O GLN C 404 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE C 409 " --> pdb=" O GLU C 405 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS C 415 " --> pdb=" O HIS C 411 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ARG C 416 " --> pdb=" O PHE C 412 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA C 423 " --> pdb=" O MET C 419 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL C 432 " --> pdb=" O ARG C 428 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE C 458 " --> pdb=" O THR C 454 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N TRP C 459 " --> pdb=" O LEU C 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 20 Processing helix chain 'D' and resid 91 through 93 No H-bonds generated for 'chain 'D' and resid 91 through 93' Processing helix chain 'D' and resid 170 through 176 removed outlier: 3.647A pdb=" N SER D 176 " --> pdb=" O GLU D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 225 removed outlier: 3.674A pdb=" N ALA D 224 " --> pdb=" O LEU D 221 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL D 225 " --> pdb=" O PHE D 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 221 through 225' Processing helix chain 'D' and resid 227 through 242 removed outlier: 3.661A pdb=" N SER D 231 " --> pdb=" O LEU D 227 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N MET D 235 " --> pdb=" O SER D 231 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N VAL D 236 " --> pdb=" O ILE D 232 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL D 237 " --> pdb=" O PHE D 233 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASP D 238 " --> pdb=" O LEU D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 244 No H-bonds generated for 'chain 'D' and resid 243 through 244' Processing helix chain 'D' and resid 245 through 248 Processing helix chain 'D' and resid 249 through 271 removed outlier: 4.219A pdb=" N SER D 253 " --> pdb=" O GLY D 249 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASP D 271 " --> pdb=" O ILE D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 308 removed outlier: 3.694A pdb=" N VAL D 285 " --> pdb=" O PRO D 281 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE D 296 " --> pdb=" O ALA D 292 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR D 301 " --> pdb=" O SER D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 332 removed outlier: 4.022A pdb=" N ILE D 332 " --> pdb=" O ARG D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 398 through 461 removed outlier: 3.706A pdb=" N SER D 408 " --> pdb=" O GLN D 404 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS D 415 " --> pdb=" O HIS D 411 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ARG D 416 " --> pdb=" O PHE D 412 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA D 423 " --> pdb=" O MET D 419 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL D 432 " --> pdb=" O ARG D 428 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE D 458 " --> pdb=" O THR D 454 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N TRP D 459 " --> pdb=" O LEU D 455 " (cutoff:3.500A) Processing helix chain 'E' and resid 13 through 20 Processing helix chain 'E' and resid 91 through 93 No H-bonds generated for 'chain 'E' and resid 91 through 93' Processing helix chain 'E' and resid 170 through 176 removed outlier: 3.647A pdb=" N SER E 176 " --> pdb=" O GLU E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 221 through 225 removed outlier: 3.673A pdb=" N ALA E 224 " --> pdb=" O LEU E 221 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL E 225 " --> pdb=" O PHE E 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 221 through 225' Processing helix chain 'E' and resid 227 through 242 removed outlier: 3.659A pdb=" N SER E 231 " --> pdb=" O LEU E 227 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N MET E 235 " --> pdb=" O SER E 231 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N VAL E 236 " --> pdb=" O ILE E 232 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL E 237 " --> pdb=" O PHE E 233 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASP E 238 " --> pdb=" O LEU E 234 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 244 No H-bonds generated for 'chain 'E' and resid 243 through 244' Processing helix chain 'E' and resid 245 through 248 Processing helix chain 'E' and resid 249 through 271 removed outlier: 4.219A pdb=" N SER E 253 " --> pdb=" O GLY E 249 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE E 267 " --> pdb=" O SER E 263 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASP E 271 " --> pdb=" O ILE E 267 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 308 removed outlier: 3.694A pdb=" N VAL E 285 " --> pdb=" O PRO E 281 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE E 296 " --> pdb=" O ALA E 292 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR E 301 " --> pdb=" O SER E 297 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 332 removed outlier: 4.022A pdb=" N ILE E 332 " --> pdb=" O ARG E 328 " (cutoff:3.500A) Processing helix chain 'E' and resid 398 through 461 removed outlier: 3.706A pdb=" N SER E 408 " --> pdb=" O GLN E 404 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE E 409 " --> pdb=" O GLU E 405 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS E 415 " --> pdb=" O HIS E 411 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ARG E 416 " --> pdb=" O PHE E 412 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA E 423 " --> pdb=" O MET E 419 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL E 432 " --> pdb=" O ARG E 428 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE E 458 " --> pdb=" O THR E 454 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N TRP E 459 " --> pdb=" O LEU E 455 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 89 removed outlier: 6.862A pdb=" N TYR A 114 " --> pdb=" O TYR A 126 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N TYR A 126 " --> pdb=" O TYR A 114 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N GLU A 122 " --> pdb=" O HIS A 118 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N TYR A 61 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N ILE A 48 " --> pdb=" O TYR A 61 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N TRP A 63 " --> pdb=" O TYR A 46 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N TYR A 46 " --> pdb=" O TRP A 63 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N ARG A 65 " --> pdb=" O ILE A 44 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N ILE A 44 " --> pdb=" O ARG A 65 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N TYR A 67 " --> pdb=" O ASP A 42 " (cutoff:3.500A) removed outlier: 8.435A pdb=" N ASP A 42 " --> pdb=" O TYR A 67 " (cutoff:3.500A) removed outlier: 9.110A pdb=" N THR A 69 " --> pdb=" O SER A 40 " (cutoff:3.500A) removed outlier: 9.615A pdb=" N SER A 40 " --> pdb=" O THR A 69 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N THR A 37 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N THR A 166 " --> pdb=" O THR A 37 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL A 39 " --> pdb=" O THR A 166 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 98 through 100 removed outlier: 4.241A pdb=" N SER A 155 " --> pdb=" O ALA A 208 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ALA A 208 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N ASN A 205 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU A 191 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ARG A 217 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N LEU A 189 " --> pdb=" O ARG A 217 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 85 through 89 removed outlier: 6.863A pdb=" N TYR B 114 " --> pdb=" O TYR B 126 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N TYR B 126 " --> pdb=" O TYR B 114 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N GLU B 122 " --> pdb=" O HIS B 118 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N TYR B 61 " --> pdb=" O ILE B 48 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N ILE B 48 " --> pdb=" O TYR B 61 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N TRP B 63 " --> pdb=" O TYR B 46 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N TYR B 46 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N ARG B 65 " --> pdb=" O ILE B 44 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N ILE B 44 " --> pdb=" O ARG B 65 " (cutoff:3.500A) removed outlier: 8.347A pdb=" N TYR B 67 " --> pdb=" O ASP B 42 " (cutoff:3.500A) removed outlier: 8.435A pdb=" N ASP B 42 " --> pdb=" O TYR B 67 " (cutoff:3.500A) removed outlier: 9.110A pdb=" N THR B 69 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 9.614A pdb=" N SER B 40 " --> pdb=" O THR B 69 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N THR B 37 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N THR B 166 " --> pdb=" O THR B 37 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N VAL B 39 " --> pdb=" O THR B 166 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 98 through 100 removed outlier: 4.241A pdb=" N SER B 155 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ALA B 208 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N ASN B 205 " --> pdb=" O ILE B 201 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU B 191 " --> pdb=" O ILE B 215 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ARG B 217 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N LEU B 189 " --> pdb=" O ARG B 217 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 85 through 89 removed outlier: 6.863A pdb=" N TYR C 114 " --> pdb=" O TYR C 126 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N TYR C 126 " --> pdb=" O TYR C 114 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N GLU C 122 " --> pdb=" O HIS C 118 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N TYR C 61 " --> pdb=" O ILE C 48 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N ILE C 48 " --> pdb=" O TYR C 61 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N TRP C 63 " --> pdb=" O TYR C 46 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N TYR C 46 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N ARG C 65 " --> pdb=" O ILE C 44 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N ILE C 44 " --> pdb=" O ARG C 65 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N TYR C 67 " --> pdb=" O ASP C 42 " (cutoff:3.500A) removed outlier: 8.435A pdb=" N ASP C 42 " --> pdb=" O TYR C 67 " (cutoff:3.500A) removed outlier: 9.109A pdb=" N THR C 69 " --> pdb=" O SER C 40 " (cutoff:3.500A) removed outlier: 9.615A pdb=" N SER C 40 " --> pdb=" O THR C 69 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N THR C 37 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N THR C 166 " --> pdb=" O THR C 37 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL C 39 " --> pdb=" O THR C 166 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 98 through 100 removed outlier: 4.241A pdb=" N SER C 155 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ALA C 208 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N ASN C 205 " --> pdb=" O ILE C 201 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU C 191 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ARG C 217 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N LEU C 189 " --> pdb=" O ARG C 217 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 85 through 89 removed outlier: 6.863A pdb=" N TYR D 114 " --> pdb=" O TYR D 126 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N TYR D 126 " --> pdb=" O TYR D 114 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLU D 122 " --> pdb=" O HIS D 118 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N TYR D 61 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N ILE D 48 " --> pdb=" O TYR D 61 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N TRP D 63 " --> pdb=" O TYR D 46 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N TYR D 46 " --> pdb=" O TRP D 63 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N ARG D 65 " --> pdb=" O ILE D 44 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N ILE D 44 " --> pdb=" O ARG D 65 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N TYR D 67 " --> pdb=" O ASP D 42 " (cutoff:3.500A) removed outlier: 8.435A pdb=" N ASP D 42 " --> pdb=" O TYR D 67 " (cutoff:3.500A) removed outlier: 9.110A pdb=" N THR D 69 " --> pdb=" O SER D 40 " (cutoff:3.500A) removed outlier: 9.615A pdb=" N SER D 40 " --> pdb=" O THR D 69 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N THR D 37 " --> pdb=" O ASN D 164 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N THR D 166 " --> pdb=" O THR D 37 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N VAL D 39 " --> pdb=" O THR D 166 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 98 through 100 removed outlier: 4.241A pdb=" N SER D 155 " --> pdb=" O ALA D 208 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ALA D 208 " --> pdb=" O SER D 155 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N ASN D 205 " --> pdb=" O ILE D 201 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU D 191 " --> pdb=" O ILE D 215 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ARG D 217 " --> pdb=" O LEU D 189 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N LEU D 189 " --> pdb=" O ARG D 217 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 85 through 89 removed outlier: 6.863A pdb=" N TYR E 114 " --> pdb=" O TYR E 126 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N TYR E 126 " --> pdb=" O TYR E 114 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLU E 122 " --> pdb=" O HIS E 118 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N TYR E 61 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N ILE E 48 " --> pdb=" O TYR E 61 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N TRP E 63 " --> pdb=" O TYR E 46 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N TYR E 46 " --> pdb=" O TRP E 63 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N ARG E 65 " --> pdb=" O ILE E 44 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N ILE E 44 " --> pdb=" O ARG E 65 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N TYR E 67 " --> pdb=" O ASP E 42 " (cutoff:3.500A) removed outlier: 8.435A pdb=" N ASP E 42 " --> pdb=" O TYR E 67 " (cutoff:3.500A) removed outlier: 9.110A pdb=" N THR E 69 " --> pdb=" O SER E 40 " (cutoff:3.500A) removed outlier: 9.615A pdb=" N SER E 40 " --> pdb=" O THR E 69 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N THR E 37 " --> pdb=" O ASN E 164 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N THR E 166 " --> pdb=" O THR E 37 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N VAL E 39 " --> pdb=" O THR E 166 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 98 through 100 removed outlier: 4.241A pdb=" N SER E 155 " --> pdb=" O ALA E 208 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ALA E 208 " --> pdb=" O SER E 155 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N ASN E 205 " --> pdb=" O ILE E 201 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU E 191 " --> pdb=" O ILE E 215 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ARG E 217 " --> pdb=" O LEU E 189 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N LEU E 189 " --> pdb=" O ARG E 217 " (cutoff:3.500A) 735 hydrogen bonds defined for protein. 2175 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: 2.82 Time building geometry restraints manager: 2.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2565 1.31 - 1.43: 4947 1.43 - 1.56: 9721 1.56 - 1.68: 47 1.68 - 1.80: 75 Bond restraints: 17355 Sorted by residual: bond pdb=" C01 CWB D 509 " pdb=" N02 CWB D 509 " ideal model delta sigma weight residual 1.445 1.184 0.261 2.00e-02 2.50e+03 1.71e+02 bond pdb=" C01 CWB B 508 " pdb=" N02 CWB B 508 " ideal model delta sigma weight residual 1.445 1.185 0.260 2.00e-02 2.50e+03 1.69e+02 bond pdb=" C01 CWB D 508 " pdb=" N02 CWB D 508 " ideal model delta sigma weight residual 1.445 1.186 0.259 2.00e-02 2.50e+03 1.68e+02 bond pdb=" C01 CWB A 508 " pdb=" N02 CWB A 508 " ideal model delta sigma weight residual 1.445 1.187 0.258 2.00e-02 2.50e+03 1.67e+02 bond pdb=" C01 CWB C 508 " pdb=" N02 CWB C 508 " ideal model delta sigma weight residual 1.445 1.187 0.258 2.00e-02 2.50e+03 1.67e+02 ... (remaining 17350 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.41: 23532 5.41 - 10.83: 166 10.83 - 16.24: 12 16.24 - 21.65: 0 21.65 - 27.07: 10 Bond angle restraints: 23720 Sorted by residual: angle pdb=" C3 NAG F 1 " pdb=" C4 NAG F 1 " pdb=" O4 NAG F 1 " ideal model delta sigma weight residual 107.29 134.36 -27.07 3.00e+00 1.11e-01 8.14e+01 angle pdb=" C3 NAG N 1 " pdb=" C4 NAG N 1 " pdb=" O4 NAG N 1 " ideal model delta sigma weight residual 107.29 134.34 -27.05 3.00e+00 1.11e-01 8.13e+01 angle pdb=" C3 NAG J 1 " pdb=" C4 NAG J 1 " pdb=" O4 NAG J 1 " ideal model delta sigma weight residual 107.29 134.30 -27.01 3.00e+00 1.11e-01 8.10e+01 angle pdb=" C3 NAG L 1 " pdb=" C4 NAG L 1 " pdb=" O4 NAG L 1 " ideal model delta sigma weight residual 107.29 134.29 -27.00 3.00e+00 1.11e-01 8.10e+01 angle pdb=" C3 NAG H 1 " pdb=" C4 NAG H 1 " pdb=" O4 NAG H 1 " ideal model delta sigma weight residual 107.29 134.26 -26.97 3.00e+00 1.11e-01 8.08e+01 ... (remaining 23715 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.56: 10175 21.56 - 43.11: 435 43.11 - 64.67: 30 64.67 - 86.23: 50 86.23 - 107.78: 20 Dihedral angle restraints: 10710 sinusoidal: 4815 harmonic: 5895 Sorted by residual: dihedral pdb=" CA LEU A 12 " pdb=" C LEU A 12 " pdb=" N LEU A 13 " pdb=" CA LEU A 13 " ideal model delta harmonic sigma weight residual 180.00 156.38 23.62 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CA LEU E 12 " pdb=" C LEU E 12 " pdb=" N LEU E 13 " pdb=" CA LEU E 13 " ideal model delta harmonic sigma weight residual 180.00 156.38 23.62 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CA LEU D 12 " pdb=" C LEU D 12 " pdb=" N LEU D 13 " pdb=" CA LEU D 13 " ideal model delta harmonic sigma weight residual 180.00 156.39 23.61 0 5.00e+00 4.00e-02 2.23e+01 ... (remaining 10707 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.170: 2769 0.170 - 0.340: 46 0.340 - 0.509: 0 0.509 - 0.679: 0 0.679 - 0.849: 10 Chirality restraints: 2825 Sorted by residual: chirality pdb=" C4 NAG F 1 " pdb=" C3 NAG F 1 " pdb=" C5 NAG F 1 " pdb=" O4 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.53 -1.68 -0.85 2.00e-01 2.50e+01 1.80e+01 chirality pdb=" C4 NAG J 1 " pdb=" C3 NAG J 1 " pdb=" C5 NAG J 1 " pdb=" O4 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.53 -1.68 -0.85 2.00e-01 2.50e+01 1.80e+01 chirality pdb=" C4 NAG N 1 " pdb=" C3 NAG N 1 " pdb=" C5 NAG N 1 " pdb=" O4 NAG N 1 " both_signs ideal model delta sigma weight residual False -2.53 -1.68 -0.85 2.00e-01 2.50e+01 1.79e+01 ... (remaining 2822 not shown) Planarity restraints: 2860 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP E 168 " 0.022 2.00e-02 2.50e+03 1.95e-02 9.51e+00 pdb=" CG TRP E 168 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP E 168 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP E 168 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP E 168 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP E 168 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP E 168 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 168 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 168 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP E 168 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 168 " 0.022 2.00e-02 2.50e+03 1.94e-02 9.37e+00 pdb=" CG TRP B 168 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP B 168 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP B 168 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 168 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 168 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 168 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 168 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 168 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP B 168 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 168 " 0.022 2.00e-02 2.50e+03 1.93e-02 9.36e+00 pdb=" CG TRP A 168 " -0.051 2.00e-02 2.50e+03 pdb=" CD1 TRP A 168 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP A 168 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A 168 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 168 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 168 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 168 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 168 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP A 168 " -0.000 2.00e-02 2.50e+03 ... (remaining 2857 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 4137 2.80 - 3.32: 14662 3.32 - 3.85: 27928 3.85 - 4.37: 30688 4.37 - 4.90: 53404 Nonbonded interactions: 130819 Sorted by model distance: nonbonded pdb=" N ASP B 91 " pdb=" OD1 ASP B 91 " model vdw 2.270 3.120 nonbonded pdb=" N ASP D 91 " pdb=" OD1 ASP D 91 " model vdw 2.271 3.120 nonbonded pdb=" N ASP A 91 " pdb=" OD1 ASP A 91 " model vdw 2.271 3.120 nonbonded pdb=" N ASP C 91 " pdb=" OD1 ASP C 91 " model vdw 2.271 3.120 nonbonded pdb=" N ASP E 91 " pdb=" OD1 ASP E 91 " model vdw 2.271 3.120 ... (remaining 130814 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 7 through 502) selection = (chain 'B' and resid 7 through 502) selection = (chain 'C' and resid 7 through 502) selection = (chain 'D' and resid 7 through 502) selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' } 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: 1.940 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: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 17.040 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.040 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: 0.000 Load rotamer database and sin/cos tables:6.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6990 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 : 0.011 0.261 17380 Z= 0.488 Angle : 1.432 34.982 23780 Z= 0.647 Chirality : 0.079 0.849 2825 Planarity : 0.006 0.046 2855 Dihedral : 13.905 107.784 6870 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 0.55 % Allowed : 6.85 % Favored : 92.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.90 (0.15), residues: 1955 helix: -2.22 (0.14), residues: 805 sheet: -2.02 (0.22), residues: 405 loop : -3.15 (0.17), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 218 TYR 0.025 0.003 TYR C 67 PHE 0.016 0.003 PHE D 193 TRP 0.052 0.003 TRP E 168 HIS 0.007 0.002 HIS D 119 Details of bonding type rmsd covalent geometry : bond 0.01069 (17355) covalent geometry : angle 1.28650 (23720) hydrogen bonds : bond 0.17637 ( 735) hydrogen bonds : angle 7.15447 ( 2175) Misc. bond : bond 0.00091 ( 5) link_BETA1-4 : bond 0.04146 ( 15) link_BETA1-4 : angle 14.25546 ( 45) link_NAG-ASN : bond 0.01063 ( 5) link_NAG-ASN : angle 4.83237 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 350 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ASN cc_start: 0.8087 (p0) cc_final: 0.7670 (p0) REVERT: A 108 LYS cc_start: 0.8130 (mttp) cc_final: 0.7750 (mtmt) REVERT: A 179 SER cc_start: 0.7943 (t) cc_final: 0.7731 (p) REVERT: A 188 GLU cc_start: 0.7890 (mt-10) cc_final: 0.7154 (mt-10) REVERT: A 197 LYS cc_start: 0.7035 (mttm) cc_final: 0.6750 (tttt) REVERT: B 17 ASP cc_start: 0.7142 (t0) cc_final: 0.6720 (m-30) REVERT: B 22 ASN cc_start: 0.7909 (p0) cc_final: 0.7346 (p0) REVERT: B 81 ASP cc_start: 0.7946 (t70) cc_final: 0.7367 (t0) REVERT: B 177 ASP cc_start: 0.7058 (t0) cc_final: 0.6834 (t0) REVERT: C 17 ASP cc_start: 0.7385 (t0) cc_final: 0.7184 (m-30) REVERT: C 81 ASP cc_start: 0.7947 (t70) cc_final: 0.7195 (t0) REVERT: C 88 ILE cc_start: 0.8266 (mt) cc_final: 0.8020 (mm) REVERT: C 105 ASP cc_start: 0.7191 (t0) cc_final: 0.6985 (t0) REVERT: D 17 ASP cc_start: 0.7303 (t0) cc_final: 0.6973 (m-30) REVERT: D 22 ASN cc_start: 0.8134 (p0) cc_final: 0.7863 (p0) REVERT: D 105 ASP cc_start: 0.7844 (t0) cc_final: 0.7443 (t0) REVERT: D 108 LYS cc_start: 0.8098 (mttp) cc_final: 0.7817 (mtmm) REVERT: D 179 SER cc_start: 0.7540 (t) cc_final: 0.7257 (p) REVERT: D 197 LYS cc_start: 0.6796 (mttm) cc_final: 0.6547 (tttt) REVERT: E 22 ASN cc_start: 0.8094 (p0) cc_final: 0.7832 (p0) REVERT: E 88 ILE cc_start: 0.8773 (mt) cc_final: 0.8524 (mp) REVERT: E 197 LYS cc_start: 0.7012 (mttm) cc_final: 0.6599 (tttt) REVERT: E 456 TRP cc_start: 0.6566 (t60) cc_final: 0.6290 (t60) outliers start: 10 outliers final: 5 residues processed: 356 average time/residue: 0.6132 time to fit residues: 243.3681 Evaluate side-chains 175 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 170 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain E residue 123 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.0870 chunk 66 optimal weight: 0.0370 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.1980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 3.9990 overall best weight: 0.3436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 ASN ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 9 GLN B 184 GLN C 82 ASN C 101 ASN D 9 GLN D 82 ASN D 111 ASN E 82 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.122980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.088975 restraints weight = 26889.200| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 2.27 r_work: 0.3014 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17380 Z= 0.128 Angle : 0.785 11.148 23780 Z= 0.354 Chirality : 0.049 0.242 2825 Planarity : 0.004 0.049 2855 Dihedral : 10.574 59.803 3025 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.67 % Allowed : 13.59 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.81 (0.18), residues: 1955 helix: 0.06 (0.18), residues: 805 sheet: -1.93 (0.23), residues: 435 loop : -2.04 (0.20), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 322 TYR 0.022 0.002 TYR C 262 PHE 0.010 0.001 PHE A 80 TRP 0.019 0.001 TRP E 168 HIS 0.004 0.001 HIS A 323 Details of bonding type rmsd covalent geometry : bond 0.00271 (17355) covalent geometry : angle 0.74036 (23720) hydrogen bonds : bond 0.04332 ( 735) hydrogen bonds : angle 4.75984 ( 2175) Misc. bond : bond 0.00045 ( 5) link_BETA1-4 : bond 0.00471 ( 15) link_BETA1-4 : angle 5.84846 ( 45) link_NAG-ASN : bond 0.00139 ( 5) link_NAG-ASN : angle 2.57059 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 213 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 ASN cc_start: 0.8526 (p0) cc_final: 0.8059 (p0) REVERT: A 81 ASP cc_start: 0.8369 (t70) cc_final: 0.7720 (t0) REVERT: A 108 LYS cc_start: 0.8715 (mttp) cc_final: 0.8439 (mtmt) REVERT: A 122 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.8116 (tt0) REVERT: A 188 GLU cc_start: 0.8584 (mt-10) cc_final: 0.8118 (mt-10) REVERT: A 197 LYS cc_start: 0.7783 (mttm) cc_final: 0.7489 (tttt) REVERT: A 235 MET cc_start: 0.7696 (mmt) cc_final: 0.7476 (mmt) REVERT: A 435 ARG cc_start: 0.7300 (mtt180) cc_final: 0.6762 (mmp-170) REVERT: B 17 ASP cc_start: 0.7919 (t0) cc_final: 0.7416 (m-30) REVERT: B 22 ASN cc_start: 0.8413 (p0) cc_final: 0.7905 (p0) REVERT: B 31 ARG cc_start: 0.8477 (mmt180) cc_final: 0.8241 (mtt-85) REVERT: B 81 ASP cc_start: 0.8633 (t70) cc_final: 0.8167 (t0) REVERT: B 307 LEU cc_start: 0.7382 (OUTLIER) cc_final: 0.7180 (tp) REVERT: C 17 ASP cc_start: 0.8109 (t0) cc_final: 0.7907 (m-30) REVERT: C 22 ASN cc_start: 0.8306 (p0) cc_final: 0.7791 (p0) REVERT: C 81 ASP cc_start: 0.8669 (t70) cc_final: 0.8282 (t0) REVERT: C 122 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.8044 (tt0) REVERT: C 315 ARG cc_start: 0.7119 (mpp80) cc_final: 0.6717 (mpp-170) REVERT: D 17 ASP cc_start: 0.8096 (t0) cc_final: 0.7846 (m-30) REVERT: D 22 ASN cc_start: 0.8572 (p0) cc_final: 0.8297 (p0) REVERT: D 197 LYS cc_start: 0.7636 (mttm) cc_final: 0.7366 (tttt) REVERT: D 435 ARG cc_start: 0.7268 (mtt180) cc_final: 0.6759 (mmp-170) REVERT: E 22 ASN cc_start: 0.8541 (p0) cc_final: 0.8289 (p0) REVERT: E 197 LYS cc_start: 0.7902 (mttm) cc_final: 0.7581 (mmmt) REVERT: E 435 ARG cc_start: 0.7333 (mtt180) cc_final: 0.6913 (mmp-170) outliers start: 67 outliers final: 26 residues processed: 267 average time/residue: 0.4982 time to fit residues: 152.1395 Evaluate side-chains 190 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 161 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 161 GLN Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 161 GLN Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 403 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 36 optimal weight: 1.9990 chunk 134 optimal weight: 4.9990 chunk 183 optimal weight: 6.9990 chunk 95 optimal weight: 0.3980 chunk 129 optimal weight: 0.7980 chunk 80 optimal weight: 0.7980 chunk 144 optimal weight: 0.8980 chunk 141 optimal weight: 0.8980 chunk 98 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 311 GLN D 9 GLN D 111 ASN E 311 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.119558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.084747 restraints weight = 27086.027| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 2.33 r_work: 0.2941 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.3605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17380 Z= 0.153 Angle : 0.750 10.189 23780 Z= 0.341 Chirality : 0.047 0.256 2825 Planarity : 0.004 0.036 2855 Dihedral : 8.675 59.769 3025 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 4.77 % Allowed : 14.85 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.19), residues: 1955 helix: 1.29 (0.19), residues: 780 sheet: -1.63 (0.23), residues: 445 loop : -1.94 (0.21), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG D 424 TYR 0.022 0.002 TYR D 262 PHE 0.018 0.001 PHE E 153 TRP 0.022 0.001 TRP E 168 HIS 0.005 0.001 HIS B 309 Details of bonding type rmsd covalent geometry : bond 0.00341 (17355) covalent geometry : angle 0.72480 (23720) hydrogen bonds : bond 0.04525 ( 735) hydrogen bonds : angle 4.31031 ( 2175) Misc. bond : bond 0.00044 ( 5) link_BETA1-4 : bond 0.00449 ( 15) link_BETA1-4 : angle 4.30553 ( 45) link_NAG-ASN : bond 0.00318 ( 5) link_NAG-ASN : angle 2.51843 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 180 time to evaluate : 0.699 Fit side-chains REVERT: A 22 ASN cc_start: 0.8674 (p0) cc_final: 0.8253 (p0) REVERT: A 81 ASP cc_start: 0.8706 (t70) cc_final: 0.8170 (t0) REVERT: A 108 LYS cc_start: 0.8836 (mttp) cc_final: 0.8494 (mtmm) REVERT: A 188 GLU cc_start: 0.8622 (mt-10) cc_final: 0.8172 (mt-10) REVERT: A 197 LYS cc_start: 0.8045 (mttm) cc_final: 0.7773 (tttm) REVERT: A 435 ARG cc_start: 0.7453 (mtt180) cc_final: 0.6967 (mmp-170) REVERT: B 17 ASP cc_start: 0.8368 (t0) cc_final: 0.7907 (m-30) REVERT: B 22 ASN cc_start: 0.8615 (p0) cc_final: 0.8082 (p0) REVERT: B 81 ASP cc_start: 0.8878 (t70) cc_final: 0.8554 (t0) REVERT: B 197 LYS cc_start: 0.8047 (mttm) cc_final: 0.7642 (tttm) REVERT: B 242 PHE cc_start: 0.8747 (OUTLIER) cc_final: 0.8215 (t80) REVERT: B 435 ARG cc_start: 0.7050 (mtt180) cc_final: 0.6537 (mmt180) REVERT: C 17 ASP cc_start: 0.8429 (t0) cc_final: 0.8066 (m-30) REVERT: C 22 ASN cc_start: 0.8496 (p0) cc_final: 0.8150 (m-40) REVERT: C 81 ASP cc_start: 0.8886 (t70) cc_final: 0.8622 (t0) REVERT: C 116 TYR cc_start: 0.9172 (OUTLIER) cc_final: 0.8473 (m-80) REVERT: C 242 PHE cc_start: 0.8714 (OUTLIER) cc_final: 0.8156 (t80) REVERT: C 315 ARG cc_start: 0.7287 (mpp80) cc_final: 0.6935 (mpp-170) REVERT: C 435 ARG cc_start: 0.7381 (mtt180) cc_final: 0.6770 (mmp-170) REVERT: D 17 ASP cc_start: 0.8533 (t0) cc_final: 0.8190 (m-30) REVERT: D 22 ASN cc_start: 0.8651 (p0) cc_final: 0.8245 (m-40) REVERT: D 197 LYS cc_start: 0.7910 (mttm) cc_final: 0.7676 (tttt) REVERT: D 435 ARG cc_start: 0.7366 (mtt180) cc_final: 0.6975 (mmp-170) REVERT: E 22 ASN cc_start: 0.8626 (p0) cc_final: 0.8373 (p0) REVERT: E 188 GLU cc_start: 0.8621 (mt-10) cc_final: 0.8126 (mt-10) REVERT: E 197 LYS cc_start: 0.8095 (mttm) cc_final: 0.7757 (tttt) REVERT: E 435 ARG cc_start: 0.7377 (mtt180) cc_final: 0.6986 (mmt180) outliers start: 87 outliers final: 42 residues processed: 253 average time/residue: 0.5052 time to fit residues: 146.0309 Evaluate side-chains 199 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 154 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 161 GLN Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 323 HIS Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 161 GLN Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 116 TYR Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 242 PHE Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 161 GLN Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 161 GLN Chi-restraints excluded: chain E residue 298 LEU Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 315 ARG Chi-restraints excluded: chain E residue 403 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 32 optimal weight: 8.9990 chunk 164 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 154 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 115 optimal weight: 0.8980 chunk 188 optimal weight: 0.5980 chunk 157 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 26 optimal weight: 7.9990 chunk 46 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 HIS ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 309 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.119768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.084650 restraints weight = 26843.237| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 2.34 r_work: 0.2931 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.4272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17380 Z= 0.123 Angle : 0.673 10.299 23780 Z= 0.307 Chirality : 0.046 0.192 2825 Planarity : 0.004 0.035 2855 Dihedral : 7.533 57.356 3025 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.84 % Allowed : 17.10 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.19), residues: 1955 helix: 1.75 (0.19), residues: 785 sheet: -1.44 (0.23), residues: 445 loop : -1.70 (0.21), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 31 TYR 0.014 0.001 TYR B 64 PHE 0.018 0.001 PHE E 153 TRP 0.013 0.001 TRP C 168 HIS 0.004 0.001 HIS A 323 Details of bonding type rmsd covalent geometry : bond 0.00270 (17355) covalent geometry : angle 0.64343 (23720) hydrogen bonds : bond 0.03955 ( 735) hydrogen bonds : angle 4.14527 ( 2175) Misc. bond : bond 0.00029 ( 5) link_BETA1-4 : bond 0.00321 ( 15) link_BETA1-4 : angle 4.42944 ( 45) link_NAG-ASN : bond 0.00051 ( 5) link_NAG-ASN : angle 1.87719 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 172 time to evaluate : 0.659 Fit side-chains REVERT: A 22 ASN cc_start: 0.8743 (p0) cc_final: 0.8368 (p0) REVERT: A 81 ASP cc_start: 0.8847 (t70) cc_final: 0.8378 (t0) REVERT: A 108 LYS cc_start: 0.8825 (mttp) cc_final: 0.8511 (mtpt) REVERT: A 188 GLU cc_start: 0.8582 (mt-10) cc_final: 0.8022 (mt-10) REVERT: A 197 LYS cc_start: 0.8108 (mttm) cc_final: 0.7835 (tttt) REVERT: A 435 ARG cc_start: 0.7643 (mtt180) cc_final: 0.7115 (mmp-170) REVERT: B 17 ASP cc_start: 0.8596 (t0) cc_final: 0.8093 (m-30) REVERT: B 22 ASN cc_start: 0.8647 (p0) cc_final: 0.8222 (m-40) REVERT: B 81 ASP cc_start: 0.8909 (t70) cc_final: 0.8655 (t0) REVERT: B 116 TYR cc_start: 0.9149 (OUTLIER) cc_final: 0.8668 (m-80) REVERT: B 197 LYS cc_start: 0.8129 (mttm) cc_final: 0.7731 (tttm) REVERT: B 238 ASP cc_start: 0.8614 (m-30) cc_final: 0.8170 (m-30) REVERT: B 410 ARG cc_start: 0.7224 (ttp80) cc_final: 0.6950 (mtp-110) REVERT: B 435 ARG cc_start: 0.7039 (mtt180) cc_final: 0.6476 (mmp-170) REVERT: C 17 ASP cc_start: 0.8531 (t0) cc_final: 0.8151 (m-30) REVERT: C 22 ASN cc_start: 0.8595 (p0) cc_final: 0.8319 (m-40) REVERT: C 81 ASP cc_start: 0.8912 (t70) cc_final: 0.8640 (t0) REVERT: C 116 TYR cc_start: 0.9154 (OUTLIER) cc_final: 0.8758 (m-80) REVERT: C 242 PHE cc_start: 0.8784 (OUTLIER) cc_final: 0.8027 (t80) REVERT: C 315 ARG cc_start: 0.7373 (mpp80) cc_final: 0.7051 (mpp-170) REVERT: C 435 ARG cc_start: 0.7421 (mtt180) cc_final: 0.6837 (mmp-170) REVERT: D 17 ASP cc_start: 0.8689 (t0) cc_final: 0.8420 (t0) REVERT: D 22 ASN cc_start: 0.8707 (p0) cc_final: 0.8306 (m-40) REVERT: D 54 LYS cc_start: 0.8628 (ttmt) cc_final: 0.8368 (ttpp) REVERT: D 197 LYS cc_start: 0.8062 (mttm) cc_final: 0.7766 (tttt) REVERT: D 296 ILE cc_start: 0.8654 (mt) cc_final: 0.8329 (mt) REVERT: D 435 ARG cc_start: 0.7435 (mtt180) cc_final: 0.7039 (mmp-170) REVERT: E 22 ASN cc_start: 0.8690 (p0) cc_final: 0.8423 (p0) REVERT: E 54 LYS cc_start: 0.8660 (ttmt) cc_final: 0.8319 (ttpp) REVERT: E 123 VAL cc_start: 0.9036 (OUTLIER) cc_final: 0.8605 (t) REVERT: E 188 GLU cc_start: 0.8590 (mt-10) cc_final: 0.8092 (mt-10) REVERT: E 197 LYS cc_start: 0.8101 (mttm) cc_final: 0.7725 (tttt) REVERT: E 435 ARG cc_start: 0.7547 (mtt180) cc_final: 0.7186 (mmt180) outliers start: 70 outliers final: 32 residues processed: 231 average time/residue: 0.5371 time to fit residues: 140.6167 Evaluate side-chains 186 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 150 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 161 GLN Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 161 GLN Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 116 TYR Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 161 GLN Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 242 PHE Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 161 GLN Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 161 GLN Chi-restraints excluded: chain E residue 162 ASP Chi-restraints excluded: chain E residue 301 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 46 optimal weight: 0.3980 chunk 18 optimal weight: 0.9990 chunk 142 optimal weight: 0.9980 chunk 85 optimal weight: 0.0570 chunk 67 optimal weight: 4.9990 chunk 49 optimal weight: 0.0870 chunk 171 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 193 optimal weight: 0.7980 chunk 183 optimal weight: 3.9990 overall best weight: 0.4676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 GLN ** C 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.120070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.084927 restraints weight = 26882.480| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 2.34 r_work: 0.2936 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.4596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 17380 Z= 0.109 Angle : 0.634 9.373 23780 Z= 0.292 Chirality : 0.044 0.176 2825 Planarity : 0.003 0.032 2855 Dihedral : 7.317 57.926 3024 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.84 % Allowed : 17.81 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.19), residues: 1955 helix: 1.98 (0.19), residues: 785 sheet: -1.28 (0.23), residues: 445 loop : -1.51 (0.22), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 31 TYR 0.012 0.001 TYR B 64 PHE 0.015 0.001 PHE E 153 TRP 0.011 0.001 TRP E 168 HIS 0.001 0.000 HIS A 323 Details of bonding type rmsd covalent geometry : bond 0.00237 (17355) covalent geometry : angle 0.61122 (23720) hydrogen bonds : bond 0.03717 ( 735) hydrogen bonds : angle 3.99844 ( 2175) Misc. bond : bond 0.00038 ( 5) link_BETA1-4 : bond 0.00243 ( 15) link_BETA1-4 : angle 3.83089 ( 45) link_NAG-ASN : bond 0.00046 ( 5) link_NAG-ASN : angle 1.82635 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 164 time to evaluate : 0.627 Fit side-chains revert: symmetry clash REVERT: A 22 ASN cc_start: 0.8782 (p0) cc_final: 0.8414 (p0) REVERT: A 81 ASP cc_start: 0.8849 (t70) cc_final: 0.8460 (t0) REVERT: A 108 LYS cc_start: 0.8832 (mttp) cc_final: 0.8546 (mtpt) REVERT: A 197 LYS cc_start: 0.8042 (mttm) cc_final: 0.7724 (tttt) REVERT: A 242 PHE cc_start: 0.8363 (OUTLIER) cc_final: 0.7919 (t80) REVERT: A 435 ARG cc_start: 0.7599 (mtt180) cc_final: 0.7074 (mmp-170) REVERT: B 17 ASP cc_start: 0.8610 (t0) cc_final: 0.8117 (m-30) REVERT: B 22 ASN cc_start: 0.8670 (p0) cc_final: 0.8259 (m-40) REVERT: B 54 LYS cc_start: 0.8546 (ttmt) cc_final: 0.8324 (ttpp) REVERT: B 81 ASP cc_start: 0.8926 (t70) cc_final: 0.8700 (t0) REVERT: B 197 LYS cc_start: 0.8035 (mttm) cc_final: 0.7727 (tttm) REVERT: B 229 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8288 (tm) REVERT: B 238 ASP cc_start: 0.8553 (m-30) cc_final: 0.8123 (m-30) REVERT: B 410 ARG cc_start: 0.7188 (ttp80) cc_final: 0.6920 (mtp-110) REVERT: B 419 MET cc_start: 0.7833 (mmm) cc_final: 0.7624 (mmt) REVERT: B 435 ARG cc_start: 0.7104 (mtt180) cc_final: 0.6570 (mmp-170) REVERT: C 17 ASP cc_start: 0.8642 (t0) cc_final: 0.8236 (m-30) REVERT: C 22 ASN cc_start: 0.8592 (p0) cc_final: 0.8328 (m-40) REVERT: C 81 ASP cc_start: 0.8849 (t70) cc_final: 0.8629 (t0) REVERT: C 91 ASP cc_start: 0.8726 (m-30) cc_final: 0.8331 (p0) REVERT: C 242 PHE cc_start: 0.8705 (OUTLIER) cc_final: 0.7965 (t80) REVERT: C 315 ARG cc_start: 0.7431 (mpp80) cc_final: 0.7093 (mpp-170) REVERT: C 435 ARG cc_start: 0.7446 (mtt180) cc_final: 0.6840 (mmp-170) REVERT: D 17 ASP cc_start: 0.8677 (t0) cc_final: 0.8473 (t0) REVERT: D 22 ASN cc_start: 0.8757 (p0) cc_final: 0.8338 (m-40) REVERT: D 54 LYS cc_start: 0.8638 (ttmt) cc_final: 0.8401 (ttpp) REVERT: D 162 ASP cc_start: 0.8748 (m-30) cc_final: 0.8492 (m-30) REVERT: D 197 LYS cc_start: 0.8081 (mttm) cc_final: 0.7825 (tttt) REVERT: D 242 PHE cc_start: 0.8566 (OUTLIER) cc_final: 0.7860 (t80) REVERT: D 311 GLN cc_start: 0.6389 (OUTLIER) cc_final: 0.6080 (pm20) REVERT: D 435 ARG cc_start: 0.7348 (mtt180) cc_final: 0.6941 (mmp-170) REVERT: E 22 ASN cc_start: 0.8692 (p0) cc_final: 0.8457 (p0) REVERT: E 54 LYS cc_start: 0.8670 (ttmt) cc_final: 0.8338 (ttpp) REVERT: E 197 LYS cc_start: 0.8059 (mttm) cc_final: 0.7734 (tttt) REVERT: E 435 ARG cc_start: 0.7529 (mtt180) cc_final: 0.7194 (mmp-170) outliers start: 70 outliers final: 36 residues processed: 229 average time/residue: 0.5057 time to fit residues: 131.7550 Evaluate side-chains 186 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 145 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 161 GLN Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 242 PHE Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 323 HIS Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 161 GLN Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 197 LYS Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 242 PHE Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 161 GLN Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 242 PHE Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 311 GLN Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 161 GLN Chi-restraints excluded: chain E residue 162 ASP Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 403 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 79 optimal weight: 0.8980 chunk 191 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 chunk 140 optimal weight: 0.9980 chunk 177 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 33 optimal weight: 10.0000 chunk 189 optimal weight: 2.9990 chunk 109 optimal weight: 0.0370 overall best weight: 1.3862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.115456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.080299 restraints weight = 26710.407| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 2.28 r_work: 0.2858 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2722 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.5296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 17380 Z= 0.185 Angle : 0.728 10.362 23780 Z= 0.336 Chirality : 0.048 0.182 2825 Planarity : 0.004 0.041 2855 Dihedral : 7.500 57.599 3024 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 4.22 % Allowed : 17.86 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.19), residues: 1955 helix: 1.88 (0.19), residues: 780 sheet: -1.22 (0.24), residues: 445 loop : -1.49 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 31 TYR 0.014 0.002 TYR A 126 PHE 0.035 0.001 PHE E 153 TRP 0.019 0.002 TRP C 168 HIS 0.003 0.001 HIS C 411 Details of bonding type rmsd covalent geometry : bond 0.00444 (17355) covalent geometry : angle 0.70524 (23720) hydrogen bonds : bond 0.04450 ( 735) hydrogen bonds : angle 4.16082 ( 2175) Misc. bond : bond 0.00048 ( 5) link_BETA1-4 : bond 0.00335 ( 15) link_BETA1-4 : angle 4.01687 ( 45) link_NAG-ASN : bond 0.00147 ( 5) link_NAG-ASN : angle 2.21084 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 148 time to evaluate : 0.630 Fit side-chains REVERT: A 22 ASN cc_start: 0.8824 (p0) cc_final: 0.8563 (m-40) REVERT: A 108 LYS cc_start: 0.8771 (mttp) cc_final: 0.7858 (mmmt) REVERT: A 188 GLU cc_start: 0.8552 (mt-10) cc_final: 0.8012 (mt-10) REVERT: A 197 LYS cc_start: 0.8037 (mttm) cc_final: 0.7763 (tttt) REVERT: A 435 ARG cc_start: 0.7750 (mtt180) cc_final: 0.7259 (mmp-170) REVERT: B 22 ASN cc_start: 0.8823 (p0) cc_final: 0.8421 (m-40) REVERT: B 52 ASP cc_start: 0.8236 (OUTLIER) cc_final: 0.7564 (t0) REVERT: B 54 LYS cc_start: 0.8689 (ttmt) cc_final: 0.8267 (ttpp) REVERT: B 197 LYS cc_start: 0.8029 (mttm) cc_final: 0.7733 (tttt) REVERT: B 229 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8287 (tm) REVERT: B 435 ARG cc_start: 0.7349 (mtt180) cc_final: 0.6802 (mmp-170) REVERT: C 22 ASN cc_start: 0.8651 (p0) cc_final: 0.8437 (m-40) REVERT: C 91 ASP cc_start: 0.8719 (m-30) cc_final: 0.8480 (p0) REVERT: C 242 PHE cc_start: 0.8856 (OUTLIER) cc_final: 0.8125 (t80) REVERT: C 294 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7675 (mp) REVERT: C 296 ILE cc_start: 0.8777 (OUTLIER) cc_final: 0.8505 (mp) REVERT: C 315 ARG cc_start: 0.7646 (mpp80) cc_final: 0.7371 (OUTLIER) REVERT: C 435 ARG cc_start: 0.7368 (mtt180) cc_final: 0.6784 (mmp-170) REVERT: D 22 ASN cc_start: 0.8899 (p0) cc_final: 0.8618 (m-40) REVERT: D 54 LYS cc_start: 0.8738 (ttmt) cc_final: 0.8497 (ttpp) REVERT: D 91 ASP cc_start: 0.8866 (OUTLIER) cc_final: 0.8465 (p0) REVERT: D 197 LYS cc_start: 0.8130 (mttm) cc_final: 0.7856 (tttt) REVERT: D 435 ARG cc_start: 0.7549 (mtt180) cc_final: 0.7134 (mmp-170) REVERT: E 22 ASN cc_start: 0.8739 (p0) cc_final: 0.8389 (m-40) REVERT: E 54 LYS cc_start: 0.8790 (ttmt) cc_final: 0.8421 (ttpp) REVERT: E 188 GLU cc_start: 0.8535 (mt-10) cc_final: 0.8080 (mt-10) REVERT: E 197 LYS cc_start: 0.8026 (mttm) cc_final: 0.7727 (tttt) REVERT: E 435 ARG cc_start: 0.7576 (mtt180) cc_final: 0.7191 (mmp-170) outliers start: 77 outliers final: 37 residues processed: 212 average time/residue: 0.5199 time to fit residues: 124.7683 Evaluate side-chains 173 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 131 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 161 GLN Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 161 GLN Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 161 GLN Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 242 PHE Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 161 GLN Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 403 LEU Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 161 GLN Chi-restraints excluded: chain E residue 162 ASP Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 403 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 116 optimal weight: 1.9990 chunk 154 optimal weight: 0.7980 chunk 1 optimal weight: 0.3980 chunk 41 optimal weight: 0.0020 chunk 89 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 145 optimal weight: 3.9990 chunk 156 optimal weight: 0.8980 chunk 123 optimal weight: 2.9990 chunk 77 optimal weight: 8.9990 chunk 29 optimal weight: 0.9980 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 195 GLN ** C 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.117670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.082683 restraints weight = 26628.270| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 2.31 r_work: 0.2894 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.5422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17380 Z= 0.115 Angle : 0.656 11.722 23780 Z= 0.299 Chirality : 0.044 0.164 2825 Planarity : 0.003 0.033 2855 Dihedral : 7.239 58.538 3024 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.51 % Allowed : 18.79 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.20), residues: 1955 helix: 2.03 (0.19), residues: 780 sheet: -1.12 (0.24), residues: 445 loop : -1.39 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 315 TYR 0.012 0.001 TYR B 64 PHE 0.014 0.001 PHE E 153 TRP 0.018 0.001 TRP B 459 HIS 0.002 0.001 HIS B 18 Details of bonding type rmsd covalent geometry : bond 0.00253 (17355) covalent geometry : angle 0.63362 (23720) hydrogen bonds : bond 0.03888 ( 735) hydrogen bonds : angle 4.06290 ( 2175) Misc. bond : bond 0.00037 ( 5) link_BETA1-4 : bond 0.00272 ( 15) link_BETA1-4 : angle 3.81254 ( 45) link_NAG-ASN : bond 0.00052 ( 5) link_NAG-ASN : angle 2.08033 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 146 time to evaluate : 0.654 Fit side-chains revert: symmetry clash REVERT: A 22 ASN cc_start: 0.8831 (p0) cc_final: 0.8593 (m-40) REVERT: A 81 ASP cc_start: 0.8927 (t70) cc_final: 0.8637 (t0) REVERT: A 108 LYS cc_start: 0.8747 (mttp) cc_final: 0.7828 (mmmt) REVERT: A 188 GLU cc_start: 0.8540 (mt-10) cc_final: 0.8011 (mt-10) REVERT: A 197 LYS cc_start: 0.8062 (mttm) cc_final: 0.7769 (tttt) REVERT: A 435 ARG cc_start: 0.7681 (mtt180) cc_final: 0.7214 (mmp-170) REVERT: B 22 ASN cc_start: 0.8810 (p0) cc_final: 0.8489 (m-40) REVERT: B 54 LYS cc_start: 0.8687 (ttmt) cc_final: 0.8418 (ttpp) REVERT: B 162 ASP cc_start: 0.8871 (m-30) cc_final: 0.8628 (m-30) REVERT: B 197 LYS cc_start: 0.7992 (mttm) cc_final: 0.7706 (tttm) REVERT: B 229 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8326 (tm) REVERT: B 435 ARG cc_start: 0.7333 (mtt180) cc_final: 0.6799 (mmp-170) REVERT: C 22 ASN cc_start: 0.8665 (p0) cc_final: 0.8444 (m-40) REVERT: C 91 ASP cc_start: 0.8670 (m-30) cc_final: 0.8447 (p0) REVERT: C 242 PHE cc_start: 0.8809 (OUTLIER) cc_final: 0.8060 (t80) REVERT: C 315 ARG cc_start: 0.7653 (mpp80) cc_final: 0.7412 (mpp-170) REVERT: C 435 ARG cc_start: 0.7436 (mtt180) cc_final: 0.6874 (mmp-170) REVERT: D 22 ASN cc_start: 0.8898 (p0) cc_final: 0.8689 (m-40) REVERT: D 54 LYS cc_start: 0.8752 (ttmt) cc_final: 0.8523 (ttpp) REVERT: D 91 ASP cc_start: 0.8865 (OUTLIER) cc_final: 0.8471 (p0) REVERT: D 197 LYS cc_start: 0.8081 (mttm) cc_final: 0.7858 (tttt) REVERT: D 435 ARG cc_start: 0.7487 (mtt180) cc_final: 0.7097 (mmp-170) REVERT: E 22 ASN cc_start: 0.8745 (p0) cc_final: 0.8427 (m-40) REVERT: E 54 LYS cc_start: 0.8794 (ttmt) cc_final: 0.8441 (ttpp) REVERT: E 123 VAL cc_start: 0.9123 (OUTLIER) cc_final: 0.8704 (t) REVERT: E 197 LYS cc_start: 0.7997 (mttm) cc_final: 0.7704 (tttt) REVERT: E 435 ARG cc_start: 0.7526 (mtt180) cc_final: 0.7193 (mmt180) outliers start: 64 outliers final: 33 residues processed: 203 average time/residue: 0.4953 time to fit residues: 114.3605 Evaluate side-chains 172 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 135 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 161 GLN Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 323 HIS Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 161 GLN Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 161 GLN Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 242 PHE Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 161 GLN Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 161 GLN Chi-restraints excluded: chain E residue 162 ASP Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 294 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 28 optimal weight: 0.9980 chunk 145 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 127 optimal weight: 0.9980 chunk 176 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 173 optimal weight: 0.1980 chunk 43 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.116894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.082216 restraints weight = 26910.095| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 2.19 r_work: 0.2893 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.5640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17380 Z= 0.146 Angle : 0.677 9.570 23780 Z= 0.311 Chirality : 0.046 0.245 2825 Planarity : 0.004 0.037 2855 Dihedral : 7.221 58.625 3024 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.07 % Allowed : 19.18 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.20), residues: 1955 helix: 1.96 (0.19), residues: 780 sheet: -1.11 (0.24), residues: 445 loop : -1.36 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 315 TYR 0.013 0.001 TYR A 67 PHE 0.022 0.001 PHE E 153 TRP 0.024 0.001 TRP B 459 HIS 0.002 0.001 HIS C 411 Details of bonding type rmsd covalent geometry : bond 0.00346 (17355) covalent geometry : angle 0.65470 (23720) hydrogen bonds : bond 0.04088 ( 735) hydrogen bonds : angle 4.08901 ( 2175) Misc. bond : bond 0.00041 ( 5) link_BETA1-4 : bond 0.00250 ( 15) link_BETA1-4 : angle 3.79404 ( 45) link_NAG-ASN : bond 0.00152 ( 5) link_NAG-ASN : angle 2.13529 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 143 time to evaluate : 0.669 Fit side-chains revert: symmetry clash REVERT: A 108 LYS cc_start: 0.8692 (mttp) cc_final: 0.7838 (mmmt) REVERT: A 188 GLU cc_start: 0.8469 (mt-10) cc_final: 0.8171 (tt0) REVERT: A 197 LYS cc_start: 0.7982 (mttm) cc_final: 0.7676 (tttt) REVERT: A 404 GLN cc_start: 0.7209 (tm-30) cc_final: 0.6716 (tp40) REVERT: A 435 ARG cc_start: 0.7637 (mtt180) cc_final: 0.7134 (mmp-170) REVERT: B 22 ASN cc_start: 0.8810 (p0) cc_final: 0.8521 (m-40) REVERT: B 54 LYS cc_start: 0.8642 (ttmt) cc_final: 0.8374 (ttpp) REVERT: B 197 LYS cc_start: 0.7972 (mttm) cc_final: 0.7682 (tttm) REVERT: B 229 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8306 (tm) REVERT: B 435 ARG cc_start: 0.7351 (mtt180) cc_final: 0.6828 (mmp-170) REVERT: C 22 ASN cc_start: 0.8689 (p0) cc_final: 0.8478 (m-40) REVERT: C 91 ASP cc_start: 0.8695 (m-30) cc_final: 0.8441 (p0) REVERT: C 242 PHE cc_start: 0.8812 (OUTLIER) cc_final: 0.8038 (t80) REVERT: C 315 ARG cc_start: 0.7728 (mpp80) cc_final: 0.7498 (mpp-170) REVERT: C 435 ARG cc_start: 0.7419 (mtt180) cc_final: 0.6834 (mmp-170) REVERT: D 54 LYS cc_start: 0.8716 (ttmt) cc_final: 0.8478 (ttpp) REVERT: D 91 ASP cc_start: 0.8787 (OUTLIER) cc_final: 0.8458 (p0) REVERT: D 197 LYS cc_start: 0.8086 (mttm) cc_final: 0.7833 (tttt) REVERT: D 435 ARG cc_start: 0.7466 (mtt180) cc_final: 0.7034 (mmp-170) REVERT: E 20 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.8612 (mp) REVERT: E 22 ASN cc_start: 0.8785 (p0) cc_final: 0.8529 (m-40) REVERT: E 54 LYS cc_start: 0.8801 (ttmt) cc_final: 0.8425 (ttpp) REVERT: E 91 ASP cc_start: 0.8718 (m-30) cc_final: 0.8508 (p0) REVERT: E 197 LYS cc_start: 0.7949 (mttm) cc_final: 0.7656 (tttt) REVERT: E 435 ARG cc_start: 0.7538 (mtt180) cc_final: 0.7173 (mmt180) outliers start: 56 outliers final: 35 residues processed: 187 average time/residue: 0.5241 time to fit residues: 110.8197 Evaluate side-chains 175 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 136 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 161 GLN Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 161 GLN Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 242 PHE Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 161 GLN Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 161 GLN Chi-restraints excluded: chain E residue 162 ASP Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 260 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 169 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 148 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 129 optimal weight: 0.9980 chunk 137 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 26 optimal weight: 4.9990 chunk 52 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 205 ASN ** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.117433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.082744 restraints weight = 26793.536| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 2.19 r_work: 0.2911 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.5765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17380 Z= 0.126 Angle : 0.655 11.320 23780 Z= 0.300 Chirality : 0.045 0.163 2825 Planarity : 0.003 0.034 2855 Dihedral : 7.103 58.748 3024 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.79 % Allowed : 19.89 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.20), residues: 1955 helix: 2.03 (0.19), residues: 780 sheet: -1.08 (0.25), residues: 445 loop : -1.32 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 315 TYR 0.012 0.001 TYR A 67 PHE 0.015 0.001 PHE E 153 TRP 0.024 0.001 TRP E 459 HIS 0.001 0.000 HIS B 309 Details of bonding type rmsd covalent geometry : bond 0.00287 (17355) covalent geometry : angle 0.63383 (23720) hydrogen bonds : bond 0.03886 ( 735) hydrogen bonds : angle 4.06123 ( 2175) Misc. bond : bond 0.00037 ( 5) link_BETA1-4 : bond 0.00288 ( 15) link_BETA1-4 : angle 3.72607 ( 45) link_NAG-ASN : bond 0.00093 ( 5) link_NAG-ASN : angle 2.05451 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 146 time to evaluate : 0.676 Fit side-chains revert: symmetry clash REVERT: A 108 LYS cc_start: 0.8661 (mttp) cc_final: 0.7728 (mmmt) REVERT: A 188 GLU cc_start: 0.8490 (mt-10) cc_final: 0.8159 (tt0) REVERT: A 197 LYS cc_start: 0.7953 (mttm) cc_final: 0.7653 (tttt) REVERT: A 404 GLN cc_start: 0.7066 (tm-30) cc_final: 0.6587 (tp40) REVERT: A 435 ARG cc_start: 0.7620 (mtt180) cc_final: 0.7136 (mmp-170) REVERT: B 22 ASN cc_start: 0.8824 (p0) cc_final: 0.8572 (m-40) REVERT: B 54 LYS cc_start: 0.8643 (ttmt) cc_final: 0.8375 (ttpp) REVERT: B 162 ASP cc_start: 0.8869 (m-30) cc_final: 0.8606 (m-30) REVERT: B 197 LYS cc_start: 0.7911 (mttm) cc_final: 0.7658 (tttm) REVERT: B 229 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8288 (tm) REVERT: B 435 ARG cc_start: 0.7301 (mtt180) cc_final: 0.6832 (mmp-170) REVERT: C 22 ASN cc_start: 0.8683 (p0) cc_final: 0.8481 (m-40) REVERT: C 91 ASP cc_start: 0.8679 (m-30) cc_final: 0.8454 (p0) REVERT: C 210 MET cc_start: 0.9606 (tpp) cc_final: 0.9312 (mmt) REVERT: C 242 PHE cc_start: 0.8771 (OUTLIER) cc_final: 0.7994 (t80) REVERT: C 435 ARG cc_start: 0.7398 (mtt180) cc_final: 0.6846 (mmp-170) REVERT: D 54 LYS cc_start: 0.8696 (ttmt) cc_final: 0.8403 (ttpp) REVERT: D 91 ASP cc_start: 0.8788 (OUTLIER) cc_final: 0.8469 (p0) REVERT: D 188 GLU cc_start: 0.8468 (mt-10) cc_final: 0.7933 (mt-10) REVERT: D 197 LYS cc_start: 0.8056 (mttm) cc_final: 0.7817 (tttt) REVERT: D 435 ARG cc_start: 0.7451 (mtt180) cc_final: 0.7025 (mmp-170) REVERT: E 20 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8566 (mp) REVERT: E 22 ASN cc_start: 0.8787 (p0) cc_final: 0.8511 (m-40) REVERT: E 54 LYS cc_start: 0.8790 (ttmt) cc_final: 0.8422 (ttpp) REVERT: E 123 VAL cc_start: 0.9106 (OUTLIER) cc_final: 0.8693 (t) REVERT: E 197 LYS cc_start: 0.7908 (mttm) cc_final: 0.7621 (tttt) REVERT: E 435 ARG cc_start: 0.7538 (mtt180) cc_final: 0.7198 (mmt180) outliers start: 51 outliers final: 35 residues processed: 188 average time/residue: 0.5629 time to fit residues: 119.1688 Evaluate side-chains 180 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 140 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 161 GLN Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 161 GLN Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 242 PHE Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 161 GLN Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 161 GLN Chi-restraints excluded: chain E residue 162 ASP Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 269 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 179 optimal weight: 0.9980 chunk 109 optimal weight: 0.5980 chunk 162 optimal weight: 2.9990 chunk 174 optimal weight: 0.7980 chunk 132 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 106 optimal weight: 4.9990 chunk 182 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 151 optimal weight: 1.9990 chunk 72 optimal weight: 7.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 205 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.117211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.082531 restraints weight = 26858.388| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 2.19 r_work: 0.2906 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.5930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17380 Z= 0.134 Angle : 0.660 9.190 23780 Z= 0.304 Chirality : 0.045 0.161 2825 Planarity : 0.004 0.035 2855 Dihedral : 7.033 58.880 3024 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.74 % Allowed : 20.16 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.20), residues: 1955 helix: 2.07 (0.19), residues: 780 sheet: -1.07 (0.25), residues: 445 loop : -1.29 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 315 TYR 0.012 0.001 TYR A 67 PHE 0.016 0.001 PHE E 153 TRP 0.028 0.001 TRP E 459 HIS 0.002 0.001 HIS E 309 Details of bonding type rmsd covalent geometry : bond 0.00314 (17355) covalent geometry : angle 0.63897 (23720) hydrogen bonds : bond 0.03885 ( 735) hydrogen bonds : angle 4.05320 ( 2175) Misc. bond : bond 0.00037 ( 5) link_BETA1-4 : bond 0.00260 ( 15) link_BETA1-4 : angle 3.67132 ( 45) link_NAG-ASN : bond 0.00144 ( 5) link_NAG-ASN : angle 2.04781 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 146 time to evaluate : 0.669 Fit side-chains revert: symmetry clash REVERT: A 108 LYS cc_start: 0.8649 (mttp) cc_final: 0.7779 (mmmt) REVERT: A 188 GLU cc_start: 0.8472 (mt-10) cc_final: 0.8163 (tt0) REVERT: A 197 LYS cc_start: 0.7963 (mttm) cc_final: 0.7679 (tttt) REVERT: A 404 GLN cc_start: 0.7097 (tm-30) cc_final: 0.6602 (tp40) REVERT: A 435 ARG cc_start: 0.7598 (mtt180) cc_final: 0.7137 (mmp-170) REVERT: B 22 ASN cc_start: 0.8838 (p0) cc_final: 0.8577 (m-40) REVERT: B 54 LYS cc_start: 0.8647 (ttmt) cc_final: 0.8382 (ttpp) REVERT: B 162 ASP cc_start: 0.8810 (m-30) cc_final: 0.8530 (m-30) REVERT: B 197 LYS cc_start: 0.7899 (mttm) cc_final: 0.7660 (tttm) REVERT: B 229 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8279 (tm) REVERT: B 435 ARG cc_start: 0.7328 (mtt180) cc_final: 0.6906 (mmp-170) REVERT: C 242 PHE cc_start: 0.8770 (OUTLIER) cc_final: 0.7906 (t80) REVERT: C 435 ARG cc_start: 0.7450 (mtt180) cc_final: 0.6917 (mmp-170) REVERT: D 52 ASP cc_start: 0.8192 (OUTLIER) cc_final: 0.7578 (t0) REVERT: D 54 LYS cc_start: 0.8718 (ttmt) cc_final: 0.8321 (ttpp) REVERT: D 91 ASP cc_start: 0.8770 (OUTLIER) cc_final: 0.8475 (p0) REVERT: D 197 LYS cc_start: 0.8058 (mttm) cc_final: 0.7826 (tttt) REVERT: D 435 ARG cc_start: 0.7441 (mtt180) cc_final: 0.7026 (mmp-170) REVERT: E 20 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8588 (mp) REVERT: E 22 ASN cc_start: 0.8805 (p0) cc_final: 0.8600 (m-40) REVERT: E 54 LYS cc_start: 0.8796 (ttmt) cc_final: 0.8428 (ttpp) REVERT: E 197 LYS cc_start: 0.7878 (mttm) cc_final: 0.7617 (tttt) REVERT: E 435 ARG cc_start: 0.7515 (mtt180) cc_final: 0.7195 (mmt180) outliers start: 50 outliers final: 35 residues processed: 186 average time/residue: 0.5318 time to fit residues: 111.8102 Evaluate side-chains 178 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 138 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 161 GLN Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 161 GLN Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 242 PHE Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 161 GLN Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 161 GLN Chi-restraints excluded: chain E residue 162 ASP Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 269 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 58 optimal weight: 0.9980 chunk 152 optimal weight: 0.9980 chunk 135 optimal weight: 0.0470 chunk 71 optimal weight: 0.0030 chunk 30 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 134 optimal weight: 0.8980 chunk 15 optimal weight: 0.0060 chunk 120 optimal weight: 2.9990 chunk 102 optimal weight: 0.2980 chunk 194 optimal weight: 2.9990 overall best weight: 0.2504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.119880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.085291 restraints weight = 26860.585| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 2.20 r_work: 0.2957 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.6006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 17380 Z= 0.101 Angle : 0.621 8.879 23780 Z= 0.285 Chirality : 0.043 0.139 2825 Planarity : 0.003 0.031 2855 Dihedral : 6.777 59.930 3024 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.41 % Allowed : 20.66 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.20), residues: 1955 helix: 2.15 (0.19), residues: 780 sheet: -1.01 (0.25), residues: 445 loop : -1.15 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 315 TYR 0.011 0.001 TYR C 67 PHE 0.012 0.001 PHE B 254 TRP 0.026 0.001 TRP C 459 HIS 0.002 0.000 HIS C 460 Details of bonding type rmsd covalent geometry : bond 0.00211 (17355) covalent geometry : angle 0.60068 (23720) hydrogen bonds : bond 0.03425 ( 735) hydrogen bonds : angle 3.96516 ( 2175) Misc. bond : bond 0.00030 ( 5) link_BETA1-4 : bond 0.00324 ( 15) link_BETA1-4 : angle 3.52841 ( 45) link_NAG-ASN : bond 0.00010 ( 5) link_NAG-ASN : angle 1.60960 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5925.92 seconds wall clock time: 101 minutes 34.27 seconds (6094.27 seconds total)